Prague, Czech Republic

The Academy of science of the Czech Republic was established in 1992 by the Czech National Council as the Czech successor of the former Czechoslovak Academy of science. The Academy is the leading non-university public research institution in the Czech Republic. It conducts both fundamental and strategic applied research.It has three scientific divisions, namely the Division of Mathematics, Physics, and Earth science, Division of Chemical and Life science, and Division of Humanities and Social science. The Academy currently manages a network of sixty research institutes and five supporting units staffed by a total of 6,400 employees, over one half of whom are university-trained researchers and Ph.D. scientists.The Head Office of the Academy and forty research institutes are located in Prague, the remaining institutes being situated throughout the country. Wikipedia.


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Patent
Academy of Sciences of the Czech Republic | Date: 2017-01-11

The present invention relates to a prostate-specific membrane antigen (PSMA)-specific binding protein, wherein the PSMA-specific binding protein is a lipocalin 2 (Lcn2)-derived binding protein and binds to PSMA with a K_(D) of 10 nM or lower. The present invention also relates to a nucleic acid molecule encoding the PSMA-specific binding protein of the invention, a vector comprising said nucleic acid molecule of the invention and a host cell transformed with the vector. Furthermore, the invention relates to a method of producing the PSMA-specific binding protein of the invention, the method comprising culturing the host cell of the invention under suitable conditions and isolating the PSMA-specific binding protein produced. The present invention further relates to a protein conjugate comprising the PSMA-specific binding protein of the invention, or the PSMA-specific binding protein produced by the method of the invention. In addition, the present invention relates to a pharmaceutical or diagnostic composition; to the PSMA-specific binding protein of the invention, the nucleic acid molecule of the invention, the vector of the invention, the host cell of the invention or the PSMA-specific binding protein produced by the method of the invention, for use in therapy and/or diagnosis, and in particular for use in the therapy and/or diagnosis of tumors, Crohns disease and/or neurological diseases.


Hackl K.,Ruhr University Bochum | Fischer F.D.,University of Leoben | Svoboda J.,Academy of Sciences of the Czech Republic
Acta Materialia | Year: 2017

We present a theory of thermal grooving, i.e. surface motion due to surface diffusion, based solely on geometrical and energetic arguments and a variational approach involving a thermodynamic extremal principle. The theory is derived for a fully three-dimensional setting. All interface and contact conditions at junction lines and points of the material aggregate are derived rigorously and without ambiguity. A finite element implementation of the model is employed. Numerical examples are presented and compared with experimental results from the literature. © 2017 Acta Materialia Inc.


Chiodaroli E.,Ecole Polytechnique Federale de Lausanne | Michalek M.,Academy of Sciences of the Czech Republic
Communications in Mathematical Physics | Year: 2017

We consider the initial value problem for the inviscid Primitive and Boussinesq equations in three spatial dimensions. We recast both systems as an abstract Euler-type system and apply the methods of convex integration of De Lellis and Székelyhidi to show the existence of infinitely many global weak solutions of the studied equations for general initial data. We also introduce an appropriate notion of dissipative solutions and show the existence of suitable initial data which generate infinitely many dissipative solutions. © 2017 Springer-Verlag Berlin Heidelberg


Kucera P.,Czech Technical University | Neustupa J.,Academy of Sciences of the Czech Republic
Nonlinearity | Year: 2017

We recall or prove a series of results on solutions to the Navier-Stokes equation with Naviers slip boundary conditions. The main theorem says that a strong solution u on any time interval (0,T ) (where 0


Chomicki G.,Ludwig Maximilians University of Munich | Janda M.,Academy of Sciences of the Czech Republic | Janda M.,National Autonomous University of Mexico | Renner S.S.,Ludwig Maximilians University of Munich
Proceedings of the Royal Society B: Biological Sciences | Year: 2017

Ant-gardens (AGs) are ant/plant mutualisms in which ants farm epiphytes in return for nest space and food rewards. They occur in the Neotropics and Australasia, but not in Africa, and their evolutionary assembly remains unclear. We here use phylogenetic frameworks for important AG lineages in Australasia, namely the ant genus Philidris and domatium-bearing ferns (Lecanopteris) and flowering plants in the Apocynaceae (Hoya and Dischidia) and Rubiaceae (Myrmecodia, Hydnophytum, Anthorrhiza, Myrmephytum and Squamellaria). Our analyses revealed that in these clades, diaspore dispersal by ants evolved at least 13 times, five times in the Late Miocene and Pliocene in Australasia and seven times during the Pliocene in Southeast Asia, after Philidris ants had arrived there, with subsequent dispersal between these two areas. A uniquely specialized AG system evolved in Fiji at the onset of the Quaternary. The farming in the same AG of epiphytes that do not offer nest spaces suggests that a broadening of the ants’ plant host spectrum drove the evolution of additional domatium-bearing AG-epiphytes by selecting on pre-adapted morphological traits. Consistent with this, we found a statistical correlation between the evolution of diaspore dispersal by ants and domatia in all three lineages. Our study highlights how host broadening by a symbiont has led to new farming mutualisms. © 2017 The Author(s) Published by the Royal Society. All rights reserved.


FermUller C.G.,Vienna University of Technology | Majer O.,Academy of Sciences of the Czech Republic
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2017

We connect two different forms of game based semantics: Hintikka’s game for Independence Friendly logic (IF logic) and Giles’s game for Łukasiewicz logic. An interpretation of truth values in [0, 1] as equilibrium values in semantic games of imperfect information emerges for a logic that extends both, Łukasiewicz logic and IF logic. We prove that already on the propositional level all rational truth values can be obtained as equilibrium values. © Springer-Verlag GmbH Germany 2017.


Polacik M.,Academy of Sciences of the Czech Republic | Smith C.,University of St. Andrews | Reichard M.,Academy of Sciences of the Czech Republic
Journal of Evolutionary Biology | Year: 2017

Organisms inhabiting unpredictable environments often evolve diversified reproductive bet-hedging strategies, expressed as production of multiple offspring phenotypes, thereby avoiding complete reproductive failure. To cope with unpredictable rainfall, African annual killifish from temporary savannah pools lay drought-resistant eggs that vary widely in the duration of embryo development. We examined the sources of variability in the duration of individual embryo development, egg production and fertilization rate in Nothobranchius furzeri. Using a quantitative genetics approach (North Carolina type II design), we found support for maternal effects rather than polyandrous mating as the primary source of the variability in the duration of embryo development. The number of previously laid eggs appeared to serve as an internal physiological cue initiating a shift from rapid-to-slow embryo developmental mode. In annual killifish, extensive phenotypic variability in progeny traits is adaptive, as the conditions experienced by parents have limited relevance to the offspring generation. In contrast to genetic control, with high phenotypic expression and heritability, maternal control of traits under natural selection prevents standing genetic diversity from potentially detrimental effects of selection in fluctuating environments. © 2017 European Society For Evolutionary Biology.


Frantal B.,Academy of Sciences of the Czech Republic | Maly J.,Academy of Sciences of the Czech Republic
Energy Policy | Year: 2017

Rebuilding and upgrading of existing nuclear power plants represent a great energy policy challenge today. In this paper, factors that affect local community support for the rebuilding of an existing nuclear power plant are explored using a regression analysis model. It is based on a survey involving nearly 600 residents of twelve municipalities located in the vicinity of the Dukovany power plant in the Czech Republic. Nearly two thirds of local population support the rebuilding of the plant. The support for rebuilding is not directly affected by distance of residence from the power plant or perceptions of its local economic impacts, but is more influenced by general perceptions of pros of nuclear power. Work in the power plant, perception of nuclear power as a clean energy contributing to climate change mitigation and negative attitude to the renewable energy development are strongest predictors of the support. In terms of energy policy implications, it seems that the education of the public and awareness of nuclear power plants as a clean, safe and landscape compatible system of energy production are more important for increasing acceptance of rebuilding projects than spatial distribution of economic benefits to local communities. © 2017 Elsevier Ltd


Venuleo M.,Marche Polytechnic University | Raven J.A.,University of Technology, Sydney | Giordano M.,Academy of Sciences of the Czech Republic
New Phytologist | Year: 2017

Contents I. II. III. IV. V. VI. VII. References Summary: The relevance of infochemicals in the relationships between organisms is emerging as a fundamental aspect of aquatic ecology. Exchanges of chemical cues are likely to occur not only between organisms of different species, but also between conspecific individuals. Especially intriguing is the investigation of chemical communication in microalgae, because of the relevance of these organisms for global primary production and their key role in trophic webs. Intraspecific communication between algae has been investigated mostly in relation to sexuality and mating. The literature also contains information on other types of intraspecific chemical communication that have not always been explicitly tagged as ways to communicate to conspecifics. However, the proposed role of certain compounds as intraspecific infochemicals appears questionable. In this article, we make use of this plethora of information to describe the various instances of intraspecific chemical communication between conspecific microalgae and to identify the common traits and ecological significance of intraspecific communication. We also discuss the evolutionary implications of intraspecific chemical communication and the mechanisms by which it can be inherited. A special focus is the genetic diversity among conspecific algae, including the possibility that genetic diversity is an absolute requirement for intraspecific chemical communication. © 2017 New Phytologist Trust.


Slampova A.,Academy of Sciences of the Czech Republic | Kuban P.,Academy of Sciences of the Czech Republic
Journal of Chromatography A | Year: 2017

A simple sample injection procedure compatible with commercial capillary electrophoresis (CE) instrumentation was developed, which enables handling sample volumes as little as 250 nL for analytical applications where sample volume availability is of concern. Single-use micro-sampling inserts were prepared by thermal modification of polypropylene micropipette tips and the inserts were accommodated in standard CE vials in CE autosampler carousel. To ensure direct contact of separation capillary injection end with sample solution and to avoid possible damage to the capillary, a soft compression spring was placed at the bottom of the vial underneath the micro-sampling insert. Injections from sub-μL samples were carried out in conventional as well as in short-end injection mode, were compatible with standard i.d./o.d. (25–100 μm/365 μm) fused silica capillaries and with various background electrolyte solutions and detection modes. Excellent repeatability of replicate injections from 250 nL to 3 μL was achieved based on RSD values of quantitative analytical measures (peak heights ≤2.4% and peak areas ≤3.7%) for CE-UV–vis, CE-ESI–MS and CE-contactless conductivity detection of model basic drugs. The achieved RSD values were comparable with those for replicate injections of the drugs from standard CE vials. The reported concept of injections from micro-sampling inserts was further demonstrated useful in evaluation of micro-electromembrane extraction (μ-EME) of model basic drugs. Sub-μL volumes of operational solutions resulted in reduced lengths of μ-EME phases and improved extraction recoveries (66–91%) were achieved. © 2017 Elsevier B.V.


Ermilov S.G.,Tyumen State University | Stary J.,Academy of Sciences of the Czech Republic
Systematic and Applied Acarology | Year: 2017

The oribatid mite family Liacaridae (Acari, Oribatida) is recorded in Vietnam for the first time. Two new species of liacarids of the genera Liacarus and Xenillus are described from Tam Dao National Park, northern Vietnam. Liacarus vietnamensis sp. nov. is similar to L. laterostris Mihelčič, 1954 in the morphology of lamellar cusps (inner teeth well-developed; interlamellar tubercle absent) and in having long interlamellar setae and short notogastral setae, but differs by the directions of lamellar cusps and morphology of bothridial setae. Xenillus tamdaoensis sp. nov. is similar to X. longipilus Pérez-Íñigo and Penã, 1995 in having long notogastral setae, insertion of notogastral setae lm posterior to la, and the presence of an interlamellar tubercle, but differs by the morphology and position of lamellar cusps, size of the interlamellar tubercle and length of interlamellar setae. © 2017 Systematic and Applied Acarology Society.


Bartkiewicz K.,Adam Mickiewicz University | Bartkiewicz K.,Academy of Sciences of the Czech Republic | Chimczak G.,Adam Mickiewicz University | Lemr K.,Academy of Sciences of the Czech Republic
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2017

We describe a direct method for experimental determination of the negativity of an arbitrary two-qubit state with 11 measurements performed on multiple copies of the two-qubit system. Our method is based on the experimentally accessible sequences of singlet projections performed on up to four qubit pairs. In particular, our method permits the application of the Peres-Horodecki separability criterion to an arbitrary two-qubit state. We explicitly demonstrate that measuring entanglement in terms of negativity requires three measurements more than detecting two-qubit entanglement. The reported minimal set of interferometric measurements provides a complete description of bipartite quantum entanglement in terms of two-photon interference. This set is smaller than the set of 15 measurements needed to perform a complete quantum state tomography of an arbitrary two-qubit system. Finally, we demonstrate that the set of nine Makhlin's invariants needed to express the negativity can be measured by performing 13 multicopy projections. We demonstrate both that these invariants are a useful theoretical concept for designing specialized quantum interferometers and that their direct measurement within the framework of linear optics does not require performing complete quantum state tomography. © 2017 American Physical Society.


Dobes F.,Academy of Sciences of the Czech Republic
Key Engineering Materials | Year: 2011

High-temperature creep of a Fe3Al-type iron aluminide alloyed by niobium and different additions of carbon was studied in the temperature range from 600 to 800 °C The alloys contained (atomic %) (i) 27.6 Al, 1.15 Nb, 0.19 C and (ii) 27.1 Al, 1.11 Nb, 0.76 C (Fe balance). Creep tests were performed in compression at constant load with stepwise loading. Stress exponent and activation energy of the creep rate were determined. Creep resistance of the low-carbon alloy is better at lower temperatures, while the opposite is true at temperature of 800 °C. © (2011) Trans Tech Publications, Switzerland.


Krepl O.,Academy of Sciences of the Czech Republic | Klusak J.,Academy of Sciences of the Czech Republic
Theoretical and Applied Fracture Mechanics | Year: 2017

A theoretical elastic stress field in the vicinity of a sharp material inclusion tip has a singular character. The power of a stress singularity, characterized by the exponents of the singularity, is different from the power of a singularity in the case of a crack in homogenous media. Stress distribution near the singular point can be described by an asymptotic expansion. The series consists of singular and non-singular terms, depending on the eigenvalue λ in the exponent of each term. The singular terms are characterized by 0


Gvozdik L.,Academy of Sciences of the Czech Republic | Kristin P.,Academy of Sciences of the Czech Republic
Journal of Experimental Biology | Year: 2017

Temperature is an important factor determining distribution and abundance of organisms. Predicting the impact of warming climate on ectotherm populations requires information about species' thermal requirements, i.e. their so-called 'thermal niche'. The characterization of thermal niche remains a complicated task. We compared the applicability of two indirect approaches, based on reaction norm (aerobic scope curve) and optimality (preferred body temperature) concepts, for indirect estimation of thermal niche while using newts, Ichthyosaura alpestris, as a study system. If the two approaches are linked, then digesting newts should keep their body temperatures close to values maximizing aerobic scope for digestion. After feeding, newts maintained their body temperatures within a narrower range than did hungry individuals. The range of preferred body temperatures was well below the temperature maximizing aerobic scope for digestion. Optimal temperatures for factorial aerobic scope fell within the preferred body temperature range of digesting individuals. We conclude that digesting newts prefer body temperatures that are optimal for the maximum aerobic performance but relative to the maintenance costs. What might be termed the 'economic' thermoregulatory response explains the mismatch between thermal physiology and behaviour in this system.


Lejcek P.,ASCR Institute of Physics Prague | Sob M.,Masaryk University | Sob M.,Academy of Sciences of the Czech Republic | Paidar V.,ASCR Institute of Physics Prague
Progress in Materials Science | Year: 2017

One of the most dangerous technical failures of materials is intergranular brittle fracture (temper embrittlement) as it proceeds very quickly and its appearance is often hardly predictable. It is known that this phenomenon is closely related to the chemistry of grain boundaries and to the difference of the segregation energies of the grain boundaries and the free surfaces (Rice–Wang model). To elucidate the effect of individual solutes on embrittlement of various materials such as steels and nickel-base superalloys, grain boundary and surface segregation was extensively studied in many laboratories. As a result, numerous data on surface and grain boundary segregation have been gathered in literature. They were obtained in two main ways, by computer simulations and from experiments. Consequently, these results are frequently applied to quantify the embrittling potency of individual solutes. Unfortunately, the values of the segregation energy of a solute at grain boundaries as well as at the surfaces obtained by various authors sometimes differ by more than one order of magnitude: such a difference is unacceptable as it cannot provide us with representative view on the problem of material temper embrittlement. In some cases it seems that these values do not properly reflect physical reality or are incorrectly interpreted. Due to the above mentioned large scatter of the segregation and embrittlement data a critical assessment of the literature results is highly needed which would enable the reader to avoid both the well known and less well known pitfalls in this field. Here we summarize the available data on interfacial segregation and embrittlement of various solutes in nickel and bcc iron and critically discuss their reliability, assessing also limitations of individual approaches employed to determine the values of segregation and strengthening/embrittling energies, such as density functional theory, Monte Carlo method, molecular statics and dynamics and tight binding on the theoretical side, and Auger electron spectroscopy, 3D tomographic atom probe, and electron microscopy techniques on the experimental side. We show that experimental methods have serious limitations which can be overcome by accepting reasonable assumptions and models. On the other hand, the theoretical approaches are limited by the size of the computational repeat cell used for the calculations of the segregation energy. In both cases, a careful critical analysis of the available segregation energy and/or enthalpy reflecting physical reality allows to assess the reliability of these values and their applicability in analysis of intergranular brittle fracture in steels and nickel-base alloys. © 2016 Elsevier Ltd


Storchova L.,Academy of Sciences of the Czech Republic
Early Science and Medicine | Year: 2016

The current study deals with the representation of gout in Bohemian humanist literature and its impact on the cultural definitions of being a humanist scholar from the 1550s to the 1620s. Bohemian humanists produced a number of brief autobiographical remarks and lengthy Latin poems dealing with gout or its personified form, podagra. After analysing Bohemian medical treatises, the author focuses on the gout-related imagery from a gender perspective. The main section of the study deals with how the disease was gendered on the level of argument and figurative speech, how its/her body and the relationships to humanist poets were described, which features were related to its/her victims and what this imagery could mean for the ways in which humanists fashioned themselves in their correspondence or casual poetry. Last but not least, the author demonstrates how gout-related imagery intermingled with social elitist discourses which enabled the articulation of the social superiority of humanist scholars and posed a challenge to the period's social hierarchies. © 2016 Koninklijke Brill NV, Leiden.


Kardosova M.,Academy of Sciences of the Czech Republic
Cell Death and Differentiation | Year: 2017

Development of hematopoietic populations through the process of differentiation is critical for proper hematopoiesis. The transcription factor CCAAT/enhancer binding protein alpha (C/EBPα) is a master regulator of myeloid differentiation, and the identification of C/EBPα target genes is key to understand this process. Here we identified the Ecotropic Viral Integration Site 2B (EVI2B) gene as a direct target of C/EBPα. We showed that the product of the gene, the transmembrane glycoprotein EVI2B (CD361), is abundantly expressed on the surface of primary hematopoietic cells, the highest levels of expression being reached in mature granulocytes. Using shRNA-mediated downregulation of EVI2B in human and murine cell lines and in primary hematopoietic stem and progenitor cells, we demonstrated impaired myeloid lineage development and altered progenitor functions in EVI2B-silenced cells. We showed that the compromised progenitor functionality in Evi2b-depleted cells can be in part explained by deregulation of cell proliferation and apoptosis. In addition, we generated an Evi2b knockout murine model and demonstrated altered properties of hematopoietic progenitors, as well as impaired G-CSF dependent myeloid colony formation in the knockout cells. Remarkably, we found that EVI2B is significantly downregulated in human acute myeloid leukemia samples characterized by defects in CEBPA. Altogether, our data demonstrate that EVI2B is a downstream target of C/EBPα, which regulates myeloid differentiation and functionality of hematopoietic progenitors.Cell Death and Differentiation advance online publication, 10 February 2017; doi:10.1038/cdd.2017.6. © 2017 Macmillan Publishers Limited, part of Springer Nature.


Kverka M.,Academy of Sciences of the Czech Republic | Tlaskalova-Hogenova H.,Academy of Sciences of the Czech Republic
Digestive Diseases | Year: 2017

In humans, the gut microbiota forms a complex ecosystem consisting of a vast number of bacteria, Archaea, fungi and viruses. It represents a major stimulus to the development of the immune system and many other physiological functions, so that it may shape the individual's susceptibility to infectious and immune-mediated diseases. The emergence of new '-omics' methods recently revolutionized the way we study the host-microbe interactions, but they also raised new questions and issues. In this review, we discuss the impact of these new data on the current and future therapies for chronic inflammatory diseases. We also outline the major conceptual, technical and interpretational issues that recently led to some misleading conclusions and discuss in brief the current research directions in the field. © 2017 S. Karger AG, Basel.


Simkanin J.,Academy of Sciences of the Czech Republic
Contributions to Geophysics and Geodesy | Year: 2016

Hydromagnetic dynamos are numerically investigated at low Prandtl, Ekman and magnetic Prandtl numbers using the PARODY dynamo code. In all the investigated cases, the generated magnetic fields are dominantly-dipolar. Convection is small-scale and columnar, while the magnetic field maintains its large-scale structure. In this study the generated magnetic field never becomes weak in the polar regions, neither at large magnetic Prandtl numbers (when the magnetic diffusion is weak), nor at low magnetic Prandtl numbers (when the magnetic diffusion is strong), which is a completely different situation to that observed in previous studies. As magnetic fields never become weak in the polar regions, then the magnetic field is always regenerated in the tangent cylinder. At both values of the magnetic Prandtl number, strong polar magnetic upwellings and weaker equatorial upwellings are observed. An occurrence of polar magnetic upwellings is coupled with a regenaration of magnetic fields inside the tangent cylinder and then with a not weakened intensity of magnetic fields in the polar regions. These new results indicate that inertia and viscosity are probably negligible at low Ekman numbers. © 2016 Ján Šimkanin.


Catecholaminergic system plays an important role in hypertension development. The available results on mRNA expression of catecholaminergic system genes in spontaneously hypertensive rats (SHR) are often contradictory. One of the possible causes might be the use of various reference genes as internal controls. In the present study, we searched for suitable reference genes in adrenal medulla or sympathetic ganglia of SHR and Wistar-Kyoto (WKY) rats, which would enable reliable comparison of mRNA expression between these two strains. The mRNA expression was measured by quantitative real-time PCR in adrenal medulla and superior cervical ganglia of 4-week-old or 24-week-old SHR and WKY rats. We evaluated 12 reference genes by three software tools (Normfinder, BestKeeper, geNorm) and compared them for the standardization of mRNA expression. Combination of reference genes Hprt1 and Ywhaz in adrenal medulla and Gapdh and 18S in sympathetic ganglia were chosen as the best ones. 18S was found as applicable reference gene in both tissues. We found many alterations in expression of catecholaminergic system genes in adrenal medulla and sympathetic ganglia of SHR. The usage of the most or the least stable reference gene as internal control changed results moderately in sympathetic ganglia but seriously in adrenal medulla. For example, tyrosine hydroxylase (Th) gene was underexpressed in adrenal medulla of adult SHR using the appropriate reference gene but unchanged after the standardization to the least stable reference gene. Our results indicate the importance of appropriate internal control. The suitability of reference genes should be checked again in the case of change in experimental conditions.


Majorowicz J.,University of Alberta | Safanda J.,Academy of Sciences of the Czech Republic
International Journal of Earth Sciences | Year: 2017

The analysis of the warming/cooling patterns from inversion of 94 well temperature logs for the study area of Central Canada shows very high variability (−1 to 3 °C). Analysis of the warming/cooling patterns in last 2–3 centuries indicates that warming has not affected the whole study area and some surface areas have significantly cooled. Regions of large cooling as well as regions of large warming are apparent. Largest cooling is observed in the NE part of the study area while large warming is observed in the area south–east of it in a ridge running NW–SE slightly north of Great Lakes. These patterns go against patterns of land development which is an unlikely factor forcing these regional scale changes derived mainly from the well sites chosen to be in remote and forested areas. © 2017 Springer-Verlag Berlin Heidelberg


Mazaira A.,Academy of Sciences of the Czech Republic | Konicek P.,Academy of Sciences of the Czech Republic
Canadian Geotechnical Journal | Year: 2015

In the last few decades, in both mining and civil engineering projects, deeper excavations have been carried out than in the past. With this increase in depth, rocks may overstress and rock failures can occur during excavation. When competent rock strata are encountered under high stress conditions, these failures can vary from superficial spalling to explosive rockburst. Intense rockbursts may cause fatal injuries to workers and significant loss of equipment and time. The occurrence of rockbursts is always difficult to predict and special steps and measures must be taken to control them. First, burst-prone zones must be predicted by an early exhaustive geological study and by the assessment of in situ stress level and orientation. Second, basic design parameters, e.g., shape, size, and excavation method, should be modified and adapted to the expected conditions to minimize rockburst risk. Third, in situ pre-conditioning methods, e.g., destress blasting, can be applied to decrease the capacity of the rock mass to store energy. Finally, special rock support and reinforcement systems, i.e., yielding systems, must be installed after excavation to ensure total stability of the opening. This paper reviews the geological and geomechanical factors that provoke and influence rockbursts in overstressed rock masses and the engineering measures taken to control them. © 2015, Canadian Science Publishing. All rights reserved.


Vavrycuk V.,Academy of Sciences of the Czech Republic | Svitek T.,Academy of Sciences of the Czech Republic | Lokajicek T.,Academy of Sciences of the Czech Republic
Geophysical Journal International | Year: 2017

Anisotropic attenuation affects seismic observations and complicates their interpretations. Its accurate determination is, however, difficult and needs extensive measurements of wavefields in many directions. So far, the traveltime and amplitude decay of waves are usually measured along a sparse grid of propagation directions, and methods for inverting for anisotropic attenuation are not fully developed. In this paper, we present theory allowing a description and parametrization of general triclinic anisotropic attenuation. We focus on a correct recalculation of ray quantities usually measured in lab to phase quantities needed in the inversion. We develop and numerically test an iterative inversion scheme for determining the parameters of anisotropic attenuation. We present a lab facility that allows for measuring anisotropic attenuation using the P-wave ultrasonic sounding of spherical samples in 132 directions distributed regularly over the sphere. The applicability of the proposed inversion method and the performance of the experimental setup are exemplified by determining triclinic anisotropic attenuation of the serpentinite rock from Val Malenco, Northern Italy. The ray velocity and ray attenuation were measured on a spherical sample of the rock with diameter of 45.5 mm at the room temperature and under two pressure levels: 0.1 and 20 MPa. The measurements confirmed that anisotropic attenuation is remarkably sensitive to confining pressure. Since cracks are closing with increasing pressure, attenuation decreases. However, changes in pressure can also induce changes in the directional variation of attenuation and rotation of anisotropy axes. The obtained results for the serpentinite rock sample are unique because they represent the first accurately determined triclinic anisotropic attenuation from lab measurements. © The Authors 2016. Published by Oxford University Press on behalf of The Royal Astronomical Society.


Breiter K.,Academy of Sciences of the Czech Republic | Skoda R.,Masaryk University
Mineralogy and Petrology | Year: 2017

Hafnium contents and Zr/Hf ratios were studied in zircons and their parent rocks from three magmatic suites associated with the Teplice caldera, Eastern Erzgebirge: rhyolite and dacite from the peraluminous Schönfeld Unit, relatively younger A-type Teplice rhyolite, and post-caldera A-type biotite and zinnwaldite granite and greisen. New data suggest that zircon crystallizing from a geochemically less evolved volatile- and water-poor melt is, compared to the host rock, relatively Hf-depleted, while zircon crystallizing from an evolved volatile- and water-rich melt has a Zr/Hf value approximately identical to that of the parental melt. Zr/Hf values in zircon did not change substantially either during greisenization, or during low-temperature alteration after metamictization. Zr/Hf values in the whole rock may serve as a sensitive indicator of magmatic fractionation of evolved granitic melts, as they are only negligibly influenced by the following hydrothermal processes. Zr/Hf values in individual cogenetic zircon grains are scattered but their general evolution trend in the rock series is consistent with the evolution of the whole-rock Zr/Hf values. © 2017 Springer-Verlag Wien


Wagner S.,Academy of Sciences of the Czech Republic | Herrmannova A.,Academy of Sciences of the Czech Republic | Sikrova D.,Academy of Sciences of the Czech Republic | Valasek L.S.,Academy of Sciences of the Czech Republic
Nucleic Acids Research | Year: 2016

The 12-subunit mammalian eIF3 is the largest and most complex translation initiation factor and has been implicated in numerous steps of translation initiation, termination and ribosomal recycling. Imbalanced eIF3 expression levels are observed in various types of cancer and developmental disorders, but the consequences of altered eIF3 subunit expression on its overall structure and composition, and on translation in general, remain unclear.We present the first complete in vivo study monitoring the effects of RNAi knockdown of each subunit of human eIF3 on its function, subunit balance and integrity. We show that the eIF3b and octameric eIF3a subunits serve as the nucleation core around which other subunits assemble in an ordered way into two interconnected modules: The yeast-like core and the octamer, respectively. In the absence of eIF3b neither module forms in vivo, whereas eIF3d knock-down results in severe proliferation defects with no impact on eIF3 integrity. Disrupting the octamer produces an array of subcomplexes with potential roles in translational regulation. This study, outlining the mechanism of eIF3 assembly and illustrating how imbalanced expression of eIF3 subunits impacts the factor's overall expression profile, thus provides a comprehensive guide to the human eIF3 complex and to the relationship between eIF3 misregulation and cancer. © The Author(s) 2016.


Demekhov A.G.,RAS Institute of Applied Physics | Taubenschuss U.,Academy of Sciences of the Czech Republic | Santolik O.,Charles University
Journal of Geophysical Research: Space Physics | Year: 2017

We present results of numerical simulations of VLF chorus emissions based on the backward wave oscillator model and compare them with Time History of Events and Macroscale Interactions during Substorms (THEMIS) spacecraft data from the equatorial chorus source region on the early morning side at a radial distance of 6 Earth radii. Specific attention is paid to the choice of simulation parameters based on experimental data. We show that with known parameters of the geomagnetic field, plasma density, and the initial wave frequency, one can successfully reproduce individual chorus elements in the simulation. In particular, the measured growth rate, wave amplitude, and frequency drift rate are in agreement with observed values. The characteristic interval between the elements has a mismatch of factor 2. The agreement becomes perfect if we assume that the inhomogeneity scale of the magnetic field along the field line is half of that obtained from the T96 model. Such an assumption can be justified since the T96 model does not fit well for the time of chorus observations, and there is a shear in the observed field which indicates the presence of local currents. © 2017. American Geophysical Union. All Rights Reserved.


Hubalek Z.,Academy of Sciences of the Czech Republic | Rudolf I.,Academy of Sciences of the Czech Republic
Medical and Veterinary Entomology | Year: 2017

A total of 7778 host-seeking adult Dermacentor reticulatus (Ixodida: Ixodidae) ticks were examined for the prevalence of Francisella tularensis holarctica (Thiotrichales: Francisellaceae) in a natural focus of tularaemia in the floodplain forest-meadow ecosystem along the lower reaches of the Dyje (Thaya) river in South Moravia (Czech Republic) between 1995 and 2013. Ticks were pooled (10 specimens per pool) and their homogenates inoculated subcutaneously in 4-week-old specific pathogen-free mice. Dead mice were sectioned, their spleens cultivated on thioglycollate-glucose-blood agar and impression smears from the spleen, liver and heart blood were Giemsa-stained. Sixty-four pools were positive for F.tularensis: the overall minimum infection rate (MIR) was 0.82%. Overall MIRs for the 4714 female and 3064 male D.reticulatus examined were 0.89 and 0.72%, respectively; MIRs fluctuated across years between 0.0 and 2.43%. The estimated bacterial load in infected ticks varied from 0.84 to 5.34 log10 infectious F.tularensis cells per tick (i.e. from about seven to 220000 cells). Ticks with low loads were more prevalent; more than 1000 infectious cells were detected in 24 ticks (0.3% of all ticks and 37.5% of infected ticks). Monitoring of D.reticulatus for the presence and cell numbers of F.tularensis may be a valuable tool in the surveillance of tularaemia. © 2017 The Royal Entomological Society.


Majer Z.,Brno University of Technology | Hutar P.,Academy of Sciences of the Czech Republic | Knesl Z.,Academy of Sciences of the Czech Republic
Key Engineering Materials | Year: 2011

In this paper polymeric particulate composites are studied (especially polypropylene (PP) matrix stuffed by rigid mineral fillers). Presently, polymeric particulate composites are frequently used in many engineering applications. The composite was modeled as a three-phase continuum matrix, interphase and particle. The properties of the particles (size, shape) have a significant effect on the global behaviour of the composite. On the basis of fracture mechanics methodology the interaction of micro-crack propagation in the matrix filled by rigid particles covered by the interphase was analyzed. The effect of the composite structure on their mechanical properties is studied here from the theoretical point of view. © (2011) Trans Tech Publications. Switzerland.


Chvatal A.,Academy of Sciences of the Czech Republic
Journal of the History of the Neurosciences | Year: 2017

The findings obtained by the famous nineteenth-century Czech scientist Jan Evangelista Purkyně (1787–1869) in the field of microscopic structure of animal and human tissues, including the brain, spinal cord, and nerves, have already been described in depth in a number of older and newer publications. The present article contains an overview of the instruments and tools that Purkyně and his assistants used for microscopic research of tissue histology. Some of these instruments were developed either by Purkyně alone, such as the microtomic compressor, or together with his assistant Adolph Oschatz, such as the microtome. A brief overview of the development of the cutting engines suggests that the first microtome, a prototype of modern sliding microtomes, was designed and constructed under the supervision of Purkyně at the Institute of Physiology in Wrocław. Purkyně and his assistants, thus, not only obtained important findings of animal and human nervous and other tissues but also substantially contributed to the development of instruments and tools for their study, a fact often forgotten today. © 2017 Taylor & Francis


Kocanova B.,Academy of Sciences of the Czech Republic
Early Science and Medicine | Year: 2017

Prague university scholars found ten questions (six quaestiones and four probleumata) of medieval meteorology remarkable enough to include them in the agenda of annual ceremonial disputations de quolibet between 1399 and 1417. The disputations resembled rhetoric tournaments where masters of the Faculty of Arts fought with each other using their polemics about scientific and political issues of the time. The six enticing quaestiones mostly concerned topics which were not sufficiently addressed by Aristotle, although they had been discussed extensively since antiquity. Above all, they concerned aspects of optical phaenomena (meteors, comets, halo effect, rainbow). The so-called probleumata, simple topics added to the quaestiones to entertain and refresh the audience, will also be discussed; unlike quaestiones, probleumata rarely referred directly to Aristotle's work. The present study examines to what extent the sources for quodlibet disputations represent relevant material for the study of the reception of meteorology in medieval education. © 2017 Koninklijke Brill NV, Leiden, The Netherlands.


Samek O.,Academy of Sciences of the Czech Republic | Zemanek P.,Academy of Sciences of the Czech Republic | Jonas A.,Academy of Sciences of the Czech Republic | Telle H.H.,University of Swansea
Laser Physics Letters | Year: 2011

Raman spectroscopy offers a powerful alternative analytical method for the detection and identification of lipids/oil in biological samples, such as algae and fish. Recent research in the authors' groups, and experimental data only very recently published by us and a few other groups suggest that Raman spectroscopy can be exploited in instances where fast and accurate determination of the iodine value (associated with the degree of lipid unsaturation) is required. Here the current status of Raman spectroscopy applications on algae is reviewed, and particular attention is given to the efforts of identifying and selecting oil-rich algal strains for the potential mass production of commercial biofuels and for utilization in the food industry. © 2011 by Astro Ltd., published exclusively by WILEY-VCH Verlag GmbH & Co. KGaA.


Heinzel P.,Academy of Sciences of the Czech Republic | Kleint L.,University of Applied Sciences and Arts Northwestern Switzerland
Astrophysical Journal Letters | Year: 2014

We present a novel observation of the white light flare (WLF) continuum, which was significantly enhanced during the X1 flare on 2014 March 29 (SOL2014-03-29T17:48). Data from the Interface Region Imaging Spectrograph (IRIS) in its near-UV channel show that at the peak of the continuum enhancement, the contrast at the quasi-continuum window above 2813 A˚ reached 100%-200% and can be even larger closer to Mg II lines. This is fully consistent with the hydrogen recombination Balmer-continuum emission, which follows an impulsive thermal and non-thermal ionization caused by the precipitation of electron beams through the chromosphere. However, a less probable photospheric continuum enhancement cannot be excluded. The light curves of the Balmer continuum have an impulsive character with a gradual fading, similar to those detected recently in the optical region on the Solar Optical Telescope on board Hinode. This observation represents a first Balmer-continuum detection from space far beyond the Balmer limit (3646 A˚), eliminating seeing effects known to complicate the WLF detection. Moreover, we use a spectral window so far unexplored for flare studies, which provides the potential to study the Balmer continuum, as well as many metallic lines appearing in emission during flares. Combined with future ground-based observations of the continuum near the Balmer limit, we will be able to disentangle various scenarios of the WLF origin. IRIS observations also provide a critical quantitative measure of the energy radiated in the Balmer continuum, which constrains various models of the energy transport and deposit during flares. © 2014. The American Astronomical Society. All rights reserved.


de Bello F.,Academy of Sciences of the Czech Republic
Global Ecology and Biogeography | Year: 2012

The relevance of neutral versus niche-based community assembly rules (i.e. the processes sorting species present in a larger geographical region into local communities) remains to be demonstrated in ecology and biogeography. To attempt to do this, a number of complex null models are increasingly being used that compare observed community functional diversity (FD, i.e. the extent of trait dissimilarity between coexisting species) with randomly simulated FD. However, little is known about the performance of these null models in detecting non-neutral community assembly rules such as trait convergence and divergence of communities (supposedly revealing habitat selection and limiting similarity, respectively). Here, using both simulated and field communities, I show that assembly rule detection varies systematically with the magnitude of the observed FD, so that these null models do not really succeed in breaking down the observed functional relationships between species. This is a particular concern, making detection of community assembly dependent on: (1) the pool of samples considered, and (2) the capacity of observed FD to correctly discriminate these rules. Null models should be more thoroughly described and validated before being considered as a magic wand to reveal assembly patterns. © 2011 Blackwell Publishing Ltd.


Lorencova E.,Charles University | Frelichova J.,Charles University | Nelson E.,University of Stirling | Vackar D.,Academy of Sciences of the Czech Republic
Land Use Policy | Year: 2013

Climatic and land use change are amongst the greatest global environmental pressures resulting from anthropogenic activities. Both significantly influence the provision of crucial ecosystem services, such as carbon sequestration, water flow regulation, and food and fibre production, at a variety of scales. The aim of this study is to provide spatially explicit information at a national level on climate and land use change impacts in order to assess changes in the provision of ecosystem services. This work provides a qualitative and quantitative analysis of the impacts on selected ecosystem services (carbon sequestration, food production and soil erosion) in the agricultural sector of the Czech Republic. This assessment shows that, historical land use trends and land use under projected climate scenarios display some shared spatial patterns. Specifically, these factors both lead to a significant decrease of arable land in the border fringes of the Czech Republic, which is to some extent replaced by grasslands, in turn affecting the provision of ecosystem services. Moreover, this assessment contributes to a useful method for integrating spatially explicit land use and climate change analysis that can be applied to other sectors or transition countries elsewhere. © 2012 Elsevier Ltd.


Heneka M.T.,Klinische Neurowissenschaften | Rodriguez J.J.,Ikerbasque | Rodriguez J.J.,Academy of Sciences of the Czech Republic | Verkhratsky A.,University of the Basque Country | And 2 more authors.
Brain Research Reviews | Year: 2010

Neuroglial cells are fundamental for control of brain homeostasis and they represent the intrinsic brain defence system. All forms in neuropathology therefore inevitably involve glia. The neurodegenerative diseases disrupt connectivity within brain circuits affecting neuronal-neuronal, neuronal-glial and glial-glial contacts. In addition neurodegenerative processes trigger universal and conserved glial reactions represented by astrogliosis and microglial activation. The complex of recently acquired knowledge allows us to regard the neurodegenerative diseases as primarily gliodegenerative processes, in which glial cells determine the progression and outcome of neuropathological process. © 2009 Elsevier B.V.


Parenti S.,Royal Observatory of Belgium | Schmieder B.,Observatoire de Paris | Heinzel P.,Academy of Sciences of the Czech Republic | Golub L.,Harvard - Smithsonian Center for Astrophysics
Astrophysical Journal | Year: 2012

The prominence-corona transition region (PCTR) plays a key role in the thermal and pressure equilibrium of solar prominences. Our knowledge of this interface is limited and several major issues remain open, including the thermal structure and, in particular, the maximum temperature of the detectable plasma. The high signal-to-noise ratio of images obtained by the Atmospheric Imaging Assembly (AIA) on NASA's Solar Dynamics Observatory clearly shows that prominences are often seen in emission in the 171 and 131 bands. We investigate the temperature sensitivity of these AIA bands for prominence observations, in order to infer the temperature content in an effort to explain the emission. Using the CHIANTI atomic database and previously determined prominence differential emission measure distributions, we build synthetic spectra to establish the main emission-line contributors in the AIA bands. We find that the Fe IX line always dominates the 171 band, even in the absence of plasma at >106 K temperatures, while the 131 band is dominated by Fe VIII. We conclude that the PCTR has sufficient plasma emitting at >4 × 105 K to be detected by AIA. © 2012. The American Astronomical Society. All rights reserved..


