Effect of Biostimulant, Manure Stabilizer, and Manure on Soil Physical Properties and Vegetation Status

Food production sustainability is one of contemporary agriculture's fundamental challenges. Farmers are currently facing high input prices in crop production and declining organic matter in the soil. For this reason, a field experiment was established to assess the effect of the biostimulant NeOsol (NS), the manure stabilizer Z'fix (ZF), farmyard manure (FM), and their combination in farm practice. In situ measurements provided information on the change in bulk density (BD), unit draft (UD), saturated hydraulic conductivity (SHC), and cone index (CI). Furthermore, the vegetation status was investigated via vegetation indices, and the yield and quality parameters were assessed. Management of the experimental field resulted in an overall decrease in BD over time for the treated variants compared to the control (CL). The decrease with time was also verified in the case of UD and CI at the depth zone of 10-20 cm. Variants FM (by 8.0%), FM_NS (by 7.3%), and FM_ZF_NS (by 3.8%) proved to have lower UD values than CL. An overall increase in SHC and in yield was observed over time. Concerning SHC, only FM (by 58.5%) proved different from CL. The yield of all the treated variants, i.e., NS (by 8.2%), FM (by 10.8%), FM_NS (by 14.1%), FM_ZF (by 17.8%), and FM_ZF_NS (by 20.1%), surpassed CL. Simultaneously, none of the examined treatments proved to have any adverse effect either on soil or on plant-related variables.

A Fast HPLC/UV Method for Determination of Ketoprofen in Cellular Media

A simple, sensitive and quick HPLC method was developed for the determination of ketoprofen in cell culture media (EMEM, DMEM, RPMI). Separation was performed using a gradient on the C18 column with a mobile phase of acetonitrile and miliQ water acidified by 0.1 % (v/v) formic acid. The method was validated for parameters including linearity, accuracy, precision, limit of quantitation and limit of detection, as well as robustness. The response was found linear over the range of 3-100 μg/mL as demonstrated by the acquired value of correlation coefficient R2=0.9997. The described method is applicable for determination of various pharmacokinetic aspects of ketoprofen in vitro.

Novel 5-Substituted Oxindole Derivatives as Bruton's Tyrosine Kinase Inhibitors: Design, Synthesis, Docking, Molecular Dynamics Simulation, and Biological Evaluation

Bruton's tyrosine kinase (BTK) is a non-RTK cytoplasmic kinase predominantly expressed by hemopoietic lineages, particularly B-cells. A new oxindole-based focused library was designed to identify potent compounds targeting the BTK protein as anticancer agents. This study used rational approaches like structure-based pharmacophore modeling, docking, and ADME properties to select compounds. Molecular dynamics simulations carried out at 20 ns supported the stability of compound 9g within the binding pocket. All the compounds were synthesized and subjected to biological screening on two BTK-expressing cancer cell lines, RAMOS and K562; six non-BTK cancer cell lines, A549, HCT116 (parental and p53-/-), U2OS, JURKAT, and CCRF-CEM; and two non-malignant fibroblast lines, BJ and MRC-5. This study resulted in the identification of four new compounds, 9b, 9f, 9g, and 9h, possessing free binding energies of -10.8, -11.1, -11.3, and -10.8 kcal/mol, respectively, and displaying selective cytotoxicity against BTK-high RAMOS cells. Further analysis demonstrated the antiproliferative activity of 9h in RAMOS cells through selective inhibition of pBTK (Tyr223) without affecting Lyn and Syk, upstream proteins in the BCR signaling pathway. In conclusion, we identified a promising oxindole derivative (9h) that shows specificity in modulating BTK signaling pathways.

