University of South Bohemia in České Budějovice
  • České Budějovice, South Bohemia, Czechia
Recent publications
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.
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.
Hydrogen has a negligible share on the global fuel market, yet it attracts a lot of investors. The main obstacle to the development of the hydrogen economy is its low cost-competitiveness. In order to meet energy demand and mitigate environmental damage, it is advisable to replace the existing fossil fuels with technologies that are more environmentally friendly and cost-competitive at the same time. Nowadays, some 97 % of hydrogen production comes from steam reforming of natural gas via energy that is obtained from fossil fuels. The production costs for 1 kg of hydrogen produced in this way, are between 2 and 4 €, while approximately 10 kg of CO2 is emitted. The production cost of hydrogen produced by electrolysis from water is about 7 €, 80 % of which is electricity cost. The production of (bio)hydrogen (via photobiological and dark fermentation techniques) from biowaste using renewable energy sources has recently come to the fore. This review discusses use of various types of nanoparticles (organic and inorganic) in (bio)hydrogen production. A diversity of organisms, in pure as well as mixed forms, could perhaps produce (bio)hydrogen using pure (preferably simple form) carbohydrates and biowaste as a feedstock in the existence of various forms of nanoparticles. Furthermore, the (bio)hydrogen production potential (and cost), have indeed been reported to change considerably depending on what type of nanoparticles used as well as their dosage.
There is a shared belief across latest literature that hydrogen and algae biodiesel are promising substitutes for fossil fuels. However, hydrogen infrastructure for everyday mobility is still in its early stage from a global perspective and there is no algae biodiesel refinery in operation. Despite all this, recent geopolitical developments have caused a tipping point to be reached in the EU and hydrogen mobility has become cheaper (7 €/100 km) than conventional fossil fuels (15.6 €/100 km) for the first time. In many other countries the breaking point is also approaching and recent methods in waste refining could make hydrogen production even cheaper (5.4 €/100 km). Switching to algae biodiesel is less technically challenging for the industry. Nevertheless, technological barriers in scaling up commercial-scale algae production make the hypothetical price of algae biodiesel far from price-competitive (292 €/100 km). At the present state of knowledge it is recommended to refine algae for non-energy purposes.
In this study the methane combustion was analysed with the TiO2 nanoparticles. A series of the simulation runs were performed by varying the fuel inlet velocity. However, the oxidizer and the nanoparticles spray were maintained constant for the entire run. The spray velocity varied from 100 m/s to 200 m/s with titanium dioxide (TiO2) nanoparticles. Using the series of the governing equation and modified Navier Stokes equation the model has been developed with the aid of numerical workbench. Three different domains are generated for fuel, oxidizer and nanoparticles. The velocity of the air and nanoparticles were maintained at constant levels and varying only the spray velocity of the fuel. Based on the findings, the mass fraction of both fuel and formation of the CO2 were dependent on the spray velocity. As the spray velocity increases the turbulence in the combustion chamber increases which ensures the higher mixing of both air–fuel and nanoparticles. From the procured findings 175 m/s and 200 m/s were the ideal range for better combustion efficiency compared to 100 m/s and 150 m/s. The simulation results have ascertained the role of the spray velocity on the emissions and the combustion efficiency of the engine. It is hoped that obtained results can provide directions to work on the combustion of the methane with the nanoparticles at the optimized spray velocity.
Production of wheat (Triticum aestivum L.) is affected by changing weather conditions, which are difficult to predict especially under climate change. Therefore, facultative varieties can be beneficial, because of their high adaptability in sowing time. Information on yield and yield components of facultative wheat in temperate climate, however, is limited. Therefore, a two-factorial experiment with the factors sowing time (autumn versus spring) and nitrogen fertilization (0, 5, 10, 15 and 20 g m⁻²) was conducted on a chernozem soil under Pannonian conditions in Eastern Austria in two seasons to assess the effects of sowing time, nitrogen fertilization and environment on yield and yield components of one facultative wheat variety. The experimental data were analyzed using principal component analysis and quantitative mixed model analysis. Grain yield of autumn-sown wheat was higher at 0 g N m⁻² and featured a higher increase with additional nitrogen fertilization compared to spring-sowing. At high nitrogen fertilization rates above 15 g m⁻², grain yield showed no response to further nitrogen fertilization. Based on ear density, grains per ear, thousand kernel weight and harvest index, the other yield and yield component parameters investigated in this study can be calculated. Ear density showed an increase with additional nitrogen fertilization, which was higher for autumn-sowing than spring-sowing. Differences in environmental conditions resulted in higher variation of grains per ear and thousand kernel weight for spring-sowing compared to autumn-sowing. Ear density, grains per ear, thousand kernel weight and harvest index featured dependencies among each other and were affected by environmental conditions during relevant developmental stages, e.g., tillering until anthesis for ear density and grains per ear as well as grain filling period after anthesis for thousand kernel weight and harvest index.