Samek O.,Academy of Sciences of the Czech Republic | Al-Marashi J.F.M.,University of Swansea | Telle H.H.,University of Swansea
Laser Physics Letters | Year: 2010

We report on an investigation into a common problem in microbiology laboratories, which is associated with the difficulty of distinguishing/recognising different strains of the genus Staphylococcus. We demonstrate the potential of Raman spectroscopy as a rapid techniques allowing for the identification of different isolates for the detection of biofilm-positive and biofilm-negative Staphylococcus epidermidis strains. For this, the recorded spectra were interpreted using the approach of principal component analysis (PCA). © 2010 by Astro Ltd.


Maslov D.A.,University of California at Riverside | Votypka J.,Charles University | Votypka J.,Academy of Sciences of the Czech Republic | Yurchenko V.,University of Ostrava | And 2 more authors.
Trends in Parasitology | Year: 2013

Monoxenous trypanosomatids, which are usually regarded as benign dwellers of the insect alimentary tract, represent a relatively obscure group within the family Trypanosomatidae. This field of study has long been in disarray with the genus level taxonomy of this group remaining artificial, species criteria elusive, host specificity and occurrence poorly known, and their diversity mostly unexplored. The time has arrived to remedy this situation: a phylogenetic approach has been applied to taxa recognition and description, and a culture-independent (PCR-based) approach for detection and identification of organisms in nature has made it feasible to study the diversity of the group. Although more than 100 typing units have been discovered recently, these appear to represent a small segment of trypanosomatid biodiversity, which still remains to be uncovered. © 2012 Elsevier Ltd.


Kumschick S.,Stellenbosch University | Hufbauer R.A.,Colorado State University | Alba C.,Academy of Sciences of the Czech Republic | Blumenthal D.M.,U.S. Department of Agriculture
Journal of Ecology | Year: 2013

Species introduced into areas outside of their native range face novel biotic and abiotic conditions, which probably impose novel selection pressures. Adaptation to these new conditions may increase the ability of introduced species to establish and spread. Like many other introduced plant populations, introduced genotypes of common mullein (Verbascum thapsus) are more successful in their introduced than in their native range, with increased growth and fecundity. These differences appear to be at least partly genetically based. The most successful introduced populations also grow in an environment that is drier and has fewer competitors than native populations. It is not known, however, whether differences between native and introduced mullein populations are related to these environmental differences between ranges. We used a common garden experiment with 23 native and 27 introduced populations of common mullein to test whether common mullein in the introduced range exhibits evolutionary shifts with respect to responses to competition, drought stress and nitrogen (N) stress. We also used choice experiments to learn whether introduced mullein is more or less resistant to a generalist herbivore than native mullein. Without competition, introduced genotypes grew larger than native genotypes under high resource availability (control) and N stress, but not water stress. Survival, however, was increased in native populations under competition and N stress. The introduced genotypes also had a lower root:shoot ratio than the native genotypes. With competition, introduced genotypes grew larger than native genotypes across all treatments, with that difference being significant under N stress. The introduced genotypes were also more resistant to a generalist herbivore. Synthesis: Together, high biomass, strong responses to high water availability and low root:shoot ratio suggest that mullein has evolved a fast-growing, weedy phenotype in its introduced range rather than adapting to a low-water environment through increased root growth. Although fast-growing plants can be more palatable to herbivores, in this case there does not appear to be a trade-off between growth and defence against a generalist herbivore. Mullein appears to have evolved to be both faster growing and better defended in the introduced range. © 2013 The Authors. Journal of Ecology © 2013 British Ecological Society.


Ha S.,Chonnam National University | Vankova R.,Academy of Sciences of the Czech Republic | Shinozaki K.,RIKEN | Tran L.-S.P.,RIKEN
Trends in Plant Science | Year: 2012

In plants, the cytokinin (CK) phytohormones regulate numerous biological processes, including responses to environmental stresses, via a complex network of CK signaling. By an unknown mechanism, stress signals are perceived and transmitted through the His-Asp phosphorelay, an important component of the CK signal transduction pathway, triggering CK-responsive genes. Because of the intensive crosstalk between CKs and abscisic acid (ABA), modulation of CK levels and their signal transduction affects both ABA-dependent and ABA-independent pathways, enabling plant adaptation to adverse conditions. This review presents our current understanding of the functions of CKs and CK signaling in the regulation of plant adaptation to stress. Biotechnological strategies based on the modulation of CK levels have been examined with the aim of stabilizing agriculture yields. © 2011 Elsevier Ltd.


Catford J.A.,University of Melbourne | Vesk P.A.,University of Melbourne | Richardson D.M.,Stellenbosch University | Pysek P.,Academy of Sciences of the Czech Republic | Pysek P.,Charles University
Global Change Biology | Year: 2012

Biological invasions are a global phenomenon that threatens biodiversity, and few, if any, ecosystems are free from alien species. The outcome of human-mediated introductions is affected by the invasiveness of species and invasibility of ecosystems, but research has primarily focused on defining, characterizing and identifying invasive species; ecosystem invasibility has received much less attention. A prerequisite for characterizing invasibility is the ability to compare levels of invasion across ecosystems. In this paper, we aim to identify the best way to quantify the level of invasion by nonnative animals and plants by reviewing the advantages and disadvantages of different metrics. We explore how interpretation and choice of these measures can depend on the objective of a study or management intervention. Based on our review, we recommend two invasion indices and illustrate their use by applying them to two case studies. Relative alien species richness and relative alien species abundance indicate the contribution that alien species make to a community. They are easy to measure, can be applied to various taxa, are independent of scale and are comparable across regions and ecosystems, and historical data are often available. The relationship between relative alien richness and abundance can indicate the presence of dominant alien species and the trajectory of invasion over time, and can highlight ecosystems and sites that are heavily invaded or especially susceptible to invasion. Splitting species into functional groups and examining invasion patterns of transformer species may be particularly instructive for gauging effects of alien invasion on ecosystem structure and function. Establishing standard, transparent ways to define and quantify invasion level will facilitate meaningful comparisons among studies, ecosystem types and regions. It is essential for progress in ecology and will help guide ecosystem restoration and management. © 2011 Blackwell Publishing Ltd.


Nejepinska J.,Academy of Sciences of the Czech Republic | Malik R.,Academy of Sciences of the Czech Republic | Filkowski J.,Friedrich Miescher Institute for Biomedical Research | Flemr M.,Academy of Sciences of the Czech Republic | And 2 more authors.
Nucleic Acids Research | Year: 2012

Double-stranded RNA (dsRNA) can enter different pathways in mammalian cells, including sequence-specific RNA interference (RNAi), sequence-independent interferon (IFN) response and editing by adenosine deaminases. To study the routing of dsRNA to these pathways in vivo, we used transgenic mice ubiquitously expressing from a strong promoter, an mRNA with a long hairpin in its 3′-UTR. The expressed dsRNA neither caused any developmental defects nor activated the IFN response, which was inducible only at high expression levels in cultured cells. The dsRNA was poorly processed into siRNAs in somatic cells, whereas, robust RNAi effects were found in oocytes, suggesting that somatic cells lack some factor(s) facilitating siRNA biogenesis. Expressed dsRNA did not cause transcriptional silencing in trans. Analysis of RNA editing revealed that a small fraction of long dsRNA is edited. RNA editing neither prevented the cytoplasmic localization nor processing into siRNAs. Thus, a long dsRNA structure is well tolerated in mammalian cells and is mainly causing a robust RNAi response in oocytes. © 2011 The Author(s).


Kueffer C.,ETH Zurich | Pysek P.,Academy of Sciences of the Czech Republic | Pysek P.,Charles University | Richardson D.M.,Stellenbosch University
New Phytologist | Year: 2013

Invasion science is a very active subdiscipline of ecology. However, some scientists contend that theoretical integration has been limited and that predictive power remains weak. This paper, focusing on plants, proposes a new multi-pronged research strategy that builds on recent advances in invasion science. More intensive studies on particular model organisms and ecosystems are needed to improve our understanding of the full suite of interacting factors that influence invasions ('model system research'). At the same time, comparative studies across many study systems are essential for unravelling the context-dependencies of insights that emerge from particular studies ('multi-site studies'); and quantitative synthesis based on large datasets should be constrained to well-defined theoretical domains ('focused meta-analysis'). We also suggest ways for better integration of information about species biology and ecosystem characteristics ('invasion syndromes'). We expect that a resulting theory of invasions will need to be conceived as a somewhat heterogeneous conglomerate of elements of varying generality and predictive power: laws that apply to well-specified domains, general concepts and theoretical frameworks that can guide thinking in research and management, and in-depth knowledge about the drivers of particular invasions. © 2013 The Authors. © 2013 New Phytologist Trust.


Prach K.,Academy of Sciences of the Czech Republic | Walker L.R.,University of Nevada, Las Vegas
Trends in Ecology and Evolution | Year: 2011

Lessons learned from the study of ecological succession have much to offer contemporary environmental problem solving but these lessons are being underutilized. As anthropogenic disturbances increase, succession is more relevant than ever. In this review, we suggest that succession is particularly suitable to address concerns about biodiversity loss, climate change, invasive species, and ecological restoration. By incorporating modern experimental techniques and linking results across environmental gradients with meta-analyses, studies of succession can substantially improve our understanding of other ecological phenomena. Succession can help predict changes in biodiversity and ecosystem services impacted by invasive species and climate change and guide manipulative responses to these disruptions by informing restoration efforts. Succession is still a critical, integrative concept that is central to ecology. © 2010 Elsevier Ltd.


Cellerino A.,Leibniz Institute for Age Research | Valenzano D.R.,Max Planck Institute for Biology of Ageing | Reichard M.,Academy of Sciences of the Czech Republic
Biological Reviews | Year: 2015

African annual fishes from the genus Nothobranchius are small teleosts that inhabit temporary water bodies subject to annual desiccation due to the alternation of the monsoon seasons. Given their unique biology, these fish have emerged as a model taxon in several biological disciplines. Their increasing popularity stems from the extremely short lifespan that is the result of their specific life-history adaptations and is retained under laboratory conditions. Nothobranchius furzeri, the most popular laboratory species, is the vertebrate species with the shortest lifespan recorded in captivity. In the laboratory, adults of different Nothobranchius species and populations live between 3 and 18months and, notably, there is a negative correlation between the captive lifespan of a species and the aridity of their habitat. Their short lifespan is coupled to rapid age-dependent functional decline and expression of cellular and molecular changes comparable to those observed in other vertebrates, including humans. The recent development of transgenesis in this species makes it possible to insert specific constructs into their genome, and the establishment of transgenic lines is facilitated by their very rapid generation time, which can be as short as 1month. This makes Nothobranchius species particularly suited for investigating biological and molecular aspects of ageing and ageing-associated dysfunctions. At the same time, they also represent a unique model taxon to investigate the evolution of life-history adaptations and their genetic architecture. We review their natural history, including phylogenetic relationships, distribution in relation to habitat conditions and natural selection for differential longevity, population structure and demography, and life cycle with emphasis on diapause that may occur at three stages during embryonic development. We further critically evaluate their use as a laboratory model for understanding the evolution of a rapid ageing rate and its consequences for other life-history traits, for cellular, molecular and integrative traits associated with the ageing process, high incidence of neoplasias, their utility for genome-wide gene-expression studies, and as a model for quantitative genetics. We summarize recent achievements in fostering Nothobranchius species as a widely applicable model system, including an annotated transcriptome, successful transgenesis, and existence of viable inbred lines. We compare the conditions they experience in the wild and in captivity and suggest that they are an ideal taxon to investigate natural genetic variation in a laboratory setting. We conclude that Nothobranchius species - and N. furzeri in particular - could become a unique model taxon that bridges interests in ecological and biomedical research. We hope that a conceptual and methodological integration of these two branches of biology will provide important new insights. © 2015 The Authors.


Pysek P.,Academy of Sciences of the Czech Republic | Pysek P.,Charles University | Richardson D.M.,Stellenbosch University
Annual Review of Environment and Resources | Year: 2010

Invasive species are a major element of global change and are contributing to biodiversity loss, ecosystem degradation, and impairment of ecosystem services worldwide. Research is shedding new light on the ecological and economic consequences of invasions. New approaches are emerging for describing and evaluating impacts of invasive species, and for translating these impacts into monetary terms. The harmful effects of invasions are now widely recognized, and multiscale programs are in place in many parts of the world to reduce current and future impacts. There has been an upsurge in scientific research aimed at guiding management interventions. Among the activities that are receiving the most attention and that have the most promise for reducing problems are risk assessment, pathway and vector management, early detection, rapid response, and new approaches to mitigation and restoration. Screening protocols to reduce new introductions are becoming more accurate and have been shown cost-effective. Copyright © 2010 by Annual Reviews. All rights reserved.


Hajek P.,Academy of Sciences of the Czech Republic | Holena M.,Academy of Sciences of the Czech Republic | Rauch J.,University of Economics in Prague
Journal of Computer and System Sciences | Year: 2010

The paper presents the history and present state of the GUHA method, its theoretical foundations and its relation and meaning for data mining. © 2009 Elsevier Inc. All rights reserved.


Soukup T.,Academy of Sciences of the Czech Republic | Smerdu V.,University of Ljubljana
Histochemistry and Cell Biology | Year: 2014

In this mini-review, we briefly present the data regarding the effect of extrinsic factors, i.e., innervation and thyroid hormones (TH) on myosin heavy chain genes and isoforms expression and consequently on muscle fiber type transitions. It has been well known that reduced neuromuscular activity, hyperthyroidism or mechanical unloading stimulate slow-to-fast fiber type transitions, while increased neuromuscular activity, hypothyroidism and higher mechanical loading result in fast to slow fiber type transitions. As there is a plethora of results on these topics, we focus mostly on data relevant to our experimental model of slow-to-fast muscle transformation following heterochronous intramuscular isotransplantation in rats with altered TH status. © 2014, Springer-Verlag Berlin Heidelberg.


Richardson D.M.,Stellenbosch University | Pysek P.,Academy of Sciences of the Czech Republic | Pysek P.,Charles University
New Phytologist | Year: 2012

Contents: Summary 383 I. Introduction 383 II. The introduction-naturalization-invasion continuum for conceptualizing biological invasions 384 III. The biogeographical background for studying naturalization: variation among populations and regions 385 IV. Factors determining naturalization in plants 388 Acknowledgements 392 References 392 Summary: The literature on biological invasions is biased in favour of invasive species - those that spread and often reach high abundance following introduction by humans. It is, however, also important to understand previous stages in the introduction-naturalization-invasion continuum ('the continuum'), especially the factors that mediate naturalization. The emphasis on invasiveness is partly because most invasions are only recognized once species occupy large adventive ranges or start to spread. Also, many studies lump all alien species, and fail to separate introduced, naturalized and invasive populations and species. These biases impede our ability to elucidate the full suite of drivers of invasion and to predict invasion dynamics, because different factors mediate progression along different sections of the continuum. A better understanding of the determinants of naturalization is important because all naturalized species are potential invaders. Processes leading to naturalization act differently in different regions and global biogeographical patterns of plant invasions result from the interaction of population-biological, macroecological and human-induced factors. We explore what is known about how determinants of naturalization in plants interact at various scales, and how their importance varies along the continuum. Research that is explicitly linked to particular stages of the continuum can generate new information that is appropriate for improving the management of biological invasions if, for example, potentially invasive species are identified before they exert an impact. © 2012 New Phytologist Trust.


Kuchta R.,Academy of Sciences of the Czech Republic | Serrano-Martinez M.E.,University of Lima | Scholz T.,Academy of Sciences of the Czech Republic
Emerging Infectious Diseases | Year: 2015

The Pacific broad tapeworm Adenocephalus pacificus (syn. Diphyllobothrium pacificum) is the causative agent of the third most common fish-borne cestodosis among humans. Although most of the nearly 1,000 cases among humans have been reported in South America (Peru, Chile, and Ecuador), cases recently imported to Europe demonstrate the potential for spread of this tapeworm throughout the world as a result of global trade of fresh or chilled marine fish and travel or migration of humans. We provide a comprehensive survey of human cases of infection with this zoonotic parasite, summarize the history of this re-emerging disease, and identify marine fish species that may serve as a source of human infection when eaten raw or undercooked. © 2015, Centers for Disease Control and Prevention (CDC). All rights reserved.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-IP | Phase: HEALTH.2011.2.3.3-1 | Award Amount: 15.69M | Year: 2011

In recent years, an increased number of zoonotic viruses and bacteria have crossed the species barrier to humans and caused or threatened to cause human pandemics with high morbidity and mortality. Because of our inability to predict the emergence of these pathogens, it is difficult to take preventive measures. It is known that zoonotic pathogens need to cross barriers at the animal-human interface, at the pathogen-host interface within humans, and at the human-human interface before they can cause a human pandemic. However, it is poorly understood which pathogen, host, arthropod vector, and environmental factors allow zoonotic pathogens to successfully cross these barriers. Therefore, our overall objective is to identify the key factors that render zoonotic pathogens prone to cross the species barrier and gain efficient transmissibility among humans. ANTIGONE has a two-pronged approach to reach this objective. First, we will perform primary research studies to fill important gaps in our understanding of how zoonotic pathogens can gain pandemic potential. These studies will focus on selected viruses and bacteria, including SARS coronavirus, , Crimean-Congo haemorrhagic fever virus, Nipah virus, Ebola virus, E. coli, M. bovis, B. burgdorferi, C. burnetii and S. suis. Integral to these activities will be a cross-disciplinary training programme for young scientists (Young ANTIGONE) and a web-based pathogen information sharing platform. Second, we will organize Dahlem studies where experts from the human and veterinary fields, from within and outside ANTIGONE, will discuss key issues in infectivity, pathogenicity, and transmissibility of zoonotic pathogens and determine general criteria to assess the risk of these pathogens to gain human pandemic potential. Together, the results of these activities will improve our ability to model and predict potential human pandemics of zoonotic origin and to develop effective and timely preventive measures.


Grant
Agency: European Commission | Branch: FP7 | Program: CSA-SA | Phase: SiS.2013.2.1.1-1 | Award Amount: 3.77M | Year: 2014

TRIGGER aims at promoting systemic interventions designed to have deep, long lasting and widespread impacts at all the different levels in 5 research organisations. The project, coordinated and co-funded by the Italian Government, assisted by an institute specialised in gender and science, involves as co-funders five universities from different EU countries (Czech Republic, France, Italy, UK, Spain). Building on the results of earlier projects, integrated actions will be implemented at each university addressing different sides of gender inequality in science, i.e.: 1) Working environment, formal/informal culture and explicit/tacit rules (awareness-raising; collection of gender-sensitive data; support in the early stages of scientific careers; promotion of work-life balance, etc.). 2) Content and methods of scientific research, to acknowledge its gender dimension and impact (updating of teaching curricula; gendering the design of research and technological innovation; allocation of funds for gendered research; contrasting stereotypes about women in science, etc.). 3) Scientific leadership at different levels (selection procedures and criteria for the evaluation of scientific merit; introduction of equality targets in decision making bodies; enhancement of women researchers visibility, etc.). Each of the 5 involved partners have designed and will carry out a tailored action plan including measures related to all 3 sides, whose relative weight depends on their specific characteristics, situations and needs. TRIGGER will be characterised by integration, customisation, systematic nature, concreteness. Public debate and awareness will be generated on these issues Europe-wide. Added value will be yielded both on the strategic level, by the strong focus on gendering research, and on the operational level, through fostering mutual learning among partners and among the different European structural change projects, giving birth to an Integrated Model.


Grant
Agency: European Commission | Branch: H2020 | Program: MSCA-ITN-ETN | Phase: MSCA-ITN-2014-ETN | Award Amount: 3.29M | Year: 2015

BACKGROUND Secure and sustainable food production in terms of quantity and quality is a major challenge facing human societies. However, food security is continuously threatened by current and invasive pest species. EU regulations for the use of pesticides are getting stricter to ensure food safety and protect ecosystem health. Biocontrol of agricultural pests by using natural enemies has great potential to deal with these two demands. CHALLENGE Controlling novel exotic pests often involves importing non-native natural enemies. Such practices are undesirable as it poses risks to local biodiversity. Optimizing existing and native biocontrol agents can reduce the dependence on imported natural enemies. OBJECTIVE BINGO will advance current knowledge in biocontrol practice through the use of natural genetic variation and by simultaneously training 13 young researchers in an extensive suite of interdisciplinary skills. This will allow them to improve the efficiency of biological pest control through selective breeding of natural enemies in a broad range of agricultural systems and environmental conditions. HOW The research projects will address current bottlenecks in biocontrol, for rearing, monitoring and performance, that include a broad range of scientific disciplines and in which state-of-the-art population genomics will be applied. Industry has a pivotal role by providing the problems for research, training, and by translating the results to capacity building and increased competitiveness. RELEVANCE BINGO will deliver improved biocontrol agents, knowledge on the genetic organisation of traits related to agents performance, genetic markers for monitoring and risk assessment, and guidelines and protocols for genetic improvement of natural enemies. Crucially, BINGO will deliver eager ESRs that have the potential to thrive in professional environments in science, industry and public bodies to ensure that the biocontrol potential is met and implemented.


Grant
Agency: European Commission | Branch: H2020 | Program: MSCA-ITN-ETN | Phase: MSCA-ITN-2016 | Award Amount: 3.87M | Year: 2017

Is there a crisis in the legitimacy of the European Union? That research question is timely and important. Investigating it is also an ideal way of training research leaders of tomorrow to rethink our assumptions about the study of legitimate political order. Whilst, however, the financial crisis has raised new questions about the legitimacy of the EU, existing theories of legitimacy crises are largely based on single-state political systems. New theory is, therefore, needed to understand what would count as legitimacy crises in the case of a non-state political system such as the EU. PLATOs (The Post-Crisis Legitimacy of the EU) ESRs will work together as a team to build new theory from 15 investigations into different standards and actors with whom the EU may need to be legitimate. ESRs will go well beyond the state-of-the-art by building a theory of legitimacy crisis in the EU from a uniquely interdisciplinary understanding of how democracy, power, law, economies and societies all fit together with institutions within and beyond the state to affect the legitimacy of contemporary political order. By developing the analytical tools needed to understand a core predicament in which the EU may both need to develop legitimate forms of political power beyond the state and find those forms of power hard to achieve, PLATO will train ESRs with the conceptual clarity needed to define new research questions at the very frontiers of their disciplines and the methodological skills needed to research those questions. They will also be prepared for careers in the non-academic sector (policy-advice, consulting, civil society, European institutions and expert bodies). PLATOs ambitious cross-university, cross-country and cross-sectoral programme of research training, supervision and secondments will pool resources from a unique network of 9 research-intensive universities and 11 non-academic partners who are themselves key users of state-of-the-art social science research.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-IP | Phase: ENV.2009.2.1.2.1;ENV.2009.2.2.1.1 | Award Amount: 9.90M | Year: 2010

Understanding how freshwater ecosystems will respond to future climate change is essential for the development of policies and implementation strategies needed to protect aquatic and riparian ecosystems. The future status of freshwater ecosystems is however, also dependent on changes in land-use, pollution loading and water demand. In addition the measures that need to be taken to restore freshwater ecosystems to good ecological health or to sustain priority species as required by EU Directives need to be designed either to adapt to future climate change or to mitigate the effects of climate change in the context of changing land-use. Generating the scientific understanding that enables such measures to be implemented successfully is the principal focus of REFRESH. It is concerned with the development of a system that will enable water managers to design cost-effective restoration programmes for freshwater ecosystems at the local and catchment scales that account for the expected future impacts of climate change and land-use change in the context of the WFD and Habitats Directive. At its centre is a process-based evaluation of the specific adaptive measures that might be taken to minimise the consequences of climate change on freshwater quantity, quality and biodiversity. The focus is on three principal climate-related and interacting pressures, increasing temperature, changes in water levels and flow regimes and excess nutrients, primarily with respect to lowland rivers, lakes and wetlands because these often pose the most difficult problems in meeting both the requirements of the WFD and Habitats Directive. REFRESH will advance our fundamental and applied science in 5 key areas: i) understanding how the functioning of freshwater ecosystems is affected by climate change; ii) new indicators of functional response and tools for assessing vulnerability; iii) modelling ecological processes; iv) integrated modelling; and v) adaptive management.


Flemr M.,Academy of Sciences of the Czech Republic | Malik R.,Academy of Sciences of the Czech Republic | Franke V.,University of Zagreb | Nejepinska J.,Academy of Sciences of the Czech Republic | And 4 more authors.
Cell | Year: 2013

Summary In mammals, a single Dicer participates in biogenesis of small RNAs in microRNA (miRNA) and RNAi pathways. In mice, endogenous RNAi is highly active in oocytes, but not in somatic cells, which we ascribe here to an oocyte-specific Dicer isoform (DicerO). DicerO lacks the N-terminal DExD helicase domain and has higher cleavage activity than the full-length Dicer in somatic cells (DicerS). Unlike Dicer S, DicerO efficiently produces small RNAs from long double-stranded (dsRNA) substrates. Expression of the DicerO isoform is driven by an intronic MT-C retrotransposon promoter, deletion of which causes loss of DicerO and female sterility. Oocytes from females lacking the MT-C element show meiotic spindle defects and increased levels of endogenous small interfering RNA (endo-siRNA) targets, phenocopying the maternal Dicer null phenotype. The alternative Dicer isoform, whose phylogenetic origin demonstrates evolutionary plasticity of RNA-silencing pathways, is the main determinant of endogenous RNAi activity in the mouse female germline. © 2013 Elsevier Inc.


Grant
Agency: European Commission | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2011-ITN | Award Amount: 4.25M | Year: 2011

RNA molecules are at the heart of life. It is now commonly admitted that nearly all the human genome is transcribed, and a wealth of new coding and non-coding RNAs have been discovered. Importantly, modern RNAs are never naked, but always exist in complex with proteins to form RNPs (Ribonucleoproteins). In the case of non-coding RNAs, these proteins are usually stably associated with the RNA and help to perform their function. In contrast, RNA binding proteins are usually transiently bound to coding RNAs, and control various aspects of their metabolism. For the next generation of scientists, a great challenge will be to understand the function and the mechanisms of action of the myriads of RNPs. The goal of this ITN (RNPnet) is first to bring together existing labs from different discipline, to join forces and tackle key questions in the field, and second, to produce highly-trained young researchers that will be sensitized to RNA and possess a multidisciplinary approach to research. The multiple expertises present in the fifteen labs of this network will be used in a highly cooperative and integrated manner. The research training will focus on studying RNPs involved in mRNA surveillance, splicing and editing. In addition, a total of fifteen meetings including two summer schools and several workshops are planed to strengthen education and interaction among participants of RNPnet. Finally, another important aspect of RNPnet is the presence of two industrial partners. Their aim is to use the enormous potential of RNA biology in therapeutic applications, either by modifying RNAs and using it as a drug, or by targeting specific RNA binding proteins with small molecules. We foresee that the presence of industrial partners will be highly beneficial for the students, and that, by exposing them to both the academic and industrial world, we will both facilitate communication between these worlds and provide to the young trainees a large panorama of their possible career.


Grant
Agency: European Commission | Branch: FP7 | Program: CP | Phase: Fission-2007-1.2-01 | Award Amount: 23.78M | Year: 2008

Actinide recycling by separation and transmutation is considered worldwide and particularly in several European countries as one of the most promising strategies to reduce the inventory of radioactive waste, thus contributing to make nuclear energy sustainable. Consistently with potentially viable recycling strategies, the Collaborative Project ACSEPT will provide a structured R&D framework to develop chemical separation processes compatible with fuel fabrication techniques, with a view to their future demonstration at the pilot level. Considering technically mature aqueous separation processes, ACSEPT will optimise and select the most promising ones dedicated to actinide partitioning and those featuring a group separation. These developments will be appropriately balanced with an exploratory research focused on the design of new molecules. In parallel, promising group actinide separation pyro-processes will be developed beyond the current state-of-the-art, as an alternative option, for a longer term. ACSEPT will also pave the way towards more integration between Partitioning and Transmutation by carrying dissolution as well as actinide conversion studies. All experimental results will be integrated by carrying out engineering and systems studies on aqueous and dry (pyro) processes to prepare for future demonstration at a pilot level. A training and education programme will also be implemented to share the knowledge among partitioning community and present and future generations of researchers. The challenging objectives of ACSEPT will be addressed by a multi-disciplinary consortium composed of European universities, nuclear research bodies and major industrial players. This consortium will generate fundamental improvements for a future design of an Advanced Processing Pilot Unit. ACSEPT will thus be an essential contribution to the demonstration, in the long term, of the potential benefits of actinide recycling to minimise the burden on the geological repositories.


Grant
Agency: European Commission | Branch: H2020 | Program: RIA | Phase: BG-02-2015 | Award Amount: 5.20M | Year: 2016

The overall goal of ClimeFish is to help ensure that the increase in seafood production comes in areas and for species where there is a potential for sustainable growth, given the expected developments in climate, thus contributing to robust employment and sustainable development of rural and coastal communities. The underlying biological models are based on single species distribution and production, as well as multispecies interactions. Forecasting models will provide production scenarios that will serve as input to socio-economic analysis where risks and opportunities are identified, and early warning methodologies are developed. Strategies to mitigate risk and utilize opportunities will be identified in co-creation with stakeholders, and will serve to strengthen the scientific advice, to improve long term production planning and the policy making process. ClimeFish will address 3 production sectors through 16 case studies involving 25 species, and study the predicted effects of 3 pre-defined climate scenarios. For 7 of these cases ClimeFish will develop specific management plans (MPs) coherent with the ecosystem approach and based on a results-based scheme that will allow regulators, fishers and aquaculture operators to anticipate, prepare and adapt to climate change while minimizing economic losses and social consequences. A guideline for how to make climate-enabled MPs will be produced, and published as a low-level, voluntary European standard after a consensus-based open consultation process. As a container for the models, scenarios and MPs ClimeFish will develop the ClimeFish Decision Support Framework (DSF) which also contains the ClimeFish Decision Support System (DSS); a software application with capabilities for what-if analysis and visualization of scenarios. The presence of key international stakeholders in the project will ensure quality and relevance of the project outputs thus ensuring uptake and significant impact also after project end.


Grant
Agency: European Commission | Branch: H2020 | Program: MSCA-RISE | Phase: MSCA-RISE-2015 | Award Amount: 243.00K | Year: 2016

Real animals and human populations are complex, involving structural relationships depending upon space and time and varied interactions between potentially many individuals. Human societies feature family units, communities, companies and nations. Some animal also have complex societies, such as primate groups and social insect colonies. Single organisms themselves can be thought of as complex ecosystems, host to many interacting life forms. Models of populations are necessarily idealised, and most involve either simple pairwise interactions or well-mixed structureless populations, or both. In this project we shall develop game-theoretical models, both general and focused on specific real population scenarios, which incorporate population structure and within population interactions which are both complex in character. We will focus on the themes of Conflict, Competition, Cooperation and Complexity inherent in the majority of real populations. There will be four complementary subprojects within the overall project. The first will focus on developing a general theory of modelling multiplayer evolutionary games in structured populations, and will feed into each of the other three subprojects. The second will consider complex foraging games, in particular games under time constraints and involving sequential decisions relating to patch choice. The third will involve developing computational models of spatio-temporal dynamics for the modelling of pandemics. The final subproject will model cancer as a complex adaptive system, where a population of tumour, normal and immune cells evolve within a human ecosystem. The four subprojects will be developed in parallel fostered by frequent research visits and interactions, each involving a team comprising of EU and North American researchers, and will feed into each other through regular interactions and meetings. The aim is to develop a rich, varied but consistent theory with wide applicability.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-CSA-Infra | Phase: INFRA-2007-2.2-01 | Award Amount: 4.16M | Year: 2008

This proposal for a major upgrade to the CESSDA Research Infrastructure is a response to the general principles and vision set out in the 2004 Blueprint for the European Research Obsrvatory for the Humanities and Social Science and will meet the goals set out in that report to strengthen interdisciplinary and cross-border collaboration and comparative research on a European dimension enhance the building of research infrastructure capacity in the less resourced European countries of today [and] it will increase the opportunity to improve knowledge on social processes and thus holds great potential in terms of advising European and national policy-makers on how to manage the challenges currently faced by the societies of Europe. Building on the existing operational structure of the Council of European Social Science Data Archives (CESSDA) network of data archives and its associated partners, this proposal for a major RI upgrade will seek to address the major gaps and deficiencies identified by the EROHS report on Research Infrastructures through the facilitation of access to and sharing of existing European and national data; the development of improved standards and documentation, and by enabling the linking of cross-national data and the generation of new and genuinely European data for the comparative researcher. Data are the single most important component necessary for a science based understanding of society and to promote and facilitate access to data is to promote research. Although there have been significant advances in recent years in making data available for scientific use, these advances have not bee European-wide. There still remains a large difference in both the actual availability of data as well as in the value that is attached to accessing data across Europe. This proposal will directly address these differences as a precursor to the implementation of an enhanced CESSDA Infrastructure.


Grant
Agency: European Commission | Branch: H2020 | Program: RIA | Phase: SFS-10a-2014 | Award Amount: 8.10M | Year: 2015

European aquaculture production provides direct employment to 80,000 people and a 3-billion annual turnover. Parasites cause severe disease outbreaks and high economic losses in finfish aquaculture. The overarching goal of ParaFishControl is to increase the sustainability and competitiveness of European Aquaculture by improving understanding of fish-parasite interactions and by developing innovative solutions and tools for the prevention, control and mitigation of the major parasites affecting Atlantic salmon, rainbow trout, common carp, European sea bass, gilthead sea bream and turbot. To achieve these objectives, ParaFishControl brings together a multidisciplinary consortium comprising 30 partners possessing world-leading, complementary, cross-cutting expertise and drawn from public and private research organisations, and the aquaculture industry. The consortium has access to excellent research facilities, diverse biological resources including host-parasite models, and state-of-the-art vaccinology, genomic, proteomic and transcriptomic technologies. The project will: 1) generate new scientific knowledge on key fish parasites, including genomics, life-cycle, invasion strategy and host-parasite interaction data, with special emphasis on host immunity, pathogen virulence and immunomodulation, providing a scientific basis for improved prophylaxis; 2) determine the transfer of parasites between farmed and wild host populations; 3) develop a wide range of novel prophylactic measures, including vaccines and functional feeds; 4) provide a range of advanced or alternative treatments for parasitic diseases; 5) develop cost-effective, specific and sensitive diagnostic tools for key parasitic diseases; 6) assess the risk factors involved in the emergence, transmission and pathogenesis of parasitic diseases; 7) map the zoonotic risks due to fish helminths and; 8) provide a catalogue of good husbandry practices to obtain safe and high-quality fish products.


Grant
Agency: European Commission | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2012-ITN | Award Amount: 4.00M | Year: 2013

INsecTIME seeks to train the next generation of ESRs in the intellectual, technological, complementary and commercial skills required for future European competitiveness in the area of biological timing, an area with considerable commercial potential. The scientific focus will be on circadian and seasonal rhythms in the model insect, Drosophila, which has proved particularly relevant for understanding temporal aspects of human health and well-being, plus non-model insects such as the parasitoid wasp and olive fruitfly, two species with major economic implications. The work is multidisciplinary, bringing together scientists from academia and the private sector with different skills in neurogenetics, genomics, life history biology, mathematical modelling, biocomputing, biological control, anatomy and population genetics. Through synergistic interactions via secondments to world class research institutions and to applied entomology and biocomputing SMEs, training workshops, and instruction in transferable skills, young researchers will learn the full-range of cutting-edge technical skills allied to an appreciation of the commercial possibilities of their work. Their obligatory secondments to SMEs will include training in the management, organisation and finance of the private sector, and be buttressed by further workshop courses in general bio-commerce, intellectual property, marketing, raising capital etc. They, and their supervisors will contribute to outreach programmes, and the ERSs and ERs will be guided in the development of their own personal career portfolios, with ESRs submitting doctoral theses. Our young researchers will represent the next crop of technically well-trained, but unusually, commercially aware, computer and mathematically literate molecular neurogeneticists, whose versatile skills will enhance pan-European collaborations for years to come.


Grant
Agency: European Commission | Branch: FP7 | Program: CSA-CA | Phase: Fission-2013-6.0.1 | Award Amount: 1.22M | Year: 2013

The objective of PLATENSO is to provide a proposal towards establishing the legal base for a European Entity on Socio-Economic matters linked to nuclear technology and to develop recommendations for research strategies in PLATENSO countries. Thereby the capabilities of research institutes in Central and Eastern European countries to take part in EU research with respect to governance, social and societal aspects is enhanced. Initially, lessons learned from earlier projects, what is the state of knowledge in societal, social and governance issues, are reviewed and summarized. The research infrastructures within which project activities and future research are to take place are mapped and efforts are made to make sure research actors frame their approaches broad enough. Research strategies are formed for research in governance, social and societal issues in which participation in EU programmes is an integrated part. The strategies are tested with case studies to make sure they are feasible to implement. A number of networking activities are carried through as a major step toward actual foundation of the strategies in PLATENSO countries. In each country a PLATENSO partner will take responsibility for building a network of research institutions in its respective country. Establishment of the legal base for a European Entity on Socio-Economic matters linked to nuclear technology has potential to overcome the barriers that still exist for taking them fully into account and to make the awareness of the social and political challenges to come to action. On the basis of exploratory studies focusing on Central and Eastern Europe and contacts with relevant stakeholders in all EU, the project will analyze main aspects with regard to the implementation of the entity (organization, legal form, communication structure, content, etc.). Major areas on social, societal and governance issues for the envisaged Entity will be proposed. A nuclear energy scenario based on the Generation 4 ALLEGRO reactor concept will be given special attention as a pilot case for the European Entity giving support to ALLEGRO in social, societal and governance issues, which will include testing the draft strategy for research. The exact forms for this will be developed in close cooperation between PLATENSO and the ALLIANCE project.


