The Czech Academy of Sciences
Recent publications
The shear strength reduction method (SSRM) is a standard method in slope stability enabling to determine the factor of safety and related failure zones. In case of the non-associated Mohr-Coulomb model, the method can oscillate with respect to the refinement of a finite element mesh. To suppress this drawback, the non-associated model is approximated by the associated one such that the strength parameters are reduced by using a function depending on a scalar factor and on the effective friction and dilatancy angles. This modification (MSSRM) can be easily implemented in commercial codes like Plaxis or Comsol Multiphysics. Next, an optimization approach to the modified SSRM (OPT-MSSRM) is introduced. It is shown that the optimization problem is well-defined and can be analyzed by variational principles. For its solution, a regularization method is combined with mesh adaptivity and implemented in Matlab. The SSRM, MSSRM and OPT-MSSRM methods are compared on numerical examples representing a case study of a real heterogeneous slope.
Cathepsin K (CatK) is a target for the treatment of osteoporosis, arthritis, and bone metastasis. Peptidomimetics with a cyanohydrazide warhead represent a new class of highly potent CatK inhibitors; however, their binding mechanism is unknown. We investigated two model cyanohydrazide inhibitors with differently positioned warheads: an azadipeptide nitrile Gü1303 and a 3-cyano-3-aza-β-amino acid Gü2602. Crystal structures of their covalent complexes were determined with mature CatK as well as a zymogen-like activation intermediate of CatK. Binding mode analysis, together with quantum chemical calculations, revealed that the extraordinary picomolar potency of Gü2602 is entropically favoured by its conformational flexibility at the nonprimed-primed subsites boundary. Furthermore, we demonstrated by live cell imaging that cyanohydrazides effectively target mature CatK in osteosarcoma cells. Cyanohydrazides also suppressed the maturation of CatK by inhibiting the autoactivation of the CatK zymogen. Our results provide structural insights for the rational design of cyanohydrazide inhibitors of CatK as potential drugs.
The nuclear pore complex (NPC) facilitates the trafficking of proteins and RNA between the nucleus and cytoplasm. The role of nucleoporins (Nups) in transport in the context of the NPC is well established, yet their function in tRNA export has not been fully explored. We selected several nucleoporins from different parts of the NPC to investigate their potential role in tRNA trafficking in Trypanosoma brucei. We show that while all of the nucleoporins studied are essential for cell viability, only TbNup62 and TbNup53a function in tRNA export. In contrast to homologs in yeast TbNup144 and TbNup158, which are part of the inner and outer ring of the NPC, have no role in nuclear tRNA trafficking. Instead, TbNup144 plays a critical role in nuclear division, highlighting the role of nucleoporins beyond nucleocytoplasmic transport. These results suggest that the location of nucleoporins within the NPC is crucial to maintaining various cellular processes.
Objective Miscarriages affect 10% of women aged 25–29, and 53% of women over 45. The primary cause of miscarriage is aneuploidy that originated in eggs. The Aurora kinase family has three members that regulate chromosome segregation. Therefore, distinguishing the roles of these isoforms is important to understand aneuploidy etiology. In meiosis, Aurora kinase A (AURKA) localizes to spindle poles, where it binds TPX2. Aurora kinase C (AURKC) localizes on chromosomes, where it replaces AURKB as the primary AURK in the chromosomal passenger complex (CPC) via INCENP binding. Although AURKA compensates for CPC function in oocytes lacking AURKB/C, it is unknown whether AURKA binds INCENP in wild type mouse oocytes. ZINC08918027 (ZC) is an inhibitor that prevents the interaction between AURKB and INCENP in mitotic cells. We hypothesized that ZC would block CPC function of any AURK isoform. Results ZC treatment caused defects in meiotic progression and spindle building. By Western blotting and immunofluorescence, we observed that activated AURKA and AURKC levels in ZC-treated oocytes decreased compared to controls. These results suggest there is a population of AURKA-CPC in mouse oocytes. These data together suggest that INCENP-dependent AURKA and AURKC activities are needed for spindle bipolarity and meiotic progression.