This study investigates the effect of the injection pressure on the spray characteristics and atomization of the fuel. The novelty of the work lies in examining the injection pressure (IP) at four different scenarios such as 180 MPa, 200 MPa, 220 MPa and 240 MPa. A series of test conducted in the single cylinder engine at three different concentrations of B10 (5% Jatropha curcas and 5% Thevetia peruviana-50 ppm of Fe 2 O 3), B20 (5% Jatropha curcas and 5% Thevetia peruviana-50 ppm of Fe 2 O 3) and B30 (5% Jatropha curcas and 5% Thevetia peruviana-50 ppm of Fe 2 O 3). All the samples were tested for performance and emission characteristics. Based on the procured results, the combination of the dual biodiesel blends improvised the production of higher brake power and lowered specific fuel consumption. Adding two blends together reduced the overall viscosity of the Thevetia peruviana (yellow oleander oil) since the viscosity of the jatropha is lower than the yellow oleander oil. As the concentration of the blends is increased there is a marginal drop in the brake thermal efficiency, however there is an improvement in the brake specific fuel consumptions. In terms of the combustion efficiency, the heat release rates were improvised upon addition of Fe 2 O 3. With regard to the emissions, there is no significant change in the NOx. Nevertheless, there is a drastic reduction in the HC and CO formation has been witnessed. Among various blends, B30 at 240 MPa of IP reported lower emissions than B10 and B20. In order to examine the fuel atomi-zation and spray characteristics, numerical modelling was applied. At 240 MPa, the fuel mixing rates were higher compared to the other injection pressure.
Gillnetting is a technique commonly used in relative abundance and biomass estimates of fish. However, due to its passive nature, the direct recalculation of the catch to reservoir volume or area is not trivial. This issue is often solved by using hydroacoustics, which provides information about fish density, though without the ability to distinguish species. However, the precision of such density estimates are also questionable. In this study, we estimated the abundance and biomass of dominant fish species before and after a biomanipulation program (fish removal) in 2020 using gillnetting and hydroacoustic surveys in a temperate reservoir. Between the two sampling periods, nearly 27,000 individuals (9000 kg) older than 0 + of bleak (Alburnus alburnus) and bream (Abramis brama) were removed during the biomanipulation program. Decreases in abundance and biomass estimates were expected for both techniques and both species. The gillnet decrease was 68% in CPUE (catch per unit of effort) and 48% in BPUE (biomass per unit of effort) for both species and all gillnets grouped together. Hydroacoustic observations showed a decrease of approximately 79% in abundance and 74% in biomass after fish reduction. Considering the numbers and biomass of fish removed, the absolute hydroacoustic estimates were underestimated for fish abundance but credibly estimated for biomass. The average weight of the fish taken was between the values of the fish caught with gillnets and the weights determined by hydroacoustics. In terms of results, both methods appear to be a suitable tool for estimating fish abundance and biomass in large inland waters, although the spatial and temporal distribution of fish of different sizes should be considered when using different sampling methods for fish monitoring.