News Article | March 2, 2017
Site: www.eurekalert.org

The Ecological Society of America (ESA) will present the 2017 awards recognizing outstanding contributions to ecology in new discoveries, teaching, sustainability, diversity, and lifelong commitment to the profession during the Society's Annual Meeting in Portland, Ore. The awards ceremony will take place during the Scientific Plenary on Monday, August 7, at 8 AM in the Oregon Ballroom, Oregon Convention Center. Learn more about ESA awards on our home website. The Eminent Ecologist Award honors a senior ecologist for an outstanding body of ecological work or sustained ecological contributions of extraordinary merit. Soil ecologist Diana Wall, the founding director of the Colorado State University's School of Global Environmental Sustainability, is world-renowned for uncovering the importance of below-ground processes. Best known for her outstanding quarter century of research in the McMurdo Dry Valleys in Antarctica, one of the more challenging environments of the planet. Her research has revealed fundamental soil processes from deserts and forests to grasslands and agricultural ecosystems to New York City's Central Park. Dr. Wall's extensive collaborative work seeks to understand how the living component of soil contributes to ecosystem processes and human wellbeing--and to in turn uncover how humans impact soils, from local to global scales. In landmark studies, she revealed the key role of nematodes and other tiny animals as drivers of decomposition rates and carbon cycling. The biodiversity in soils, she found, influences ecosystem functioning and resilience to human disturbance, including climate change. She demonstrated that the biodiversity belowground can at times be decoupled from biodiversity aboveground. Her focus on nematodes in soils in very harsh environments, from the cold, dry Antarctic to hot, dry deserts, opened up a perspective on how life copes with extreme environments. She has a laudable record of publishing excellent papers in top-ranked scientific journals. Dr. Wall has played a vital role as an ecological leader, chairing numerous national and international committees and working groups and serving as president of the Ecological Society of America in 1999. She is a Fellow of ESA, the American Association for the Advancement of Science, and the Society of Nematologists. In 2013, she received the Tyler Prize for Environmental Achievement for her outspoken efforts as an ambassador for the environmental and economic importance of soils and ecology. Currently, she is scientific chair of the Global Soil Biodiversity Initiative, which works to advance soil biodiversity for use in policy and management of terrestrial ecosystems. Dr. Wall is well-respected in her role as mentor of young scientists, over several generations, and as a communicator of science outside the usual academic arenas. Odum Award recipients demonstrate their ability to relate basic ecological principles to human affairs through teaching, outreach, and mentoring activities.? Kathleen Weathers is a senior scientist and the G.Evelyn Hutchinson chair of ecology at the Cary Institute of Ecosystem Studies, where she focuses on freshwater ecosystems. For more than a decade, she has been dedicated to advancing bottom-up network science, creating training opportunities for graduate students and tools for citizen science engagement. Her efforts strive to equip the next generation of ecologists and managers with the skills needed to protect freshwater resources. Dr Weathers played a guiding role in the formation of the Global Lake Ecological Observatory Network (GLEON), and currently acts as co-chair. A part of this international grassroots collaboration she helped develop Lake Observer, a crowd-sourcing App that streamlines the way that researchers and citizen scientists record water quality observations in lakes, rivers, and streams. Dr. Weathers has made it a priority to mentor students and early-career scientists participating in GLEON, with an eye toward diversity, inclusion, and instruction. She helped empower GLEON's student association, which contributes meaningfully to governance and training within the broader network. She also spearheaded the development of the GLEON Fellows Program, a two-year graduate immersion in data analysis, international collaboration, effective communication, and team science. The GLEON Fellows Program has emerged as a model for training initiatives in macrosystem ecology, and will affect the ecological community positively for decades to come, as participants carry their training forward to other institutions and endeavors. The Distinguished Service Citation recognizes long and distinguished volunteer service to ESA, the scientific community, and the larger purpose of ecology in the public welfare. Debra Peters is the founding editor-in-chief of ESA's newest journal, Ecosphere, created in 2010 to offer a rapid path to publication for research reports from across the spectrum of ecological science, including interdisciplinary studies that may have had difficulty finding a home within the scope of the existing ESA family of journals. In her hands the online-only, open-access journal has claimed a successful niche in the ecological publications landscape, expanding to publish over 400 manuscripts in 2016. Dr. Peters, an ecologist for the United States Department of Agriculture Agricultural Research service's (USDA-ARS) Jornada Experimental Range and lead principal investigator for the Jornada Basin Long Term Ecological Research program in Las Cruces, New Mexico, has served on the editorial boards of ESA's journals Ecological Applications, Ecology and Ecological Monographs. She chaired the society's Rangeland Section, was a founding member and chair of the Southwest Chapter, and has served as member-at-large on the Governing Board. As program chair for the 98th Annual Meeting of the society, she inaugurated the wildly popular Ignite talks, which give speakers the opportunity to present conceptual talks that do not fit into the standard research presentation format. Dr. Peters has greatly contributed to the broader research enterprise as senior advisor to the chief scientist at the USDA, and as a member of the National Ecological Observatory Network's (NEON) Board of Directors. She has provided this quite amazing array of services in support of the society and her profession while maintaining an outstanding level of research productivity and scientific leadership in landscape-level, cross-scale ecosystem ecology. Many of her more than 100 research publication have been cited more than 100 times. Her fine record of research led to her election as a Fellow of ESA and the American Association for the Advancement of Science. In all respects, Debra Peters exemplifies distinguished service to the ESA, and to science. ESA's Commitment to Human Diversity in Ecology award recognizes long-standing contributions of an individual towards increasing the diversity of future ecologists through mentoring, teaching, or outreach. Gillian Bowser, research scientist in Colorado State University's Natural Resource Ecology Laboratory, is honored for her joyful and successful recruitment and retention of under-represented students to the study of ecology, to public service in support of the natural world, and to empowerment of women and minorities worldwide. The Cooper Award honors the authors of an outstanding publication in the field of geobotany, physiographic ecology, plant succession or the distribution of plants along environmental gradients. William S. Cooper was a pioneer of physiographic ecology and geobotany, with a particular interest in the influence of historical factors, such as glaciations and climate history, on the pattern of contemporary plant communities across landforms. University of Waterloo, Ontario professor Andrew Trant and colleagues at the University of Victoria and the Hakai Institute in British Columbia revealed a previously unappreciated historical influence on forest productivity: long-term residence of First Nations people. Counter to a more familiar story of damage to ecosystems inflicted by people and their intensive use of resources, the activities of native people on the Central Coast of British Columbia enhanced the fertility of the soil around habitation sites, leading to greater productivity of the dominant tree species, the economically and culturally valuable western redcedar (Thuja plicata Donn ex D. Don). Through a combination of airborne remote sensing and on-the-ground field work, the authors showed that forest height, width, canopy cover, and greenness increased on and near shell middens. They presented the first documentation of influence on forest productivity by the daily life activities of traditional human communities. The Mercer Award recognizes an outstanding and recently-published ecological research paper by young scientists. Biological invasions, and migrations of native species in response to climate change, are pressing areas of interest in this time of global change. Fragmentation of the landscape by natural and human-made barriers slows the velocity of spread, but it is not known how patchy habitat quality might influence the potential for evolution to accelerate invasions. Jennifer Williams, an assistant professor at the University of British Columbia, and colleagues implemented a creative experimental design using the model plant species Arabidopsis thaliana that allowed them to disentangle ecological and evolutionary dynamics during population expansion. Some plant populations were allowed to evolve, while others were continually reset to their original genetic composition. The authors convincingly demonstrate that rapid evolution can influence the speed at which populations spread, especially in fragmented landscapes. The Sustainability Science Award recognizes the authors of the scholarly work that makes the greatest contribution to the emerging science of ecosystem and regional sustainability through the integration of ecological and social sciences. Sustainability challenges like air pollution, biodiversity loss, climate change, energy and food security, disease spread, species invasion, and water shortages and pollution are often studied, and managed, separately, although they the problems they present are interconnected. Jianguo Liu and colleagues provide a framework for addressing global sustainability challenges from a coupled human and natural systems approach that incorporates both socioeconomic and environmental factors. They review several recent papers that have quantified at times conflicting efforts to provide ecosystem services, when these efforts are examined in a global perspective. The authors argue for the need to quantify spillover systems and feedbacks and to integrate analyses over multiple spatial and temporal scales. This will likely require the development of new analytical frameworks both to understand the social ecological mechanisms involved and to inform management and policy decisions for global sustainability. The Innovation in Sustainability Science Award recognizes the authors of a peer-reviewed paper published in the past five years exemplifying leading-edge work on solution pathways to sustainability challenges. One of the biggest challenges facing development of effective policy to address sustainability issues is that the concepts and vocabulary used by scientists to define and promote sustainability rarely translate into effective policy, because they do not include measures of success. This challenge is particularly apparent in the concept of stability and resilience, terms which are frequently used in policy statements and have long been the subject of empirical and theoretical research in ecology, but for which there are no easily defined and quantified metrics. Ian Donohue and colleagues argue that much of the fault for this disconnect lies with the academic community. They summarize and analyze a number of examples to support their claim that ecologists have taken a one-dimensional approach to quantifying stability and disturbance when these are actually multi-dimensional processes. They argue that this has led to confused communication of the nature of stability, which contributes to the lack of adoption of clear policies. They propose three areas where future research is needed and make clear recommendations for better integrating the multidimensional nature of stability into research, policy and actions that should become a priority for all involved in sustainability science. The Whittaker Award recognizes an ecologist with an earned doctorate and an outstanding record of contributions in ecology who is not a U.S. citizen and who resides outside the United States. Petr Pyšek, the chair of the Department of Invasion Ecology at the Academy of Sciences of the Czech Republic, is honored for his pioneering and insightful work in invasion ecology. Dr. Pyšek is editor-in-chief of Preslia (Journal of the Czech Botanical Society) and serves on the editorial boards of Biological Invasions, Diversity and Distributions, Folia Geobotanica, and Perspectives on Plant Ecology, Evolution and Systematics. The Shreve award supplies $1,000-2,000 to support ecological research by graduate or undergraduate student members of ESA in the hot deserts of North America (Sonora, Mohave, Chihuahua, and Vizcaino). Daniel Winkler, a PhD student with Travis Huxman at University of California Irvine, studies the invasion of Sahara mustard (Brassica tournefortii) in the Mojave, Sonoran, and Chihuahuan deserts. His dissertation focuses on determining the source populations of Sahara mustard and whether plasticity in functional traits is allowing the species to spread. Funds from the Forrest Shreve Student Research Fund will be used to process samples for leaf stable isotopes and elemental stoichiometry, allowing for a comparison of functional traits indicative of local adaptation and the species' plasticity. Daniel was a National Park Service Young Leaders in Climate Change Fellow and a NSF EAPSI Research Fellow. Learn more about the August 7-12, 2017 ESA Annual Meeting on the meeting website: http://esa. ESA welcomes attendance from members of the press and waives registration fees for reporters and public information officers. To apply, please contact ESA Communications Officer Liza Lester directly at llester@esa.org. The Ecological Society of America (ESA), founded in 1915, is the world's largest community of professional ecologists and a trusted source of ecological knowledge, committed to advancing the understanding of life on Earth. The 10,000 member Society publishes five journals and a membership bulletin and broadly shares ecological information through policy, media outreach, and education initiatives. The Society's Annual Meeting attracts 4,000 attendees and features the most recent advances in ecological science. Visit the ESA website at http://www. .


Van Rijt S.H.,University of Warwick | Kostrhunova H.,Academy of Sciences of the Czech Republic | Brabec V.,Academy of Sciences of the Czech Republic | Sadler P.J.,University of Warwick
Bioconjugate Chemistry | Year: 2011

Attaching peptides to metallodrugs may result in improved biological properties of the complexes. The potential use of cell penetrating peptides (CPPs) as cell delivery vectors is attractive, since directed cell uptake of (metallo)drugs remains a major challenge in anticancer drug design. In this work, we report the synthesis of peptide conjugates of the organometallic Os II anticancer complex [(η 6-biphenyl)Os(picolinate) Cl] with different arginine (Arg) chain lengths. Complexes conjugated to Arg 5 or Arg 8 at the 5-position of the picoline ring increase Os uptake into A2780 human ovarian cancer cells by ca. 2× and 10×, respectively, whereas a single Arg had no effect. Furthermore, a 15-fold increase in binding of Os to DNA, a potential target for these complexes, was observed for Arg 8 compared to the Arg 1 conjugate. The Arg 5 and Arg 8 conjugates exhibited fast kinetics of binding to calf thymus DNA and an ability to precipitate DNA at very low concentrations. In serum-free medium, the Arg 8 complex was cytotoxic (IC 50 33 μM) and appears to be a rare example of a bioactive organometallic peptide conjugate. Experiments on CHO cells deficient in DNA repair suggested that unrepaired DNA damage contributes to the cytotoxicity of the Arg 5 and Arg 8 conjugates. These studies demonstrate the potential for use of cell- and nucleus-penetrating peptides in targeting organometallic arene anticancer complexes. © 2011 American Chemical Society.


Reblova K.,Academy of Sciences of the Czech Republic | Reblova K.,Masaryk University | Sponer J.,Academy of Sciences of the Czech Republic | Sponer J.,Masaryk University | Lankas F.,Czech Institute of Organic Chemistry And Biochemistry
Nucleic Acids Research | Year: 2012

The L1 stalk is a key mobile element of the large ribosomal subunit which interacts with tRNA during translocation. Here, we investigate the structure and mechanical properties of the rRNA H76/H75/H79 three-way junction at the base of the L1 stalk from four different prokaryotic organisms. We propose a coarse-grained elastic model and parameterize it using large-scale atomistic molecular dynamics simulations. Global properties of the junction are well described by a model in which the H76 helix is represented by a straight, isotropically flexible elastic rod, while the junction core is represented by an isotropically flexible spherical hinge. Both the core and the helix contribute substantially to the overall H76 bending fluctuations. The presence of wobble pairs in H76 does not induce any increased flexibility or anisotropy to the helix. The half-closed conformation of the L1 stalk seems to be accessible by thermal fluctuations of the junction itself, without any long-range allosteric effects. Bending fluctuations of H76 with a bulge introduced in it suggest a rationale for the precise position of the bulge in eukaryotes. Our elastic model can be generalized to other RNA junctions found in biological systems or in nanotechnology. © 2012 The Author(s).


Stengl V.,Academy of Sciences of the Czech Republic | Henych J.,Academy of Sciences of the Czech Republic | Henych J.,J.E. Purkyne University in Ústí nad Labem
Nanoscale | Year: 2013

Intense ultrasound in a pressurized batch reactor was used for preparation of monolayered MoS2 nanosheets from natural mineral molybdenite. Exfoliation of bulk MoS2 using ultrasound is an attractive route to large-scale preparation of monolayered crystals. To evaluate the quality of delamination, methods like X-ray diffraction, Raman spectroscopy and microscopic techniques (TEM and AFM) were employed. From single- or few-layered products obtained from intense sonication, MoS2 quantum dots (MoSQDs) were prepared by a one-pot reaction by refluxing exfoliated nanosheets of MoS 2 in ethylene glycol under atmospheric pressure. The synthesised MoSQDs were characterised by photoluminescence spectroscopy and laser-scattering particle size analysis. Our easy preparation leads to very strongly green luminescing quantum dots. © The Royal Society of Chemistry 2013.


Hervik S.,University of Stavanger | Pravda V.,Academy of Sciences of the Czech Republic | Pravdova A.,Academy of Sciences of the Czech Republic
Classical and Quantum Gravity | Year: 2014

Universal spacetimes are spacetimes for which all conserved symmetric rank-2 tensors, constructed as contractions of polynomials from the metric, the Riemann tensor and its covariant derivatives of arbitrary order, are multiples of the metric. Consequently, metrics of universal spacetimes solve vacuum equations of all gravitational theories, with the Lagrangian being a polynomial curvature invariant constructed from the metric, the Riemann tensor and its derivatives of arbitrary order. In the literature, universal metrics are also discussed as metrics with vanishing quantum corrections and as classical solutions to string theory. Widely known examples of universal metrics are certain Ricci-flat pp waves. In this paper, we start a general study of the geometric properties of universal metrics in arbitrary dimension and arrive at a broader class of such metrics. In contrast with pp waves, these universal metrics also admit a non-vanishing cosmological constant and in general do not have to possess a covariant constant or recurrent null vector field. First, we show that a universal spacetime is necessarily a constant curvature invariant spacetime, i.e. all curvature invariants constructed from the Riemann tensor and its derivatives are constant. Then we focus on type N spacetimes, where we arrive at a simple necessary and sufficient condition: a type N spacetime is universal if and only if it is an Einstein Kundt spacetime. A class of type III Kundt universal metrics is also found. Several explicit examples of universal metrics are presented. © 2014 IOP Publishing Ltd.


Pravenec M.,Academy of Sciences of the Czech Republic | Kurtz T.W.,University of California at San Francisco
Current Hypertension Reports | Year: 2010

The spontaneously hypertensive rat (SHR) is the most widely used animal model of essential hypertension and associated metabolic disturbances. Multiple quantitative trait loci associated with hemodynamic and metabolic parameters have been mapped in the SHR. Recently, it has become possible to identify some of the specific quantitative trait gene (QTG) variants that underlie quantitative trait loci linked to complex cardiovascular and metabolic traits in SHR related strains. Recombinant inbred strains derived from SHR and Brown Norway progenitors, together with SHR congenic and transgenic strains, have proven useful for establishing the identity of several QTGs in SHR models. It is anticipated that the combined use of linkage analyses and gene expression profiles, together with the recently available genome sequences of both the SHR and Brown Norway strains and new methods for manipulating the rat genome, will soon accelerate progress in identifying QTGs for complex traits in SHR-related strains.


Schwarz A.,Academy of Sciences of the Czech Republic | Von Reumont B.M.,Natural History Museum in London | Erhart J.,Academy of Sciences of the Czech Republic | Chagas A.C.,National Institute of Allergy and Infectious Diseases | And 2 more authors.
FASEB Journal | Year: 2013

Tick salivary gland (SG) proteins possess powerful pharmacologic properties that facilitate tick feeding and pathogen transmission. For the first time, SG transcriptomes of Ixodes ricinus, an important disease vector for humans and animals, were analyzed using next-generation sequencing. SGs were collected from different tick life stages fed on various animal species, including cofeeding of nymphs and adults on the same host. Four cDNA samples were sequenced, discriminating tick SG transcriptomes of early- and late-feeding nymphs or adults. In total, 441,381,454 pyrosequencing reads and 67,703,183 Illumina reads were assembled into 272,220 contigs, of which 34,560 extensively annotated coding sequences are disclosed; 8686 coding sequences were submitted to GenBank. Overall, 13% of contigs were classified as secreted proteins that showed significant differences in the transcript representation among the 4 SG samples, including high numbers of sample-specific transcripts. Detailed phylogenetic reconstructions of two relatively abundant SG-secreted protein families demonstrated how this study improves our understanding of the molecular evolution of hematophagy in arthropods. Our data significantly increase the available genomic information for I. ricinus and form a solid basis for future tick genome/transcriptome assemblies and the functional analysis of effectors that mediate the feeding physiology and parasite-vector interaction of I. ricinus.-Schwarz, A., von Reumont, B.M., Erhart, J., Chagas, A.C., Ribeiro, J.M.C., Kotsyfakis, M. De novo Ixodes ricinus salivary gland transcriptome analysis using two next-generation sequencing methodologies. © FASEB.


Sojka D.,Academy of Sciences of the Czech Republic | Franta Z.,Academy of Sciences of the Czech Republic | Horn M.,Czech Institute of Organic Chemistry And Biochemistry | Caffrey C.R.,University of California at San Francisco | And 2 more authors.
Trends in Parasitology | Year: 2013

Blood-protein digestion is a key physiological process providing essential nutrients for ticks and is a prerequisite for the transmission of tick-borne pathogens. Recently, substantial progress has been made in determining the proteolytic machinery in tick gut tissue, which is based on a dynamic multienzyme network capable of processing a vast amount of host blood. In this article we summarize our current knowledge of the molecular mechanisms of tick hematophagy and their similarities to those of Platyhelminthes, nematodes, and Plasmodium. Future research perspectives, including the potential for rational control of ticks and transmitted diseases, are also discussed. © 2013 Elsevier Ltd.


Malina J.,Academy of Sciences of the Czech Republic | Scott P.,University of Warwick | Brabec V.,Academy of Sciences of the Czech Republic
Nucleic Acids Research | Year: 2015

Loss of a base in DNA leading to creation of an abasic (AP) site leaving a deoxyribose residue in the strand, is a frequent lesion that may occur spontaneously or under the action of various physical and chemical agents. Progress in the understanding of the chemistry and enzymology of abasic DNA largely relies upon the study of AP sites in synthetic duplexes. We report here on interactions of diastereomerically pure metallo-helical 'flexicate' complexes, bimetallic triple-stranded ferro-helicates [Fe2(NN-NN)3]4+ incorporating the common NN-NN bis(bidentate) helicand, with short DNA duplexes containing AP sites in different sequence contexts. The results show that the flexicates bind to AP sites in DNA duplexes in a shape-selective manner. They preferentially bind to AP sites flanked by purines on both sides and their binding is enhanced when a pyrimidine is placed in opposite orientation to the lesion. Notably, the Λ-enantiomer binds to all tested AP sites with higher affinity than the Δ-enantiomer. In addition, the binding of the flexicates to AP sites inhibits the activity of human AP endonuclease 1, which is as a valid anticancer drug target. Hence, this finding indicates the potential of utilizing well-defined metallo-helical complexes for cancer chemotherapy. © 2015 The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.


Ostapovets A.,Academy of Sciences of the Czech Republic | Ostapovets A.,ASCR Institute of Physics Prague | Serra A.,Polytechnic University of Catalonia
Philosophical Magazine | Year: 2014

A model of twin growth in magnesium is presented together with the analysis of defects responsible for this growth. The twin interface is represented by and basal-prismatic facets. Disclinations are situated in the facet junctions creating dipoles superimposed on basal-prismatic and conjugate twin facets. The migration of facets is mediated by the conservative motion of interfacial disconnections. The interfaces contain twinning disconnections. The facet junctions serve as sources and sinks for these defects. Two types of disconnections (and) were observed in basal-prismatic boundary. The dipoles of disconnections were nucleated in the vicinity of existing defects of this type. Interaction of this dipole with existing leads to the creation of a disconnection, which is later absorbed in the facet junction. The nucleation of dipoles was not observed. In twin embryo growth, the basal-prismatic segments remain coherent with a fixed length, while the twin segments grow indefinitely. © 2014 © 2014 Taylor & Francis.


Guttman A.,University of Pannonia | Guttman A.,Academy of Sciences of the Czech Republic
TrAC - Trends in Analytical Chemistry | Year: 2013

In N-glycosylation analysis of biopharmaceuticals, analytical need depends on the phase of the manufacturing process. All important glycoanalysis steps are thoroughly discussed. Carbohydrate sequencing by exoglycosidase arrays is described in conjunction with capillary electrophoresis (CE) to identify linkage and positional isomers. A possible automated workflow for N-glycosylation based on CE is outlined. © 2013.


Kuzmiak V.,Academy of Sciences of the Czech Republic | Eyderman S.,Academy of Sciences of the Czech Republic | Vanwolleghem M.,University Paris - Sud
Physical Review B - Condensed Matter and Materials Physics | Year: 2012

We have demonstrated numerically by using of Fourier modal method (FMM) that the interface between a metal and a uniformly magnetized two-dimensional photonic crystal fabricated from a transparent dielectric magneto-optical (MO) material possesses a one-way frequency range in which a surface plasmon polariton (SPP) is allowed to propagate only in one direction. The time-reversal symmetry breaking is implied by the MO properties of the photonic crystal material, namely, bismuth iron garnet (BIG), which may be magnetically saturated by fields of the order of tens of milli tesla. The results obtained by FMM have been validated by a theoretical model and a standard plane-wave method that yield separately a nonreciprocal dispersion relation for the SPP and the band structure of the two-dimensional magneto-optical photonic crystal (2D MOPhC), respectively. These spectra represent the key characteristics assuring the functionality of the one-way waveguide associated with the both underlying mechanisms, namely, time-reversal symmetry breaking and a suppression of disorder-induced backscattering. By using a generalized finite-difference time-domain (FDTD) method, which allows studying the propagation of electromagnetic (EM) waves through media with a tensor MO permittivity, we studied transport properties of the one-way waveguide. We examined the influence of specific types of boundary conditions on one-way functionality in the presence of a static external magnetic field and have shown that the SPP can be dynamically controlled by applying a time-dependent magnetic field. By evaluating the Fourier transform of the energy density, we have analyzed the behavior of the field patterns observed in the waveguide in the case of ac magnetic field, and have interpreted new and interesting features associated with the redistribution of the EM field that may offer new mechanisms for dynamical control of SPP flow. © 2012 American Physical Society.


Wimmer Z.,Academy of Sciences of the Czech Republic | Zarevucka M.,Czech Institute of Organic Chemistry And Biochemistry
International Journal of Molecular Sciences | Year: 2010

Different types of enzymes such as lipases, several phosphatases, dehydrogenases, oxidases, amylases and others are well suited for the reactions in SC-CO2. The stability and the activity of enzymes exposed to carbon dioxide under high pressure depend on enzyme species, water content in the solution and on the pressure and temperature of the reaction system. The three-dimensional structure of enzymes may be significantly altered under extreme conditions, causing their denaturation and consequent loss of activity. If the conditions are less adverse, the protein structure may be largely retained. Minor structural changes may induce an alternative active protein state with altered enzyme activity, specificity and stability. © 2010 by the authors; licensee Molecular Diversity Preservation International.


Kurtz T.W.,University of California at San Francisco | Dominiczak A.F.,University of Glasgow | Dicarlo S.E.,Wayne State University | Pravenec M.,Academy of Sciences of the Czech Republic | Morris R.C.,University of California at San Francisco
Hypertension | Year: 2015

This critical review directly challenges the prevailing theory that a transient increase in cardiac output caused by genetically mediated increases in activity of the ENaC in the aldosterone sensitive distal nephron, or of the NCC in the distal convoluted tubule, accounts entirely for the hemodynamic initiation of all Mendelian forms of salt-dependent hypertension (Figure 1).2,3,7,8 The prevailing theory of how genetic mutations enable salt to hemodynamically initiate Mendelian forms of salt-dependent hypertension in humans (Figure 1)2 depends on the results of salt-loading studies of cardiac output and systemic vascular resistance in nongenetic models of hypertension that lack appropriate normal controls. The theory is inconsistent with the results of studies that include measurements of the initial hemodynamic changes induced by salt loading in normal, salt-resistant controls. The present analysis, which takes into account the results of salt-loading studies that include the requisite normal controls, indicates that mutation-induced increases in the renal tubular activity of ENaC or NCC that lead to transient increases in cardiac output will generally not be sufficient to enable increases in salt intake to initiate the increased BP that characterizes Mendelian forms of salt-dependent hypertension (Table). The present analysis also raises questions about whether mutation-dependent increases in renal tubular activity of ENaC or NCC are even necessary to account for increased risk for salt-dependent hypertension in most patients with such mutations. We propose that for the genetic alterations underlying Mendelian forms of salt-dependent hypertension to enable increases in salt intake to initiate the increased BP, they must ften cause vasodysfunction, ie, an inability to normally vasodilate and decrease systemic vascular resistance in response to increases in salt intake within dietary ranges typically observed in most modern societies. A subnormal ability to vasodilate in response to salt loading could be caused by mutation-related disturbances originating in the vasculature itself or in sites outside the vasculature (eg, brain or adrenal glands) that have the capacity to affect vascular function. © 2015 American Heart Association, Inc.


Jansa J.,Academy of Sciences of the Czech Republic | Jansa J.,ETH Zurich | Erb A.,ETH Zurich | Oberholzer H.-R.,ART Agroscope Reckenholz Tänikon | And 2 more authors.
Molecular Ecology | Year: 2014

Arbuscular mycorrhizal fungi (AMF) are ubiquitous soil fungi, forming mutualistic symbiosis with a majority of terrestrial plant species. They are abundant in nearly all soils, less diverse than soil prokaryotes and other intensively studied soil organisms and thus are promising candidates for universal indicators of land management legacies and soil quality degradation. However, insufficient data on how the composition of indigenous AMF varies along soil and landscape gradients have hampered the definition of baselines and effect thresholds to date. Here, indigenous AMF communities in 154 agricultural soils collected across Switzerland were profiled by quantitative real-time PCR with taxon-specific markers for six widespread AMF species. To identify the key determinants of AMF community composition, the profiles were related to soil properties, land management and site geography. Our results indicate a number of well-supported dependencies between abundances of certain AMF taxa and soil properties such as pH, soil fertility and texture, and a surprising lack of effect of available soil phosphorus on the AMF community profiles. Site geography, especially the altitude and large geographical distance, strongly affected AMF communities. Unexpected was the apparent lack of a strong land management effect on the AMF communities as compared to the other predictors, which could be due to the rarity of highly intensive and unsustainable land management in Swiss agriculture. In spite of the extensive coverage of large geographical and soil gradients, we did not identify any taxon suitable as an indicator of land use among the six taxa we studied. © 2014 John Wiley & Sons Ltd.


Howson S.E.,University of Warwick | Bolhuis A.,University of Bath | Brabec V.,Academy of Sciences of the Czech Republic | Clarkson G.J.,University of Warwick | And 3 more authors.
Nature Chemistry | Year: 2012

The helicates-chiral assemblies of two or more metal atoms linked by short or relatively rigid multidentate organic ligands-may be regarded as non-peptide mimetics of α-helices because they are of comparable size and have shown some relevant biological activity. Unfortunately, these beautiful helical compounds have remained difficult to use in the medicinal arena because they contain mixtures of isomers, cannot be optimized for specific purposes, are insoluble, or are too difficult to synthesize. Instead, we have now prepared thermodynamically stable single enantiomers of monometallic units connected by organic linkers. Our highly adaptable self-assembly approach enables the rapid preparation of ranges of water-stable, helicate-like compounds with high stereochemical purity. One such iron(II) 'flexicate' system exhibits specific interactions with DNA, promising antimicrobial activity against a Gram-positive bacterium (methicillin-resistant Staphylococcus aureus, MRSA252), but also, unusually, a Gram-negative bacterium (Escherichia coli, MC4100), as well as low toxicity towards a non-mammalian model organism (Caenorhabditis elegans). © 2011 Macmillan Publishers Limited. All rights reserved.


Antvorskov J.C.,Rigshospitalet Ole | Josefsen K.,Rigshospitalet Ole | Engkilde K.,Rigshospitalet Ole | Funda D.P.,Rigshospitalet Ole | And 2 more authors.
Diabetologia | Year: 2014

Gluten proteins differ from other cereal proteins as they are partly resistant to enzymatic processing in the intestine, resulting in a continuous exposure of the proteins to the intestinal immune system. In addition to being a disease-initiating factor in coeliac disease (CD), gluten intake might affect type 1 diabetes development. Studies in animal models of type 1 diabetes have documented that the pathogenesis is influenced by diet. Thus, a gluten-free diet largely prevents diabetes in NOD mice while a cereal-based diet promotes diabetes development. In infants, amount, timing and mode of introduction have been shown to affect the diabetogenic potential of gluten, and some studies now suggest that a gluten-free diet may preserve beta cell function. Other studies have not found this effect. There is evidence that the intestinal immune system plays a primary role in the pathogenesis of type 1 diabetes, as diabetogenic T cells are initially primed in the gut, islet-infiltrating T cells express gut-associated homing receptors, and mesenteric lymphocytes transfer diabetes from NOD mice to NOD/severe combined immunodeficiency (SCID) mice. Thus, gluten may affect diabetes development by influencing proportional changes in immune cell populations or by modifying the cytokine/chemokine pattern towards an inflammatory profile. This supports an important role for gluten intake in the pathogenesis of type 1 diabetes and further studies should be initiated to clarify whether a gluten-free diet could prevent disease in susceptible individuals or be used with newly diagnosed patients to stop disease progression. © 2014 The Author(s).


Ozdener M.H.,Monell Chemical Senses Center | Subramaniam S.,University of Burgundy | Sundaresan S.,Washington University in St. Louis | Sery O.,Academy of Sciences of the Czech Republic | And 5 more authors.
Gastroenterology | Year: 2014

Background & Aims It is important to increase our understanding of gustatory detection of dietary fat and its contribution to fat preference. We studied the roles of the fat taste receptors CD36 and GPR120 and their interactions via Ca2+ signaling in fungiform taste bud cells (TBC). Methods We measured Ca2+ signaling in human TBC, transfected with small interfering RNAs against messenger RNAs encoding CD36 and GPR120 (or control small interfering RNAs). We also studied Ca2+ signaling in TBC from CD36-/- mice and from wild-type lean and obese mice. Additional studies were conducted with mouse enteroendocrine cell line STC-1 that express GPR120 and stably transfected with human CD36. We measured release of serotonin and glucagon-like peptide-1 from human and mice TBC in response to CD36 and GPR120 activation. Results High concentrations of linoleic acid induced Ca2+ signaling via CD36 and GPR120 in human and mice TBC, as well as in STC-1 cells, and low concentrations induced Ca2+ signaling via only CD36. Incubation of human and mice fungiform TBC with lineoleic acid down-regulated CD36 and up-regulated GPR120 in membrane lipid rafts. Obese mice had decreased spontaneous preference for fat. Fungiform TBC from obese mice had reduced Ca2+ and serotonin responses, but increased release of glucagon-like peptide-1, along with reduced levels of CD36 and increased levels of GPR120 in lipid rafts. Conclusions CD36 and GPR120 have nonoverlapping roles in TBC signaling during orogustatory perception of dietary lipids; these are differentially regulated by obesity. © 2014 by the AGA Institute.


Polivka T.,University of South Bohemia | Polivka T.,Academy of Sciences of the Czech Republic | Frank H.A.,University of Connecticut
Accounts of Chemical Research | Year: 2010

Carotenoids are naturally occurring pigments that absorb light in the spectral region in which the sun irradiates maximally. These molecules transfer this energy to chlorophylls, initiating the primary photochemical events of photosynthesis. Carotenoids also regulate the flow of energy within the photosynthetic apparatus and protect it from photoinduced damage caused by excess light absorption. To carry out these functions in nature, carotenoids are bound in discrete pigment-protein complexes in the proximity of chlorophylls. A few three-dimensional structures of these carotenoid complexes have been determined by X-ray crystallography. Thus, the stage is set for attempting to correlate the structural information with the spectroscopic properties of carotenoids to understand the molecular mechanism(s) of their function in photosynthetic systems. In this Account, we summarize current spectroscopic data describing the excited state energies and ultrafast dynamics of purified carotenoids in solution and bound in light-harvesting complexes from purple bacteria, marine algae, and green plants. Many of these complexes can be modified using mutagenesis or pigment exchange which facilitates the elucidation of correlations between structure and function. We describe the structural and electronic factors controlling the function of carotenoids as energy donors. We also discuss unresolved issues related to the nature of spectroscopically dark excited states, which could play a role in light harvesting. To illustrate the interplay between structural determinations and spectroscopic investigations that exemplifies work in the field, we describe the spectroscopic properties of four light-harvesting complexes whose structures have been determined to atomic resolution. The first, the LH2 complex from the purple bacterium Rhodopseudomonas acidophila, contains the carotenoid rhodopin glucoside. The second is the LHCII trimeric complex from higher plants which uses the carotenoids lutein, neoxanthin, and violaxanthin to transfer energy to chlorophyll. The third, the peridinin-chlorophyll-protein (PCP) from the dinoflagellate Amphidinium carterae, is the only known complex in which the bound carotenoid (peridinin) pigments outnumber the chlorophylls. The last is xanthorhodopsin from the eubacterium Salinibacter ruber. This complex contains the carotenoid salinixanthin, which transfers energy to a retinal chromophore. The carotenoids in these pigment-protein complexes transfer energy with high efficiency by optimizing both the distance and orientation of the carotenoid donor and chlorophyll acceptor molecules. Importantly, the versatility and robustness of carotenoids in these light-harvesting pigment-protein complexes have led to their incorporation in the design and synthesis of nanoscale antenna systems. In these bioinspired systems, researchers are seeking to improve the light capture and use of energy from the solar emission spectrum. © 2010 American Chemical Society.


Svozil D.,Institute of Chemical Technology Prague | Hobza P.,Czech Institute of Organic Chemistry And Biochemistry | Hobza P.,Palacky University | Sponer J.,Academy of Sciences of the Czech Republic
Journal of Physical Chemistry B | Year: 2010

High level ab initio methods have been used to study stacking interactions in ten unique base pair steps both in A-RNA and in B-DNA duplexes. The protocol for selection of geometries based on molecular dynamics (MD) simulations is proposed, and its suitability is demonstrated by comparison with stacking in steps at fiber diffraction geometries. It is shown that fiber diffraction geometries are not sufficiently accurate for interaction energy calculations. In addition, the protocol for selection of geometries based on MD simulations allows for the evaluation of the variability of the intrinsic stacking energies along the MD trajectories. The uncertainty in stacking energies (difference between the most and least stable geometry) due to the dynamical nature of systems can be, in some cases, as large as 3.0 kcal• mol-1, which is almost 50% of the actual sequence dependence of base stacking energies (the energy difference between the most and least stable sequences). Thus, assessing the relative magnitude of the gas phase stacking energy using a single geometry for each sequence is insufficient to obtain an unambiguous order of gas phase stacking energies in canonical double helices. Though the ordering of ten unique dinucleotide steps cannot be definitive, some general conclusions were drawn. The stacking energies of base pair steps in A-RNA are more evenly separated compared to B-DNA, and their ordering is less sensitive to the dynamics of the system compared to be B-DNA. The most stable step both in B-DNA and A-RNA is the CG/CG step that is well separated from the second most stable step GC/GC. Also the least stable step (the CC/GG step) is well separated from the rest of the structures. The calculations further show that B-DNA stacking is favorable only marginally (on average by 1.14 kcal • mol-1 per base pair step) over A-RNA stacking, and this difference vanishes after subtracting the stabilizing van der Waals effect of the thymine 5-methyl group that is absent in RNA. Basically, no correlation between the sequence dependence of gas phase stacking energies and the sequence dependence of ΔG°37 free energies used in nearest-neighbor models was found either for B-DNA or for A-RNA. This reflects the complexity of the balance of forces that are responsible for the sequence dependence of thermodynamics stability of nucleic acids, which masks the effect of the intrinsic interactions between the stacked base pairs. © 2010 American Chemical Society.


Sato K.,Osaka University | Bergqvist L.,Uppsala University | Kudrnovsky J.,ASCR Institute of Physics Prague | Dederichs P.H.,Jülich Research Center | And 9 more authors.
Reviews of Modern Physics | Year: 2010

This review summarizes recent first-principles investigations of the electronic structure and magnetism of dilute magnetic semiconductors (DMSs), which are interesting for applications in spintronics. Details of the electronic structure of transition-metal-doped III-V and II-VI semiconductors are described, especially how the electronic structure couples to the magnetic properties of an impurity. In addition, the underlying mechanism of the ferromagnetism in DMSs is investigated from the electronic structure point of view in order to establish a unified picture that explains the chemical trend of the magnetism in DMSs. Recent efforts to fabricate high- TC DMSs require accurate materials design and reliable TC predictions for the DMSs. In this connection, a hybrid method (ab initio calculations of effective exchange interactions coupled to Monte Carlo simulations for the thermal properties) is discussed as a practical method for calculating the Curie temperature of DMSs. The calculated ordering temperatures for various DMS systems are discussed, and the usefulness of the method is demonstrated. Moreover, in order to include all the complexity in the fabrication process of DMSs into advanced materials design, spinodal decomposition in DMSs is simulated and we try to assess the effect of inhomogeneity in them. Finally, recent works on first-principles theory of transport properties of DMSs are reviewed. The discussion is mainly based on electronic structure theory within the local-density approximation to density-functional theory. © 2010 The American Physical Society.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: ENV.2007.2.1.4.1. | Award Amount: 4.58M | Year: 2008

European soil biodiversity is pivotal for delivering food, fiber and biofuels and carbon storage. However, the demand is greater than the amount of soil available, as production of biofuels competes with areas for food production and nature. Moreover, intensified land use reduces soil biodiversity and the resulting ecosystem services. SOILSERVICE will value soil biodiversity through the impact on ecosystem services and propose how these values can be granted through payments. SOILSERVICE will combine interdisciplinary empirical studies and soil biodiversity surveys to construct soil food web models and determine effects of changing soil biodiversity on stability and resilience of carbon, nitrogen and phosphorus cycling, as well as assess consequences for outbreaks of pests or invasive species. SOILSERVICE will link ecological and economic models to develop a system for valuing soil biodiversity in relation to ecosystem services. Objectives: Develop methods to value soil ecosystem services during different pressure of land use and changes in soil biodiversity. Field and modelling studies will determine to what spatial and temporal scales soil biodiversity and soil ecosystem services are vulnerable to disturbance. Detecting processes that indicate when ecosystems are approaching the limits of their natural functioning or productive capacity. Establishing methods to determine and predict sustainability of ecosystem services at different types of land use Building scenarios to identify economical and social drivers of how land use such as biofuel production and land abandonment can influence soil biodiversity and ecosystem services over European scale. Interacting with EU policies and strategies with results on which services are at threat and mitigating changes in soil biodiversity to achieve a sustainable use of soils. Our results contribute to a European knowledge-based competitive economy and to a future EU directive on soils.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: SEC-2012.4.4-2 | Award Amount: 4.42M | Year: 2013

COUNTERFOG will be a new, rapid response system for collapsing all kinds of dispersed agents (smoke, fog, spores, etc.) by using a fog made of a solution that could eventually contain any kind of neutralizing component. It will be a permanent installation in large public buildings like railway stations but also a portable COUNTERFOG for use outdoors, used to counteract a CBRN attack in its earliest stages, greatly reducing the number of potential fatalities. In fact, COUNTERFOG will use the same weapon as a CBRN attack: a dispersed state with a large surface/volume ratio. It will penetrate all the intricate holes CBRN agents are able to infiltrate. As it needs a minimum quantity of decontaminant, it is intrinsically an environmental-friendly and electric-compatible system. It would have three benefits: Firstly, to neutralize and collapse the CBRN cloud, secondly, to rapidly decontaminate all the affected people in that area, and finally, to rapidly decontaminate any equipment and the facility itself. Because of the large-scale fogging capacity of up to three components, choice of pressures and capability to simultaneously emulsify liquids and disperse solid particles and an enormous surface/volume ratio, it will be possible to counteract a CBRN cloud in large, open areas. Nozzle, sensor and solid mesoporous particles will be technological keys. A Fog Dynamic Laboratory will be designed, built and used in the project to test the ability such a system has to condense different kinds of smokes, clouds or fogs and its ability to simultaneously neutralize different kinds of CBRN agents and combined incidents (fire & CBRN). Full scale tests will be also performed. Eventually, the real applicability, side effects and compatibility with conventional fire protection facilities will also investigated, a detailed marketing plan prepared and a diffusion campaign implemented. Furthermore, a spin-off company will be set up in order to exploit the results most effectively.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: SEC-2011.7.5-2;SEC-2011.6.4-1 | Award Amount: 4.68M | Year: 2012

SECONOMICS goal is synthesizing sociological, economic and security science into a usable, concrete, actionable knowledge for policy makers and social planners responsible for citizens security. The project is driven by industry case studies and will specifically identify security threats in transport (air and urban and super urban metro) and critical infrastructure. The research focus places social science and political science at the heart of the modeling framework. In particular the project seeks to explore the challenges of pan European coordination in security outcomes for transport and critical infrastructure. The contribution of the project will be in developing and furthering the state of the art in modelling security problems in a technological and socio economic context and then applying state of the art risk assessments and analysis of the social context to develop optimal policies. The outputs are twofold: first assessment of the future and emerging threats in the identified areas with rigorous modeling of the optimal mechanisms for mitigation within the policy domain. Second, and more crucially, a generalized policy toolkit that will assist decision makers in identifying and reacting coherently (within the appropriate social context) to future and emerging threats that may arrive long after the project has been completed. The lasting impactof SECONOMICS will be a methodological revolution driven by a common, but diverse set, of modelling tools and utilizing recent advances in modelling technology that seamlessly transverses the social, economic and technological domains.