Information about cholesterol subcellular localization and transport pathways inside cells is essential for understanding and treatment of cholesterol-related diseases. However, there is a lack of reliable tools to monitor it. This work follows the fate of Sterolight, a BODIPY-labelled sterol, within the cell and demonstrates it as a suitable probe for visualization of sterol/lipid trafficking. Sterolight enters cells through an energy-independent process and knockdown experiments suggest caveolin-1 as its potential cellular carrier. Intracellular transport of Sterolight is a rapid process, and transfer from ER and mitochondria to lysosomes and later to lipid droplets requires the participation of active microtubules, as it can be inhibited by the microtubule disruptor nocodazole. Excess of the probe is actively exported from cells, in addition to being stored in lipid droplets, to re-establish the sterol balance. Efflux occurs through a mechanism requiring energy and may be selectively poisoned with verapamil or blocked in cells with mutated cholesterol transporter NPC1. Sterolight is efficiently transferred within and between different cell populations, making it suitable for monitoring numerous aspects of sterol biology, including the live tracking and visualization of intracellular and intercellular transport.
The Laser Interferometer Space Antenna (LISA) has the potential to reveal wonders about the fundamental theory of nature at play in the extreme gravity regime, where the gravitational interaction is both strong and dynamical. In this white paper, the Fundamental Physics Working Group of the LISA Consortium summarizes the current topics in fundamental physics where LISA observations of gravitational waves can be expected to provide key input. We provide the briefest of reviews to then delineate avenues for future research directions and to discuss connections between this working group, other working groups and the consortium work package teams. These connections must be developed for LISA to live up to its science potential in these areas.
This work demonstrates the facile preparation of one-dimensional nanostructures of poly(N-methyl pyrrole) (PNMPy) with the guidance of anionic organic dyes, methyl orange (MO) or Acid Blue 25 (AB). The addition of MO dye to polymerization mixture resulted in a nanotubular morphology of PNMPy, whereas nanofibers were obtained with AB dye. In order to examine the effects on yield and conductivity of the obtained polymers, various concentrations of dye ranging from 5 mM to 40 mM with fixed molar ratio of the N-methyl pyrrole to oxidant were used. Addition of both the dyes showed enhancement in the conductivity of PNMPy by one order of magnitude independent on the dye concentration. FTIR and Raman spectroscopies were used to investigate the molecular structure of PNMPy and the possible interaction with dyes. Additionally, the enhanced specific surface areas were attained for both PNMPy nanotubes and nanofibers. The presence of either dye, displayed a pronounced effect on electrochemical activity, as higher gravimetric capacitances were achieved by 1-D nanostructures.
Prey can ease the burden of exploitation by attracting a third party that interferes with their predators. Such is the case for plant-ant or aphid-ant mutualisms, where the victim supplies food to the ants, while the ants attack or drive away the offenders. Since ants are adaptive foragers, defense services can be altered by alternative food sources (e.g., other plants, or human-supplied resource). This article explores the prey-predator-ant system, using a model that combines predator-prey population dynamics with ant optimal foraging, where ants consume prey-supplied resources or alternative resources. Feedbacks between prey-predator dynamics and adaptive ant foraging leads to complex dynamics. For a given ant colony size and supply rate of alternative resources, prey can coexist with predators at alternative stable states, or along alternative limit cycles. Limit cycles extend the scope of defensive mutualism beyond the point where ants would abandon prey in favor of alternative resources under equilibrium conditions. These results highlight the importance of trait-mediated indirect interactions for natural mutualistic–antagonistic systems, and potential outcomes of manipulating ant defense services using baits in the case of agriculture.
To determine the toxicity and bioaccumulation of copper, adult oribatid soil mites Oppia nitens were exposed for 28 days to LUFA 2.2 soil spiked at concentrations of 0–6400 mg Cu kg⁻¹ dry soil. Effects on survival and reproduction were related to total and available (0.01 M CaCl2 extractable and pore water) concentrations in the soil and concentrations in the animals. The mites showed a concentration-dependent uptake of copper, which, however, decreased at toxic concentrations. Overall bioaccumulation factors were low, suggesting a low tendency for copper bioaccumulation. The estimated median lethal concentration (LC50) values were 3251 mg Cu kg⁻¹ dry soil, 1130 mg Cu kg⁻¹ dry soil, 1977 mg Cu L⁻¹ pore water, and 592 mg Cu kg⁻¹ dry body weight, and the estimated 50 % effective concentrations (EC50) for effects of copper on reproduction were 589 mg Cu kg⁻¹ dry soil, 116 mg Cu kg⁻¹ dry soil, 78.5 mg Cu L⁻¹ pore water, and 413 mg Cu kg⁻¹ dry body weight, based on measured soil total concentrations, 0.01 M CaCl2 extractable, porewater, and internal concentrations, respectively. The results show that the mite O. nitens is a suitable test organism for measuring metal bioavailability and toxicity in soil.
