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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.


Kvasz L.,Academy of Sciences of the Czech Republic
History of Mechanism and Machine Science | Year: 2015

In this paper we try to distinguish two different styles of experimental practice - roughly speaking the Galilean and the Newtonian. They differ in the way they intertwine mathematics and experimentation. We offer a theoretical reconstruction of the transition from the Galilean to the Newtonian experimental practice. It seems that this transition was brought about by gradual changes of the conceptual framework for the representation of motion. The aim of the paper is to argue that in many of these changes Cartesian physics played an important role. © 2015 Springer Science+Business Media Dordrecht.


Balik A.,University of Cambridge | Balik A.,Academy of Sciences of the Czech Republic | Penn A.C.,University of Cambridge | Nemoda Z.,University of Cambridge | Greger I.H.,University of Cambridge
Nucleic Acids Research | Year: 2013

RNA editing by adensosine deaminases is a widespread mechanism to alter genetic information in metazoa. In addition to modifications in non-coding regions, editing contributes to diversification of protein function, in analogy to alternative splicing. However, although splicing programs respond to external signals, facilitating fine tuning and homeostasis of cellular functions, a similar regulation has not been described for RNA editing. Here, we show that the AMPA receptor R/G editing site is dynamically regulated in the hippocampus in response to activity. These changes are bi-directional, reversible and correlate with levels of the editase Adar2. This regulation is observed in the CA1 hippocampal subfield but not in CA3 and is thus subfield/celltype-specific. Moreover, alternative splicing of the flip/flop cassette downstream of the R/G site is closely linked to the editing state, which is regulated by Ca 2+. Our data show that A-to-I RNA editing has the capacity to tune protein function in response to external stimuli. © 2012 The Author(s).


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.


Karlicky M.,Academy of Sciences of the Czech Republic | Kontar E.P.,University of Glasgow
Astronomy and Astrophysics | Year: 2012

Aims. We investigate the effects of acceleration during non-linear electron-beam relaxation in magnetized plasma in the case of electron transport in solar flares. Methods. The evolution of electron distribution functions is computed using a three-dimensional particle-in-cell electromagnetic code. Analytical estimations under simplified assumptions are made to provide comparisons. Results. We show that, during the non-linear evolution of the beam-plasma system, the accelerated electron population appears. We found that, although the electron beam loses its energy efficiently to the thermal plasma, a noticeable part of the electron population is accelerated. For model cases with initially monoenergetic beams in uniform plasma, we found that the amount of energy in the accelerated electrons above the injected beam-electron energy varies depending the plasma conditions and could be around 10-30% of the initial beam energy. Conclusions. This type of acceleration could be important for the interpretation of non-thermal electron populations in solar flares. Its neglect could lead to the over-estimation of accelerated electron numbers. The results emphasize that collective plasma effects should not be treated simply as an additional energy-loss mechanism, when hard X-ray emission in solar flares is interpreted, notably in the case of RHESSI data. © 2012 ESO.


Slama K.,Academy of Sciences of the Czech Republic
European Journal of Entomology | Year: 2015

This article is a comprehensive summary of the 50-year history of physiological investigations in the Czech Republic into the mode of action of the corpus allatum hormone (CAH) in insects, which is commonly known as the juvenile hormone (JH). During this period 4000 synthetic JH- mimetic bioanalogues were tested. The sesquiterpenoid epoxy-homofarnesoate (JH-I), which is generally thought to be the true JH of insects, is an excretory product of the male colleterial gland, not an insect hormone. There are two principal hormones produced by the insect neuroendocrine system: activation hormone (AH) produced by neurosecretory cells in the brain and JH secreted by the corpora allata. The prothoracic glands are a subordinated target of JH, not PTTH; they are not involved in the regulation of moulting in insects. The development of larval, pupal and adult structures depends primarily on inherited instructions encoded within the genome, not on high, medium or low concentrations of JH. At the level of epidermal cells, the responses to JH are always "all-or-none" with intermediate forms mosaic mixtures of cells of previous and future developmental stages. There are two alternative theorical explanations of the action of insect hormones. The Gilbert-Riddiford theory proposes that insect development is stimulated by a moulting hormone (ecdysone) released from the PG in response to the prothoracicotropic hormone (PTTH) from the brain. Formation of larval, pupal and adult epidermal strucures depends, respectively, on high, medium or low concentrations of JH. The alternative hormonal theory of Novák-Sláma argues that PG is not involved in the regulation of insect moults. High, medium or low concentrations of JH have nothing in common with the selective formation of larval, pupal or adult structural characters. The immature stages of certain insect groups undergo an autonomic (hormone independent), genetically programmed morphogenesis, which can be extended over several moulting cycles. Comparative endocrinological studies revealed several common evolutionary links between the neuroendocrine systems of insects and humans. The neurosecretory cells (NSC) in the insect brain and the NSC in the human hypothalamus are homologous as are the neurohaemal organs (CC) in insects and the neurohypophysis in humans, and the glandular CA in insects is anatomically and physiologically homologous with the human adenohypophysis. The centrally produced hormones (AH and CAH) alter the transcriptional potential the cellular genome. AH switches on genes at the most suitable moments for initiating inherited developmental programmes; JH determines in which direction the development should proceed, i.e. larval somatic growth or morphogenesis.


Mares P.,Academy of Sciences of the Czech Republic
Naunyn-Schmiedeberg's Archives of Pharmacology | Year: 2014

Ifenprodil, an antagonist of NMDA receptors containing the NR2B subunit, was expected to exhibit anticonvulsant action in rat pups up to the third postnatal week because of predominance of NR2B subunit at early development. Cortical epileptic afterdischarges (ADs) were used to study possible effects on threshold current intensities and duration of ADs in 12-, 15-, 18-, and 25-day-old rats. A series of 18 stimulation series with stepwise increasing current intensities (from 0.2 to 15 mA) was applied with 10-min intervals. The first experiment studied rats pretreated with ifenprodil (20 or 40 mg/kg), the second experiment studied an effect of ifenprodil on already present ADs-the dose of 20 mg/kg was administered after stimulation with the 3.5-mA current intensity. Pretreatment with ifenprodil resulted in an anticonvulsant effect in 15-day-old rats only, on the contrary, proconvulsant action was found in 18- and 25-day-old animals (decrease of thresholds especially for transition into the second, limbic type of ADs and increase in duration of ADs). Anticonvulsant effect was found in 12-, 15-, and 18-day-old rats in the second experiment-ADs were shortened. In contrast, no effect was observed in 25-day-old animals. An anticonvulsant action of ifenprodil is not only age-dependent but also activation-dependent. © 2014 Springer-Verlag.


Adamec L.,Academy of Sciences of the Czech Republic
Aquatic Botany | Year: 2011

Firing and resetting of traps in aquatic Utricularia species are associated with water flows and trap volume changes. In this study, trap thickness was used as a measure of water flow and was monitored automatically using an electronic position sensor. Isolated traps from three aquatic Utricularia species were monitored over the course of 1-2 days to verify spontaneous firings (without any mechanical stimulation) and describe their basic characteristics. Isolated traps of three Utricularia species were initially fired by mechanical stimulation and allowed to naturally reset within a period of 24-48. h. Within this resting period, spontaneous firings were found in the traps of all species and in two trap age categories of U. vulgaris. The timing of spontaneous firings was found to be irregular. Spontaneous firings ranged between 0.29 and 2.4 during the 24-h resting period and the mean time between two spontaneous firings was highly variable within each species (319-891. min). There was no quantitative difference between spontaneous and mechanically stimulated firings of the traps. Spontaneous firings could explain how phytoplankton or detritus enters traps even when no prey species are present. © 2010 Elsevier B.V.


Janouskova M.,Academy of Sciences of the Czech Republic | Pavlikova D.,Czech University of Life Sciences
Plant and Soil | Year: 2010

The aim of the study was to assess how the extraradical mycelium (ERM) of arbuscular mycorrhizal (AM) fungi contributes to Cd immobilization in the rhizosphere. Substrates prepared by cultivation of AM and non-mycorrhizal tobacco (Nicotiana tabacum L.) in quartz sand in two experiments were amended with Cd in a range of concentrations and Cd immobilization was assessed as Cd toxicity using root growth tests. Split-root plants, inoculated at one part of the root system, and hyphal compartments colonized by ERM only were used to separate the effects of ERM from plant-mediated effects of mycorrhiza and from the effects of roots. AM decreased Cd toxicity in the substrates obtained by 12 weeks of cultivation (Experiment 1), while the effect was less clear after 8 weeks (Experiment 2). No indication was found for an involvement of plant-mediated effects; in contrast, the effect of ERM could be clearly demonstrated. Lower Cd toxicity in the substrates colonized by ERM was related to ERM-induced alkalinization, but not directly to ERM density. It is concluded that the ERM of AM fungi may enhance Cd immobilisation in soil not only due to its high Cd sorption capacity but also by its activity. © 2010 Springer Science+Business Media B.V.


Sroubek Z.,Academy of Sciences of the Czech Republic
Nuclear Instruments and Methods in Physics Research, Section B: Beam Interactions with Materials and Atoms | Year: 2010

Available experimental data on the kinetic electron emission from metals bombarded by low energy atomic particles below the classical threshold were analyzed in terms of one-electron non-adiabatic model and in terms of phenomenological many-electron models. Total electron yields as a function of the particle velocity for several distinctly different substrate-particle systems were successfully interpreted using a phenomenological model. The essential microscopic mechanism of the model is the valence electron Auger interaction which leads to the Boltzmann - like energy distribution of the excited electrons in the impact zone. © 2010 Elsevier B.V. All rights reserved.


Dostal P.,Academy of Sciences of the Czech Republic
Basic and Applied Ecology | Year: 2010

The invasive behaviour of exotic species is assumed to be due to the reduced impact of enemies on their performance, along with other possible mechanisms. I studied whether the seeds of exotics (6 species) are less impacted by seed predators and seed fungal pathogens than the seeds of their related natives (5 species). I also explored whether the co-occurrence of related natives and the time since introduction increased the percentage of lost seeds in exotics. Seeds were either left unprotected during a period of seven months or treated with fungicide, protected by seed predator exclosures or subjected to both treatments. Both treatments improved seed survival rate. Fungicide treatment had more positive effect on seeds of native than of exotic species but the fungicide-by-origin interaction was insignificant. When exotic species only were considered, fungicide had neutral effect on survival of their seeds, irrespective of the co-occurrence of related natives in the vegetation. Time since introduction was shown not to influence the proportion of seeds lost due to fungi or seed predators. Though the results of this study did not support enemy release as a possible mechanism causing the invasiveness of exotic species, it identified fungal pathogens as an enemy group with possibly differential impacts on native and exotic seeds, which thus deserves attention in future studies. © 2010.


A revision of the diversity and distribution of Potamogeton hybrids in the Czech Republic is presented. Thorough examination of herbarium material and recent extensive field studies revealed the present and/or past occurrence of eight Potamogeton hybrids in the Czech Republic. In addition to morphological characters, stem anatomy and/or molecular analysis were used to identify some of the hybrids. All the hybrids detected are between broad-leaved species of the genus, suggesting that hybrids between linear-leaved species may be overlooked because of the overall morphological similarity of taxa within this group. Four of the hybrids identified, P nitens, P. ×olivaceus, P. ×sparganiifolius and P. ×undulatus, are recorded for the first time from the Czech Republic. Four of the hybrids are now extinct in the Czech Republic and the extant hybrids are rare. The occurrence of P. ×lintonii was not confirmed; the previous record was based on extreme forms of P. gramineus. The name P. ×concinnitus, proposed for a putative hybrid combination "P. pusillus × P. crispus", was lectotypified and reduced to a synonym of P. crispus. Although the absolute number of finds of specimens of Potamogeton hybrids per decade is increasing, this is not a result of more frequent hybridization but of an increase in recording activity. Most records for recent decades are associated with targeted research by a few experts. The typical habitat of Potamogeton hybrids in the Czech Republic are ponds that were previously drained in summer and allowed to dry out. Many historical localities disappeared when the traditional fishpond management was largely abandoned and fish farming become more intensive. In the 19th century in particular some hybrids were recorded also in rivers but these occurrences generally disappeared after the extensive channelling of rivers at the beginning of the 20th century. Many hybrids occur at the same localities as their parents but it is documented that hybrids can persist vegetatively in the absence of the parental species, presumably as relics of the previous presence of the parent plants. Although almost all Potamogeton hybrids are consistently sterile, a cultivation experiment showed that P. ×angustifolius set seeds that were fertile and successfully produced adult plants.


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.


Discontinuous respiration in diapausing pupae of Cecropia silkworms was monitored by means of several electronic methods, including recording changes in haemocoelic pressure, monitoring respiratory movements by strain-gauge sensors and nanorespirographic recording of O2 consumption and CO2 output. It appears that, in contrast to previous concepts of stereotypic discontinuous respiration cycles (DGC) driven by accumulation of gaseous CO2 in the body, the new results indicate that CO2 remains dissolved in liquid carbonate buffers during interburst periods. In other words, there is no accumulation of gaseous CO2 within the air filled tracheal space between the bursts. The bursts of CO2 are caused by homeostatically regulated enzymatic hydration by carbonic anhydrase of metabolically produced carbonic acid. The chemically produced gaseous CO2 was exhaled mainly by a bulk outflow through selectively opened or pulsating spiracles. The output of CO2 was enhanced by actively regulated, unidirectional ventilation. The deep depressions in haemocoelic pressure, caused by permanent closure of all spiracular valves for long periods, appeared to be a specific feature of diapausing saturniid pupae. Physiologically, it has circulatory, not respiratory functions. The original definition of spiracular "fluttering"resulted from a misinterpretation of previously unknown extracardiac pulsations in haemocoelic pressure. The coordinated pulsation of the spiracular valves with extracardiac pulsations produce a very efficient, unidirectional ventilation of the whole tracheal system. According to the new results, the discontinuous respiration cycles of diapausing Cecropia pupae can be briefly described as follows: (1) Spiracular valves are kept permanently closed during the periods of deep depressions, they remain closed for some 99% of the time with occasional snap opening (passive inspirations) during prolonged interburst periods and more than 50% closed during the bursts; (2) During the long interburst periods, CO2 is retained in liquid carbonate buffers, while the relatively high (after the burst) or low (toward the next burst) rate of O2 consumption creates an internal vacuum, which is homeostatically compensated for by the snap-opening of one or just a few spiracular valves (passive suction inspirations); (3) The CO2 gas, produced enzymatically by carbonic anhydrase, enters the air filled tracheal system and leaves the body by diffusion, a bulk outflow, or actively regulated unidirectional ventilation ("fluttering"spiracles). The selective advantage of this actively regulated respiratory system for water retention in pupae is discussed. © 2003 Institute of Entomology.


Hanel L.,Academy of Sciences of the Czech Republic
Applied Soil Ecology | Year: 2010

Secondary succession of nematodes was studied in 1-48-year-old abandoned fields on cambisols in South Bohemia, Czech Republic, and compared with cultivated field and sub-climax oak forests. Bacterivores were the predominant group in the cultivated field whereas in forests root-fungal feeders (mainly Filenchus) were almost as abundant as bacterivores. The total abundance of nematodes in the cultivated field averaged 868×103indm-2. During the first three years of succession the abundance practically did not change (775×103indm-2), the fauna was still similar to that in cultivated field but the biomass increased mainly due to Aporcelaimellus. Then the abundance increased up to 3731×103indm-2 in 7-8-year-old abandoned fields, plant parasites (Helicotylenchus) dominated and the fungal-based decomposition channel was activated. Later the abundance stabilised at between 1086 and 1478×103indm-2 in 13-25-year-old successional meadow stages with high population densities of omnivores and predators. The total abundance of nematodes was low in the 12-13-year-old willow shrub stage (594×103indm-2), increased in the 35-48-year-old birch shrub stage (1760×103indm-2) and the nematode fauna developed towards a forest community. The diversity and maturity of nematode communities generally increased with the age of abandoned fields but the highest values were in meadow stages (81-113 species, 57-68 genera, MI 2.73-3.30). The development of meadow arrested succession towards forests or diverted succession towards a waterlogged ecosystem. The succession of nematodes was influenced by the method of field abandonment (bare soil vs. legume cover, mowing) that affected the formation of either a shrub or meadow stage, and by the soil water status. The composition of the nematode fauna indicated that the soil food web could recover faster from agricultural disturbance under successive meadows than under shrubs. © 2010 Elsevier B.V.


Sera B.,Academy of Sciences of the Czech Republic
Polish Journal of Ecology | Year: 2010

The study examines the vegetation diversity (235 herbaceous species) in variable road-site types in terms of life history components (life traits) like life form, type of pollination, seed dispersal, spreading ability, life strategy according to Grimes classification, and in terms of habitat preferences using Ellenberg s indicator value (in relation to light, temperature, moisture, nitrogen, soil pH and soil salinity). Plants reGIStered as alien species were evaluated also according to invasive status, level of abundance, introduction mode and land use habitat. Study localities (9 sites) were situated in the Českomoravska highlands and the South Bohemian regions (Czech Republic). The plant species were recorded in the bands (width in range of 1.5-3.0 m) along the verge of two types of roads (motorways with median stripes) and secondary roads (II and III classes). In total - road length of about 15 km and the total area of roadside vegetation of about 8 ha were surveyed. The annual/therophyte species with a tendency to seed dispersed by wind, preferring a light and dry habitat, and having the RC (competitive - ruderal) life strategy were mainly found along the motorways. It means that road verges along motorways are quite insolated and constitute the dry habitats, probably suitable for ruderal, weedy, non-native, and invasive species. On the contrary, species with a tendency to vegetative reproduction and the C (competitive) strategy occur mainly along the secondary roads. It seems that the secondary roads are alternative habitats for grassland flora. Species occurred on the verges of the secondary roads do not belong to the particular group of the life traits. The salt tolerant species Puccinellia distans (Jacq.) Pari, was found along all types of roads. Almost 24% of all recorded herbaceous species growing in road-sites were alien species.


Adamec L.,Academy of Sciences of the Czech Republic
Flora: Morphology, Distribution, Functional Ecology of Plants | Year: 2010

Tissue N, P, K, Ca, and Mg content was estimated in traps and photosynthetic and carnivorous shoots in five aquatic carnivorous plant species from an outdoor culture: Aldrovanda vesiculosa, Utricularia vulgaris, U. reflexa, U. intermedia, and U. stygia, for the determination of the mineral cost of carnivory. In three species with monomorphic shoots (A. vesiculosa, U. vulgaris, U. reflexa), tissue P and K content in traps was significantly higher than that in their photosynthetic shoots, whereas N content was about the same. In U. stygia and U. intermedia with dimorphic shoots, tissue N and P content was markedly the highest in photosynthetic shoots followed by traps, while it was lowest in carnivorous shoots. In all five species, trap K content was significantly (2-4 times) higher than that in photosynthetic and carnivorous shoots. In all species, the values of the mineral cost of carnivory - the proportion of mineral nutrient amount contained in traps or carnivorous shoots to that in the total plant biomass - were within 19-61% for N, 33-76% P, 51-78% K, 26-70% Ca, and 34% for Mg. A new concept of the ecological cost-benefit relationships of plant carnivory, based on the mineral benefit of prey capture and mineral costs associated with trap production, is introduced for aquatic carnivorous plants. The evolution of this plant group is considered to show the optimization of these mineral cost-benefit relationships. © 2010 Elsevier GmbH.


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.


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.


Kalinova J.,University of South Bohemia | Vrchotova N.,Academy of Sciences of the Czech Republic
Food Chemistry | Year: 2011

Common buckwheat (Fagopyrum esculentum Moench) is a pseudocereal that is cultivated for its achenes that possess a high level of flavonoids. Some scientific studies have found that the growing conditions can significantly affect the flavonoid content in conventional and organic food products. Hence, the present study compared conventionally and organically produced common buckwheat with respect to the content of selected flavonoids, thousand achenes weight and achene yield. Three buckwheat varieties were grown with organic and conventional crop management under the same environmental conditions. The thousand achenes weight and achene yield were not significantly influenced by way of crop management. The level of rutin, epicatechin, catechin, and epicatechin gallate in buckwheat groats (hulled achenes) were quantified with high pressure liquid chromatography. Only rutin and epicatechin gallate reached significantly higher level in organic groats. However, the differences were influenced by environmental conditions in the given year and variety. © 2011 Elsevier Ltd. All rights reserved.


Svoboda J.,Academy of Sciences of the Czech Republic | Fischer F.D.,University of Leoben
Acta Materialia | Year: 2014

The coarsening of precipitates in a matrix with a non-zero volume fraction is treated by assuming that the exchange of matter between the precipitates occurs by diffusion in the matrix within finite zones surrounding the precipitates. The thermodynamic extremal principle is used for the derivation of evolution equations for the precipitate radii. Accordingly, non-steady-state and steady-state distribution functions are deduced, depending on the system parameter characterizing the finite diffusion zones. The distribution functions tend exactly to the established Lifshitz-Slyozov-Wagner distribution for a zero volume fraction of the precipitates. The steady-state distribution functions are expressed by means of distinct volume-fraction-dependent parameters, which are presented by analytical expressions and in diagrams. To treat non-steady-state systems, ensembles of up to 106 precipitates can easily be handled by standard computational methods. © 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.


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.


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).


Cai B.,University of Nebraska Medical Center | Katafiasz D.,University of Nebraska Medical Center | Horejsi V.,Academy of Sciences of the Czech Republic | Naslavsky N.,University of Nebraska Medical Center
Traffic | Year: 2011

EHD1 regulates the trafficking of multiple receptors from the endocytic recycling compartment (ERC) to the plasma membrane. However, the potential role of EHD1 in regulating the family of glycosylphosphatidylinositol-anchored proteins (GPI-APs) has not been determined. Here we demonstrate a novel role for EHD1 in regulating the trafficking of CD59, an endogenous GPI-AP, at early stages of trafficking through the endocytic pathway. EHD1 displays significant colocalization with newly internalized CD59. Upon EHD1 depletion, there is a rapid Rab5-independent coalescence of CD59 in the ERC region. However, expression of an active Arf6 mutant (Q67L), which traps internalized pre-sorting endosomal cargo in phosphatidylinositol(4,5)-bisphosphate enriched vacuoles, prevents this coalescence. It is of interest that sustained PKC activation leads to a similar coalescence of CD59 at the ERC, and treatment of EHD1-depleted cells with a PKC inhibitor (Go6976) blocked this rapid relocation of CD59. However, unlike sustained PKC activation, EHD1 depletion does not induce the translocation of PKCα to ERC. The results presented herein provide evidence that EHD1 is involved in the control of CD59 transport from pre-sorting endosomes to the ERC in a PKC-dependent manner. However, the mechanisms of EHD1-induced coalescence of CD59 at the ERC differ from those induced by sustained PKC activation. © 2010 John Wiley & Sons A/S.


Hansel R.,Goethe University Frankfurt | Lohr F.,Goethe University Frankfurt | Foldynova-Trantirkova S.,Academy of Sciences of the Czech Republic | Bamberg E.,Max Planck Institute of Biophysics | And 2 more authors.
Nucleic Acids Research | Year: 2011

G-quadruplex topologies of telomeric repeat sequences from vertebrates were investigated in the presence of molecular crowding (MC) mimetics, namely polyethylene glycol 200 (PEG), Ficoll 70 as well as Xenopus laevis egg extract by CD and NMR spectroscopy and native PAGE. Here, we show that the conformational behavior of the telomeric repeats in X. laevis egg extract or in Ficoll is notably different from that observed in the presence of PEG. While the behavior of the telomeric repeat in X. laevis egg extract or in Ficoll resembles results obtained under dilute conditions, PEG promotes the formation of high-order parallel topologies. Our data suggest that PEG should not be used as a MC mimetic. © 2011 The Author(s).


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.