Grant
Agency: European Commission | Branch: FP7 | Program: CP | Phase: Fission-2012-2.3.1 | Award Amount: 10.27M | Year: 2013

Nuclear power plays a key role in limiting EUs greenhouse gases emissions, and makes an important contribution to improve European Unions independence, security and diversity of energy supply. However, its social acceptance is closely linked to an enhanced safety in the management of long-lived radioactive waste contributing to resource efficiency and cost-effectiveness of this energy and ensuring a robust and socially acceptable system of protection of man and environment. Among the different strategies, partitioning and transmutation (P&T) allows a reduction of the amount, the radiotoxicity and the thermal power of these wastes, leading to an optimal use of geological repository sites. In line with the Strategic Research Agenda of SNE-TP, the SACSESS collaborative project will provide a structured framework to enhance the fuel cycle safety associated to P&T. In addition, safety studies will be performed for each selected process to identify weak points to be studied further. These data will be integrated to optimise flowsheets and process operation conditions. A training and education programme will be implemented in close collaboration with other European initiatives, addressing safety issues of nuclear energy industry. The multidisciplinary consortium composed of European universities, nuclear research bodies, TSOs and industrial stakeholders will generate fundamental safety improvements on the future design of an Advanced Processing Unit. SACSESS will thus be an essential contribution to the demonstration of the potential benefits of actinide partitioning to the global safety of the long-lived waste management.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH.2013.2.3.4-1 | Award Amount: 3.82M | Year: 2013

Background Ixodes ricinus transmits bacterial, protozoal and viral pathogens that cause Lyme borreliosis, babesiosis and tick-borne encephalitis respectively and exceedingly affect Central and Eastern Europe (CEE). During feeding, ticks introduce salivary proteins in the skin that interfere with host defense mechanisms. However, in animals repeated tick infestations as well as vaccination against selected tick proteins can lead to decreased pathogen transmission by inhibiting tick feeding - known as tick immunity - or by neutralizing tick proteins that facilitate the transmission of tick-borne pathogens (TBPs). Also humans with hypersensitivity to tick-bites have a lower risk of contracting tick-borne diseases (TBDs). Therefore, anti-tick vaccines encompass an innovative strategy to prevent TBDs in humans, or animals and wildlife to indirectly reduce the risk of contracting TBDs for humans. Overall Objective To identify and characterize tick proteins involved in tick immunity and TBP transmission and to use this knowledge to develop anti-tick vaccines to prevent multiple human TBDs. Methods Using state of the art proteomic and transcriptomic approaches we will identify and characterize novel tick salivary gland proteins, which will be subsequently assessed as anti-tick vaccines to protect against LB, babesiosis and TBE in animal models. In addition, through an integrated and multidisciplinary approach involving CEE public health institutes, health organizations and industrial companies we will examine how to develop anti-tick vaccines and implement these in public health systems. Impact ANTIDotE will deliver 1) essential knowledge on the biological mechanisms involved in the pathogenesis of TBDs, 2) proof of concept of an anti-tick vaccine protecting against multiple human TBPs and 3) plans for exploitation and implementation of anti-tick vaccines, significantly contributing to downscaling the severe medical and economic burden that TBDs have on societies.


Riedl J.,Czech Institute of Organic Chemistry And Biochemistry | Pohl R.,Czech Institute of Organic Chemistry And Biochemistry | Ernsting N.P.,Humboldt University of Berlin | Orsag P.,Academy of Sciences of the Czech Republic | And 3 more authors.
Chemical Science | Year: 2012

Solvatochromic fluorescent 4-aminophthalimide (API) and 4-(N,N-dimethylamino)phthalimide (DAPI) were attached covalently to 2′-deoxycytidine or -adenosine via a non-conjugated propargyl linker by Sonogashira cross-coupling reactions of N-propargylphthalimides with halogenated nucleosides. The nucleosides were phosphorylated to triphosphates and enzymatically incorporated into oligonucleotides by DNA polymerases. API-labelled DNA was used for the detection of DNA protein interactions with either the sequence-specific p53 protein or a non-specific single strand binding (SSB) protein. Both proteins changed the polarity around the fluorophore and increased (2-3 fold) the intensity of API fluorescence. © 2012 The Royal Society of Chemistry.


News Article | January 15, 2017
Site: www.techtimes.com

A gruesome tapeworm that was once believed to infect only fish in Asia has been found in salmon netted in Alaska. A new study, which was published in the Centers for Disease Control and Prevention's journal Emerging Infectious Diseases, hint of the growing dangers of eating sashimi and sushi. Americans who love to eat raw or undercooked fish may now have higher risk of getting an infection from parasites as researchers discovered Japanese broad tapeworm in wild pink salmon caught in Alaska. The Japanese broad tapeworm, Diphyllobothrium nihonkaiense, was first recognized as a human parasite in 1986. It has been reported in 2,000 illnesses in Japan and other parts of Asia and is known to affect humans who eat infected fish in eastern Russia and Japan. Now, the tapeworm was found in salmon caught in the North American waters off the coast of Alaska. In 2013, Jayde Ferguson, from Department of Fish and Game, and colleagues, examined 64 wild Alaskan salmon. By observing the musculature and the internal organs of the fish under a magnifying glass, the researchers discovered larvae measuring up to 15 millimeters long. Gene sequencing later revealed that these were Japanese tapeworms. Based on the findings, four species of Pacific salmon are now known to be carriers of the Japanese tapeworm infection namely the chum salmon, pink salmon, masu salmon, and sockeye salmon. "We report finding Japanese broad tapeworm plerocercoids in North America," Ferguson and colleagues reported. "Our main intent is to alert parasitologists and medical doctors about the potential danger of human infection with this long tapeworm resulting from consumption of infected salmon imported (on ice) from the Pacific coast of North America and elsewhere." The health effects of Japanese tapeworm infection are not generally serious. Most infections, in fact, go unnoticed because the parasites tend to cause few symptoms. Some of those infected may only experience nausea or slight abdominal discomfort but there are instances when the infection can become a serious medical problem. In 2012, a Japanese man who enjoyed eating chilled salmon suffered from gastrointestinal distress. A meter-long "tape-shaped object" later emerged from his anus which turned out to be the parasitic Japanese broad tapeworm. "The infections can have a substantial emotional impact on patients and their families," said study author Roman Kuchta, from the Academy of Sciences of the Czech Republic. "More severe cases may require specialized consultations and complementary analyses, which are costly." Scientists also warned that the problem may spread if nothing is done about it. Global importation and the increasing popularity of eating raw fish help spread the parasite. Salmon is often packed and transported in ice but not frozen. The tapeworm's larvae can possibly survive the trip and infect consumers in different countries worldwide which include New Zealand, China, and some parts of the United States. © 2017 Tech Times, All rights reserved. Do not reproduce without permission.


Vrba L.,Arizona Cancer Center | Vrba L.,Academy of Sciences of the Czech Republic | Garbe J.C.,Lawrence Berkeley National Laboratory | Stampfer M.R.,Arizona Cancer Center | And 3 more authors.
Genome Research | Year: 2011

Epigenetic mechanisms are important regulators of cell type-specific genes, including miRNAs. In order to identify cell type-specific miRNAs regulated by epigenetic mechanisms, we undertook a global analysis of miRNA expression and epigenetic states in three isogenic pairs of human mammary epithelial cells (HMEC) and human mammary fibroblasts (HMF), which represent two differentiated cell types typically present within a given organ, each with a distinct phenotype and a distinct epigenotype. While miRNA expression and epigenetic states showed strong interindividual concordance within a given cell type, almost 10% of the expressed miRNA showed a cell type-specific pattern of expression that was linked to the epigenetic state of their promoter. The tissue-specific miRNA genes were epigenetically repressed in nonexpressing cells by DNA methylation (38%) and H3K27me3 (58%), with only a small set of miRNAs (21%) showing a dual epigenetic repression where both DNA methylation and H3K27me3 were present at their promoters, such as MIR10A and MIR10B. Individual miRNA clusters of closely related miRNA gene families can each display cell type-specific repression by the same or complementary epigenetic mechanisms, such as the MIR200 family, and MIR205, where fibroblasts repress MIR200C/141 by DNA methylation, MIR200A/200B/429 by H3K27me3, and MIR205 by both DNA methylation and H3K27me3. Since deregulation of many of the epigenetically regulated miRNAs that we identified have been linked to disease processes such as cancer, it is predicted that compromise of the epigenetic control mechanisms is important for this process. Overall, these results highlight the importance of epigenetic regulation in the control of normal cell type-specific miRNA expression. © 2011 by Cold Spring Harbor Laboratory Press.


Biedermann D.,Academy of Sciences of the Czech Republic | Vavrikova E.,Academy of Sciences of the Czech Republic | Cvak L.,R.Ø.S.A. | Kren V.,Academy of Sciences of the Czech Republic
Natural Product Reports | Year: 2014

Covering: 1959 to 2013 Silybin, a secondary metabolite isolated from the seeds of the blessed milk thistle (Silybum marianum) was discovered as the first member of a new family of natural compounds called flavonolignans in 1959. Over the years it has received the research attention of many organic chemists. This research has resulted in a number of semisynthetic derivatives prepared in an effort to modulate and better target the biological activities of silybin or to improve its physical properties, such as its solubility. A fundamental breakthrough in silybin chemistry was the determination of the absolute configurations of silybin A and silybin B, and the development of methods for their separation. This review covers articles dealing with silybin chemistry and also summarizes all the derivatives prepared. This journal is © the Partner Organisations 2014.


Turek I.,Academy of Sciences of the Czech Republic | Kudrnovsky J.,ASCR Institute of Physics Prague | Carva K.,Charles University
Physical Review B - Condensed Matter and Materials Physics | Year: 2012

We present results of systematic fully relativistic first-principles calculations of the uniaxial magnetic anisotropy energy (MAE) of a disordered and partially ordered tetragonal Fe-Co alloy using the coherent potential approximation (CPA). This alloy has recently become a promising system for thin ferromagnetic films with a perpendicular magnetic anisotropy. We find that existing theoretical approaches to homogeneous random bulk Fe-Co alloys, based on a simple virtual crystal approximation (VCA), overestimate the maximum MAE values obtained in the CPA by a factor of 4. This pronounced difference is ascribed to the strong disorder in the minority spin channel of real alloys, which is neglected in the VCA and which leads to a broadening of the d-like eigenstates at the Fermi energy and to the reduction of the MAE. The ordered Fe-Co alloys with a maximum L10-like atomic long-range order can exhibit high values of the MAE, which, however, get dramatically reduced by small perturbations of the perfect order. © 2012 American Physical Society.


Turek I.,Academy of Sciences of the Czech Republic | Kudrnovsky J.,ASCR Institute of Physics Prague | Drchal V.,ASCR Institute of Physics Prague
Physical Review B - Condensed Matter and Materials Physics | Year: 2012

We present an ab initio theory of transport quantities of metallic ferromagnets developed in the framework of the fully relativistic tight-binding linear muffin-tin orbital method. The approach is based on the Kubo-Středa formula for the conductivity tensor, on the coherent potential approximation for random alloys, and on the concept of interatomic electron transport. The developed formalism is applied to pure 3d transition metals (Fe, Co, Ni) and to random Ni-based ferromagnetic alloys (Ni-Fe, Ni-Co, Ni-Mn). High values of the anisotropic magnetoresistance (AMR), found for Ni-rich alloys, are explained by a negligible disorder in the majority spin channel, while a change of the sign of the anomalous Hall effect (AHE) on alloying is interpreted as a band-filling effect without a direct relation to the high AMR. The influence of disorder on the AHE in concentrated alloys is investigated as well. © 2012 American Physical Society.


Tian F.,Stevens Institute of Technology | Kanka J.,Academy of Sciences of the Czech Republic | Du H.,Stevens Institute of Technology
Optics Express | Year: 2012

Regular and cascaded long period gratings (LPG, C-LPG) of periods ranging from 460 to 590 μm were inscribed in an endlessly single mode photonic crystal fiber (PCF) using CO2 laser for sensing measurements of helium, argon and acetylene. High index sensitivities in excess of 1700 nm/RIU were achieved in both grating schemes with a period of 460 μm. The sharp interference fringes in the transmission spectrum of C-PCF-LPG afforded not only greatly enhanced sensing resolution, but also accuracy when the phase-shift of the fringe pattern is determined through spectral processing. Comparative numerical and experimental studies indicated LP01 to LP03 mode coupling as the principal coupling step for both PCF-LPG and C-PCF-LPG with emergence of multimode coupling at shorter grating periods or longer resonance wavelengths. © 2012 Optical Society of America.


Chen H.,Stevens Institute of Technology | Tian F.,Stevens Institute of Technology | Chi J.,Stevens Institute of Technology | Kanka J.,Academy of Sciences of the Czech Republic | Du H.,Stevens Institute of Technology
Optics Letters | Year: 2014

An unclad, multi-mode single crystal sapphire fiber was used as a platform, and immobilized colloidal Ag nanoparticles (NPs) were used as enabler, for evanescent-field fiber-optic sensing via surface-enhanced Raman scattering (SERS) of Rhodamine 6G (R6G) solution. The dependence of the measured Raman intensity on NP coverage density (to a maximum of 120 particles/μm2) as well as the coverage length (to a maximum of 6 cm) was investigated. We demonstrate the utility of SERS-active sapphire fibers for sensitive measurements (10-8 M R6G). We further reveal, with the aid of theoretical analysis, that multi-mode fiber offers a significant advantage compared to its single-mode counterpart because the former allows two orders of magnitude higher particle coverage density than the latter to maximize SERS benefit, while maintaining the dominance of Raman gain despite the competitive interplay of NP-induced absorption and scattering loss along the interaction path length. © 2014 Optical Society of America


Hansen K.A.,University of Aarhus | Koucky M.,Academy of Sciences of the Czech Republic | Lauritzen N.,University of Aarhus | Miltersen P.B.,University of Aarhus | Tsigaridas E.P.,University of Aarhus
Proceedings of the Annual ACM Symposium on Theory of Computing | Year: 2011

Shapley's discounted stochastic games, Everett's recursive games and Gillette's undiscounted stochastic games are classical models of game theory describing two-player zero-sum games of potentially infinite duration. We describe algorithms for exactly solving these games. When the number of positions of the game isbconstant, our algorithms run in polynomial time. © 2011 ACM.


Le Comber S.C.,Queen Mary, University of London | Ainouche M.L.,University of Rennes 1 | Kovarik A.,Academy of Sciences of the Czech Republic | Leitch A.R.,Queen Mary, University of London
New Phytologist | Year: 2010

•One little understood feature of polyploid speciation is the transition from polysomic to disomic inheritance, and much recent attention has focused on the role of pairing genes in this process.•Using computer simulations we studied the effects of mutations, chromosomal inversions, chiasma, neofunctionalization, subfunctionalization and selection on the evolution of disomic inheritance in a polyploid over 10 000 generations.•We show that: the evolution of pairing genes is not essential for the establishment of disomic inheritance, as genetic drift, coupled with a threshold for homologue pairing fidelity, is sufficient to explain the transition from polysomic to disomic inheritance; high rates of recombination increase the number of generations required for disomic inheritance to become established; both neofunctionalization and subfunctionalization speed up the transition to disomic inheritance.•The data suggest that during polyploid species establishment, selection will favour reduced chiasma number and/or more focused distribution. The data also suggest a new role for subfunctionalization in that it can drive disomic inheritance. The evolution of subfunctionalization in genes across the genome will then act to maintain genes in syntenic blocks and may explain why such regions are so highly conserved. © The Authors (2009). Journal compilation © New Phytologist Trust (2009).


Kudrnovsky J.,ASCR Institute of Physics Prague | Drchal V.,ASCR Institute of Physics Prague | Turek I.,Academy of Sciences of the Czech Republic
Physical Review B - Condensed Matter and Materials Physics | Year: 2013

We estimate the anomalous Hall effect of selected Heusler alloys from first principles. An emphasis is put on the effect of the native disorder which is often present in the stoichiometric samples. Such disorder can strongly influence both the magnetic and transport properties of these alloys. We employ a recently developed fully relativistic Kubo-Středa approach adapted to disordered multisublattice systems in which the chemical disorder is described in terms of the coherent potential approximation. As case studies we choose half-metallic Heusler alloys Co2CrAl and Co2MnAl, as well as the spin gapless semiconductor alloy Mn2CoAl for which experimental and theoretical studies appeared recently. We demonstrate that proper inclusion of disorder significantly improves agreement between the experiment and theory. © 2013 American Physical Society.


Slama K.,Academy of Sciences of the Czech Republic | Lukas J.,Czech Republic Crop Research Institute
Journal of Insect Physiology | Year: 2011

Larvae of the greater waxmoth (Galleria mellonella) become paralysed by the venom of the braconid wasp (Habrobracon hebetor) a few minutes after intoxication. The profound neuromuscular paralysis, which may last for several weeks, includes all somatic muscles that are innervated through neuromuscular transmission. The peristaltic contractions of the heart and intestine, which are regulated by the depolarisation potentials of the myocardium or intestinal epithelial muscles, remain unaffected and fully functional. Heartbeat patterns and intestinal pulsations were monitored in the motionless, paralysed larvae by means of advanced electrocardiographic recording methods (contact thermography, pulse-light optocardiography). The records revealed more or less constant cardiac pulsations characterised by 20-25 systolic contractions per minute. The contractions were peristaltically propagated in the forward (anterograde) direction, with a more or less constant speed of 10. mm per second (23-25 °C). Additional electrocardiographic investigations on larvae immobilised by decapitation revealed the autonomic (brain independent) nature of heartbeat regulation. Sectioning performed in the middle of the heart (4th abdominal segment) seriously impaired the pacemaker rhythmicity and slowed down the rate of heartbeat in the anterior sections. By contrast, the functions of the posterior compartments of the disconnected heart remained unaffected. These results confirmed our previous conclusions about the existence of an autonomic, myogenic, pacemaker nodus in the terminal part of an insect heart. They show an analogy to the similar myogenic, sinoatrial or atrioventricular nodi regulating rhythmicity of the human heart. Peristaltic contractions of the intestine also represent a purely myogenic system, which is fully functional in larvae with complete neuromuscular paralysis. Unlike the constant anterograde direction of the heartbeat, intestinal peristaltic waves periodically reversed anterograde and retrograde directions. A possibility that the functional similarity between insect and human hearts may open new avenues in the field of comparative cardiology has been discussed. © 2010 Elsevier Ltd.


Broz P.,Academy of Sciences of the Czech Republic | Hauber E.,German Aerospace Center
Icarus | Year: 2012

Based on theoretical grounds, explosive basaltic volcanism should be common on Mars, yet the available morphological evidence is sparse. We test this hypothesis by investigating a unique unnamed volcanic field north of the shield volcanoes Biblis Patera and Ulysses Patera on Mars, where we observe several small conical edifices and associated lava flows. Twenty-nine volcanic cones are identified and the morphometry of many of these edifices is determined using established morphometric parameters such as basal width, crater width, height, slope, and their respective ratios. Their morphology, morphometry, and a comparison to terrestrial analogues suggest that they are martian equivalents of terrestrial pyroclastic cones, the most common volcanoes on Earth. The cones are tentatively interpreted as monogenetic volcanoes. According to absolute model age determinations, they formed in the Amazonian period. Our results indicate that these pyroclastic cones were formed by explosive activity. The cone field is superposed on an old, elevated window of fractured crust which survived flooding by younger lava flows. It seems possible that a more explosive eruption style was common in the past, and that wide-spread effusive plain-style volcanism in the Late Amazonian has buried much of its morphological evidence in Tharsis. © 2011 Elsevier Inc.


Nemecek J.,R.Ø.S.A. | Lhotsky O.,DEKONTA a.s. | Cajthaml T.,Academy of Sciences of the Czech Republic
Science of the Total Environment | Year: 2014

Because of its high toxicity and mobility, hexavalent chromium is considered to be a high priority pollutant. This study was performed to carry out a pilot-scale in-situ remediation test in the saturated zone of a historically Cr(VI)-contaminated site using commercially available nanoscale zero-valent iron (nZVI). The site was monitored before and after the nZVI application by means of microbial cultivation tests, phospholipid fatty acid analysis (PLFA) and toxicological tests with Vibrio fischeri. Injection of nZVI resulted in a rapid decrease in the Cr(VI) and total Cr concentrations in the groundwater without any substantial effect on its chemical properties. The ecotoxicological test with V. fischeri did not indicate any negative changes in the toxicity of the groundwater following the application of nZVI and no significant changes were observed in cultivable psychrophilic bacteria densities and PLFA concentrations in the groundwater samples during the course of the remediation test. However, PLFA of soil samples revealed that the application of nZVI significantly stimulated the growth of Gram-positive bacteria. Principle component analysis (PCA) was applied to the PLFA results for the soil samples from the site in order to explain how Cr(VI) reduction and the presence of Fe influence the indigenous populations. The PCA results clearly indicated a negative correlation between the Cr concentrations and the biota before the application of nZVI and a significant positive correlation between bacteria and the concentration of Fe after the application of nZVI. © 2013 Elsevier B.V.


Slanina F.,ASCR Institute of Physics Prague | Slanina F.,Academy of Sciences of the Czech Republic
European Physical Journal B | Year: 2011

The dynamics of the model of agents with limited confidence introduced by Hegselmann and Krause exhibits multiple well-separated regimes characterised by the number of distinct clusters in the stationary state. We present indications that there are genuine dynamical phase transitions between these regimes. The main indicator is the divergence of the average evolution time required to reach the stationary state. The slowdown close to the transition is connected with the emergence of the groups of mediator agents which are very small but have decisive role in the process of social convergence. More detailed study shows that the histogram of the evolution times is composed of several peaks. These peaks are unambiguously interpreted as corresponding to mediator groups consisting of one, two, three etc. agents. Detailed study reveals that each transition possesses also an internal fine structure. © EDP Sciences, Societa Italiana di Fisica, Springer-Verlag 2009.


Reddy V.,University of Portsmouth | Markova G.,Academy of Sciences of the Czech Republic | Wallot S.,University of Aarhus
PLoS ONE | Year: 2013

Anticipation of the actions of others is often used as a measure of action understanding in infancy. In contrast to studies of action understanding which set infants up as observers of actions directed elsewhere, in the present study we explored anticipatory postural adjustments made by infants to one of the most common adult actions directed to them - picking them up. We observed infant behavioural changes and recorded their postural shifts on a pressure mat in three phases: (i) a prior Chat phase, (ii) from the onset of Approach of the mother's arms, and (iii) from the onset of Contact. In Study 1, eighteen 3-month-old infants showed systematic global postural changes during Approach and Contact, but not during Chat. There was an increase in specific adjustments of the arms (widening or raising) and legs (stiffening and extending or tucking up) during Approach and a decrease in thrashing/general movements during Contact. Shifts in postural stability were evident immediately after onset of Approach and more slowly after Contact, with no regular shifts during Chat. In Study 2 we followed ten infants at 2, 3 and 4 months of age. Anticipatory behavioural adjustments during Approach were present at all ages, but with greater differentiation from a prior Chat phase only at 3 and 4 months. Global postural shifts were also more phase differentiated in older infants. Moreover, there was significantly greater gaze to the mother's hands during Approach at 4 months. Early anticipatory adjustments to being picked up suggest that infants' awareness of actions directed to the self may occur earlier than of those directed elsewhere, and thus enable infants' active participation in joint actions from early in life. © 2013 Reddy et al.


Solc P.,Academy of Sciences of the Czech Republic | Schultz R.M.,University of Pennsylvania | Motlik J.,Academy of Sciences of the Czech Republic
Molecular Human Reproduction | Year: 2010

Mammalian oocytes are arrested at prophase I until puberty when luteinizing hormone (LH) induces resumption of meiosis of follicle-enclosed oocytes. Resumption of meiosis is tightly coupled with regulating cyclin-dependent kinase 1 (CDK1) activity. Prophase I arrest depends on inhibitory phosphorylation of CDK1 and anaphase-promoting complex-(APC-CDH1)-mediated regulation of cyclin B levels. Prophase I arrest is maintained by endogenously produced cyclic adenosine monophosphate (cAMP), which activates protein kinase A (PKA) that in turn phosphorylates (and activates) the nuclear kinase WEE2. In addition, PKA-mediated phosphorylation of the phosphatase CDC25B results in its cytoplasmic retention. The combined effect maintains low levels of CDK1 activity that are not sufficient to initiate resumption of meiosis. LH triggers synthesis of epidermal growth factor-like factors in mural granulosa cells and leads to reduced cGMP transfer from cumulus cells to oocytes via gap junctions that couple the two cell types. cGMP inhibits oocyte phosphodiesterase 3A (PDE3A) and a decline in oocyte cGMP results in increased PDE3A activity. The ensuing decrease in oocyte cAMP triggers maturation by alleviating the aforementioned phosphorylations of WEE2 and CDC25B. As a direct consequence CDC25B translocates into the nucleus. The resulting activation of CDK1 also promotes extrusion of WEE2 from the nucleus thereby providing a positive amplification mechanism for CDK1 activation. Other kinases, e.g. protein kinase B, Aurora kinase A and polo-like kinase 1, also participate in resumption of meiosis. Mechanisms governing meiotic prophase I arrest and resumption of meiosis share common features with DNA damage-induced mitotic G2-checkpoint arrest and checkpoint recovery, respectively. These common features include CDC14B-dependent activation of APC-CDH1 in prophase I arrested oocytes or G2-arrested somatic cells, and CDC25B-dependent cell cycle resumption in both oocytes and somatic cells. © The Author 2010. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved.


Kubicka D.,Academy of Sciences of the Czech Republic | Kaluza L.,Czech Institute of Chemical Process Fundamentals
Applied Catalysis A: General | Year: 2010

Deoxygenation of vegetable oils has a potential to become an important process for production of biofuels. The present work focuses on investigation of Ni, Mo, and NiMo sulfided catalysts prepared by impregnation in deoxygenation of rapeseed oil at 260-280 °C, 3.5 MPa and 0.25-4 h-1 in a fixed-bed reactor. The activity of the catalysts decreased in the order NiMo/Al2O3 > Mo/Al2O3 > Ni/Al2O3. The catalysts exhibited significantly different product distributions. The bimetallic NiMo catalysts showed higher yields of hydrocarbons than the monometallic catalysts at a given conversion. Apart from the various oxygenated product intermediates, NiMo/Al2O3 yielded a mixture of decarboxylation and hydrodeoxygenation hydrocarbon products while Ni/Al2O3 yielded only decarboxylation hydrocarbon products and Mo/Al2O3 yielded almost exclusively hydrodeoxygenation hydrocarbon products. The effect of Ni/(Ni + Mo) atomic ratio in the range 0.2-0.4 on the activity and selectivity was not significant. © 2009 Elsevier B.V. All rights reserved.


Broz P.,Academy of Sciences of the Czech Republic | Broz P.,Charles University | Hauber E.,German Aerospace Center
Journal of Geophysical Research E: Planets | Year: 2013

Hydrovolcanism is a common natural phenomenon on Earth and should be common on Mars, too, since its surface shows widespread evidence for volcanism and near-surface water. We investigate fields of pitted cones in the Nephentes/Amenthes region at the southern margin of the ancient impact basin, Utopia, which were previously interpreted as mud volcanoes. The cone fields contain pitted and breached cones with associated outgoing flow-like landforms. Based on stratigraphic relations, we determined a Hesperian or younger model age. We test the hypothesis of a (hydro)volcanic origin. Based on a detailed morphological and morphometrical analysis and an analysis of the regional context, an igneous volcanic origin of these cones as hydrovolcanic edifices produced by phreatomagmatic eruptions is plausible. Several lines of evidence suggest the existence of subsurface water ice. The pitted cones display well-developed wide central craters with floor elevations below the preeruptive surface. Their morphometry and the overall appearance are analogous to terrestrial tuff cones and tuff rings. Mounds that are also observed in the same region resemble terrestrial lava domes. The hydrovolcanic interaction between ascending magma and subsurface water and/or water ice may explain the formation of the pitted cones, although other scenarios such as mud volcanism cannot be ruled out. Together with the mounds, the cones might represent effusive and explosive edifices of a monogenetic volcanic field composed of lava domes, tuff rings, tuff cones, and possibly maars. © 2013. American Geophysical Union. All Rights Reserved.


Raven J.A.,University of Technology, Sydney | Beardall J.,Monash University | Giordano M.,Marche Polytechnic University | Giordano M.,Academy of Sciences of the Czech Republic
Photosynthesis Research | Year: 2014

Minimum energy (as photon) costs are predicted for core reactions of photosynthesis, for photorespiratory metabolism in algae lacking CO2 concentrating mechanisms (CCMs) and for various types of CCMs; in algae, with CCMs; allowance was made for leakage of CO2 from the internal pool. These predicted values are just compatible with the minimum measured photon costs of photosynthesis in microalgae and macroalgae lacking or expressing CCMs. More energy-expensive photorespiration, for example for organisms using Rubiscos with lower CO2-O2 selectivity coefficients, would be less readily accommodated within the lowest measured photon costs of photosynthesis by algae lacking CCMs. The same applies to the cases of CCMs with higher energy costs of active transport of protons or inorganic carbon species, or greater allowance for significant leakage from the accumulated intracellular pool of CO2. High energetic efficiency can involve a higher concentration of catalyst to achieve a given rate of reaction, adding to the resource costs of growth. There are no obvious mechanistic interpretations of the occurrence of CCMs algae adapted to low light and low temperatures using the rationales adopted for the occurrence of C4 photosynthesis in terrestrial flowering plants. There is an exception for cyanobacteria with low-selectivity Form IA or IB Rubiscos, and those dinoflagellates with low-selectivity Form II Rubiscos, for which very few natural environments have high enough CO2:O2 ratios to allow photosynthesis in the absence of CCMs. © 2014 Springer Science+Business Media Dordrecht.


Molnar P.,ASCR Institute of Physics Prague | Ostapovets A.,ASCR Institute of Physics Prague | Ostapovets A.,Academy of Sciences of the Czech Republic | Jager A.,ASCR Institute of Physics Prague
Materials and Design | Year: 2014

Attractiveness of magnesium alloys for structural applications is caused by their intrinsic properties i.e. low density and high specific strength. The main challenge in development of magnesium alloys is connected with requirement to fulfill the main function of structural materials i.e. to bear load. Wrought magnesium alloys possess strong basal texture which causes anisotropy of mechanical properties. It would be interesting to find out the way how to benefit from this anisotropic behavior of magnesium alloys. One way is to take into account strong basal texture and {1 0 -1 2} twinning in magnesium alloys under compressive deformation. Parallelepiped samples of AZ31 magnesium alloy were successively deformed in compression with 3.5% strain along two perpendicular directions. During first compression the sample contracts along the RD direction parallel to compression axis, elongates only in one perpendicular ND direction and no deformation is observed in third perpendicular TD direction. Subsequent compression along the ND direction recovers the initial shape of the sample. Microstructure analyses shows that the {1 0 -1 2} twinning is the main deformation mode during compression along the RD direction and twin variants which gives 0% strain to TD direction are predominant in microstructure. Twin-free microstructure is observed after subsequent compression along the ND direction. Crystallographic analyzes and calculations explain why reversible motion of twin boundaries is more favorable than nucleation of other twin variants in matrix grains during compression along the ND direction. The experiment presented in this article profile wrought magnesium alloy as smart material and emphasize the importance of strong {0 0 0 1} <1 0 -1 0> texture and {1 0 -1 2} twinning in obtaining the properties characteristic for smart materials. In the presented case, it is the ability to produce and recover significant strains in a controlled manner under compressive stress. © 2013 Elsevier Ltd.


Hocek M.,Gilead Sciences | Fojta M.,Academy of Sciences of the Czech Republic
Chemical Society Reviews | Year: 2011

Basic aspects of DNA electrochemistry with a strong focus on the use of modified nucleobases as redox probes for electrochemical bioanalysis are reviewed. Intrinsic electrochemical properties of nucleobases in combination with artificial redox-active nucleobase modifications are frequently applied in this field. Synthetic approaches (both chemical and enzymatic) to base-modified nucleic acids are briefly summarized and their applications in redox labelling are discussed. Finally, analytical applications including DNA hybridization, primer extension, PCR, SNP typing, DNA damage and DNA-protein interaction analysis are presented (critical review, 91 references). © The Royal Society of Chemistry 2011.


Srivastava K.,Karlsruhe Institute of Technology | Groger R.,Academy of Sciences of the Czech Republic | Weygand D.,Karlsruhe Institute of Technology | Gumbsch P.,Karlsruhe Institute of Technology | Gumbsch P.,Fraunhofer Institute for Mechanics of Materials
International Journal of Plasticity | Year: 2013

A computational framework for the discrete dislocation dynamics simulation of body-centered cubic (bcc) metals which incorporates atomistic simulation results is developed here on the example of tungsten. Mobility rules for the a/2〈111〉 screw dislocations are based on the kink-pair mechanism. The fundamental physical quantity controlling the kink-pair nucleation, the stress-dependent activation enthalpy, is obtained by fitting the line-tension model to atomistic data extending the approach by Gröger et al. (2008a,b) and Gröger and Vitek (2008c). In agreement with atomistic simulation, kink-pair nucleation is assumed to occur only on {110} planes. It is demonstrated that slip of the crystal along high-index planes like {112} which is often observed in experiments is obtained by the glide of the dislocation on two or more {110} planes. It is shown that such an atomistic based description of the dislocation mobility provides a physical basis to naturally explain many experimentally observed phenomena in bcc metals like the tension-compression asymmetry, the orientation dependence of loading, temperature dependence of yield stress and the crystallography of slip. © 2013 Elsevier Ltd. All rights reserved.


Pavela R.,Czech Republic Crop Research Institute | Vrchotova N.,Academy of Sciences of the Czech Republic
Industrial Crops and Products | Year: 2013

The essential oil (EO) and extracts (EXs) obtained from the seeds of Angelica archangelica were used to determine the efficacy in terms of chronic and acute toxicity, antifeedancy and growth inhibition of Spodoptera littoralis larvae. The EO and the EXs were analyzed by GC/MS and HPLC. The EO contained β-phellandrene as the major substance (60%). Furanocoumarins were identified in the EXs obtained using organic solvents, with the majority content of imperatorin (50-56%). Their varying efficacy was caused by the different composition of the EO and EXs obtained. Significant acute toxicity was caused only by the EO (LD 50 96μg/larva). Significantly higher chronic toxicity was found for the EXs obtained using organic solvents (LD 50 was estimated at 0.32, 0.82 and 0.52mgg -1 for benzene, acetone and methanol, respectively), compared to the EO (LD 50 7.53mgg -1). All the tested EXs and the EO caused growth inhibition. The highest larval growth inhibition was caused by the benzene extract, with ED 50 estimated at 2.4μgg -1. All EXs and the EO also showed antifeedant activity. However, the benzene extract showed the highest efficacy (ED 50 0.31μgcm -2), while the least efficacy was shown by the water extract (ED 50 1.92μgcm -2). In order to determine the dependence of biological efficacy of the EXs, LD 50 and ED 50 values were subjected to regression and correlation analysis. The analysis showed dependence between the total content of furanocoumarins in the extracts and chronic toxicity (R 2=0.8451; P<0.01) or larval growth inhibition (R 2=0.8941; P<0.01). This dependence was also confirmed for all individual furanocoumarins except bergapten, which showed no dependence.Based on a comparison of the determined efficacy and yield of the extracts, extracts from A. archangelica seeds obtained using methanol can be recommended as suitable for the development of botanical insecticides against S. littoralis larvae. © 2012 Elsevier B.V.


Tomas R.,Academy of Sciences of the Czech Republic | Koval M.,R.Ø.S.A. | Foret F.,Academy of Sciences of the Czech Republic
Journal of Chromatography A | Year: 2010

Capillary isotachophoresis with coupled columns provides efficient means for rapid electrophoretic analysis of sample volumes of up to 10 μl or more. Commercially available instruments are commonly equipped with conductivity and UV absorbance detectors; however, their on-line coupling with electrospray mass spectrometry is highly desirable. In this work we have modified the commercial coupled column isotachophoresis system for direct connection to an ion trap mass spectrometer. The design included attachment of an elution block with a short capillary transfer line directing the separated zones towards the mass spectrometer. The modification further included separation of the injection and electrode blocks from the separation columns by semipermeable membranes eliminating unwanted fluid movements in the wide bore fluoropolymer separation capillaries. Fused silica capillaries with varying internal diameter were connected as a transfer line between the elution block and mass spectrometer. The transfer line served also as the ESI tip of the sheathless electrospray interface. During the analysis the first, wide bore preseparation capillary with 0.8. mm internal diameter served for removal of the bulk sample components and preseparation of the potentially interfering analytes. After the electronic column switching the separation was finished in a 0.3. mm internal diameter capillary and the separated ITP zones were transferred in-line by a spray liquid towards the mass spectrometer. The instrumentation was tested for determination of vitamins in whole blood analysis and separation of tryptic peptides. © 2010 Elsevier B.V.


Weinberg R.F.,Monash University | Hasalova P.,Czech Geological Survey | Hasalova P.,Academy of Sciences of the Czech Republic
Lithos | Year: 2015

Water-fluxed melting, also known as fluid- or water-present melting, is a fundamental process in the differentiation of continents but its importance has been underestimated in the past 20. years during which research efforts focused mostly on dehydration melting reactions involving hydrate phases, in the absence of a separate aqueous phase. The presence of a free aqueous phase in anatectic terranes influences all major physical and chemical aspects of the melting process, from melt volumes, viscosity and ability to segregate from rock pores, to melt chemical and isotopic composition. A review of the literature shows that melting due to the fluxing of aqueous fluids is a widespread process that can take place in diverse tectonic environments. Active tectono-magmatic processes create conditions for the release of aqueous fluids and deformation-driven, transient high permeability channels, capable of fluxing high-temperature regions of the crust where they trigger voluminous melting. Water-fluxed melting can be either congruent in regions at the water-saturated solidus, or incongruent at suprasolidus, P-T conditions. Incongruent melting reactions can give rise to peritectic hornblende, or to nominally anhydrous minerals such as garnet, sillimanite or orthopyroxene. In this case, the presence of an aqueous phase is indicated by a mismatch between the large melt fraction generated and the much smaller fractions predicted in its absence. The relatively small volumes of aqueous fluids compared to that of rocks imply that melting reactions are generally rock buffered. Fluids tend to move upwards and down temperature. However, there are cases in which pressure gradients drive fluids up temperature, potentially fluxing suprasolidus terranes. Crustal regions at conditions equivalent to the water-saturated solidus represent a natural impediment to the up-temperature migration of aqueous fluids because they are consumed in melting reactions. In this case, continued migration into supra-solidus terranes take place through the migration of water-rich melts. Thus, melts become the transport agent of water into supra-solidus terranes and responsible for water-fluxed melting. Other processes, such as the relatively rapid fluid migration through fractures, also allow regional aqueous fluids to by-pass the water-saturated solidus fluid trap and trigger melting above solidus conditions. When aqueous fluids or hydrous melts flux rocks at supra-solidus conditions, they equilibrate with the surroundings through further melting, decreasing water activity and giving rise to undersaturated melts. It is in these conditions that hornblende or anhydrous peritectic phases are stabilized. Unlike dehydration melting, the melt fraction generated in this case is not limited by the water contained in hydrous minerals but by the volume of water added to the system. Unlike melting at the water-saturated solidus, these melts are capable of rising without freezing and do give rise to upper crustal granitic bodies. © 2014 Elsevier B.V.


Groger R.,Academy of Sciences of the Czech Republic | Vitek V.,University of Pennsylvania
Acta Materialia | Year: 2013

The recently formulated constrained nudged elastic band method with atomic relaxations (NEB + r) (Gröger R, Vitek V. Model Simul Mater Sci Eng 2012;20:035019) is used to investigate the dependence of the Peierls barrier of 1/2〈1 1 1âŒ̈ screw dislocations in body-centered cubic metals on non-glide stresses. These are the shear stresses parallel to the slip direction acting in the planes of the 〈1 1 1âŒ̈ zone different from the slip plane, and the shear stresses perpendicular to the slip direction. Both these shear stresses modify the structure of the dislocation core and thus alter both the Peierls barrier and the related Peierls stress. Understanding of this effect of loading is crucial for the development of mesoscopic models of thermally activated dislocation motion via formation and propagation of pairs of kinks. The Peierls stresses and related choices of the glide planes determined from the Peierls barriers agree with the results of molecular statics calculations (Gröger R, Bailey AG, Vitek V. Acta Mater 2008;56:5401), which demonstrates that the NEB + r method is a reliable tool for determining the variation in the Peierls barrier with the applied stress. However, such calculations are very time consuming, and it is shown here that an approximate approach of determining the stress dependence of the Peierls barrier (proposed in Gröger R, Vitek V. Acta Mater 2008;56:5426) can be used, combined with test calculations employing the NEB + r method.


Grant
Agency: European Commission | Branch: FP7 | Program: MC-IRG | Phase: FP7-PEOPLE-2009-RG | Award Amount: 100.00K | Year: 2009

Schistosomiasis caused by trematode parasites, the Schistosoma bloodflukes, represents one of the most serious chronic infections in the developing world with more then 200 million people infected and many more at risk. Schistosomes reside in the portal and mesenteric or bladder and survive for many years producing hundreds of fertilized eggs per day. Chronic infections can persist for decades and severe morbidity results from host immune responses to eggs in tissues. Disease symptoms include; spleno- and hepatomegalies due to an immune-mediated entrapment (granulomas) of schistosome eggs, periportal fibrosis, portal hypertension, urinary obstruction, bladder carcinoma, sterility, malnutrition, developmental retardation. Resistant isolates of S. mansoni in some regions have been already reported from treated patients. Their evasive and immuno-modulatory strategies are key players in host-parasite interactions. Their bioactive molecules involved in these processes represent interesting subject for pharmacology. One group, proteases function at the host-parasite interface facilitating migration, immune evasion and digestion of host proteins. Besides of relatively well characterized enzymes there are groups of proteases which were surprisingly neglected. One of them is a group which belongs to the class of serine proteases, Clan PA trypsin-like family S1. These schistosomal proteases share similarities to several human regulatory factors such as mammalian kallikrein, epithelial transmembrane proteases, protein C-anticoagulation factor. This probably arose due to co-existence with the mammalian hosts and needs to actively interact with their physiological processes involving proteolysis (anticoagulation, vasodilatation, immuno-evasion). If hypothesis is valid, proteases may represent attractive bioactive pharmacokinetic molecules for further research. At last, it may have impact on better understanding of diseases, leading subsequently to new disease treatments.


