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Background: Pleuronectiformes, also known as flatfish, are important model and economic animals. However, a comprehensive genome survey of their important organelles, mitochondria, has been limited. Therefore, we aim to analyze the genomic structure, codon preference, nucleotide diversity, selective pressure and repeat sequences, as well as reconstruct the phylogenetic relationship using the mitochondrial genomes of 111 flatfish species. Results: Our analysis revealed a conserved gene content of protein-coding genes and rRNA genes, but varying numbers of tRNA genes and control regions across species. Various gene rearrangements were found in flatfish species, especially for the rearrangement of nad5-nad6-cytb block in Samaridae family, the swapping rearrangement of nad6 and cytb gene in Bothidae family, as well as the control region translocation and tRNA-Gln gene inversion in the subfamily Cynoglossinae, suggesting their unique evolutionary history and/or functional benefit. Codon usage showed obvious biases, with adenine being the most frequent nucleotide at the third codon position. Nucleotide diversity and selective pressure analysis suggested that different protein-coding genes underwent varying degrees of evolutionary pressure, with cytb and cox genes being the most conserved ones. Phylogenetic analysis using both whole mitogenome information and concatenated independently aligned protein-coding genes largely mirrored the taxonomic classification of the species, but showed different phylogeny. The identification of simple sequence repeats and various long repetitive sequences provided additional complexity of genome organization and offered markers for evolutionary studies and breeding practices. Conclusions: This study represents a significant step forward in our comprehension of the flatfish mitochondrial genomes, providing valuable insights into the structure, conservation and variation within flatfish mitogenomes, with implications for understanding their evolutionary history, functional genomics and fisheries management. Future research can delve deeper into conservation biology, evolutionary biology and functional usages of variations. [ABSTRACT FROM AUTHOR]

Background: The confused taxonomic classification of Crucigenia is mainly inferred through morphological evidence and few nuclear genes and chloroplast genomic fragments. The phylogenetic status of C. quadrata, as the type species of Crucigenia, remains considerably controversial. Additionally, there are currently no reports on the chloroplast genome of Crucigenia. Results: In this study, we utilize molecular phylogenetics and comparative genomics to show that C. quadrata belongs to Chlorophyceae rather than Trebouxiophyceae. The Bayesian and maximum likelihood (ML) phylogenetic trees support a monophyletic group of C. quadrata and Scenedesmaceae (Chlorophyceae) species. Our study presents the first complete chloroplast genome of C. quadrata, which is 197,184 bp in length and has a GC content of 31%. It has a typical quadripartite structure, and the chloroplast genome codons exhibit usage bias. Nucleotide diversity analysis highlights six genes (ccsA, psbF, chlN, cemA, rps3, rps18) as hotspots for genetic variation. Coding gene sequence divergence analyses indicate that four genes (cemA, clpP, psaA, rps3) are subject to positive selection. Conclusions: The determination of the phylogenetic status and the comparative chloroplast genomic analyses of C. quadrata will not only be useful in enhancing our understanding of the intricacy of Crucigenia taxonomy but also provide the important basis for studying the evolution of the incertae sedis taxa within Trebouxiophyceae. [ABSTRACT FROM AUTHOR]

Background: The genus Impatiens, which includes both annual and perennial herbs, holds considerable ornamental, economic, and medicinal value. However, it posed significant challenges for taxonomic and systematic reconstruction. This was largely attributed to its high intraspecific diversity and low interspecific variation in morphological characteristics. In this study, we sequenced samples from 12 Impatiens species native to China and assessed their phylogenetic resolution using the complete chloroplast genome, in conjunction with published samples of Impatiens. In addition, a comparative analysis of chloroplast genomes were conducted to explore the evolution of the chloroplast genome in Impatiens. Results: The chloroplast genomes of 12 Impatiens species exhibited high similarity to previously published samples in terms of genome size, gene content, and sequence. The chloroplast genome of Impatiens exhibited a typical four-part structure, with lengths ranging from 146,987 bp(I. morsei)- 152,872 bp(I. jinpingensis). Our results identified 10 mutant hotspot regions (rps16, rps16-trnG, trnS-trnR, and rpoB-trnC) that could serve as effective molecular markers for phylogenetic analyses and species identification within the Impatiens. Phylogenetic analyses supported the classification of Impatiens as a monophyletic taxon. The identified affinities supported the taxonomic classification of the subgenus Clavicarpa within the Impatiens, with subgenus Clavicarpa being the first taxon to diverge. In phylogenetic tree,the Impatiens was divided into eight distinct clades. The results of ancestral trait reconstruction suggested that the ancestral traits of Impatiens included a perennial life cycle, four sepals and three pollen grooves. However, the ancestral morphology regarding fruit shape, flower colour, and spacing length remained ambiguous. Conclude: Our study largely supported the family-level taxonomic treatment of Impatiens species in China and demonstrated the utility of whole chloroplast genome sequences for phylogenetic resolution. Comparative analysis of the chloroplast genomes of Impatiens facilitated the development of molecular markers.The results of ancestral trait reconstruction showed that the ancestor type of habit was perennial, the number of sepals was 4, and morphology and number of aperture was 3 colpus. The traits of capsule shape, flower colour, and spur length underwent a complex evolutionary process. Our results provided data support for further studies and some important new insights into the evolution of the Impatiens. [ABSTRACT FROM AUTHOR]