Reblova M.,Academy of Sciences of the Czech Republic | Seifert K.A.,Agriculture and Agri Food Canada
Studies in Mycology | Year: 2011

Sterigmatobotrys macrocarpa is a conspicuous, lignicolous, dematiaceous hyphomycete with macronematous, penicillate conidiophores with branches or metulae arising from the apex of the stipe, terminating with cylindrical, elongated conidiogenous cells producing conidia in a holoblastic manner. The discovery of its teleomorph is documented here based on perithecial ascomata associated with fertile conidiophores of S. macrocarpa on a specimen collected in the Czech Republic; an identical anamorph developed from ascospores isolated in axenic culture. The teleomorph is morphologically similar to species of the genera Carpoligna and Chaetosphaeria, especially in its nonstromatic perithecia, hyaline, cylindrical to fusiform ascospores, unitunicate asci with a distinct apical annulus, and tapering paraphyses. Identical perithecia were later observed on a herbarium specimen of S. macrocarpa originating in New Zealand. Sterigmatobotrys includes two species, S. macrocarpa, a taxonomic synonym of the type species, S. elata, and S. uniseptata. Because no teleomorph was described in the protologue of Sterigmatobotrys, we apply Article 59.7 of the International Code of Botanical Nomenclature. We epitypify (teleotypify) both Sterigmatobotrys elata and S. macrocarpa to give the genus holomorphic status, and the name S. macrocarpa is adopted for the holomorph. To evaluate the ordinal and familial affinities of Sterigmatobotrys and its relationships with the morphologically similar genera Carpoligna and Chaetosphaeria, phylogenetic relationships were inferred based on aligned sequences of the large subunit nuclear ribosomal DNA (ncLSU rDNA). © 2011 by the CBS Fungal Biodiversity Centre.


Pospiskova K.,Palacky University | Safarik I.,Academy of Sciences of the Czech Republic | Safarik I.,Palacky University
Carbohydrate Polymers | Year: 2013

Extremely simple procedures for the preparation of magnetic chitosan enzyme carriers have been developed and used for the immobilization of lipase and β-galactosidase as model enzymes. In the first case commercially available magnetite microparticles were entrapped in chitosan gel, while in the second case magnetic iron oxides microparticles were synthesized in chitosan matrix from ferrous sulfate using microwave irradiation. Immobilized enzymes showed long-term stability without leaching of enzyme from the support and enabled their repeated use without significant loss of activity. © 2013 Elsevier Ltd. All rights reserved.


Franova J.,Academy of Sciences of the Czech Republic
Bulletin of Insectology | Year: 2011

Polymerase chain reaction (PCR) with subsequent restriction fragment length polymorphism (RFLP) analysis is often used for phytoplasma identification and classification. Although these techniques are very sensitive and specific, in some cases, nonspecific reactions, false positives and negatives results, as well as unusual or illegible profiles after RFLP analyses, amplification of plant host́s DNA or other difficulties occurred. Experiences with suitability of positive and negative controls integration in PCR, evaluation of critical samples and other difficulties in phytoplasma PCR/RFLP identification are reported.


Garcia S.,University of Barcelona | Garnatje T.,Institute Botanic Of Barcelona Ibb Csic Icub | Kovarik A.,Academy of Sciences of the Czech Republic
Chromosoma | Year: 2012

Number, position and structure of the 5S and 18S- 5.8S-26S ribosomal DNA (rDNA) loci are important species characteristics. In recent decades, we have witnessed accumulation of rDNA data, and there is a need to compile, store and analyse this information, and to make it accessible to a broader scientific community. An online resource, accessible at www.plantrdnadatabase.com, has been developed to accomplish these goals. Current knowledge regarding chromosomal rDNA sites is provided for more than 1,000 plant species (including more than 1,400 different accessions). The data comes from fluorescent in situ hybridisation experiments (FISH) from more than 300 publications. Additional information is also displayed, such as ploidy level, mutual arrangement of rRNA genes, genome size and life cycle. The webpage is intuitive and user-friendly, including different search options, and currently holds information published (or in press) up until January 2011; frequent updates are planned. We expect this database to be used for data-mining, analysing rDNAs from different angles, unit organisation, distribution, evolution and linkage of rDNA patterns with phylogenetic relationships. © Springer-Verlag 2012.


Adamec L.,Academy of Sciences of the Czech Republic
Central European Journal of Biology | Year: 2010

In this study, O2-based dark respiration rate (RD) in leaf and trap cuttings was compared in 9 terrestrial carnivorous plant species of 5 genera to decide whether traps represent a greater energetic (maintanence) cost than leaves or photosynthetic parts of traps. RD values of cut strips of traps or leaves of terrestrial carnivorous plants submerged in water ranged between 2.2 and 8.4 nmol g-1 s-1 (per unit dry weight) in pitcher traps of the genera Sarracenia, Nepenthes, and Cephalotus, while between 7.2 and 25 nmol g-1DW s-1 in fly-paper or snapping traps or leaves of Dionaea and Drosera. No clear relationship between RD values of traps (or pitcher walls) and leaves (or pitcher wings or petioles) was found. However, RD values of separated Drosera prolifera tentacles exceeded those of leaf lamina 7.3 times. © Versita Warsaw and Springer-Verlag Berlin Heidelberg.


Fischer F.D.,University of Leoben | Svoboda J.,Academy of Sciences of the Czech Republic | Petryk H.,Polish Academy of Sciences
Acta Materialia | Year: 2014

Mathematical and physical aspects of the applicability of the Onsager, Prigogine as well as the Glansdorff and Ziegler thermodynamic extremal principles (TEPs) to non-equilibrium thermodynamics are examined for systems at fixed temperature with respect to their ability to provide kinetic equations approved in materials science. TEPs represent an alternative to the classical phenomenological equations approach. As TEPs are, more or less, a pure mathematical tool, they cannot significantly contribute to a deeper physical understanding. However, if a system can be described by discrete characteristic (thermodynamic) parameters, it is demonstrated that application of Onsager's TEP or Ziegler's TEP represents a systematic way to derive a set of explicit evolution equations for these parameters. This approach can significantly simplify the treatment of the problem and, thus, can also be applied to rather complex systems, for which the classical approach, involving application of phenomenological equations, fails. The application of TEPs is demonstrated on plasticity with respect to constitutive equations as well as on grain growth and coarsening with respect to evolution equations of discrete parameters. No exploitation of Prigogine's TEP has been reported for applications in materials science. Contrarily, Prigogine's TEP can be invalidated if the coefficients of the dissipation function depend on the evolution of state variables with time. This is demonstrated by a further practical example worked out for the solute drag phenomenon. Glansdorff's and Prigogine's evolution criterion, however, is always fulfilled near the equilibrium state of convex Gibbs energy. Extensions of TEPs to non-linear non-equilibrium thermodynamics are demonstrated for homogeneous and quasi-homogeneous dissipation functions. © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.


Karlicky M.,Academy of Sciences of the Czech Republic
Research in Astronomy and Astrophysics | Year: 2014

This review summarizes new trends in studies of magnetic reconnection in solar flares. It is shown that plasmoids play a very important role in this primary flare process. Using the results of magnetohydrodynamic and particle-in-cell simulations, we describe how the plasmoids are formed, how they move and interact, and how a flare current sheet is fragmented into a cascade of plasmoids. Furthermore, it is shown that during the interactions of these plasmoids electrons are not only very efficiently accelerated and heated, but electromagnetic (radio) emission is also produced. We also describe possible mechanisms for the triggering of magnetic reconnection. The relevant X-ray and radio signatures of these processes (such as radio drifting pulsation structures, narrowband dm-spikes, and the loop-top and above-the-loop-top X-ray sources) are then described. It is shown that plasmoids can also be formed in kinked magnetic ropes. A mapping of X-points of the magnetic reconnection on the chromosphere (as e.g. a splitting of flare ribbons) is mentioned. Supporting EUV and white-light observations of plasmoids are added. The significance of all these processes for the fast magnetic reconnection and electron acceleration is outlined. Their role in fusion experiments is briefly mentioned. © 2014 National Astronomical Observatories of Chinese Academy of Sciences and IOP Publishing Ltd..


Adamec L.,Academy of Sciences of the Czech Republic
Plant Signaling and Behavior | Year: 2011

Aquatic Utricularia species usually grow in standing, nutrientpoorhumic waters. They take up all necessary nutrients eitherdirectly from the water by rootless shoots or from animal preyby traps. The traps are hollow bladders, 1-6 mm long withelastic walls and have a mobile trap door. The inner part ofthe trap is densely lined with quadrifid and bifid glands andthese are involved in the secretion of digestive enzymes,resorption of nutrients and pumping out the water. The trapscapture small aquatic animals but they also host a communityof microorganisms considered as commensals. How do theseperfect traps function, kill and digest their prey? How dothey provide ATP energy for their demanding physiologicalfunctions? What are the nature of the interactions betweenthe traps and the mutualistic microorganisms living insideas commensals? In this minireview, all of these questions areconsidered from an ecophysiologist's point of view, basedon the most recent literature data and unpublished results. Anew concept on the role of the commensal community for theplants is presented. © 2011 Landes Bioscience.


Moravec F.,Academy of Sciences of the Czech Republic | Justine J.-L.,CNRS Systematics, Biodiversity and Evolution Institute
Parasite | Year: 2014

A recent examination of newly obtained specimens of philometrid nematodes (Philometridae) parasitising carangid and serranid fishes off New Caledonia, South Pacific, revealed the presence of several nematodes of the genus Philometra Costa, 1845, including three new species: P. austropacifica n. sp. (males and females) from the ovary of Alepes vari (Carangidae), P. piscaria n. sp. (males) from the ovary of Epinephelus coioides (Serranidae), and P. selaris n. sp. (males) probably from the abdominal cavity (found in washings) of Selar crumenophthalmus (Carangidae). The new species are characterised mainly by the length and structure of the spicules and gubernaculum, body size, their location in the host and the type of host. Philometra austropacifica n. sp. is the first known nominal gonad-infecting species of Philometra parasitising a carangid fish. In addition, the gravid female of P. fasciati Moravec & Justine, 2008 from the ovary of Epinephelus fasciatus (Serranidae) is described for the first time. Carangid host fish were identified by both morphology and DNA barcoding. © EDP Sciences, 2014.


Reblova M.,Academy of Sciences of the Czech Republic | Gams W.,Molenweg 15 | Seifert A.,Agriculture and Agri Food Canada
Studies in Mycology | Year: 2011

We examined the phylogenetic relationships of two species that mimic Chaetosphaeria in teleomorph and anamorph morphologies, Chaetosphaeria tulasneorum with a Cylindrotrichum anamorph and Australiasca queenslandica with a Dischloridium anamorph. Four data sets were analysed: a) the internal transcribed spacer region including ITS1, 5.8S rDNA and ITS2 (ITS), b) nc28S (ncLSU) rDNA, c) nc18S (ncSSU) rDNA, and d) a combined data set of ncLSU-ncSSU-RPB2 (ribosomal polymerase B2). The traditional placement of Ch. tulasneorum in the Microascales based on ncLSU sequences is unsupported and Australiasca does not belong to the Chaetosphaeriaceae. Both holomorph species are nested within the Glomerellales. A new genus, Reticulascus, is introduced for Ch. tulasneorum with associated Cylindrotrichum anamorph; another species of Reticulascus and its anamorph in Cylindrotrichum are described as new. The taxonomic structure of the Glomerellales is clarified and the name is validly published. As delimited here, it includes three families, the Glomerellaceae and the newly described Australiascaceae and Reticulascaceae. Based on ITS and ncLSU rDNA sequence analyses, we confirm the synonymy of the anamorph genera Dischloridium with Monilochaetes. Consequently Dischloridium laeënse, type species of the genus, and three related species are transferred to the older genus Monilochaetes. The teleomorph of D. laeënse is described in Australiasca as a new species. The Plectosphaerellaceae, to which the anamorph genus Stachylidium is added, is basal to the Glomerellales in the three-gene phylogeny. Stilbella annulata also belongs to this family and is newly combined in Acrostalagmus. Phylogenetic analyses based on ncLSU, ncSSU, and combined ncLSU-ncSSU-RPB2 sequences clarify family relationships within the Microascales. The family Ceratocystidaceae is validated as a strongly supported monophyletic group consisting of Ceratocystis, Cornuvesica, Thielaviopsis, and the type species of Ambrosiella. The new family Gondwanamycetaceae, a strongly supported sister clade to the Ceratocystidaceae, is introduced for the teleomorph genus Gondwanamyces and its Custingophora anamorphs. Four families are accepted in the Microascales, namely the Ceratocystidaceae, Gondwanamycetaceae, Halosphaeriaceae, and Microascaceae. Because of a suggested affinity of a Faurelina indica isolate to the Microascales, the phylogenetic position of the Chadefaudiellaceae is reevaluated. Based on the results from a separate ncLSU analysis of the Dothideomycetes, Faurelina is excluded from the Microascales and placed in the Pleosporales. © 2011 by the CBS Fungal Biodiversity Centre.


Vlcek C.,Academy of Sciences of the Czech Republic | Marande W.,University of Montreal | Marande W.,French Natural History Museum | Teijeiro S.,University of Montreal | And 2 more authors.
Nucleic Acids Research | Year: 2011

Arguably, the most bizarre mitochondrial DNA (mtDNA) is that of the euglenozoan eukaryote Diplonema papillatum. The genome consists of numerous small circular chromosomes none of which appears to encode a complete gene. For instance, the cox1 coding sequence is spread out over nine different chromosomes in non-overlapping pieces (modules), which are transcribed separately and joined to a contiguous mRNA by trans-splicing. Here, we examine how many genes are encoded by Diplonema mtDNA and whether all are fragmented and their transcripts trans-spliced. Module identification is challenging due to the sequence divergence of Diplonema mitochondrial genes. By employing most sensitive protein profile search algorithms and comparing genomic with cDNA sequence, we recognize a total of 11 typical mitochondrial genes. The 10 protein-coding genes are systematically chopped up into three to 12 modules of 60-350bp length. The corresponding mRNAs are all trans-spliced. Identification of ribosomal RNAs is most difficult. So far, we only detect the 3′-module of the large subunit ribosomal RNA (rRNA); it does not trans-splice with other pieces. The small subunit rRNA gene remains elusive. Our results open new intriguing questions about the biochemistry and evolution of mitochondrial trans-splicing in Diplonema. © 2010 The Author(s).


Lopez C.A.,Zernike Institute for Advanced Materials | Sovova Z.,University of South Bohemia | Sovova Z.,Academy of Sciences of the Czech Republic | Van Eerden F.J.,Zernike Institute for Advanced Materials | And 2 more authors.
Journal of Chemical Theory and Computation | Year: 2013

We present an extension of the Martini coarse-grained force field to glycolipids. The glycolipids considered here are the glycoglycerolipids monogalactosyldiacylglycerol (MGDG), sulfoquinovosyldiacylglycerol (SQDG), digalactosyldiacylglycerol (DGDG), and phosphatidylinositol (PI) and its phosphorylated forms (PIP, PIP2), as well as the glycosphingolipids galactosylceramide (GCER) and monosialotetrahexosylganglioside (GM1). The parametrization follows the same philosophy as was used previously for lipids, proteins, and carbohydrates focusing on the reproduction of partitioning free energies of small compounds between polar and nonpolar solvents. Bonded parameters are optimized by comparison to lipid conformations sampled with an atomistic force field, in particular with respect to the representation of the most populated states around the glycosidic linkage. Simulations of coarse-grained glycolipid model membranes show good agreement with atomistic simulations as well as experimental data available, especially concerning structural properties such as electron densities, area per lipid, and membrane thickness. Our coarse-grained model opens the way to large scale simulations of biological processes in which glycolipids are important, including recognition, sorting, and clustering of both external and membrane bound proteins. © 2013 American Chemical Society.


Ruzicka V.,Academy of Sciences of the Czech Republic
Polish Journal of Ecology | Year: 2011

The purpose of the study is to find which habitats within Central Europe support the persistence of isolated populations of spider species of both boreal and Alpine origins. Twenty-five species exhibited disjunctive distributions with their main sub-area in the tundra or boreal forest, and isolated sub-areas in the temperate zone of Central Europe. Six species exhibited disjunctive distributions with their main sub-area in the Alps, and isolated sub-areas in the temperate zone in Central Europe. Only (approximately) one-third of the species of boreal origin have the same habitat, as in the boreal zone. Twothirds of the species inhabit different habitats, or have narrowed their ecological valency. Screes play an important role in the survival of these isolated populations of species of boreal origin in the temperate zone, together with mountain summits, mountain forests, and peat bogs. Extensive complexes of sandstone rocks also enables the survival of isolated populations of species of boreal origin.


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.


Stockelova T.,Academy of Sciences of the Czech Republic
Science Technology and Human Values | Year: 2012

Science policies and science studies largely share an understanding of scientific knowledge and objects as immutable mobiles. This article shows how the analysis of research assessment in a non-Anglophone country and its effects on social sciences can shed new light on this shared notion. The preference for immutable mobiles in assessment regimes pushes social scientists to publish in specialized, usually Anglophone journals, which can result in the attenuation of local relevance of the knowledge they produce and contribute to the performance of globally converging societies. The author argues that the observed consequences for the social sciences in non-Anglophone countries underscore a larger problem with both the policy ideal and the science and technology studies (STS) idea of immutable mobiles on two counts: the relation of the social and natural sciences to society and the engagement of sciences with the multiplicity of societies as well as natures. © SAGE Publications 2012.


Lebeda O.,Academy of Sciences of the Czech Republic | Pruszynski M.,Institute of Nuclear Chemistry and Technology of Poland
Applied Radiation and Isotopes | Year: 2010

Cross-sections for the proton induced reactions on natural molybdenum leading to 93mTc, 93m+gTc, 94Tc, 94mTc, 95Tc, 95mTc, 96m+gTc, 99mTc, 90Mo, 93mMo, 99Mo, 90m+gNb, 92mNb, 95Nb and 89m+gZr were measured in the proton energy range 8.4-37.1MeV on the cyclotron U-120M at the Institute of Nuclear Physics AS CR. Special attention was paid to excitation functions and thick target yields for the formation of 95mTc, a suitable tracer for 99Tc, of 96m+gTc, which was proposed as a proton beam monitor, and of 99mTc and 99Mo, the most widespread radionuclide generator pair in nuclear medicine. If appropriate, obtained data are compared with the heretofore published cross-sections. © 2010 Elsevier Ltd.


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.


Reblova M.,Academy of Sciences of the Czech Republic
Fungal Diversity | Year: 2011

The phylogenetic relationship of Jattaea and Wegelina, two morphologically related genera of the Calosphaeriales, is analyzed in two molecular analyses using the Internal transcribed spacer region of the DNA operon, and the nuclear large and small subunits of ribosomal DNA combined with the second largest subunit of RNA polymerase for a multigene analysis. For each data set maximum likelihood, maximum parsimony and Bayesian analyses were performed. Type and herbarium material of two lectotype species Jattaea algeriensis and Wegelina discreta were examined and correlated with results from in vitro studies. The phylogenetic analyses show that both species are congeneric. The name Jattaea is accepted to include species with hyaline, allantoid to suballantoid ascospores in clavate, stipitate asci without apical annulus borne on individual cells on ascogenous hyphae and with phialophora-like anamorphs produced in axenic culture. Twelve species are accepted in Jattaea, the concept of the genus is outlined and a key to its species is provided. The genus Wegelina is reduced to its synonymy. Molecular data also show that septation of ascospores, a diagnostic feature used to separate calosphaeria-like fungi into the genus Phragmocalosphaeria, does not appear to be relevant in distinguishing genera in the Calosphaeriales. Therefore, Jattaea includes species with both one-celled and septate ascospores and Phragmocalosphaeria is accepted as its generic synonym. The genus Jattaea and its phialophora-like anamorphs is compared with other genera of the Calosphaeriales and the phylogenetically related Togniniaceae. The revision of four species of Ceratostomella, i.e., C. echinella, C. leptorrhyncha, C. mali and C. microspora, revealed their striking morphological similarities with the Calosphaeriaceae and the Togniniaceae. These are identified as species of Jattaea, Togninia and Togniniella and the respective new combinations are proposed. © 2011 Kevin D. Hyde.


Walch S.K.,Max Planck Institute for Astrophysics | Whitworth A.P.,University of Cardiff | Bisbas T.,University College London | Wunsch R.,Academy of Sciences of the Czech Republic | Hubber D.,University of Sheffield
Monthly Notices of the Royal Astronomical Society | Year: 2012

Feedback from massive stars is believed to be a key element in the evolution of molecular clouds. We use high-resolution 3D smoothed particle hydrodynamics simulations to explore the dynamical effects of a single O7 star-emitting ionizing photons at 10 49s -1 and located at the centre of a molecular cloud with mass 10 4M ⊙ and radius 6.4pc; we also perform comparison simulations in which the ionizing star is removed. The initial internal structure of the cloud is characterized by its fractal dimension, which we vary between D=2.0 and 2.8, and the standard deviation of the approximately log-normal initial density PDF, which is σ 10 = 0.38 for all clouds. (i) As regards star formation, in the short term ionizing feedback is positive, in the sense that star formation occurs much more quickly (than in the comparison simulations), in gas that is compressed by the high pressure of the ionized gas. However, in the long term ionizing feedback is negative, in the sense that most of the cloud is dispersed with an outflow rate of up to ~10 -2M ⊙yr -1, on a time-scale comparable with the sound-crossing time for the ionized gas (~1-2 Myr ), and triggered star formation is therefore limited to a fewper cent of the cloud's mass. We will describe in greater detail the statistics of the triggered star formation in a companion paper. (ii) As regards the morphology of the ionization fronts (IFs) bounding the Hii region and the systematics of outflowing gas, we distinguish two regimes. For low D≲2.2, the initial cloud is dominated by large-scale structures, so the neutral gas tends to be swept up into a few extended coherent shells, and the ionized gas blows out through a few large holes between these shells; we term these Hii regions shell dominated. Conversely, for high D≳2.6, the initial cloud is dominated by small-scale structures, and these are quickly overrun by the advancing IF, thereby producing neutral pillars protruding into the Hii region, whilst the ionized gas blows out through a large number of small holes between the pillars; we term these Hii regions pillar dominated. (iii) As regards the injection of bulk kinetic energy, by ~1Myr, the expansion of the Hii region has delivered a mass-weighted rms velocity of ~6kms -1; this represents less than 0.1per cent of the total energy radiated by the O7 star. © 2012 The Authors Monthly Notices of the Royal Astronomical Society. © 2012 RAS.


Adamec L.,Academy of Sciences of the Czech Republic
Fundamental and Applied Limnology | Year: 2011

Turions are overwintering, dormant organs, produced by aquatic plants. In spring, aerobic dark respiration (RD) and photosynthetic rates (PN) were measured as criteria of metabolic activity and photosynthetic capacity in dormant turions of 7 temperate aquatic plant species. These rates were also measured in old, original turion segments and in the newly formed shoots of sprouting turions. Two non-carnivorous rooting species (Caldesia parnassifolia, Hydrocharis morsus-ranae) and 5 carnivorous rootless species (Aldrovanda vesiculosa, Utricularia vulgaris, U. australis, U. stygia, U. bremii) were studied. RD values of dormant turions per unit fresh weight (range 1.1- 5.4 mmol kg-1 FW h-1) were significantly lower (1.9 -13 times) for all species, except A. vesiculosa, than those for old segments of sprouting turions (range 5.2 -14 mmol kg-1 FW h-1). However, RD and PN values of old and newly formed turion segments in U. australis and U. stygia were similar. PN values of dormant turions under optimum conditions were either very low or negative, while PN values of old segments of sprouting turions of all species except H. morsus-ranae were very high (18 - 94 mmol kg-1 FW h-1). In a N- and P-free solution, turions of all species except A. vesiculosa formed distinct new organs after 6 - 20 days. In conclusion, the intensity of metabolism (both RD and PN) in sprouting turions reaches the level of adult shoots or leaves of the same species. Turions of aquatic plants also function as important storage organs for mineral nutrients (N, P, S and Mg) to ensure the growth of new organs. © 2011 E. Schweizerbart'sche Verlagsbuchhandlung, Stuttgart, Germany.


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.