Investigation of the potential effects of estrogen receptor modulators on immune checkpoint molecules

Immune checkpoints regulate the immune system response. Recent studies suggest that flavonoids, known as phytoestrogens, may inhibit the PD-1/PD-L1 axis. We explored the potential of estrogens and 17 Selective Estrogen Receptor Modulators (SERMs) as inhibiting ligands for immune checkpoint proteins (CTLA-4, PD-L1, PD-1, and CD80). Our docking studies revealed strong binding energy values for quinestrol, quercetin, and bazedoxifene, indicating their potential to inhibit PD-1 and CTLA-4. Quercetin and bazedoxifene, known to modulate EGFR and IL-6R alongside estrogen receptors, can influence the immune checkpoint functionality. We discuss the impact of SERMs on PD-1 and CTLA-4, suggesting that these SERMs could have therapeutic effects through immune checkpoint inhibition. This study highlights the potential of SERMs as inhibitory ligands for immune checkpoint proteins, emphasizing the importance of considering PD-1 and CTLA-4 inhibition when evaluating SERMs as therapeutic agents. Our findings open new avenues for cancer immunotherapy by exploring the interaction between various SERMs and immune checkpoint pathways.

Climate regulation processes are linked to the functional composition of plant communities in European forests, shrublands, and grasslands

Terrestrial ecosystems affect climate by reflecting solar irradiation, evaporative cooling, and carbon sequestration. Yet very little is known about how plant traits affect climate regulation processes (CRPs) in different habitat types. Here, we used linear and random forest models to relate the community-weighted mean and variance values of 19 plant traits (summarized into eight trait axes) to the climate-adjusted proportion of reflected solar irradiation, evapotranspiration, and net primary productivity across 36,630 grid cells at the European extent, classified into 10 types of forest, shrubland, and grassland habitats. We found that these trait axes were more tightly linked to log evapotranspiration (with an average of 6.2% explained variation) and the proportion of reflected solar irradiation (6.1%) than to net primary productivity (4.9%). The highest variation in CRPs was explained in forest and temperate shrubland habitats. Yet, the strength and direction of these relationships were strongly habitat-dependent. We conclude that any spatial upscaling of the effects of plant communities on CRPs must consider the relative contribution of different habitat types.

Correction: Krbata et al. Effect of Supercritical Bending on the Mechanical & Tribological Properties of Inconel 625 Welded Using the Cold Metal Transfer Method on a 16Mo3 Steel Pipe. Materials 2023, 16, 5014

In the original publication [...].

Assessment of refining efficiency during the refining cycle in a foundry degassing unit in industrial conditions

The article focuses on the issue of improving the efficiency of a Foundry Degassing Unit (FDU) via operational testing of aluminium alloys during casting at MOTOR JIKOV Slévárna a.s.. As part of the research, the efficiency of the refining process in the FDU was assessed. The main emphasis was placed on determining the moment of the greatest decrease in the hydrogen content in the melt and whether it is possible to shorten the refining cycle. The values of the Dichte Index were determined, on the basis of which the degassing curve was plotted and the progress of the melt degassing was assessed. To ensure the required quality of castings, the maximum allowable value of the Dichte Index ranged from 3 to 4%. During the process, the temperature drop during the refining cycle was also determined. The total temperature drop from pouring the melt into the ladle to the end of refining ranged from 26 to 32 °C, which is within the acceptable limits of the foundry. Based on the knowledge resulting from the operational experiments, recommendations were formulated to optimize the refining technology at the FDU for the MOTOR JIKOV Slévárna a.s. foundry.

Radioreparative Effect of Diode Laser on Leukopoiesis Recovery: A Pilot Study

The aim of the present study was to investigate the effect of laser therapy on leukopoiesis recovery after irradiation with ionizing radiation. A dose of ionizing radiation was used that induced the hematological form of radiation sickness, reducing the number of blood cells. Subsequently, mice were treated with non-ionizing laser radiation. Based on the examination of the peripheral blood, the study found that laser therapy significantly impacted the number of eosinophils and basophils two weeks after irradiation. Laser therapy also led to the faster reparation of the lymphocyte lineage of white blood cells (WBCs). The research showed that the examined therapeutic laser had a long-term radioreparative effect on gamma-irradiated mice, improving the absolute counts of different lines of WBCs. The results of this study could have implications for the treatment of radiation sickness in humans.

