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The genetic diversity of the gut microbiota has a central role in host health. Here, we created pangenomes for 728 human gut prokaryotic species, quadrupling the genes of strain-specific genomes. Each of these species has a core set of a thousand genes, differing even between closely related species, and an accessory set of genes unique to the different strains. Functional analysis shows high strain variability associates with sporulation, whereas low variability is linked with antibiotic resistance. We further map the antibiotic resistome across the human gut population and find 237 cases of extreme resistance even to last-resort antibiotics, with a predominance among Enterobacteriaceae. Lastly, the presence of specific genes in the microbiota relates to host age and sex. Our study underscores the genetic complexity of the human gut microbiota, emphasizing its significant implications for host health. The pangenomes and antibiotic resistance map constitute a valuable resource for further research. [Display omitted] • Pangenomes showcase the extensive genetic diversity of the human gut microbiota • High strain-level variability associates with species' capacity to sporulate • Extreme antibiotic resistance is widespread in the healthy, non-hospitalized population • The presence of specific microbial genes relates to host age and sex Shoer et al. showcase the extensive genetic diversity of the human gut microbiota and its implications for the host. They find high strain-level variability associates with species' capacity to sporulate, while low variability associates with carrying antibiotic resistance genes. Their insights into microbial evolution open avenues for targeted microbiota interventions. [ABSTRACT FROM AUTHOR]

The aggregation of alpha-synuclein (aSyn) represents a neuropathological hallmark observed in a group of neurodegenerative disorders collectively known as synucleinopathies. Despite their shared characteristics, these disorders manifest diverse clinical and pathological phenotypes. The mechanism underlying this heterogeneity is thought to be due to the diversity in the aSyn strains present across the diseases. In this perspective, we will explore recent findings on aSyn strains and discuss recent discoveries about Lewy bodies' composition. We further discuss the current hypothesis for aSyn spreading and emphasize the emerging biomarker field demonstrating promising results. A comprehension of these mechanisms holds substantial promise for future clinical applications. This understanding can pave the way for the development of personalized medicine strategies, specifically targeting the unique underlying causes of each synucleinopathy. Such advancements can revolutionize therapeutic approaches and significantly contribute to more effective interventions in the intricate landscape of neurodegenerative disorders. In this perspective, Lázaro and Lee explore the diverse characteristics of Lewy bodies (LBs) and alpha-synuclein (aSyn) strains, their roles in synucleinopathies, and the mechanisms of aSyn aggregation and propagation. They highlight emerging biomarkers and AI integration for early diagnosis and personalized treatment strategies. [ABSTRACT FROM AUTHOR]

Two‐dimensional (2D) Janus materials are a fascinating class of materials resulting from their unique electronic and magnetic properties induced by mirror symmetry breaking. However, 2D Janus materials with intrinsic magnetism remain rather rare, casting a mysterious veil over magnetism. In this work, the electronic and magnetic properties of Janus Mn2GeX (X = As, Sb) monolayers using the first‐principles calculations are investigated. The results demonstrate that these Janus materials exhibit excellent mechanical and dynamic stability, indicating their potential for future applications in nanoscale spintronic devices. Interestingly, the Janus Mn2GeAs$\left(\text{Mn}\right)_{2} \text{GeAs}$ and Mn2GeSb$\left(\text{Mn}\right)_{2} \text{GeSb}$ monolayers possess exciting half‐metallic character with wide half‐metallic gaps of 0.29 and 0.18 eV, and spin gaps of 1.68 and 1.62 eV, respectively. Their calculated ground state exhibits a strong preference for ferromagnetic ordering, with a Curie temperature (Tc$T_{c}$) of 630 and 590 K, respectively. Additionally, the ferromagnetism of Janus Mn2GeX (X = As, Sb) monolayers is robust against biaxial strain ranging from −6% to 6%. Under 6% tensile strain, the calculated Tc$T_{c}$ of the Mn2GeSb$\left(\text{Mn}\right)_{2} \text{GeSb}$ monolayer is 639 K, which represents a 9% increase compared to the Tc$T_{c}$ observed in the unstrained condition. All these intriguing electronic and magnetic properties make the Janus Mn2GeX (X = As, Sb) monolayers an appealing candidate for applications in nanoscale spintronic devices. [ABSTRACT FROM AUTHOR]

BaTiO3 (BT), a lead‐free ferroelectric material, is employed in energy‐conversion devices, including actuators and capacitors. However, its ferroelectric properties, such as the piezoelectric coefficient and Curie temperature, fall short of those of harmful lead‐based ferroelectrics, such as Pb(Zrx, Ti1−x)O3. In this study, a BT crystal is examined under biaxial strain (i.e., strain in the a‐ and b‐directions of the unit cell) to investigate the alterations in its ferroelectric properties. The piezoelectric coefficient, Curie temperature, polarization magnitude, and coercive electric field are calculated under varying biaxial strains using molecular dynamics simulations. The simulations utilize a core–shell‐type interatomic potential developed from first‐principles electronic structure calculations. In the findings, it is revealed that 1) the Curie temperature, polarization magnitude, and coercive electric field increase, whereas the piezoelectric coefficient in the c‐direction decreases under biaxial compression; 2) modifications in the ferroelectric properties depend on the area of ab‐plane and not on its aspect ratio. Comprehensive analyses of the Ti‐displacement distribution offer microscopic insights into strain‐induced shifts in ferroelectric properties. [ABSTRACT FROM AUTHOR]

The possibility of Fe loaded on BP (Fe@BP) as an efficient gas sensor for the detection of toxic gases such as NO2, NO, and CO is studied by the first‐principles calculation, and it is proposed that Fe@BP is an excellent gas‐sensitive material. The adsorption behaviors of gases on Fe@BP were analyzed in terms of adsorption configurations and electronic properties. It is found that all gases adsorbed on Fe@BP exhibit significantly enhanced interactions, and the adsorption intensity is much larger than that of molecules adsorbed on the surface of pure BP. Fe@BP has high selectivity for toxic and ambient gas molecules. In addition, the adsorption strength of NO2 and NO molecules on Fe@BP increases after compression strain is applied (within −3%), while the adsorption strength of CO decreases gradually. After the tensile strain is applied, the adsorption intensity of NO2 and NO is decreased, but that of CO is increased gradually. It is speculated that the strain causes changes in the electronic structure, which affects the adsorption behavior. The adsorption of NO has a stronger strain sensitivity. For these reasons, Fe@BP with high adsorption strength and strain selection is the ideal gas‐sensitive material. [ABSTRACT FROM AUTHOR]