Feld C.K.,University of Duisburg - Essen | de Bello F.,Academy of Sciences of the Czech Republic | de Bello F.,University of South Bohemia | Doledec S.,CNRS Ecology of Natural and Anthropized Hydrosystems Laboratory
Freshwater Biology | Year: 2014

Lotic ecosystems worldwide are being increasingly modified hydromorphologically, for example, by damming, fragmentation, flow regulation and channel modification. Serious threats to riverine biodiversity are suspected, yet available field data are few and rarely address the various taxonomic, functional and phylogenetic components of biodiversity. We examined benthic macroinvertebrate diversity along a gradient of hydromorphological alteration across 65 lowland river sites in the Netherlands, Germany and Poland. We calculated eight metrics describing taxonomic diversity (richness, rarefied richness, Shannon's and Simpson's diversity, Pielou's evenness), functional diversity (mean trait diversity) and phylogenetic diversity (mean taxonomic distinctness and its variance). Threshold Indicator Taxa ANalysis (TITAN) and Non-metric Multidimensional Scaling (NMS) showed detailed changes in taxonomic and trait composition, respectively, with increasing hydromorphological alteration. TITAN revealed a gradual turnover under increasing impact in which taxon losses were almost balanced by gains. NMS illustrated a high degree of concordance in the traits possessed by the taxa lost and gained at the gradient's end points. Although a biologically meaningful hydromorphological gradient was evident, the biodiversity response was modest (Spearman's ρ < |0.32| for all metrics). Pielou's evenness and mean taxonomic distinctness actually increased at impaired sites. Our results suggest that taxonomic and trait replacement with hydromorphological alteration is not followed by changes in whole-community diversity. This implies some redundancy in these systems, with ecologically similar species replacing those lost through environmental change. The results highlight how whole-community-based diversity, although frequently calculated and interpreted for decades in ecology and conservation biology, is not the all-purpose concept to detect and assess the various facets of biodiversity loss. Therefore, we suggest that concerted effort is needed to develop and test novel indicators of biodiversity, capable of detecting biodiversity loss, or other changes, in response to the main environmental stressors of lotic ecosystems. © 2013 John Wiley & Sons Ltd.


Krasowska A.,Wroclaw University | Sigler K.,Academy of Sciences of the Czech Republic
Frontiers in Cellular and Infection Microbiology | Year: 2014

Cell surface hydrophobicity (CSH) plays a crucial role in the attachment to, or detachment from the surfaces. The influence of CSH on adhesion of microorganisms to biotic and abiotic surfaces in medicine as well as in bioremediation and fermentation industry has both negative and positive aspects. Hydrophobic microorganisms cause the damage of surfaces by biofilm formation; on the other hand, they can readily accumulate on organic pollutants and decompose them. Hydrophilic microorganisms also play a considerable role in removing organic wastes from the environment because of their high resistance to hydrophobic chemicals. Despite the many studies on the environmental and metabolic factors affecting CSH, the knowledge of this subject is still scanty and is in most cases limited to observing the impact of hydrophobicity on adhesion, aggregation or flocculation. The future of research seems to lie in finding a way to managing the microbial adhesion process, perhaps by steering cell hydrophobicity. © 2014 Krasowska and Sigler.


Mares P.,Academy of Sciences of the Czech Republic
Epilepsy Research | Year: 2012

GABA B receptors mediate inhibition at early stages of development but mixed anti-and proconvulsant action of their agonists affecting all receptors was found in immature rats. Positive allosteric modulators of GABA B receptors potentiate only already active GABA B receptors and therefore more specific action is expected. Possible anticonvulsant action of CGP7930 was studied in a model of pentetrazol-induced seizures previously used for studies with agonists baclofen and SKF97541.Pentetrazol (100. mg/kg) was administered subcutaneously in male rats 7, 12, 18, 25 and 90 days old pretreated with CGP7930 in doses 1-40. mg/kg i.p. High doses of CGP7930 suppressed generalized tonic-clonic seizures in all five age groups. Animals 18 and less days old exhibited a specific suppression of the tonic phase after lower doses of CGP7930. Twelve-day-old rats were the most sensitive to anticonvulsant effect of CGP7930 (even the 2-mg/kg dose suppressed the tonic phase whereas 20-mg/kg dose was active in other age groups). Minimal clonic seizures (mS) were moderately potentiated by low doses of CGP7930 in 18-day-old but suppressed by the highest dose in 25-day-old rats. The 60-mg/kg dose of PTZ induced only mS in 4 out of 9 25-day-old rats; the 40-mg/kg dose of CGP7930 combined with this lower dose of PTZ resulted in the only proconvulsant effect - generalized tonic-clonic seizures appeared in two rats. Results from 12-day-old rats suggest a possibility to find an age-specific anticonvulsant among positive allosteric modulators of GABA B receptors. © 2012 Elsevier B.V.


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).


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.


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.


Kroupa A.,Academy of Sciences of the Czech Republic
Computational Materials Science | Year: 2013

The Calphad method is very important method for the modelling of thermodynamic properties and phase diagrams of multicomponent systems. The method is based on a semi-empirical approach and sequential modelling from simpler to more complicated systems. Therefore reliable experimental data are necessary for the description of the thermodynamic and phase properties of unary and binary systems. Basic principles of the method will be described in this paper, especially from the point of view of preparing the reliable theoretical thermodynamic description of simpler systems, which allow reliable prediction and assessment of higher order systems. The thermodynamic data, describing assessed binary and ternary systems are collected in the form of the thermodynamic databases, which allow (together with proper software) the prediction of properties for multicomponent systems corresponding to real materials. The software packages, based on Calphad method, are currently the only theoretical tools, applicable for complex materials as steels, superalloys, etc. The thermodynamic databases and outputs of the theoretical calculations are also important for many other applications and multi-scale simulations. They serve as input for phase field simulations, diffusion processes modelling, phase transformations, material properties and structure morphology development, including the processes on interface. © 2012 Elsevier B.V. All rights reserved.


Cajthaml T.,Academy of Sciences of the Czech Republic
Environmental Microbiology | Year: 2014

Without any doubt, endocrine-disrupting compounds (EDCs) represent an environmental risk for wildlife and human beings. Endocrine-disrupting effects were found for many chemicals in products for personal use, industrial compounds and even in classical persistent organic pollutants (POPs). In order to understand the fate of EDCs in the environment, it is highly important to identify and to clarify the biodegradation mechanisms that can lead to their decomposition. Ligninolytic fungi (LF) are interesting microorganisms that are capable of participating in a variety of versatile decomposition mechanisms. The microorganisms represent a useful model group and, moreover, LF or their enzymes can be actively used for decontamination. Potential optimization of the decontamination process provides another important reason why it is necessary for understanding the mechanisms of EDC transformation. This minireview summarizes current knowledge about the LF biodegradation mechanisms of the most important micropollutants (xenoestrogens), including nonylphenols, bisphenol A and 17α-ethinylestradiol and polychlorinated biphenyls as POPs with endocrine-disrupting potency. Generally, LF exhibit the ability to either polymerize the target pollutants or to substantially decompose the original structure using ligninolytic enzymes and cytochrome P-450. Moreover, most of the transformation processes are accompanied by reduction of the endocrine-disrupting activity or ecotoxicity. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.


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.


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.


Halacka K.,Academy of Sciences of the Czech Republic
Open Life Sciences | Year: 2015

Gill characteristics and the size and number of erythrocytes were observed for three species of goby: Neogobius melanostomus, N. fluviatilis and N. kessleri. While erythrocyte size was similar in all species, N. fluviatilis had a statistically higher erythrocyte count. Significant differences were found in gill apparatus structure, with N. melanostomus having 25% and 50% greater gill contact area than N. kessleri and N. fluviatilis, respectively. Secretory goblet cells, which produce a protective mucous, were also present in highest numbers in N. melanostomus gill tissues. These physiological and morphological differences may be one reason for differences observed in the invasiveness of these three species. © 2015 Karel Halačka 2015.


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.


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


Krejci A.,University of South Bohemia | Krejci A.,Academy of Sciences of the Czech Republic
Biochemical Society Transactions | Year: 2012

There is an intimate, yet poorly understood, link between cellular metabolic status, cell signalling and transcription. Central metabolic pathways are under the control of signalling pathways and, vice versa, the cellular metabolic profile influences cell signalling through the incorporation of various metabolic sensors into the signalling networks. Thus information about nutrients availability directly and crucially influences crucial cell decisions. In the present review, I summarize our current knowledge of various metabolic sensors and give some examples of the integration of metabolically derived inputs into the signalling system and the regulation of transcription. I also discuss the Warburg effect where the crosstalk between metabolism and signalling is used to orchestrate rapid cell growth and division. It is becoming clear that future research will concentrate on the collection of small-molecule metabolites, whose concentration fluctuates in response to cellular energy levels, searching for their sensors that connect them to the signalling and transcriptional networks. © The Authors Journal compilation © 2012 Biochemical Society.


Adamec L.,Academy of Sciences of the Czech Republic
Plant signaling & behavior | Year: 2011

Aquatic Utricularia species usually grow in standing, nutrient-poor humic waters. They take up all necessary nutrients either directly from the water by rootless shoots or from animal prey by traps. The traps are hollow bladders, 1-6 mm long with elastic walls and have a mobile trap door. The inner part of the trap is densely lined with quadrifid and bifid glands and these are involved in the secretion of digestive enzymes, resorption of nutrients and pumping out the water. The traps capture small aquatic animals but they also host a community of microorganisms considered as commensals. How do these perfect traps function, kill and digest their prey? How do they provide ATP energy for their demanding physiological functions? What are the nature of the interactions between the traps and the mutualistic microorganisms living inside as commensals? In this mini review, all of these questions are considered from an ecophysiologist's point of view, based on the most recent literature data and unpublished results. A new concept on the role of the commensal community for the plants is presented.


Palus M.,Academy of Sciences of the Czech Republic
Entropy | Year: 2014

An information-theoretic approach for detecting interactions and information transfer between two systems is extended to interactions between dynamical phenomena evolving on different time scales of a complex, multiscale process. The approach is demonstrated in the detection of an information transfer from larger to smaller time scales in a model multifractal process and applied in a study of cross-scale interactions in atmospheric dynamics. Applying a form of the conditional mutual information and a statistical test based on the Fourier transform and multifractal surrogate data to about a century long records of daily mean surface air temperature from various European locations, an information transfer from larger to smaller time scales has been observed as the influence of the phase of slow oscillatory phenomena with the periods around 6-11 years on the amplitudes of the variability characterized by the smaller temporal scales from a few months to 4-5 years. These directed cross-scale interactions have a non-negligible effect on interannual air temperature variability in a large area of Europe. © 2014 by the author.


This study represents the first formal combined (morphological and molecular) phylogenetic analysis of the highly diversified subfamily Baetinae (sensu Kazlauskas 1972). Taxonomic sampling comprised the majority of different Palaearctic lineages within the subfamily recognised so far. The data set of 47 coded morphological characters was analysed together with the partial mitochondrial DNA cytochrome oxidase c subunit I gene (COI) sequences using parsimony and Bayesian inference. From the eight genera and species-groups investigated, three were supported as monophyletic in the analyses. The monophyly of another three genera/species-groups could not be tested because only a single species was included in the sampling. The remaining two subgenera/species-groups were recovered as paraphyletic at least using one methodological approach. A monophyletic group comprising the genera Labiobaetis + Nigrobaetis + Alainites was supported as a sister lineage to the genus Baetis s.str. Morphological characters were mapped on a cladogram, clade robustness was tested by multiple approaches and alternative views to the taxonomy of the subfamily were discussed. Intraspecific and interspecific divergences in the COI sequence were estimated for the species studied. The existence of a distinct 'barcoding gap' was not supported. Baetis rhodani and Alainites muticus exhibited unusually high values of intraspecific variability pointing to the possible existence of cryptic species. © 2012 Copyright Taylor and Francis Group, LLC.


Valasek L.S.,Academy of Sciences of the Czech Republic
Current Protein and Peptide Science | Year: 2012

Protein synthesis is a fundamental biological mechanism bringing the DNA-encoded genetic information into life by its translation into molecular effectors - proteins. The initiation phase of translation is one of the key points of gene regulation in eukaryotes, playing a role in processes from neuronal function to development. Indeed, the importance of the study of protein synthesis is increasing with the growing list of genetic diseases caused by mutations that affect mRNA translation. To grasp how this regulation is achieved or altered in the latter case, we must first understand the molecular details of all underlying processes of the translational cycle with the main focus put on its initiation. In this review I discuss recent advances in our comprehension of the molecular basis of particular initiation reactions set into the context of how and where individual eIFs bind to the small ribosomal subunit in the pre-initiation complex. I also summarize our current knowledge on how eukaryotic initiation factor eIF3 controls gene expression in the gene-specific manner via reinitiation. © 2012 Bentham Science Publishers.


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.


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.


Petrzik K.,Academy of Sciences of the Czech Republic
Journal of Phytopathology | Year: 2012

Conserved block III of the RNA polymerase L gene is predicted to be essential for RNA polymerase function of cytorhabdoviruses and may be a target in exploring evolutionary relationships among rhabdoviruses. Sequence comparison of an amplified segment of the polymerase gene isolated from six English ivy samples revealed its high similarity with known plant cytorhabdoviruses. Lettuce yellow mottle virus was recognized as a closely related virus with 79.6% aa identity in the amplified region of the CB2 isolate and around 70% aa identity for the CB1, CB6 and CB18 isolates. The CB11 and CB16 isolates show a closer relationship to Raspberry vein chlorosis virus, with 75 and 69% aa identity, respectively. These data in combination with phylogenetic analyses resulted in discrimination of four new rhabdoviruses. The names Ivy latent viruses 1, 2, 3 and 4 (IvLV1, IvLV2, IvLV3 and IvLV4) are proposed for these viruses. © 2012 Blackwell Verlag GmbH.


A new species of gobioid fish Pirskenius Obrhelová, 1961 (P. radoni sp. nov.) is described from Oligocene strata of the České Středohoří Mountains and compared with related species. The new species is characterized by a unique combination of characters that allow it to be separated from P. diatomaceus Obrhelová, 1961. The taxonomic position of the genus Pirskenius is discussed, and its affinity to the family Eleotridae is indicated. The new record documents, together with P. diatomaceus, the oldest known skeletal record of the Eleotridae. © 2013 Springer-Verlag Berlin Heidelberg.


Krizek M.,Academy of Sciences of the Czech Republic
New Astronomy | Year: 2012

The Hubble constant is split into two terms H = H1 + H 2, where H1 is a decreasing function due to the Big Bang and the subsequent gravitational interaction that slows the expansion of the Universe and H2 is an increasing function that corresponds to dark energy which accelerates this expansion. For T = 13.7 Gyr we prove that H 2(T) > 5 m/(yr AU). This is a quite large number and thus the impact of dark energy, which is spread almost everywhere uniformly, should be observable not only on large scales, but also in our Solar system. In particular, we show that Earth, Mars and other planets were closer to the Sun 4.5 Gyr ago. The recession speed ≈5.3 m/yr of the Earth from the Sun seems to be just right for an almost constant influx of solar energy from the origin of life on Earth up to the present over which time the Sun's luminosity has increased approximately linearly. This presents further support for the Anthropic Principle. Namely, the existence of dark energy guarantees very stable conditions for the development of intelligent life on Earth over a period of 3.5 Gyr. © 2011 Elsevier B.V. All rights reserved.


Fiala Z.,Academy of Sciences of the Czech Republic
Acta Mechanica | Year: 2015

While the position and shape of a deformed body take place in the usual three-dimensional Euclidean space (Formula presented.) , a corresponding progress of the deformation tensor makes up a trajectory in the space of all symmetric positive-definite matrices (Formula presented.) —a negatively curved Riemannian symmetric manifold. In this context, we prove that a well-known relation (Formula presented.) between deformation rate (Formula presented.) and symmetric velocity gradient (Formula presented.) , via deformation gradient (Formula presented.) , can be actually interpreted as an equation of Lie-type describing evolution of the right Cauchy–Green deformation tensor (Formula presented.) on the configuration space (Formula presented.). As a consequence, this interpretation leads to geometrically consistent time-discrete integration schemes for finite deformation processes, such as the Runge–Kutta–Munthe-Kaas method. The need to solve such an equation arises from an incremental numerical modelling of deformations of nonlinear materials. In parallel, the exposition is accompanied by an analysis of evolution of the deformation gradient (Formula presented.) on the general linear group of all non-singular matrices (Formula presented.). © 2014, Springer-Verlag Wien.


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.


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.


Falandysz J.,University of Gdansk | Borovicka J.,Nuclear Physics Institute of Czech Republic | Borovicka J.,Academy of Sciences of the Czech Republic
Applied Microbiology and Biotechnology | Year: 2013

This article reviews and updates data on macro and trace elements and radionuclides in edible wild-grown and cultivated mushrooms. A huge biodiversity of mushrooms and spread of certain species over different continents makes the study on their multi-element constituents highly challenging. A few edible mushrooms are widely cultivated and efforts are on to employ them (largely Agaricus spp., Pleurotus spp., and Lentinula edodes) in the production of selenium-enriched food (mushrooms) or nutraceuticals (by using mycelia) and less on species used by traditional medicine, e.g., Ganoderma lucidum. There are also attempts to enrich mushrooms with other elements than Se and a good example is enrichment with lithium. Since minerals of nutritional value are common constituents of mushrooms collected from natural habitats, the problem is however their co-occurrence with some hazardous elements including Cd, Pb, Hg, Ag, As, and radionuclides. Discussed is also the problem of erroneous data on mineral compounds determined in mushrooms. © 2012 The Author(s).


Tabatadze N.,Northwestern University | Smejkalova T.,Northwestern University | Smejkalova T.,Academy of Sciences of the Czech Republic | Woolley C.S.,Northwestern University
Endocrinology | Year: 2013

Acute 17β-estradiol (E2) signaling in the brain is mediated by extranuclear estrogen receptors. Here we used biochemical methods to investigate the distribution, posttranslational modification, and E2 regulation of estrogen receptor-α (ERα) in synaptosomal fractions isolated by differential centrifugation from the adult female rat hippocampus. We find that ERα is concentrated presynaptically and is highly enriched with synaptic vesicles. Immunoisolation of vesicles using vesicle subtype-specific markers showed that ERα is associated with both glutamate and γ-aminobutyric acid-containing neurotransmitter vesicles as well as with some large dense core vesicles. Experiments using broad spectrum and residue-specific phosphatases indicated that a portion of ERα in synaptosomal fractions is phosphorylated at serine/threonine residues leading to a mobility shift in SDS-PAGE and creating a double band on Western blots. The phosphorylated form of ERα runs in the upper of the two bands and is particularly concentrated with synaptic vesicles. Finally, we used E2 with or without the acyl protein thioesterase 1 inhibitor, Palmostatin B, to show that 20 min of E2 treatment of hippocampal slices depletes ERα from the synaptosomal membrane by depalmitoylation. We found no evidence that E2 regulates phosphorylation of synaptosomal ERα on this time scale. These studies begin to fill the gap between detailed molecular characterization of extranuclear ERα in previous in vitro studies and acute E2 modulation of hippocampal synapses in the adult brain. Copyright © 2013 by The Endocrine Society.


Vavrycuk V.,Academy of Sciences of the Czech Republic
Geophysical Journal International | Year: 2014

Stress inversions from focal mechanisms require knowledge of which nodal plane is the fault. If such information is missing, and faults and auxiliary nodal planes are interchanged, the stress inversions can produce inaccurate results. It is shown that the linear inversion method developed by Michael is reasonably accurate when retrieving the principal stress directions even when the selection of fault planes in focal mechanisms is incorrect. However, the shape ratio is more sensitive to the proper choice of the fault and substituting the faults by auxiliary nodal planes introduces significant errors. This difficulty is removed by modifying Michael's method and inverting jointly for stress and for fault orientations. The fault orientations are determined by applying the fault instability constraint and the stress is calculated in iterations. As a by-product, overall friction on faults is determined. Numerical tests show that the new iterative stress inversion is fast and accurate and performs much better than the standard linear inversion. The method is exemplified on real data from central Crete and from the West- Bohemia swarm area of the Czech Republic. The joint iterative inversion identified correctly 36 of 38 faults in the central Crete data. In the West Bohemia data, the faults identified by the inversion were close to the principal fault planes delineated by foci clustering. The overall friction on faults was estimated to be 0.75 and 0.85 for the central Crete and West Bohemia data, respectively. © The Authors 2014. Published by Oxford University Press on behalf of The Royal Astronomical Society.


Heyrovsky M.,Academy of Sciences of the Czech Republic
Journal of Solid State Electrochemistry | Year: 2011

Polarography was first developed as an automated method of voltage-controlled electrolysis with dropping mercury electrode. The spontaneously renewed pure electrode surface provided reproducible electrochemical results which enabled scientists to work out adequate theory and rich analytical applications. The original method was then instrumentally modified in various ways. Later, hanging mercury drop was added as an alternative indicator electrode-in this way, polarography turned formally into voltammetry with mercury drop electrodes. Beside, in potential-controlled electrolysis, the mercury drop electrodes have been also used in current-controlled electrolysis (chronopotentiometry)-there, it has provided new experimental effects. Polarography has thus gradually covered a wide field of electrolytic methods based on the use of mercury electrodes, in which it continues developing. © 2011 Springer-Verlag.


Kalina J.,Academy of Sciences of the Czech Republic
Journal of Forensic Sciences | Year: 2012

Image analysis methods commonly used in forensic anthropology do not have desirable robustness properties, which can be ensured by robust statistical methods. In this paper, the face localization in images is carried out by detecting symmetric areas in the images. Symmetry is measured between two neighboring rectangular areas in the images using a new robust correlation coefficient, which down-weights regions in the face violating the symmetry. Raw images of faces without usual preliminary transformations are considered. The robust correlation coefficient based on the least weighted squares regression yields very promising results also in the localization of such faces, which are not entirely symmetric. Standard methods of statistical machine learning are applied for comparison. The robust correlation analysis can be applicable to other problems of forensic anthropology. © 2011 American Academy of Forensic Sciences.


Stibr B.,Academy of Sciences of the Czech Republic
Journal of Organometallic Chemistry | Year: 2015

The chemistry of the nido-5,6-C2B8H12 dicarbaborane, the most significant compound of the 10-vertex dicarbaborane series, has been discussed in this review within the contexts of reactivity and reaction mechanism. Chemical transformations of this carborane led to the isolation of the whole series of other compounds that now start playing ever increasing role in developing new carborane chemistry. Overviewed are procedures leading to closo and open-structured (nido and arachno) dicarbaboranes together with principles of their substitution on cluster-carbon and boron vertexes. © 2015 Elsevier B.V.


Malek T.,Academy of Sciences of the Czech Republic
Classical and Quantum Gravity | Year: 2014

We study extended Kerr-Schild (xKS) spacetimes, i.e. extensions of the Kerr-Schild (KS) ansatz where, in addition to the null KS vector, a spacelike vector field appears in the metric. In contrast to the KS case, we obtain only a necessary condition under which the KS vector is geodetic. However, it is shown that this condition becomes sufficient if we appropriately restrict the geometry of the null KS and spacelike vector. It turns out that xKS spacetimes with a geodetic KS vector are of Weyl type I and the KS vector has the same optical properties in the full and background spacetimes. In the case of Kundt xKS spacetimes, the compatible Weyl types are further restricted and a few examples of such metrics are provided. The relation of pp-waves to the class of Kundt xKS spacetimes is briefly discussed. We also show that the CCLP black hole, as an example of an expanding xKS spacetime, is of Weyl type Ii, which specializes to type D in the uncharged or non-rotating limit, and that its optical matrix satisfies the optical constraint. © 2014 IOP Publishing Ltd.


Groger R.,Academy of Sciences of the Czech Republic
Philosophical Magazine | Year: 2014

By direct application of stress in molecular statics calculations we identify the stress components that affect the glide of 1/2111 screw dislocations in bcc tungsten. These results prove that the hydrostatic stress and the normal stress parallel to the dislocation line do not play any role in the dislocation glide. Therefore, the Peierls stress of the dislocation cannot depend directly on the remaining two normal stresses that are perpendicular to the dislocation but, instead, on their combination that causes an equibiaxial tension-compression (and thus shear) in the plane perpendicular to the dislocation line. The Peierls stress of 1/2111 screw dislocations then depends only on the orientation of the plane in which the shear stress parallel to the Burgers vector is applied and on the magnitude and orientation of the shear stress perpendicular to the slip direction. © 2014 Taylor & Francis.