Disease-associated nonsense and frame-shift variants resulting in the truncation of the GluN2A or GluN2B C-terminal domain decrease NMDAR surface expression and reduce potentiating effects of neurosteroids

N-methyl-D-aspartate receptors (NMDARs) play a critical role in normal brain function, and variants in genes encoding NMDAR subunits have been described in individuals with various neuropsychiatric disorders. We have used whole-cell patch-clamp electrophysiology, fluorescence microscopy and in-silico modeling to explore the functional consequences of disease-associated nonsense and frame-shift variants resulting in the truncation of GluN2A or GluN2B C-terminal domain (CTD). This study characterizes variant NMDARs and shows their reduced surface expression and synaptic localization, altered agonist affinity, increased desensitization, and reduced probability of channel opening. We also show that naturally occurring and synthetic steroids pregnenolone sulfate and epipregnanolone butanoic acid, respectively, enhance NMDAR function in a way that is dependent on the length of the truncated CTD and, further, is steroid-specific, GluN2A/B subunit-specific, and GluN1 splice variant-specific. Adding to the previously described effects of disease-associated NMDAR variants on the receptor biogenesis and function, our results improve the understanding of the molecular consequences of NMDAR CTD truncations and provide an opportunity for the development of new therapeutic neurosteroid-based ligands.

Liposomes Affect Protein Release and Stability of ITA-Modified PLGA-PEG-PLGA Hydrogel Carriers for Controlled Drug Delivery

Fat grafting, a key regenerative medicine technique, often requires repeat procedures due to high-fat reabsorption and volume loss. Addressing this, a novel drug delivery system uniquely combines a thermosensitive, FDA-approved hydrogel (itaconic acid-modified PLGA-PEG-PLGA copolymer) with FGF2-STAB, a stable fibroblast growth factor 2 with a 21-day stability, far exceeding a few hours of wild-type FGF2's stability. Additionally, the growth factor was encapsulated in "green" liposomes prepared via the Mozafari method, ensuring pH protection. The system, characterized by first-order FGF2-STAB release, employs green chemistry for biocompatibility, bioactivity, and eco-friendliness. The liposomes, with diameters of 85.73 ± 3.85 nm and 68.6 ± 2.2% encapsulation efficiency, allowed controlled FGF2-STAB release from the hydrogel compared to the unencapsulated FGF2-STAB. Yet, the protein compromised the carrier's hydrolytic stability. Prior tests were conducted on model proteins human albumin (efficiency 80.8 ± 3.2%) and lysozyme (efficiency 81.0 ± 2.7%). This injectable thermosensitive system could advance reconstructive medicine and cosmetic procedures.

Forest carbon stock development following extreme drought-induced dieback of coniferous stands in Central Europe: a CBM-CFS3 model application

BACKGROUND

We analyze the forest carbon stock development following the recent historically unprecedented dieback of coniferous stands in the Czech Republic. The drought-induced bark-beetle infestation resulted in record-high sanitary logging and total harvest more than doubled from the previous period. It turned Czech forestry from a long-term carbon sink offsetting about 6% of the country's greenhouse gas emissions since 1990 to a significant source of CO2 emissions in recent years (2018-2021). In 2020, the forestry sector contributed nearly 10% to the country's overall GHG emissions. Using the nationally calibrated Carbon Budget Model of the Canadian Forest Sector (CBM-CFS3) at a regional (NUTS3) spatial resolution, we analyzed four scenarios of forest carbon stock development until 2070. Two critical points arise: the short-term prognosis for reducing current emissions from forestry and the implementation of adaptive forest management focused on tree species change and sustained carbon accumulation.