Background: The microbiome greatly affects health and wellbeing. Evolutionarily, it is doubtful that a host would rely on chance alone to pass on microbial colonization to its offspring. However, the literature currently offers only limited evidence regarding two alternative hypotheses: active microbial shaping by host genetic factors or transmission of a microbial maternal legacy. Results: To further dissect the influence of host genetics and maternal inheritance, we collected two-cell stage embryos from two representative wild types, C57BL6/J and BALB/c, and transferred a mixture of both genotype embryos into hybrid recipient mice to be inoculated by an identical microbiome at birth. Conclusions: Observing the offspring for six generations unequivocally emphasizes the impact of host genetic factors over maternal legacy in constant environments, akin to murine laboratory experiments. Interestingly, maternal legacy solely controlled the microbiome in the first offspring generation. However, current evidence supporting maternal legacy has not extended beyond this initial generation, resolving the aforementioned debate. BvkFmArGExF4DhB6h6D8wq Video Abstract [ABSTRACT FROM AUTHOR]

The article discusses the development of a new toolkit called CyDotian, which is designed to study repetitive DNA sequences within genes. The toolkit bridges the gap between existing tools that focus on genomic repeats and those that analyze all repeats within a gene. CyDotian can extract repeat sequences, calculate repeat density, and provide statistical evidence about repeats within sequences. The article provides examples of how CyDotian can be used to study intragenic repeats in different species and demonstrates its potential applications in genetic research. The toolkit is freely available for public use on GitHub. [Extracted from the article]

Background: Over the last two decades, hybridization has been a powerful tool used to construct superior yeast for brewing and winemaking. Novel hybrids were primarily constructed using at least one Saccharomyces cerevisiae parent. However, little is known about hybrids used for other purposes, such as targeted flavor production, for example, 2-phenylethanol (2-PE). 2-PE, an aromatic compound widely utilised in the food, cosmetic, and pharmaceutical industries, presents challenges in biotechnological production due to its toxic nature. Consequently, to enhance productivity and tolerance to 2-PE, various strategies such as mutagenesis and genetic engineering are extensively explored to improved yeast strains. While biotechnological efforts have predominantly focused on S. cerevisiae for 2-PE production, other Saccharomyces species and their hybrids remain insufficiently described. Results: To address this gap, in this study, we analysed a new interspecies yeast hybrid, II/6, derived from S. uvarum and S. kudriavzevii parents, in terms of 2-PE bioconversion and resistance to its high concentration, comparing it with the parental strains. Two known media for 2-PE biotransformation and three different temperatures were used during this study to determine optimal conditions. In 72 h batch cultures, the II/6 hybrid achieved a maximum of 2.36 ± 0.03 g/L 2-PE, which was 2–20 times higher than the productivity of the parental strains. Our interest lay not only in determining whether the hybrid improved in productivity but also in assessing whether its susceptibility to high 2-PE titers was also mitigated. The results showed that the hybrid exhibited significantly greater resistance to the toxic product than the original strains. Conclusions: The conducted experiments have confirmed that hybridization is a promising method for modifying yeast strains. As a result, both 2-PE production yield and tolerance to its inhibitory effects can be increased. Furthermore, this strategy allows for the acquisition of non-GMO strains, alleviating concerns related to additional legislative requirements or consumer acceptance issues for producers. The findings obtained have the potential to contribute to the development of practical solutions in the future. [ABSTRACT FROM AUTHOR]