Psidium cattleyanum (Myrtaceae) is a widespread invasive species in several countries, particularly on oceanic islands. The species was first recorded in South Africa in 1948 and has since established self-sustaining populations. We present the first comprehensive evaluation of the invasiveness of P. cattleyanum in South Africa by: 1) mapping the current distribution of the species; 2) estimating its potential range using species distribution models in MaxEnt; 3) analysing the risk posed to South Africa using the risk analysis for alien taxa framework; and 4) developing recommendations for regulation. Psidium cattleyanum was recorded at 52 sites in four provinces across South Africa, with the population in the Western Cape being the first substantial invasive population reported from a temperate winter-rainfall region globally. Invasive populations were assessed in detail at four sites: Newlands Forest (Western Cape; n=2193 plants; covering ∼12 ha), Eshowe (KwaZulu-Natal; n=1561, ∼7.6 ha), Southbroom (KwaZulu-Natal; n = 449, ∼2.9 ha), and George (Western Cape; n=214, ∼2.4 ha). At all four sites the species is self-sustaining and there is evidence of spread. In South Africa, the east coast is climatically suitable for the species to expand its range. Although damaging invasions of P. cattleyanum have only been recorded on several islands to date, we find no reason to suggest that climatically suitable continental regions (including parts of South Africa) will not suffer harmful impacts if invasions progress unmanaged. As such, we support the current regulation of P. cattleyanum in South Africa, whereby the species must be controlled as part of a national management plan (category 1b) noting that while it is advisable to ban cultivation, the forcible removal of plants from people's gardens should perhaps only be prioritised if such plantings clearly pose a high risk (i.e., in climatically suitable regions near to riparian areas or natural areas).
Risk-taking in birds is often measured as the flight initiation distance (FID), the distance at which individuals take flight when approached by a potential predator (typically a human). The ecological factors that affect avian FID have received great attention over the past decades and meta-analyses and comparative analyses have shown that FID is correlated with body mass, flock size, starting distance of the approaching human, density of potential predators, as well as varying along rural to urban gradients. However, surprisingly, only few studies (mainly on reptiles and mammals) have explored effects of different types of refugia and their availability on animal escape decisions. We used Bayesian regression models (controlling for the phylogenetic relatedness of bird species) to explore changes in escape behaviour recorded in European cities in relationship to the birds' distance to the nearest refuge and distance fled to the refuge. In our analyses, we also included information on the type of refuge, built-up and vegetation cover, starting distance, flock size, urbanization level, and type of urban habitat. We found that birds preferred tree refuges over artificial and bush refuges. Birds escaped earlier if the distance to the nearest refuge of any type was longer and if birds fled longer distances to the refuge. FID was shorter when birds used bushes as refugia or landed on the ground after flushing compared to using artificial refugia. Similarly, the distance fled to a refuge was shortest when using bushes, and increased when escaping to artificial substrates and trees. Birds were more timid in suburban than core areas of cities, cemeteries than parks, and in areas with higher bush cover but lower cover of built-up areas and trees. Our findings provide novel information regarding the importance of refuge proximity and type as factors affecting the escape behaviour of urban birds.
