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Joskowiak A.,Institute of Nanoscience and Nanotechnology | Joskowiak A.,IBB Institute for Biotechnology And Bioengineering | Stasio N.,Institute of Nanoscience and Nanotechnology | Chu V.,Institute of Nanoscience and Nanotechnology | And 4 more authors.
Biosensors and Bioelectronics | Year: 2012

Two-dimensional fluorescence spectroscopy (2D FS) provides a non-invasive means to assess cell condition without the introduction of changes to the cell environment. The method relies on the measurement of the excitation-emission fluorescence intensity matrix of key intrinsic fluorophores, like aromatic amino acids, enzyme cofactors, and vitamins. Commonly used detection systems are complex, with multiple bandpass filters, and are hard to miniaturize. Here, an amorphous silicon photodetector array system integrated with amorphous silicon-carbon alloy filters designed to detect three key fluorophores - tryptophan (Trp), reduced nicotine adenine dinucleotide (NADH) and flavin adenine dinucleotide (FAD) - is demonstrated. These intrinsic fluorophores were detected in pure solutions and also in suspended yeast cells. The array system was used to monitor changes in intrinsic fluorophore concentration when a yeast cell solution was subject to a thermal shock stress. © 2012 Elsevier B.V.


Salamalikis V.,University of Patras | Argiriou A.A.,University of Patras | Dotsika E.,Institute of Nanoscience and Nanotechnology
Science of the Total Environment | Year: 2016

In dry and warm environments sub-cloud evaporation influences the falling raindrops modifying their final stable isotopic content. During their descent from the cloud base towards the ground surface, through the unsaturated atmosphere, hydrometeors are subjected to evaporation whereas the kinetic fractionation results to less depleted or enriched isotopic signatures compared to the initial isotopic composition of the raindrops at cloud base. Nowadays the development of Generalized Climate Models (GCMs) that include isotopic content calculation modules are of great interest for the isotopic tracing of the global hydrological cycle. Therefore the accurate description of the underlying processes affecting stable isotopic content can improve the performance of iso-GCMs. The aim of this study is to model the sub-cloud evaporation effect using a) mixing and b) numerical isotope evaporation models. The isotope-mixing evaporation model simulates the isotopic enrichment (difference between the ground and the cloud base isotopic composition of raindrops) in terms of raindrop size, ambient temperature and relative humidity (RH) at ground level. The isotopic enrichment (δδ) varies linearly with the evaporated raindrops mass fraction of the raindrop resulting to higher values at drier atmospheres and for smaller raindrops. The relationship between δδ and RH is described by a 'heat capacity' model providing high correlation coefficients for both isotopes (R2>80%) indicating that RH is an ideal indicator of the sub-cloud evaporation effect. Vertical distribution of stable isotopes in falling raindrops is also investigated using a numerical isotope-evaporation model. Temperature and humidity dependence of the vertical isotopic variation is clearly described by the numerical isotopic model showing an increase in the isotopic values with increasing temperature and decreasing RH. At an almost saturated atmosphere (RH=95%) sub-cloud evaporation is negligible and the isotopic composition hardly changes even at high temperatures while at drier and warm conditions the enrichment of 18O reaches up to 20‰, depending on the raindrop size and the initial meteorological conditions. © 2015 Elsevier B.V.


Salamalikis V.,University of Patras | Argiriou A.A.,University of Patras | Dotsika E.,Institute of Nanoscience and Nanotechnology
Journal of Hydrology | Year: 2016

In this paper the periodic patterns of the isotopic composition of precipitation (δ18O) for 22 stations located around Central Europe are investigated through sinusoidal models and wavelet analysis over a 23 years period (1980/01-2002/12). The seasonal distribution of δ18O follows the temporal variability of air temperature providing seasonal amplitudes ranging from 0.94‰ to 4.47‰ the monthly isotopic maximum is observed in July. The isotopic amplitude reflects the geographical dependencies of the isotopic composition of precipitation providing higher values when moving inland. In order to describe the dominant oscillation modes included in δ18O time series, the Morlet Continuous Wavelet Transform is evaluated. The main periodicity is represented at 12-months (annual periodicity) where the wavelet power is mainly concentrated. Stations (i.e. Cuxhaven, Trier, etc.) with limited seasonal isotopic effect provide sparse wavelet power areas at the annual periodicity mode explaining the fact that precipitation has a complex isotopic fingerprint that cannot be examined solely by the seasonality effect. Since temperature is the main contributor of the isotopic variability in mid-latitudes, the isotope-temperature effect is also investigated. The isotope-temperature slope ranges from 0.11‰/°C to 0.47‰/°C with steeper values observed at the southernmost stations of the study area. Bivariate wavelet analysis is applied in order to determine the correlation and the slope of the δ18O - temperature relationship over the time-frequency plane. High coherencies are detected at the annual periodicity mode. The time-frequency slope is calculated at the annual periodicity mode ranging from 0.45‰/°C to 0.83‰/°C with higher values at stations that show a more distinguishable seasonal isotopic behavior. Generally the slope fluctuates around a mean value but in certain cases (sites with low seasonal effect) abrupt slope changes are derived and the slope becomes strongly unstable. © 2016 Elsevier B.V.