Background: Tandem repeats are specific sequences in genomic DNA repeated in tandem that are present in all organisms. Among the subcategories of TRs we have Satellite repeats, that is divided into macrosatellites, minisatellites, and microsatellites, being the last two of specific interest because they can identify polymorphisms between organisms due to their instability. Currently, most mining tools focus on Simple Sequence Repeats (SSR) mining, and only a few can identify SSRs in the coding regions. Results: We developed a microsatellite mining software called SATIN (Micro and Mini SATellite IdentificatioN tool) based on a new sliding window algorithm written in C and Python. It represents a new approach to SSR mining by addressing the limitations of existing tools, particularly in coding region SSR mining. SATIN is available at https://github.com/labgm/SATIN.git. It was shown to be the second fastest for perfect and compound SSR mining. It can identify SSRs from coding regions plus SSRs with motif sizes bigger than 6. Besides the SSR mining, SATIN can also analyze SSRs polymorphism on coding-regions from pre-determined groups, and identify SSRs differentially abundant among them on a per-gene basis. To validate, we analyzed SSRs from two groups of Escherichia coli (K12 and O157) and compared the results with 5 known SSRs from coding regions. SATIN identified all 5 SSRs from 237 genes with at least one SSR on it. Conclusions: The SATIN is a novel microsatellite search software that utilizes an innovative sliding window technique based on a numerical list for repeat region search to identify perfect, and composite SSRs while generating comprehensible and analyzable outputs. It is a tool capable of using files in fasta or GenBank format as input for microsatellite mining, also being able to identify SSRs present in coding regions for GenBank files. In conclusion, we expect SATIN to help identify potential SSRs to be used as genetic markers. [ABSTRACT FROM AUTHOR]

Amyotrophic Lateral Sclerosis (ALS) is a devastating neurodegenerative disorder characterized by the progressive loss of motor neurons, with genetic and environmental factors contributing to its complex pathogenesis. Dysregulated immune responses and altered energetic metabolism are key features, with emerging evidence implicating the gut microbiota (GM) in disease progression. We investigated the interplay among genetic background, GM composition, metabolism, and immune response in two distinct ALS mouse models: 129Sv_G93A and C57Ola_G93A, representing rapid and slow disease progression, respectively. Using 16 S rRNA sequencing and fecal metabolite analysis, we characterized the GM composition and metabolite profiles in non-transgenic (Ntg) and SOD1G93A mutant mice of both strains. Our results revealed strain-specific differences in GM composition and functions, particularly in the abundance of taxa belonging to Erysipelotrichaceae and the levels of short and medium-chain fatty acids in fecal samples. The SOD1 mutation induces significant shifts in GM colonization in both strains, with C57Ola_G93A mice showing changes resembling those in 129 Sv mice, potentially affecting disease pathogenesis. ALS symptom progression does not significantly alter microbiota composition, suggesting stability. Additionally, we assessed systemic immunity and inflammatory responses revealing strain-specific differences in immune cell populations and cytokine levels. Our findings underscore the substantial influence of genetic background on GM composition, metabolism, and immune response in ALS mouse models. These strain-specific variations may contribute to differences in disease susceptibility and progression rates. Further elucidating the mechanisms underlying these interactions could offer novel insights into ALS pathogenesis and potential therapeutic targets. [ABSTRACT FROM AUTHOR]

Background: Aquilegia is a model system for studying the evolution of adaptive radiation. However, very few studies have been conducted on the Aquilegia mitochondrial genome. Since mitochondria play a key role in plant adaptation to abiotic stress, analyzing the mitochondrial genome may provide a new perspective for understanding adaptive evolution. Results: The Aquilegia amurensis mitochondrial genome was characterized by a circular chromosome and two linear chromosomes, with a total length of 538,736 bp; the genes included 33 protein-coding genes, 24 transfer RNA (tRNA) genes and 3 ribosomal RNA (rRNA) genes. We subsequently conducted a phylogenetic analysis based on single nucleotide polymorphisms (SNPs) in the mitochondrial genomes of 18 Aquilegia species, which were roughly divided into two clades: the European-Asian clade and the North American clade. Moreover, the genes mttB and rpl5 were shown to be positively selected in European-Asian species, and they may help European and Asian species adapt to environmental changes. Conclusions: In this study, we assembled and annotated the first mitochondrial genome of the adaptive evolution model plant Aquilegia. The subsequent analysis provided us with a basis for further molecular studies on Aquilegia mitochondrial genomes and valuable information on adaptive evolution in Aquilegia. [ABSTRACT FROM AUTHOR]