RESULTS

This study used four different spruce forest dieback scenarios to assess the impact of adaptive forest management on the forest carbon stock change and CO2 emissions, tree species composition, harvest possibilities, and forest structure in response to the recent unprecedented calamitous dieback in the Czech Republic. The model analysis indicates that Czech forestry may stabilize by 2025 Subsequently, it may become a sustained sink of about 3 Mt CO2 eq./year (excluding the contribution of harvested wood products), while enhancing forest resilience by the gradual implementation of adaptation measures. The speed of adaptation is linked to harvest intensity and severity of the current calamity. Under the pessimistic Black scenario, the proportion of spruce stands declines from the current 43-20% by 2070, in favor of more suited tree species such as fir and broadleaves. These species would also constitute over 50% of the harvest potential, increasingly contributing to harvest levels like those generated by Czech forestry prior to the current calamity. The standing stock would only be recovered in 50 years under the optimistic Green scenario.

CONCLUSION

The results show progress of adaptive management by implementing tree species change and quantify the expected harvest and mitigation potential in Czech forestry until 2070.

Mechanical Properties of MiniBars™ Basalt Fiber-Reinforced Geopolymer Composites

Fly ash-based geopolymers represent a new material, which can be considered an alternative to ordinary Portland cement. MiniBars™ are basalt fiber composites, and they were used to reinforce the geopolymer matrix for the creation of unidirectional MiniBars™ reinforced geopolymer composites (MiniBars™ FRBCs). New materials were obtained by incorporating variable amount of MiniBars™ (0, 12.5, 25, 50, 75 vol.% MiniBars™) in the geopolymer matrix. Geopolymers were prepared by mixing fly ash powder with Na2SiO3 and NaOH as alkaline activators. MiniBars™ FRBCs were cured at 70 °C for 48 h and tested for different mechanical properties. Optical microscopy and SEM were employed to investigate the fillers and MiniBars™ FRBC. MiniBars™ FRBC showed increasing mechanical properties by an increased addition of MiniBars™. The mechanical properties of MiniBars™ FRBC increased more than the geopolymer wtihout MiniBars™: the flexural strength > 11.59-25.97 times, the flexural modulus > 3.33-5.92 times, the tensile strength > 3.50-8.03 times, the tensile modulus > 1.12-1.30 times, and the force load at upper yield tensile strength > 4.18-7.27 times. SEM and optical microscopy analyses were performed on the fractured surface and section of MiniBars™ FRBC and confirmed a good geopolymer network around MiniBars™. Based on our results, MiniBars™ FRBC could be a very promising green material for buildings.

Major tree species of Central European forests differ in their proportion of positive, negative, and nonstationary growth trends

Temperate forests are undergoing significant transformations due to the influence of climate change, including varying responses of different tree species to increasing temperature and drought severity. To comprehensively understand the full range of growth responses, representative datasets spanning extensive site and climatic gradients are essential. This study utilizes tree-ring data from 550 sites from the temperate forests of Czechia to assess growth trends of six dominant Central European tree species (European beech, Norway spruce, Scots pine, silver fir, sessile and pedunculate oak) over 1990-2014. By modeling mean growth series for each species and site, and employing principal component analysis, we identified the predominant growth trends. Over the study period, linear growth trends were evident across most sites (56% increasing, 32% decreasing, and 10% neutral). The proportion of sites with stationary positive trends increased from low toward high elevations, whereas the opposite was true for the stationary negative trends. Notably, within the middle range of their distribution (between 500 and 700 m a.s.l.), Norway spruce and European beech exhibited a mix of positive and negative growth trends. While Scots pine growth trends showed no clear elevation-based pattern, silver fir and oaks displayed consistent positive growth trends regardless of site elevation, indicating resilience to the ongoing warming. We demonstrate divergent growth trajectories across space and among species. These findings are particularly important as recent warming has triggered a gradual shift in the elevation range of optimal growth conditions for most tree species and has also led to a decoupling of growth trends between lowlands and mountain areas. As a result, further future shifts in the elevation range and changes in species diversity of European temperate forests can be expected.