Pigment is the most attractive attribute and integral part of human life. The source of the pigment used for different applications is chemically synthesised. However, pigment produced from natural sources (such as plants and microorganisms) can also be applied as a coloring agent. In addition to being colorants, many natural pigments are also fascinating bioactive substances with possible health benefits. Agrochemicals, food, medicine, pharmacology, cosmetics, and numerous other industries use these compounds. In this study, a total of 7 pigmented colonies were isolated from the soil samples of different areas of Assam. Out of 7 pigmented colonies, 3 colonies showed orange color and 4 colonies showed yellow color. Based on the similarity of growth pattern and high intensity of pigmentation one colony from each pigment was picked for further studies. The isolated orange and yellow pigments were denoted as S1 and S2, respectively. With the help of Bergey's Manual of Determinative Bacteriology the isolated pigmented strains were preliminary identified based on their morphological, microscopic, and biochemical characteristics and after that 16S rRNA gene sequencing helped to identify the bacteria at the species level and the strains were identified as (S1) Micrococcus aloeverae ON377368 and (S2) Exiguobacterium aestuarii ON377409. The identified strains Micrococcus aloeverae and Exiguobacterium aestuarii showed a high pigment production rate at specific optimized conditions such as at temperature 37°C, pH 6, and NaCl concentrations at 1.5-2% and strains also showed a good characteristic growth pattern at a specific time interval. Therefore, the present study may be a helpful step towards the large-scale manufacture of pigments and the extraction, purification, and characterization of the pigment extracted from these strains will lead to provide a potent eco-friendly natural dye in the industrial sector. [ABSTRACT FROM AUTHOR]

The problem of submerged body motion in a frozen channel is considered. The fluid in the channel is assumed to be inviscid and incompressible. Fluid flow is the potential. The ice cover has non-uniform compression along the principal coordinates. The damping of hydroelastic waves generated by the motion of submerged body is modeled by taking into account porosity of ice. The submerged body is modeled as a dipole, the potential of which is determined using mirror images from the channel walls. The main problem of the submerged body motion at constant speed along the central line of the channel is considered. Two subproblems are addressed: comparison of damping effects of the porosity and viscosity of ice and investigation of effects of symmetrically variable ice thickness relative to the central line of the channel. It was found that the most important compressive stress is the stress in the direction of the motion of the submerged body. The speed of the body, which was subcritical for uncompressed ice, may become critical or supercritical. Compressive stresses perpendicular to the direction of motion do not qualitatively change the character of the ice response. These stresses, in combination with compressive stresses along the direction of motion, strengthen the effect of the latter, making the transition from subcritical to supercritical regime faster. [ABSTRACT FROM AUTHOR]

Since prion diseases result from infection and neurodegeneration of the central nervous system (CNS), experimental characterizations of prion strain properties customarily rely on the outcomes of intracerebral challenges. However, natural transmission of certain prions, including those causing chronic wasting disease (CWD) in elk and deer, depends on propagation in peripheral host compartments prior to CNS infection. Using gene-targeted GtE and GtQ mice, which accurately control cellular elk or deer PrP expression, we assessed the impact that peripheral or intracerebral exposures play on CWD prion strain propagation and resulting CNS abnormalities. Whereas oral and intraperitoneal transmissions produced identical neuropathological outcomes in GtE and GtQ mice and preserved the naturally convergent conformations of elk and deer CWD prions, intracerebral transmissions generated CNS prion strains with divergent biochemical properties in GtE and GtQ mice that were changed compared to their native counterparts. While CWD replication kinetics remained constant during iterative peripheral transmissions and brain titers reflected those found in native hosts, serial intracerebral transmissions produced 10-fold higher prion titers and accelerated incubation times. Our demonstration that peripherally and intracerebrally challenged Gt mice develop dissimilar CNS diseases which result from the propagation of distinct CWD prion strains points to the involvement of tissue-specific cofactors during strain selection in different host compartments. Since peripheral transmissions preserved the natural features of elk and deer prions, whereas intracerebral propagation produced divergent strains, our findings illustrate the importance of experimental characterizations using hosts that not only abrogate species barriers but also accurately recapitulate natural transmission routes of native strains. [ABSTRACT FROM AUTHOR]

In order to explore the differences of taste and metabolites of different Ganoderma lucidum strains, the fruiting bodies of different Ganoderma lucidum strains were taken as samples, the taste of aqueous extracts of 21 different Ganoderma lucidum strains were determined by electronic tongue. The non-targeted metabonomics techniques of ultra high performance liquid chromatography and mass spectrometry were used. Combined with principal component analysis (PCA) and orthogonal partial least square discriminant analysis (OPLS-DA) and other statistical methods based on the results of taste cluster analysis, three different Ganoderma lucidum strains (GL229, GL219, GL236) were selected for metabolite identification and analysis. The results showed that the response values of sour, umami, bitter and salty taste of water extracts of different Ganoderma lucidum strains were quite different. A total of 6057 metabolites were identified from the water extracts of three different Ganoderma lucidum strains. There were 1282, 1311 and 1966 differential metabolites between GL219 and GL229, GL236 and GL229, GL219 and GL236, respectively. There were 123 differential metabolites among the three control groups, including organic acids and their derivatives, benzene ring compounds, organic oxygen compounds, organic heterocyclic compounds, lipids and lipid compounds. The main differential metabolites were Jamaicamide C, 2-isopropylmalicacid, 1-naphthylamine, tyramine, genipin and so on. The differential metabolites L-glutamine, glutamine, cinchonine, solanidine, phenylacetaldehyde and dehydrocholicacid were flavor substances, which contributed to the taste differences of water extracts of different Ganoderma lucidum strains. This study showed that metabonomics could be used to analyze the compositions differences of Ganoderma lucidum with different taste. Therefore, it could provide a theoretical basis for the material basis of Ganoderma lucidum taste.