Sediment fingerprinting is widely used in drainage basin analysis to identify the provenance and source contributions of sediments (or other material) in transit from source-to-sink. By enabling source areas of sediment supply to be targeted, the method has become an integral part of sustainable landscape management. The precision and accuracy of sediment fingerprinting is contingent on the choice of mixing model, which quantifies the contribution of potential sediment sources by minimizing the difference between observed properties of sink samples and characteristic properties of the sources. Here, we apply a set of frequentist and Bayesian mixing models with the aim of identifying the optimum composite fingerprint of four sediment sources (viz., agricultural land, rangeland, gullies, and landslides) in a small catchment draining the Iranian Loess Plateau in the Golestan province of northeastern Iran. Forty-four soil samples were collected from the four potential source zones. Based on seven synthetic mixtures with known source contributions we compared the performance of a frequentist Monte Carlo model, GLUE model, a Bayesian end-member model (BEMMA), MixSIAR Bayesian model, and a Brewer Bayesian model. We found that, in terms of uncertainty estimation, the best results were obtained with GLUE and BEMMA. Applying GLUE to our study catchment, we estimated the following source contributions to an earth dam reservoir: agricultural land (55.8 %), rangeland (33.7 %), gullies (15.7 %), and landslides (14.2 %), confirming the view that agriculture is the main cause of reservoir sedimentation. All source contributions exhibited high variability, which we attribute to storm frequency, sediment delivery due to hillslope-sink connectivity, and human activities involving removal of vegetation.
The causes of decreasing plant species richness include abandonment of traditional management and the spread of invasive species, even in alpine habitats. Studies on the restoration and management of alpine habitats are predominantly focused on vascular plants, although an important part of alpine vegetation and its diversity is formed by bryophytes. We used bryophytes to indicate changes that occur after the clearcutting of nonindigenous dwarf pine (Pinus mugo Turra) and attempted to reveal the community to which the development of bryophyte species structure was directed. We compared species richness and composition between surveys to test for changes in spatial heterogeneity bryophyte communities. We also tried to reveal the main ecological drivers of the restoration process. The study was performed in the (sub)alpine area of the Eastern High Sudetes Mts. (the Czech Republic). We estimated bryophyte species cover and compared the composition of the bryophyte community in autochthonous grassland areas, areas under the dwarf pine canopy, and clearcut areas to reveal the pattern of shifts 9 years after the treatment. We also measured soil characteristics to reveal the environmental habitat conditions. Evidence of taxonomic homogenization of habitat after dwarf pine removal was found. Light conditions and attributes of litter were the driving factors of successional changes in the bryophyte communities, which led to taxonomic homogenization. This finding explains the slow restoration process due to dwarf pine legacy on the clearcut area. The succession trends were also shaped by unobserved factors, such as climate change and environmental eutrophication. We highly recommended active management and long-term monitoring.
Synthesized cement systems made with variable C3A/C4AF ratios, containing C3S, gypsum and, optionally, calcite, were stored long-term at humid conditions at 5 or 20 °C, without any protection against atmospheric carbonation. Analytical techniques able to assess both the crystalline and amorphous phases were used. Experimental results were compared with thermodynamic simulations. The systems with C3A/C4AF < 1 better preserved the soundness of the CSH phase, which hosted iron, and prevented thaumasite formation. The addition of calcite in these systems inhibited carbonation. When occurred (mixtures without calcite), the carbonation was significantly more intense at ambient temperature. In the systems that underwent extensive deterioration, cross-linking of silicate structures, AFt decomposition, and iron release from the deteriorating CSH, occurred, while Al-incorporating amorphous silica, calcium carbonate polymorphs and hydrous iron oxide formed. The presence of unreacted C3A in the systems with C3A/C4AF = 1, suggested that CSH decomposition was contributed by available sulfates.
In this paper we propose a novel form known as the steel-PEC spliced frame beam (SPSFB), which is intended to maintain the advantages of the PEC beam while reducing the consumption of steel. In the SPSFB, an independent H-beam (mid-portion beam) is replaced by the PEC beam with a thinner flange. The PEC and stub beams are connected by web bolts, a welded flange, and a girth welded flange cover plate to improve flexural capacity. Low cycle loading tests were conducted on five SPSFB specimens testing the variables of the concrete strength, the length of the stub beam, and the length of flange-plates. Two failure modes were observed, and the related seismic behavior was investigated. When the damage occurred at the bottom of the PEC beam, higher grade concrete was correlated with better seismic performance. When the damage occurred at the bottom of the stub beam, setting an appropriate length of stub beam and flange-plate can improve the hysteretic capacity and further reduce steel consumption. Based on elastic and plastic analysis, the bearing capacities and deformation were calculated. The calculated results agreed well with the experimental results.