Seismic Beacon-A New Instrument for Detection of Changes in Rock Massif

The seismic beacon is a new instrument that allows for the measurement of changes in a rock massif with high sensitivity. It is based on effects, which affect the propagation of harmonic seismic waves generated continuously with stable and precise frequency and amplitude. These seismic waves are registered by a system of seismic stations. The amplitude of the seismic signal is very small, and it is normally hidden in a seismic noise. Special techniques are applied to increase the signal-to-noise ratio. In 2020, the first prototype of the seismic beacon was constructed in a laboratory, and field tests were performed in 2022 and 2023. During the tests, the changes in spectral amplitude and phase of seismic waves were detected, which is interpreted as the changes in material properties. These measurements testified the basic functionality of the device. The seismic beacon has been developed primarily for the detection of critical stress before an earthquake, which is manifested by non-linear effects such as higher harmonics generation. In addition, it could be used, for example, in the detection of magma movements, groundwater level changes, changes in hydrocarbon saturation in rocks during the extraction of oil and natural gas, or the penetration of gases and liquids into the earth's crust.

Survivability and proliferation of microorganisms in bentonite with implication to radioactive waste geological disposal: strong effect of temperature and negligible effect of pressure

As bentonite hosts a diverse spectrum of indigenous microorganisms with the potential to influence the long-term stability of deep geological repositories, it is essential to understand the factors influencing microbial activity under repository conditions. Here, we focus on two factors, i.e., temperature and swelling pressure, using a suspension of Cerny Vrch bentonite to boost microbial activity and evaluate microbial response. Suspensions were exposed either to different pressures (10, 12 and 15 MPa; to simulate the effect of swelling pressure) or elevated temperatures (60, 70, 80 and 90 °C; to simulate the effect of cannister heating) for four weeks. Each treatment was followed by a period of anaerobic incubation at atmospheric pressure/laboratory temperature to assess microbial recovery after treatment. Microbial load and community structure were then estimated using molecular-genetic methods, with presence of living cells confirmed through microscopic analysis. Our study demonstrated that discrete application of pressure did not influence on overall microbial activity or proliferation, implying that pressure evolution during bentonite swelling is not the critical factor responsible for microbial suppression in saturated bentonites. However, pressure treatment caused significant shifts in microbial community structure. We also demonstrated that microbial activity decreased with increasing temperature, and that heat treatment strongly influenced bentonite microbial community structure, with several thermophilic taxa identified. A temperature of 90 °C proved to be limiting for microbial activity and proliferation in all bentonite suspensions. Our study emphasizes the crucial role of a deep understanding of microbial activity under repository-relevant conditions in identifying possible strategies to mitigate the microbial potential within the deep geological repository and increase its long-term stability and safety.

Determining the Mouth-to-Microphone Distance in Rigid Laryngoscopy: A Simple Solution Based on the Newly Measured Values of the Depth of Endoscope Insertion into the Mouth

Mouth-to-microphone (MTM) distance is important when measuring the sound of voice. However, determining the MTM distance for laryngoscope-mounted microphones during laryngoscopic examinations is cumbersome. We introduce a novel solution for such cases, using the depth of insertion of the laryngoscope into the mouth DI as a reference distance. We measured the average insertion depth, DI, in 60 adult women and 60 adult men for rigid laryngoscopes with 70° and 90° view. We found the DI for the 70°/90° laryngoscope to be 9.7 ± 0.9/9.4 ± 0.6 cm in men, 8.9 ± 0.9/8.7 ± 0.7 cm in women, and 9.3 ± 0.9/9.0 ± 0.7 cm in all adults. Using these values, we show that, for microphones fixed at 15-40 cm from the tip of the laryngoscope, the final MTM distances are between 5 and 35 cm from the lips, and the standard uncertainties of these distances are between 16% and 2.5%. Our solution allows laryngologists and laryngoscope manufacturers to set and estimate the MTM distance for any rigid laryngeal endoscope with a microphone attached with reasonable accuracy, avoiding the need to measure this distance in vivo in routine practice.