The aim of the study is to obtain a comprehensive characterization of Yersinia pseudotuberculosis strains from the Aksai high-mountain and Balkhash desert foci of plague in Central Asia. Materials and methods. Investigation of the cultural, morphological and biochemical properties of the examined strains was carried out using conventional methods of laboratory diagnostics. Ion S5 XL System (Thermo Fischer Scientific) was used for whole-genome sequencing. Data processing and sequence assembly of raw reads de novo were performed using Ion Torrent Suite software package 5.12 and Newbler gsAssembler 2.6 (454 Life Sciences). To search for marker SNPs, the Wombac 2.0 program based on the BioLinux 8.0 operating system was applied. When constructing the dendrogram, the Maximum Likelihood method, the PhyML 3.1 program and the HKY85 model were used. Results and discussion. The studied strains from the Aksai high-mountain and Balkhash desert foci have properties characteristic of the Y. pseudotuberculosis species, are prototrophs and do not contain the pYV plasmid. According to phylogenetic analysis based on identified 109,641 core SNPs, they are closely related to strains of the pseudotuberculosis microbe from the Sarydzhaz high-mountain focus in the Kyrgyz Republic and the Republic of Kazakhstan, as well as to the O:3 serovar strain from Turkmenistan. The cluster of these Central Asian strains on the phylogenetic tree of Y. pseudotuberculosis is localized next to strains of the pseudotuberculosis microbe of O:3 serovar from various regions of the world. The results obtained testify to the circulation of a separate phylogeographic population of Y. pseudotuberculosis in the territory of natural plague foci in Central Asia. The characterized Y. pseudotuberculosis strains and their whole genome sequences can be used as reference ones for the Aksai and Balkhash natural plague foci of Central Asia.

Micrococcus sp. PNS1, Ochrobactrum sp. PNS5, Stenotrophomonas sp. PNS6, Pseudomonas sp. PNB3, Brevibacterium sp. PNB5, Achromobacter sp. PNB6, and Bosea sp. PNB7 were isolated from the PN2 and PN2-B associations and screened for their ability to degrade mono-hydroxylated biphenyls with hydroxyl groups at the C3 or C4 atoms in the biphenyl molecule. The maximum degradation efficiency was 98 % for 3-hydroxybiphenyl and up to 100 % for 4-hydroxybiphenyl with various strains. All strains showed amplification of a fragment of the bphA gene encoding biphenyl-2,3-dioxygenase biosynthesis. Sequence analysis of the bphA gene revealed a distinct branch on the tree topology, indicating its similarity level with known sequences of this gene. Pseudomonas sp. PNB3 was found to possess the benA gene encoding benzoate-1,2-dioxygenase biosynthesis and positioned on the same evolutionary branch as the benA gene from the well-known biphenyl degrader Pseudomonas putida KT2440. The results obtained demonstrate that the transformation of 3-hydroxy- and 4-hydroxybiphenyls by the isolated strains occurs through dioxygenation of the unsubstituted ring of the biphenyl molecule, with subsequent cleavage into 3- and 4-hydroxybenzoic acids, respectively. Therefore, the strains that were examined are promising for potential application in technologies aimed at degrading both chlorobiphenyls and hydroxylated biphenyls.

Pigment is the most attractive attribute and integral part of human life. The source of the pigment used for different applications is chemically synthesised. However, pigment produced from natural sources (such as plants and microorganisms) can also be applied as a coloring agent. In addition to being colorants, many natural pigments are also fascinating bioactive substances with possible health benefits. Agrochemicals, food, medicine, pharmacology, cosmetics, and numerous other industries use these compounds. In this study, a total of 7 pigmented colonies were isolated from the soil samples of different areas of Assam. Out of 7 pigmented colonies, 3 colonies showed orange color and 4 colonies showed yellow color. Based on the similarity of growth pattern and high intensity of pigmentation one colony from each pigment was picked for further studies. The isolated orange and yellow pigments were denoted as S1 and S2, respectively. With the help of Bergey’s Manual of Determinative Bacteriology the isolated pigmented strains were preliminary identified based on their morphological, microscopic, and biochemical characteristics and after that 16S rRNA gene sequencing helped to identify the bacteria at the species level and the strains were identified as (S1) Micrococcus aloeverae ON377368 and (S2) Exiguobacterium aestuarii ON377409. The identified strains Micrococcus aloeverae and Exiguobacterium aestuarii showed a high pigment production rate at specific optimized conditions such as at temperature 37°C, pH 6, and NaCl concentrations at 1.5-2% and strains also showed a good characteristic growth pattern at a specific time interval. Therefore, the present study may be a helpful step towards the large-scale manufacture of pigments and the extraction, purification, and characterization of the pigment extracted from these strains will lead to provide a potent eco-friendly natural dye in the industrial sector.

The current research explored the biocontrol ability of two strains of Trichoderma fungi on infected Freesia corm by Fusarium disease. Enhancements in plant growth and performance were evaluated in response to the Trichoderma fungi in laboratory and greenhouse conditions. Laboratory experiments included five Trichoderma strains, i.e., T1, T20, and Th4, related to T. harzianum species, T2 related to T. atroviride species, and Tvi related to T. virens species. A dual culture test and investigation of the inhibition and colonization rate were carried out with 11 treatments in three replications. Results revealed that strains T1 and T2 completely covered the pathogen in 96 h of culture by 70.02% and 68.98% and successfully inhibited the colonization of the disease agent by 84.53% and 82.72%, respectively, compared to the other strains. Then, a greenhouse experiment was performed with eight treatments, using suspensions of Trichoderma strains separately or combined with the presence of Fusarium fungus isolate on Freesia cultivation. The results showed that the strains at different levels were able to increase the growth and yield of Freesia plants and control Fusarium disease. In general, the T2 strain was more effective in increasing plant growth and flower stem height in Freesia. The T1 strain specifically improved the corm diameter. Both T1 and T2 strains demonstrated effectiveness in controlling and reducing the severity of Fusarium disease and enhancing the growth quality of Freesia. [ABSTRACT FROM AUTHOR]