The boreal forest is an important global carbon (C) sink. Since low soil nitrogen (N) availability is commonly a key constraint on forest productivity, the prevalent view is that increased N input enhances its C sink-strength. This understanding however relies primarily on observations of increased aboveground tree biomass and soil C stock following N fertilization, whereas empirical data evaluating the effects on the whole ecosystem-scale C balance are lacking. Here we use a unique long-term experiment consisting of paired forest stands with eddy covariance measurements to explore the effect of ecosystem-scale N fertilization on the C balance of a managed boreal pine forest. We find that the annual C uptake (i.e. net ecosystem production, NEP) at the fertilized stand was 16 ± 2% greater relative to the control stand by the end of the first decade of N addition. Subsequently, the ratio of NEP between the fertilized and control stand remained at a stable level during the following five years with an average NEP to N response of 7 ± 1 g C per g N. Our study reveals that this non-linear response of NEP to long-term N fertilization was the result of a cross-seasonal feedback between the N-induced increases in both growing-season C uptake and subsequent winter C emission. We further find that one decade of N addition altered the sensitivity of ecosystem C fluxes to key environmental drivers resulting in divergent responses to weather patterns. Thus, our study highlights the need to account for ecosystem-scale responses to perturbations to improve our understanding of nitrogen-carbon-climate feedbacks in boreal forests.
The photo-excited triplet state of Zn-protoporphyrin IX located in the heme pocket of human neuroglobin has been investigated by time-resolved EPR coupled to magnetophotoselection. The triplet state in the protein matrix has been compared with the model complex in organic glass, considering both non-coordinating and coordinating solvent mixtures. The protein matrix plays an important role in stabilizing the coordination of the embedded chromophore, resulting in a more homogeneous environment relative to that of the chromophore in a glassy solvent, even in the presence of an axial nitrogenous ligand like pyridine. The EPR spectral parameters point out a slow Jahn–Teller interconversion between slightly different triplet states, both in organic solvent and in the protein matrix. The EPR-magnetophotoselection allows us to propose a reinterpretation of the assignment of the Q bands in the electronic absorption spectrum.
Some forms of national identification facilitate criticism of one's own country and nation, whereas others prevent it. The critical form of national identification – constructive patriotism – is characterized by the willingness to criticise the group in order to improve it. The uncritical form of national identification – glorification – is characterized by seeing the group as superior to others and by intolerance of criticism of the group. We used dual-process theories to examine whether differences in thinking style and cognitive ability help predict the emergence of the critical and uncritical form of national identification. We ran three correlational studies (total N = 2509) in Poland including two samples representative of Polish society. We ran an internal meta-analysis to summarise the obtained results from all studies. We found that constructive patriotism was positively linked with need for cognition (i.e., the willingness to engage in slow, effortful information processing; for the random effect model r = 0.18). Constructive patriotism was also positively linked with cognitive ability (r = 0.07). In contrast, glorification was negatively associated with need for cognition (r = -0.26) and cognitive ability (r = -0.09). Glorification was also positively linked with faith in intuition (r = 0.14).
Heat transfer in a synthetic impinging jet in the range of pulse frequencies is studied experimentally and numerically. A heat flux sensor is used to measure averaged and pulsating heat transfer at the point of flow stagnation. Mean and fluctuational structure and heat transfer in a synthetic impinging air jet are simulated using the axisymmetric non-steady-state Reynolds averaged Navier-Stokes equations and the Reynolds stress model. The measured results on the instantaneous and pulsation values of the heat flux at the stagnation point and along the radius of the target surface are obtained. The experimental spectra of heat flux fluctuations on the plate are given. The measurements and numerical predictions of the heat transfer are carried out with variation in the nozzle-to-target distance, and frequency of pulsations of the synthetic jets.
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3,210 members
Jan Rozman
  • Institute of Molecular Genetics
Thibault JY. Derrien
  • Institute of Physics
Holger Kruse
  • Institute of Biophysics
Jaroslav Hlinka
  • Institute of Computer Sciences, Department of Complex Systems
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Pod Vodárenskou věží 2, 18207, Prague, Czechia
Head of institution
prof. RNDr. Eva Zažímalová, CSc
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www.cs.cas.cz
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