Background: The impact of probiotic strains on host health is widely known. The available studies on the interaction between bacteria and the host are focused on the changes induced by bacteria in the host mainly. The studies determining the changes that occurred in the bacteria cells are in the minority. Within this paper, we determined what happens to the selected Bifidobacterium adolescentis and Bifidobacterium longum ssp. longum in an experimental environment with the intestinal epithelial layer. For this purpose, we tested the bacteria cells' viability, redox activity, membrane potential and enzymatic activity in different environments, including CaCo-2/HT-29 co-culture, cell culture medium, presence of inflammatory inductor (TNF-α) and oxygen. Results: We indicated that the external milieu impacts the viability and vitality of bacteria. Bifidobacterium adolescentis decrease the size of the live population in the cell culture medium with and without TNF-α (p < 0.001 and p < 0.01 respectively). In contrast, Bifidobacterium longum ssp. longum significantly increased survivability in contact with the eukaryotic cells and cell culture medium (p < 0.001). Bifidobacterium adolescentis showed significant changes in membrane potential, which was decreased in the presence of eukaryotic cells (p < 0.01), eukaryotic cells in an inflammatory state (p < 0.01), cell culture medium (p < 0.01) and cell culture medium with TNF-α (p < 0.05). In contrast, Bifidobacterium longum ssp. longum did not modulate membrane potential. Instead, bacteria significantly decreased the redox activity in response to milieus such as eukaryotic cells presence, inflamed eukaryotic cells as well as the culture medium (p < 0.001). The redox activity was significantly different in the cells culture medium vs the presence of eukaryotic cells (p < 0.001). The ability to β-galactosidase production was different for selected strains: Bifidobacterium longum ssp. longum indicated 91.5% of positive cells, whereas Bifidobacterium adolescentis 4.34% only. Both strains significantly reduced the enzyme production in contact with the eukaryotic milieu but not in the cell culture media. Conclusion: The environmental-induced changes may shape the probiotic properties of bacterial strains. It seems that the knowledge of the sensitivity of bacteria to the external environment may help to select the most promising probiotic strains, reduce research costs, and contribute to greater reproducibility of the obtained probiotic effects. Highlights: • External/experimental milieu impacts the viability and vitality of bacteria. • Bacteria differ in their response to the environments. • Environmental-induced changes may shape the probiotic properties of bacterial strains. • The knowledge of the sensitivity of bacteria to the external environment may help to select the most promising probiotic strains, reduce research costs, and contribute to greater reproducibility of the obtained probiotic effects. [ABSTRACT FROM AUTHOR]

Background: Antimicrobial resistance (AMR) is a growing global health threat that contributes to substantial neonatal mortality. Bangladesh has reported some of the highest rates of AMR among bacteria causing neonatal sepsis. As AMR colonization among newborns can predispose to infection with these bacteria, we aimed to characterize the frequency of and risk factors for colonization of mothers and newborns during hospitalization for delivery. Methods: We enrolled pregnant women presenting for delivery to a tertiary care hospital in Faridpur, Bangladesh. We collected vaginal and rectal swabs from mothers pre- and post-delivery, rectal swabs from newborns, and swabs from the hospital environment. Swabs were plated on agars selective for extended-spectrum-beta-lactamase producing bacteria (ESBL-PB) and carbapenem-resistant bacteria (CRB). We performed logistic regression to determine factors associated with ESBL-PB/CRB colonization. Results: We enrolled 177 women and their newborns during February-October 2020. Prior to delivery, 77% of mothers were colonized with ESBL-PB and 15% with CRB. 79% of women underwent cesarean deliveries (C-section). 98% of women received antibiotics. Following delivery, 98% of mothers and 89% of newborns were colonized with ESBL-PB and 89% of mothers and 72% of newborns with CRB. Of 290 environmental samples, 77% were positive for ESBL-PB and 69% for CRB. Maternal pre-delivery colonization was associated with hospitalization during pregnancy (RR for ESBL-PB 1.24, 95% CI 1.10–1.40; CRB 2.46, 95% CI 1.39–4.37). Maternal post-delivery and newborn colonization were associated with C-section (RR for maternal CRB 1.31, 95% CI 1.08–1.59; newborn ESBL-PB 1.34, 95% CI 1.09–1.64; newborn CRB 1.73, 95% CI 1.20–2.47). Conclusions: In this study, we observed high rates of colonization with ESBL-PB/CRB among mothers and newborns, with pre-delivery colonization linked to prior healthcare exposure. Our results demonstrate this trend may be driven by intense use of antibiotics, frequent C-sections, and a contaminated hospital environment. These findings highlight that greater attention should be given to the use of perinatal antibiotics, improved surgical stewardship for C-sections, and infection prevention practices in healthcare settings to reduce the high prevalence of colonization with AMR organisms. [ABSTRACT FROM AUTHOR]