Background. Annual studies of West Nile virus (WNV) circulating in endemic areas are necessary to characterize its properties and track them over time. Given the lack of specific antiviral therapy for West Nile fever (WNF), it is of interest to study sensitivity to drugs widely used in modern practice. The aim of the study is to study the sensitivity of West Nile virus strains circulating in the Russian Federation in 2018–2021 to drugs used to treat viral infections.Material and methods. The sensitivity of WNV strains to ribavirin, riamilovir, and umifenovir was determined using Vero cell culture.Results and discussion. A study of the sensitivity of WNV strains circulating in the Russian Federation in 2018–2021 to therapeutic drugs used to treat viral infections showed their heterogeneity in this regard. Thus, 5 strains (WNV_Volgograd_601/18, Volgograd_723/18, Volgograd_830/18, Voronezh_794/21, Astrachan_962/21) out of 10 studied were characterized by some differences in resistance to ribavirin and riamilovir. No statistically significant differences were revealed when comparing drug resistance indicators of the group of WNV strains of the «old» genovariant with those of the «new» group.Conclusion. Further analysis of the genome of the studied WNV strains will allow us to establish genetic characteristics, which may contribute to the establishment of molecular mechanisms of resistance to ribavirin, riamilovir, and umifenovir.

Abstract Synucleinopathies are a group of neurodegenerative disorders characterized by the presence of misfolded α-Synuclein (αSyn) in the brain. These conditions manifest with diverse clinical and pathophysiological characteristics. This disease diversity is hypothesized to be driven by αSyn strains with differing biophysical properties, potentially influencing prion-type propagation and consequentially the progression of illness. Previously, we investigated this hypothesis by injecting brain lysate (seeds) from deceased individuals with various synucleinopathies or human recombinant αSyn preformed fibrils (PFFs) into transgenic mice overexpressing either wild type or A53T human αSyn. In the studies herein, we expanded on these experiments, utilizing a panel of antibodies specific for the major carboxyl-terminally truncated forms of αSyn (αSynΔC). These modified forms of αSyn are found enriched in human disease brains to inform on potential strain-specific proteolytic patterns. With monoclonal antibodies specific for human αSyn cleaved at residues 103, 114, 122, 125, and 129, we demonstrate that multiple system atrophy (MSA) seeds and PFFs induce differing neuroanatomical spread of αSyn pathology associated with host specific profiles. Overall, αSyn cleaved at residue 103 was most widely present in the induced pathological inclusions. Furthermore, αSynΔC-positive inclusions were present in astrocytes, but more frequently in activated microglia, with patterns dependent on host and inoculum. These findings support the hypothesis that synucleinopathy heterogeneity might stem from αSyn strains with unique biochemical properties that include proteolytic processing, which could result in dominant strain properties.

Abstract A comprehensive mathematical model is proposed to study two strains of dengue virus with saturated incidence rates and quarantine measures. Imperfect dengue vaccination is also assumed in the model. Existence, uniqueness and stability of the proposed model are proved using the results from fixed point and degree theory. Additionally, well constructed Lyapunov function candidates are also applied to prove the global stability of infection-free equilibria. It is also demonstrated that the model is generalized Ulam-Hyers stable under some appropriate conditions. The model is fitted to the real data of dengue epidemic taken from the city of Espirito Santo in Brazil. For the approximate solution of the model, a non-standard finite difference(NSFD) approach is applied. Sensitivity analysis is also carried out to show the influence of different parameters involved in the model. The behaviour of the NSFD is also assessed under different denominator functions and it is observed that the choice of the denominator function could influence the solution trajectories. Different scenario analysis are also assessed when the reproduction number is below or above one. Furthermore, simulations are also presented to assess the epidemiological impact of dengue vaccination and quarantine measures for infected individuals.

The dieback disease is caused by the phytopathogen Lasiodiplodia theobromae that affects farmer's production; it is characterized by its ability to survive through pycnidia and chlamydospores in soil and crop residues, it spreads to plant tissues to remain endophytic until the host crop becomes vulnerable by mechanical damage or nutrient deficiency leading to death of young branches, mummification and fruit rot. Due to the persistent mode of L. theobromae, the research focused on the simultaneous depuration of strains of the phytopathogen isolated from banana and raspberry with the objective of detecting the mycelial growth rate against fungicides of different mode of action, establishing by means of a toxicity scale at one of the concentrations 10; 1; 0,1; 0,01 and 0,001 µg mL-1 as efficient with propiconazole, mancozeb, iprodione, difenoconazole and cyproconazole, respectively in their order. There was 100% growth inhibition with propiconazole and difenoconazole at a concentration of 10 µg mL-1 that allows them to be effective fungicides in the control of the phytopathogen, while mancozeb, iprodione and cyproconazole were harmless to L. theobromae, because they allowed its mycelial growth in the research. [ABSTRACT FROM AUTHOR]

Thanks to the capabilities of distributed fibre optic sensors (DFOS), a significant increase in their applications within civil and geotechnical engineering has been observed during the last few years. In contrast to conventional spot gauges, the main advantage of this technology is direct damage detection, as the information is gained over the entire measurement path. This diagnostic solution is especially suitable for safety-critical infrastructure, including bridges. However, to utilise the benefits of the DFOS approach, appropriate interrogators, sensors, and installation methods must be adopted. The article briefly discusses possible solutions available on the market, indicating their specific advantages and limitations. Then, several practical case studies related to bridge monitoring in Poland are presented. The review shows various possible applications, from long measurement sections over entire spans to small-size structural components. Some are truly new and pioneer solutions, solving different technical problems in bridge engineering. Presented applications supported by in situ data proved the possible high-quality performance of DFOS-based systems for measurements of concrete, steel and composite bridges in actual operating conditions. [ABSTRACT FROM AUTHOR]