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.


Kirchhoff H.,Washington State University | Sharpe R.M.,Washington State University | Herbstova M.,Washington State University | Herbstova M.,Academy of Sciences of the Czech Republic | And 2 more authors.
Plant Physiology | Year: 2013

The photosynthetic performance of plants is crucially dependent on the mobility of the molecular complexes that catalyze the conversion of sunlight to metabolic energy equivalents in the thylakoid membrane network inside chloroplasts. The role of the extensive folding of thylakoid membranes leading to structural differentiation into stacked grana regions and unstacked stroma lamellae for diffusion-based processes of the photosynthetic machinery is poorly understood. This study examines, to our knowledge for the first time, the mobility of photosynthetic pigment-protein complexes in unstacked thylakoid regions in the C3 plant Arabidopsis (Arabidopsis thaliana) and agranal bundle sheath chloroplasts of the C4 plants sorghum (Sorghum bicolor) and maize (Zea mays) by the fluorescence recovery after photobleaching technique. In unstacked thylakoid membranes, more than 50% of the protein complexes are mobile, whereas this number drops to about 20% in stacked grana regions. The higher molecular mobility in unstacked thylakoid regions is explained by a lower protein-packing density compared with stacked grana regions. It is postulated that thylakoid membrane stacking to form grana leads to protein crowding that impedes lateral diffusion processes but is required for efficient light harvesting of the modularly organized photosystem II and its lightharvesting antenna system. In contrast, the arrangement of the photosystem I light-harvesting complex I in separate units in unstacked thylakoid membranes does not require dense protein packing, which is advantageous for protein diffusion. © 2012 American Society of Plant Biologists. All Rights Reserved.


Stibr B.,Academy of Sciences of the Czech Republic
Journal of Organometallic Chemistry | Year: 2013

New approaches to the synthesis of carboranes and heterocarboranes based on addition reactions of highly nucleophilic boron-cluster anions are briefly overviewed together with some mechanistic aspects. The anions, in which the negative charge is accumulated on the open face of the cage, become capable of coordinating to the most electrophilic center of the reacting substrate and are activated for addition reactions to multiply bonded substrates. Additions to cyanides, nitriles, isocyanides, aldehydes, and acyl chlorides lead usually to the insertion of one more carbon vertex into the boron framework, though the products may be in some cases unusual or unexpected. The methods based on nucleophilic addition have become an effective synthetic tool in the area of general carborane chemistry, though this specific field of cluster chemistry has still been far from being fully explored. One of the aims of this overview is to encourage a younger generation of chemists to return to building-up new borane clusters. © 2013 Elsevier B.V. All rights reserved.


Cupera J.,Academy of Sciences of the Czech Republic
Mathematical Biosciences and Engineering | Year: 2014

Leaky integrate-and-Fire neuronal models with reversal potentials have a number of difierent difiusion approximations, each depending on the form of the amplitudes of the postsynaptic potentials. Probability distributions of the First-passage times of the membrane potential in the original model and its difiusion approximations are numerically compared in order to Find which of the approximations is the most suitable one. The properties of the random amplitudes of postsynaptic potentials are discussed. It is shown on a simple example that the quality of the approximation depends directly on them.


Ellison A.M.,Harvard University | Adamec L.,Academy of Sciences of the Czech Republic
Oikos | Year: 2011

Identification of tradeoffs among physiological and morphological traits and their use in cost-benefit models and ecological or evolutionary optimization arguments have been hallmarks of ecological analysis for at least 50 years. Carnivorous plants are model systems for studying a wide range of ecophysiological and ecological processes and the application of a cost-benefit model for the evolution of carnivory by plants has provided many novel insights into trait-based cost-benefit models. Central to the cost-benefit model for the evolution of botanical carnivory is the relationship between nutrients and photosynthesis; of primary interest is how carnivorous plants efficiently obtain scarce nutrients that are supplied primarily in organic form as prey, digest and mineralize them so that they can be readily used, and allocate them to immediate versus future needs. Most carnivorous plants are terrestrial - they are rooted in sandy or peaty wetland soils - and most studies of cost-benefit tradeoffs in carnivorous plants are based on terrestrial carnivorous plants. However approximately 10% of carnivorous plants are unrooted aquatic plants. Here we ask whether the cost-benefit model applies equally well to aquatic carnivorous plants and what general insights into tradeoff models are gained by this comparison. Nutrient limitation is more pronounced in terrestrial carnivorous plants, which also have much lower growth rates and much higher ratios of dark respiration to photosynthetic rates than aquatic carnivorous plants. Phylogenetic constraints on ecophysiological tradeoffs among carnivorous plants remain unexplored. Despite differences in detail, the general cost-benefit framework continues to be of great utility in understanding the evolutionary ecology of carnivorous plants. We provide a research agenda that if implemented would further our understanding of ecophysiological tradeoffs in carnivorous plants and also would provide broader insights into similarities and differences between aquatic and terrestrial plants of all types. © 2011 The Authors.


Sysala S.,Academy of Sciences of the Czech Republic
Mathematics and Computers in Simulation | Year: 2012

Some elasto-plasticity models with hardening are discussed and some incremental finite element methods with different time discretisation schemes are considered. The corresponding one-time-step problems lead to variational equations with various non-linear operators. Common properties of the non-linear operators are derived and consequently a general problem is formulated. The problem can be solved by Newton-like methods. First, the semismooth Newton method is analysed. The local superlinear convergence is proved in dependence on the finite element discretisation parameter. Then it is introduced a modified semismooth Newton method which contain suitable "damping" in each Newton iteration in addition. The determination of the damping coefficients uses the fact that the investigated problem can be formulated as a minimisation one. The method is globally convergent, independently on the discretisation parameter. Moreover the local superlinear convergence also holds. The influence of inexact inner solvers is also discussed. The method is illustrated on a numerical example. © 2012 IMACS. Published by Elsevier B.V. All rights reserved.


Chvalovsky K.,Academy of Sciences of the Czech Republic | Chvalovsky K.,Charles University
Fuzzy Sets and Systems | Year: 2012

We prove that the axiom expressing that the multiplicative conjunction of two formulae implies the first one of them is redundant in the standard Hilbert-style calculi of Hájeks basic logic BL and Esteva and Godos monoidal t-norm based logic MTL. This proof does not use the axiom expressing that multiplicative conjunction is commutative, which is already known to be redundant. Therefore both of these axioms are simultaneously redundant. We also show that all the other axioms are independent of each other. © 2011 Elsevier B.V.


Vejchodsky T.,Academy of Sciences of the Czech Republic
Mathematics and Computers in Simulation | Year: 2012

The paper is devoted to complementary approaches in a posteriori error estimation for a diffusion-reaction model problem. These approaches provide sharp and guaranteed upper bounds for the energy norm of the error and they are independent from the way how the approximate solution is obtained. In particular, the estimator naturally includes all sources of errors of any conforming approximation, like the discretization error, the error in the solver of linear algebraic systems, the quadrature error, etc. The paper recapitulates three complementarity approaches, proves sufficient and necessary conditions for the efficiency and asymptotic exactness of the error estimators, constructs an approximation by the method of hypercircle such that its error can be computed exactly, and presents numerical tests showing robustness of these approaches. © 2011 IMACS. Published by Elsevier B.V. All rights reserved.


Tokarev M.V.,Laboratory of High Energy Physics | Zborovsky I.,Academy of Sciences of the Czech Republic
Physics of Atomic Nuclei | Year: 2012

Experimental data on inclusive spectra measured in heavy-ion collisions at RHIC and SPS over a wide range of the energy √ GeV are analyzed in the framework of z scaling. A microscopic scenario of constituent interactions in the framework of this approach is discussed. Dependence of the energy loss on the momentum of the produced hadron, energy, and centrality of the collision, is studied. Self-similarity of the constituent interactions in terms of momentum fractions is used to characterize the nuclear medium by "specific heat" and colliding nuclei by fractal dimensions. Preferable kinematical regions for search for signatures of the phase transition of the nuclearmatter produced inHIC are discussed. Discontinuity of "specific heat" is assumed to be a signature of the phase transition and the Critical Point. © 2012 Pleiades Publishing, Ltd.


Krivan V.,Academy of Sciences of the Czech Republic | Krivan V.,National Institute for Mathematical and Biological Synthesis
Journal of Theoretical Biology | Year: 2011

This article re-analyses a prey-predator model with a refuge introduced by one of the founders of population ecology Gause and his co-workers to explain discrepancies between their observations and predictions of the Lotka-Volterra prey-predator model. They replaced the linear functional response used by Lotka and Volterra by a saturating functional response with a discontinuity at a critical prey density. At concentrations below this critical density prey were effectively in a refuge while at a higher densities they were available to predators. Thus, their functional response was of the Holling type III. They analyzed this model and predicted existence of a limit cycle in predator-prey dynamics. In this article I show that their model is ill posed, because trajectories are not well defined. Using the Filippov method, I define and analyze solutions of the Gause model. I show that depending on parameter values, there are three possibilities: (1) trajectories converge to a limit cycle, as predicted by Gause, (2) trajectories converge to an equilibrium, or (3) the prey population escapes predator control and grows to infinity. © 2011 Elsevier Ltd.


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.


Revilla T.A.,Academy of Sciences of the Czech Republic
Journal of Theoretical Biology | Year: 2015

Many mutualisms involve inter-specific resource exchanges, making consumer-resource approaches ideal for studying their dynamics. Also in many cases these resources are short lived (e.g. flowers) compared with the population dynamics of their producers and consumers (e.g. plants and insects), which justifies a separation of time scales. As a result, we can derive the numerical response of one species with respect to the abundance of another. For resource consumers, the numerical responses can account for intra-specific competition for mutualistic resources (e.g. nectar), thus connecting competition theory and mutualism mechanistically. For species that depend on services (e.g. pollination, seed dispersal), the numerical responses display saturation of benefits, with service handling times related with rates of resource production (e.g. flower turnover time). In both scenarios, competition and saturation have the same underlying cause, which is that resource production occurs at a finite velocity per individual, but their consumption tracks the much faster rates of population growth characterizing mutualisms. The resulting models display all the basic features seen in many models of facultative and obligate mutualisms, and they can be generalized from species pairs to larger communities. © 2015 Elsevier Ltd.


Ralph S.J.,Griffith University | Rodriguez-Enriquez S.,National Institute of Cardiology | Neuzil J.,Griffith University | Neuzil J.,Academy of Sciences of the Czech Republic | Moreno-Sanchez R.,National Institute of Cardiology
Molecular Aspects of Medicine | Year: 2010

Mitochondria are emerging as idealized targets for anti-cancer drugs. One reason for this is that although these organelles are inherent to all cells, drugs are being developed that selectively target the mitochondria of malignant cells without adversely affecting those of normal cells. Such anti-cancer drugs destabilize cancer cell mitochondria and these compounds are referred to as mitocans, classified into several groups according to their mode of action and the location or nature of their specific drug targets. Many mitocans selectively interfere with the bioenergetic functions of cancer cell mitochondria, causing major disruptions often associated with ensuing overloads in ROS production leading to the induction of the intrinsic apoptotic pathway. This in-depth review describes the bases for the bioenergetic differences found between normal and cancer cell mitochondria, focussing on those essential changes occurring during malignancy that clinically may provide the most effective targets for mitocan development. A common theme emerging is that mitochondrially mediated ROS activation as a trigger for apoptosis offers a powerful basis for cancer therapy. Continued research in this area is likely to identify increasing numbers of novel agents that should prove highly effective against a variety of cancers with preferential toxicity towards malignant tissue, circumventing tumor resistance to the other more established therapeutic anti-cancer approaches. Crown Copyright © 2009.


Stastna M.,Academy of Sciences of the Czech Republic | Van Eyk J.E.,Cedars Sinai Medical Center
Proteomics | Year: 2015

The alteration in proteome composition induced by environmental changes and various pathologies is accompanied by the modifications of proteins by specific cotranslational and PTMs. The type and site stoichiometry of PTMs can affect protein functions, alter cell signaling, and can have acute and chronic effects. The particular interest is drawn to those amino acid residues that can undergo several different PTMs. We hypothesize that these selected amino acid residues are biologically rare and act within the cell as molecular switches. There are, at least, 12 various lysine modifications currently known, several of them have been shown to be competitive and they influence the ability of a particular lysine to be modified by a different PTM. In this review, we discuss the PTMs that occur on lysine, specifically neddylation and sumoylation, and the proteomic approaches that can be applied for the identification and quantification of these PTMs. Of interest are the emerging roles for these modifications in heart disease and what can be inferred from work in other cell types and organs. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Svoboda P.,Academy of Sciences of the Czech Republic
RNA Biology | Year: 2010

Small RNA molecules regulating gene expression received a status of omnipresent master regulators of eukaryotic lives with almost supernatural powers. Mammals hold at least three mechanisms employing small RNA molecules for regulating gene expression. One of these mechanisms, the microRNA (miRNA) pathway, currently involves over a thousand of genome-encoded different miRNAs that are claimed to extend their control over more than a half of a genome. Here, I discuss how and why mouse oocytes and early embryos ignore the regulatory power of miRNAs, adding another surprising feature to the field of small RNAs.


Stros M.,Academy of Sciences of the Czech Republic
Biochimica et Biophysica Acta - Gene Regulatory Mechanisms | Year: 2010

HMGB proteins are members of the High Mobility Group (HMG) superfamily, possessing a unique DNA-binding domain, the HMG-box, which can bind non-B-type DNA structures (bent, kinked and unwound) with high affinity, and also distort DNA by bending/looping and unwinding. HMGBs (there are four HMGBs in mammals, HMGB1-4) are highly abundant and ubiquitously expressed non-histone proteins, acting as DNA chaperones influencing multiple processes in chromatin such as transcription, replication, recombination, DNA repair and genomic stability. Although HMGB1 is a nuclear protein, it can be secreted into the extracellular milieu as a signaling molecule when cells are under stress, in particular, when necrosis occurs. Mammalian HMGBs contain two HMG-boxes arranged in tandem, share more than 80% identity and differ in the length (HMGB1-3) or absence (HMGB4) of the acidic C-tails. The acidic tails consist of consecutive runs of only Glu/Asp residues of various length, and modulate the DNA-binding properties and functioning of HMGBs. HMGBs are subject to post-translational modifications which can fine-tune interactions of the proteins with DNA/chromatin and determine their relocation from the nucleus to the cytoplasm and secretion. Association of HMGBs with chromatin is highly dynamic, and the proteins affect the chromatin fiber as architectural factors by transient interactions with nucleosomes, displacement of histone H1, and facilitation of nucleosome remodeling and accessibility of the nucleosomal DNA to transcription factors or other sequence-specific proteins. © 2009 Elsevier B.V. All rights reserved.


Reini M.,Academy of Sciences of the Czech Republic
Future Oncology | Year: 2010

MHC class I downregulation is a general mechanism by which tumor cells can escape from T-cell-mediated immunity. This downregulation also represents a serious obstacle to the development of effective antitumor immunotherapy or vaccination. Therefore, successful immunotherapeutic and vaccination protocols should be optimized against tumors with distinct cell surface expression of the MHC class I molecules. Mechanisms leading to protective immunity may vary in different models with respect to the particular tumors (e.g., in their levels of residual expression of the MHC class I molecules on tumor cells or inducibility of MHC class I expression). Notably, both CD8 + cell-mediated immunity and MHC class I-unrestricted mechanisms can take place against MHC class I-deficient tumors. Since MHC class I downregulation is frequently reversible by cytokines and also by the activation of epigenetically silenced genes, an attractive strategy is to elicit specific cell-mediated immunity combined with restoration of MHC class I expression on tumor cells. © 2010 Future Medicine Ltd.


Tomasetti M.,Marche Polytechnic University | Neuzil J.,Griffith University | Neuzil J.,Academy of Sciences of the Czech Republic | Dong L.,Griffith University
Biochimica et Biophysica Acta - General Subjects | Year: 2014

Background Mitochondria, essential to the cell homeostasis maintenance, are central to the intrinsic apoptotic pathway and their dysfunction is associated with multiple diseases. Recent research documents that microRNAs (miRNAs) regulate important signalling pathways in mitochondria, and many of these miRNAs are deregulated in various diseases including cancers. Scope of review In this review, we summarise the role of miRNAs in the regulation of the mitochondrial bioenergetics/function, and discuss the role of miRNAs modulating the various metabolic pathways resulting in tumour suppression and their possible therapeutic applications. Major conclusions MiRNAs have recently emerged as key regulators of metabolism and can affect mitochondria by modulating mitochondrial proteins coded by nuclear genes. They were also found in mitochondria. Reprogramming of the energy metabolism has been postulated as a major feature of cancer. Modulation of miRNAs levels may provide a new therapeutic approach for the treatment of mitochondria-related pathologies, including neoplastic diseases. General significance The elucidation of the role of miRNAs in the regulation of mitochondrial activity/bioenergetics will deepen our understanding of the molecular aspects of various aspects of cell biology associated with the genesis and progression of neoplastic diseases. Eventually, this knowledge may promote the development of innovative pharmacological interventions. This article is part of a Special Issue entitled Frontiers of Mitochondrial Research. © 2013 Elsevier B.V.


Stibr B.,Academy of Sciences of the Czech Republic
Journal of Organometallic Chemistry | Year: 2012

Iron is one of the most abundant elements on the Earth and its chemistry has been therefore rapidly developed. As a part of the chemistry these complexes, a short review on the synthesis of bis-(arene) iron complexes and reactions associated with direct and indirect replacement of arene ligands in these complexes is presented. These reactions lead to a broad variety of novel iron sandwich compounds that now play an important role in the development of specific areas of metaloorganic and metallacarborane chemistry of iron. The review comprises recent synthetic routes and approaches to iron sandwich complexes, of which the most significant have been arene and cyclohexadienyl ferradicarba- and ferratricarba-boranes, together with new types of piano-stool structured compounds. The reader will also find references to methods of structural characterization of individual compounds in this area of chemistry. © 2012 Elsevier B.V. All rights reserved.


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.


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.


Kurkova V.,Academy of Sciences of the Czech Republic
Neural Networks | Year: 2012

Integral transforms with kernels corresponding to computational units are exploited to derive estimates of network complexity. The estimates are obtained by combining tools from nonlinear approximation theory and functional analysis together with representations of functions in the form of infinite neural networks. The results are applied to perceptron networks. © 2012 Elsevier Ltd.


Bures Z.,Academy of Sciences of the Czech Republic
Biological Cybernetics | Year: 2012

In the nervous system, the representation of signals is basedpredominantly on the rate and timingof neuronal discharges. In most everyday tasks, the brain has to carry out a variety of mathematical operations on the discharge patterns. Recent findings show that even single neurons are capable of performing basic arithmetic on the sequences of spikes. However, the interaction of the two spike trains, and thus the resulting arithmetic operation may be influenced by the stochastic properties of the interacting spike trains. If we represent the individual discharges as events of a random point process, then an arithmetical operation is given by the interaction of two point processes. Employing a probabilistic model based on detection of coincidence of random events and complementary computer simulations, we show that the point process statistics control the arithmetical operation being performed and, particularly, that it is possible to switch from subtraction to division solely by changing the distribution of the inter-event intervals of the processes. Consequences of the model for evaluation of binaural information in the auditory brainstem are demonstrated. The results accentuate the importance of the stochastic properties of neuronal discharge patterns for information processing in the brain; further studies related to neuronal arithmetic should therefore consider the statistics of the interacting spike trains. © 2011 Springer-Verlag.


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.


Bukovsky A.,Academy of Sciences of the Czech Republic
Anatomical Record | Year: 2011

Stem cell niche consists of perivascular compartment, which connects the stem cells to the immune and vascular systems. During embryonic period, extragonadal primordial germ cells colonize coelomic epithelium of developing gonads. Subsequently, ovarian stem cells (OSC) produce secondary germ cells under the influence of OSC niche, including immune system-related cells and hormonal signaling. The OSC in fetal and adult human ovaries serve as a source of germ and granulosa cells. Lack of either granulosa or germ cell niche will result in premature ovarian failure in spite of the presence of OSC. During perinatal period, the OSC transdifferentiate into fibroblast-like cells forming the ovarian tunica albuginea resistant to environmental threats. They represent mesenchymal precursors of epithelial OSC during adulthood. The follicular renewal during the prime reproductive period (PRP) ensures that there are fresh eggs available for a healthy progeny. End of PRP is followed by exponentially growing fetal genetic abnormalities. The OSC are present in adult, aging, and postmenopausal ovaries, and differentiate in vitro into new oocytes. During in vitro development of large isolated oocytes reaching 200 μm in diameter, an ancestral mechanism of premeiotic nurse cells, which operates during oogenesis in developing ovaries from invertebrates to mammalian species, is utilized. In vitro developed eggs could be used for autologous IVF treatment of premature ovarian failure. Such eggs are also capable to produce parthenogenetic embryos like some cultured follicular oocytes. The parthenotes produce embryonic stem cells derived from inner cell mass, and these cells can serve as autologous pluripotent stem cells. © 2011 Wiley-Liss, Inc.


Pajtasz-Piasecka E.,Polish Academy of Sciences | Indrova M.,Academy of Sciences of the Czech Republic
Immunotherapy | Year: 2010

Dendritic cells (DCs) are believed to be the most potent antigen-presenting cells able to link the innate and adaptive immune systems. Many studies have focused on different immunotherapeutic approaches to applying DCs as tools to improve anticancer therapy. Although a number of investigations suggesting the benefit of DC-based vaccination during anticancer therapy have been reported, the general knowledge regarding the ultimate methods of DC-vaccine preparation is still unsatisfactory. In this article, the perspectives of DC-based anti-tumor immunotherapy and optimizing strategies of DC vaccination in humans in light of results obtained in mouse models are discussed. © 2010 Future Medicine Ltd.


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.


Honzatko P.,Academy of Sciences of the Czech Republic
Optics Communications | Year: 2010

I present new method of phase modulation to amplitude modulation conversion (PM/AM conversion) that utilizes integrating capabilities of fiber Bragg grating (FBG). I found that the wavelength converter based on fiber cross-phase modulation (XPM) and new method of PM/AM conversion have an order of magnitude higher conversion efficiency then the wavelength converter based on sideband filtration method and up to 6 dB higher conversion efficiency then the converter based on the nonlinear optical loop mirror. Numerical analysis and experimental results are provided for bit rates up to 40 Gb/s. © 2009 Elsevier B.V. All rights reserved.


Ostadalova I.,Center for Cardiovascular Research | Ostadalova I.,Academy of Sciences of the Czech Republic
Physiological Research | Year: 2012

Selenium is a trace element that is essential for living organism. Its beneficial effect is, however, expressed in a very narrow dosage range: The high and low doses of selenium are connected with pathological manifestations. The toxicity depends on the chemical form of selenium, state of organism, interactions with heavy metals and on the stage of ontogenetic development. Whereas one dose of sodium selenite (20 μmol/kg b.w.) is lethal in adult rats, suckling rats are entirely resistant. However, within one week after administration of the same dose, cataract of eye lens developed. The highest incidence of cataract was observed in 10-day-old animals and it decreased until day 20. From postnatal day 20 to day 40 the rats were resistant to both the lethal and cataractogenic effects of selenium. The incidence of cataract may be suppressed by premature weaning, lower hydration of suckling, change of water soluble/water insoluble lens protein ratio, thyroxine treatment, and by interaction with mercury. By means of its oxidative and reduction properties, selenium is involved in the maintenance of the cell redox homeostasis. Typical example is its possible cardioprotective effect: Selenium decreased number of arrhythmias, reduced infarct size and improved the contractile recovery after ischemia/reperfusion injury. Selenium supplementation may thus increase cardiac tolerance to ischemic damage. © 2012 Institute of Physiology.