PubMed | Imperial College London, Institute of Nanoscience and Nanotechnology and Bulgarian Academy of Science
Type: | Journal: Scientific reports | Year: 2017

The most powerful method for protein structure determination is X-ray crystallography which relies on the availability of high quality crystals. Obtaining protein crystals is a major bottleneck, and inducing their nucleation is of crucial importance in this field. An effective method to form crystals is to introduce nucleation-inducing heterologous materials into the crystallization solution. Porous materials are exceptionally effective at inducing nucleation. It is shown here that a combined diffusion-adsorption effect can increase protein concentration inside pores, which enables crystal nucleation even under conditions where heterogeneous nucleation on flat surfaces is absent. Provided the pore is sufficiently narrow, protein molecules approach its walls and adsorb more frequently than they can escape. The decrease in the nucleation energy barrier is calculated, exhibiting its quantitative dependence on the confinement space and the energy of interaction with the pore walls. These results provide a detailed explanation of the effectiveness of porous materials for nucleation of protein crystals, and will be useful for optimal design of such materials.


Proenca M.P.,CSIC - Institute of Materials Science | Proenca M.P.,University of Porto | Merazzo K.J.,CSIC - Institute of Materials Science | Vivas L.G.,CSIC - Institute of Materials Science | And 6 more authors.
Nanotechnology | Year: 2013

A comparative study on the structural and magnetic properties of highly ordered hexagonal arrays of Co nanoholes, nanowires, nanopillars and nanotubes, with tuned pore/wire/tube diameters, is here presented. The magnetic interactions and their dependence on the geometric features of the arrays were studied using first-order reversal curves (FORCs). For all nanostructures we observe an increase of the magnetostatic interactions with the templates' pore diameter, with the higher (smaller) values found for the nanowire (nanohole) arrays. For the smallest diameters studied (35 nm), all types of arrays could be considered as almost isolated nanostructures, where local interactions prevail. In particular, both nanotube and nanohole arrays exhibit considerable local magnetostatic interactions coming from the stray fields within each void or empty core. On the other hand, the coercivity is found to decrease with diameter for the elongated nanostructures, while it increases with the pore diameter for the nanohole arrays. This behavior is associated with the magnetization reversal mechanisms present in each array. This work highlights a versatile route to tailor the size, geometrical arrangement and magnetostatic interactions of ordered arrays and demonstrates their importance for the tuning of the magnetic behavior of nanometric devices. © 2013 IOP Publishing Ltd.


Stavros P.,Japan National Institute of Radiological Sciences | Saridakis E.,Institute of Nanoscience and Nanotechnology | Nounesis G.,Japan National Institute of Radiological Sciences
Biopolymers | Year: 2016

X-ray crystallography is the most powerful method for determining three-dimensional structures of proteins to (near-)atomic resolution, but protein crystallization is a poorly explained and often intractable phenomenon. Differential Scanning Calorimetry was used to measure the thermodynamic parameters (ΔG, ΔH, ΔS) of temperature-driven unfolding of two globular proteins, lysozyme, and ribonuclease A, in various salt solutions. The mixtures were categorized into those that were conducive to crystallization of the protein and those that were not. It was found that even fairly low salt concentrations had very large effects on thermodynamic parameters. High concentrations of salts conducive to crystallization stabilized the native folded forms of proteins, whereas high concentrations of salts that did not crystallize them tended to destabilize them. Considering the ΔH and TΔS contributions to the ΔG of unfolding separately, high concentrations of crystallizing salts were found to enthalpically stabilize and entropically destabilize the protein, and vice-versa for the noncrystallizing salts. These observations suggest an explanation, in terms of protein stability and entropy of hydration, of why some salts are good crystallization agents for a given protein and others are not. This in turn provides theoretical insight into the process of protein crystallization, suggesting ways of predicting and controlling it. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 642–652, 2016. © 2016 Wiley Periodicals, Inc.