This paper deals with the application of deposition analysis to an unusual type of features in the Late Bronze Age settlements in Central Europe. These are long narrow trenches (referred to as ‘long pits’ in this text) with characteristic standard form and alignment, as well as find contents, including high amounts of secondary-burned pottery fragments. In the context of prehistoric research, these features represent a relatively new phenomenon that has attracted attention in the last two decades due to new excavations in Bohemia and Bavaria. Based on the finds from Březnice (Czechia), the authors conclude that the long pits were connected with the closing rituals following the abandonment and burial of dwellings. Although no houses were directly documented on this site, their presence must be assumed, and their cultural biography can be reconstructed from the depositional characteristics of the accompanying finds. In order to fully understand the processes of deposition, the authors find it useful to focus not only on human agency but also on the relationships between the things themselves. This way, houses are understood as the central element of a hybrid actor-network. Their role may have been strengthened by their ontological status of living beings.
Development of primary spruce forests is driven by a series of disturbances, which also have an important influence on the understorey vegetation and its diversity. Early post-disturbance processes have been intensively studied, however, very little is known about the long-term effects of disturbances on the understorey. We quantified disturbance history using dendrochronological methods to investigate its impact on vascular plant diversity and understorey species composition. We sampled 141 plots randomly assigned throughout primary stands located in the zone of natural montane acidophilous forests dominated by Picea abies (L.) Karst. in the Western Carpathians. Dendrochronological, dendrometric, and environmental parameters were related to understorey properties using ordination methods and a Bayesian approach using multilevel linear models (GLMM). Time since the last disturbance (23–260 years ago; mostly windstorms and bark beetle outbreaks) had a significant effect on understorey species composition of the current communities, and it also interacted with disturbance severity to influence species diversity. The effect of disturbances on the understorey was largely mediated by the alteration of stand structure (age, DBH, canopy openness), Vaccinium myrtillus L. cover, and topsoil chemical properties. A period of severe disturbances between 1860 and 1890 resulted in a legacy of our current, relatively homogeneous spruce stands with less diverse sciophilous understorey dominated by V. myrtillus, which is in contrast to heterogeneous stands (in terms of age and spatial structure) driven by small-scale, lower-severity disturbances, which led to an understorey enriched by species with higher demands on light and topsoil quality (higher K concentration and lower C/N ratio). All developmental pathways following disturbances create a unique complex of spatiotemporal understorey variability in the montane spruce forests. Therefore, to preserve their full diversity, disturbances of all severities and sizes should be accepted as natural drivers, both in the field of nature conservation and close-to-nature forestry efforts.
The response of biodiversity to natural and anthropogenic disturbances is a central topic in applied ecology. Climate change has altered forest disturbance regimes, resulting in global increases in stand-replacing disturbances, which are regularly followed by the removal of trees (salvage logging). Yet, the mid- to long-term effects of disturbances and salvage logging and the importance of species relative abundances on β-diversity remain unclear. We compared the β-diversity of 13 taxonomic groups in intact forest, unlogged windthrow, and salvage-logged windthrow plots 11 years after a windthrow. Hill numbers were used to quantify differences in between-treatment and within-treatment β-diversity for rare, common, and dominant species. We found that over a decade post-disturbance, both windthrow and salvage logging led to significant changes in between-treatment β-diversity of all 13 taxonomic groups. In addition, differences in between- and within-treatment β-diversity were more pronounced for rare species than for common and dominant ones. Windthrow led to the homogenization of communities of most saproxylic and half of the non-saproxylic studied groups. However, contrary to our expectation, salvage logging did not further increase community homogenization for any taxonomic group or Hill number. Moreover, salvage logging even reversed the community homogenization caused by the windthrow for saproxylic groups, leading to more heterogeneous communities. This effect was likely caused by the relatively high amount and diversity of deadwood found on the salvage-logged plots. Our study suggests that differences in within-treatment β-diversity between salvaged and unsalvaged windthrows tend to vanish over time, whereas differences between-treatments persisted, especially for saproxylic groups and rare species. This finding underlines the importance of preserving the characteristic communities in unsalvaged wind-disturbed forests in the mid- to long-term. Therefore, we recommend a management strategy that balances the amount of salvage-logged areas with that of set-aside areas.