Mares P.,Academy of Sciences of the Czech Republic
Physiological Research | Year: 2012

Models of basic types of epileptic seizures are elaborated not only in adult but also in immature rodents. It is important because at least half of human epilepsies starts during infancy and childhood. This paper presents a review of chemically and electrically induced models of generalized convulsive and nonconvulsive (absence) seizures as well as models of partial simple (neocortical) and complex (limbic) seizures in immature rats. These models can also serve as a tool for study the development of central nervous system and motor abilities because the level of maturation is reflected in seizure semiology. Age-dependent models of epileptic seizures (absences and flexion seizures) are discussed. Models of seizures in immature animals should be used for testing of potential antiepileptic drugs. © 2012 Institute of Physiology.


Matteini L.,University of Paris Descartes | Landi S.,University of Florence | Velli M.,Jet Propulsion Laboratory | Hellinger P.,Academy of Sciences of the Czech Republic
Journal of Geophysical Research: Space Physics | Year: 2010

Using numerical simulations in a hybrid regime, we studied the evolution of large-amplitude Alfvn waves subject to modulational and decay instabilities, including the effects of ion kinetics. We considered both a monochromatic and incoherent spectrum of waves, different wave polarizations and amplitudes, and different plasma regimes, ranging from β < 1 to β > 1. We found in all cases that ion dynamics affects the instability evolution and saturation; as a feedback, wave-particle interactions provide a nonlinear trapping of resonant particles that importantly change the properties of the ion velocity distribution functions. In particular, we observed a proton acceleration along the magnetic field and in some cases the formation of a parallel velocity beam traveling faster than the rest of the distribution. For the range of parameters used in our simulations, the fundamental ingredient in generating an ion beam is observed to be the parallel electric field carried by the density fluctuations driven by the ion-acoustic modes generated by the parametric instabilities. Copyright © 2010 by the American Geophysical Union.


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.


Reichard M.,Academy of Sciences of the Czech Republic | Polacik M.,University of St. Andrews
Biological Journal of the Linnean Society | Year: 2010

Allopatric populations separated by vicariance events are expected to evolve reproductive isolating mechanisms as a result of disparate selection pressures and genetic drift. The appearance of reproductive isolating mechanisms may vary across taxa with differences in the opportunity for mate choice, and may be asymmetrical. In addition, premating barriers may be affected by individual mating experience. We used choice and no-choice experiments to investigate reproductive isolation between two allopatric (island and mainland) and colour-differentiated populations of an African annual fish, Nothobranchius korthausae. Assortative mating under experimental conditions was limited and asymmetrical. Preference for sympatric males was only expressed in nonvirgin females from one population. Virgin fish from both populations mated indiscriminately. No difference in the number of eggs laid, fertilization rate and hatching success was detected in no-choice experiments. All mating combinations produced viable offspring and no postmating barriers were detected in terms of the performance and fertility of F1 hybrids. Overall, we found little evidence for significant reproductive isolation, which is in contrast with the related killifish taxa in which assortative mating can be strong, even among allopatric populations with no colour differentiation. © 2010 The Linnean Society of London.


Lastovicka J.,Academy of Sciences of the Czech Republic
Annales Geophysicae | Year: 2012

Origin of long-term trends in the thermosphere-ionosphere system has been discussed since the beginning of trend studies. The two most prioritized explanations have been those via long-term increase of atmospheric concentration of greenhouse gases and long-term increase of geomagnetic activity throughout the 20th century. Secular changes of the Earth's main magnetic field play an important role in trends in a limited region. Recently, Walsh and Oliver (2011) suggested that the long-term cooling of the upper thermosphere (above 200 km) may be due largely to the stratospheric ozone depletion. Here, we show that the role of ozone is very important in the mesosphere and lower thermosphere but not in the upper thermosphere. The suggestion of Walsh and Oliver (2011) is based on historical (before 1988) data from Saint-Santin radar, whereas more recent data do not support their conclusion. © Author(s) 2012.


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.


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..


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.


Hodek I.,Academy of Sciences of the Czech Republic
Psyche | Year: 2012

Recent studies dealing with adult (reproductive) diapause in the Coleoptera are reviewed, as a kind of supplement to the classic compendia. In the first two sections, the general characteristics of adult diapause are described and principal terms explained. Original articles dealing with 19 species from nine coleopteran families (Coccinellidae, Chrysomelidae, Bruchidae, Curculionidae, Carabidae, Silphidae, Scolytidae, Scarabaeidae, and Endomychidae) are reviewed. Finally attempts are made at generalisations from the papers reviewed, and hypotheses on diapause evolution are inferred. A polyphenic character of diapause is a prominent feature in C. septempunctata and L. decemlineata, but has been found also in other Coleoptera and in insects generally and often generates voltinism heterogeneity within populations. © 2012 Ivo Hodek.


Komarek J.,Academy of Sciences of the Czech Republic
Fottea | Year: 2012

The criteria for systematic classification of Cyanoprokaryota (Cyanobacteria, Cyanophyta) were changed considerably in last decades. The molecular and morphological analyses, ecological characterization and biochemical markers are indispensable premises for modern cyanobacterial taxonomic re-classification. Many genera were divided, newly described and numerous species were transferred in generic entities, characterized on the basis of molecular, ecological and revised morphological criteria. All of the proposed taxonomic changes are included in the manuscript of the recently prepared 3 rd volume of "Cyanoprokaryotes" in the frame of the new edited compendium Süsswasserflora von Mitteleuropa' (2 nd edition, volume 19/3, Heterocytous genera). The used taxonomic status of many taxa is already clearly revised in numerous modern publications, but in several cases the nomenclatural consequences were not yet validly published (new combinations, few new names of taxa). However, it is necessary to publish validly the corrected names before edition of any monographic review. The valid nomenclatural transfer of 9 species, one new name and description of two species, the changed position of which follows without doubts from the recent modern revisions, are therefore included in the present article. The validation is published in agreement with the last edition of Botanical Nomenclatoric Code (ICBN; McNeill et al., ed. 2007). All the mentioned species belong to the heterocytous monophyletic group Nostocales (or Nostochineae, respectively), and are arranged alphabetically. © Czech Phycological Society (2012).


Kaminek M.,Academy of Sciences of the Czech Republic
Journal of Plant Growth Regulation | Year: 2015

Existence of compound(s) inducing cell division in excised plant tissues was spotted more than 100 years ago. Since then research of cytokinins (CKs), plant hormones which in cooperation with other phytohormones, namely auxin, control cytokinesis, and a number of other physiological processes in plants, has advanced correspondingly to the progress in other fields of life sciences. This historical overview is focused on major topics of CK research including (1) discovery of CKs, (2) search for natural CKs, (3) role of CKs in transfer RNA, (4) biosynthesis (5) metabolism, (6) signaling of CKs, and (7) molecular probing of the physiological functions of CKs. Some parts of these subjects can already be assessed within the context of an appropriate time span necessary for critical evaluation. I have used this opportunity to present also some personal recollections, namely those of Prof Folke Skoog, in whose laboratory the first CK, kinetin, was discovered. © 2015, Springer Science+Business Media New York.


Karlicky M.,Academy of Sciences of the Czech Republic
Astronomy and Astrophysics | Year: 2014

Context. During solar flares several types of radio bursts are observed. The fine striped structures of the type IV solar radio bursts are called zebras. Analyzing them provides important information about the plasma parameters of their radio sources. We present a new analysis of zebras. Aims. Power spectra of the frequency variations of zebras are computed to estimate the spectra of the plasma density variations in radio zebra sources. Methods. Frequency variations of zebra lines and the high-frequency boundary of the whole radio burst were determined with and without the frequency fitting. The computed time dependencies of these variations were analyzed with the Fourier method. Results. First, we computed the variation spectrum of the high-frequency boundary of the whole radio burst, which is composed of several zebra patterns. This power spectrum has a power-law form with a power-law index-1.65. Then, we selected three well-defined zebra-lines in three different zebra patterns and computed the spectra of their frequency variations. The power-law indices in these cases are found to be in the interval between-1.61 and-1.75. Finally, assuming that the zebra-line frequency is generated on the upper-hybrid frequency and that the plasma frequency ωpe is much higher than the electron-cyclotron frequency ωce, the Fourier power spectra are interpreted to be those of the electron plasma density in zebra radio sources. © 2013 ESO.


Palus M.,Academy of Sciences of the Czech Republic
Physical Review Letters | Year: 2014

Interactions between dynamics on different temporal scales of about a century long record of data of the daily mean surface air temperature from various European locations have been detected using a form of the conditional mutual information, statistically tested using the Fourier-transform and multifractal surrogate data methods. An information transfer from larger to smaller time scales has been observed as the influence of the phase of slow oscillatory phenomena with the periods around 6-11 yr on the amplitudes of the variability characterized by the smaller temporal scales from a few months to 4-5 yr. The overall effect of the slow oscillations on the interannual temperature variability within the range 1-2 C has been observed in large areas of Europe. © 2014 American Physical Society.


Jirout J.,Academy of Sciences of the Czech Republic
Fungal Ecology | Year: 2015

The objective of the study was to identify N2O-producing fungi isolated from six qualitatively different sections of an overwintering pasture with substantial cattle impact. 80 out of 164 fungal isolates were considered as N2O-producers in nitrite-containing medium, representing 33 fungal species of 23 different genera. Ability to produce N2O was newly reported in eight genera: Arthrinium, Gibellulopsis, Ilyonectria, Lichtheimia, Paraphaeosphaeria, Purpureocillium, Tolypocladium and Westerdykella. Three levels of fungal N2O-productivity were assigned according to the fraction of nitrite-N transformed into N2O-N: < 1%, 1-10%, over 10%. Fungi capable of high and moderate transformation rates were predominantly isolated from sections under current or past cattle impact, where they contributed with a maximum of 65% of the total N2O emissions. There was no significant effect of cultivation conditions on the fraction of N2O-producing fungi. The results demonstrate that N2O-producing fungi are a common constituent of fungal communities in soils impacted by overwintering cattle. © 2015 Elsevier Ltd and The British Mycological Society.


Rohacek K.,Academy of Sciences of the Czech Republic
Photosynthesis Research | Year: 2010

A new method of the chlorophyll (Chl) a fluorescence quenching analysis is described, which allows the calculation of values of (at least) three components of the non-photochemical quenching of the variable Chl a fluorescence (qN) using a non-linear regression of a multi-exponential function within experimental data. Formulae for coefficients of the "energy"-dependent (ΔpH-dependent) quenching (qE), the state-transition quenching (qT) and the photo/inhibitory quenching (qI) of Chl a fluorescence were found on the basis of three assumptions: (i) the dark relaxation kinetics of qN, as well as of all its components, is of an exponential nature, (ii) the superposition principle is valid for individual Chl a fluorescence quenching processes and (iii) the same reference fluorescence level (namely the maximum variable Chl a fluorescence yield in the dark-adapted state, FV) is used to define both qN and its components. All definitions as well as the algorithms for analytical recognition of the qN components are theoretically clarified and experimentally tested. The described theory results in a rather simple equation allowing to compute values for all qN components (qE, qT, qI) as well as the half-times of relaxation (τ1/2) of corresponding quenching processes. It is demonstrated that under the above assumptions it holds: qN = qE + qT + qI. The theoretically derived equations are tested, and the results obtained are discussed for non-stressed and stressed photosynthetically active samples. Semi-empirical formulae for a fast estimation of values of the qN components from experimental data are also given. © 2010 Springer Science+Business Media B.V.


Jirout J.,Academy of Sciences of the Czech Republic
Ecological Indicators | Year: 2015

The aim of this work was to describe changes in fatty acid profiles of fungi growing under artificial conditions of oxygen depletion. In total, 133 fungal strains belonging to eight orders were isolated from cattle impacted soils and tested. The analysis of the ten most frequent fatty acids revealed significant shift in fatty acids composition as a result of decreasing oxygen level. Taxonomic- as well as aeration-dependent changes in the amounts of fungal biomarker fatty acids (18:1ω9 and 18:2ω6,9) were found. Therefore, the ratio of these two fatty acids could be considered as an indicator of anaerobic, microaerobic or aerobic conditions in soil. Moreover, fatty acid-based estimation of fungal biomass in soils should be performed as a sum of both biomarker fatty acids and with respect to the soil characteristics as well as to the composition of fungal community. © 2015 Elsevier Ltd. All rights reserved.


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.


Fiala K.,Academy of Sciences of the Czech Republic
Ekologia Bratislava | Year: 2010

Total belowground plant biomass (TBB, comprising both living and dead plant parts), percentage proportion (PLBB) and amount of living biomass (LBB), as well as, yearly net belowground biomass production (BNBP) and root turnover (TO) were assessed and compared in various stands of grasslands studied in the Czech Republic northeaster part of USA and in Cuban savannas. TBB assessed in 45 different grassland stands varied in a broad range of values. There was mostly only 1000 to 1500 g DM m -2 in fresh moist meadows and dry grasslands but 2500 to 3500 g DM m -2 in old wet and moist meadows. Higher values (up to 3000 g DM m -2) were also found in mountain grasslands of dearcut areas. PLBB in TBB and LBB were also considerably variable (mostly ranged from 10 to 80% of living parts and from 260 to 2300 g DM m -2). Values of PLBB and LBB gradually increase and TBB decrease from wet meadows through moist and fresh moist meadows to dearcut grasslands. The highest values of LBB were also recorded in the centre of soil moisture gradient of a natural meadow hydrosere (1500 to 1700 g DM m -2). The lowest values of BNBP were recorded in unmowed Polygalo-Nardetum stands (750-950 g DM m -2 yr -1) and the highest ones in unmowed Polygono-Cirsietum palustris (1300 g DM m -2 yr -1). 500 g DM m -2 yr -2 was estimated in a savannas community. Obtained results suggest that TO period of total belowground plant mass is mostly about two to three years in mesophytic meadows and probably longer in stands growing in either dry or wet habitats. Meadow stands rich in plant species and with greater amount of LBB were more resistant to mowing, i.e., the decrease in both TBB and LBB was slower.


Arslan A.,Selcuk University | Zima J.,Academy of Sciences of the Czech Republic
Folia Zoologica | Year: 2014

Available data on karyotypes of the mammals from Turkey and neighbouring regions (the Balkans, the Caucasus, and the Middle East) were summarized and reviewed in respect of their implications to taxonomy and systematics. In this review, previously unpublished data are presented in 20 species. Terrestrial mammals were taken into consideration, both the native and introduced. Altogether, 156 species occurring in the region concerned were included. The karyotype was studied in 109 of these species in Turkey, in most other species data are available from other geographic regions, and only three species remain unstudied cytogenetically. Intraspecific chromosomal variation (polymorphism or polytypy) was reported in 22 species. A karyotype different from the findings made in other regions was reported in Turkish populations of 17 species. Possible future directions of the cytogenetic investigations of mammals in the region are proposed.


Polivka T.,University of South Bohemia | Polivka T.,Academy of Sciences of the Czech Republic | Chabera P.,Lund University | Kerfeld C.A.,University of California at Berkeley | Kerfeld C.A.,U.S. Department of Energy
Biochimica et Biophysica Acta - Bioenergetics | Year: 2013

The Orange Carotenoid Protein (OCP) is a photoactive water soluble protein that is crucial for photoprotection in cyanobacteria. When activated by blue-green light, it triggers quenching of phycobilisome fluorescence and regulates energy flow from the phycobilisome to the reaction center. The OCP contains a single pigment, the carotenoid 3′-hydroxyechinenone (hECN). Binding to the OCP causes a conformational change in hECN leading to an extension of its effective conjugation length. We have determined the S 1 energy of hECN in organic solvent and compared it with the S 1 energy of hECN bound to the OCP. In methanol and n-hexane, hECN has an S1 energy of 14,300 cm- 1, slightly higher than carotenoids with shorter conjugation lengths such as zeaxanthin or β-carotene; this is consistent with the proposal that the presence of the conjugated carbonyl group in hECN increases its S1 energy. The S 1 energy of hECN in organic solvent is independent of solvent polarity. Upon binding to the OCP, the S1 energy of hECN is further increased to 14,700 cm- 1, underscoring the importance of protein binding which twists the conjugated carbonyl group into s-trans conformation and enhances the effect of the carbonyl group. Activated OCP, however, has an S1 energy of 14,000 cm- 1, indicating that significant changes in the vicinity of the conjugated carbonyl group occur upon activation. © 2012 Elsevier B.V.


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.


Scott J.,Rutherford Appleton Laboratory | Tuma M.,Academy of Sciences of the Czech Republic
ACM Transactions on Mathematical Software | Year: 2014

This article focuses on the design and development of a new robust and efficient general-purpose incomplete Cholesky factorization package HSL MI28, which is available within the HSL mathematical software library. It implements a limited memory approach that exploits ideas from the positive semidefinite Tismenetsky-Kaporin modification scheme and, through the incorporation of intermediate memory, is a generalization of the widely used ICFS algorithm of Lin and Moré. Both the density of the incomplete factor and the amount of memory used in its computation are under the user's control. The performance of HSL-MI28 is demonstrated using extensive numerical experiments involving a large set of test problems arising from a wide range of real-world applications. The numerical experiments are used to isolate the effects of scaling, ordering, and dropping strategies so as to assess their usefulness in the development of robust algebraic incomplete factorization preconditioners and to select default settings for HSL-MI28. They also illustrate the significant advantage of employing a modest amount of intermediate memory. Furthermore, the results demonstrate that, with limited memory, high-quality yet sparse general-purpose preconditioners are obtained. Comparisons are made with ICFS, with a level-based incomplete factorization code and, finally, with a state-of-the-art direct solver. © 2014 ACM.


Breiter K.,Academy of Sciences of the Czech Republic
Mineralogy and Petrology | Year: 2016

The chemical compositions of zircon and monazite and the relationships between the contents of Th, U, Y, and REE in both minerals and in the bulk samples of their parental rocks were studied in three Variscan composite peraluminous granite plutons in the Bohemian Massif. It was established that granites of similar bulk composition contain zircon and monazite of significantly different chemistry. Monazite typically contains 5–13 wt% (rarely up to 28 wt%) ThO2, 0.4–2 wt% (up to 8.2 wt%) UO2, and 0.5–2 wt% (up to 5 wt%) Y2O3, whereas zircon typically contains less than 0.1 wt% (rarely up to 1.7 wt%) ThO2, less than 1 wt% UO2 (in the Plechý/Plockenstein granite, commonly, 1–2 wt% and scarcely up to 4.8 wt% UO2), and less than 1 wt% Y2O3 (in the Nejdek pluton often 2–5, maximally 7 wt% Y2O3). Monazite is an essential carrier of thorium, hosting more than 80 % of Th in all studied granites. Monazite also appears to be an important carrier of Y (typically 14–16 %, and in the Melechov pluton, up to 81 % of the total rock content) and U (typically 18–35 % and occasionally 6–60 % of the total rock budget). The importance of zircon for the rock budget of all the investigated elements in granites is lower: 4–26 % U, 5–17 % Y, and less than 5 % Th. © 2016 Springer-Verlag Wien


Daniel M.,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: 2013

This theoretical contribution studies mathematical properties of plausibility conflict of belief functions. The analysis is performed for belief functions defined on 2-element frames, then the results are generalized to general finite frames. After that, an analogous analysis of Liu's degree of conflict is presented, to enable its comparison to the plausibility conflict. To be more efficient, a simplification of formula and computation of Liu's degree of conflict is suggested. A series of examples and graphical demonstrations are included. © 2013 Springer-Verlag.


Stibr B.,Academy of Sciences of the Czech Republic
Journal of Organometallic Chemistry | Year: 2015

The chemistry of the nido-5,6-C2B8H12 dicarbaborane, the most significant compound of the 10-vertex dicarbaborane series, has been discussed in this review within the contexts of reactivity and reaction mechanism. Chemical transformations of this carborane led to the isolation of the whole series of other compounds that now start playing ever increasing role in developing new carborane chemistry. Overviewed are procedures leading to closo and open-structured (nido and arachno) dicarbaboranes together with principles of their substitution on cluster-carbon and boron vertexes. © 2015 Elsevier B.V. All rights reserved.


Slama K.,Academy of Sciences of the Czech Republic
Journal of Insect Physiology | Year: 2012

Recent electrocardiographic (ECG) studies of insect hearts revealed the presence of human-like, involuntary and purely myogenic hearts. Certain insects, like a small light-weight species of hoverfly (Episyrphus balteatus), have evolved a very efficient cardiac system comprised of a compact heart ventricle and a narrow tube of aorta, which evolved as an adaptation to sustained hovering flights. Application of thermocardiographic and optocardiographic ECG methods revealed that adult flies of this species use the compact muscular heart chamber (heart ventricle) for intensive pumping of insect " blood" (haemolymph) into the head and thorax which is ringed all over with indirect flight musculature. The recordings of these hearts revealed extremely high, record rates of forward-directed, anterograde heartbeat (up to 10. Hz), associated with extremely enhanced synchronic (not peristaltic) propagation of systolic myocardial contractions (32.2. mm/s at room temperature). The relatively slow, backward-directed or retrograde cardiac contractions occurred only sporadically in the form of individual or twinned pulses replacing occasionally the resting periods. The compact heart ventricle contained bi-directional lateral apertures, whose opening and closure diverted the intracardiac anterograde " blood" streams between the abdominal haemocoelic cavity and the aortan artery, respectively. The visceral organs of this flying machine (crop, midgut) exhibited myogenic, extracardiac peristaltic pulsations similar to heartbeat, including the periodically reversed forward and backward direction of the peristaltic waves. The tubular crop contracted with a periodicity of 1. Hz, both forwards and backwards, with propagation of the peristaltic waves at 4.4. mm/s. The air-inflated and blindly ended midgut contracted at 0.2. Hz, with a 0.9. mm/s propagation of the peristaltic contraction waves. The neurogenic system of extracardiac haemocoelic pulsations, widely engaged in the regulation of circulatory and respiratory functions in other insect species, has been replaced here by a more economic, myogenic pulsation of the visceral organs as a light-weight evolutionary adaptation to prolonged hovering flight. Striking structural, functional and even genetic similarities found between the hearts of Episyrphus, Drosophila and human hearts, have been practically utilised for inexpensive testing of new cardioactive or cardioinhibitory drugs on insect heart. © 2012 Elsevier Ltd.


Karlick M.,Academy of Sciences of the Czech Republic
Astrophysical Journal | Year: 2012

We investigate processes in the electron-beam-return-current system in the impulsive phase of solar flares to answer a question about the formation of the n-electron distribution detected in this phase of solar flares. An evolution of the electron-beam-return-current system with an initial local density depression is studied using a three-dimensional electromagnetic particle-in-cell model. In the system the strong double layer is formed. Its electric field potential increases with the electron beam flux. In this electric field potential, the electrons of background plasma are strongly accelerated and propagate in the return-current direction. The high-energy part of their distribution at the high-potential side of the strong double layer resembles that of the n-distribution. Thus, the detection of the n-distributions, where a form of the high-energy part of the distribution is the most important, can indicate the presence of strong double layers in solar flares. The similarity between processes in solar flare loops and those in the downward current region of the terrestrial aurora, where the double layers were observed by FAST satellite, supports this idea. © 2012 The American Astronomical Society. All rights reserved.


Nemecek J.,R.O.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.


Kuban P.,Academy of Sciences of the Czech Republic | Hauser P.C.,University of Basel
Electrophoresis | Year: 2013

The developments in the field of capacitively coupled contactless conductivity detection in the approximate period from July 2010 to June 2012 are traced. Few reports concerning fundamental studies or new detector designs have appeared. On the other hand, applications in standard CZE are flourishing and contactless conductivity measurements are increasingly being employed as part of novel or more sophisticated experimental systems. Work on the lab-on-chip devices integrating contactless conductivity detection is continuing. A range of reports on the use of the simple yet powerful detection technique of contactless conductivity measurements in chromatographic separation as well as for analytical methods not including a separation step have also appeared. © 2012.


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.


Gvozdik L.,Academy of Sciences of the Czech Republic
Biology Letters | Year: 2012

Thermoregulatory behaviour represents an important component of ectotherm non-genetic adaptive capacity that mitigates the impact of ongoing climate change. The buffering role of behavioural thermoregulation has been attributed solely to the ability to maintain near optimal body temperature for sufficiently extended periods under altered thermal conditions. The widespread occurrence of plastic modification of target temperatures that an ectotherm aims to achieve (preferred body temperatures) has been largely overlooked. I argue that plasticity of target temperatures may significantly contribute to an ectotherm's adaptive capacity. Its contribution to population persistence depends on both the effectiveness of acute thermoregulatory adjustments (reactivity) in buffering selection pressures in a changing thermal environment, and the total costs of thermoregulation (i.e. reactivity and plasticity) in a given environment. The direction and magnitude of plastic shifts in preferred body temperatures can be incorporated into mechanistic models, to improve predictions of the impact of global climate change on ectotherm populations. © 2011 The Royal Society.