Complete genome sequence of Xanthomonas phage M29, a new member of Foxunavirus isolated in the Czech Republic

The newly discovered Xanthomonas phage M29 (Xp M29) is the first lytic phage infecting Xanthomonas campestris pv. campestris (Xcc) that was isolated from cabbage leaves in the Czech Republic. The phage consists of icosahedral head approximately 60 nm in diameter and a probably contractile tail of 170 nm. The complete genome size was 42 891 bp, with a G + C content of 59.6%, and 69 ORFs were predicted on both strands. Pairwise nucleotide comparison showed the highest similarity with the recently described Xanthomonas phage FoX3 (91.2%). Bacteriophage Xp M29 has a narrow host range infecting 5 out of 21 isolates of Xcc. Xp M29 is a novel species in a newly formed genus Foxunavirus assigned directly to the class Caudoviricetes.

Conserved temperature requirements but contrasting responses to humidity across oviposition preferences in temperate grasshoppers

The right choice of an oviposition site is a crucial task for oviparous species without maternal care. In contrast to well investigated biotic factors, e.g., larval food preferences, parasitism, predation, and competition avoiding, abiotic factors affecting oviposition preferences in insects have been rarely investigated in comparative studies. To improve our current understanding of oviposition site selection in Orthoptera, we investigated the influence of substrate temperature and moisture on the oviposition behaviour of 14 temperate grasshopper species. Conspecific groups of adults were kept in arenas with simultaneous temperature and moisture gradients. For each ootheca produced during the experiment (n = 1192) we recorded its depth and local microclimatic conditions. Our results indicate that microclimatic oviposition preferences significantly differ among species, however, correlations between adult habitat preferences and microclimatic oviposition preferences were surprisingly weak. Even oligothermic species preferred substrate temperatures around 30 °C and some xerothermic species preferred higher humidity. The hypothesized tendency to place oothecae closer to the ground within grass tussocks under hot and dry conditions was confirmed. It is possible that species evaluate microclimatic conditions for oviposition in the context of occupied habitat, i.e., in a relative rather than absolute manner.

Insight into the Li-Storage Property of Surface-Modified Ti2Nb10O29 Anode Material for High-Rate Application

Ti-based anode materials are considered to be an alternative to graphite anodes to accomplish high-rate application requirements. Ti2Nb10O29 (TNO15) has attracted much attention due to its high lithium storage capacity through the utilization of multiple redox couples and a suitable operating voltage window of 1.0 to 2.0 V vs Li/Li+. However, poor intrinsic electronic conductivity has limited the futuristic applicability of this material to the battery anode. In this work, we report the modification of TNO15 by introducing oxygen vacancies and using few-layered carbon and copper coatings on the surface to improve its Li+ storage property. With the support of the galvanostatic intermittent titration technique (GITT), we found that the diffusion coefficient of carbon/copper coated TNO15 is 2 orders of magnitude higher than that of the uncoated sample. Here, highly conductive copper metal on the surface of the carbon-coated oxygen-vacancy-incorporated TNO15 increases the overall electronic and ionic conductivity. The prepared TNO15-800-C-Cu-700 half-cell shows a significant rate capability of 92% when there is a 10-fold increase in the current density. In addition, the interconnected TNO15 nanoparticles create a porous microsphere structure, which enables better Li-ion transportation during charge/discharge process, and experiences an enhancement after the carbon and copper coating on the surface of the primary TNO15 nanocrystallites.