Zahradnik J.,Charles University | Plesinger A.,Academy of Sciences of the Czech Republic
Bulletin of the Seismological Society of America | Year: 2010

Broadband observations of small earthquakes at short epicentral distances reveal a mixture of near-field effects and instrumental artifacts. We investigated these phenomena at a station equipped with an STS-2 and CMG-40T sensor situated almost above shallow M 3.0 to 3.8 events (peak ground acceleration 2 × 10-1 m/sec2). The horizontal components were systematically accompanied by tiltlike disturbances, and the tilt obtained from the STS-2 records exceeded more than 10 times the values predicted by the source model. We also observed a so far uncommonly recognized type of disturbance, whose shape is the first derivative of the tiltlike disturbance. The most likelyexplanationseemstobeclippingofhigh-frequency signal peaks within the sensor system. A computational model of a broadband feedback velocimeter as a linear dynamic system with saturation proved this interpretation on a qualitative level. Generally, any asymmetry in the transfer of high frequencies in the feedback velocimeter would produce along-period disturbance of this type.Users of near-faultbroad-band velocigrams may numerically simulate the disturbances, without any knowledge of their physical nature, and subtract them from the records. The decontaminated records still may have a strange, bow-shaped form, related to the near-field ramp and the static displacement (of the order of 1 × 10-5 m in this article). The effects studied in this article seem to have a general character, for apparently any feedback-controlled broadband velocimeter.


MacEk M.,Charles University | Dobes J.,Academy of Sciences of the Czech Republic | Cejnar P.,Charles University
Physical Review C - Nuclear Physics | Year: 2010

We observe an adiabatic separation of collective rotations built upon a subset of intrinsic vibrational states within the interacting boson model (IBM) in the parameter domains corresponding to axially deformed ground state. The effect is not limited only to the low-lying states and closely follows the variation of quantum and classical measures of regularity. It leads to the existence of rotational bands even close to the highest accessible energies in specific regions within the IBM symmetry triangle. We propose a more general effect of regular intrinsic dynamics on the adiabatic separation of intrinsic and collective motion. © 2010 The American Physical Society.


Tashpulatov S.N.,Charles University | Tashpulatov S.N.,Academy of Sciences of the Czech Republic
Energy Policy | Year: 2013

Price fluctuations that partially comove with demand are a specific feature inherent to liberalized electricity markets. The regulatory authority in Great Britain, however, believed that sometimes electricity prices were significantly higher than what was expected and, therefore, introduced price-cap regulation and divestment series. In this study, I analyze how the introduced institutional changes and regulatory reforms affected the dynamics of daily electricity prices in the England and Wales wholesale electricity market during 1990-2001.This research finds that the introduction of price-cap regulation did achieve the goal of lowering the price level at the cost of higher price volatility. Later, the first series of divestments is found to be successful at lowering price volatility, which however happens at the cost of a higher price level. Finally, this study also documents that the second series of divestments was more successful at lowering both the price level and volatility. © 2013 Elsevier Ltd.


Ouda L.,Academy of Sciences of the Czech Republic | Druga R.,Charles University | Syka J.,Academy of Sciences of the Czech Republic
Brain Structure and Function | Year: 2012

SMI-32 antibody recognizes a non-phosphorylated epitope of neurofilament proteins, which are thought to be necessary for the maintenance of large neurons with highly myelinated processes. We investigated the distribution and quantity of SMI-32-immunoreactive(-ir) neurons in individual parts of the rat auditory system. SMI-32-ir neurons were present in all auditory structures; however, in most regions they constituted only a minority of all neurons (10-30%). In the cochlear nuclei, a higher occurrence of SMI-32-ir neurons was found in the ventral cochlear nucleus. Within the superior olivary complex, SMI-32-ir cells were particularly abundant in the medial nucleus of the trapezoid body (MNTB), the only auditory region where SMI-32-ir neurons constituted an absolute majority of all neurons. In the inferior colliculus, a region with the highest total number of neurons among the rat auditory subcortical structures, the percentage of SMI-32-ir cells was, in contrast to the MNTB, very low. In the medial geniculate body, SMI-32-ir neurons were prevalent in the ventral division. At the cortical level, SMI-32-ir neurons were found mainly in layers III, V and VI. Within the auditory cortex, it was possible to distinguish the Te1, Te2 and Te3 areas on the basis of the variable numerical density and volumes of SMI-32-ir neurons, especially when the pyramidal cells of layer V were taken into account. SMI-32-ir neurons apparently form a representative subpopulation of neurons in all parts of the rat central auditory system and may belong to both the inhibitory and excitatory systems, depending on the particular brain region. © 2011 Springer-Verlag.


Bauer M.,Charles University | Bauer M.,Academy of Sciences of the Czech Republic | Cassar A.,University of San Francisco | Chytilova J.,Charles University | And 2 more authors.
Psychological Science | Year: 2014

In suggesting that new nations often coalesce in the decades following war, historians have posed an important psychological question: Does the experience of war generate an enduring elevation in people's egalitarian motivations toward their in-group? We administered social-choice tasks to more than 1,000 children and adults differentially affected by wars in the Republic of Georgia and Sierra Leone. We found that greater exposure to war created a lasting increase in people's egalitarian motivations toward their in-group, but not their out-groups, during a developmental window starting in middle childhood (around 7 years of age) and ending in early adulthood (around 20 years of age). Outside this window, war had no measurable impact on social motivations in young children and had only muted effects on the motivations of older adults. These "war effects" are broadly consistent with predictions from evolutionary approaches that emphasize the importance of group cooperation in defending against external threats, though they also highlight key areas in need of greater theoretical development. © The Author(s) 2013.


Zobel M.,University of Tartu | Moora M.,Academy of Sciences of the Czech Republic | Herben T.,Charles University
Oikos | Year: 2010

Patterns of clonal growth and their controls on the level of individuals have been studied thoroughly, but little is known about the actual clonal mobility of plant individuals in vegetation and about its role in generating vegetation patterns and influencing species coexistence. Current evidence shows that communities are composed of spatially nonmobile 'matrix-forming species' and mobile 'inter-matrix' species, while local between-species variation in clonal mobility has been shown to be positively correlated to small-scale richness. We identify two major gaps in the knowledge. (1) Clonal mobility has a strong species-specific component, but the existing information is mainly qualitative and describes the potential mobility of species the best. Also, species may respond by their clonal growth in a plastic way to some environmental stimuli, such as neighbors or abiotic environment, but this data comes almost exclusively from artificial conditions. We know very little of the actual spatial mobility of clonal plant individuals in the field and of the factors that determine it. (2) Theoretical research indicates that localized dispersal plays prime role in determination of community structure. While clonal mobility shares many important features with the seed dispersal, it also shows important differences to it, such as in dispersal kernel (non-monotonic in clonal dispersal), role of microsite limitation, and role of plasticity. We have little information how systematic are these differences, and whether these differences in dispersal can play any role in shaping community dynamics. We conclude that clonal mobility has an important role in structuring plant communities in a small scale and propose further studies to address specific mechanisms, as well as community context of evolution of clonality. © 2010 The Authors.


Hedl R.,Academy of Sciences of the Czech Republic | Kopecky M.,Academy of Sciences of the Czech Republic | Kopecky M.,Charles University | Komarek J.,Agency for Nature Conservation and Landscape Protection of the Czech Republic
Diversity and Distributions | Year: 2010

Aim: Lowland woodlands in Europe went through dramatic changes in management in the past century. This article investigates the influence of two key factors, abandonment of coppicing and increased pressure of ungulates, in thermophilous oakwoods. We focused on three interconnected topics: (1) Has the assumed successional trend lead to impoverishment of the vegetation assemblages? (2) Has it resulted in vegetation homogenization? (3) Are the thermophilous oakwoods loosing their original character? Location: Czech Republic, Central Europe. Methods: The vegetation in 46 semi-permanent plots was recorded three times: firstly, shortly after the abandonment of coppicing (1953) and then, after four to six decades of secondary succession and strong game impact (1992 and 2006). Overall trends and changes in species spectra were analysed. Results: There is a marked successional shift towards species-poorer communities growing in cooler, moister and nutrient-richer conditions. The change was significantly different in parts affected and unaffected by high numbers of ungulates yet only for herbs, not the woody species. However, observed change in species composition was not accompanied by significant homogenization process that is the general process reported from elsewhere. A sharp decline in plant species typical for thermophilous woodland communities and in endangered species indicates that the original character of the woodland has been gradually lost. Main conclusions: Thermophilous oakwoods have been largely replaced by mesic forests. Lowland oakwoods in continental parts of Europe historically depended on active management, which kept the understorey conditions light and warm. Successional processes in the 20th century caused a critical loss of species diversity at various spatial levels. However, artificially high numbers of ungulates, which otherwise have a negative impact, probably held up succession, so that the changes may still be reversible. © 2010 Blackwell Publishing Ltd.


Skalova H.,Academy of Sciences of the Czech Republic | Havlickova V.,Academy of Sciences of the Czech Republic | Pysek P.,Academy of Sciences of the Czech Republic | Pysek P.,Charles University
Annals of Botany | Year: 2012

Background and AimsInvasiveness of some alien plants is associated with their traits, plastic responses to environmental conditions and interpopulation differentiation. To obtain insights into the role of these processes in contributing to variation in performance, we compared congeneric species of Impatiens (Balsaminaceae) with different origin and invasion status that occur in central Europe.MethodsNative I. noli-tangere and three alien species (highly invasive I. glandulifera, less invasive I. parviflora and potentially invasive I. capensis) were studied and their responses to simulated canopy shading and different nutrient and moisture levels were determined in terms of survival and seedling traits.Key Results and ConclusionsImpatiens glandulifera produced high biomass in all the treatments and the control, exhibiting the 'Jack-and-master' strategy that makes it a strong competitor from germination onwards. The results suggest that plasticity and differentiation occurred in all the species tested and that along the continuum from plasticity to differentiation, the species at the plasticity end is the better invader. The most invasive species I. glandulifera appears to be highly plastic, whereas the other two less invasive species, I. parviflora and I. capensis, exhibited lower plasticity but rather strong population differentiation. The invasive Impatiens species were taller and exhibited higher plasticity and differentiation than native I. noli-tangere. This suggests that even within one genus, the relative importance of the phenomena contributing to invasiveness appears to be species'specific. © 2012 The Author. Published by Oxford University Press on behalf of the Annals of Botany Company.


Skalova H.,Academy of Sciences of the Czech Republic | Moravcova L.,Academy of Sciences of the Czech Republic | Pysek P.,Academy of Sciences of the Czech Republic | Pysek P.,Charles University
Perspectives in Plant Ecology, Evolution and Systematics | Year: 2011

Invasion of some alien plants is considered to be associated with inter-population differentiation and adaptations to local conditions. To obtain an insight into these processes it is convenient to compare invasive plants with their native congeners. The intra-specific differentiation during invasion was studied using four Impatiens (Balsaminaceae) species in Central Europe: native Impatiens noli-tangere and three aliens (highly invasive Impatiens glandulifera, less invasive Impatiens parviflora and potentially invasive Impatiens capensis). Differentiation in traits important for the establishment (germination; seedling emergence; seedling frost resistance) was measured in a laboratory and an experimental garden using seed collected from five natural populations of each species. Frost resistance of I. capensis, currently invasive in Western Europe, was within the scope of other congeners and it does not seem to be a barrier to spread of the species into Central Europe. Among-population differences were found within all species except I. capensis. In I. noli-tangere, I. glandulifera and I. parviflora the differences were related to the climatic characteristics in early spring at the source localities, which indicates that individuals may be adapted to local conditions. The differences found between the populations of I. noli-tangere, I. glandulifera and I. parviflora are likely to reflect the frost sensitivity of the species. In the highly frost-sensitive I. parviflora differentiation was found both in germination and frost resistance of individual populations. In I. glandulifera the differences among populations in frost sensitivity depended on temperature at the seed source and corresponded to the pattern of emergence of seedlings in the garden. In the native I. noli-tangere, the differences among populations in the time of germination depended on temperature at the seed-source locality. Since local adaptations were indicated both in native and invasive species studied, they are unlikely to provide the invasive Impatiens species with an advantage against the native congener, at least in terms of the traits investigated. © 2011 Perspectives in Plant Ecology, Evolution and Systematics.


Palacky J.,Charles University | Vorlickova M.,Academy of Sciences of the Czech Republic | Vorlickova M.,Masaryk University | Kejnovska I.,Academy of Sciences of the Czech Republic | And 2 more authors.
Nucleic Acids Research | Year: 2013

DNAconcentrationhasbeenrecentlysuggestedtobe the reason why different arrangements are revealed for K+-stabilized human telomere quadruplexes by experimental methods requiring DNA concentrations differing by orders of magnitude. AsRamanspectroscopy can be applied to DNA samples ranging from those accessible by absorption and CD spectroscopies up to extremely concentrated solutions, gels and even crystals; it has been used here to clarify polymorphism of a core human telomeric sequence G3(TTAG 3)3 in the presence of K+and Na+ ions throughout wide range of DNA concentrations. We demonstrate that the K+-structure of G3(TTAG3)3 at low DNA concentration is close to the antiparallel fold of Na+-stabilized quadruplex. On the increase of G 3(TTAG3)3 concentration, a gradual transition from antiparallel to intramolecular parallel arrangement was observed, but only for thermodynamically equilibrated K+-stabilized samples. The transition is synergically supported by increased K+ concentration. However, even for extremely high G3(TTAG3)3 and K +concentrations, an intramolecular antiparallel quadruplex is spontaneously formed from desalted non-quadruplex single-strand after addition of K+ ions. Thermal destabilization or long dwell time are necessary to induce interquadruplex transition. On the contrary, Na+-stabilized G 3(TTAG3)3 retains its antiparallel folding regardless of the extremely high DNA and/or Na+concentrations, thermal destabilization or annealing. © 2012 The Author(s).


Skora R.,Charles University | Turek I.,Academy of Sciences of the Czech Republic
Journal of Physics Condensed Matter | Year: 2012

Results of first-principles calculations of the Fe/GaAs/Ag(001) epitaxial tunnel junctions reveal that hybridization of interface resonances formed at both interfaces can enhance the tunnelling anisotropic magnetoresistance (TAMR) of the systems. This mechanism is manifested by a non-monotonic dependence of the TAMR effect on the thickness of the tunnel barrier, with a maximum for intermediate thicknesses. A detailed scan of k-resolved transmissions over the two-dimensional Brillouin zone proves an interplay between a few hybridization-induced hot spots and a contribution to the tunnelling from the vicinity of the point. This interpretation is supported by calculated properties of a simple tight-binding model of the junction, which reproduce qualitatively most of the features of the first-principles theory. © 2012 IOP Publishing Ltd.


Simova I.,Charles University | Simova I.,Academy of Sciences of the Czech Republic | Herben T.,Charles University | Herben T.,Academy of Sciences of the Czech Republic
Proceedings of the Royal Society B: Biological Sciences | Year: 2012

Plant nuclear genome size (GS) varies over three orders of magnitude and is correlated with cell size and growth rate. We explore whether these relationships can be owing to geometrical scaling constraints. These would produce an isometric GS-cell volume relationship, with the GS-cell diameter relationship with the exponent of 1/3. In the GS-cell division relationship, duration of processes limited by membrane transport would scale at the 1/3 exponent, whereas those limited by metabolism would show no relationship. We tested these predictions by estimating scaling exponents from 11 published datasets on differentiated and meristematic cells in diploid herbaceous plants. We found scaling of GS-cell size to almost perfectly match the prediction. The scaling exponent of the relationship between GS and cell cycle duration did not match the prediction. However, this relationship consists of two components: (i) S phase duration, which depends on GS, and has the predicted 1/3 exponent, and (ii) a GS-independent threshold reflecting the duration of the G1 and G2 phases. The matcheswe found for the relationships between GS and both cell size and S phase duration are signatures of geometrical scaling. We propose that a similar approach can be used to examine GS effects at tissue and whole plant levels. © 2011 The Royal Society.


Sponer J.,Academy of Sciences of the Czech Republic | Sponer J.,Masaryk University | Cang X.,CAS Shanghai Institute of Materia Medica | Cheatham T.E.,University of Utah
Methods | Year: 2012

The article reviews the application of biomolecular simulation methods to understand the structure, dynamics and interactions of nucleic acids with a focus on explicit solvent molecular dynamics simulations of guanine quadruplex (G-DNA and G-RNA) molecules. While primarily dealing with these exciting and highly relevant four-stranded systems, where recent and past simulations have provided several interesting results and novel insight into G-DNA structure, the review provides some general perspectives on the applicability of the simulation techniques to nucleic acids. © 2012 Elsevier Inc.


Rosero A.,Charles University | Zarsky V.,Charles University | Zarsky V.,Academy of Sciences of the Czech Republic | Cvrckova F.,Charles University
Journal of Experimental Botany | Year: 2013

Plant cell growth and morphogenesis depend on remodelling of both actin and microtubule cytoskeletons. AtFH1 (At5g25500), the main housekeeping Arabidopsis formin, is targeted to membranes and known to nucleate and bundle actin. The effect of mutations in AtFH1 on root development and cytoskeletal dynamics was examined. Consistent with primarily actin-related formin function, fh1 mutants showed increased sensitivity to the actin polymerization inhibitor latrunculin B (LatB). LatB-treated mutants had thicker, shorter roots than wild-type plants. Reduced cell elongation and morphological abnormalities were observed in both trichoblasts and atrichoblasts. Fluorescently tagged cytoskeletal markers were used to follow cytoskeletal dynamics in wild-type and mutant plants using confocal microscopy and VAEM (variable-angle epifluorescence microscopy). Mutants exhibited more abundant but less dynamic F-actin bundles and more dynamic microtubules than wild-type seedlings. Treatment of wild-type seedlings with a formin inhibitor, SMIFH2, mimicked the root growth and cell expansion phenotypes and cytoskeletal structure alterations observed in fh1 mutants. The results suggest that besides direct effects on actin organization, the in vivo role of AtFH1 also includes modulation of microtubule dynamics, possibly mediated by actin-microtubule cross-talk. © 2012 © 2012 The Authors.


Bar T.,Labonnet Ltd. | Kubista M.,TATAA Biocenter | Kubista M.,Academy of Sciences of the Czech Republic | Tichopad A.,Academy of Sciences of the Czech Republic | Tichopad A.,Charles University
Nucleic Acids Research | Year: 2012

Quantitative real-time PCR (qPCR) is the method of choice for specific and sensitive quantification of nucleic acids. However, data validation is still a major issue, partially due to the complex effect of PCR inhibition on the results. If undetected PCR inhibition may severely impair the accuracy and sensitivity of results. PCR inhibition is addressed by prevention, detection and correction of PCR results. Recently, a new family of computational methods for the detection of PCR inhibition called kinetics outlier detection (KOD) emerged. KOD methods are based on comparison of one or a few kinetic parameters describing a test reaction to those describing a set of reference reactions. Modern KOD can detect PCR inhibition reflected by shift of the amplification curve by merely half a cycle with specificity and sensitivity >90. Based solely on data analysis, these tools complement measures to improve and control pre-analytics. KOD methods do not require labor and materials, do not affect the reaction accuracy and sensitivity and they can be automated for fast and reliable quantification. This review describes the background of KOD methods, their principles, assumptions, strengths and limitations. Finally, the review provides recommendations how to use KOD and how to evaluate its performance. © 2012 The Author(s).


Kolarik M.,Academy of Sciences of the Czech Republic | Kolarik M.,Charles University | Jankowiak R.,Agricultural University of Krakow
Microbial Ecology | Year: 2013

Fungi from the genus Geosmithia (Ascomycota: Hypocreales) are associated with bark beetles (Coleoptera: Scolytinae), though little is known about ecology, diversity, and distribution of these fungi across beetle and its host tree species. This study surveyed the diversity, distribution and vector affinity of Geosmithia isolated from subcortical insects that colonized trees from the family Pinaceae in Central and Northeastern Europe. Twelve Geosmithia species were isolated from 85 plant samples associated with 23 subcortical insect species (including 14 bark beetle species). Geosmithia community composition was similar across different localities and vector species; although the fungal communities associated with insects that colonized Pinus differed from that colonizing other tree species (Abies, Larix, and Picea). Ten Geosmithia species from four independent phylogenetic lineages were not reported previously from vectors feeding on other plant families and seem to be restricted to the vectors from Pinaceae only. We conclude that presence of such substrate specificity suggests a long and stable association between Geosmithia and bark beetles. © 2013 Springer Science+Business Media New York.


Volarik D.,Mendel University in Brno | Hedl R.,Academy of Sciences of the Czech Republic
Forest Ecology and Management | Year: 2013

Silver fir (Abies alba Mill.) is a tree species distributed mainly in central Europe. It once was a dominant tree species within some forests of this region. The causes for its rapid decline in the past two centuries have not yet been sufficiently explained. It is argued that human activities have been largely responsible for expansions and contractions of silver fir populations. On the basis of the current distribution of silver fir, historical maps and palaeoecological data, we describe the expansion of silver fir forests. We use fine resolution at the landscape level, an approach that has so far been neglected. Our study area lies in the northern part of the White Carpathian Mountains, Czech Republic. The area comprises 7045. ha, 65% of which is covered by forests. This landscape was shaped by early modern colonization from the 16th century onwards and has changed greatly since the decline of its traditional utilization in the 19th and 20th centuries. The area of forests almost doubled from 1838 to 2005 while the area of pastures and arable land decreased. We identified 172. ha of silver fir forests by field mapping, which represent 2.5% of the whole study area and 3.8% of its forested part. We used land use history variables (based on subsequent land cover maps from 1838, 1882 and 1956) and terrain variables (derived from a digital elevation model) in a logistic regression to model the probability of silver fir forest occurrence. Land use history was highly significantly correlated with the occurrence of silver fir forests. Approximately 59% of silver fir forests occur on land used as pastures in 1838, 28% are on former arable land, meadows and fallows, while only 13% have been forested continuously since the 19th century. We know from historical sources that the surrounding forests (now mainly Norway spruce monocultures) were dominated by silver fir up to the 1860s. Silver fir can act as a pioneer species. It can invade former agricultural land, which probably ensures the survival and periodical expansion of silver fir-dominated forests. Although silver fir has been thought to decline under human pressure, we suggest that the opposite may occur at the landscape level. © 2012 Elsevier B.V.


Dostal P.,Academy of Sciences of the Czech Republic | Paleckova M.,Charles University
Biological Invasions | Year: 2011

The naturalisation hypothesis has been gaining attention recently as a possible mechanism to explain variations in invasion success. It predicts that exotic genera with native representatives should be less successful because of an overlap in resource use and of the existence of common specialised enemies. In this study, we tested whether native congenerics have more negative impact on exotic species than heterogenerics by increasing the effects of soil pathogens. We sampled soil in populations of three exotic species (Epilobium ciliatum, Impatiens parviflora and Stenactis annua) at sites with and without respective congeneric species. This soil was used as an inoculum for cultivating the first plant cohort, which included exotics, as well as native congenerics and heterogenerics. The conditioned soil was subsequently used for cultivating the second cohort of plants (exotics only). We found no consistent impact of relatedness of conditioning species on exotic growth. Although soil conditioned by congeneric E. hirsutum had the largest reduction on the performance of E. ciliatum, the final biomass of S. annua was lowest when grown in soil conditioned by itself. There was no effect of stimulating species on the biomass of I. parviflora. In both experimental phases, performance of exotics was improved when cultivated with sterilised inoculua, indicating the dominance of soil generalist pathogens. However, the biomass of S. annua was increased most by congeneric-stimulated inoculum from congeneric sites, suggesting a possible role for specialised symbionts. Our results suggest that variations in invasion success of at least some exotics may be affected by species-specific interactions mediated by the soil biota. © 2010 Springer Science+Business Media B.V.


Krejci P.,Masaryk University | Krejci P.,Academy of Sciences of the Czech Republic | Krejci P.,University of California at Los Angeles
Mutation Research - Reviews in Mutation Research | Year: 2014

Somatic mutations in receptor tyrosine kinase FGFR3 cause excessive cell proliferation, leading to cancer or skin overgrowth. Remarkably, the same mutations inhibit chondrocyte proliferation and differentiation in developing bones, resulting in skeletal dysplasias, such as hypochondroplasia, achondroplasia, SADDAN and thanatophoric dysplasia. A similar phenotype is observed in Noonan syndrome, Leopard syndrome, hereditary gingival fibromatosis, neurofibromatosis type 1, Costello syndrome, Legius syndrome and cardiofaciocutaneous syndrome. Collectively termed RASopathies, the latter syndromes are caused by germline mutations in components of the RAS/ERK MAP kinase signaling pathway. This article considers the evidence suggesting that FGFR3 activation in chondrocytes mimics the activation of major oncogenes signaling via the ERK pathway. Subsequent inhibition of chondrocyte proliferation in FGFR3-related skeletal dysplasias and RASopathies is proposed to result from activation of defense mechanisms that originally evolved to safeguard mammalian organisms against cancer. © 2013 Elsevier B.V.


Stepanova K.,Academy of Sciences of the Czech Republic | Stepanova K.,Charles University | Sinkora M.,Academy of Sciences of the Czech Republic
Developmental and Comparative Immunology | Year: 2012

The expression of selected molecules was chosen to study porcine γδ lymphocytes and their CD2/CD8 subsets in different lymphoid organs in vivo and in vitro. Results indicate that many γδ T cells can constitutively express CD25 and MHC-II and that the frequency of γδ T cells positive for CD25, CD11b, SWC1 and SWC7 can be increased by stimulation. A diversified TCRδ repertoire was found inside CD25 +, CD11b +, SWC1 - and CD45RA - cells. Ontogenetic studies revealed various age and/or colonization dependency for expression of all studied molecules except of SWC7. Findings generally indicate that CD25 represent an activation molecule that probably marks a functionally distinct subsets, expression of CD11b is perhaps connected to early functions of naive γδ T cells in the periphery, SWC1 is lineage specific marker, SWC7 may represent an activation molecule with intrinsic or transient expression, and the expression of CD45RA/RC most likely defines naive and terminally differentiated cells. © 2011 Elsevier Ltd.


Svanda M.,Academy of Sciences of the Czech Republic | Svanda M.,Charles University
Astrophysical Journal Letters | Year: 2012

I analyze the maps recording the travel-time shifts caused by averaged plasma anomalies under an "average supergranule," constructed by means of statistical averaging over 5582 individual supergranules with large divergence signals detected in two months of Helioseismic and Magnetic Imager Dopplergrams. By utilizing a three-dimensional validated time-distance inversion code, I measure a peak vertical velocity of 117 ± 2ms-1 at depths around 1.2 Mm in the center of the supergranule and a root-mean-square vertical velocity of 21ms-1 over the area of the supergranule. A discrepancy between this measurement and the measured surface vertical velocity (a few ms-1) can be explained by the existence of the large-amplitude vertical flow under the surface of supergranules with large divergence signals, recently suggested by Duvall & Hanasoge. © 2012. The American Astronomical Society. All rights reserved.


Zurmanova J.,Charles University | Soukup T.,Academy of Sciences of the Czech Republic
Physiological Research | Year: 2013

We studied the expression of myosin heavy chain isoforms at mRNA and protein levels as well as fiber type composition in the fast extensor digitorum longus (EDL) and slow soleus (SOL) twitch muscles of adult inbred Lewis strain rats. Comparison of the results from Real Time RT-PCR, SDS-PAGE and fiber type analysis showed corresponding proportions of MyHC transcripts (MyHC-1, -2a, -2x/d, -2b), protein isoforms (MyHC-1, -2a, -2x/d, -2b) and fiber types (type 1, 2A, 2X/D, 2B) in both muscles. Furthermore, we found that slow MyHC-1 mRNA expression in the SOL was up to three orders higher than that of fast MyHC transcripts. This finding can explain the predominance of MyHC-1 isoform and fiber type 1 and the absence of pure 2X/D and 2B fibers in the SOL muscle. Based on our data presenting quantitative evidence of corresponding proportions between mRNA level, protein content and fiber type composition, we suggest that the Real Time RT-PCR technique can be used as a routine method for analysis of muscle composition changes and could be advantageous for the analysis of scant biological samples such as muscle biopsies in humans. © 2013 Institute of Physiology v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic.


Cap M.,Charles University | Stepanek L.,Charles University | Harant K.,Charles University | Harant K.,Academy of Sciences of the Czech Republic | And 2 more authors.
Molecular Cell | Year: 2012

Nutrient sensing and metabolic reprogramming are crucial for metazoan cell aging and tumor growth. Here, we identify metabolic and regulatory parallels between a layered, multicellular yeast colony and a tumor-affected organism. During development, a yeast colony stratifies into U and L cells occupying the upper and lower colony regions, respectively. U cells activate a unique metabolism controlled by the glutamine-induced TOR pathway, amino acid-sensing systems (SPS and Gcn4p) and signaling from mitochondria with lowered respiration. These systems jointly modulate U cell physiology, which adapts to nutrient limitations and utilize the nutrients released from L cells. Stress-resistant U cells share metabolic pathways and other similar characteristics with tumor cells, including the ability to proliferate. L cells behave similarly to stressed and starving cells, which activate degradative mechanisms to provide nutrients to U cells. Our data suggest a nutrient flow between both cell types, resembling the Cori cycle and glutamine-NH 4 + shuttle between tumor and healthy metazoan cells. © 2012 Elsevier Inc.


Brom C.,Charles University | Preuss M.,Charles University | Klement D.,Academy of Sciences of the Czech Republic
Computers and Education | Year: 2011

Curricular schooling can benefit from the usage of educational computer games, but it is difficult to integrate them in the formal schooling system. Here, we investigate one possible approach to this integration, which capitalizes on using a micro-game that can be played with a teacher's guidance as a supplement after a traditional expository lecture followed by a debriefing. The game's purpose is to reinforce and integrate part of the knowledge learnt during the lecture. We investigated feasibility of this approach in a quasi-experimental study in 70 min long seminars on the topic of animal learning at 5 classes at 4 different high-schools in the Czech Republic. Each class was divided to two groups randomly. After an expository lecture, the game group played a game called Orbis Pictus Bestialis while the control group received an extra lecture that used media-rich materials. The time allotment was the same in both groups. We investigated the immediate and one month delayed effects of the game on students' knowledge reinforced and integrated by the game as well as on knowledge learnt during the expository lecture but not strengthened by the game. We also investigated students' overall appeal towards the seminar and its perceived educational value. Data from 100 students were analysed. The results showed that a) the game-playing is comparable to the traditional form of teaching concerning immediate knowledge gains and has a significant medium positive effect size regarding retention, b) the game-playing is not detrimental to information transmitted in the expository lecture but not strengthened by the game, c) perceived educational value and the overall appeal were high in the game group, nevertheless the perceived educational value was slightly lower in the game group comparing to the traditional group. Our results suggest that the proposed approach of harnessing educational computer games at high-schools is promising. © 2011 Elsevier Ltd. All rights reserved.


Horak P.,Charles University | Mikes L.,Charles University | Lichtenbergova L.,Charles University | Skala V.,Charles University | And 2 more authors.
Clinical Microbiology Reviews | Year: 2015

Cercarial dermatitis (swimmer’s itch) is a condition caused by infective larvae (cercariae) of a species-rich group of mammalian and avian schistosomes. Over the last decade, it has been reported in areas that previously had few or no cases of dermatitis and is thus considered an emerging disease. It is obvious that avian schistosomes are responsible for the majority of reported dermatitis outbreaks around the world, and thus they are the primary focus of this review. Although they infect humans, they do not mature and usually die in the skin. Experimental infections of avian schistosomes in mice show that in previously exposed hosts, there is a strong skin immune reaction that kills the schistosome. However, penetration of larvae into naive mice can result in temporary migration from the skin. This is of particular interest because the worms are able to migrate to different organs, for example, the lungs in the case of visceral schistosomes and the central nervous system in the case of nasal schistosomes. The risk of such migration and accompanying disorders needs to be clarified for humans and animals of interest (e.g., dogs). Herein we compiled the most comprehensive review of the diversity, immunology, and epidemiology of avian schistosomes causing cercarial dermatitis. © 2015, American Society for Microbiology. All Rights Reserved.


Valentova J.V.,Academy of Sciences of the Czech Republic | Havlicek J.,Charles University
PLoS ONE | Year: 2013

Previous research has shown that lay people can accurately assess male sexual orientation based on limited information, such as face, voice, or behavioral display. Gender-atypical traits are thought to serve as cues to sexual orientation. We investigated the presumed mechanisms of sexual orientation attribution using a standardized set of facial and vocal stimuli of Czech men. Both types of stimuli were rated for sexual orientation and masculinity-femininity by non-student heterosexual women and homosexual men. Our data showed that by evaluating vocal stimuli both women and homosexual men can judge sexual orientation of the target men in agreement with their self-reported sexual orientation. Nevertheless, only homosexual men accurately attributed sexual orientation of the two groups from facial images. Interestingly, facial images of homosexual targets were rated as more masculine than heterosexual targets. This indicates that attributions of sexual orientation are affected by stereotyped association between femininity and male homosexuality; however, reliance on such cues can lead to frequent misjudgments as was the case with the female raters. Although our study is based on a community sample recruited in a non-English speaking country, the results are generally consistent with the previous research and thus corroborate the validity of sexual orientation attributions. © 2013 Valentova, Havlček.


Urban P.,Academy of Sciences of the Czech Republic | Musilova V.,Academy of Sciences of the Czech Republic | Skrbek L.,Charles University
Physical Review Letters | Year: 2011

We present an experimental study of turbulent Rayleigh-Bénard convection (RBC) in a cylindrical cell of height 0.3m, diameter 0.3m. It is designed to minimize the influence of its structure on the convective flow of cryogenic He4 gas of Prandtl number Pr1, with the aim of resolving existing contradictions in Nusselt (Nu) versus Rayleigh number (Ra) scaling. For 7.2×106≤R1011 our data agree with suitably corrected data from similar cryogenic experiments and are consistent with NuRa2/7. On approaching Ra1011 our data display a crossover to NuRa1/3 that approximately holds up to Ra≅4.6×1013; there is no sign of a transition to the ultimate Kraichnan regime. Differences in Nu(Ra) scaling observed in similar RBC experiments for Ra1011 cannot be explained due to the difference in Pr, but seem to depend also on experimental details. © 2011 American Physical Society.


Veis L.,Charles University | Veis L.,Academy of Sciences of the Czech Republic | Pittner J.,Academy of Sciences of the Czech Republic
Journal of Chemical Physics | Year: 2010

Quantum computers are appealing for their ability to solve some tasks much faster than their classical counterparts. It was shown in [Aspuru-Guzik, Science 309, 1704 (2005)] that they, if available, would be able to perform the full configuration interaction (FCI) energy calculations with a polynomial scaling. This is in contrast to conventional computers where FCI scales exponentially. We have developed a code for simulation of quantum computers and implemented our version of the quantum FCI algorithm. We provide a detailed description of this algorithm and the results of the assessment of its performance on the four lowest lying electronic states of CH2 molecule. This molecule was chosen as a benchmark, since its two lowest lying A1 1 states exhibit a multireference character at the equilibrium geometry. It has been shown that with a suitably chosen initial state of the quantum register, one is able to achieve the probability amplification regime of the iterative phase estimation algorithm even in this case. © 2010 American Institute of Physics.


Prochazkova D.,Academy of Sciences of the Czech Republic | Bousova I.,Charles University | Wilhelmova N.,Academy of Sciences of the Czech Republic
Fitoterapia | Year: 2011

The interest in possible health benefits of flavonoids has increased owing to their potent antioxidant and free radical scavenging activities observed in vitro. Nevertheless, the antioxidant efficacy of flavonoids in vivo is less documented and their prooxidant properties have been actually described in vivo. Due to their prooxidant properties, they are able to cause oxidative damage by reacting with various biomolecules, such as lipids, proteins and DNA. Hence, the aim of this review is to discuss both the antioxidant and prooxidant effects of flavonoids. © 2011 Elsevier B.V. All rights reserved.


Svanda M.,Academy of Sciences of the Czech Republic | Svanda M.,Charles University
Astrophysical Journal | Year: 2013

The consistency of time-distance inversions for horizontal components of the plasma flow on supergranular scales in the upper solar convection zone is checked by comparing the results derived using two k-ω filtering procedures - ridge filtering and phase-speed filtering - commonly used in time-distance helioseismology. I show that both approaches result in similar flow estimates when finite-frequency sensitivity kernels are used. I further demonstrate that the performance of the inversion improves (in terms of a simultaneously better averaging kernel and a lower noise level) when the two approaches are combined together in one inversion. Using the combined inversion, I invert for horizontal flows in the upper 10 Mm of the solar convection zone. The flows connected with supergranulation seem to be coherent only for the top ∼5 Mm; deeper down there is a hint of change of the convection scales toward structures larger than supergranules. © 2013. The American Astronomical Society. All rights reserved..


Epanchin-Niell R.S.,Resources for the Future | Haight R.G.,U.S. Department of Agriculture | Berec L.,Academy of Sciences of the Czech Republic | Kean J.M.,Agresearch Ltd. | Liebhold A.M.,U.S. Department of Agriculture
Ecology Letters | Year: 2012

Cost-effective surveillance strategies are needed for efficient responses to biological invasions and must account for the trade-offs between surveillance effort and management costs. Less surveillance may allow greater population growth and spread prior to detection, thereby increasing the costs of damages and control. In addition, surveillance strategies are usually applied in environments under continual invasion pressure where the number, size and location of established populations are unknown prior to detection. We develop a novel modeling framework that accounts for these features of the decision and invasion environment and determines the long term sampling effort that minimises the total expected costs of new invasions. The optimal solution depends on population establishment and growth rates, sample sensitivity, and sample, eradication, and damage costs. We demonstrate how to optimise surveillance systems under budgetary constraints and find that accounting for spatial heterogeneity in sampling costs and establishment rates can greatly reduce management costs. © 2012 Blackwell Publishing Ltd/CNRS.


Sykova E.,Academy of Sciences of the Czech Republic | Forostyak S.,Charles University
Laser Therapy | Year: 2013

Background. A number of cardiovascular, neurological, musculoskeletal and other diseases have a limited capacity for repair and only a modest progress has been made in treatment of brain diseases. The discovery of stem cells has opened new possibilities for the treatment of these maladies, and cell therapy now stands at the cutting-edge of modern regenerative medicine and tissue engineering. Experimental data and the first clinical trials employing stem cells have shown their broad therapeutic potential and have brought hope to patients suffering from devastating pathologies of different organs and systems. Aims. Here, we briefly review the main achievements and trends in cell-based therapy, with an emphasis on the main types of stem cells. embryonic, mesenchymal stromal and induced pluripotent cells. Discussion. Many questions regarding the application of stem cells remain unanswered, particularly tumorigenicity, immune rejection and danger of gene manipulation. Currently, only MSC seems to be safe and might be considered to be a leading candidate for human application to treat pathologies that affect the cardiovascular, neurological and musculoskeletal systems. © 2013 JMLL, Tokyo, Japan.


Satori C.P.,University of Minnesota | Henderson M.M.,University of Minnesota | Krautkramer E.A.,University of Minnesota | Kostal V.,Tescan | And 3 more authors.
Chemical Reviews | Year: 2013

The role that organelle analysis has played in understanding biology is studied. Organelle analysis enables a more specific description of the molecular, biochemical, and physiological processes associated with diseases, embryonic development, tissue differentiation, organism aging, disease treatments, and organism response to pathogens. Confocal microscopy has become a routine tool for investigating subcellular organization, organelle networks, and organelle dynamics in cellular and tissue samples. Most organelles have a dynamic, three-dimensional (3D) organization inside the cell, which is tightly connected to their physiological functions. Due to this, a single 2D image inherently limits the information acquired about the distribution of a particular property within the organelle. The combination of subcellular fractionation with 'omic' technologies has become a powerful resource to characterize and catalogue the various subcellular environments in a cell.


Meyerson L.A.,University of Rhode Island | Meyerson L.A.,Academy of Sciences of the Czech Republic | Cronin J.T.,Louisiana State University
Biological Invasions | Year: 2013

We found a new non-native haplotype of Phragmites australis in North America that provides convincing evidence for multiple introductions of this highly invasive reed from Europe. Prior to our detection of this new non-native haplotype, invasion of North America by this reed grass was thought to be limited to a single cp-DNA haplotype-haplotype M. However, we found two sites colonized by haplotype L1 in Quebec, Canada, a haplotype native to northern Europe, Great Britain and Romania. Because the invasion of North America by P. australis is ongoing, and because there is evidence for intra- and inter-specific hybridization and increased fecundity resulting from outcrossing, more attention should be paid to genetic differences and associated vigor of populations of introduced Phragmites across North America. © 2013 Springer Science+Business Media Dordrecht.


Pleskot R.,Academy of Sciences of the Czech Republic | Li J.,Purdue University | Zarsky V.,Academy of Sciences of the Czech Republic | Zarsky V.,Charles University | And 2 more authors.
Trends in Plant Science | Year: 2013

Plants respond to diverse biotic and abiotic stimuli as well as to endogenous developmental cues. Many of these stimuli result in altered activity of phospholipase D (PLD), an enzyme that hydrolyzes structural phospholipids producing phosphatidic acid (PA). PA is a key signaling intermediate in animals, but its targets in plants are relatively uncharacterized. Recent studies have demonstrated that the cytoskeleton is a major target of PLD-PA signaling and identified a positive feedback loop between actin turnover and PLD activity. Moreover, two cytoskeletal proteins, capping protein and MAP65-1, have been identified as PA-binding proteins regulating actin and microtubule organization and dynamics. In this review, we highlight the role of the PLD-PA module as an important hub for housekeeping and stress-induced regulation of membrane-associated cytoskeletal dynamics. © 2013 Elsevier Ltd.