Background: Microbial communities play a crucial role in ecosystem function through metabolic interactions. Genome-scale modeling is a promising method to understand these interactions and identify strategies to optimize the community. Flux balance analysis (FBA) is most often used to predict the flux through all reactions in a genome-scale model; however, the fluxes predicted by FBA depend on a user-defined cellular objective. Flux sampling is an alternative to FBA, as it provides the range of fluxes possible within a microbial community. Furthermore, flux sampling can capture additional heterogeneity across a population, especially when cells exhibit sub-maximal growth rates. Results: In this study, we simulate the metabolism of microbial communities and compare the metabolic characteristics found with FBA and flux sampling. With sampling, we find significant differences in the predicted metabolism, including an increase in cooperative interactions and pathway-specific changes in predicted flux. Conclusions: Our results suggest the importance of sampling-based approaches to evaluate metabolic interactions. Furthermore, we emphasize the utility of flux sampling in quantitatively studying interactions between cells and organisms. [ABSTRACT FROM AUTHOR]

Background: Sphaeropteris brunoniana and Alsophila latebrosa are both old relict and rare tree ferns, which have experienced the constant changes of climate and environment. However, little is known about their high-quality genetic information and related research on environmental adaptation mechanisms of them. In this study, combined with PacBio and Illumina platforms, transcriptomic analysis was conducted on the roots, rachis, and pinna of S. brunoniana and A. latebrosa to identify genes and pathways involved in environmental adaptation. Additionally, based on the transcriptomic data of tree ferns, chloroplast genes were mined to analyze their gene expression levels and RNA editing events. Results: In the study, we obtained 11,625, 14,391 and 10,099 unigenes of S. brunoniana root, rachis, and pinna, respectively. Similarly, a total of 13,028, 11,431 and 12,144 unigenes were obtained of A. latebrosa root, rachis, and pinna, respectively. According to the enrichment results of differentially expressed genes, a large number of differentially expressed genes were enriched in photosynthesis and secondary metabolic pathways of S. brunoniana and A. latebrosa. Based on gene annotation results and phenylpropanoid synthesis pathways, two lignin synthesis pathways (H-lignin and G-lignin) were characterized of S. brunoniana. Among secondary metabolic pathways of A. latebrosa, three types of WRKY transcription factors were identified. Additionally, based on transcriptome data obtained in this study, reported transcriptome data, and laboratory available transcriptome data, positive selection sites were identified from 18 chloroplast protein-coding genes of four tree ferns. Among them, RNA editing was found in positive selection sites of four tree ferns. RNA editing affected the protein secondary structure of the rbcL gene. Furthermore, the expression level of chloroplast genes indicated high expression of genes related to the chloroplast photosynthetic system in all four species. Conclusions: Overall, this work provides a comprehensive transcriptome resource of S. brunoniana and A. latebrosa, laying the foundation for future tree fern research. [ABSTRACT FROM AUTHOR]

Background: Sphaeropteris brunoniana and Alsophila latebrosa are both old relict and rare tree ferns, which have experienced the constant changes of climate and environment. However, little is known about their high-quality genetic information and related research on environmental adaptation mechanisms of them. In this study, combined with PacBio and Illumina platforms, transcriptomic analysis was conducted on the roots, rachis, and pinna of S. brunoniana and A. latebrosa to identify genes and pathways involved in environmental adaptation. Additionally, based on the transcriptomic data of tree ferns, chloroplast genes were mined to analyze their gene expression levels and RNA editing events. Results: In the study, we obtained 11,625, 14,391 and 10,099 unigenes of S. brunoniana root, rachis, and pinna, respectively. Similarly, a total of 13,028, 11,431 and 12,144 unigenes were obtained of A. latebrosa root, rachis, and pinna, respectively. According to the enrichment results of differentially expressed genes, a large number of differentially expressed genes were enriched in photosynthesis and secondary metabolic pathways of S. brunoniana and A. latebrosa. Based on gene annotation results and phenylpropanoid synthesis pathways, two lignin synthesis pathways (H-lignin and G-lignin) were characterized of S. brunoniana. Among secondary metabolic pathways of A. latebrosa, three types of WRKY transcription factors were identified. Additionally, based on transcriptome data obtained in this study, reported transcriptome data, and laboratory available transcriptome data, positive selection sites were identified from 18 chloroplast protein-coding genes of four tree ferns. Among them, RNA editing was found in positive selection sites of four tree ferns. RNA editing affected the protein secondary structure of the rbcL gene. Furthermore, the expression level of chloroplast genes indicated high expression of genes related to the chloroplast photosynthetic system in all four species. Conclusions: Overall, this work provides a comprehensive transcriptome resource of S. brunoniana and A. latebrosa, laying the foundation for future tree fern research. [ABSTRACT FROM AUTHOR]