Flexible Hybrid and Single-Component Aerogels: Synthesis, Characterization, and Applications

The inherent disadvantages of traditional nonflexible aerogels, such as high fragility and moisture sensitivity, severely restrict their applications. To address these issues, different techniques have been used to incorporate the flexibility in aerogel materials; hence, the term "flexible aerogels" was introduced. In the case of introducing flexibility, the organic part is induced with the inorganic part (flexible hybrid aerogels). Additionally, some more modern research is also available in the fabrication of hybrid flexible aerogels (based on organic-organic), the combination of two organic polymers. Moreover, a new type (single-component flexible aerogels) are quite a new category composed of only single materials; this category is very limited, charming to make the flexible aerogels pure from single polymers. The present review is composed of modern techniques and studies available to fabricate hybrid and single-component flexible aerogels. Their synthesis, factors affecting their parameters, and limitations associated with them are explained deeply. Moreover, a comparative analysis of drying methods and their effectiveness in the development of structures are described in detail. The further sections explain their properties and characterization methods. Eventually, their applications in a variety of multifunctional fields are covered. This article will support to introduce the roadmap pointing to a future direction in the production of the single-component flexible aerogel materials and their applications.

PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning

PredictONCO 1.0 is a unique web server that analyzes effects of mutations on proteins frequently altered in various cancer types. The server can assess the impact of mutations on the protein sequential and structural properties and apply a virtual screening to identify potential inhibitors that could be used as a highly individualized therapeutic approach, possibly based on the drug repurposing. PredictONCO integrates predictive algorithms and state-of-the-art computational tools combined with information from established databases. The user interface was carefully designed for the target specialists in precision oncology, molecular pathology, clinical genetics and clinical sciences. The tool summarizes the effect of the mutation on protein stability and function and currently covers 44 common oncological targets. The binding affinities of Food and Drug Administration/ European Medicines Agency -approved drugs with the wild-type and mutant proteins are calculated to facilitate treatment decisions. The reliability of predictions was confirmed against 108 clinically validated mutations. The server provides a fast and compact output, ideal for the often time-sensitive decision-making process in oncology. Three use cases of missense mutations, (i) K22A in cyclin-dependent kinase 4 identified in melanoma, (ii) E1197K mutation in anaplastic lymphoma kinase 4 identified in lung carcinoma and (iii) V765A mutation in epidermal growth factor receptor in a patient with congenital mismatch repair deficiency highlight how the tool can increase levels of confidence regarding the pathogenicity of the variants and identify the most effective inhibitors. The server is available at https://loschmidt.chemi.muni.cz/predictonco.

FireProt 2.0: web-based platform for the fully automated design of thermostable proteins

Thermostable proteins find their use in numerous biomedical and biotechnological applications. However, the computational design of stable proteins often results in single-point mutations with a limited effect on protein stability. However, the construction of stable multiple-point mutants can prove difficult due to the possibility of antagonistic effects between individual mutations. FireProt protocol enables the automated computational design of highly stable multiple-point mutants. FireProt 2.0 builds on top of the previously published FireProt web, retaining the original functionality and expanding it with several new stabilization strategies. FireProt 2.0 integrates the AlphaFold database and the homology modeling for structure prediction, enabling calculations starting from a sequence. Multiple-point designs are constructed using the Bron-Kerbosch algorithm minimizing the antagonistic effect between the individual mutations. Users can newly limit the FireProt calculation to a set of user-defined mutations, run a saturation mutagenesis of the whole protein or select rigidifying mutations based on B-factors. Evolution-based back-to-consensus strategy is complemented by ancestral sequence reconstruction. FireProt 2.0 is significantly faster and a reworked graphical user interface broadens the tool's availability even to users with older hardware. FireProt 2.0 is freely available at http://loschmidt.chemi.muni.cz/fireprotweb.