Kalina J.,Academy of Sciences of the Czech Republic
Journal of Mathematical Imaging and Vision | Year: 2012

This paper is devoted to highly robust statistical methods with applications to image analysis. The methods of the paper exploit the idea of implicit weighting, which is inspired by the highly robust least weighted squares regression estimator.We use a correlation coefficient based on implicit weighting of individual pixels as a highly robust similarity measure between two images. The reweighted least weighted squares estimator is considered as an alternative regression estimator with a clear interpretation. We apply implicit weighting to dimension reduction by means of robust principal component analysis. Highly robust methods are exploited in tasks of face localization and face detection in a database of 2D images. In this context we investigate a method for outlier detection and a filter for image denoising based on implicit weighting. © Springer Science+Business Media, LLC 2011.


Perina J.,Palacky University | Krepelka J.,Academy of Sciences of the Czech Republic
Optics Communications | Year: 2011

Joint photon-number and integrated-intensity probability distributions are used for description of time evolution of optical parametric process including processes of frequency conversion, parametric amplification and subharmonic generation taking into account losses and noise. Using these tools quantum entanglement of modes based on the separability criteria is considered and nonclassical properties of the process under discussion are demonstrated by means of conditional probability distributions and their Fano factors, difference-number probability distributions, quantum oscillations, squeezing of vacuum fluctuations and negative values of the joint wave probability quasidistributions in time evolution. Sub-Poissonian and sub-shot-noise properties are illustrated for spontaneous process and stimulated process by means of chaotic light and squeezed light. Also the multimode processes are investigated in the spirit of the Mandel-Rice photocount formula. The description is applied to interpretation of experimental data. © 2011 Elsevier B.V. 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.


Pravenec M.,Academy of Sciences of the Czech Republic
Methods in molecular biology (Clifton, N.J.) | Year: 2010

The spontaneously hypertensive rat (SHR) is the most widely used animal model of essential hypertension and accompanying metabolic disturbances. In this model, the use of whole genome sequencing and gene expression profiling techniques, linkage and correlation analyses in recombinant inbred strains, and in vitro and in vivo functional studies in congenic and transgenic lines has recently enabled molecular identification of quantitative trait loci (QTLs) relevant to the metabolic syndrome: (1) a deletion variant in Cd36 (fatty acid translocase) responsible for QTLs on chromosome 4 associated with dyslipidemia, insulin resistance and hypertension, (2) mutated Srebf1 (sterol regulatory element binding factor 1) as a QTL on chromosome 10 influencing dietary-induced changes in hepatic cholesterol levels, and (3) Ogn (osteoglycin) as a QTL on chromosome 17 associated with left ventricular hypertrophy. In addition, selective replacement of the mitochondrial genome of the SHR with the mitochondrial genome of the Brown Norway rat influenced several major metabolic risk factors for type 2 diabetes and provided evidence that spontaneous variation in the mitochondrial genome per se can promote systemic metabolic disturbances relevant to the pathogenesis of metabolic syndrome. Owing to recent progress in the development of rat genomic resources, the pace of QTL identification and discovery of new disease mechanisms can be expected to accelerate in the near future.


Liska J.,Academy of Sciences of the Czech Republic
Preslia | Year: 2012

This review of the lichen flora of the Czech Republic deals with the history of the research and highlights the most important summarizing publications. The diversity of the lichen flora is discussed and compared with that recorded in neighbouring countries. The main phytogeographic elements are outlined and illustrated with representative examples. The threat to the lichen flora in the Czech Republic is discussed in terms of the recently published Red List (version 1.1) and several endangered ecological groups of lichens with examples of the most threatened and extinct species are identified. Changes in the lichen flora along with the main causal factors are discussed. Air pollution, in particular sulphur dioxide was the most serious damaging factor in the 20th century. However, there has been a change in the trend in airpollution over the last two decades, with a decrease in sulphur and increase in nitrogen emissions, which has resulted in recolonization by formerly vanishing species of nitrophytic lichens (e.g. Xanthoriaparietina) and decrease in the abundance of the toxitolerant acidophytic species Lecanora conizaeoides. Ongoing present changes are very dynamic and not yet fully recognized. Therefore, field surveys are very important and will result in the recording of further species new to the Czech lichen flora.


Krahulec F.,Academy of Sciences of the Czech Republic
Preslia | Year: 2012

A brief history of the botanical research on the flora and vegetation in the Czech Republic is presented. This is done in the context of the progress in botany in neighbouring countries as well as the development of the society, especially the establishment of scientific institutions in the different countries. Important botanists who worked in other countries, but spent part of their life in what is now the Czech Republic, are also listed.


Kaplan Z.,Academy of Sciences of the Czech Republic
Preslia | Year: 2012

A review of the flora and phytogeography of the Czech Republic is given. The diversity of plants in this country reflects its geographic position in the centre of Europe, local natural conditions and the effect of intense human activity on the landscape. The Czech flora includes 148 families, 916 genera, 3557 species (plus 194 additional subspecies) and 609 hybrid vascular plants. Families richest in species are Asteraceae (662 species), Rosaceae (316), Poaceae (275), Fabaceae (170), Brassicaceae (148), Cyperaceae (127), Lamiaceae (112), Caryophyllaceae (108) and Apiaceae (100). Most of these species are native and 36.0% are alien. The spectrumoflife-forms is dominated by hemicryptophytes (45.7%), followed by therophytes (22.3%), phanerophytes (14.4%), geophytes (9.3%), chamaephytes (5.1%) and hydrophytes (3.2%), while the percentage of epiphytes is negligible (only two species). Several species that occur in the Czech Republic are relicts from glacial and early postglacial periods. Examples of arctic, boreal, alpine, steppe and other sorts of relicts are listed. Because of the relatively small size of this country and the considerable climatic and vegetational changes caused by glaciations, which repeatedly eliminated the local flora, endemism is relatively low in the Czech Republic. All endemics are of Quaternary age (neoendemics). A revised list of endemic species and subspecies includes 74 taxa endemic to the Czech Republic and adjacent border regions, which is 2% of the total vascular plant diversity. Of these, 48 taxa are strictly Czech endemics (defined by the borders of the country), the distributions of the other 26 taxa extend slightly beyond the borders of this country (mostly by less than 1 km) in the summit areas of the Krkonose/Karkonosze Mts and/or in the Kralicky Sneznlk/Snieznik Klodzki Mts. Hieracium and Sorbus are the genera with the greatest number of endemics (25 and 11 species and subspecies, respectively). Patterns in the distribution and occurrence of endemics in different types ofhabitat are discussed. The greatest concentration of endemics is in the Krkonose Mts, where they occur mostly in subalpine habitats, such as natural grasslands above the timberline, summit rocks and rocky slopes, and various sites in glacial cirques including avalanche tracks. Other endemics of subalpine habitats occur in the Kralicky Sneznik Mts and Hruby Jesenik Mts. Endemics at low altitudes mostly occur on rocky outcrops and in associated open thermophilous forests and grasslands, less frequently on open sandy areas, in fens and various types offorest. Maps of the distribution of endemics in the Czech Republic are presented. The majority of Czech endemics are rare and/or strongly endangered and included on the Red List of the Czech flora, and seven are extinct or missing. Changes in understanding of Czech endemics are reviewed and evolution of endemics discussed. The Czech Republic is situated at the intersection of several important European migration routes. The Czech flora is composed of almost all the floristic elements that occur in central Europe of which the Central-European geoelement is dominant. Other well represented geoelements include the Central-European-(sub-)alpine, Arctic-alpine, Boreal, Sub-boreal, Sub-Atlantic, Sub-Mediterranean, Pontic, Sub-pontic and South-Siberian. Examples of all geoelements are listed. The limits of the distributions of a number of widespread species are in the Czech Republic. These species are distinguished as boundary or outlying elements. Examples of species that in the Czech Republic are at the limits of their distributions, which range in different directions, are listed. Groups of species with similar ecogeographic features within the Czech Republic are distinguished as regional types of distribution (phytochorotypes). 15 basic phyto-chorotypes are listed, defined and illustrated using maps. Phytogeographical division of the Czech Republic is described. Three principal phytogeographical regions are recognized within the country, which are based on the dominant flora and vegetation that reflects specific regional topography and climatic conditions. These regions are further subdivided into phytogeographical provinces, districts and subdistricts. All of these phytogeographical units (phytochoria) are listed and their position illustrated on a map.


Folbergrova J.,Academy of Sciences of the Czech Republic | Kunz W.S.,University of Bonn
Mitochondrion | Year: 2012

Mitochondrial dysfunction has been identified as one potential cause of epileptic seizures. Impaired mitochondrial function has been reported for the seizure focus of patients with temporal lobe epilepsy and Ammon's horn sclerosis and of adult and immature animal models of epilepsy. Since mitochondrial oxidative phosphorylation provides the major source of ATP in neurons and mitochondria participate in cellular Ca 2+ homeostasis and generation of reactive oxygen species, their dysfunction strongly affects neuronal excitability and synaptic transmission. Therefore, mitochondrial dysfunction is proposed to be highly relevant for seizure generation. Additionally, mitochondrial dysfunction is known to trigger neuronal cell death, which is a prominent feature of therapy-resistant epilepsy. For this reason mitochondria have to be considered as promising targets for neuroprotective strategies in epilepsy. © 2011 Elsevier B.V. and Mitochondria Research Society.


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.


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.


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.


Palecek E.,Academy of Sciences of the Czech Republic
Electrochimica Acta | Year: 2016

Recently we have shown that, in difference to most of polysaccharides, which are considered as electroinactive, chitosan samples containing both glucosamine (GlcN) and N-acetylated glucosamine (GlcNAc) residues are involved in the catalytic hydrogen evolution reaction (CHER) at mercury electrodes, and can be determined by voltammetric or chronopotentiometric stripping. Here we show that polysaccharides and oligosaccharides composed of GlcN, but not those containing only GlcNAc residues, take part in CHER, allowing their easy label-free electrochemical detection. GlcNAc-containing oligosaccharides can be easily transformed into electroactive species by deacetylation using hot KOH treatment. This procedure can be applied also to electroinactive GlcNAc-containing glycans, frequently occurring in glycoproteins, allowing their electrochemical determination at submicromolar level. © 2015 Published by Elsevier Ltd.


Vohradsky J.,Academy of Sciences of the Czech Republic
Nucleic Acids Research | Year: 2012

Cell cycle is controlled by the activity of protein family of cyclins and cyclin-dependent kinases that are periodically expressed during cell cycle and that are conserved among different species. Genomewide location analysis found that cyclins are controlled by a small number of transcription factors that form closed network of genes controlling each other. To investigate gene expression dynamics of this network, we developed a general procedure for stochastic simulation of gene expression process. Using the binding data, we simulated gene expression of all genes of the network for all possible combinations of regulatory interactions and by statistical comparison with experimentally measured time series excluded those interactions that formed gene expression temporal profiles significantly different from the measured ones. These experiments led to a new definition of the cyclins regulatory network coherent with the binding experiments which are kinetically plausible. Level of influence of individual regulators in control of the regulated genes is defined. Simulation results indicate particular mechanism of regulatory activity of protein complexes involved in the control of cyclins. © The Author(s) 2012.


Farra V.,University Paris Diderot | Psencik I.,Academy of Sciences of the Czech Republic
Geophysics | Year: 2013

We tested alternative expressions for the P- and SV-wave moveout formulas in VTI media based on the weak-anisotropy (WA) approximation. Our moveout formulas represent expansions with respect to small parameters, which are related to deviations of anisotropy from isotropy. First-order P-wave formulas depend on four parameters, two-way zero-offset traveltime T0 related to the vertical velocity α0, the depth H of the single horizontal reflector, and two WA parameters εW and δW. The first-order SV-wave formulas depend on three parameters, again on T0, now related to the SV-wave vertical velocity β0, depth H, and the WA version of parameter σ. The secondorder formulas are slightly more complicated. The P- and SV-wave formulas depend on an additional parameter r, the ratio of the SV- and P-wave vertical velocities. The SV-wave formula depends, in addition, on the WA parameters εW Because the dependence of the moveout formulas on r is very weak, r can be specified as a typical SV- to P-wave velocity ratio, and the number of parameters necessary to specify the second-order formulas is four for both waves. The formulas are relatively simple, highly accurate around zero offset, and yield an exact long-offset asymptote. Their accuracy at intermediate offsets depends on deviations of ray- and phase-velocity directions. These formulas are also applicable in cases in which the reflected ray is situated in a plane of symmetry of an orthorhombic medium, whose other symmetry plane is horizontal. This also includes any HTI medium with an axis of symmetry in the plane containing the reflected ray. © 2013 Society of Exploration Geophysicists.


Balogova M.,University of P.J. Safarik | Gvozdik L.,Academy of Sciences of the Czech Republic
PLoS ONE | Year: 2015

Many ectotherms effectively reduce their exposure to low or high environmental temperatures using behavioral thermoregulation. In terrestrial ectotherms, thermoregulatory strategies range from accurate thermoregulation to thermoconformity according to the costs and limits of thermoregulation, while in aquatic taxa the quantification of behavioral thermoregulation have received limited attention. We examined thermoregulation in two sympatric newt species, Ichthyosaura alpestris and Lissotriton vulgaris, exposed to elevated water temperatures under semi-natural conditions. According to a recent theory, we predicted that species for which elevated water temperatures pose a lower thermal quality habitat, would thermoregulate more effectively than species in thermally benign conditions. In the laboratory thermal gradient, L. vulgaris maintained higher body temperatures than I. alpestris. Semi-natural thermal conditions provided better thermal quality of habitat for L. vulgaris than for I. alpestris. Thermoregulatory indices indicated that I. alpestris actively thermoregulated its body temperature, whereas L. vulgaris remained passive to the thermal heterogeneity of aquatic environment. In the face of elevated water temperatures, sympatric newt species employed disparate thermoregulatory strategies according to the species-specific quality of the thermal habitat. Both strategies reduced newt exposure to suboptimal water temperatures with the same accuracy but with or without the costs of thermoregulation. The quantification of behavioral thermoregulation proves to be an important conceptual and methodological tool for thermal ecology studies not only in terrestrial but also in aquatic ectotherms. © 2015 Balogová, Gvoždík. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


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.


Sokol Z.,Academy of Sciences of the Czech Republic
Atmospheric Research | Year: 2011

The aim of this paper is to determine whether the assimilation of extrapolated radar reflectivity can improve very short range precipitation forecasts in the summer season. The COSMO NWP model, with a horizontal resolution of 2.8. km, is applied, and radar reflectivity data are assimilated using a water vapour correction method. Two model runs are compared: the first run assimilates observed radar reflectivity, and the second run assimilates observed and extrapolated radar reflectivity. The extrapolation is performed by the COTREC method, and the length of extrapolation is 1. h. Hourly precipitation forecasts are compared and evaluated subjectively, both visually and by the Fractions Skill Score for three events with severe convective precipitation in the model domain. The results of the comparisons indicate that the assimilation of extrapolated radar reflectivity in most cases improves the accuracy of precipitation forecasts for the second and third lead hours. In general, hourly precipitation forecasts by the COSMO NWP model with the assimilation of radar reflectivity show reasonable skill for the first and the second hours. © 2010 Elsevier B.V.


Malik J.,Academy of Sciences of the Czech Republic
Journal of Sound and Vibration | Year: 2013

The original Tacoma suspension bridge was completed on 10 June 1940 and opened to traffic on 1 July 1940. The bridge was stable with respect to torsional oscillation until 7 November 1940. That day at 10 a.m. the diagonal tie attached to the midspan band of one main cable loosened and the cable began to slip through the band. Just after the loosening of the tie torsional oscillations appeared, lasted for more than 1 h, and resulted in the collapse of the center span at 11:10 a.m. In this paper a continuous model of the original Tacoma suspension bridge is proposed. This model describes the mutual interaction of the main cables, central span, and hangers. The reaction of the ties attached to the midspan bands is included in the model, so it is possible to study the situation when only one midspan band loosens. The model is described by a system of variational equations which are derived from the Hamilton variational principle. Three different eigenvalue and eigenvector problems are formulated and analyzed. The problems correspond to the situations when the both midspans are loosened, the both midspan bands are fixed, and one midspan band is fixed and the other is loosened. The analysis of the three eigenvalue and eigenvector problems against flutter is carried out, which reveals possible reasons of the collapse. © 2013 Elsevier Ltd. All rights reserved.


Perina J.,Academy of Sciences of the Czech Republic
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2013

Quantum pulsed second-subharmonic generation in a planar waveguide with a small periodic corrugation at the surface is studied. Backscattering of the interacting fields on the corrugation enhances the nonlinear interaction, giving larger values of squeezing. The problem of backscattering is treated by perturbation theory, using the Fourier transform for nondispersion propagation, and by numerical approach in the general case. Optimum spectral modes for squeezed-light generation are found using the Bloch-Messiah reduction. An improvement in squeezing and increase of the numbers of generated photons are quantified for the corrugation resonating with the fundamental and second-subharmonic field. Splitting of the generated pulse by the corrugation is predicted. © 2013 American Physical Society.


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.


Vlasakova B.,Academy of Sciences of the Czech Republic
Journal of Tropical Ecology | Year: 2015

The effective floral neighbourhood is the radius around a plant where the density of flowering plants and other factors affect visitation rates and pollination success of plants. This study aims to determine this radius and focuses on the effects of conspecific plant density, plant sex and the amount of shrub vegetation on visitation rates of Clusia blattophila, a dioecious bush pollinated by Amazonina platystylata cockroaches. The number of visits did not differ between flower sexes but cockroaches spent less time on the rewardless female flowers. The density effect was scale dependent. The distribution of flowering individuals within the 15-m radius had a significant positive effect on flower visitation rates. At a larger scale (35-45-m radius), an increase in density of male plants led to a decrease in visitation rates, indicating competition for pollinators. Within the smaller radius, the facilitative effect was probably induced by elevated floral advertisement and high mobility of cockroaches at this scale. Within the larger radii, the results indicated that cockroach mobility was restricted and population density was stable at this scale. Density of male plants affected visitation rates because only male plants reward pollinators. Hence, male plants were the true competitors. Copyright © 2014 Cambridge University Press.


Gvozdik L.,Academy of Sciences of the Czech Republic
Evolutionary Biology | Year: 2015

A continuing issue in evolutionary thermal biology is the mismatch between preferred body temperatures (Tpref) and optimal temperatures (Topt) for whole-animal performance. Using phylogenetic comparative analyses, I examined the hypothesis that a difference in the rates at which Tpref and Topt evolve causes the mismatch in a lineage of European newts. In a laboratory thermal gradient, newts maintained body temperatures that were on average 8 °C below Topt for maximum swimming velocity. The lower boundary of the Tpref range evolved faster than the mean Tpref, the upper boundary of the Tpref range, and Topt. The strong evolutionary co-variation between mean Tpref and its boundaries prevented the shift of mean Tpref away from Topt. This suggests that the variation in evolutionary rates has a limited potential to modify the disparity between thermal optima and preferenda. © 2015, Springer Science+Business Media New York.


Schauer P.,Academy of Sciences of the Czech Republic
Nuclear Instruments and Methods in Physics Research, Section B: Beam Interactions with Materials and Atoms | Year: 2011

To enhance the detective quantum efficiency (DQE) of scintillation electron detectors for scanning electron microscopes or scanning transmission electron microscopes (S(T)EM), the cathodoluminescence (CL) decay kinetics of YAG:Ce single crystal scintillators is studied in this paper. Some possibilities for reductions of decay time and afterglow of the mentioned scintillators are presented. The pulse mode utilizing a blanking system and 10 keV electrons for the excitation and a sampling oscilloscope for the CL detection were used for the measurement of decay characteristics. The CL decay characteristics of YAG:Ce single crystals of different Ce concentrations, pulled by the Czochralski method and cleaned and annealed under specific conditions, were measured in dependence on excitation pulse duration and on the specimen temperature. To interpret the presented results, a kinetic model of cathodoluminescence of the YAG:Ce single crystals was created. The effects of quenching impurities and of defect centers in YAG:Ce were specified. © 2011 Elsevier B.V. All rights reserved.


Jirousek R.,Academy of Sciences of the Czech Republic | Shenoy P.P.,University of Kansas
International Journal of Approximate Reasoning | Year: 2014

Compositional models were initially described for discrete probability theory, and later extended for possibility theory and for belief functions in Dempster-Shafer (D-S) theory of evidence. Valuation-based system (VBS) is an unifying theoretical framework generalizing some of the well known and frequently used uncertainty calculi. This generalization enables us to not only highlight the most important theoretical properties necessary for efficient inference (analogous to Bayesian inference in the framework of Bayesian network), but also to design efficient computational procedures. Some of the specific calculi covered by VBS are probability theory, a version of possibility theory where combination is the product t-norm, Spohn's epistemic belief theory, and D-S belief function theory. In this paper, we describe compositional models in the general framework of VBS using the semantics of no-double counting, which is central to the VBS framework. Also, we show that conditioning can be expressed using the composition operator. We define a special case of compositional models called decomposable models, again in the VBS framework, and demonstrate that for the class of decomposable compositional models, conditioning can be done using local computation. As all results are obtained for the VBS framework, they hold in all calculi that fit in the VBS framework. For the D-S theory of belief functions, the compositional model defined here differs from the one studied by Jiroušek, Vejnarová, and Daniel. The latter model can also be described in the VBS framework, but with a combination operator that is different from Dempster's rule of combination. For the version of possibility theory in which combination is the product t-norm, the compositional model defined here reduces to the one studied by Vejnarová. © 2013 Elsevier Inc. All rights reserved.


Wood-inhabiting taxa of the Sordariomycetidae comprise several distantly related monotypic or small genera, which lack familial or ordinal affiliation and share a simple and inconspicuous morphology of dark ascomata with carbonaceous walls and long necks, stipitate asci and hyaline ellipsoidal, fusiform to cylindrical ascospores. Recent collections of an undescribed fungus and of Ceratosphaeria abietis reveal two additional evolutionary lineages characterized by this simple and indistinct teleomorph morphology. Phylogenetic analysis of three genes, small and large subunit nuclear ribosomal DNA (nc28S and nc18S rDNA) combined with the second largest subunit of RNA polymerase II (rpb2), supports the recognition of two new genera, Ceratolenta and Platytrachelon for C. abietis. Platytrachelon abietis is redescribed and illustrated based on additional collections. In culture it produced a dematiaceous hyphomycetous anamorph with blastic conidiogenesis and ellipsoidal, septate, pale brown conidia. It was associated with a synanamorph producing cylindrical, strongly curved hyaline conidia. Molecular data suggest a relationship of Platytrachelon with the Papulosaceae, while Ceratolenta forms a monophylum on a separate branch. Both taxonomic novelties possess striking morphological similarities with Ceratosphaeria, Lentomitella and Rhodoveronaea, which recently were reinstated based on DNA sequence data. A key to morphologically similar wood-inhabiting fungi classified in the Sordariomycetidae is provided. © 2013 by The Mycological Society of America.