Background: Methane (CH4) is a major greenhouse gas, and ruminants are one of the sources of CH4 which is produced by the rumen microbiota. Modification of the rumen microbiota compositions will impact the CH4 production. In this study, the effects of melatonin on methane production in cows were investigated both in the in vitro and in vivo studies. Results: Melatonin treatment significantly reduced methane production in both studies. The cows treated with melatonin reduced methane emission from their respiration by approximately 50%. The potential mechanisms are multiple. First, melatonin lowers the volatile fatty acids (VFAs) production in rumen and reduces the raw material for CH4 synthesis. Second, melatonin not only reduces the abundance of Methanobacterium which are responsible for generating methane but also inhibits the populations of protozoa to break the symbiotic relationship between Methanobacterium and protozoa in rumen to further lowers the CH4 production. The reduced VFA production is not associated with food intake, and it seems also not to jeopardize the nutritional status of the cows. This was reflected by the increased milk lipid and protein contents in melatonin treated compared to the control cows. It is likely that the energy used to synthesize methane is saved to compensate the reduced VFA production. Conclusion: This study enlightens the potential mechanisms by which melatonin reduces rumen methane production in dairy cows. Considering the greenhouse effects of methane on global warming, these findings provide valuable information using different approaches to achieve low carbon dairy farming to reduce the methane emission. 6uXNnBCVHjJWi7WJQ32EAM Video Abstract [ABSTRACT FROM AUTHOR]

Background: Recent studies have shown that gut microbiome plays important roles in response to radiation exposure. IL-18, an inflammatory cytokine, is highly elevated in mice, mini-pigs and nonhuman primates after radiation exposure. Blocking IL-18 using its endogenous binding protein (IL-18BP) increases mice survival after radiation exposure by decreasing bone marrow interferon-gamma levels. Methods: To further characterize the roles of IL-18 in response to radiation, both wild type and IL-18 knockout (IL-18 KO) mice were exposed to 9.0 Gy total body irradiation (TBI). The 30-day survival result demonstrated that IL-18 KO mice were significantly more resistant to radiation compared to the wild type mice (p < 0.0001). Mouse faecal samples were collected at pre-radiation (d0), d1, d3, d7, d14, d21 and d29 after radiation exposure. Microbiome profiling was performed on the faecal samples using 16S and ITS sequencing technology. Results: Data analysis showed that there was significant difference in the bacterial microbiome between wild type and IL-18 KO mice. Cohousing of wild type and IL-18 KO mice decreased the bacterial microbiome difference between the two genotypes. Much fewer bacterial genera were significantly changed in wild type mice than the IL-18 KO mice after radiation exposure. The different composition of the IL-18 KO mice and wild type mice persisted even after radiation exposure. Bacterial genera that significantly correlated with other genera were identified in the IL-18 KO and wild type mice. The metabolic pathways that differentially expressed in both genotypes were identified. The animal bacterial microbiome data could be used to predict the animal's radiation status. The fungal microbiome had no significant difference regarding genotype or time after radiation exposure. Conclusion: The current study helps understand the gut microbiome in different genetic backgrounds and its temporal changes after radiation exposure. Our data provide insight into the mechanisms underlying radiation-induced toxicity and help identify bacteria important in response to radiation. [ABSTRACT FROM AUTHOR]