Thermoelectric materials convert heat into electricity, with a broad range of applications near room temperature (RT). However, the library of RT high‐performance materials is limited. Traditional high‐temperature synthetic methods constrain the range of materials achievable, hindering the ability to surpass crystal structure limitations and engineer defects. Here, a solution‐based synthetic approach is introduced, enabling RT synthesis of powders and exploration of densification at lower temperatures to influence the material's microstructure. The approach is exemplified by Ag2Se, an n‐type alternative to bismuth telluride. It is demonstrated that the concentration of Ag interstitials, grain boundaries, and dislocations are directly correlated to the sintering temperature, and achieve a figure of merit of 1.1 from RT to 100 °C after optimization. Moreover, insights into and resolve Ag2Se's challenges are provided, including stoichiometry issues leading to irreproducible performances. This work highlights the potential of RT solution synthesis in expanding the repertoire of high‐performance thermoelectric materials for practical applications. [ABSTRACT FROM AUTHOR]

Synucleinopathies are a group of neurodegenerative disorders characterized by the presence of misfolded α-Synuclein (αSyn) in the brain. These conditions manifest with diverse clinical and pathophysiological characteristics. This disease diversity is hypothesized to be driven by αSyn strains with differing biophysical properties, potentially influencing prion-type propagation and consequentially the progression of illness. Previously, we investigated this hypothesis by injecting brain lysate (seeds) from deceased individuals with various synucleinopathies or human recombinant αSyn preformed fibrils (PFFs) into transgenic mice overexpressing either wild type or A53T human αSyn. In the studies herein, we expanded on these experiments, utilizing a panel of antibodies specific for the major carboxyl-terminally truncated forms of αSyn (αSynΔC). These modified forms of αSyn are found enriched in human disease brains to inform on potential strain-specific proteolytic patterns. With monoclonal antibodies specific for human αSyn cleaved at residues 103, 114, 122, 125, and 129, we demonstrate that multiple system atrophy (MSA) seeds and PFFs induce differing neuroanatomical spread of αSyn pathology associated with host specific profiles. Overall, αSyn cleaved at residue 103 was most widely present in the induced pathological inclusions. Furthermore, αSynΔC-positive inclusions were present in astrocytes, but more frequently in activated microglia, with patterns dependent on host and inoculum. These findings support the hypothesis that synucleinopathy heterogeneity might stem from αSyn strains with unique biochemical properties that include proteolytic processing, which could result in dominant strain properties. [ABSTRACT FROM AUTHOR]

Simple Summary: The Retinta cattle breed from Spain is derived from two ancestral bovine lineages, which are clearly characterized based on coat color: blond and brown/red. Currently, despite a great level of admixture, two pure genetic lines remain (Retinto Extremeño and Andalusian Blond). This study analyzed the genealogy and genetics of over 22,000 animals, revealing high genetic diversity overall, but lower diversity within each subpopulation, with the Retinto line having the greatest influence on the breed. A special subgroup within the Andalusian Blond lineage, known as the Tamarona cow, was identified as genetically unique and should be protected due to its small population size. Preserving genetic diversity within the Retinta breed is crucial to ensure sustainable breeding in the breed's natural environment. The Retinta breed, an autochthonous type of Spanish beef cattle, is highly adapted to breeding in its natural environment, which is characterized by a Mediterranean climate. The origins of this breed can be traced to two ancestral bovine stocks, which gave rise to distinct morphotypes differentiated primarily by coat color, alongside other significant traits such as growth, morphological conformation and temperament. Specifically, one morphotype comprises blond animals (Rubia Andaluza), genetically resembling the ancestral Bos taurus Aquitanicus, while the other encompasses brown- and red-colored animals (Retinta Extremeña) originating from Bos taurus Turdenatus stock. Over decades, these populations have undergone hybridization, leading to a unified population, albeit with the original subpopulations largely maintaining their genetic integrity. The objective of this study was to undertake genealogical and genomic characterization of these genetic lines, including a particular subpopulation within the blond animals (Tamarona cow). To achieve this, the genealogical records of 22,004 active animals were analyzed, and over 63,000 SNPs from a total of 1030 animals were examined for genomic characterization. Genealogical analysis revealed pedigree completeness and a high level of effective population size (Ne) across the entire population, yet relatively low Ne values within each pure line (ranging from 28.38 to 34.47). These findings underscore the ongoing efforts of the National Association of Retinta Breeders (ACRE) over the past decades to mitigate the loss of variability in this breed. The genomic characterization highlights the persistent differences within the original population and the predominant influence of the Retinto line within the current breed, as evidenced by principal component analysis (PCA) and admixture analysis. Furthermore, the identification of the Tamarona subpopulation within the blond lineage underlines its unique genetic composition, warranting its recognition as an official genetic line within the current Retinta breed. Given the small population size of these lines, particularly the Tamarona subpopulation, protective measures are imperative to preserve this distinct gene pool. Such measures would enhance the genetic diversity of the Retinta breed, which is essential for sustainable breeding practices in its natural habitats. [ABSTRACT FROM AUTHOR]

The crack formations in AlGaN templates for deep ultraviolet (DUV) light‐emitting diodes (LEDs) are investigated and successfully suppressed. The strain values in AlGaN thick layers on sapphire substrates by in situ wafer curvature measurements and ex situ X‐ray diffraction measurements are evaluated. It is found that the tensile strain during the AlGaN thick layer growth comes from a thermal expansion difference between the AlGaN thick layer and the sapphire substrate as the temperature changes from the AlN nucleation layer growth to the AlGaN thick layer growth. When the temperature change is 100 °C and less, the tensile strain of 0.1% and less is observed during the AlGaN thick layer growth, resulting in no crack formations in the AlGaN thick layer. Furthermore, a DUV LED layer structure grown on such a crack‐free AlGaN template shows no crack formations. Thus, to suppress crack formation in templates fabricated for DUV LEDs, their growth temperature must be optimized by considering thermal expansions caused by the changes in the growth temperature from the nucleation layer to the thick layer. [ABSTRACT FROM AUTHOR]