Ueta Y.,University of Occupational and Environmental Health Japan | Dayanithi G.,Academy of Sciences of the Czech Republic | Fujihara H.,University of Occupational and Environmental Health Japan
Hormones and Behavior | Year: 2011

Arginine vasopressin (AVP) is involved in the homeostatic responses numerous life-threatening conditions, for example, the promotion of water conservation during periods of dehydration, and the activation of the hypothalamo-pituitary adrenal axis by emotional stress. Recently, we generated new transgenic animals that faithfully express an AVP-enhanced green fluorescent protein (eGFP) fusion gene in the paraventricular nucleus (PVN), the supraoptic nucleus (SON) and the suprachiasmatic nucleus (SCN) of the hypothalamus. In these transgenic rats, marked increases in eGFP fluorescence and fusion gene expression were observed in the magnocellular division of the PVN and the SON, but not the SCN, after osmotic challenges, such as dehydration and salt loading, and both acute and chronic nociceptive stimuli. In the parvocellular division of the PVN, eGFP expression was increased after acute and chronic pain, bilateral adrenalectomy, endotoxin shock and restraint stress. In the extra-hypothalamic areas of the brain, eGFP expression was induced in the locus coeruleus after the intracerebroventricular administration of colchicine. Next, we generated another transgenic rat that expresses a fusion gene comprised of c- fos promoter-enhancer sequences driving the expression of monomeric red fluorescent protein 1 (mRFP1). In these transgenic rats, abundant nuclear fluorescence of mRFP1 was observed in the PVN, the SON and other osmosensitive areas after acute osmotic stimulation. Finally, we generated a double transgenic rat that expresses both the AVP-eGFP and c- fos-mRFP1 fusion genes. In this double transgenic rat, we have observed nuclear mRFP1 fluorescence in eGFP-positive neurons after acute osmotic stimulation. These unique transgenic rats provide an exciting new tool to examine neuroendocrine responses to physiological and stressful stimuli in both in vivo and in vitro preparations. © 2010 Elsevier Inc.


Svoboda J.,Academy of Sciences of the Czech Republic | Fischer F.D.,University of Leoben | McDowell D.L.,Georgia Institute of Technology
Acta Materialia | Year: 2012

Thermodynamics employs quantities that characterize the state of the system and provides driving forces for system evolution. These quantities can be applied by means of the thermodynamic extremal principle to obtain models and consequently constitutive equations for the evolution of the thermodynamic systems. The phase field method is a promising tool for simulation of the microstructure evolution in complex systems but introduces several parameters that are not standard in thermodynamics. The purpose of this paper is to show how the phase field method equations can be derived from the thermodynamic extremal principle, allowing the common treatment of the phase field parameters together with standard thermodynamic parameters in future applications. Fixed values of the phase field parameters may, however, not guarantee fixed values of thermodynamic parameters. Conditions are determined, for which relatively stable values of the thermodynamic parameters are guaranteed during phase field method simulations of interface migration. Finally, analytical relations between the thermodynamic and phase field parameters are found and verified for these simulations. A slight dependence of the thermodynamic parameters on the driving force is determined for the cases examined. © 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.


Islam B.,Queens University of Belfast | Sgobba M.,Queens 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.


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.


Fischer F.D.,University of Leoben | Svoboda J.,Academy of Sciences of the Czech Republic
Progress in Materials Science | Year: 2014

Diffusion of elements and vacancies is embedded in the framework of continuum mechanics and thermodynamics. The evolution equations for the site fractions of the substitutional and interstitial elements as well as the vacancies are derived. Each possible activity of vacancies, from no to non-ideal and ideal sources and sinks for vacancies, is taken into account. Manning's theory is implemented considering the vacancy wind effect. Furthermore, the role of a stress state is rigorously treated and shows its different influence on substitutional and interstitial elements as well as on vacancies. The reader is provided by the full set of diffusion equations for each kind of vacancy activity. Physically most relevant types of boundary condition, representing closed system with different activities of vacancies at its surface, are studied in detail. The theoretical framework is demonstrated by two illustrative examples emphasizing the interaction of bulk diffusion with an internal phase interface and/or the surface of the system expressed by contact conditions taking into account the properties of the interface or the surface. © 2013 Elsevier Ltd. All rights reserved.


Zdansky K.,Academy of Sciences of the Czech Republic
Nanoscale Research Letters | Year: 2011

Depositions on surfaces of semiconductor wafers of InP and GaN were performed from isooctane colloid solutions of palladium (Pd) nanoparticles (NPs) in AOT reverse micelles. Pd NPs in evaporated colloid and in layers deposited electrophoretically were monitored by SEM. Diodes were prepared by making Schottky contacts with colloidal graphite on semiconductor surfaces previously deposited with Pd NPs and ohmic contacts on blank surfaces. Forward and reverse current-voltage characteristics of the diodes showed high rectification ratio and high Schottky barrier heights, giving evidence of very small Fermi level pinning. A large increase of current was observed after exposing diodes to flow of gas blend hydrogen in nitrogen. Current change ratio about 700,000 with 0.1% hydrogen blend was achieved, which is more than two orders-of-magnitude improvement over the best result reported previously. Hydrogen detection limit of the diodes was estimated at 1 ppm H 2/N 2. The diodes, besides this extremely high sensitivity, have been temporally stable and of inexpensive production. Relatively more expensive GaN diodes have potential for functionality at high temperatures. © 2011 Zdansky.


Kysely J.,Academy of Sciences of the Czech Republic
International Journal of Climatology | Year: 2010

The study examines whether recent occurrences of severe heat waves in central Europe were exceptional in the context of past fluctuations, and estimates their recurrence probabilities under several climate change scenarios. Using data from a network of meteorological stations in the Czech Republic since 1961, it is found that 1994 was the year with the most severe heat waves over majority of the area. The other seasons with enhanced heat wave characteristics were 1992,2003 and 2006. Analysis of the long-term temperature series at Prague-Klementinum reveals that the July 2006 heat wave, covering 33 consecutive days, was the longest and most severe individual heat wave since 1775. Probabilities of long and severe heat waves are estimated from daily temperature series generated by a first-order autoregressive model with a deterministic component (incorporating a seasonal cycle and a long-term trend). The model is validated with respect to the simulation of heat waves in present climate (1961-2006) and subsequently run under several assumptions reflecting various rates of summer warming over 2007-2100. The return period of a heat wave reaching or exceeding the length of the 2006 heat wave in Prague is estimated to be around 120 years in 2006. Owing to an increase in mean summer temperatures, probabilities of very long heat waves have already risen by an order of magnitude over the recent 25 years, and are likely to increase by another order of magnitude by around 2040 under the summer warming rate assumed by the mid-scenario. Even the lower bound scenario yields a considerable decline of return periods associated with intense heat waves. Nevertheless, the most severe recent heat waves appear to be typical rather of a late 21st century than a mid-21st century climate. © 2009 Royal Meteorological Society.


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.


Horst B.,Adam Mickiewicz University | Bartkiewicz K.,Academy of Sciences of the Czech Republic | Miranowicz A.,Adam Mickiewicz University
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2013

Amplitude damping changes entangled pure states into usually less-entangled mixed states. We show, however, that even local amplitude damping of one or two qubits can result in mixed states more entangled than pure states if one compares the relative entropy of entanglement (REE) for a given degree of the Bell-Clauser-Horne-Shimony-Holt inequality violation (referred to as nonlocality). By applying Monte Carlo simulations, we find the maximally entangled mixed states and show that they are likely to be optimal by checking the Karush-Kuhn-Tucker conditions, which generalize the method of Lagrange multipliers for this nonlinear optimization problem. We show that the REE for mixed states can exceed that of pure states if the nonlocality is in the range (0,0.82) and the maximal difference between these REEs is 0.4. A former comparison of the REE for a given negativity showed analogous property but the corresponding maximal difference in the REEs is one order smaller (i.e., 0.039) and the negativity range is (0,0.53) only. For appropriate comparison, we normalized the nonlocality measure to be equal to the standard entanglement measures, including the negativity, for arbitrary two-qubit pure states. We also analyze the influence of the phase-damping channel on the entanglement of the initially pure states. We show that the minimum of the REE for a given nonlocality can be achieved by this channel, contrary to the amplitude-damping channel. © 2013 American Physical Society.


Ratschan S.,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: 2010

Safety verification of hybrid systems is undecidable, except for very special cases. In this paper, we circumvent undecidability by providing an algorithm that can verify safety and provably terminates for all robust and safe problem instances. It need not necessarily terminate for problem instances that are unsafe or non-robust. A problem instance x is robust iff the given property holds not only for x itself, but also when x is perturbed a little bit. Since, in practice, well-designed hybrid systems are usually robust, this implies that the algorithm terminates for the cases occurring in practice. In contrast to earlier work, our result holds for a very general class of hybrid systems, and it uses a continuous time model. © 2010 Springer-Verlag.


Valdes J.J.,Academy of Sciences of the Czech Republic
Parasites & vectors | Year: 2014

BACKGROUND: Ticks counteract host inflammatory responses by secreting proteins from their saliva that compete for histamine binding. Among these tick salivary proteins are lipocalins, antiparallel beta-barrel proteins that sequester small molecules. A tick salivary lipocalin has been structurally resolved and experimentally shown to efficiently compete for histamine with its native receptor (e.g., H1 histamine receptor). To date, molecular dynamics simulations focus on protein-protein and protein-ligand interactions, but there are currently no studies for simultaneous ligand exploration between two competing proteins.METHODS: Aided by state-of-the-art, high-throughput computational methods, the current study simulated and analyzed the dynamics of competitive histamine binding at the tick-host interface using the available crystal structures of both the tick salivary lipocalin histamine-binding protein from Rhipicephalus appendiculatus and the human histamine receptor 1.RESULTS: The attraction towards the tick salivary lipocalin seems to depend on the protonated (adding a hydrogen ion) state of histamine since the current study shows that as histamine becomes more protonated it increases its exploration for the tick salivary lipocalin. This implies that during tick feeding, histamine may need to be protonated for the tick salivary lipocalin to efficiently sequester it in order to counteract inflammation. Additionally, the beta-hairpin loops (at both ends of the tick salivary lipocalin barrel) were reported to have a functional role in sequestering histamine and the results in the current study concur and provide evidence for this hypothesis. These beta-hairpin loops of the tick salivary lipocalin possess more acidic residues than a structurally similar but functionally unrelated lipocalin from the butterfly, Pieris brassicae; comparative results indicate these acidic residues may be responsible for the ability of the tick lipocalin to out-compete the native (H1) receptor for histamine.CONCLUSIONS: Three explanatory types of data can be obtained from the current study: (i) the dynamics of multiple binding sites, (ii) competition between two proteins for a ligand, and (iii) the intrinsic molecular components involved in the competition. These data can provide further insight at the atomic level of the host-tick interface that cannot be experimentally determined. Additionally, the methods used in this study can be applied in rationally designing drugs.


The aim was to estimate the impacts of invasive Impatiens parviflora on forests' herbal layer communities. A replicated Before-After-Control-Impact field experiment and comparisons with adjacent uninvaded plots were used. The alien's impact on species richness was tested using hierarchical generalized mixed effect models with Poisson error structure. Impact on species composition was tested using multivariate models (DCA, CCA, RDA) and Monte-Carlo permutation tests. Removal plots did not differ in native species richness from neither invaded nor adjacent uninvaded plots, both when the treatment's main effect or its interaction with sampling time was tested (Chi2 = 0.4757, DF = 2, p = 0.7883; Chi2 = 7.229, DF = 8, p = 0.5121 respectively). On the contrary, ordination models revealed differences in the development of plots following the treatments (p = 0.034) with the invaded plots differing from the adjacent uninvaded (p = 0.002). Impatiens parviflora is highly unlikely to impact native species richness of invaded communities, which may be associated with its limited ability to create a dense canopy, a modest root system or the fact the I. parviflora does not represent a novel and distinctive dominant to the invaded communities. Concerning its potential impacts on species composition, the presence of native clonal species (Athyrium filix-femina, Dryopteris filix-mas, Fragaria moschata, Luzula luzuloides, Poa nemoralis) on the adjacent uninvaded plots likely makes them different from the invaded plots. However, these competitive and strong species are more likely to prevent the invasion of I. parviflora on the adjacent uninvaded plots rather than being themselves eliminated from the invaded communities. © 2012 Hejda.


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.


Kubinova S.,Academy of Sciences of the Czech Republic
Future Neurology | Year: 2015

Restoration of lost neuronal function after spinal cord injury still remains a considerable challenge for current medicine. Over the last decade, regenerative medicine has recorded rapid and promising advancements in stem cell research, genetic engineering and the progression of new sophisticated biomaterials as well as nanotechnology. This advancement has also been reflected in neural tissue engineering, where, along with the development of a new generation of well-designed biopolymer scaffolds, multifactorial therapeutic strategies are being validated in order to determine the greatest possible repair efficacy of the complex CNS pathophysiology. Much attention is currently focused on the designing of multifunctional polymer scaffolds as systems for targeted drug or gene delivery, electrical stimulation or as substrates creating a special micro-environment, promoting the growth and desired differentiation of various cell lines. In this review, the latest advances in biomaterial technology together with various combinatorial strategies designed to treat spinal cord injury treatment are summarized and discussed. © 2015 Future Medicine Ltd.


The Rhinanthoid clade of the family Orobanchaceae comprises plants displaying a hemiparasitic or holoparasitic strategy of resource acquisition. Some of its species (mainly Rhinanthus spp.) are often used as models for studies of hemiparasite physiology. Although there is a well-developed concept covering their physiological processes, most recent studies have neglected the existence of hydathode trichomes present on leaves of these hemiparasitic plants. As a first step for the proposed integration of these structures in the theory of physiological processes of the hemiparasites, we described the outer micromorphology and ultrastructure of the hydathode trichomes on leaves of hemiparasitic Rhinanthus alectorolophus and Odontites vernus with scanning and transmission electron microscopy (SEM and TEM, respectively). The TEM inspections of both types of trichome revealed typical ultrastructural features: labyrinthine cell wall, high content of cytoplasm in cells with numerous mitochondria and presence of plasmodesmata. All these features indicate high metabolic activity complying with their function as glandular trichomes actively secreting water. The active secretion of water by the hydathode trichomes (evidence for which is summarised here) also presents a possible mechanism explaining results of previous gas exchange measurements detecting high dark respiration and transpiration rates and a tight inter-correlation between them in hemiparasitic Orobanchaceae. In addition, this process is hypothesised to have allowed multiple evolutionary transitions from facultative to obligate hemiparasitism and unique xylem-feeding holoparasitism of Lathraea with a long-lived underground stage featuring a rhizome covered by scales of leaf origin. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.


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..


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.


Fiala Z.,Academy of Sciences of the Czech Republic
Annals of Physics | Year: 2011

The starting point in the geometrical setting of solid mechanics is to represent deformation process of a solid body as a trajectory in a convenient space with Riemannian geometry, and then to use the corresponding tools for its analysis. Based on virtual power of internal stresses, we show that such a configuration space is the (globally) symmetric space of symmetric positive-definite real matrices. From this unifying point of view, we shall analyse the logarithmic strain, the stress rate, as well as linearization and intrinsic integration of corresponding evolution equation. © 2011 Elsevier Inc.


Mares P.,Academy of Sciences of the Czech Republic
Epilepsy Research | Year: 2010

Epileptic seizures activate not only excitatory but also inhibitory systems what results in an arrest of seizures. Our recent data indicate that GABAergic inhibition plays an important role in this process in cortically elicited seizures. We started to study the role of GABA-B receptors in cortical epileptic afterdischarges (ADs) in immature rats 12, 18 and 25 days old with implanted electrodes. Low-frequency stimulation of sensorimotor cortical area was repeated with increasing intensities of stimulation current. Thresholds for movements directly elicited by stimulation, for spike-and-wave type of AD, for clonic seizures accompanying this type of ADs and for transition into limbic type of AD were decreased by the 200. mg/kg dose of a GABA-B receptor antagonist CGP35348 in all three age groups. Duration of ADs was markedly increased by 50, 100 as well as 200. mg/kg dose of CGP35348. The effects were best expressed in 18-day-old rats. To conclude, GABA-B receptors play an important role in generation and especially in arrest of cortical seizures in immature rats. © 2010 Elsevier B.V.


Homolka L.,Academy of Sciences of the Czech Republic
Fungal Biology | Year: 2014

Basidiomycetes are used in industrial processes, in basic or applied research, teaching, systematic and biodiversity studies. Efficient work with basidiomycete cultures requires their reliable source, which is ensured by their safe long-term storage. Repeated subculturing, frequently used for the preservation, is time-consuming, prone to contamination, and does not prevent genetic and physiological changes during long-term maintenance. Various storage methods have been developed in order to eliminate these disadvantages. Besides lyophilization (unsuitable for the majority of basidiomycetes), cryopreservation at low temperatures seems to be a very efficient way to attain this goal. Besides survival, another requirement for successful maintenance of fungal strains is the ability to preserve their features unchanged. An ideal method has not been created so far. Therefore it is highly desirable to develop new or improve the current preservation methods, combining advantages and eliminate disadvantages of individual techniques. Many reviews on preservation of microorganisms including basidiomycetes have been published, but the progress in the field requires an update. Although herbaria specimens of fungi (and of basidiomycetes in particular) are very important for taxonomic and especially typological studies, this review is limited to live fungal cultures. © 2013 The British Mycological Society.


Adamek Z.,University of South Bohemia | Marsalek B.,Academy of Sciences of the Czech Republic
Aquaculture International | Year: 2013

Bioturbation of bottom sediments at the sediment-water interface is currently gaining more attention in studies dealing with the functioning of aquatic ecosystems. Such bioturbation can be caused by a variety of benthic macroinvertebrates or benthivorous fish that forage and burrow various bottom tubes, holes and pits. Thus, the processes involved may either be a result of direct interception by benthic animals, e. g., through bioresuspension of particles or through food ingestion and biodeposition, or of other indirect effects, e. g., changes in the physical properties of sediments or through the constructions mentioned above, along with corresponding changes in pond ecosystem functioning. The most distinct effect of benthivorous fish bioturbation activities is an increase in the turbidity of the water, which can lead to many subsequent knock-on effects, including inhibition of phytoplankton and submersed macrophyte growth with resulting alterations in physico-chemical water conditions. The importance of benthic macroinvertebrates and fish in bioturbation processes is also indicated by an increase in the numbers of resting cyanobacterial colonies recruited due to bioturbation of bottom sediments. © 2012 Springer Science+Business Media B.V.


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.


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.


Vasicek Z.,Academy of Sciences of the Czech Republic
Acta Geologica Polonica | Year: 2010

The taxonomic and stratigraphic study of rich ammonite material from the Lower Cretaceous deposits of the Butkov Quarry, near Ladce (Manín Unit, Slovak Central Carpathians) is presented. More than 55 ammonite species are recognised and twenty-one biostratigraphically significant ammonite species are described, with one species, Sarasinella subdensicostata, described as new. the recognised taxa document an interval from the Upper Valanginian through to the Lower Hauterivian. the ammonite assemblage represents the Mediterranean bioprovince, with only a single species, Dichotomites evolutus, from the Boreal bioprovince.a new ammonite zone, the Teschenites flucticulus Zone, is proposed for the basal Hauterivian in the Western Carpathians.


Bruce A.W.,University of South Bohemia | Bruce A.W.,Academy of Sciences of the Czech Republic
Reproductive BioMedicine Online | Year: 2013

The divergence of two differentiating extraembryonic cell types (trophectoderm and primitive endoderm) from the pluripotent epiblast population (the source of fetal progenitor cells) by the blastocyst stage of mouse development relies upon the activation and execution of lineage-specific gene expression programmes. While our understanding of the central transcription factor 'effectors' directing these cell-fate choices has accumulated rapidly, what is less clear is how the differential expression of such genes within the diverging lineages is initially generated. This review summarizes and consolidates current understanding. I introduce the traditional concept and importance of a cell's spatial location within the embryo, referencing recent mechanistic and molecular insights relating to cell fate. Additionally, I address the growing body of evidence that suggests that heterogeneities among blastomeres precede, and possibly inform, their spatial segregation in the embryo. I also discuss whether the origins of such early heterogeneity are stochastic and/or indicative of intrinsic properties of the embryo. Lastly, I argue that the robustness and regulative capacity of preimplantation embryonic development may reflect the existence of multiple converging, if not wholly redundant, mechanisms that act together to generate the necessary diversity of inter-cell-lineage gene expression patterns. Following conception, the early mammalian embryo undergoes a series of cell divisions. The divisions not only increase the number of cells but also lead to the generation of three different cell classes. These cell classes ensure that the early embryo is able to implant into the mothers womb and continue successful development until birth. In order to generate these three types of cells, specific genes need to be activated or shut down to ensure they can develop properly and permit further embryogenesis. The process of acquiring the correct genetic expression patterns is controlled by specialized proteins called transcription factors. As the three specialized types of cells arise, they require the correct set of transcription factors but little is known about how this process is regulated. In this review summary, I introduce some recent evidence about how this is achieved and how the potential processes involved can contribute to the robust nature of early mammalian embryo development. © 2013, Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.


Prikryl J.,Academy of Sciences of the Czech Republic
IEEE Conference on Intelligent Transportation Systems, Proceedings, ITSC | Year: 2013

This paper introduces a new model of traffic flow between two signalized intersections. The model originated from our effort to improve older, macroscopic model [5] based on the conservation law of vehicles. In order to keep the proposed model simple and numerically tractable, we make several simplifications: we do not take into account acceleration and deceleration of vehicles and different preferences of drivers and we classify the movements of vehicles into two classes: (i) a stopped vehicle, waiting in a queue, and (ii) a vehicle moving with a constant cruising speed. Under these assumptions the flow of vehicles between two intersections can be described by a piece-wise linear function as a combination of several 'ramp' functions. We demonstrate the behavior of the proposed model on an simulated scenario of two signalized intersections. © 2013 IEEE.


Jarusek J.,Academy of Sciences of the Czech Republic
Zeitschrift fur Angewandte Mathematik und Physik | Year: 2015

For the static contact problem with limited interpenetration with obstacle, the existence of solutions is proved. The frictionless case is studied at first, and then the problem with Coulomb friction is investigated as well. The body has nowhere a Dirichlet boundary value condition prescribed. In both cases, if the prescribed depth of the interpenetration tends to 0, the solutions tend to a solution of the appropriate unilateral contact problem. © 2015, Springer Basel.


Michalek M.,Academy of Sciences of the Czech Republic
Journal of Mathematical Fluid Mechanics | Year: 2015

A stability result for the compressible Navier–Stokes system with transport equation for entropy s is shown. The proof comes as an outcome of the isentropic case and additional properties of the effective viscous flux. We deal with the pressure term in the form $${\rho^{\gamma}e^{s}}$$ργes with adiabatic index $${\gamma>3\slash 2}$$γ>3/2; therefore the crucial renormalization method is restricted. © 2015, Springer Basel.


Shackell N.L.,Bedford Institute of Oceanography | Ricard D.,Academy of Sciences of the Czech Republic | Stortini C.,Dalhousie University
PLoS ONE | Year: 2014

Global scale forecasts of range shifts in response to global warming have provided vital insight into predicted species redistribution. We build on that insight by examining whether local warming will affect habitat on spatiotemporal scales relevant to regional agencies. We used generalized additive models to quantify the realized habitat of 46 temperate/boreal marine species using 41+ years of survey data from 35°N-48°N in the Northwest Atlantic. We then estimated change in a "realized thermal habitat index" under short-term (2030) and long-term (2060) warming scenarios. Under the 2030 scenario, ∼10% of species will lose realized thermal habitat at the national scale (USA and Canada) but planktivores are expected to lose significantly in both countries which may result in indirect changes in their predators' distribution. In contrast, by 2060 in Canada, the realized habitat of 76% of species will change (55% will lose, 21% will gain) while in the USA, the realized habitat of 85% of species will change (65% will lose, 20% will gain). If all else were held constant, the ecosystem is projected to change radically based on thermal habitat alone. The magnitude of the 2060 warming projection (∼1.5-3°C) was observed in 2012 affirming that research is needed on effects of extreme "weather" in addition to increasing mean temperature. Our approach can be used to aggregate at smaller spatial scales where temperate/boreal species are hypothesized to have a greater loss at ∼40°N. The uncertainty associated with climate change forecasts is large, yet resource management agencies still have to address climate change. How? Since many fishery agencies do not plan beyond 5 years, a logical way forward is to incorporate a "realized thermal habitat index" into the stock assessment process. Over time, decisions would be influenced by the amount of suitable thermal habitat, in concert with gradual or extreme warming. © 2014 Shackell et al.