To understand the spatiotemporal overlap in the habitat use of sympatric predators, we studied longitudinal activity and reservoir section and depth use of pike (Esox lucius), pikeperch (Sander lucioperca) and catfish (Silurus glanis) in the Římov Reservoir, using an autonomous telemetry system for 11 months. We found significant differences among these species in studied parameters that varied considerably over tracked period. Pike consistently used the same sections of the reservoir, while pikeperch and catfish frequently visited a tributary during the warm season (late spring and early autumn), and moved closer to the dam during the cold season (late autumn to early spring). Pike longitudinal activity was highest in the cold season, pikeperch in the warm season, and catfish activity peaked in both seasons. Overlap in the depth use among species was higher in the warm season, when all species used the upper layer of the water column, and lower in the cold season, when pikeperch and catfish used deeper areas. These results demonstrated overlay and temporal variation of habitat use among these predators, as well as potential spatiotemporal space for their direct ecological interactions.
The application of environmental DNA (eDNA) metabarcoding has revolutionised large scale biodiversity monitoring of aquatic ecosystems. Validation studies have been performed mainly in laboratories and mesocosm experiments, however large-scale field experiments are necessary to verify the robustness of eDNA based monitoring for more specific applications and different environmental conditions. Here, eDNA samples were collected from three fishponds with high fish density and broad species diversity during summer and autumn. This sampling design included a large number of spatial replicates evenly spaced across the pond surface and samples from the inflow, while pooled samples were used to test the effect of filtration volumes on detectability. Most common species were detected using eDNA, but rare species were often missed out under these high stocking densities. Average read counts and site occupancy positively correlated strongly with species abundance and biomass, with the exception of samples affected by PCR inhibition. Higher diversity detections were observed in autumn compared to summer samplings and in running compared to standing water. Fish communities detected in pooled samples reflect the overall community structure, and the species detectability increases with higher filtration volumes. This work highlights how eDNA based surveys can be optimised based on sampling conditions to achieve the highest overall detection, which has important implications for applying this method to aid management and policy initiatives.
Air transport plays an inevitable role in the transportation sector. In the modern world, the aviation contribution is very immense to establish worldwide developments. However, the emission released by the aviation industry is massively high. Due to the sudden increase in the air traffic the contribution of global CO2 and CO have increased in recent years. Hence the aviation sector seeks the replacement for fossil fuels. In this study, the micro gas turbine engine has been experimentally studied for different engine speeds and throttle position. The gas turbine was allowed to run in the different test fuels such as, Jet-A, A20 (20% microalgae 80% Jet-A) and A30 (30% microalgae 70% Jet-A) and the predicted results were compared. In addition to the typical experimental calibrations, machine learning has been applied to examine the differences in the both performance and emission characteristics of the biofuel blends with approximately 51 different fuel combinations using LSTM networks. Based on the predicted results, introduction of the biofuel affects the production of the static thrust. On the contrary, the emissions of the CO and CO2 were very low compared to Jet-A. With regard to the nitrogen of the oxides, no massive reduction has been witnessed despite running at different fuel conditions. Besides, the marginal decrease in the NOx was observed above 75000 rpm.
Nitric oxide (NO) is an ancestral key signalling molecule essential for life and has enormous versatility in biological systems, including cardiovascular homeostasis, neurotransmission and immunity. Although our knowledge of NO synthases (Nos), the enzymes that synthesize NO in vivo , is substantial, the origin of a large and diversified repertoire of nos gene orthologues in fishes with respect to tetrapods remains a puzzle. The recent identification of nos3 in the ray-finned fish spotted gar, which was considered lost in this lineage, changed this perspective. This finding prompted us to explore nos gene evolution, surveying vertebrate species representing key evolutionary nodes. This study provides noteworthy findings: first, nos2 experienced several lineage-specific gene duplications and losses. Second, nos3 was found to be lost independently in two different teleost lineages, Elopomorpha and Clupeocephala. Third, the expression of at least one nos paralogue in the gills of developing shark, bichir, sturgeon, and gar, but not in lamprey, suggests that nos expression in this organ may have arisen in the last common ancestor of gnathostomes. These results provide a framework for continuing research on nos genes’ roles, highlighting subfunctionalization and reciprocal loss of function that occurred in different lineages during vertebrate genome duplications.