The Basal Chote Event, slightly above the Lower-Middle Devonian boundary in the Prague Synform, is significant not only for its faunal and lithological changes but also for its distinct and widely correlatable magnetic susceptibility (MS), gamma spectrometric (GRS), and geochemical patterns. The upper part of the Tebotov Limestone was composed of calcisiltic material deposited from distal storm or turbidite currents, which alternate with slowly deposited and condensed hemipelagic material. The lower part of the overlying ChoteLimestone was also composed of turbidite deposits. A more proximal depositional environment is recorded in the Na Škrábku Quarry whereas the Prastav Quarry represents a more distal environment. A decrease in the proportion of pelagic components was observed toward the event datum and an increase in the amount of recycled lithoclastic-skeletal detritus carbonate material. A similar trend is displayed by the shallow-water stratigraphic equivalents in the ervenỳ Quarry. The MS record across the studied interval produces a smooth curve below the first event-related beds (Tebotov and Suchomasty Limestone), a drop in MS values at the event base (base of the Choteand Acanthopyge Limestone), and a rapid increase in MS values with high-magnitude and high-amplitude oscillations above the first event-related dark beds. The GRS record shows a reversal in the Th/U ratio at the event base from Th/U. 1 to Th/U < 1. The upper part of the event-related interval is characterized by a GRS-U peak. REE distributions show very uniform patterns both in the deeper-water facies and shallow-water open ocean facies, indicative of their origin by aeolian atmospheric deposition. Light and heavy mineral assemblages are dominated by paramagnetic (kaolinite, muscovite, chlorite, feldspars, pyroxene and amphiboles, apatite, and barite) and ferromagnetic minerals (mostly Fe oxides or oxyhydroxides). The MS and GRS records, together with the lithological character of the sediments, suggest the sea-level rise at the Basal Chote event interval. © 2010 Elsevier B.V.


Stejskalova E.,Academy of Sciences of the Czech Republic | Stejskalova E.,Charles University | Stanek D.,Academy of Sciences of the Czech Republic
Journal of Cell Science | Year: 2014

The nuclear SMN complex localizes to specific structures called nuclear gems. The loss of gems is a cellular marker for several neurodegenerative diseases. Here, we identify that the U1-snRNPspecific protein U1-70K localizes to nuclear gems, and we show that U1-70K is necessary for gem integrity. Furthermore, we show that the interaction between U1-70K and the SMN complex is RNA independent, and we map the SMN complex binding site to the unstructured N-terminal tail of U1-70K. Consistent with these results, the expression of the U1-70K N-terminal tail rescues gem formation. These findings show that U1-70K is an SMN-complexassociating protein, and they suggest a new function for U1-70K in the formation of nuclear gems. © 2014. Published by The Company of Biologists Ltd.


Hulme P.E.,Lincoln University at Christchurch | Pysek P.,Lincoln University at Christchurch | Pysek P.,Academy of Sciences of the Czech Republic | Pysek P.,Charles University | And 7 more authors.
Trends in Ecology and Evolution | Year: 2013

Quantitative assessments of alien plant impacts are essential to inform management to ensure that resources are prioritized against the most problematic species and that restoration targets the worst-affected ecosystem processes. Here, we present the first detailed critique of quantitative field studies of alien plant impacts and highlight biases in the biogeography and life form of the target species, the responses assessed, and the extent to which spatial variability is addressed. Observed impacts often fail to translate to ecosystem services or evidence of environmental degradation. The absence of overarching hypotheses regarding impacts has reduced the consistency of approaches worldwide and prevented the development of predictive tools. Future studies must ensure that the links between species traits, ecosystem stocks, and ecosystem flows, as well as ecosystem services, are explicitly defined. © 2012 Elsevier Ltd.


Vecer J.,Charles University | Vesela P.,Academy of Sciences of the Czech Republic | Malinsky J.,Academy of Sciences of the Czech Republic | Herman P.,Charles University
FEBS Letters | Year: 2014

We report sphingolipid-related reorganization of gel-like microdomains in the plasma membrane of living Saccharomyces cerevisiae using trans-Parinaric acid (t-PnA) and 1,6-diphenyl-1,3,5-hexatriene (DPH). Compared to control, the gel-like domains were significantly reduced in the membrane of a sphingolipid-deficient lcb1-100 mutant. The same reduction resulted from sphingolipid depletion by myriocin. The phenotype could be reverted when a myriocin-induced block in sphingolipid biosynthesis was bypassed by exogenous dihydrosphingosine. Lipid order of less-ordered membrane regions decreased with sphingolipid depletion as well, as documented by DPH fluorescence anisotropy. The data indicate that organization of lateral microdomains is an essential physiological role of these structural lipids.


Malinsky J.,Academy of Sciences of the Czech Republic | Opekarova M.,Academy of Sciences of the Czech Republic | Grossmann G.,Carnegie Institution for Science | Grossmann G.,University of Heidelberg | Tanner W.,University of Regensburg
Annual Review of Plant Biology | Year: 2013

The existence of specialized microdomains in plasma membranes, postulated for almost 25 years, has been popularized by the concept of lipid or membrane rafts. The idea that detergent-resistant membranes are equivalent to lipid rafts, which was generally abandoned after a decade of vigorous data accumulation, contributed to intense discussions about the validity of the raft concept. The existence of membrane microdomains, meanwhile, has been verified by unequivocal independent evidence. This review summarizes the current state of research in plants and fungi with respect to common aspects of both kingdoms. In these organisms, principally immobile microdomains large enough for microscopic detection have been visualized. These microdomains are found in the context of cell-cell interactions (plant symbionts and pathogens), membrane transport, stress, and polarized growth, and the data corroborate at least three mechanisms of formation. As documented in this review, modern methods of visualization of lateral membrane compartments are also able to uncover the functional relevance of membrane microdomains. © Copyright ©2013 by Annual Reviews. All rights reserved.


Malek T.,Charles University | Pravda V.,Academy of Sciences of the Czech Republic
Classical and Quantum Gravity | Year: 2011

General properties of Kerr-Schild spacetimes with an (A)dS background in arbitrary dimension n > 3 are studied. It is shown that the geodetic Kerr-Schild vector k is a multiple WAND of the spacetime. Einstein Kerr-Schild spacetimes with non-expanding k are shown to be of Weyl type N, while the expanding spacetimes are of type II or D. It is shown that this class of spacetimes obeys the optical constraint. This allows us to solve Sachs equation, determine r-dependence of boost weight zero components of the Weyl tensor and discuss curvature singularities. © 2011 IOP Publishing Ltd.


Sedmera D.,Academy of Sciences of the Czech Republic | Sedmera D.,Charles University
Cardiovascular Research | Year: 2011

Function of the developing heart is dictated by changes in its morphology. For simplicity, we distinguish four stages with different contraction mechanics and conduction parameters. Straight or looped tubular hearts, similar to those of invertebrates such as Drosophila or Ciona, operate as suction pumps and are characterized by a caudally localized pacemaker and slow, peristaltoid conduction and contraction. There is a complete occlusion of the lumen during systole. When the atrial and ventricular chambers appear, the preseptation heart is in many functional aspects similar to the adult heart, but the same function is achieved by different means. There are parallels in design among the hearts of lower vertebrates, such as a spongy ventricle without coronary vasculature and a myocardial atrioventricular canal. Even after septation, considerable maturation of cardiac morphology and function occurs during the foetal and early postnatal period. © 2011 The Author.


Grulich M.,Academy of Sciences of the Czech Republic | Grulich M.,Charles University | Stepanek V.,Academy of Sciences of the Czech Republic | Kyslik P.,Academy of Sciences of the Czech Republic
Biotechnology Advances | Year: 2013

Penicillin G acylases (PGAs) are robust industrial catalysts used for biotransformation of β-lactams into key intermediates for chemical production of semi-synthetic β-lactam antibiotics by hydrolysis of natural penicillins. They are used also in reverse, kinetically controlled synthetic reactions for large-scale productions of these antibiotics from corresponding beta-lactam nuclei and activated acyl donors. Further biocatalytic applications of PGAs have recently been described: catalysis of peptide syntheses and the resolutions of racemic mixtures for the production of enantiopure active pharmaceutical ingredients that are based on enantioselective acylation or chiral hydrolysis. Moreover, PGAs rank among promiscuous enzymes because they also catalyze reactions such as trans-esterification, Markovnikov addition or Henry reaction. This particular biocatalytic versatility represents a driving force for the discovery of novel members of this enzyme family and further research into the catalytic potential of PGAs. This review deals with biocatalytic applications exploiting enantioselectivity and promiscuity of prokaryotic PGAs that have been recently reported. Biocatalytic applications are discussed and presented with reaction substrates converted into active compounds useful for the pharmaceutical industry. © 2013 Elsevier Inc.


Koukol O.,Charles University | Baldrian P.,Academy of Sciences of the Czech Republic
Soil Biology and Biochemistry | Year: 2012

Twelve unrelated microfungi from Scots pine (. Pinus sylvestris) needle litter were selected to represent supposedly different ecophysiological traits. In order to explore the differences in their involvement in decomposition, activities of their hydrolytic enzymes were compared. Most strains were able to degrade cellulose. The highest exocellulase, β-xylosidase and N-acetylglucosaminidase activities were found in . Verticicladium trifidum. . Oidiodendron griseum and . Allantophomopsis lycopodina were strongly cellulolytic and hemicellulolytic as well. The overlap in the microfungal utilization of cellulose suggests the overlap of nutritional niches of unrelated fungal taxa and competition for carbon sources. Production of the protein-degrading enzymes, arylsulphatase, phosphomonoesterase and phosphodiesterase by litter microfungi was mostly low. © 2012 Elsevier Ltd.


Dewangan S.,Indian School of Mines | Chattopadhyaya S.,Indian School of Mines | Hloch S.,Technical University of Košice | Hloch S.,Academy of Sciences of the Czech Republic
Rock Mechanics and Rock Engineering | Year: 2015

Conical pick is a widely used tool for cutting coal in mines. It has a cemented carbide tip inserted in a steel body. Cemented carbide has been in use for many years for coal/rock cutting because it has the optimum combination of hardness, toughness and resistance against abrasive wear. As coal/rock is a heterogeneous substance, the cutting tool has to undergo various obstructions at the time of excavation that cause the tool to wear out. The cracks and fractures developing in the cemented carbide limit the life of the tool. For a long time, different wear mechanisms have been studied to develop improved grades of cemented carbide with high wear resistance properties. The research is still continuing. Moreover, due to the highly unpredictable nature of coal/rock, it is not easy to understand the wear mechanisms. In the present work, an attempt has been made to understand the wear mechanisms in four conical picks, which were used in a continuous miner machine for underground mining of coal. The wearing pattern of the conical pick indicates damage in its cemented carbide tip as well as the steel body. The worn out parts of the tools have been critically examined using scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) point analysis. Mainly four types of wear mechanisms, namely, coal/rock intermixing, plastic deformation, rock channel formation and crushing and cracking, have been detected. The presence of coal/rock material and their respective concentrations in the selected area of worn out surface were observed using the spectra generated by EDX analysis. © 2014, Springer-Verlag Wien.


Vackar D.,Charles University | Vackar D.,Academy of Sciences of the Czech Republic
Ecological Indicators | Year: 2012

The Ecological Footprint and Biocapacity have been compared with several commonly used environmental indices measuring various aspects of ecological sustainability and biodiversity. We found that the Ecological Footprint and Biocapacity are closely related especially to the Human Appropriation of Net Primary Production (HANPP). On the other hand, the Ecological Footprint is negatively related to other measures of ecosystem health and biodiversity such as the Ecosystem Wellbeing Index (EWI). We explored patterns of correlation between the Ecological Footprint and ecosystem and biodiversity measures, including threatened species numbers. Our results support previous findings that human economic activity and environmental pressures are related to threats to biodiversity. This analysis provides evidence that the Ecological Footprint is a meaningful ecological indicator which can be compared to equivalent measures of the appropriation of ecosystem productive capacity and land use pressures. © 2011 Elsevier Ltd.


Kowarik I.,TU Berlin | Pysek P.,Academy of Sciences of the Czech Republic | Pysek P.,Charles University
Diversity and Distributions | Year: 2012

Aim: Biological invasions are a major threat to biodiversity, and The ecology of invasions by animals and plants by Charles Elton (1958) is often recognized as the starting point for modern invasion research. Yet there were predecessors in invasion research whose contribution to the development of ideas and concepts in this field is often underestimated. To contribute to a balanced perception of pioneers in invasion research, we retrace the work of the Swiss botanist Albert Thellung (1881-1928) whose main work, La flore adventice de Montpellier, appeared 100 years ago, in 1912, and illustrate how his ideas contributed to the current state of the art in the fields of invasion science and biogeography. Location: None. Methods: We discuss conceptual approaches in the invasion-related work by Albert Thellung. Results: Thellung's early work covered topics that are still central to widely used invasion frameworks. He promoted concepts to classify alien species (degree of naturalization, introduction pathways and time period of introduction) and adopted these systematically at a regional scale in his alien flora of Montpellier, comprising 800 non-native species. He introduced an exact population-based definition of naturalization, with links to environmental barriers, and elaborated the first assessment of pathway efficiency by relating introduction modes to naturalization. With conceptual papers and a first review of human-mediated plant introductions, Thellung stimulated further research on plant invasions as well as modern terminological frameworks for alien plants. Main conclusions: Albert Thellung was an outstanding member of the group of pre-Eltonian invasion scientists. He opened up focussed research in the field of alien plants in Europe, and his theoretical approaches were a powerful step towards unifying concepts in invasion ecology. © 2012 Blackwell Publishing Ltd.


Dostal P.,Academy of Sciences of the Czech Republic | Mullerova J.,Academy of Sciences of the Czech Republic | Pysek P.,Academy of Sciences of the Czech Republic | Pysek P.,Charles University | And 2 more authors.
Ecology Letters | Year: 2013

Many exotic plant invaders pose a serious threat to native communities, but little is known about the dynamics of their impacts over time. In this study, we explored the impact of an invasive plant Heracleum mantegazzianum (giant hogweed) at 24 grassland sites invaded for different periods of time (from 11 to 48 years). Native species' richness and productivity were initially reduced by hogweed invasion but tended to recover after ~30 years of hogweed residence at the sites. Hogweed cover declined over the whole period assessed. A complementary common garden experiment suggested that the dynamics observed in the field were due to a negative plant-soil feedback; hogweed survival and biomass, and its competitive ability were lower when growing in soil inocula collected from earlier-invaded grasslands. Our results provide evidence that the initial dominance of an invasive plant species and its negative impact can later be reversed by stabilising processes. © 2013 John Wiley & Sons Ltd/CNRS.


Kubinova S.,Academy of Sciences of the Czech Republic | Sykova E.,Academy of Sciences of the Czech Republic | Sykova E.,Charles University
Regenerative Medicine | Year: 2012

Spinal cord injury (SCI) is a devastating traumatic injury resulting in paralysis or sensory deficits due to tissue damage and the poor ability of axons to regenerate across the lesion. Despite extensive research, there is still no effective treatment that would restore lost function after SCI. A possible therapeutic approach would be to bridge the area of injury with a bioengineered scaffold that would create a stimulatory environment as well as provide guidance cues for the re-establishment of damaged axonal connections. Advanced scaffold design aims at the fabrication of complex materials providing the concomitant delivery of cells, neurotrophic factors or other bioactive substances to achieve a synergistic effect for treatment. This review summarizes the current utilization of scaffolding materials for SCI treatment in terms of their physicochemical properties and emphasizes their use in combination with various cell types, as well as with other combinatorial approaches promoting spinal cord repair. © 2012 Future Medicine Ltd.


Zarsky V.,Charles University | Potocky M.,Academy of Sciences of the Czech Republic
Biochemical Society Transactions | Year: 2010

The Rho/Rop small GTPase regulatory module is central for initiating exocytotically ACDs (active cortical domains) in plant cell cortex, and a growing array of Rop regulators and effectors are being discovered in plants. Structural membrane phospholipids are important constituents of cells as well as signals, and phospholipid-modifying enzymes are well known effectors of small GTPases. We have shown that PLDs (phospholipases D) and their product, PA (phosphatidic acid), belong to the regulators of the secretory pathway in plants. We have also shown that specific NOXs (NADPH oxidases) producing ROS (reactive oxygen species) are involved in cell growth as exemplified by pollen tubes and root hairs. Most plant cells exhibit several distinct plasma membrane domains (ACDs), established and maintained by endocytosis/exocytosis-driven membrane protein recycling. We proposed recently the concept of a 'recycling domain' (RD), uniting the ACD and the connected endosomal recycling compartment (endosome), as a dynamic spatiotemporal entity. We have described a putative GTPase-effector complex exocyst involved in exocytic vesicle tethering in plants. Owing to the multiplicity of its Exo70 subunits, this complex, along with many RabA GTPases (putative recycling endosome organizers), may belong to core regulators of RD organization in plants. ©The Authors.


Suda J.,Charles University | Suda J.,Academy of Sciences of the Czech Republic | Herben T.,Charles University | Herben T.,Academy of Sciences of the Czech Republic
Proceedings of the Royal Society B: Biological Sciences | Year: 2013

Genome duplication (polyploidy) is a recurrent evolutionary process in plants, often conferring instant reproductive isolation and thus potentially leading to speciation. Outcome of the process is often seen in the field as different cytotypes co-occur in many plant populations. Failure of meiotic reduction during gametogenesis is widely acknowledged to be the main mode of polyploid formation. To get insight into its role in the dynamics of polyploidy generation under natural conditions, and coexistence of several ploidy levels, we developed a general gametic model for diploid-polyploid systems. This model predicts equilibrium ploidy frequencies as functions of several parameters, namely the unreduced gamete proportions and fertilities of higher ploidy plants. We used data on field ploidy frequencies for 39 presumably autopolyploid plant species/populations to infer numerical values of the model parameters (either analytically or using an optimization procedure). With the exception of a few species, the model fit was very high. The estimated proportions of unreduced gametes (median of 0.0089) matched published estimates well. Our results imply that conditions for cytotype coexistence in natural populations are likely to be less restrictive than previously assumed. In addition, rather simple models show sufficiently rich behaviour to explain the prevalence of polyploids among flowering plants. © 2012 The Author(s) Published by the Royal Society. All rights reserved.


Niedermeyer T.H.J.,University of Greifswald | Niedermeyer T.H.J.,Cyano Biotech GmbH | Strohalm M.,Academy of Sciences of the Czech Republic
PLoS ONE | Year: 2012

Natural or synthetic cyclic peptides often possess pronounced bioactivity. Their mass spectrometric characterization is difficult due to the predominant occurrence of non-proteinogenic monomers and the complex fragmentation patterns observed. Even though several software tools for cyclic peptide tandem mass spectra annotation have been published, these tools are still unable to annotate a majority of the signals observed in experimentally obtained mass spectra. They are thus not suitable for extensive mass spectrometric characterization of these compounds. This lack of advanced and user-friendly software tools has motivated us to extend the fragmentation module of a freely available open-source software, mMass (http://www.mmass.org), to allow for cyclic peptide tandem mass spectra annotation and interpretation. The resulting software has been tested on several cyanobacterial and other naturally occurring peptides. It has been found to be superior to other currently available tools concerning both usability and annotation extensiveness. Thus it is highly useful for accelerating the structure confirmation and elucidation of cyclic as well as linear peptides and depsipeptides. © 2012 Niedermeyer, Strohalm.


Zou X.,Rutgers University | Zou X.,Jilin University | Huang X.,Rutgers University | Goswami A.,Rutgers University | And 4 more authors.
Angewandte Chemie - International Edition | Year: 2014

Despite being technically possible, splitting water to generate hydrogen is still practically unfeasible due mainly to the lack of sustainable and efficient catalysts for the half reactions involved. Herein we report the synthesis of cobalt-embedded nitrogen-rich carbon nanotubes (NRCNTs) that 1) can efficiently electrocatalyze the hydrogen evolution reaction (HER) with activities close to that of Pt and 2) function well under acidic, neutral or basic media alike, allowing them to be coupled with the best available oxygen-evolving catalysts - which also play crucial roles in the overall water-splitting reaction. The materials are synthesized by a simple, easily scalable synthetic route involving thermal treatment of Co2+-embedded graphitic carbon nitride derived from inexpensive starting materials (dicyandiamide and CoCl2). The materials' efficient catalytic activity is mainly attributed to their nitrogen dopants and concomitant structural defects. The water-splitting reaction still remains far from being practically feasible because of the unavailability of effective catalysts for the hydrogen evolution reaction (HER). A simple synthetic route gives to nitrogen-rich carbon nanotubes that electrocatalyze HER with activities close to that of Pt, and function well under acidic, neutral, or basic media allowing them to be coupled with the best oxygen-evolving catalysts available. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Svanda M.,Academy of Sciences of the Czech Republic | Svanda M.,Charles University
Astronomy and Astrophysics | Year: 2015

Aims. Recent studies have shown that time-distance inversions for flows start to be dominated by a random noise at a depth of only a few Mm. It was proposed that the ensemble averaging might be a solution for learning about the structure of the convective flows, e.g. about the depth structure of supergranulation. Methods. Time-distance inversion is applied to the statistical sample of ~ 104 supergranules, which allows the inversion cost function to be regularised weakly about the random-noise term and thus provides a much better localisation in space. We compare these inversions at four depths (1.9, 2.9, 4.3, and 6.2 Mm) when using different spatio-temporal filtering schemes in order to gain confidence about these inferences. Results. The flows inferred by using different spatio-temporal filtering schemes are different (even by the sign) even though the formal averaging kernels and the random-noise levels are very similar. The inverted flows changes its sign several times with depth. I suggest that this is due to the inaccuracies in the forward problem that are possibly amplified by the inversion. It is also possible that other time-distance inversions are affected by this. © ESO, 2015.


Vachova L.,Academy of Sciences of the Czech Republic | Cap M.,Charles University | Palkova Z.,Charles University
Oxidative Medicine and Cellular Longevity | Year: 2012

When growing on solid surfaces, yeast, like other microorganisms, develops organized multicellular populations (colonies and biofilms) that are composed of differentiated cells with specialized functions. Life within these populations is a prevalent form of microbial existence in natural settings that provides the cells with capabilities to effectively defend against environmental attacks as well as efficiently adapt and survive long periods of starvation and other stresses. Under such circumstances, the fate of an individual yeast cell is subordinated to the profit of the whole population. In the past decade, yeast colonies, with their complicated structure and high complexity that are also developed under laboratory conditions, have become an excellent model for studies of various basic cellular processes such as cell interaction, signaling, and differentiation. In this paper, we summarize current knowledge on the processes related to chronological aging, adaptation, and longevity of a colony cell population and of its differentiated cell constituents. These processes contribute to the colony ability to survive long periods of starvation and mostly differ from the survival strategies of individual yeast cells. © 2012 Libuše Váchová et al.


Obsil T.,Charles University | Obsil T.,Academy of Sciences of the Czech Republic | Obsilova V.,Academy of Sciences of the Czech Republic
Seminars in Cell and Developmental Biology | Year: 2011

The 14-3-3 proteins, a family of conserved regulatory molecules, participate in a wide range of cellular processes through binding interactions with hundreds of structurally and functionally diverse proteins. Several distinct mechanisms of the 14-3-3 protein function were described, including conformational modulation of the bound protein, masking of its sequence-specific or structural features, and scaffolding that facilitates interaction between two simultaneously bound proteins. Details of these functional modes, especially from the structural point of view, still remain mostly elusive. This review gives an overview of the current knowledge concerning the structure of 14-3-3 proteins and their complexes as well as the insights it provides into the mechanisms of their functions. We discuss structural basis of target recognition by 14-3-3 proteins, common structural features of their complexes and known mechanisms of 14-3-3 protein-dependent regulations. © 2011 Elsevier Ltd.


Obsil T.,Charles University | Obsil T.,Academy of Sciences of the Czech Republic | Obsilova V.,Academy of Sciences of the Czech Republic
Biochimica et Biophysica Acta - Molecular Cell Research | Year: 2011

The FOXO forkhead transcription factors are involved in metabolism control, cell survival, cellular proliferation, DNA damage repair response, and stress resistance. Their transcriptional activity is regulated through a number of posttranslational modifications, including phosphorylation, acetylation and ubiquitination. The recently determined three-dimensional structures of FOXO forkhead domains bound to DNA enable to explain the structural basis for DNA recognition by FOXO proteins and its regulation. The aim of this review is to summarize the recent structural characterization of FOXO proteins, the mechanisms of DNA recognition and the role of posttranslational modifications in the regulation of FOXO DNA-binding properties. This article is part of a Special Issue entitled: PI3K-AKT-FOXO axis in cancer and aging. © 2010 Elsevier B.V.


Malek T.,Charles University | Pravda V.,Academy of Sciences of the Czech Republic
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2011

We study exact vacuum solutions to quadratic gravity (QG) of the Weyl types N and III. We show that in an arbitrary dimension all Einstein spacetimes of the Weyl type N with an appropriately chosen effective cosmological constant Λ are exact solutions to QG and we refer to explicitly known metrics within this class. For type III Einstein spacetimes, an additional constraint follows from the field equations of QG and examples of spacetimes obeying such constraint are given. However, type III pp waves do not satisfy this constraint and thus do not solve QG. For type N, we also study a wider class of spacetimes admitting a pure radiation term in the Ricci tensor. In contrast to the Einstein case, the field equations of generic QG determine optical properties of the geometry and restrict such exact solutions to the Kundt class. We provide examples of these metrics. © 2011 American Physical Society.


Flegr J.,Charles University | Hodny Z.,Academy of Sciences of the Czech Republic
Parasites and Vectors | Year: 2016

Background: A recent study performed on 1.3 million patients showed a strong association between being bitten by a cat and probability of being diagnosed with depression. Authors suggested that infection with cat parasite Toxoplasma could be the reason for this association. Method: A cross sectional internet study on a non-clinical population of 5,535 subjects was undertaken. Results: The subjects that reported having been bitten by a dog and a cat or scratched by a cat have higher Beck depression score. They were more likely to have visited psychiatrists, psychotherapists and neurologists in past two years, to have been previously diagnosed with depression (but not with bipolar disorder). Multivariate analysis of models with cat biting, cat scratching, toxoplasmosis, the number of cats at home, and the age of subjects as independent variables showed that only cat scratching had positive effect on depression (p=0.004). Cat biting and toxoplasmosis had no effect on the depression, and the number of cats at home had a negative effect on depression (p=0.021). Conclusions: Absence of association between toxoplasmosis and depression and five times stronger association of depression with cat scratching than with cat biting suggests that the pathogen responsible for mood disorders in animals-injured subjects is probably not the protozoon Toxoplasma gondii but another organism; possibly the agent of cat-scratched disease - the bacteria Bartonella henselae. © 2015 Flegr and Hodný.


Honza M.,Academy of Sciences of the Czech Republic | Honza M.,Charles University
Proceedings. Biological sciences / The Royal Society | Year: 2014

Interspecific brood parasitism represents a prime example of the coevolutionary arms race where each party has evolved strategies in response to the other. Here, we investigated whether common cuckoos (Cuculus canorus) actively select nests within a host population to match the egg appearance of a particular host clutch. To achieve this goal, we quantified the degree of egg matching using the avian vision modelling approach. Randomization tests revealed that cuckoo eggs in naturally parasitized nests showed lower chromatic contrast to host eggs than those assigned randomly to other nests with egg-laying date similar to naturally parasitized clutches. Moreover, egg matching in terms of chromaticity was better in naturally parasitized nests than it would be in the nests of the nearest active non-parasitized neighbour. However, there was no indication of matching in achromatic spectral characteristics whatsoever. Thus, our results clearly indicate that cuckoos select certain host nests to increase matching of their own eggs with host clutches, but only in chromatic characteristics. Our results suggest that the ability of cuckoos to actively choose host nests based on the eggshell appearance imposes a strong selection pressure on host egg recognition.


Kusova K.,Academy of Sciences of the Czech Republic | Pelant I.,Academy of Sciences of the Czech Republic | Valenta J.,Charles University
Light: Science and Applications | Year: 2015

Strain-engineered silicon nanocrystals (SiNCs) have recently been shown to possess direct bandgap. Here, we report the observation of a rich structure in the single-nanocrystal photoluminescence spectra of strain-engineered direct-bandgap SiNCs in the temperature range of 9-300 K. The relationship between individual types of spectra is discussed, and the numerical modeling of spectral diffusion of the experimentally acquired spectra reveals a common origin for most types. The intrinsic spectral shape is shown to be a structure that contains three peaks, approximately 150 meV apart, each of which possesses a Si phonon substructure. Narrow spectral lines, reaching ≤1 meV at 20 K, are detected. The observed temperature dependence of the spectral structure can be assigned to the radiative recombination of positively charged trions, in contrast to several previous reports linking a very similar shape to phonons in the surface capping layers. Our result serves as strong additional support for the direct-bandgap nature of the investigated SiNCs. © 2015 CIOMP.


Abraham V.,Charles University | Kozakova R.,Academy of Sciences of the Czech Republic
Review of Palaeobotany and Palynology | Year: 2012

We estimated relative pollen productivity estimates (PPE), key parameters for the quantitative interpretation of pollen data, for 13 taxa using modern pollen assemblages from 54 sites and recent vegetation data. Vegetation mapping in the area covered a minimum radius of 2. km around each sampling site. Vegetation data were weighted by the Prentice model, i.e. weighting by distance and by the dispersal-deposition parameters of different pollen types. PPE values were calculated by three submodels of the Extended R-value model. ERV 1 produced the best goodness of fit. The PPEs for . Urtica and . Sambucus nigra are published here for the first time, and the PPE for the Chenopodiaceae represents the first estimate for Europe. Values for the other ten taxa (Poaceae, . Pinus, . Salix, . Fraxinus, . Quercus, . Tilia, . Artemisia, . Plantago lanceolata, . Alnus and Cerealia) are comparable with or fall within the ranges of values published in previous studies. Herb taxa produce ca 3-11 times more pollen than the Poaceae. Herbs produce even more pollen than trees, whose production is 1-6 times higher than that of the Poaceae. The lowest pollen producers are the Cerealia, producing 20 times less pollen than the Poaceae. Our estimate of the relevant source area of pollen (RSAP) of 1050. m is relatively high compared to other studies in semi-open landscapes. This is possibly caused by the uneven pattern of some taxa in the vegetation mosaic (. Pinus, . P. lanceolata, . Salix and . Alnus). The distance of 1100. m, at which all taxa are present around each site, is similar to the RSAP distance (1050. m). © 2012 Elsevier B.V.


Kuzel R.,Charles University | Bursik J.,Academy of Sciences of the Czech Republic
Thin Solid Films | Year: 2013

A simple and illustrative method of different fast X-ray diffraction sample scans (omega, phi, psi) was applied to the analysis of preferred grain orientation of cubic KTaO3 thin film deposited on highly textured polycrystalline Pt(111) interlayer on Si single crystalline substrate. The material has a tendency to create many different oriented domains - texture components with strongly dominating (100) orientation. By fast subsequent sample scans (ψ-scans) the components with very narrow distribution of orientations were discovered (gradual texture component stripping) and estimated. By comparison with the detector scan taken at low angle of incidence as it is common for thin film analysis it was found that there is also a background of misoriented crystallites in this film together with many texture components. Using only standard single symmetric θ-2θ or asymmetric grazing incidence scans can easily lead to overlooking of important microstructural features. © 2012 Elsevier B.V.


Flegr J.,Charles University | Lenochova P.,Charles University | Hodny Z.,Academy of Sciences of the Czech Republic | Vondrova M.,Charles University
PLoS Neglected Tropical Diseases | Year: 2011

Background: Latent toxoplasmosis, a lifelong infection with the protozoan Toxoplasma gondii, has cumulative effects on the behaviour of hosts, including humans. The most impressive effect of toxoplasmosis is the "fatal attraction phenomenon," the conversion of innate fear of cat odour into attraction to cat odour in infected rodents. While most behavioural effects of toxoplasmosis were confirmed also in humans, neither the fatal attraction phenomenon nor any toxoplasmosis-associated changes in olfactory functions have been searched for in them. Principal Findings: Thirty-four Toxoplasma-infected and 134 noninfected students rated the odour of urine samples from cat, horse, tiger, brown hyena and dog for intensity and pleasantness. The raters were blind to their infection status and identity of the samples. No signs of changed sensitivity of olfaction were observed. However, we found a strong, gender dependent effect of toxoplasmosis on the pleasantness attributed to cat urine odour (p = 0.0025). Infected men rated this odour as more pleasant than did the noninfected men, while infected women rated the same odour as less pleasant than did noninfected women. Toxoplasmosis did not affect how subjects rated the pleasantness of any other animal species' urine odour; however, a non-significant trend in the same directions was observed for hyena urine. Conclusions: The absence of the effects of toxoplasmosis on the odour pleasantness score attributed to large cats would suggest that the amino acid felinine could be responsible for the fatal attraction phenomenon. Our results also raise the possibility that the odour-specific threshold deficits observed in schizophrenia patients could be caused by increased prevalence of Toxoplasma-infected subjects in this population rather than by schizophrenia itself. The trend observed with the hyena urine sample suggests that this carnivore, and other representatives of the Feliformia suborder, should be studied for their possible role as definitive hosts in the life cycle of Toxoplasma. © 2011 Flegr et al.


Filla J.,Academy of Sciences of the Czech Republic | Filla J.,Charles University | Honys D.,Academy of Sciences of the Czech Republic
Amino Acids | Year: 2012

Rapid changes of protein phosphorylation play a crucial role in the regulation of many cellular processes. Being post-translationally modified, phosphoproteins are often present in quite low abundance and tend to co-exist with their unphosphorylated isoform within the cell. To make their identification more practicable, the use of enrichment protocols is often required. The enrichment strategies can be performed either at the level of phosphoproteins or at the level of phosphopeptides. Both approaches have their advantages and disadvantages. Most enriching strategies are based on chemical modifications, affinity chromatography to capture peptides and proteins containing negatively charged phosphate groups onto a positively charged matrix, or immunoprecipitation by phospho-specific antibodies. In this article, the most up-to-date enrichment techniques are discussed, taking into account their optimization, and highlighting their advantages and disadvantages. Moreover, these methods are compared to each other, revealing their complementary nature in providing comprehensive coverage of the phosphoproteome. © 2012 Springer-Verlag.


Zarsky V.,Charles University | Zarsky V.,Academy of Sciences of the Czech Republic
Protoplasma | Year: 2012

Being a professor of physiology in Wrocław/Breslau till the half of nineteenth century, Jan Evangelista Purkyně/Purkinje made, along with his students, many crucial discoveries combining original experimental approaches with new advanced microscopy and histology techniques. Here, he established first Institute of Physiology worldwide and created a framework for the new science of cellular physiology. With his work, he not only substantially contributed to the establishment of cellular and protoplasmic concepts in biology but represented a rare type of Central European scholar by bridging communities separated by ethnicity and language. © 2012 Springer-Verlag.


Kubinova S.,Academy of Sciences of the Czech Republic | Sykova E.,Academy of Sciences of the Czech Republic | Sykova E.,Charles University
Nanomedicine | Year: 2010

The use of nanotechnology in cell therapy and tissue engineering offers promising future perspectives for brain and spinal cord injury treatment. Stem cells have been shown to selectively target injured brain and spinal cord tissue and improve functional recovery. To allow cell detection, superparamagnetic iron-oxide nanoparticles can be used to label transplanted cells. MRI is then a suitable method for the in vivo tracking of grafted cells in the host organism. CNS, and particularly spinal cord, injury is accompanied by tissue damage and the formation of physical and biochemical barriers that prevent axons from regenerating. One aspect of nanomedicine is the development of biologically compatible nanofiber scaffolds that mimic the structure of the extracellular matrix and can serve as a permissive bridge for axonal regeneration or as a drug-delivery system. The incorporation of biologically active epitopes and/or the utilization of these scaffolds as stem cell carriers may further enhance their therapeutic efficacy. © 2010 Future Medicine Ltd.


Markova S.,Academy of Sciences of the Czech Republic | Searle J.B.,Cornell University | Kotlik P.,Academy of Sciences of the Czech Republic
Heredity | Year: 2014

Gene duplication plays an important role in the origin of evolutionary novelties, but the mechanisms responsible for the retention and functional divergence of the duplicated copy are not fully understood. The α;-globin genes provide an example of a gene family with different numbers of gene duplicates among rodents. Whereas Rattus and Peromyscus each have three adult α;-globin genes (HBA-T1, HBA-T2 and HBA-T3), Mus has only two copies. High rates of amino acid evolution in the independently derived HBA-T3 genes of Peromyscus and Rattus have been attributed to positive selection. Using RACE PCR, reverse transcription-PCR (RT-PCR) and RNA-seq, we show that another rodent, the bank vole Clethrionomys glareolus, possesses three transcriptionally active α;-globin genes. The bank vole HBA-T3 gene is distinguished from each HBA-T1 and HBA-T2 by 20 amino acids and is transcribed 23- and 4-fold lower than HBA-T1 and HBA-T2, respectively. Polypeptides corresponding to all three genes are detected by electrophoresis, demonstrating that the translated products of HBA-T3 are present in adult erythrocytes. Patterns of codon substitution and the presence of low-frequency null alleles suggest a postduplication relaxation of purifying selection on bank vole HBA-T3. © 2014 Macmillan Publishers Limited.


Plavcova E.,Academy of Sciences of the Czech Republic | Plavcova E.,Charles University | Kysely J.,Academy of Sciences of the Czech Republic
Tellus, Series A: Dynamic Meteorology and Oceanography | Year: 2011

Reproduction of daily maximum and minimum temperatures, including tails of their distributions and links to large-scale circulation, is evaluated in an ensemble of high-resolution regional climate model (RCM) simulations over the Czech Republic. RCM data for recent climate (1961-1990) are validated against observed data gridded from a high-density station network. We find large biases in mean monthly temperatures and in seasonal extremes, which are significant in most RCMs throughout the year. The results suggest that an RCM's formulation plays a much more important role in summer, whereas in winter RCM performance is closely linked to the driving GCM. Biases are usually larger for extremes than central parts of temperature distributions, and RCMs tend to underestimate the severity of extremes in both seasons. Substantial underestimation of diurnal temperature range throughout the year in all RCMs and a shift of maximum in its annual cycle suggest general errors in simulating climate processes affecting the difference between daytime and nighttime temperatures. Some features of the temperature biases in RCMs are related to deficiencies in the simulation of atmospheric circulation, particularly too strong advection and overestimation of westerly flow at the expense of easterly flow in most RCMs. The general biases in simulating anticyclonic, cyclonic and straight flow also contribute to the underestimated diurnal temperature range. ©2011 The Authors Tellus A©2011 John Wiley & Sons A/S.


Franek P.,Academy of Sciences of the Czech Republic | Krcal M.,Charles University
Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms | Year: 2014

We study the problem of robust satisfiability of systems of nonlinear equations, namely, whether for a given continuous function f: K → R n on a finite simplicial complex K and α > 0, it holds that each function g: K→Rn such that \\g - f//∞ ≤ a, has a root in K. Via a reduction to the extension problem of maps into a sphere, we show that this problem is decidable if dim K ≤ 2n - 3. This is a substantial extension of previous computational applications of topological degree and related concepts in numerical and interval analysis. Via a reverse reduction we prove that the problem is undecidable when dim K ≥ 2n - 2, where the threshold comes from the stable range in homotopy theory. For the lucidity of our exposition, we focus on the setting when f is piecewise linear. Such functions can approximate general continuous functions, and thus we get approximation schemes and undecidability of the robust satisfiability in other possible settings. Copyright © 2014 by the Society for Industrial and Applied Mathematics.


Bartos M.,Academy of Sciences of the Czech Republic | Janecek S.,Academy of Sciences of the Czech Republic | Janecek S.,Charles University
Current Biology | Year: 2014

Specific pollen placement by zygomorphic flowers on pollinators is one of the key innovations of angiosperm evolution [1]. In most phylogenetic lineages that have evolved zygomorphic flowers, reproductive organs are positioned either in the lower or upper part of the flower. Although these specific positions largely enhance pollen economy, they also represent architectural constraints such that flowers are able to place pollen only on the dorsal or ventral part of pollinators' bodies [2]. Such constraints can lead to interspecific pollen placement in situations where phylogenetically related species with the same floral architecture share pollinators [3]. © 2014 Elsevier Ltd.


Sykova E.,Charles University | Sykova E.,Academy of Sciences of the Czech Republic
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2014

Volume transmission is a form of intercellular communication that does not require synapses; it is based on the diffusion of neuroactive substances across the brain extracellular space (ECS) and their binding to extrasynaptic high-affinity receptors on neurons or glia. Extracellular diffusion is restricted by the limited volume of the ECS, which is described by the ECS volume fraction a, and the presence of diffusion barriers, reflected by tortuosity l, that are created, for example, by fine astrocytic processes or extracellular matrix (ECM) molecules. Organized astrocytic processes, ECM scaffolds or myelin sheets channel the extracellular diffusion so that it is facilitated in a certain direction, i.e. anisotropic. The diffusion properties of the ECS are profoundly influenced by various processes such as the swelling and morphological rebuilding of astrocytes during either transient or persisting physiological or pathological states, or the remodelling of the ECM in tumorous or epileptogenic tissue, during Alzheimer’s disease, after enzymatic treatment or in transgenic animals. The changing diffusion properties of the ECM influence neuron-glia interaction, learning abilities, the extent of neuronal damage and even cell migration. From a clinical point of view, diffusion parameter changes occurring during pathological states could be important for diagnosis, drug delivery and treatment. © 2014 The Author(s) Published by the Royal Society. All rights reserved.