Xu M.,Florida International University | Lai Y.,Florida International University | Jiang Z.,Florida International University | Terzidis M.A.,National Research Council Italy | And 4 more authors.
Nucleic Acids Research | Year: 2014

5',8-cyclo-2'-deoxypurines (cdPus) are common forms of oxidized DNA lesions resulting from endogenous and environmental oxidative stress such as ionizing radiation. The lesions can only be repaired by nucleotide excision repair with a low efficiency. This results in their accumulation in the genome that leads to stalling of the replication DNA polymerases and poor lesion bypass by translesion DNA polymerases. Trinucleotide repeats (TNRs) consist of tandem repeats of Gs and As and therefore are hotspots of cdPus. In this study, we provided the first evidence that both (5'R)- and (5'S)-5',8-cyclo-2'-deoxyadenosine (cdA) in a CAG repeat tract caused CTG repeat deletion exclusively during DNA lagging strand maturation and base excision repair. We found that a cdA induced the formation of a CAG loop in the template strand, which was skipped over by DNA polymerase β (pol β) lesion bypass synthesis. This subsequently resulted in the formation of a long flap that was efficiently cleaved by flap endonuclease 1, thereby leading to repeat deletion. Our study indicates that accumulation of cdPus in the human genome can lead to TNR instability via a unique lesion bypass by pol β. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.


Kritikos G.,Institute of Nanoscience and Nanotechnology | Vergadou N.,Institute of Nanoscience and Nanotechnology | Economou I.G.,Institute of Nanoscience and Nanotechnology | Economou I.G.,Texas A&M University at Qatar
Journal of Physical Chemistry C | Year: 2016

We present a molecular dynamics simulation study of 1-octyl-3-methylimidazolium tricyanomethanide ([Omim+][TCM-]) ionic liquid capped by two silica planar surfaces. The study extends over a wide temperature range and various interwall distances. Our results indicate that the structure and dynamics of the confined system is significantly affected by the width of the film. At the shortest interwall distance of 25 Å, which is comparable to the ion pair dimensions, the bulk structure is breached. The dynamics of the cation in the adsorbed layer is accelerated for the time scale of 1 ns and decelerates for longer time scales. In the most confined film, we observe a suppression of the cooperative characteristics in the diffusion. The whole phenomenon seems to be related to an Arrhenius behavior. Our proposed model suggests a stable, static liquid path in the center of the pore that facilitates the diffusion. The simulations results are consistent with a recent experimental study on the same confined system. © 2015 American Chemical Society.


Vivas L.G.,CSIC - Institute of Materials Science | Vazquez M.,CSIC - Institute of Materials Science | Escrig J.,University of Santiago de Chile | Allende S.,University of Santiago de Chile | And 4 more authors.
Physical Review B - Condensed Matter and Materials Physics | Year: 2012

Ordered arrays of Co xNi 1-x nanowires (0


Sousa C.T.,Institute of Nanoscience and Nanotechnology | Nunes C.,University of Porto | Proenca M.P.,Institute of Nanoscience and Nanotechnology | Leitao D.C.,Institute of Nanoscience and Nanotechnology | And 4 more authors.
Colloids and Surfaces B: Biointerfaces | Year: 2012

A novel pH-sensitive drug delivery system based on functionalized silica nanotubes was developed for the incorporation of non-steroidal anti-inflammatory drugs (NSAIDs), aimed at a tailored drug release in acidic conditions characteristic of inflamed tissues. Silica nanotubes (SNTs) were synthesized by a nanoporous alumina template assisted sol-gel method. Inner surfaces were physically and chemically modified to improve both the functionalization and subsequent incorporation of the drug. Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS) and transmission electron microscopy (TEM) were used to characterize the designed nanocarriers and their functionalization. To achieve the highest degree of functionalization, three types of aminosilanes were tested and calcination conditions were optimized. APTES was shown to be the most effective aminosilane regarding the functionalization of the SNTs' inner surface and an adequate calcination temperature (220 °C) was found to attain mechanical stability without compromising functionalization efficiency. Finally, the incorporation of naproxen into the nanotubes was accessed by fluorescence measurements and drug release studies were performed, revealing that the electrostatic linkage ensures effective release of the drug in the acidic pH typical of inflamed cells, while maintaining the SNT-drug conjugates stable at the typical bloodstream pH. © 2012 Elsevier B.V.

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