Explorative Image Analysis of Methylene Blue Interactions with Gelatin in Polypropylene Nonwoven Fabric Membranes: A Potential Future Tool for the Characterization of the Diffusion Process

This manuscript explores the interaction between methylene blue dye and gelatin within a membrane using spectroscopy and image analysis. Emphasis is placed on methylene blue's unique properties, specifically its ability to oscillate between two distinct resonance states, each with unique light absorption characteristics. Image analysis serves as a tool for examining dye diffusion and absorption. The results indicate a correlation between dye concentrations and membrane thickness. Thinner layers exhibit a consistent dye concentration, implying an even distribution of the dye during the diffusion process. However, thicker layers display varying concentrations at different edges, suggesting the establishment of a diffusion gradient. Moreover, the authors observe an increased concentration of gelatin at the peripheries rather than at the center, possibly due to the swelling of the dried sample and a potential water concentration gradient. The manuscript concludes by suggesting image analysis as a practical alternative to spectral analysis, particularly for detecting whether methylene blue has been adsorbed onto the macromolecular network. These findings significantly enhance the understanding of the complex interactions between methylene blue and gelatin in a membrane and lay a solid foundation for future research in this field.

Rotation-based schedules in elementary schools to prevent COVID-19 spread: a simulation study

Rotations of schoolchildren were considered as a non-pharmacological intervention in the COVID-19 pandemic. This study investigates the impact of different rotation and testing schedules.We built an agent-based model of interactions among pupils and teachers based on a survey in an elementary school in Prague, Czechia. This model contains 624 schoolchildren and 55 teachers and about 27 thousands social contacts in 10 layers. The layers reflect different types of contacts (classroom, cafeteria, etc.) in the survey. On this multi-graph structure we run a modified SEIR model of covid-19 infection. The parameters of the model are calibrated on data from the outbreak in the Czech Republic in spring 2020. Weekly rotations of in-class and distance learning are an effective preventative measure in schools reducing the spread of covid-19 by 75-81% . Antigen testing twice a week or PCR once a week significantly reduces infections even when using tests with a lower sensitivity. The structure of social contacts between pupils and teachers strongly influences the transmission. While the density of contact graphs for older pupils is 1.5 times higher than for younger pupils, the teachers' network is an order of magnitude denser. Teachers moreover act as bridges between groups of children, responsible for 14-18% of infections in the secondary school compared to 8-11% in the primary school. Weekly rotations with regular testing are a highly effective non-pharmacological intervention for the prevention of covid-19 spread in schools and a way to keep schools open during an epidemic.

Plant Growth-Promoting Endophytic Bacteria Isolated from Miscanthus giganteus and Their Antifungal Activity

Modern technologies can satisfy human needs only with the use of large quantities of fertilizers and pesticides that are harmful to the environment. For this reason, it is possible to develop new technologies for sustainable agriculture. The process could be carried out by using endophytic microorganisms with a (possible) positive effect on plant vitality. Bacterial endophytes have been reported as plant growth promoters in several kinds of plants under normal and stressful conditions. In this study, isolates of bacterial endophytes from the roots and leaves of Miscanthus giganteus plants were tested for the presence of plant growth-promoting properties and their ability to inhibit pathogens of fungal origin. Selected bacterial isolates were able to solubilize inorganic phosphorus, fix nitrogen, and produce phytohormones, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, and siderophore. Leaf bacterial isolate Pantoea ananat is 50 OL 2 had high production of siderophores (zone ≥ 5 mm), and limited phytohormone production, and was the only one to show ACC deaminase activity. The root bacterial isolate of Pseudomonas libanensis 5 OK 7A showed the best results in phytohormone production (N6-(Δ2-isopentenyl)adenine and indole-3-acetic acid, 11.7 and 12.6 ng·mL-1, respectively). Four fungal cultures-Fusarium sporotrichioides DBM 4330, Sclerotinia sclerotiorum SS-1, Botrytis cinerea DS 90 and Sphaerodes fimicola DS 93-were used to test the antifungal activity of selected bacterial isolates. These fungal cultures represent pathogenic families, especially for crops. All selected root endophyte isolates inhibited the pathogenic growth of all tested fungi with inhibition percentages ranging from 30 to 60%. Antifungal activity was also tested in two forms of immobilization of selected bacterial isolates: one in agar and the other on dextrin-coated cellulose carriers. These results demonstrated that the endophytic Pseudomonas sp. could be used as biofertilizers for crops.