Reblova M.,Academy of Sciences of the Czech Republic | Untereiner W.A.,Brandon University | Reblova K.,Masaryk University
PLoS ONE | Year: 2013

Cyphellophora and Phialophora (Chaetothyriales, Pezizomycota) comprise species known from skin infections of humans and animals and from a variety of environmental sources. These fungi were studied based on the comparison of cultural and morphological features and phylogenetic analyses of five nuclear loci, i.e., internal transcribed spacer rDNA operon (ITS), large and small subunit nuclear ribosomal DNA (nuc28S rDNA, nuc18S rDNA), β-tubulin, DNA replication licensing factor (mcm7) and second largest subunit of RNA polymerase II (rpb2). Phylogenetic results were supported by comparative analysis of ITS1 and ITS2 secondary structure of representatives of the Chaetothyriales and the identification of substitutions among the taxa analyzed. Base pairs with non-conserved, co-evolving nucleotides that maintain base pairing in the RNA transcript and unique evolutionary motifs in the ITS2 that characterize whole clades or individual taxa were mapped on predicted secondary structure models. Morphological characteristics, structural data and phylogenetic analyses of three datasets, i.e., ITS, ITS-β-tubulin and 28S-18S-rpb2-mcm7, define a robust clade containing eight species of Cyphellophora (including the type) and six species of Phialophora. These taxa are now accommodated in the Cyphellophoraceae, a novel evolutionary lineage within the Chaetothyriales. Cyphellophora is emended and expanded to encompass species with both septate and nonseptate conidia formed on discrete, intercalary, terminal or lateral phialides. Six new combinations in Cyphellophora are proposed and a dichotomous key to species accepted in the genus is provided. Cyphellophora eugeniae and C. hylomeconis, which grouped in the Chaetothyriaceae, represent another novel lineage and are introduced as the type species of separate genera. © 2013 Réblová et al.


Lee K.P.,University of Geneva | Piskurewicz U.,University of Geneva | Tureckova V.,Academy of Sciences of the Czech Republic | Carat S.,Ecole Polytechnique Federale de Lausanne | And 4 more authors.
Genes and Development | Year: 2012

Phytochromes phyB and phyA mediate a remarkable developmental switch whereby, early upon seed imbibition, canopy light prevents phyB-dependent germination, whereas, later on, it stimulates phyA-dependent germination. Using a seed coat bedding assay where the growth of dissected embryos is monitored under the influence of dissected endosperm, allowing combinatorial use of mutant embryos and endosperm, we show that canopy light specifically inactivates phyB activity in the endosperm to override phyA-dependent signaling in the embryo. This interference involves abscisic acid (ABA) release from the endosperm and distinct spatial activities of phytochrome signaling components. Under the canopy, endospermic ABA opposes phyA signaling through the transcription factor (TF) ABI5, which shares with the TF PIF1 several target genes that negatively regulate germination in the embryo. ABI5 enhances the expression of phytochrome signaling genes PIF1, SOMNUS, GAI, and RGA, but also of ABA and gibberellic acid (GA) metabolic genes. Over time, weaker ABA-dependent responses eventually enable phyA-dependent germination, a distinct type of germination driven solely by embryonic growth. © 2012 by Cold Spring Harbor Laboratory Press.


Prochazkova G.,Institute of Chemical Technology Prague | Safarik I.,Academy of Sciences of the Czech Republic | Safarik I.,Palacky University | Branyik T.,Institute of Chemical Technology Prague
Bioresource Technology | Year: 2013

To make magnetic harvesting a more viable option, a suspension of inexpensive iron oxide magnetic microparticles (IOMMs) prepared by microwave treatment is presented as a new agent for separating Chlorella vulgaris from a highly diluted suspension. Separation efficiencies were tested under various conditions (model environment, cultivation media, different pH), revealing not only a dependency on the pH and amount of IOMMs, but also the influence of the ions present in the culture medium. Phosphorus ions were identified as the medium component interfering with algae-IOMMs interactions that are essential for magnetic cell separations in the culture medium. Phosphorus limited C. vulgaris cells were magnetically separated from the medium at separation efficiencies of over 95% at a 3:1 mass ratio of IOMMs to microalgae. A rapid and complete demagnetization of harvested algae was achieved by acidic treatment (10vol.% H2SO4) at 40°C under the influence of ultrasound. © 2012 Elsevier Ltd.


Hubackova S.,Academy of Sciences of the Czech Republic | Krejcikova K.,Academy of Sciences of the Czech Republic | Bartek J.,Academy of Sciences of the Czech Republic | Bartek J.,Danish Cancer Society | Hodny Z.,Academy of Sciences of the Czech Republic
Aging | Year: 2012

Many cancers arise at sites of infection and inflammation. Cellular senescence, a permanent state of cell cycle arrest that provides a barrier against tumorigenesis, is accompanied by elevated proinflammatory cytokines such as IL1, IL6, IL8 and TNFα. Here we demonstrate that media conditioned by cells undergoing any of the three main forms of senescence, i.e. replicative, oncogene-and drug-induced, contain high levels of IL1, IL6, and TGFβ capable of inducing reactive oxygen species (ROS)-mediated DNA damage response (DDR). Persistent cytokine signaling and activated DDR evoke senescence in normal bystander cells, accompanied by activation of the JAK/STAT, TGFβ/SMAD and IL1/NFκB signaling pathways. Whereas inhibition of IL6/STAT signaling had no effect on DDR induction in bystander cells, inhibition of either TGFβ/SMAD or IL1/NFκB pathway resulted in decreased ROS production and reduced DDR in bystander cells. Simultaneous inhibition of both TGFβ/SMAD and IL1/NFκB pathways completely suppressed DDR indicating that IL1 and TGFβ cooperate to induce and/or maintain bystander senescence. Furthermore, the observed IL1-and TGFβ-induced expression of NAPDH oxidase Nox4 indicates a mechanistic link between the senescence-associated secretory phenotype (SASP) and DNA damage signaling as a feature shared by development of all major forms of paracrine bystander senescence. © Hubackova et al.


Krahulcova A.,Academy of Sciences of the Czech Republic | Rotreklova O.,Masaryk University
Preslia | Year: 2010

This paper reviews recent use of flow cytometry in studies on apomictic plant taxa. The most of apomictic angiosperms are polyploid, often differing in ploidy level from their sexual counterparts within the agamic complex. Flow cytometry is widely used for screening the ploidy levels of mature plants and their seed generated both in the field and in experiments. Routine ploidy screening often accompanied by molecular markers distinguishing individual genotypes are used to reveal novel insights into the biosystematics and population biology of apomictic taxa. Apomixis (asexual seed formation) is mostly facultative, operating together with other less frequent reproductive pathways within the same individual. The diversity in modes of reproduction in apomicts is commonly reflected in the ploidy structure of their progeny in mixed-cytotype populations. Thus, flow cytometry facilitates the detection and quantification of particular progeny classes generated by different reproductive pathways. The specific embryo/endosperm ploidy ratios, typical of the different reproductive pathways, result from modifications of double fertilization in sexual/apomictic angiosperms. Thus, the reproductive origin of seed can be identified, including autonomous or pseudogamous apomixis, haploid parthenogenesis and sexual reproduction, involving either reduced or unreduced gametes. Collectively, flow cytometry has been used to address the following research topics: (i) assessing the variation in ploidy levels and genome sizes in agamic complexes, (ii) detection and quantification of different reproductive modes in facultative apomicts, (iii) elucidation of processes in populations with coexisting sexual and apomictic biotypes, (iv) evolution of agamic complexes, and (v) genetic basis of apomixis. The last topic is of paramount importance to crop breeding: the search for candidate gene(s) responsible for apomixis is the main objective of many research programmes. A list of the angiosperm taxa that could provide model systems for such research is provided.


Malina J.,Academy of Sciences of the Czech Republic | Hannon M.J.,University of Birmingham | Brabec V.,Academy of Sciences of the Czech Republic
FEBS Journal | Year: 2014

Bulged DNA structures are of general biological significance because of their important roles in a number of biochemical processes. Compounds capable of targeting bulged DNA sequences can be used as probes for studying their role in nucleic acid function, or could even have significant therapeutic potential. The interaction of [Fe2L3]4+ metallosupramolecular helicates (L = C25H20N4) with DNA duplexes containing bulges has been studied by measurement of the DNA melting temperature and gel electrophoresis. This study was aimed at exploring binding affinities of the helicates for DNA bulges of various sizes and nucleotide sequences. The studies reported herein reveal that both enantiomers of [Fe2L3]4+ bind to DNA bulges containing at least two unpaired nucleotides. In addition, these helicates show considerably enhanced affinity for duplexes containing unpaired pyrimidines in the bulge and/or pyrimidines flanking the bulge on both sides. We suggest that the bulge creates the structural motif, such as the triangular prismatic pocket formed by the unpaired bulge bases, to accommodate the [Fe2L3] 4+ helicate molecule, and is probably responsible for the affinity for duplexes with a varying number of bulge bases. Our results reveal that DNA bulges represent another example of unusual DNA structures recognized by dinuclear iron(II) ([Fe2L3]4+) supramolecular helicates. © 2013 FEBS.


Palecek E.,Academy of Sciences of the Czech Republic | Tkac J.,Slovak Academy of Sciences | Bartosik M.,Masaryk Memorial Cancer Institute | Bertok T.,Slovak Academy of Sciences | And 2 more authors.
Chemical Reviews | Year: 2015

Significant progress has been done in the electrochemical (EC) analysis of practically all proteins, based on the electroactivity of amino acid (aa) residues in proteins. From a transducer point of view, it can be anticipated that many different ways of how nanomaterials can be integrated into the EC detection platform of detection will be developed. This can be done by direct modification of electroactive surfaces by nanomaterials or by advanced patterning protocol and by using nanomaterials as amplification tags, helping to produce lectin biosensors/biochips working in an ultrasensitive and selective way. Further, it can be anticipated that EC-based biosensors will compete in a future with instrumental techniques or lectin microarrays only if such devices are integrated into a biochip format offering multiplexed glycan measurements. Moreover, it has been shown that some glucosamine-containing poly- and oligosaccharides are electroactive under conditions close to physiological and that most polysaccharides and glycans can be transformed into electrochemically active substances by a simple chemical modification. Usually 4-10 biomarkers have to be detected to obtain good specificity and selectivity of detection. EC detection appears particularly advantageous for the preparation of low-density chips with this number of biomarkers.


Burketova L.,Academy of Sciences of the Czech Republic | Trda L.,Academy of Sciences of the Czech Republic | Ott P.G.,Hungarian Academy of Sciences | Valentova O.,Institute of Chemical Technology Prague
Biotechnology Advances | Year: 2015

An increasing demand for environmentally acceptable alternative for traditional pesticides provides an impetus to conceive new bio-based strategies in crop protection. Employing induced resistance is one such strategy, consisting of boosting the natural plant immunity. Upon infections, plants defend themselves by activating their immune mechanisms. These are initiated after the recognition of an invading pathogen via the microbe-associated molecular patterns (MAMPs) or other microbe-derived molecules. Triggered responses inhibit pathogen spread from the infected site. Systemic signal transport even enables to prepare, i.e. prime, distal uninfected tissues for more rapid and enhanced response upon the consequent pathogen attack. Similar defense mechanisms can be triggered by purified MAMPs, pathogen-derived molecules, signal molecules involved in plant resistance to pathogens, such as salicylic and jasmonic acid, or a wide range of other chemical compounds. Induced resistance can be also conferred by plant-associated microorganisms, including beneficial bacteria or fungi. Treatment with resistance inducers or beneficial microorganisms provides long-lasting resistance for plants to a wide range of pathogens. This study surveys current knowledge on resistance and its mechanisms provided by microbe-, algae- and plant-derived elicitors in different crops. The main scope deals with bacterial substances and fungus-derived molecules chitin and chitosan and algae elicitors, including naturally sulphated polysaccharides such as ulvans, fucans or carageenans. Recent advances in the utilization of this strategy in practical crop protection are also discussed. © 2015 Elsevier Inc.


Janouskovec J.,University of British Columbia | Horak A.,University of British Columbia | Horak A.,Academy of Sciences of the Czech Republic | Barott K.L.,San Diego State University | And 2 more authors.
Current Biology | Year: 2012

The presence of relict non-photosynthetic plastids in obligate intracellular apicomplexan parasites (e.g. Plasmodium) has proved puzzling in many ways, but the recent discovery of their photosynthetic relative, Chromera velia, has begun to shed much-needed light on the origin and evolution of these plastids [1,2]. The intense interest that this single species has generated demonstrates how surprisingly little we know about photosynthetic relatives of apicomplexans as a whole. Here, we investigate global plastid diversity and distribution by comprehensively searching existing prokaryotic sequence surveys for eukaryotic plastids. From more than 1.6 million bacterial sequences, we identified 9,799 plastid-derived sequences, most of which were previously mis-labeled as 'novel bacteria' sequences. 98.8% of these plastid-derived sequences could be assigned to well-defined algal lineages, most often green algae, diatoms, and haptophytes. The exceptions were 121 sequences, all of which were related to apicomplexan parasites, and nearly all of which were derived from coral reef environments. Close relatives of C. velia were rare, but two other clusters were more common and globally distributed, one of which was tightly associated with corals. Overall, all of the major new lineages of algae we discovered were related to apicomplexans, suggesting that apicomplexans represent a large pool of unexplored algal diversity. © 2012 Elsevier Ltd.


Henych T.,Masaryk University | Henych T.,Academy of Sciences of the Czech Republic | Pravec P.,Academy of Sciences of the Czech Republic
Monthly Notices of the Royal Astronomical Society | Year: 2013

Photometric observations of asteroids showthat some of them are in non-principal axis rotation state (free precession), called tumbling. Collisions between asteroids have been proposed as a possible asteroid rotation excitation mechanism. We simulated subcatastrophic collisions between asteroids of various physical and material parameters to find out whether they could be responsible for the excited rotation. For every simulated target body after the collision, we computed its rotational light curve and found that tumbling was photometrically detectable for the rotational axis misalignment angle β greater than about 15°.We found that subcatastrophic collisions are a plausible cause of non-principal axis rotation for small slowly rotating asteroids. The determining parameter is the ratio of the projectile orbital angular momentum to the target rotational angular momentum, and we derived an approximate relation between this ratio and the angle β.We also compared the limiting energy for the onset of tumbling with the shattering energy. Slowly rotating asteroids of diameter 100 m and larger can be rotationally excited by collisions with energies below the shattering limit. © 2013 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.


Masoodi M.,Nestlé | Kuda O.,Academy of Sciences of the Czech Republic | Rossmeisl M.,Academy of Sciences of the Czech Republic | Flachs P.,Academy of Sciences of the Czech Republic | Kopecky J.,Academy of Sciences of the Czech Republic
Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids | Year: 2015

Obesity-associated low-grade inflammation of white adipose tissue (WAT) contributes to development of insulin resistance and other disorders. Accumulation of immune cells, especially macrophages, and macrophage polarization from M2 to M1 state, affect intrinsic WAT signaling, namely anti-inflammatory and proinflammatory cytokines, fatty acids (FA), and lipid mediators derived from both n- 6 and n- 3 long-chain PUFA such as (i) arachidonic acid (AA)-derived eicosanoids and endocannabinoids, and (ii) specialized pro-resolving lipid mediators including resolvins derived from both eicosapentaenoic (EPA) and docosahexaenoic acid (DHA), lipoxins (AA metabolites), protectins and maresins (DHA metabolites). In this respect, potential differences in modulating adipocyte metabolism by various lipid mediators formed by inflammatory M1 macrophages typical of obese state, and non-inflammatory M2 macrophages typical of lean state remain to be established. Studies in mice suggest that (i) transient accumulation of M2 macrophages could be essential for the control of tissue FA levels during activation of lipolysis, (ii) currently unidentified M2 macrophage-borne signaling molecule(s) could inhibit lipolysis and re-esterification of lipolyzed FA back to triacylglycerols (TAG/FA cycle), and (iii) the egress of M2 macrophages from rebuilt WAT and removal of the negative feedback regulation could allow for a full unmasking of metabolic activities of adipocytes. Thus, M2 macrophages could support remodeling of WAT to a tissue containing metabolically flexible adipocytes endowed with a high capacity of both TAG/FA cycling and oxidative phosphorylation. This situation could be exemplified by a combined intervention using mild calorie restriction and dietary supplementation with EPA/DHA, which enhances the formation of "healthy" adipocytes. This article is part of a Special Issue entitled Oxygenated metabolism of PUFA: analysis and biological relevance." © 2014 Elsevier B.V. All rights reserved.


Kysely J.,Academy of Sciences of the Czech Republic | Picek J.,Technical University of Liberec | Beranova R.,Academy of Sciences of the Czech Republic
Global and Planetary Change | Year: 2010

The paper presents a methodology for estimating high quantiles of distributions of daily temperature in a non-stationary context, based on peaks-over-threshold analysis with a time-dependent threshold expressed in terms of regression quantiles. The extreme value models are applied to estimate 20-yr return values of maximum daily temperature over Europe in transient global climate model (GCM) simulations for the 21st century. A comparison of scenarios of changes in the 20-yr return temperatures based on the non-stationary peaks-over-threshold models with conventional stationary models is performed. It is demonstrated that the application of the stationary extreme value models in temperature data from GCM scenarios yields results that may be to a large extent biased, while the non-stationary models lead to spatial patterns that are robust and enable one to detect areas where the projected warming in the tail of the distribution of daily temperatures is largest. The method also allows splitting the projected warming of extremely high quantiles into two parts that reflect change in the location and scale of the distribution of extremes, respectively. Spatial patterns of the two components differ significantly in the examined climate change projections over Europe. © 2010 Elsevier B.V.


Krystof V.,Academy of Sciences of the Czech Republic | Uldrijan S.,Masaryk University
Current Drug Targets | Year: 2010

Poor therapeutic outcomes and serious side effects, together with acquired resistance to multiple drugs, are common problems of current cancer therapies. Therefore, there is an urgent need for new cancer-targeted drugs, which has led (inter alia) to the development of molecules that can specifically inhibit cyclin-dependent kinases (CDKs). In addition to their cell cycle regulatory functions, CDKs, especially CDK7 and CDK9, play important roles in the regulation of RNA polymerase II-mediated transcription. Here, we report on progress in the preclinical development of CDK inhibitors and their anticancer activities. Special attention is paid to the action mechanisms of the pan-specific CDK inhibitors flavopiridol and roscovitine, which have already entered phase II clinical trials as treatments for various tumours. The links between their ability to inhibit transcription and sensitisation of some types of cancer to apoptosis, mechanisms leading to p53 activation, and their synergistic cooperation with common DNA damaging drugs are also discussed. It has been demonstrated that drug-resistant cancer cells can arise during therapeutic application of small molecule protein kinase inhibitors. Clinical resistance to CDK inhibitors has not yet been described, but by comparing CDKs to other kinases, and CDK inhibitors to other clinically used protein kinase inhibitors, we also discuss possible mechanisms that could lead to resistance to CDK inhibitors. © 2010 Bentham Science Publishers Ltd.


Mikeskova H.,Academy of Sciences of the Czech Republic | Mikeskova H.,Institute of Chemical Technology Prague | Novotny C.,Academy of Sciences of the Czech Republic | Svobodova K.,Academy of Sciences of the Czech Republic
Applied Microbiology and Biotechnology | Year: 2012

In recent works, microbial consortia consisting of various bacteria and fungi exhibited a biodegradation performance superior to single microbial strains. A highly efficient biodegradation of synthetic dyes, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, and other organic pollutants can be achieved by mixed microbial cultures that combine degradative enzyme activities inherent to individual consortium members. This review summarizes biodegradation results obtained with defined microbial cocultures and real microbial consortia. The necessity of using a proper strategy for the microbial consortium development and optimization was clearly demonstrated. Molecular genetic and proteomic techniques have revolutionized the study of microbial communities, and techniques such as the denaturing gradient gel electrophoresis, rRNA sequencing, and metaproteomics have been used to identify consortium members and to study microbial population dynamics. These analyses could help to further enhance and optimize the natural activities of mixed microbial cultures. © Springer-Verlag 2012.


Vsianska M.,Masaryk University | Vsianska M.,Academy of Sciences of the Czech Republic | Sob M.,Masaryk University | Sob M.,Academy of Sciences of the Czech Republic
Progress in Materials Science | Year: 2011

We present a detailed theoretical study of segregation and strengthening/embrittling energy of sp-elements from the 3rd, 4th and 5th period (Al, Si, P, S, Ga, Ge, As, Se, In, Sn, Sb and Te) at the Σ5(2 1 0) grain boundary (GB) in fcc ferromagnetic nickel. For comparison, we investigate also the segregation of these impurities at the (2 1 0) free surface (FS). On the basis of ab initio electronic structure calculations, full relaxation of the geometric configuration of the GB and FS without and with impurities is performed and the effect of impurities on the distribution of magnetic moments is analysed. Whereas there is a slight enhancement of magnetization at the clean GB and FS with respect to bulk nickel (3-7% and 24%, respectively), the studied impurities entirely kill or strongly reduce ferromagnetism at the GB and in its immediate neighbourhood so that magnetically dead layers are formed. This effect, which is due to the hybridization of the impurity sp-states and nickel d-states, is even more pronounced at the impurity-decorated (2 1 0) FS. We determine the preferred segregation sites at the Σ5(2 1 0) GB for the sp-impurities studied, their segregation enthalpies and strengthening/ embrittling energies with their decomposition into the chemical and mechanical components. We find interstitially segregated Si as a GB cohesion enhancer, substitutionally segregated Al and interstitially segregated P with none or minimum strengthening effect and interstitially segregated S, Ge, As, Se and substitutionally segregated Ga, In, Sn, Sb and Te as GB embrittlers in nickel. As there is very little experimental information on GB segregation in nickel most of the present results are theoretical predictions which may motivate future experimental work. © 2011 Elsevier Ltd. All rights reserved.


Vita M.,Academy of Sciences of the Czech Republic | Vita M.,Masaryk University
Fuzzy Sets and Systems | Year: 2014

Fuzzification of special types of filters on several different algebras of many-valued logics has been very popular in recent years. The main aim of this paper is to point out some general principles concerning particular results about fuzzification of special types of filters. We introduce the notion of a fuzzy t-filter which generalizes most types of special fuzzy filters (e.g. fuzzy implicative, fuzzy boolean, fuzzy fantastic, etc.) and prove some basic properties of fuzzy t-filters. © 2013 Elsevier B.V. All rights reserved.


Partyka J.,Academy of Sciences of the Czech Republic | Partyka J.,Masaryk University | Foret F.,Academy of Sciences of the Czech Republic
Journal of Chromatography A | Year: 2012

Cationic derivatization of oligosaccharides by quaternary ammonium label was investigated for capillary electrophoretic separation with transient isotachophoretic preconcentration (t-ITP) as detected by capacitively coupled contactless conductivity detection (C4D). Dextran ladder, prepared by partial hydrolysis of dextran, isomaltotriose, maltopentaose and maltoheptaose were derivatized by reductive amination with (2-aminoethyl)trimethylammonium chloride. This label provides permanent positive charge potentially also useful for mass spectrometry ionization. Capillary electrophoresis (CE) separations of the oligosaccharides were tested in zone electrophoretic (CZE) and combined t-ITP/CZE modes. The transient isotachophoretic preconcentration was performed by injecting the sample solution complemented by ammonium acetate into the acetic acid background electrolyte. In this case the ammonium ions served as leading electrolyte followed by the sample zone and the background electrolyte of acetic acid acted as terminating electrolyte. The oligosaccharides were focused into narrow zones by ITP principles and during the course of migration through the separation capillary relaxed into zone electrophoretic separation mode. The separated ones were detected by C4D detector with detection limits in the nanomolar concentration range. © 2012 Elsevier B.V.


Simacek P.,Institute of Chemical Technology Prague | Kubicka D.,Academy of Sciences of the Czech Republic | Sebor G.,Institute of Chemical Technology Prague | Pospisil M.,Institute of Chemical Technology Prague
Fuel | Year: 2010

This paper deals with the hydroprocessing of rapeseed oil as a source of hydrocarbon-based biodiesel. Rapeseed oil was hydroprocessed in a laboratory flow reactor under four combinations of reaction conditions at temperatures 310 and 360 °C and under hydrogen pressure of 7 and 15 MPa. A commercial hydrotreating Ni-Mo/alumina catalyst was used. Reaction products contained mostly n-heptadecane and n-octadecane accompanied by low concentrations of other n-alkanes and i-alkanes. Reaction product obtained at 360 °C and 7 MPa was blended into mineral diesel fuel in several concentration levels ranging from 5 to 30 wt.%. It was found, that most of the standard parameters were similar to or better than those of pure mineral diesel. On the other hand, low-temperature properties were worse, even after addition of high concentrations of flow improvers. © 2009 Elsevier Ltd. All rights reserved.


Bacakova L.,Academy of Sciences of the Czech Republic | Filova E.,Academy of Sciences of the Czech Republic | Parizek M.,Academy of Sciences of the Czech Republic | Ruml T.,Institute of Chemical Technology Prague | Svorcik V.,Institute of Chemical Technology Prague
Biotechnology Advances | Year: 2011

The interaction of cells and tissues with artificial materials designed for applications in biotechnologies and in medicine is governed by the physical and chemical properties of the material surface. There is optimal cell adhesion to moderately hydrophilic and positively charged substrates, due to the adsorption of cell adhesion-mediating molecules (e.g. vitronectin, fibronectin) in an advantageous geometrical conformation, which makes specific sites on these molecules (e.g. specific amino acid sequences) accessible to cell adhesion receptors (e.g. integrins). Highly hydrophilic surfaces prevent the adsorption of proteins, or these molecules are bound very weakly. On highly hydrophobic materials, however, proteins are adsorbed in rigid and denatured forms, hampering cell adhesion. The wettability of the material surface, particularly in synthetic polymers, can be effectively regulated by physical treatments, e.g. by irradiation with ions, plasma or UV light. The irradiation-activated material surface can be functionalized by various biomolecules and nanoparticles, and this further enhances its attractiveness for cells and its effectiveness in regulating cell functions. Another important factor for cell-material interaction is surface roughness and surface topography. Nanostructured substrates (i.e. substrates with irregularities smaller than 100. nm), are generally considered to be beneficial for cell adhesion and growth, while microstructured substrates behave more controversially (e.g. they can hamper cell spreading and proliferation but they enhance cell differentiation, particularly in osteogenic cells). A factor which has been relatively less investigated, but which is essential for cell-material interaction, is material deformability. Highly soft and deformable substrates cannot resist the tractional forces generated by cells during cell adhesion, and cells are not able to attach, spread and survive on such materials. Local variation in the physical and chemical properties of the material surface can be advantageously used for constructing patterned surfaces. Micropatterned surfaces enable regionally selective cell adhesion and directed growth, which can be utilized in tissue engineering, in constructing microarrays and in biosensorics. Nanopatterned surfaces are an effective tool for manipulating the type, number, spacing and distribution of ligands for cell adhesion receptors on the material surface. As a consequence, these surfaces are able to control the size, shape, distribution and maturity of focal adhesion plaques on cells, and thus cell adhesion, proliferation, differentiation and other cell functions. © 2011 Elsevier Inc.


Pavelka S.,Academy of Sciences of the Czech Republic | Pavelka S.,Masaryk University
Physiological Research | Year: 2014

We newly elaborated and adapted several radiometric enzyme assays for the determination of activities of the key enzymes engaged in the biosynthesis (thyroid peroxidase, TPO) and metabolic transformations (conjugating enzymes and iodothyronine deiodinases, IDs) of thyroid hormones (THs) in the thyroid gland and in peripheral tissues, especially in white adipose tissue (WAT). We also elaborated novel, reliable radiometric methods for extremely sensitive determination of enzyme activities of IDs of types 1, 2 and 3 in microsomal fractions of different rat and human tissues, as well as in homogenates of cultured mammalian cells. The use of optimized TLC separation of radioactive products from the unconsumed substrates and film-less autoradiography of radiochromatograms, taking advantage of storage phosphor screens, enabled us to determine IDs enzyme activities as low as 10-18 katals. In studies of the interaction of fluoxetine (Fluox) with the metabolism of THs, we applied adapted radiometric enzyme assays for iodothyronine sulfotransferases (ST) and uridine 5'-diphosphoglucuronyltransferase (UDP-GT). Fluox is the most frequently used representative of a new group of non-tricyclic antidepressant drugs - selective serotonin re-uptake inhibitors. We used the elaborated assays for quantification the effects of Fluox and for the assessment of the degree of potential induction of rat liver ST and/or UDP-GT enzyme activities by Fluox alone or in combination with T3. Furthermore, we studied possible changes in IDs activities in murine adipose tissue under the conditions that promoted either tissue hypertrophy (obesogenic treatment) or involution (caloric restriction), and in response to leptin, using our newly developed radiometric enzyme assays for IDs. Our results suggest that deiodinase D1 has a functional role in WAT, with D1 possibly being involved in the control of adipose tissue metabolism and/or accumulation of the tissue. Significant positive correlation between specific enzyme activity of D1 in WAT and plasma leptin levels was found. The newly developed and adapted radiometric enzyme assays proved to be very useful tools for studies of factors modulating THs metabolism, not only in model animals but also in clinical studies of human obesity. © 2014 Institute of Physiology v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic.


Danihelka J.,Masaryk University | Danihelka J.,Academy of Sciences of the Czech Republic | Chrtek J.,Academy of Sciences of the Czech Republic | Kaplan Z.,Academy of Sciences of the Czech Republic
Preslia | Year: 2012

A checklist of vascular plants of the Czech Republic is provided, based on the Kubat et al's Key to the flora of the Czech Republic from 2002 and volumes 7 and 8 of the Flora of the Czech Republic as taxonomic reference, and incorporating numerous floristic, taxonomic and nomenclatural novelties. Native, alien, both naturalized and casual, as well as frequently cultivated taxa are included. Species, subspecies, nothospecies and nothosubspecies, and some frequently used variety names are listed. For cultivated plants, the taxonomic rank of Group is widely applied. For practical purposes, 188 species aggregates and other informal species groups are defined. References are made to corresponding taxonyms in the Key or the two Flora volumes when name or orthography changes occurred. Most important changes in nomenclature, taxonomy, recently described taxa and additions to the country's flora are annotated. The flora of the Czech Republic includes 3557 species (plus 194 additional subspecies) and 609 (plus 13 additional nothospecies) hybrids. Of these, 2256 species are native, 464 naturalized (228 archaeophytes and 236 neophytes) and 837 casual aliens. Further, 324 cultivated taxa of different ranks are listed. The list includes categorizations of alien species of Pysek et al.'s second edition of the Catalogue of alien plants of the Czech Republic and Red List categorizations of Grulich's third edition of the Red List of vascular plants of the Czech Republic, both published in Preslia in 2012.


Reblova M.,Academy of Sciences of the Czech Republic | Reblova K.,Masaryk University
Mycological Progress | Year: 2013

In a case study of fungi of the class Sordariomycetes, we evaluated the effect of multiple sequence alignment (MSA) on the reliability of the phylogenetic trees, topology and confidence of major phylogenetic clades. We compared two main approaches for constructing MSA based on (1) the knowledge of the secondary (2D) structure of ribosomal RNA (rRNA) genes, and (2) automatic construction of MSA by four alignment programs characterized by different algorithms and evaluation methods, CLUSTAL, MAFFT, MUSCLE, and SAM. In the primary fungal sequences of the two functional rRNA genes, the nuclear small and large ribosomal subunits (18 S and 28 S), we identified four and six, respectively, highly variable regions, which correspond mainly to hairpin loops in the 2D structure. These loops are often positioned in expansion segments, which are missing or are not completely developed in the Archaeal and Eubacterial kingdoms. Proper sorting of these sites was a key for constructing an accurate MSA. We utilized DNA sequences from 28 S as an example for one-gene analysis. Five different MSAs were created and analyzed with maximum parsimony and maximum likelihood methods. The phylogenies inferred from the alignments improved with 2D structure with identified homologous segments, and those constructed using the MAFFT alignment program, with all highly variable regions included, provided the most reliable phylograms with higher bootstrap support for the majority of clades. We illustrate and provide examples demonstrating that re-evaluating ambiguous positions in the consensus sequences using 2D structure and covariance is a promising means in order to improve the quality and reliability of sequence alignments. © 2012 German Mycological Society and Springer.


Vita M.,Academy of Sciences of the Czech Republic | Vita M.,Masaryk University
Information Sciences | Year: 2014

In this paper we introduce a notion of a t-filter on residuated lattices which is a generalization of several special types of filters. We provide some basic properties of t-filters and show how particular results about special types of filters (e.g. Extension property, Triple of equivalent characteristics, and Quotient characteristics) are uniformly covered by this simple general framework. © 2013 Elsevier Inc. All rights reserved.


Mozgova I.,Masaryk University | Mokros P.,Masaryk University | Fajkus J.,Masaryk University | Fajkus J.,Academy of Sciences of the Czech Republic
Plant Cell | Year: 2010

Chromatin Assembly Factor 1 (CAF1) is a three-subunit H3/H4 histone chaperone responsible for replication-dependent nucleosome assembly. It is composed of CAC 1-3 in yeast; p155, p60, and p48 in humans; and FASCIATA1 (FAS1), FAS2, and MULTICOPY SUPPRESSOR OF IRA1 in Arabidopsis thaliana. We report that disruption of CAF1 function by fas mutations in Arabidopsis results in telomere shortening and loss of 45S rDNA, while other repetitive sequences (5S rDNA, centromeric 180-bp repeat, CACTA, and Athila) are unaffected. Substantial telomere shortening occurs immediately after the loss of functional CAF1 and slows down at telomeres shortened to median lengths around 1 to 1.5 kb. The 45S rDNA loss is progressive, leaving 10 to 15% of the original number of repeats in the 5th generation of mutants affecting CAF1, but the level of the 45S rRNA transcripts is not altered in these mutants. Increasing severity of the fas phenotype is accompanied by accumulation of anaphase bridges, reduced viability, and plant sterility. Our results show that appropriate replicationdependent chromatin assembly is specifically required for stable maintenance of telomeres and 45S rDNA. © 2010 American Society of Plant Biologists.


Vlasak J.,Academy of Sciences of the Czech Republic | Kout J.,University of West Bohemia
Mycological Progress | Year: 2011

Sequencing of the ribosomal ITS region was used to resolve the relationship among USA collections of the morphological species Fomitiporia robusta. F. robusta corresponding to European collections was not found and its occurrence in the USA is regarded as questionable. Birch-growing fungus from mid-western and eastern United States known as Phellinus bakeri is a closely related polypore, but because of the absence of typical F. robusta here, it should be considered a separate species. Oak-growing pileate fungus from the south-eastern USA, also known as Fomes calkinsii, is a distinct species, rather distant from the European F. robusta. New combinations Fomitiporia bakeri and F. calkinsii are proposed. Notes on other similar species are provided. © 2010 German Mycological Society and Springer.


Renciuk D.,University of Zürich | Renciuk D.,Academy of Sciences of the Czech Republic | Blacque O.,University of Zürich | Vorlickova M.,University of Zürich | And 2 more authors.
Nucleic Acids Research | Year: 2013

5-Hydroxymethylcytosine (5-hmC) was recently identified as a relatively frequent base in eukaryotic genomes. Its physiological function is still unclear, but it is supposed to serve as an intermediate in DNA de novo demethylation. Using X-ray diffraction, we solved five structures of four variants of the d(CGCG AATTCGCG) dodecamer, containing either 5-hmC or 5-methylcytosine (5-mC) at position 3 or at position 9. The observed resolutions were between 1.42 and 1.99A ̊ . Cytosine modification in all cases influences neither the whole B-DNA double helix structure nor the modified base pair geometry. The additional hydroxyl group of 5-hmC with rotational freedom along the C5-C5A bond is preferentially oriented in the 3′ direction. A comparison of thermodynamic properties of the dodecamers shows no effect of 5-mC modification and a sequence-dependent only slight destabilizing effect of 5-hmC modification. Also taking into account the results of a previous functional study [Münzel et al. (2011) (Improved synthesis and mutagenicity of oligonucleotides containing 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine. Chem. Eur. J., 17, 13782-13788)], we conclude that the 5 position of cytosine is an ideal place to encode epigenetic information. Like this, neither the helical structure nor the thermodynamics are changed, and polymerases cannot distinguish 5-hmC and 5-mC from unmodified cytosine, all these effects are making the former ones non-mutagenic. © The Author(s) 2013. Published by Oxford University Press.


Simacek P.,Institute of Chemical Technology Prague | Kubicka D.,Academy of Sciences of the Czech Republic
Fuel | Year: 2010

Hydrocracking of pure petroleum vacuum distillate and the same fraction containing 5 wt.% of rapeseed oil was carried out at 400 and 420 °C and under a hydrogen pressure of 18 MPa over commercial Ni-Mo catalyst. Reaction products were separated by distillation into kerosene, gas oil and the residue. Fuel properties of fractions suitable for diesel production were evaluated (gas oils and remixed blends of kerosene and gas oil). Gas oils obtained from co-processing showed very good fuel properties as the remixed distillates did. Gas oil obtained from co-processing at 420 °C showed also reasonable key low-temperature properties (cloud point: -23 °C, CFPP: -24 °C) similar to those of gas oil obtained from pure petroleum raw material processing. © 2009 Elsevier Ltd. All rights reserved.


Vsianska M.,Masaryk University | Sob M.,Masaryk University | Sob M.,Academy of Sciences of the Czech Republic
Physical Review B - Condensed Matter and Materials Physics | Year: 2011

With the help of ab initio electronic structure calculations, we study segregation of the sp elements from the 13th-16th group and the third, fourth, and fifth period of the Periodic Table (i.e., Al, Si, P, S, Ga, Ge, As, Se, In, Sn, Sb, and Te) at the Σ5(210) grain boundary (GB) and (210) free surface (FS) in fcc ferromagnetic nickel, and analyze the geometric configuration and the distribution of magnetic moments at the GB and FS without and with impurities. Whereas there is a slight enhancement of magnetization at the clean GB and FS with respect to bulk nickel (3-7% and 24%, respectively), most of these impurities nearly kill or substantially reduce the magnetic moments at the FS and, when segregating interstitially at the GB (i.e., Si, P, S, Ge, As, and Se), they produce magnetically dead layers at the boundary. We demonstrate that the existence of magnetically dead layers is a common phenomenon at the sp-impurity-decorated GB and FS in nickel. It is caused by a strong hybridization of sp states of the impurities with the d states of nickel and a redistribution of electron states in both majority and minority bands. © 2011 American Physical Society.


Kotik M.,Academy of Sciences of the Czech Republic | Archelas A.,Aix - Marseille University | Wohlgemuth R.,Sigma-Aldrich
Current Organic Chemistry | Year: 2012

The number of synthetic applications of epoxide hydrolases in organic chemistry has reached a remarkable level. This has been due to a tremendous amount of work dedicated to the discovery of novel epoxide hydrolases from various biological sources, understanding the structure and function of these widespread enzymes and last but not least, the stabilization of these biocatalysts by various means for production purposes. © 2012 Bentham Science Publishers.


Allender E.,Rutgers University | Koucky M.,Academy of Sciences of the Czech Republic
Journal of the ACM | Year: 2010

We observe that many important computational problems in NC1 share a simple self-reducibility property. We then show that, for any problem A having this self-reducibility property, A has polynomial-size TC0 circuits if and only if it has TC0 circuits of size n 1+ε for every ε > 0 (counting the number of wires in a circuit as the size of the circuit). As an example of what this observation yields, consider the Boolean Formula Evaluation problem (BFE), which is complete for NC1 and has the self-reducibility property. It follows from a lower bound of Impagliazzo, Paturi, and Saks, that BFE requires depth d TC 0 circuits of size n1+εd. If one were able to improve this lower bound to show that there is some constant ε > 0 (independent of the depth d) such that every TC0 circuit family recognizing BFE has size at least n1+ε, then it would follow that TC 0≠NC1. We show that proving lower bounds of the form n1+ε is not ruled out by the Natural Proof framework of Razborov and Rudich and hence there is currently no known barrier for separating classes such as ACC0, TC0 and NC1 via existing natural approaches to proving circuit lower bounds. We also show that problems with small uniform constant-depth circuits have algorithms that simultaneously have small space and time bounds. We then make use of known time-space tradeoff lower bounds to show that SAT requires uniform depth d TC0 and AC 0[6] circuits of size n1+c for some constant c depending on d. © 2010 ACM.


Majer Z.,Brno University of Technology | Hutar P.,Academy of Sciences of the Czech Republic
Key Engineering Materials | Year: 2012

In this paper polymer particulate composite was studied. The composite was modeled as a three-phase continuum - soft matrix, interphase and rigid particles. On the basis of fracture mechanics methodology the interaction of micro-crack propagation in the soft matrix filled by rigid particles (covered by the interphase) was analyzed. The properties of soft matrix (elasto-plastic material) were determined from the experiment and they were used for estimations of the crack behavior. © (2012) Trans Tech Publications.


Balbuena J.A.,University of Valencia | Miguez-Lozano R.,University of Valencia | Blasco-Costa I.,Academy of Sciences of the Czech Republic
PLoS ONE | Year: 2013

We present Procrustean Approach to Cophylogeny (PACo), a novel statistical tool to test for congruence between phylogenetic trees, or between phylogenetic distance matrices of associated taxa. Unlike previous tests, PACo evaluates the dependence of one phylogeny upon the other. This makes it especially appropriate to test the classical coevolutionary model that assumes that parasites that spend part of their life in or on their hosts track the phylogeny of their hosts. The new method does not require fully resolved phylogenies and allows for multiple host-parasite associations. PACo produces a Procrustes superimposition plot enabling a graphical assessment of the fit of the parasite phylogeny onto the host phylogeny and a goodness-of-fit statistic, whose significance is established by randomization of the host-parasite association data. The contribution of each individual host-parasite association to the global fit is measured by means of jackknife estimation of their respective squared residuals and confidence intervals associated to each host-parasite link. We carried out different simulations to evaluate the performance of PACo in terms of Type I and Type II errors with respect to two similar published tests. In most instances, PACo performed at least as well as the other tests and showed higher overall statistical power. In addition, the jackknife estimation of squared residuals enabled more elaborate validations about the nature of individual links than the ParaFitLink1 test of the program ParaFit. In order to demonstrate how it can be used in real biological situations, we applied PACo to two published studies using a script written in the public-domain statistical software R. © 2013 Balbuena et al.