Kostal L.,Academy of Sciences of the Czech Republic
Brain Research | Year: 2012

The limits on maximum information that can be transferred by single neurons help us to understand how sensory and other information is being processed in the brain. In this paper we approximately calculate the information capacity of the perfect integrate-and-fire neuronal model in dependence on the stimulus range, assuming the simplest form of temporal coding scheme. We couple the information transfer with metabolic cost of neuronal activity and we find that the optimal information per metabolic cost ratios may occur for a relatively small stimulus range. This article is part of a Special Issue entitled Neural Coding. © 2011 Elsevier B.V. All rights reserved.


Celik L.,Academy of Sciences of the Czech Republic
International Journal of Industrial Organization | Year: 2016

Television (TV) stations forego millions of dollars of advertising revenues by airing tune-ins (preview advertisements) for their upcoming programs. In this paper, I analyze the equilibrium as well as welfare properties of tune-ins in a duopolistic TV market that lasts for two periods. Importantly, each TV station is fully informed about its own as well as its rival's program. Viewers receive information via tune-ins, if any, or alternatively by sampling a program for a few minutes (and switching across stations). I find that equilibrium tune-in decisions do not necessarily depend on TV stations' knowledge of their rival's program. In this case, the opportunity costs of tune-ins could be so high that a regime without any tune-ins may be socially better. However, when tune-ins depend on both of the upcoming programs, it is possible that they enhance welfare by helping viewers avoid some of the inefficient program sampling they would otherwise do in a regime without any tune-ins. © 2015 Elsevier B.V.


Alba C.,Colorado State University | Alba C.,Academy of Sciences of the Czech Republic | Hufbauer R.,Colorado State University
Biological Invasions | Year: 2012

Biogeographic data describing performance differences in native and introduced populations of invasive species are increasingly coming to light, revealing that introduced populations often perform better than their native conspecifics. However, this pattern is not universal, nor is it well studied in species that fall on the more "benign" end of the invasion spectrum. Furthermore, performance data are infrequently linked with variation in key environmental factors experienced by populations in each range, making it difficult to assess which factors are typically associated with shifts in performance. Here we assessed performance in native and introduced populations of Verbascum thapsus (common mullein), an herbaceous biennial that was initially introduced to the eastern US from Europe, but which has subsequently expanded its range into semi-arid mountainous regions of the western US, where it appears to be more problematic. Indeed, we found that introduced populations were larger than native populations, with over half of them comprising more than 500 individuals, a size seldom achieved in the native range. We further explored the role that abiotic factors (latitude, elevation, and precipitation) might serve in shaping performance in European and western US populations, and quantified variation in two biotic factors relevant to invasion: herbivory, and the potential for competition from co-occurring vegetation (as well as its inverse, the availability of bare ground). When the influence of abiotic factors was not considered, introduced mullein performed better than native mullein in terms of plant density and plant size (i. e., number of leaves and area covered by the basal rosette). When the influence of abiotic factors was statistically taken into account, the difference in the density of native and introduced populations remained strong, while the difference in number of leaves was reduced, though it remained significant. In contrast, controlling for abiotic factors reversed the pattern for plant area such that plants in introduced populations performed less well than natives. These results suggest that the difference in climate experienced by native and introduced populations is an important driver of mullein performance only for plant area. Thus, increased performance in western US population likely hinges in part on shifts in biotic factors. Indeed, we found a reduction in the prevalence of several herbivore guilds on introduced relative to native mullein, accompanied by a significant decrease in chewing damage in introduced populations. We also found differences in the potential for competition: cover of vegetation is significantly higher in native mullein populations than in introduced populations, and increasing cover of vegetation is associated with declining performance (i. e., density) of native populations but not introduced populations. In sum, the introduced populations performed better than the native populations in several respects; thus, although mullein is considered a relatively 'benign' introduced species, it has the potential to differentially impact resident communities in its native and introduced ranges. Additionally, despite the disparity in abiotic conditions experienced by native and introduced populations, these factors do not appear to consistently drive differences in performance. Instead, evidence suggests that enemy escape and shifts in the competitive regime may facilitate mullein invasion. We use our data to propose hypotheses to be tested experimentally. © 2012 Springer Science+Business Media B.V.


Husnik F.,University of South Bohemia | Chrudimsky T.,University of South Bohemia | Hypsa V.,University of South Bohemia | Hypsa V.,Academy of Sciences of the Czech Republic
BMC Biology | Year: 2011

Background: The bacterial family Enterobacteriaceae gave rise to a variety of symbiotic forms, from the loosely associated commensals, often designated as secondary (S) symbionts, to obligate mutualists, called primary (P) symbionts. Determination of the evolutionary processes behind this phenomenon has long been hampered by the unreliability of phylogenetic reconstructions within this group of bacteria. The main reasons have been the absence of sufficient data, the highly derived nature of the symbiont genomes and lack of appropriate phylogenetic methods. Due to the extremely aberrant nature of their DNA, the symbiotic lineages within Enterobacteriaceae form long branches and tend to cluster as a monophyletic group. This state of phylogenetic uncertainty is now improving with an increasing number of complete bacterial genomes and development of new methods. In this study, we address the monophyly versus polyphyly of enterobacterial symbionts by exploring a multigene matrix within a complex phylogenetic framework.Results: We assembled the richest taxon sampling of Enterobacteriaceae to date (50 taxa, 69 orthologous genes with no missing data) and analyzed both nucleic and amino acid data sets using several probabilistic methods. We particularly focused on the long-branch attraction-reducing methods, such as a nucleotide and amino acid data recoding and exclusion (including our new approach and slow-fast analysis), taxa exclusion and usage of complex evolutionary models, such as nonhomogeneous model and models accounting for site-specific features of protein evolution (CAT and CAT+GTR). Our data strongly suggest independent origins of four symbiotic clusters; the first is formed by Hamiltonella and Regiella (S-symbionts) placed as a sister clade to Yersinia, the second comprises Arsenophonus and Riesia (S- and P-symbionts) as a sister clade to Proteus, the third Sodalis, Baumannia, Blochmannia and Wigglesworthia (S- and P-symbionts) as a sister or paraphyletic clade to the Pectobacterium and Dickeya clade and, finally, Buchnera species and Ishikawaella (P-symbionts) clustering with the Erwinia and Pantoea clade.Conclusions: The results of this study confirm the efficiency of several artifact-reducing methods and strongly point towards the polyphyly of P-symbionts within Enterobacteriaceae. Interestingly, the model species of symbiotic bacteria research, Buchnera and Wigglesworthia, originated from closely related, but different, ancestors. The possible origins of intracellular symbiotic bacteria from gut-associated or pathogenic bacteria are suggested, as well as the role of facultative secondary symbionts as a source of bacteria that can gradually become obligate maternally transferred symbionts. © 2011 Husník et al; licensee BioMed Central Ltd.


The criteria for taxonomic classification of cyanobacteria were radically changed in the last few decades after application of data obtained from EM studies and after use of phylogenetic analyses, mainly derived from molecular sequencing. These changes provided important knowledge of phylogeny of cyanobacteria, and they must be also expressed in the systematic review, usable for ecologists and experimental laboratories. This paper presents short descriptions of modern families with cyanobacterial genera containing planktic types after the latest revisions. The phylogenetic position of the main planktic genera was revised and controlled. © 2015 Springer International Publishing Switzerland


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.


Svoboda J.,Academy of Sciences of the Czech Republic | Fischer F.D.,University of Leoben | Abart R.,Free University of Berlin
Acta Materialia | Year: 2010

In many multi-component systems, phases can be considered stoichiometric. If two phases not stably coexisting are brought into contact, multiple new phases may nucleate at the interface and develop into a sequence of layers with different phase compositions, which grow between the original phases. Inert markers at the original contact may show "splitting" of the marker (Kirkendall) plane, called polyfurcation. Nearly exclusively binary systems have been studied theoretically or experimentally. A thermodynamic model for the kinetics of diffusional phase transformation in multi-component systems and motion of the polyfurcated Kirkendall plane is derived by the thermodynamic extremal principle. The degrees of freedom of the system are discussed rigorously. The model is demonstrated on simulations of kinetics in binary three-phase and ternary four-phase systems. © 2010 Acta Materialia Inc.


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.


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.


The main goal of this article is to summarize results of palaeoecological investigations of a classical and iconic site in the Czech Republic, the former Komoranské jezero lake. This lake persisted in north-western Bohemia from at least the Weichselian Late Glacial until quite recently. Pollen and palaeoalgological analyses of coccal green algae were carried out on several sedimentary sequences sampled within the framework of palaeobotanical and archaeological salvage research from 1970s to 1990s. The results are published here jointly for the first time. They make it possible to reconstruct both the lacustrine environment and upland vegetation in the wider surroundings of the lake. The Komoranské jezero lake in the late-glacial period was cold and oligotrophic. Its nutrient status gradually changed and became mesotrophic and dystrophic locally in the early Holocene and eutrophic from the Middle Holocene onwards. Unfortunately, big differences in geomorphology and environmental conditions together with long-distance (and likely even fluvial) transport of pollen make the reconstruction of upland vegetation somewhat difficult. Immigration of climatically demanding species into the area started already in the Preboreal period (before 8200 uncal. yr BP). Maximum expansion of broadleaved forests occurred in the Atlantic period (between 6000 and 7000 uncal. yr BP). At the same time, afforestation spreading from the lowlands (200 to 400 m altitude) up to the mountain ridges (around 1000ma.s.l.) of the Krušné hory Mts attained its maximum level. Based on continually increased presence of non-arboreal pollen we hypothesize that open grassland biotopes (continental-type steppe vegetation) persisted in the wider region from the late glacial throughout the entire Holocene. First clear evidence of a human effect on vegetation in promoting expansion of secondary grasslands is dated in pollen diagrams to around 4000 uncal. yr BP (i.e. the Subboreal period).


Komarek J.,Academy of Sciences of the Czech Republic | Komarek J.,University of South Bohemia
Hydrobiologia | Year: 2010

Taxonomic classification is a method for recognizing and registering the world's organism diversity, in the context of continual changing knowledge about evolutionary (genetic) and ecological relations and phenotype variation. The present system of cyanobacteria must be modified according to combined markers, in which molecular data (as an indisputable genetic basis) should be correlated with biochemical, ultrastructural, phenotypic and ecological data. New data are necessary in order to correct or up date the system; thus, the classification must continually be revised and supplemented. The greatest problem is to transfer all modern data derived from molecular investigations to experimental research and establish the necessary and correct nomenclatural rules for scientific practice. The molecular approach must be the baseline for the reorganisation of our knowledge; however, it should explain and be in agreement with morphological and ecological variation of cyanobacterial genotypes. The present article summarizes the main conclusions, derived from modern cyanobacterial diversity studies. © Springer Science+Business Media B.V. 2009.


Szabo P.,Academy of Sciences of the Czech Republic
Biological Reviews | Year: 2014

The term 'historical ecology' has been used with various meanings since the first half of the 20th century. Studies labelled as historical ecology have been produced in at least four academic disciplines: history, ecology, geography and anthropology. Although all those involved seem to agree that historical ecology concerns the historical interconnectedness of nature and human culture, this field of study has no unified methodology, specialized institutional background and common publication forums. Knowledge of the development of historical ecology is also limited. As a result, the current multitude of definitions of historical ecology is accompanied by divergent opinions as to where the origins of the field are to be sought. In this review, I follow the development of historical ecology from the 18th century to the present. In the first part, I briefly describe some early examples of historical ecological investigations, followed by a description of the various scientific strands in the 20th century that contributed to the formation of historical ecology. In the second part, I discuss the past five decades of historical ecological investigations in more detail, focusing mostly (but not exclusively) on works that their respective authors identified as historical ecology. I also examine the appearance and interconnectedness of the two main trends (ecological and anthropological) in historical ecological research. In the last part, I attempt to outline the future of historical ecology based on common features in existing research. It appears that at present historical ecology is at a crossroads. With rapidly growing interest in historical ecological research, it may move towards institutionalization or remain an umbrella term. © 2014 Cambridge Philosophical Society.


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.


Henoux J.C.,University of Paris Descartes | Karlicky M.,Academy of Sciences of the Czech Republic
Astronomy and Astrophysics | Year: 2013

Context. The impact polarization of optical chromospheric lines in solar flares is still being debated. For this reason, additional observations and improved flare atmosphere models are needed still. Aims. The polarization-free telescope THEMIS used in multiline 2 MulTiRaies (MTR) mode allows accurate simultaneous linear polarization measurements in various spectral lines. Methods. In the 2001 June 15 flare, Hα, Hβ, and Mg D2 lines linear impact polarization was reported as present in THEMIS 2 MTR observations. In this paper, THEMIS data analysis was extended to the Na D2 line. Sets of I ± U and I ± Q flare Stokes S 2D-spectra were corrected from dark-current, spectral-line curvature and from transmission differences. Then, we derived the linear polarization degree P and polarization orientation angle α 2D-spectra. No change in relative positioning could be found that would reduce the Stokes parameters U and Q values. No V and I crosstalks could explain our results either. Results. The Na D2 line is linearly polarized with a polarization degree exceeding 5% at some locations. The polarization was found to be radial at outer ribbons edges, and tangential at their inner edges. This orientation change may be due to differences in electron distribution functions on the opposite borders of flare chromospheric ribbons. Electron beams propagating along magnetic field lines, together with return currents, could explain both radial and tangential polarization. At the inner ribbon edges, intensity profile-width enlargements and blueshifts in polarization profiles are observed. This suggests chromospheric evaporation. © 2013 ESO.


Bezdek A.,Academy of Sciences of the Czech Republic
Journal of Geodynamics | Year: 2010

The proposed calibration method uses the precise kinematic positions derived from the data of the GPS receivers aboard the twin GRACE satellites (POD, Precise Orbit Determination). The total satellite accelerations are obtained numerically as a second derivative of the kinematic positions, from these the modelled forces of gravitational origin are subtracted. The resulting nongravitational accelerations then serve as a calibration standard for the uncalibrated accelerometer data. The calibration parameters for the GRACE accelerometers have already been published using other methods. The aim of our study was to obtain not only the calibrated accelerometer measurements, but also a statistically correct estimate of their uncertainty.The main problem in the application of a numerical derivative to observational data is the amplification of noise, especially at high frequencies. Besides, the filter of the numerical derivative introduces the correlation structure in the noise, which complicates the uncertainty estimates using the ordinary least squares. We succeeded in solving both of these problems by using the generalized least squares (GLS) method.Using the proposed procedure, the calibration parameters for all three accelerometer data components were obtained. To remove the serial correlation in the POD positions, we used the GLS method together with a fitted autoregressive process. In this way, a realistic estimate of accuracy of the calibrated accelerometer data was obtained for the along-track component. The time evolution of the calibration parameters over a 1.5-year period (08/2002-03/2004) display approximately constant scale factors and slowly changing biases for both GRACE A and B satellites, which is in accordance with the results in the references. © 2010 Elsevier Ltd.


Svoboda J.,Academy of Sciences of the Czech Republic | Fischer F.D.,University of Leoben
Acta Materialia | Year: 2011

The formation of stoichiometric MpXq hollow nanospheres by reaction of metallic M nanospheres with the gaseous X phase must be preceded by the formation of a sufficiently thick MpXq nanoshell on the metallic core of phase M. During this stage, high supersaturation of vacancies in the M core and/or hydrostatic stress in the M core, due to the misfit between the core and the nanoshell, are developed and provide favourable conditions for the hollow nucleation. The misfit is caused by the Kirkendall effect. Based on the application of the thermodynamic extremal principle, a kinetic model of MpXq nanoshell formation is derived. The kinetics is driven by the change of the chemical energy due to reaction of the M and X components, the interface and surface energies, and the elastic strain energy due to misfit strain of the whole system. The model is used for simulation of the Cu2O shell growth kinetics due to oxidation of a Cu nanosphere, and the results of the simulations are discussed. © 2010 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.


Wiedermann J.,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: 2012

The quest for understanding the working of artificial minds attaining a human-like cognition is culminating. While still inspired by the functionality of biological brains, the realization of thinking machines need not slavishly copy the principles used by their living pendants. Achieving a higher-level artificial intelligence no longer seems to be a matter of a fundamental scientific breakthrough but rather a matter of exploiting our best algorithmic theories of thinking machines supported by our most advanced robotic and real time data processing technologies. We review recent examples of such theories, ideas and machines which could pave the road towards building interesting artificial brains. © 2012 Springer-Verlag.


Wiedermann J.,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: 2012

We will give plausible arguments in favor of a claim that we already have sufficient knowledge to understand the working of interesting artificial minds attaining a high-level cognition, consciousness included. Achieving a higher-level AI seems to be not a matter of a fundamental scientific breakthrough but rather a matter of exploiting our best theories of artificial minds and our most advanced data processing technologies. We list the theories we have in mind and illustrate their role and place on the example of a high-level architecture of a conscious cognitive agent with a potential to pass the Turing test. © 2012 Springer-Verlag.


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.


Vavrycuk V.,Academy of Sciences of the Czech Republic
Geophysical Journal International | Year: 2010

The behaviour of rays at interfaces in anisotropic viscoelastic media is studied using three different approaches: the real elastic ray theory, the real viscoelastic ray theory and the complex ray theory. In solving the complex eikonal equation, the highest accuracy is achieved by the complex ray theory. The real elastic and viscoelastic ray theories are less accurate but computationally more effective. In all three approaches, the rays obey Snell's law at the interface, but its form is different for each approach. The complex Snell's law constrains the complex tangential components of the slowness vector. The real viscoelastic and elastic Snell's laws constrain the real tangential components of the slowness vector. In the viscoelastic ray theory, the Snell's law is supplemented by the condition of the stationary slowness vector of scattered waves. The accuracy of all three ray theoretical approaches is numerically tested by solving the complex eikonal equation and by calculating the R/T coefficients. The models of the medium consist of attenuating isotropic and anisotropic homogeneous half-spaces with attenuation ranging from extremely strong (Q= 2.5-3) to moderate (Q = 25-30). Numerical modelling shows that solving the complex eikonal equation by the real viscoelastic ray approach is at least 20 times more accurate than solving it by the real elastic ray approach. Also the R/T coefficients are reproduced with a higher accuracy by the real viscoelastic ray approach than by the elastic ray approach. © 2010 The Author Journal compilation © 2010 RAS.


Ctyroky J.,Academy of Sciences of the Czech Republic
Journal of Lightwave Technology | Year: 2012

Recently, we described a simple but efficient 2-D bidirectional eigenmode expansion propagation algorithm based on Fourier series expansion for modeling optical field distribution in waveguide devices. Complex coordinate transformation was used as an efficient absorbing boundary condition. In this paper, we systematically extend this algorithm to 3-D structures. © 2012 IEEE.


Komarek J.,Academy of Sciences of the Czech Republic | Komarek J.,University of South Bohemia
Hydrobiologia | Year: 2010

The taxonomy of cyanobacteria has been substantially modified in the last few decades, particularly after application of modern ultrastructural and molecular methods. The group of heterocytous cyanobacteria (Nostocales) was found to be monophyletic, but the concept and content of different genera must be continually corrected and revised. The widespread introduction of the molecular approach (especially 16S rRNA gene sequencing) has confirmed almost all traditional genera based on distinct and morphologically recognizable type species, but indicated also broader diversity resulting in separation of more genetic and generic entities in several genera. The combination of molecular and phenotype analyses enables also a better and more objective definition of criteria for describing newly researched generic units, discovered from various habitats in the biosphere. Here, the nostocacean generic taxa are reviewed after recent necessary taxonomic corrections. Nostocacean cyanobacteria are filamentous, heterocytous, not branched and not polarized morphotypes, classified traditionally into one family (Nostocaceae). The main part of the review focuses on the genera containing planktic species. © Springer Science+Business Media B.V. 2009.


Mason N.W.H.,Landcare Research | De Bello F.,Academy of Sciences of the Czech Republic | De Bello F.,University of South Bohemia
Journal of Vegetation Science | Year: 2013

Functional trait diversity provides a powerful means of addressing ecology's persistent questions, through its dual role as an indicator of mechanisms driving differences in species composition between communities and as a predictor of ecosystem-level processes. Functional traits provide a means of testing mechanisms behind species turnover between communities because environmental heterogeneity, competition and disturbance influence species fitness via their traits. Functional traits also provide a link between species and multiple ecosystem-level processes, such as primary productivity, nutrient fluxes and resilience, since species influence these processes via their traits. This special issue demonstrates that functional diversity offers a practical means of investigating ecology's persistent questions. © 2013 International Association for Vegetation Science.


Novak K.,Academy of Sciences of the Czech Republic
Annals of Applied Biology | Year: 2010

The supernodulating mutants of legumes lack the internal regulation of the number of symbiotic root nodules that harbour N2-fixing nodule bacteria. On one hand, these mutants represent an efficient tool for dramatic increase in the degree of rhizobial symbiosis development. The trait of released nodulation is often associated with the desirable resistance of nodule initiation and functioning to the inhibition by ambient nitrate. On the other hand, the more intense and stable atmospheric nitrogen fixation of supernodulated plants is devalued by plant growth depression that results from the disproportion between the photosynthetic capacity of the shoot and the catabolic demands of symbiotic nodules. The deleterious effects of excessive nodulation can be neutralised or alleviated by a breeding strategy aimed at creating an ideotype of N2-fixing legume. The growth depression can be diminished by the reduction in the nodule number typical for supernodulators, that is, 6-10-fold of the wild type, to the level found permissive for the particular crop. This shift should be accompanied with breeding aimed at the increased photosynthetic capacity of the shoot. Forage varieties of legumes represent a reserve of high photosynthetic and shoot growth capacity, thanks to a long-term breeding history for green biomass accumulation. Moreover, the deleterious effects of supernodulation are less perceived after introgression into the background of forage varieties in view of different criteria in their evaluation, such as nitrogen accumulation and biomass production per crop area unit. The growth of supernodulators can be further corrected by breeding for auxiliary traits such as long-vine shoot architecture, a longer vegetation period and late flowering. The same strategy is applicable to the compensation for inherent pleiotropic changes in plant development, which are often associated with primarily symbiotic mutations. Supporting evidence for the efficiency of the described approach has already been reported. © 2010 Association of Applied Biologists.


Neustupa J.,Academy of Sciences of the Czech Republic
Archive for Rational Mechanics and Analysis | Year: 2010

We prove the existence of a weak solution to the steady Navier-Stokes problem in a three dimensional domain Ω, whose boundary ∂Ω consists of M unbounded components Γ1, . . ., ΓM and N - M bounded components ΓM+1, . . ., ΓN. We use the inhomogeneous Dirichlet boundary condition on ∂Ω. The prescribed velocity profile α on ∂Ω is assumed to have an L3-extension to Ω with the gradient in L2(Ω)3×3. We assume that the fluxes of α through the bounded components ΓM+1, . . ., ΓN of ∂Ω are "sufficiently small", but we impose no restriction on the size of fluxes through the unbounded components Γ1, . . ., ΓM. © 2010 Springer-Verlag.


Hejda M.,Academy of Sciences of the Czech Republic
Biological Invasions | Year: 2013

Invasions are associated with loss of diversity and changes in species composition. This study aims to provide evidence if this loss happens at random or if the loss is related to functional traits of native species. Traits of species in communities dominated by 13 plants alien to Central Europe were compared to those found in the adjacent uninvaded vegetation. There is a weak but significant non-random pattern in the distribution of traits between the invaded and adjacent uninvaded vegetation. For example, species possessing a taproot, annuals but also juveniles of trees tend to be proportionally more abundant in the invaded vegetation, suggesting they are impacted less than species with high clonal index, perennial polycarpic species and species without a taproot, which are proportionally more represented in the uninvaded vegetation. Fast laterally spreading species, trees' juveniles and woody species in general are proportionally more frequent in the invaded vegetation, while biennials, slow laterally spreading species but also shrubs are proportionally more frequent in the uninvaded vegetation. Juveniles of trees may compete successfully with the aliens due to being adapted to thrive in low light conditions. Annuals may thrive in the invaded communities by possessing a life strategy different from most of the selected aliens. Possessing a taproot appears to be another trait important for the successful coexistence with the dominant invasive aliens, possibly pointing to the importance of underground competition. Clonal perennial polycarpic herbs are species functionally most similar to most of the selected aliens, and these species were found to be most underrepresented in the invaded vegetation. © 2013 Springer Science+Business Media Dordrecht