A comprehensive mathematical model is proposed to study two strains of dengue virus with saturated incidence rates and quarantine measures. Imperfect dengue vaccination is also assumed in the model. Existence, uniqueness and stability of the proposed model are proved using the results from fixed point and degree theory. Additionally, well constructed Lyapunov function candidates are also applied to prove the global stability of infection-free equilibria. It is also demonstrated that the model is generalized Ulam-Hyers stable under some appropriate conditions. The model is fitted to the real data of dengue epidemic taken from the city of Espirito Santo in Brazil. For the approximate solution of the model, a non-standard finite difference(NSFD) approach is applied. Sensitivity analysis is also carried out to show the influence of different parameters involved in the model. The behaviour of the NSFD is also assessed under different denominator functions and it is observed that the choice of the denominator function could influence the solution trajectories. Different scenario analysis are also assessed when the reproduction number is below or above one. Furthermore, simulations are also presented to assess the epidemiological impact of dengue vaccination and quarantine measures for infected individuals. [ABSTRACT FROM AUTHOR]

The characteristics of linear hydroelastic waves propagating in a channel covered with compressed ice are investigated. The channel has a rectangular cross-section and is assumed to be infinite in length. The fluid in the channel is non-viscous and incompressible; its flow is potential. The ice cover is modelled by an elastic plate of constant thickness frozen to the channel walls. Principal attention is paid to the investigation of the influence of ice compression on the parameters of hydroelastic waves. The problem is solved in a coupled hydroelastic formulation. The profiles of propagating waves in the channel are sought in the form of series on the normal modes of a dry plate. The modes are defined analytically through trigonometric and hyperbolic functions. It is shown that compression in the longitudinal and transverse directions has different effects on the dispersion relations of these hydroelastic waves, their shape and phase, as well as on the critical velocities and strains distribution. [ABSTRACT FROM AUTHOR]

This research evaluated the structural behavior of precast concrete box culverts (PCBCs) reinforced with glass fiber-reinforced polymer (GFRP) bars, both experimentally and theoretically. Four full-scale specimens with a span of 1500 mm (59.06 in.), a rise of 1500 mm (59.06 in.), and a joint length of 1219 mm (48 in.) were prepared, along with one specimen with a span of 1800 mm (70.87 in.). Four specimens were reinforced with GFRP bars, and one specimen with steel bars as a reference. The PCBCs were tested up to failure under a concentrated load over a contact area of 250 x 600 mm (9.8 x 23.6 in.) on the top slab. The load plate simulated the footprint of the truck wheel load (87.5 kN [19.67 kip] CL-625 truck) according to the Canadian Highway Bridge Design Code. The investigated test parameters were the longitudinal reinforcement stiffness (GFRP versus steel), the longitudinal GFRP reinforcement ratios, specimen clear span, and slab thickness. Two-way shear failure was observed in all the tested specimens as a result of the concentrated load acting on the top slab. The test results revealed that increasing the longitudinal reinforcement ratio, as well as increasing the top-slab thickness, resulted in higher load-carrying capacity, lower deflection, and lower concrete and reinforcement strains. The experimental shear strengths were compared to the values predicted using current code provisions for two-way shear resistance equations. The results show that the punching-shear resistance equation in CSA S806-12 provided good yet conservative predictions of the shear capacity of the PCBCs' top slab. The Canadian Highway Bridge Design Code does not provide an equation for two-way shear design of FRP-reinforced concrete members. The two-way shear equation available for steel-reinforced concrete members was modified to take into account the characteristics of FRP bars. The modified equation produced predictions consistent with the experimental results. Moreover, the findings of this study demonstrate the feasibility and effectiveness of using GFRP bars as internal reinforcement for PCBCs as an alternative to steel bars. [ABSTRACT FROM AUTHOR]

ABSTRACT Despite the importance of intra-species variants of viruses for causing disease and/or disrupting ecosystem functioning, there is no universally applicable standard to define these. A (natural) gap in whole-genome average nucleotide identity (ANI) values around 95% is commonly used to define species, especially for bacteriophages, but whether a similar gap exists within species that can be used to define intra-species units has not been evaluated yet. Whole-genome comparisons among members of 1,016 bacteriophage (Caudoviricetes) species revealed a region of low frequency of ANI values around 99.2%–99.8%, showing threefold or fewer pairs than expected for an even distribution. This second gap is prevalent in viruses infecting various cultured or uncultured hosts from a variety of environments, although a few exceptions to this pattern were also observed (3.7% of total species) and are likely attributed to cultivation biases or other factors. Similar results were observed for a limited set of eukaryotic viruses that are adequately sampled, including SARS-CoV-2, whose ANI-based clusters matched well with the WHO-defined variants of concern, indicating that our findings from bacteriophages might be more broadly applicable and the ANI-based clusters may represent functionally and/or ecologically distinct units. These units appear to be predominantly driven by (high) ecological cohesiveness coupled to either frequent recombination for bacteriophages or selection and clonal evolution for other viruses such as SARS-CoV-2, indicating that fundamentally different underlying mechanisms could lead to similar diversity patterns. Accordingly, we propose the ANI gap approach outlined above for defining viral intra-species units, for which we propose the term genomovars.IMPORTANCEViral species are composed of an ensemble of intra-species variants whose individual dynamics may have major implications for human and animal health and/or ecosystem functioning. However, the lack of universally accepted standards to define these intra-species variants has led researchers to use different approaches for this task, creating inconsistent intra-species units across different viral families and confusion in communication. By comparing hundreds of mostly bacteriophage genomes, we show that there is a widely distributed natural gap in whole-genome average nucleotide identity values in most, but not all, of these species that can be used to define intra-species units. Therefore, these results advance the molecular toolbox for tracking viral intra-species units and should facilitate future epidemiological and environmental studies.