Andreu Saura and Alexandra Zakharova contributed equally and authors' order was based on alphabetical order of last names. ABSTRACT Leishmaniaviruses (LRVs) have been demonstrated to enhance progression of leishmaniasis, a vector-transmitted disease with a wide range of clinical manifestations that is caused by flagellates of the genus Leishmania. Here, we used two previously proposed strategies of the LRV ablation to shed light on the relationships of two Leishmania spp. with their respective viral species (L. guyanensis, LRV1 and L. major, LRV2) and demonstrated considerable difference between two studied systems. LRV1 could be easily eliminated by the expression of exogenous capsids regardless of their origin (the same or distantly related LRV1 strains, or even LRV2), while LRV2 was only partially depleted in the case of the native capsid overexpression. The striking differences were also observed in the effects of complete viral elimination with 2'C-methyladenosine (2-CMA) on the transcriptional profiles of these two Leishmania spp. While virtually no differentially expressed genes were detected after the LRV1 removal from L. guyanensis, the response of L. major after ablation of LRV2 involved 87 genes, the analysis of which suggested a considerable stress experienced even after several passages following the treatment. This effect on L. major was also reflected in a significant decrease of the proliferation rate, not documented in L. guya-nensis and naturally virus-free strain of L. major. Our findings suggest that integration of L. major with LRV2 is deeper compared with that of L. guyanensis with LRV1. We presume this determines different effects of the viral presence on the Leishmania spp. infections. IMPORTANCE Leishmania spp. represent human pathogens that cause leishmaniasis, a widespread parasitic disease with mild to fatal clinical manifestations. Some strains of leishmaniae bear leishmaniaviruses (LRVs), and this has been shown to aggravate disease course. We investigated the relationships of two distally related Leishmania spp. with their respective LRVs using different strategies of virus removal. Our results suggest the South American L. guyanensis easily loses its virus with no important consequences for the parasite in the laboratory culture. Conversely, the Old-World L. major is refractory to virus removal and experiences a prominent stress if this removal is nonetheless completed. The drastically different levels of integration between the studied Leishmania spp. and their viruses suggest distinct effects of the viral presence on infections in these species of parasites.
We report for the first time the use of two live-cell imaging agents from the group of luminescent transition metal complexes (IRAZOLVE-MITO and REZOLVE-ER) as cathodoluminescent probes. This first experimental demonstration shows the application of both probes for the identification of cellular structures at the nanoscale and near the native state directly in the cryo-scanning electron microscope. This approach can potentially be applied to correlative and multimodal approaches and used to target specific regions within vitrified samples at low electron beam energies.
The extent to which chemicals bioaccumulate in aquatic and terrestrial organisms represents a fundamental consideration for chemicals management efforts intended to protect public health and the environment from pollution and waste. Many chemicals, including most pharmaceuticals and personal care products (PPCPs), are ionizable across environmentally relevant pH gradients, which can affect their fate in aquatic and terrestrial systems. Existing mathematical models describe the accumulation of neutral organic chemicals and weak acids and bases in both fish and plants. Further model development is hampered, however, by a lack of mechanistic insights for PPCPs that are predominantly or permanently ionized. Targeted experiments across environmentally realistic conditions are needed to address the following questions: (1) What are the partitioning and sorption behaviors of strongly ionizing chemicals among species? (2) How does membrane permeability of ions influence bioaccumulation of PPCPs? (3) To what extent are salts and associated complexes with PPCPs influencing bioaccumulation? (4) How do biotransformation and other elimination processes vary within and among species? (5) Are bioaccumulation modelling efforts currently focussed on chemicals and species with key data gaps and risk profiles? Answering these questions promises to address key sources of uncertainty for bioaccumulation modeling of ionizable PPCPs and related contaminants. This article is protected by copyright. All rights reserved.
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2,819 members
Jan Valdman
  • Institute of Mathematics
Jan Zenka
  • Department of Medical Biology (KME)
Ivo Bukovsky
  • Department o Computer Science
Frantisek Weyda
  • Department of Medical Biology (KME)
Martin Pech
  • Department of Management
Branisovska 31, 37005, České Budějovice, South Bohemia, Czechia
Head of institution
Bohumil Jiroušek, Rector
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