Background: Methane (CH4) is a major greenhouse gas, and ruminants are one of the sources of CH4 which is produced by the rumen microbiota. Modification of the rumen microbiota compositions will impact the CH4 production. In this study, the effects of melatonin on methane production in cows were investigated both in the in vitro and in vivo studies. Results: Melatonin treatment significantly reduced methane production in both studies. The cows treated with melatonin reduced methane emission from their respiration by approximately 50%. The potential mechanisms are multiple. First, melatonin lowers the volatile fatty acids (VFAs) production in rumen and reduces the raw material for CH4 synthesis. Second, melatonin not only reduces the abundance of Methanobacterium which are responsible for generating methane but also inhibits the populations of protozoa to break the symbiotic relationship between Methanobacterium and protozoa in rumen to further lowers the CH4 production. The reduced VFA production is not associated with food intake, and it seems also not to jeopardize the nutritional status of the cows. This was reflected by the increased milk lipid and protein contents in melatonin treated compared to the control cows. It is likely that the energy used to synthesize methane is saved to compensate the reduced VFA production. Conclusion: This study enlightens the potential mechanisms by which melatonin reduces rumen methane production in dairy cows. Considering the greenhouse effects of methane on global warming, these findings provide valuable information using different approaches to achieve low carbon dairy farming to reduce the methane emission. 6uXNnBCVHjJWi7WJQ32EAM Video Abstract [ABSTRACT FROM AUTHOR]

Background: The design of ecologically sustainable and plant-beneficial soil systems is a key goal in actively manipulating root-associated microbiomes. Community engineering efforts commonly seek to harness the potential of the indigenous microbiome through substrate-mediated recruitment of beneficial members. In most sustainable practices, microbial recruitment mechanisms rely on the application of complex organic mixtures where the resources/metabolites that act as direct stimulants of beneficial groups are not characterized. Outcomes of such indirect amendments are unpredictable regarding engineering the microbiome and achieving a plant-beneficial environment. Results: This study applied network analysis of metagenomics data to explore amendment-derived transformations in the soil microbiome, which lead to the suppression of pathogens affecting apple root systems. Shotgun metagenomic analysis was conducted with data from ‘sick’ vs ‘healthy/recovered’ rhizosphere soil microbiomes. The data was then converted into community-level metabolic networks. Simulations examined the functional contribution of treatment-associated taxonomic groups and linked them with specific amendment-induced metabolites. This analysis enabled the selection of specific metabolites that were predicted to amplify or diminish the abundance of targeted microbes functional in the healthy soil system. Many of these predictions were corroborated by experimental evidence from the literature. The potential of two of these metabolites (dopamine and vitamin B12) to either stimulate or suppress targeted microbial groups was evaluated in a follow-up set of soil microcosm experiments. The results corroborated the stimulant’s potential (but not the suppressor) to act as a modulator of plant beneficial bacteria, paving the way for future development of knowledge-based (rather than trial and error) metabolic-defined amendments. Our pipeline for generating predictions for the selective targeting of microbial groups based on processing assembled and annotated metagenomics data is available at . Conclusions: This research demonstrates how genomic-based algorithms can be used to formulate testable hypotheses for strategically engineering the rhizosphere microbiome by identifying specific compounds, which may act as selective modulators of microbial communities. Applying this framework to reduce unpredictable elements in amendment-based solutions promotes the development of ecologically-sound methods for re-establishing a functional microbiome in agro and other ecosystems. E7XdzHk-x_xNr6tGiZLY1V Video Abstract [ABSTRACT FROM AUTHOR]

Background: 2-Phenylethanol (2-PE), a higher alcohol with a rose-like odor, inhibits growth of the producer strains. However, the limited knowledge regarding 2-PE tolerance mechanisms renders our current knowledge base insufficient to inform rational design. Results: To improve the growth phenotype of Saccharomyces cerevisiae under a high 2-PE concentration, adaptive laboratory evolution (ALE) was used to generate an evolved 19–2 strain. Under 2-PE stress, its OD600 and growth rate increased by 86% and 22% than that of the parental strain, respectively. Through whole genome sequencing and reverse engineering, transcription factor Pdr1p mutation (C862R) was revealed as one of the main causes for increased 2-PE tolerance. Under 2-PE stress condition, Pdr1p mutation increased unsaturated fatty acid/saturated fatty acid ratio by 42%, and decreased cell membrane damage by 81%. Using STRING website, we identified Pdr1p interacted with some proteins, which were associated with intracellular ergosterol content, reactive oxygen species (ROS), and the ATP-binding cassette transporter. Also, the results of transcriptional analysis of genes encoded these proteins confirmed that Pdr1p mutation induced the expression of these genes. Compared with those of the reference strain, the ergosterol content of the PDR1_862 strain increased by 72%–101%, and the intracellular ROS concentration decreased by 38% under 2-PE stress. Furthermore, the Pdr1p mutation also increased the production of 2-PE (11% higher). Conclusions: In the present work, we have demonstrated the use of ALE as a powerful tool to improve yeast tolerance to 2-PE. Based on the reverse engineering, transcriptional and physiological analysis, we concluded that Pdr1p mutation significantly enhanced the 2-PE tolerance of yeast by regulating the fatty acid proportion, intracellular ergosterol and ROS. It provides new insights on Pdr1p mediated 2-PE tolerance, which could help in the design of more robust yeasts for natural 2-PE synthesis. [ABSTRACT FROM AUTHOR]