The human gut microbiome harbors substantial ecological diversity at the species level as well as at the strain level within species. In healthy hosts, species abundance fluctuations in the microbiome are thought to be stable, and these fluctuations can be described by macroecological laws. However, it is less clear how strain abundances change over time. An open question is whether individual strains behave like species themselves, exhibiting stability and following the macroecological relationships known to hold at the species level, or whether strains have different dynamics, perhaps due to the relatively close phylogenetic relatedness of cocolonizing lineages. Here, we analyze the daily dynamics of intraspecific genetic variation in the gut microbiomes of four healthy, densely longitudinally sampled hosts. First, we find that the overall genetic diversity of a large majority of species is stationary over time despite short-term fluctuations. Next, we show that fluctuations in abundances in approximately 80% of strains analyzed can be predicted with a stochastic logistic model (SLM), an ecological model of a population experiencing environmental fluctuations around a fixed carrying capacity, which has previously been shown to capture statistical properties of species abundance fluctuations. The success of this model indicates that strain abundances typically fluctuate around a fixed carrying capacity, suggesting that most strains are dynamically stable. Finally, we find that the strain abundances follow several empirical macroecological laws known to hold at the species level. Together, our results suggest that macroecological properties of the human gut microbiome, including its stability, emerge at the level of strains. IMPORTANCE To date, there has been an intense focus on the ecological dynamics of the human gut microbiome at the species level. However, there is considerable genetic diversity within species at the strain level, and these intraspecific differences can have important phenotypic effects on the host, impacting the ability to digest certain foods and metabolize drugs. Thus, to fully understand how the gut microbiome operates in times of health and sickness, its ecological dynamics may need to be quantified at the level of strains. Here, we show that a large majority of strains maintain stable abundances for periods of months to years, exhibiting fluctuations in abundance that can be well described by macroecological laws known to hold at the species level, while a smaller percentage of strains undergo rapid, directional changes in abundance. Overall, our work indicates that strains are an important unit of ecological organization in the human gut microbiome.

Abstract Organophosphate compounds are widely used in agricultural activities to optimize food production. Contamination of field soil by these compounds may result in detrimental effects on soil biota. The aim of the present study was to isolate microorganisms from field soils and evaluate the strains on ability to degrade organophosphates as single isolate and as a consortium. Isolated strains were identified using both biochemical and molecular techniques. Results revealed that, out of the 46 isolated strains, three isolates herein referred to as S6, S36 and S37 showed an average diazinon degradation rate of 76.4%, 76.7% and 76.8% respectively, of the initial dose (50 ppm) within 11 days of incubation in mineral medium. Notably, isolates S36 and S37 were more effective than S6 in degrading diazinon by 40% in soil aliquot after 11 days and therefore were evaluated on biochemical reactions and molecular identification. The isolates showed variable biochemical characteristics. However, both isolates possessed catalase enzyme, but lacked oxidase enzyme. Molecular characterization showed that, the closest species for S36 and S37 were Priestia megaterium and P. arybattia, respectively, based on 16S rRNA gene similarity (> 99%). Combination of the strains increased diazinon degradation ability by 45% compared to single strain treatment. Chlorpyrifos was the most highly degraded organophosphate, compared to phorate and cadusafos. Therefore it is expected that the pesticide-degrading bacteria could be a solution to soil health improvement and contribution to the production of safe agricultural products.

Surveys were conducted to assess Citrus tristeza virus (CTV) in California. Orchard surveys in central California during 2009 to 2013 estimated CTV incidence from 0.05% to 2.9%. Similar surveys in Ventura, Riverside, San Bernardino, and San Diego Counties in 2020-22 estimated CTV incidence from 6.3% to 34.9% while CTV was rarely found in the other five counties surveyed. T30 comprised over 95% of CTV detected alone or in mixtures with other strains in southern California and constituted 59% of 550 CTV accessions maintained in Tulare, California. VT, RB, and S1 genotypes were also found but T36 was rarely detected. No evidence of CTV-induced economic damage was noted except for occasional CTV quick decline on sour orange rootstock.

Elucidating the sources of a microbiome can provide insight into the ecological dynamics responsible for the formation of these communities. Source tracking approaches to date leverage species abundance information; however, single nucleotide variants (SNVs) may be more informative because of their high specificity to certain sources. To overcome the computational burden of utilizing all SNVs for a given sample, we introduce a novel method to identify signature SNVs for source tracking. Signature SNVs used as input into a previously designed source tracking algorithm, FEAST, can more accurately estimate contributions than species and provide novel insights, demonstrated in three case studies.

BackgroundMetagenomics analyses can be negatively impacted by DNA contamination. While external sources of contamination such as DNA extraction kits have been widely reported and investigated, contamination originating within the study itself remains underreported.ResultsHere, we applied high-resolution strain-resolved analyses to identify contamination in two large-scale clinical metagenomics datasets. By mapping strain sharing to DNA extraction plates, we identified well-to-well contamination in both negative controls and biological samples in one dataset. Such contamination is more likely to occur among samples that are on the same or adjacent columns or rows of the extraction plate than samples that are far apart. Our strain-resolved workflow also reveals the presence of externally derived contamination, primarily in the other dataset. Overall, in both datasets, contamination is more significant in samples with lower biomass.ConclusionOur work demonstrates that genome-resolved strain tracking, with its essentially genome-wide nucleotide-level resolution, can be used to detect contamination in sequencing-based microbiome studies. Our results underscore the value of strain-specific methods to detect contamination and the critical importance of looking for contamination beyond negative and positive controls. Video Abstract.