Penn A.C.,University of Cambridge | Penn A.C.,Institut Universitaire de France | Penn A.C.,French National Center for Scientific Research | Balik A.,University of Cambridge | And 2 more authors.
Nucleic Acids Research | Year: 2013

Adenosine-to-Inosine (A-to-I) RNA editing is a post-transcriptional mechanism, evolved to diversify the transcriptome in metazoa. In addition to wide-spread editing in non-coding regions protein recoding by RNA editing allows for fine tuning of protein function. Functional consequences are only known for some editing sites and the combinatorial effect between multiple sites (functional epistasis) is currently unclear. Similarly, the interplay between RNA editing and splicing, which impacts on post-transcriptional gene regulation, has not been resolved. Here, we describe a versatile antisense approach, which will aid resolving these open questions. We have developed and characterized morpholino oligos targeting the most efficiently edited site-the AMPA receptor GluA2 Q/R site. We show that inhibition of editing closely correlates with intronic editing efficiency, which is linked to splicing efficiency. In addition to providing a versatile tool our data underscore the unique efficiency of a physiologically pivotal editing site. © 2012 The Author(s).


Arino J.,Autonomous University of Barcelona | Ramos J.,University of Cordoba, Spain | Sychrova H.,Academy of Sciences of the Czech Republic
Microbiology and Molecular Biology Reviews | Year: 2010

The maintenance of appropriate intracellular concentrations of alkali metal cations, principally K+ and Na+, is of utmost importance for living cells, since they determine cell volume, intracellular pH, and potential across the plasma membrane, among other important cellular parameters. Yeasts have developed a number of strategies to adapt to large variations in the concentrations of these cations in the environment, basically by controlling transport processes. Plasma membrane high-affinity K+ transporters allow intracellular accumulation of this cation even when it is scarce in the environment. Exposure to high concentrations of Na+ can be tolerated due to the existence of an Na+, K+-ATPase and an Na +, K+/H+-antiporter, which contribute to the potassium balance as well. Cations can also be sequestered through various antiporters into intracellular organelles, such as the vacuole. Although some uncertainties still persist, the nature of the major structural components responsible for alkali metal cation fluxes across yeast membranes has been defined within the last 20 years. In contrast, the regulatory components and their interactions are, in many cases, still unclear. Conserved signaling pathways (e.g., calcineurin and HOG) are known to participate in the regulation of influx and efflux processes at the plasma membrane level, even though the molecular details are obscure. Similarly, very little is known about the regulation of organellar transport and homeostasis of alkali metal cations. The aim of this review is to provide a comprehensive and up-to-date vision of the mechanisms responsible for alkali metal cation transport and their regulation in the model yeast Saccharomyces cerevisiae and to establish, when possible, comparisons with other yeasts and higher plants. Copyright © 2010, American Society for Microbiology. All Rights Reserved.


Ramos J.,University of Cordoba, Spain | Arino J.,Autonomous University of Barcelona | Sychrova H.,Academy of Sciences of the Czech Republic
FEMS Microbiology Letters | Year: 2011

To maintain optimal intracellular concentrations of alkali-metal-cations, yeast cells use a series of influx and efflux systems. Nonconventional yeast species have at least three different types of efficient transporters that ensure potassium uptake and accumulation in cells. Most of them have Trk uniporters and Hak K +-H + symporters and a few yeast species also have the rare K + (Na +)-uptake ATPase Acu. To eliminate surplus potassium or toxic sodium cations, various yeast species use highly conserved Nha Na + (K +)/H + antiporters and Na + (K +)-efflux Ena ATPases. The potassium-specific yeast Tok1 channel is also highly conserved among various yeast species and its activity is important for the regulation of plasma membrane potential. © 2011 Federation of European Microbiological Societies.


Feireisl E.,Academy of Sciences of the Czech Republic | Novotny A.,University of Toulon
Archive for Rational Mechanics and Analysis | Year: 2012

The Navier-Stokes-Fourier system describing the motion of a compressible, viscous and heat conducting fluid is known to possess global-in-time weak solutions for any initial data of finite energy. We show that a weak solution coincides with the strong solution, emanating from the same initial data, as long as the latter exists. In particular, strong solutions are unique within the class of weak solutions. © 2012 Springer-Verlag.


Seitl S.,Academy of Sciences of the Czech Republic | Vesely V.,Brno University of Technology | Routil L.,Brno University of Technology
Computers and Structures | Year: 2011

The stress intensity factor and the T-stress for the near-crack-tip field for wedge splitting test (WST) specimens with several variants of boundary conditions are computed using finite element software. The WST is a convenient alternative to classical fracture tests (bending, tensile) for the quasi-brittle fracture of building materials. The WST specimen is investigated within the framework of two-parameter fracture mechanics; near-crack-tip stress field parameters are determined and compared with those of the compact tension specimen due to its shape similarity to the WST. The sensitivity of the values of these parameters to the boundary conditions is also shown. © 2011 Civil-Comp Ltd and Elsevier Ltd. All rights reserved.


Verkhratsky A.,University of Manchester | Verkhratsky A.,Academy of Sciences of the Czech Republic
Neurochemistry International | Year: 2010

Neuronal-glial networks are the substrate for the brain function. Evolution of the nervous system resulted in the appearance of highly specialized neuronal web optimized for rapid information transfer. This neuronal web is embedded into glial syncytium, thereby creating sophisticated neuronal-glial circuitry were both types of neural cells are working in concert, ensuring amplification of brain computational power. In addition neuroglial cells are fundamental for control of brain homeostasis and they represent the intrinsic brain defence system, being thus intimately involved in pathogenesis of neurological diseases. © 2010 Elsevier Ltd.


Feireisl E.,Academy of Sciences of the Czech Republic | Jin B.J.,Mokpo National University | Novotny A.,University of Toulon
Journal of Mathematical Fluid Mechanics | Year: 2012

We introduce the notion of relative entropy for the weak solutions to the compressible Navier-Stokes system. In particular, we show that any finite energy weak solution satisfies a relative entropy inequality with respect to any couple of smooth functions satisfying relevant boundary conditions. As a corollary, we establish the weak-strong uniqueness property in the class of finite energy weak solutions, extending thus the classical result of Prodi and Serrin to the class of compressible fluid flows. © 2012 Springer Basel AG.


Kainen P.C.,Georgetown University | Kurkova V.,Academy of Sciences of the Czech Republic | Sanguineti M.,University of Genoa
IEEE Transactions on Information Theory | Year: 2012

The role of input dimension d is studied in approximating, in various norms, target sets of -variable functions using linear combinations of adjustable computational units. Results from the literature, which emphasize the number n of terms in the linear combination, are reformulated, and in some cases improved, with particular attention to dependence on . For worst-case error, upper bounds are given in the factorized form ε (d)κ(n), where κ is nonincreasing (typically κ (n) ̃ n -1/2). Target sets of functions are described for which the function ε is a polynomial. Some important cases are highlighted where ε decreases to zero as d → ∞. For target functions, extent (e.g., the size of domains in ℝ d where they are defined), scale (e.g., maximum norms of target functions), and smoothness (e.g., the order of square-integrable partial derivatives) may depend on , and the influence of such dimension-dependent parameters on model complexity is considered. Results are applied to approximation and solution of optimization problems by neural networks with perceptron and Gaussian radial computational units. © 2011 IEEE.


Feireisl E.,Academy of Sciences of the Czech Republic | Feireisl E.,Erwin Schroedinger International Institute for Mathematical Physics | Novotny A.,University of Toulon
Communications in Mathematical Physics | Year: 2013

We consider the full Navier-Stokes-Fourier system in the singular limit for the small Mach and large Reynolds and Péclet numbers, with ill prepared initial data on R 3. The Euler-Boussinesq approximation is identified as the limit system. © 2013 Springer-Verlag Berlin Heidelberg.


Malinsky J.,Academy of Sciences of the Czech Republic | Opekarova M.,Academy of Sciences of the Czech Republic | Tanner W.,University of Regensburg
Yeast | Year: 2010

The plasma membrane of Saccharomyces cerevisiae contains large microdomains enriched in ergosterol, which house at least nine integral proteins, including proton symporters. The domains adopt a characteristic structure of furrow-like invaginations typically seen in freeze-fracture pictures of fungal cells. Being stable for the time comparable with the cell cycle duration, they might be considered as fixed islands (rafts) in an otherwise fluid yeast plasma membrane. Rapidly moving endocytic marker proteins avoid the microdomains; the domain-accumulated proton symporters consequently show a reduced rate of substrate-induced endocytosis and turnover. Copyright © 2010 John Wiley & Sons, Ltd.


Zavyalova U.,Fritz Haber Institute of the Max Planck Society | Holena M.,University of Rostock | Holena M.,Academy of Sciences of the Czech Republic | Schlogl R.,Fritz Haber Institute of the Max Planck Society | Baerns M.,Fritz Haber Institute of the Max Planck Society
ChemCatChem | Year: 2011

A database consisting of 1870 data sets on catalyst compositions and their performances in the oxidative coupling of methane was compiled. For this goal, about 1000 full-text references from the last 30years have been analyzed and about 420 of them, which contained all the necessary information, were selected for the data extraction. The accumulated data were subject to statistical analysis: analysis of variance, correlation analysis, and decision tree. On the basis of the results, 18 catalytic key elements were selected from originally 68 elements. All oxides of the selected elements, which positively affect the selectivity to C 2 products, show strong basicity. Analysis of binary and ternary interactions between the selected key elements shows that high-performance catalysts are mainly based on Mg and La oxides. Alkali (Cs, Na) and alkaline-earth (Sr, Ba) metals used as dopants increase the selectivity of the host oxides, whereas dopants such as Mn, W, and the Cl anion have positive effects on the catalyst activity. The maximal C 2 selectivities for the proposed catalyst compositions range from 72 to 82%, and the respective C 2 yields range from 16 to 26%. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Patent
ETH Zurich and Academy of Sciences of the Czech Republic | Date: 2016-02-10

A hypervalent iodine of formula (I) or formula (II)


Stastna M.,Johns Hopkins University | Stastna M.,Academy of Sciences of the Czech Republic | Van Eyk J.E.,Johns Hopkins University
Proteomics | Year: 2012

The proteins secreted by various cells (the secretomes) are a potential rich source of biomarkers as they reflect various states of the cells at real time and at given conditions. To have accessible, sufficient and reliable protein markers is desirable as they mark various stages of disease development and their presence/absence can be used for diagnosis, prognosis, risk stratification and therapeutic monitoring. As direct analysis of blood/plasma, a common and noninvasive patient screening method, can be difficult for candidate protein biomarker identification, the alternative/complementary approaches are required, one of them is the analysis of secretomes in cell conditioned media in vitro. As the proteins secreted by cells as a response to various stimuli are most likely secreted into blood/plasma, the identification and pre-selection of candidate protein biomarkers from cell secretomes with subsequent validation of their presence at higher levels in serum/plasma is a promising approach. In this review, we discuss the proteins secreted by three progenitor cell types (smooth muscle, endothelial and cardiac progenitor cells) and two adult cell types (neonatal rat ventrical myocytes and smooth muscle cells) which can be relevant to cardiovascular research and which have been recently published in the literature. We found, at least for secretome studies included in this review, that secretomes of progenitor and adult cells overlap by 48% but the secretomes are very distinct among progenitor cell themselves as well as between adult cells. In addition, we compared secreted proteins to protein identifications listed in the Human Plasma PeptideAtlas and in two reports with cardiovascular-related proteins and we performed the extensive literature search to find if any of these secreted proteins were identified in a biomarker study. As expected, many proteins have been identified as biomarkers in cancer but 18 proteins (out of 62) have been tested as biomarkers in cardiovascular diseases as well. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Stastna M.,Johns Hopkins University | Stastna M.,Academy of Sciences of the Czech Republic | Van Eyk J.E.,Johns Hopkins University
Proteomics | Year: 2012

Protein isoforms/splice variants can play important roles in various biological processes and can potentially be used as biomarkers or therapeutic targets/mediators. Thus, there is a need for efficient and, importantly, accurate methods to distinguish and quantify specific protein isoforms. Since protein isoforms can share a high percentage of amino acid sequence homology and dramatically differ in their cellular concentration, the task for accuracy and efficiency in methodology and instrumentation is challenging. The analysis of intact proteins has been perceived to provide a more accurate and complete result for isoform identification/quantification in comparison to analysis of the corresponding peptides that arise from protein enzymatic digestion. Recently, novel approaches have been explored and developed that can possess the accuracy and reliability important for protein isoform differentiation and isoform-specific peptide targeting. In this review, we discuss the recent development in methodology and instrumentation for enhanced detection of protein isoforms as well as the examples of their biological importance. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Ctyroky J.,Academy of Sciences of the Czech Republic | Kwiecien P.,Czech Technical University | Richter I.,Czech Technical University
Journal of Lightwave Technology | Year: 2010

Recently we described the implementation of complex coordinate transformation as boundary conditions into a bidirectional eigenmode expansion propagation algorithm based on Fourier series expansion for modeling optical field distribution in waveguide devices. In this communication we report on the implementation of an additional coordinate transformation known as adaptive spatial resolution into this algorithm. It helps significantly reduce the number of expansion terms needed to reach required accuracy especially for photonics structures containing layers of very different thicknesses and/or optical properties, e.g., metal layers. © 2010 IEEE.


Cermak T.,University of Minnesota | Baltes N.J.,University of Minnesota | Cegan R.,Academy of Sciences of the Czech Republic | Zhang Y.,University of Electronic Science and Technology of China | Voytas D.F.,University of Minnesota
Genome Biology | Year: 2015

Background: The use of homologous recombination to precisely modify plant genomes has been challenging, due to the lack of efficient methods for delivering DNA repair templates to plant cells. Even with the advent of sequence-specific nucleases, which stimulate homologous recombination at predefined genomic sites by creating targeted DNA double-strand breaks, there are only a handful of studies that report precise editing of endogenous genes in crop plants. More efficient methods are needed to modify plant genomes through homologous recombination, ideally without randomly integrating foreign DNA. Results: Here, we use geminivirus replicons to create heritable modifications to the tomato genome at frequencies tenfold higher than traditional methods of DNA delivery (i.e., Agrobacterium). A strong promoter was inserted upstream of a gene controlling anthocyanin biosynthesis, resulting in overexpression and ectopic accumulation of pigments in tomato tissues. More than two-thirds of the insertions were precise, and had no unanticipated sequence modifications. Both TALENs and CRISPR/Cas9 achieved gene targeting at similar efficiencies. Further, the targeted modification was transmitted to progeny in a Mendelian fashion. Even though donor molecules were replicated in the vectors, no evidence was found of persistent extra-chromosomal replicons or off-target integration of T-DNA or replicon sequences. Conclusions: High-frequency, precise modification of the tomato genome was achieved using geminivirus replicons, suggesting that these vectors can overcome the efficiency barrier that has made gene targeting in plants challenging. This work provides a foundation for efficient genome editing of crop genomes without the random integration of foreign DNA. © 2015 Čermák et al.


Fischer F.D.,University of Leoben | Svoboda J.,Academy of Sciences of the Czech Republic | Appel F.,Helmholtz Center Geesthacht | Kozeschnik E.,Vienna University of Technology
Acta Materialia | Year: 2011

The equilibrium site fraction of vacancies increases with temperature and, thus, annealing and rapid quenching may lead to states with a significant vacancy supersaturation. Excess vacancies can then gradually annihilate at available sinks represented by jogs at dislocations, by grain boundaries or free surfaces. Significant supersaturation by vacancies may also lead to the nucleation and growth of Frank loops acting as additional sinks. Three models corresponding to three different annihilation mechanisms are developed in this paper. They refer to annihilation of excess vacancies at jogs at dislocation with a constant density, at homogeneously distributed Frank loops with a constant density and at grain boundaries. The simulations based on the models are performed for individual annihilation mechanisms under isothermal and non-isothermal conditions as well as for simultaneous annihilation of vacancies at Frank loops and dislocation jogs and grain boundaries using different cooling conditions. © 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.


Melchin M.J.,St. Francis Xavier University | Mitchell C.E.,State University of New York at Buffalo | Holmden C.,University of Saskatchewan | Storch P.,Academy of Sciences of the Czech Republic
Bulletin of the Geological Society of America | Year: 2013

The Late Ordovician (Katian-Hirnantian) through earliest Silurian (Rhuddanian) interval was a time of varying climate and sea level, marked by a peak glacial episode in the early-mid-Hirnantian. Synthesis of recently published data permits global correlation of at least two cycles of glacial advance and retreat with a distinct interglacial period that is recognizable in sequence-stratigraphic and chemostratigraphic records in many parts of the world. A period of warming and sea-level rise during the late Katian is marked by the widespread occurrences of oceanic anoxia in paleotropical and subtropical localities, mostly confined to regions of inferred upwelling and semirestricted marine basins. Nitrogen isotope data show that the regions of oceanic anoxia were marked by intense water-column denitrification in which cyanobacteria were the principal source of fixed N. In the overlying peak glacial interval of the Hirnantian, sedimentary successions from localities representing a wide range of water depths and paleolatitudes indicate that anoxia was restricted during the early-mid-Hirnantian. The shift to more positive N isotope values also suggests less intense water-column denitrification. In the overlying late Hirnantian and early Rhuddanian, the distribution of black shales reaches its greatest extent in the studied interval. Localities showing evidence of anoxia are globally spread over all paleolatitudes and water depths for which data are available, indicating a Rhuddanian ocean anoxic event comparable to examples from the Mesozoic. It is accompanied by a return to intensely denitrifying conditions within the water column, as indicated by the shift to negative N isotope values. The two phases of Hirnantian mass extinction coincide with rapid, climate-driven changes in oceanic anoxia. The first extinction occurred at the onset of glaciation and with the loss of anoxic conditions at the end of the Katian. The second extinction occurred at the demise of glaciation and coincided with the return of anoxic conditions during the late Hirnantian- early Rhuddanian. Integration of our N isotope data with graptolite biodiversity records suggests that the extinctions were profoundly infl uenced by changes occurring at the base of the marine food web, i.e., redoxdriven changes in nutrient cycling and primary producer communities. © 2013 Geological Society of America.


Dibble K.L.,University of Rhode Island | Meyerson L.A.,University of Rhode Island | Meyerson L.A.,Academy of Sciences of the Czech Republic
PLoS ONE | Year: 2012

Roads, bridges, and dikes constructed across salt marshes can restrict tidal flow, degrade habitat quality for nekton, and facilitate invasion by non-native plants including Phragmites australis. Introduced P. australis contributes to marsh accretion and eliminates marsh surface pools thereby adversely affecting fish by reducing access to intertidal habitats essential for feeding, reproduction, and refuge. Our study assessed the condition of resident fish populations (Fundulus heteroclitus) at four tidally restricted and four tidally restored marshes in New England invaded by P. australis relative to adjacent reference salt marshes. We used physiological and morphological indicators of fish condition, including proximate body composition (% lipid, % lean dry, % water), recent daily growth rate, age class distributions, parasite prevalence, female gravidity status, length-weight regressions, and a common morphological indicator (Fulton's K) to assess impacts to fish health. We detected a significant increase in the quantity of parasites infecting fish in tidally restricted marshes but not in those where tidal flow was restored to reduce P. australis cover. Using fish length as a covariate, we found that unparasitized, non-gravid F. heteroclitus in tidally restricted marshes had significantly reduced lipid reserves and increased lean dry (structural) mass relative to fish residing in reference marshes. Fish in tidally restored marshes were equivalent across all metrics relative to those in reference marshes indicating that habitat quality was restored via increased tidal flushing. Reference marshes adjacent to tidally restored sites contained the highest abundance of young fish (ages 0-1) while tidally restricted marshes contained the lowest. Results indicate that F. heteroclitus residing in physically and hydrologically altered marshes are at a disadvantage relative to fish in reference marshes but the effects can be reversed through ecological restoration. © 2012 Dibble, Meyerson.


Moravec F.,Academy of Sciences of the Czech Republic | Manoharan J.,Annamalai University
Parasitology Research | Year: 2014

Based on light and scanning electron microscopical studies, two new gonad-infecting species of Philometra Costa, 1845 (Nematoda: Philometridae) are described from marine fishes of the genus Lutjanus Bloch (Lutjanidae, Perciformes) in the Bay of Bengal, off the eastern coast of India: Philometra argentimaculati sp. n. and Philometra fulvi sp. n. from the mangrove red snapper Lutjanus argentimaculatus (Forsskål) and blacktail snapper Lutjanus fulvus (Foerster), respectively. P. argentimaculati is mainly characterised by the body length of male 2.56-3.07 mm, needle-like spicules 183-228 μm long, length of the gubernaculum at 90-120 μm, distal end of the gubernaculum with lamellar structures without a dorsal protuberance and by the dorsally non-interrupted male caudal mound. P. fulvi differs from all Philometra spp. with described males in the rectangular shape of the distal tip of the gubernaculum and is noted for the length of needle-like spicules 123-138 μm, that of the gubernaculum 69-93 μm and for the presence of a dorsal protuberance and lamella-like structures on the gubernaculum distal end. These are the first nominal species of philometrids reported from fishes of the family Lutjanidae in the region of the Indian Ocean. A necessity of further detailed studies on philometrids parasitising marine fishes worlwide is stressed. © 2014 Springer-Verlag Berlin Heidelberg.


This is the first report on the structural identity of a neuropeptide of the insect order Grylloblattodea. A peptide was isolated and sequenced from the retrocerebral corpora cardiaca-corpora allata complex of the ice crawler, Galloisiana yuasai. The sequence of the peptide was deduced from the multiple MSN electrospray mass data as that of an octapeptide: pGlu-Val-Asn-Phe-Ser-Pro-Thr-Trp amide. The retention time on reversed-phase HPLC and the CID MS2 mass spectra of a synthetic peptide with the same primary structure were exactly the same as of the natural peptide. The sequence represents a novel peptide of the adipokinetic hormone family which contains presently 50 members. The primary structure differs in only one position to a few previously discovered AKHs. A scenario is outlined that makes it likely that the most recently discovered insect order, the Mantophasmatodea, and the Grylloblattodea are closely related. © 2009 Elsevier Inc.


Alves R.J.V.,Federal University of Rio de Janeiro | Kolbek J.,Academy of Sciences of the Czech Republic
Plant Ecology | Year: 2010

A number of floristic and vegetation studies apply the terms campo rupestre, campo de altitude (or Brazilian páramo), and Tepui to neotropical azonal outcrop and montane vegetation. All of these are known to harbor considerable numbers of endemic plant species and to share several genera. In order to determine whether currently known combinations of vascular plant genera could help circumscribe and distinguish these vegetation types, we selected 25 floras which did not exclude herbs and compiled them into a single database. We then compared the Sørensen similarities of the genus-assemblages using the numbers of native species in the resulting 1945 genera by multivariate analysis. We found that the circumscription of campo rupestre and other Neotropical outcrop vegetation types may not rely exclusively on a combination of genera. © 2009 Springer Science+Business Media B.V.


Gioria M.,Academy of Sciences of the Czech Republic | Gioria M.,University College Dublin | Osborne B.A.,University College Dublin
Frontiers in Plant Science | Year: 2014

Invasions by alien plants provide a unique opportunity to examine competitive interactions among plants. While resource competition has long been regarded as a major mechanism responsible for successful invasions, given a well-known capacity for many invaders to become dominant and reduce plant diversity in the invaded communities, few studies have measured resource competition directly or have assessed its importance relative to that of other mechanisms, at different stages of an invasion process. Here, we review evidence comparing the competitive ability of invasive species vs. that of cooccurring native plants, along a range of environmental gradients, showing that many invasive species have a superior competitive ability over native species, although invasive congeners are not necessarily competitively superior over native congeners, nor are alien dominants are better competitors than native dominants. We discuss how the outcomes of competition depend on a number of factors, such as the heterogeneous distribution of resources, the stage of the invasion process, as well as phenotypic plasticity and evolutionary adaptation, which may result in increased or decreased competitive ability in both invasive and native species. Competitive advantages of invasive species over natives are often transient and only important at the early stages of an invasion process. It remains unclear how important resource competition is relative to other mechanisms (competition avoidance via phenological differences, niche differentiation in space associated with phylogenetic distance, recruitment and dispersal limitation, indirect competition, and allelopathy). Finally, we identify the conceptual and methodological issues characterizing competition studies in plant invasions, and we discuss future research needs, including examination of resource competition dynamics and the impact of global environmental change on competitive interactions between invasive and native species. © 2014 Gioria and Osborne.


Gioria M.,University College Dublin | Pysek P.,Academy of Sciences of the Czech Republic | Moravcova L.,Academy of Sciences of the Czech Republic
Preslia | Year: 2012

Invasions by alien plant species significantly affect biodiversity and ecosystem functioning. Investigations of the soil seed banks of invasive plant species and changes in the composition and structure of resident seed banks following plant invasions can provide valuable insight into the long-term implications of plant invasions. Soil seed banks play a major role as reservoirs of species and genetic diversity and allow for the persistence of a species at a locality, buffering environmental changes that may occur over time. Despite the emerging body of literature on ecological impacts of invasive plants on the diversity of resident communities, the long-term implications of impoverished soil seed banks for vegetation dynamics and ecosystem functioning have only recently begun receiving attention. Evidence has so far indicated that there is a correlation between the invasiveness of a species and the characteristics of its seed bank, and that changes in the seed banks of resident communities associated with plant invasions affect their biotic resistance to primary and secondary invasions. To promote the study of soil seed banks in the context of invasive species, we (i) summarize the functional roles of soil seed banks; (ii) describe how the capacity to form a seed bank may contribute to a species' invasiveness using data from the flora of the Czech Republic, showing an increasing representation of species capable of forming long-term persistent seed bank from casual to naturalized to invasion stage; (iii) assess the impact of invasive plants on seed banks of resident communities, including the potential creation of conditions that favour secondary invasions by other alien species or native weeds, and long-term implications of such impact; and (iv) describe the potential effects of climate change on the soil seed bank in the context of plant invasions. We conclude with highlighting promising avenues for future research on invaded soil seed banks, and emphasize the importance of this knowledge in the development of control programs and restoration strategies.


Alba C.,Colorado State University | Alba C.,Academy of Sciences of the Czech Republic | Deane Bowers M.,University of Colorado at Boulder | Hufbauer R.,Colorado State University
Ecology | Year: 2012

Optimal defense theory posits that plants with limited resources deploy chemical defenses based on the fitness value of different tissues and their probability of attack. However, what constitutes optimal defense depends on the identity of the herbivores involved in the interaction. Generalists, which are not tightly coevolved with their many host plants, are typically deterred by chemical defenses, while coevolved specialists are often attracted to these same chemicals. This imposes an "evolutionary dilemma" in which generalists and specialists exert opposing selection on plant investment in defense, thereby stabilizing defenses at intermediate levels. We used the natural shift in herbivore community composition that typifies many plant invasions to test a novel, combined prediction of optimal defense theory and the evolutionary dilemma model: that the within-plant distribution of defenses reflects both the value of different tissues (i.e., young vs. old leaves) and the relative importance of specialist and generalist herbivores in the community. Using populations of Verbascum thapsus exposed to ambient herbivory in its native range (where specialist and generalist chewing herbivores are prevalent) and its introduced range (where only generalist chewing herbivores are prevalent), we illustrate significant differences in the way iridoid glycosides are distributed among young and old leaves. Importantly, high-quality young leaves are 6.53 more highly defended than old leaves in the introduced range, but only 23 more highly defended in the native range. Additionally, defense levels are tracked by patterns of chewing damage, with damage restricted mostly to low-quality old leaves in the introduced range, but not the native range. Given that whole-plant investment in defense does not differ between ranges, introduced mullein may achieve increased fitness simply by optimizing its within-plant distribution of defense in the absence of certain specialist herbivores. © 2012 by the Ecological Society of America.


Moravec F.,Academy of Sciences of the Czech Republic | Manoharan J.,Annamalai University
Acta Parasitologica | Year: 2014

Based on light and scanning electron microscopical studies, two new and one specifically not identified gonad-infecting species of Philometra Costa, 1845 (Nematoda: Philometridae) are described from the ovary of marine fishes of the genus Epinephelus Bloch (Serranidae, Perciformes) in the Bay of Bengal, off the eastern coast of India: P. indica sp. nov. (male and females) from the honeycomb grouper E. merra Bloch, P. tropica sp. nov. (males and females) from the duskytail grouper E. bleekeri (Vaillant) and Philometra sp. (only females) from the cloudy grouper E. erythrurus (Valenciennes). Philometra indica is mainly characterized by the length of spicules 192-195 μm and the gubernaculum 84 μm, the distal tip of the gubernaculum without a dorsal protuberance, and by the presence of five pairs of caudal papillae. Philometra tropica is mainly characterized by the spicules conspicuously ventrally distended at their posterior halves, the distal tip of the gubernaculum with a dorsal protuberance, and the presence of three pairs of caudal papillae. © 2014 Versita Warsaw.


Tobin P.C.,U.S. Department of Agriculture | Berec L.,Academy of Sciences of the Czech Republic | Liebhold A.M.,U.S. Department of Agriculture
Ecology Letters | Year: 2011

Biological invasions are a global and increasing threat to the function and diversity of ecosystems. Allee effects (positive density dependence) have been shown to play an important role in the establishment and spread of non-native species. Although Allee effects can be considered a bane in conservation efforts, they can be a benefit in attempts to manage non-native species. Many biological invaders are subject to some form of an Allee effect, whether due to a need to locate mates, cooperatively feed or reproduce or avoid becoming a meal, yet attempts to highlight the specific exploitation of Allee effects in biological invasions are surprisingly unprecedented. In this review, we highlight current strategies that effectively exploit an Allee effect, and propose novel means by which Allee effects can be manipulated to the detriment of biological invaders. We also illustrate how the concept of Allee effects can be integral in risk assessments and in the prioritization of resources allocated to manage non-native species, as some species beset by strong Allee effects could be less successful as invaders. We describe how tactics that strengthen an existing Allee effect or create new ones could be used to manage biological invasions more effectively. © 2011.


Cifra M.,Academy of Sciences of the Czech Republic | Cifra M.,Czech Technical University | Fields J.Z.,CATX Inc. | Farhadi A.,Rush University Medical Center
Progress in Biophysics and Molecular Biology | Year: 2011

Chemical and electrical interaction within and between cells is well established. Just the opposite is true about cellular interactions via other physical fields. The most probable candidate for an other form of cellular interaction is the electromagnetic field. We review theories and experiments on how cells can generate and detect electromagnetic fields generally, and if the cell-generated electromagnetic field can mediate cellular interactions. We do not limit here ourselves to specialized electro-excitable cells. Rather we describe physical processes that are of a more general nature and probably present in almost every type of living cell. The spectral range included is broad; from kHz to the visible part of the electromagnetic spectrum. We show that there is a rather large number of theories on how cells can generate and detect electromagnetic fields and discuss experimental evidence on electromagnetic cellular interactions in the modern scientific literature. Although small, it is continuously accumulating. © 2010 Elsevier Ltd.


Lazar J.,Academy of Sciences of the Czech Republic | Lazar J.,University of South Bohemia | Lazar J.,Columbia University | Bondar A.,Academy of Sciences of the Czech Republic | And 3 more authors.
Nature Methods | Year: 2011

Membrane proteins are a large, diverse group of proteins, serving a multitude of cellular functions. They are difficult to study because of their requirement of a lipid membrane for function. Here we show that two-photon polarization microscopy can take advantage of the cell membrane requirement to yield insights into membrane protein structure and function, in living cells and organisms. The technique allows sensitive imaging of G-protein activation, changes in intracellular calcium concentration and other processes, and is not limited to membrane proteins. Conveniently, many suitable probes for two-photon polarization microscopy already exist. © 2011 Nature America, Inc. All rights reserved.


Piliarik M.,Academy of Sciences of the Czech Republic | Sipova H.,Academy of Sciences of the Czech Republic | Kvasnicka P.,Academy of Sciences of the Czech Republic | Galler N.,University of Graz | And 2 more authors.
Optics Express | Year: 2012

We report on a new biosensor with localized surface plasmons (LSP) based on an array of gold nanorods and the total internal reflection imaging in polarization contrast. The sensitivity of the new biosensor is characterized and a model detection of DNA hybridization is carried out. The results are compared with a reference experiment using a conventional high-resolution surface plasmon resonance (SPR) biosensor. We show that the LSP-based biosensor delivers the same performance as the SPR system while involving significantly lower surface densities of interacting molecules. We demonstrate a limit of detection of 100 pM and a surface density resolution of only 35 fg×mm-2 that corresponds to less than one DNA molecule per nanoparticle on average. © 2011 Optical Society of America.


Yatskiv R.,Academy of Sciences of the Czech Republic | Grym J.,Academy of Sciences of the Czech Republic | Zdansky K.,Academy of Sciences of the Czech Republic | Piksova K.,Czech Technical University
Carbon | Year: 2012

A method is described for the fabrication of highly rectifying Schottky contacts on n-type ZnO (O and Zn polar face) single crystals, both bare and partially covered with Pt nanoparticles, coated with mechanically deposited colloidal graphite. A layer of Pt nanoparticles deposited by in situ pulsed electrophoretic deposition from isooctane colloid solutions is inserted between the graphite and the ZnO surface serves to dissociate hydrogen molecules in hydrogen sensing elements based on the highly rectifying Schottky barriers. The sensing elements are sensitive to gas mixtures with a low hydrogen concentration down to 10 ppm and show an extremely fast response above 1000 ppm. © 2012 Elsevier Ltd. All rights reserved.


Patent
Czech Technical University and Academy of Sciences of the Czech Republic | Date: 2014-09-16

A layer protecting the surface of zirconium alloys used as materials for nuclear reactors is formed by a homogenous polycrystalline diamond layer prepared by chemical vapor deposition method. This diamond layer is 100 nm to 50 m thick and the size of the crystalline cores in the layer ranges from 10 nm to 500 nm. Maximum content of non-diamond carbon is 25 mol %, total content of non-carbon impurities is maximum up to 0.5 mol %, RMS surface roughness of the polycrystalline diamond layer has a value less than 40 nm and thermal conductivity of the layer ranges from 1000 to 1900 Wm^(1)K^(1). Coating of the zirconium alloys surface with the described polycrystalline diamond layer serves as a zirconium alloys surface protection against undesirable changes and processes in the nuclear reactor environment.


Butler J.E.,University of Iowa | Sinkora M.,Academy of Sciences of the Czech Republic
Journal of Leukocyte Biology | Year: 2013

Artiodactyls possess GALT that appears in fetal life and is located at the extreme end of the ileum. These IPP contain mostly B cells and in volute early in postnatal life. Rabbits have a similarly located lymphoid organ, called the sacculus rotundus. Studies in sheep and rabbits have led to the concept that the lower hindgut GALT represents primary lymphoid tissue for B cells and is necessary for normal B cell development, analogous to the bursa of Fabricius. This review traces the history of the observations and theories that have led to the existing concept concerning the role of lower GALT. We then review recent data from piglets with resected IPP that challenges the concept that the IPP is primary B cell lymphoid tissue and that artiodactyls and rabbits are members of the GALT group in the same context as gallinaceous birds. Eliminating the IPP as the primary lymphoid tissue for B cells leads to the hypothesis that the IPP acts as first-responder mucosal lym-phoid tissue. © Society for Leukocyte Biology.


Jindra M.,Academy of Sciences of the Czech Republic | Palli S.R.,University of Kentucky | Riddiford L.M.,Howard Hughes Medical Institute
Annual Review of Entomology | Year: 2013

The molecular action of juvenile hormone (JH), a regulator of vital importance to insects, was until recently regarded as a mystery. The past few years have seen an explosion of studies of JH signaling, sparked by a finding that a JH-resistance gene, Methoprene-tolerant (Met), plays a critical role in insect metamorphosis. Here, we summarize the recently acquired knowledge on the capacity of Met to bind JH, which has been mapped to a particular ligand-binding domain, thus establishing this bHLH-PAS protein as a novel type of an intracellular hormone receptor. Next, we consider the significance of JH-dependent interactions of Met with other transcription factors and signaling pathways. We examine the regulation and biological roles of genes acting downstream of JH and Met in insect metamorphosis. Finally, we discuss the current gaps in our understanding of JH action and outline directions for future research. © 2013 by Annual Reviews. All rights reserved.


Bucur D.,CNRS Mathematics Laboratory | Feireisl E.,Academy of Sciences of the Czech Republic | Necasova S.,Academy of Sciences of the Czech Republic
Archive for Rational Mechanics and Analysis | Year: 2010

We consider a family of solutions to the evolutionary Navier-Stokes system supplemented with the complete slip boundary conditions on domains with rough boundaries. We give a complete description of the asymptotic limit by means of Γ-convergence arguments, and identify a general class of boundary conditions. © 2009 Springer-Verlag.


Moravec F.,Academy of Sciences of the Czech Republic | Bakenhaster M.,Florida Fish And Wildlife Conservation Commission
Journal of Parasitology | Year: 2012

The following 3 species of Philometra Costa, 1845 (Nematoda: Philometridae) were recorded from marine fishes off Florida: Caranginema americanum Moravec, Montoya-Mendoza and Salgado-Maldonado, 2008 from the subcutaneous tissue of the crevalle jack Caranx hippos (Linnaeus) (Carangidae); Philometra charlestonensis Moravec, de Buron, Baker and González-Solís, 2008 from the gonads (ovaries) of the scamp Mycteroperca phenax Jordan and Swain (Serranidae); and Philometra sp. (only subgravid females) from the gonads (ovaries) of the Atlantic needlefish Strongylura marina (Walbaum) (Belonidae). The male of C. americanum, the type species of Caranginema Moravec, Montoya-Mendoza, and Salgado-Maldonado, 2008, is described for the first time. Its general morphology is similar to that of males of Philometra and Philometroides species. The males of C. americanum are mainly characterized by an elongate body, 3.13-3.28 mm long, a markedly elongate esophagus, and spicules and a gubernaculum 69-75 μm and 48-51 μm long, respectively. The present findings of C. americanum and P. charlestonensis represent new geographical records. The gonad-infecting Philometra sp. from S. marina probably belongs to an undescribed species. © 2012 American Society of Parasitologists.


Simon T.,Ruhr University Bochum | Kroger A.,Ruhr University Bochum | Somsen C.,Ruhr University Bochum | Dlouhy A.,Academy of Sciences of the Czech Republic | Eggeler G.,Ruhr University Bochum
Acta Materialia | Year: 2010

In situ and post-mortem diffraction contrast transmission electron microscopy (TEM) was used to study the multiplication of dislocations during a thermal martensitic forward and reverse transformation in a NiTi shape memory alloy single crystal. An analysis of the elongated dislocation loops which formed during the transformation was performed. It is proposed that the stress field of an approaching martensite needle activates an in-grown dislocation segment and generates characteristic narrow and elongated dislocation loops which expand on {1 1 0}B2 planes parallel to {0 0 1}B19′ compound twin planes. The findings are compared with TEM results reported in the literature for NiTi and other shape memory alloys. It is suggested that the type of dislocation multiplication mechanism documented in the present study is generic and that it can account for the increase in dislocation densities during thermal and stress-induced martensitic transformations in other shape memory alloys. © 2010.


Islam B.,Queen's University of Belfast | Sgobba M.,Queen's University of Belfast | Laughton C.,University of Nottingham | Orozco M.,Barcelona Institute for Research in Biomedicine | And 4 more authors.
Nucleic Acids Research | Year: 2013

The human telomeric DNA sequence with four repeats can fold into a parallel-stranded propellertype topology. NMR structures solved under molecular crowding experiments correlate with the crystal structures found with crystal-packing interactions that are effectively equivalent to molecular crowding. This topology has been used for rationalization of ligand design and occurs experimentally in a number of complexes with a diversity of ligands, at least in the crystalline state. Although G-quartet stems have been well characterized, the interactions of the TTA loop with the G-quartets are much less defined. To better understand the conformational variability and structural dynamics of the propeller-type topology, we performed molecular dynamics simulations in explicit solvent up to 1.5 ks. The analysis provides a detailed atomistic account of the dynamic nature of the TTA loops highlighting their interactions with the G-quartets including formation of an A:A base pair, triad, pentad and hexad. The results present a threshold in quadruplex simulations, with regards to understanding the flexible nature of the sugar-phosphate backbone in formation of unusual architecture within the topology. Furthermore, this study stresses the importance of simulation time in sampling conformational space for this topology. © The Author(s) 2013.


Pepino M.Y.,Center for Human Nutrition | Kuda O.,Academy of Sciences of the Czech Republic | Samovski D.,Center for Human Nutrition | Abumrad N.A.,Center for Human Nutrition | Abumrad N.A.,University of Washington
Annual Review of Nutrition | Year: 2014

CD36 (cluster of differentiation 36) is a scavenger receptor that functions in high-affinity tissue uptake of long-chain fatty acids (FAs) and contributes under excessive fat supply to lipid accumulation and metabolic dysfunction. This review describes recent evidence regarding the CD36 FA binding site and a potential mechanism for FA transfer. It also presents the view that CD36 and FA signaling coordinate fat utilization, a view that is based on newly identified CD36 actions that involve oral fat perception, intestinal fat absorption, secretion of the peptides cholecystokinin and secretin, regulation of hepatic lipoprotein output, activation of beta oxidation by muscle, and regulation of the production of the FA-derived bioactive eicosanoids. Thus abnormalities of fat metabolism and the associated pathology might involve dysfunction of CD36-mediated signal transduction in addition to the changes in FA uptake. Copyright ©2014 by Annual Reviews. All rights reserved.