Metal halide perovskites (MHPs) exhibit strong spin‐orbit coupling and structural inversion asymmetry, making them ideal for testbeds of Rashba effects and for use in spin‐related optoelectronic and spintronic applications. However, the Rashba band splitting is mainly observed in bulk MHPs so far and is rarely observed in thin films. In this study, a direct observation of Rashba band splitting in MHP thin films at room temperature is reported. By employing a silicone rubber substrate with a high thermal expansion coefficient, the out‐of‐plane tensile strain significantly reduces the activation energy of ion migration in these thin films and leads to a considerable amount of point defects. These point defects disrupt the inversion symmetry and ultimately give rise to the Rashba band splitting. These findings open up new possibilities for manipulating Rashba effects in MHP thin films through device engineering. [ABSTRACT FROM AUTHOR]

The shiitake mushroom (Lentinula edodes) is globally valued for its nutrition and medicinal properties. New technologies aim to increase production with less environmental impact, considering materials such as charcoal for substrate enrichment. This manuscript evaluated the effect of fine charcoal (FC) on the substrate formulation of two L. edodes strains (LED 20/11 and LED 20/12). The substrate consisted of 72% eucalyptus sawdust, 12.5% rice bran, 12.5% wheat bran, and 3% calcium carbonate (control treatment without charcoal). Treatments with FC proportionally reduced the use of sawdust, with doses of 1%, 2%, 4%, 8%, and 16% (relative to the substrate material). Yield, mushroom number, and mushroom weight were evaluated. The concentration of FC significantly affected the parameters analyzed, especially at the 4% dose. A negative correlation between mushroom number and weight was observed. For yield, the control treatment and the lowest dose of FC (1%) had the highest yields for the first harvest. Strain LED 20/12 showed lower yield variability due to the percentage of FC applied to the substrate. The incorporation of FC into the substrate for shiitake cultivation demonstrates efficacy; however, both the concentration and strain used are limiting factors for its applicability. [ABSTRACT FROM AUTHOR]

Simple Summary: Uterine health is crucial for cows to become pregnant and maintain farm profitability. However, when cows suffer from uterine diseases, it not only affects their fertility but also leads to increased antibiotic usage, impacting both animal health and farm economics. Probiotics, which are beneficial bacteria, offer a promising solution to improve cow health and reproductive success. Research suggests that certain probiotics can enhance cow fertility. Administering these probiotics directly into the cow's vagina may strengthen uterine health, especially after giving birth. While initial findings are promising, further large-scale studies are needed to confirm their effectiveness. This paper underscores the importance of establishing clear guidelines for using probiotics in cow management, including selecting appropriate strains and administering them correctly. Moving forward, continued research is necessary to fully understand the benefits of probiotics in maintaining cow health and improving fertility. Uterine disease in cattle impairs reproductive performance and profitability and increases antibiotic use and antimicrobial resistance. Thus, probiotics offer a promising alternative therapy. This review presents conceptual findings on the efficacy of probiotics in managing uterine diseases and fertility in cows. Probiotics containing Lactobacillus spp. and Bifidobacterium spp. individually or as composite formulations are known to improve fertility. Strategic intravaginal administration of these formulations would likely enhance uterine immunity, particularly during the postpartum period. While current findings on the benefits to uterine health are encouraging, there is still significant knowledge missing, including a lack of empirical information from large-scale field trials. This review underscores the need for evidence-based guidelines for probiotics, such as genomic selection of formulations, targeted delivery, or potential synergy with other interventions. Future research should address these gaps to maximize the potential of probiotics in managing uterine diseases and enhancing the reproductive health of dairy cattle. [ABSTRACT FROM AUTHOR]

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This study was conducted to evaluate the effect of strains on growth performance and morphometric traits of two strains of commercial pullets (Isa brown and Nera black). A total of 90 chicks (45 chicks per strain) were purchased from a reputable hatchery. Each strain was further replicated three times with 15 birds per replicate. Growth performance and morphometric trait measurements were determined from 0 - 10 weeks of age. The growth performance traits studied were body weight (BW), weight gain (WG), feed intake (FI) and feed conversion ratio (FCR). The morphometric traits measured were body length (BL), wing length (WL), shank length (SL), breast girth (BG) and neck length (NL). Data obtained were subjected to an independent t-test using the SPSS package. The results indicated that BW and other growth performance traits (FI, WG and FCR) were significantly influenced (p<0.05) by the strain of pullets. Nera black pullets consistently had higher BW, WG, FI and FCR than Isa brown at all ages studied. However, morphometric traits were not affected by strains. It was also indicated in the study that regardless of strain, BW and all morphometric traits increased in mean values with the advancing age of the birds. Nera black was identified as having better BW because it had the highest mean value in BW and other performance traits and could be recommended to farmers for an increase in productivity. [ABSTRACT FROM AUTHOR]

The processes of elastic and elastoplastic deformation in concentration zones are analyzed for the case of different levels of rated stresses and resistance with respect to plastic strains. Based on the calculated and experimental data, it is shown that, with a decrease in the strengthening index in the inelastic region, the inhomogeneity of the strain distribution exhibits an increase. At the same time, the strain concentration coefficients increase and the stress concentration coefficients decrease. Special cases are considered when the latter are less than unity. This is important for justifying the strength, service life, survivability, and safety of new objects of the technosphere made of special structural materials and operated under extreme thermomechanical loading conditions, including the conditions inherent in nuclear power plants in normal modes and emergency situations. [ABSTRACT FROM AUTHOR]

Medical application of femtosecond laser irradiation for possible cancer treatment is a primary interest for this study. In this study the effects of femtosecond laser irradiation time, treatment wavelength and strain type upon the structure of DNA from methicillin-resistant Staphylococcus aureus (strain I) and methicillin-susceptible Staphylococcus aureus (strain II) is presented using Fourier transform infrared (FT-IR) spectroscopy. Six sets of irradiation parameters are considered for the bacterial strains. Fourier transform infrared spectra of genomic nucleic acids extracted from the two Staphylococcus aureus bacterial strains were characterized for control and irradiated samples. FT-IR assignments and structure of nucleic acids subgroups were analyzed from 800 to 1800 cm−1. In particular, the bands at 1074 cm−1 [PO2− symmetric stretching (υsPO2−)], 1233 cm−1 (antisymmetric stretching υaPO2−, possible A-form), 1330 cm−1 [deoxyadenosine (dA)], 1400 cm−1 (C3'-endo/anti, A-form), 1540 cm−1 [deoxycytidine (dC)] and 1650 cm−1 [deoxycytidine (dC) (C2 = O2)] were considered to evaluate the structural changes of DNA functional groups following irradiation. [ABSTRACT FROM AUTHOR]