Vibrio vulnificus is a pathogenic bacterium that causes disease in marine fish, affecting fish farming and human health worldwide. In May 2021, in the Bohai Bay region, a disease broke out in commercially farmed pearl gentian grouper (♀Epinephelus fuscoguttatus × ♂Epinephelus lanceolatus), causing huge economic losses. The diseased fish had skin lesions, water accumulation in their abdomens, and showed tissue and organ damage. V. vulnificus biotype 2 has been reported in eels and other marine fish, but it is less reported in pearl gentian grouper. In this study, the pathogenic strain isolated from diseased fish was identified as V. vulnificus EPL 0201 biotype 2 on the basis of physiological and biochemical characteristics and the results of 16S rRNA gene and gyrB sequencing, virulence gene detection, and recursive infection experiments. To gain a comprehensive understanding of the pathogenicity and drug resistance of this strain, whole-genome sequencing was performed. Whole-genome analysis showed that the gene map of this strain was complete. The Virulence Factor Database annotation results showed that this strain had the key virulence factor genes vvhA and rtxA, which cause host disease. In addition, this strain had genes conferring resistance against cephalosporins, aminoglycosides, tetracyclines, and sulfonamides. Antimicrobial susceptibility testing confirmed the presence of these resistance genes identified in the genome. The results of this study show that V. vulnificus EPL 0201 biotype 2 is a multi-drug resistant strain with high pathogenicity. [ABSTRACT FROM AUTHOR]

Bioremediation of atrazine-contaminated soil is considered a safe and effective approach in removing contaminates from the soil. However, the effects of adding foreign organisms to assist bioremediation on soil environmental quality and ecosystem are unclear. Here, the ecological remediation potential of strain Paenarthrobacter ureafaciens ZF1 on atrazine-contaminated soil was investigated through miniature experiments using variations in soil enzymes and bacterial communities as indicators. The results showed that strain ZF1 accelerated atrazine degradation, which could completely degrade atrazine at concentrations of 100 mg·L− 1 atrazine within 2 h in liquid medium and could remove up to 99.3% of atrazine (100 mg·kg− 1 in soil) within 6 days. During soil bioremediation, atrazine promoted the activities of urease and cellulase, and inhibited the activities of sucrase and catalase, while the strain ZF1 significantly promoted the activities of these four enzymes. High-throughput sequencing of 16S rRNA genes showed that ZF1 affected the relative abundance and bacterial community structure, and promoted bacterial diversity and evenness. Furthermore, redundancy analysis revealed a certain correlation among the strain ZF1, atrazine residue, soil enzyme activity, and soil bacterial community. The strain ZF1 in this work demonstrated remarkable potential for ecological restoration, and can be an effective and environmentally friendly alternative in remediating atrazine-contaminated soil. [ABSTRACT FROM AUTHOR]

Background: The large genus Ficus comprises approximately 800 species, most of which possess high ornamental and ecological values. However, its evolutionary history remains largely unknown. Plastome (chloroplast genome) analysis had become an essential tool for species identification and for unveiling evolutionary relationships between species, genus and other rank groups. In this work we present the plastomes of ten Ficus species. Results: The complete chloroplast (CP) genomes of eleven Ficus specimens belonging to ten species were determined and analysed. The full length of the Ficus plastome was nearly 160 kbp with a similar overall GC content, ranging from 35.88 to 36.02%. A total of 114 unique genes, distributed in 80 protein-coding genes, 30 tRNAs, and 4 rRNAs, were annotated in each of the Ficus CP genome. In addition, these CP genomes showed variation in their inverted repeat regions (IR). Tandem repeats and mononucleotide simple sequence repeat (SSR) are widely distributed across the Ficus CP genome. Comparative genome analysis showed low sequence variability. In addition, eight variable regions to be used as potential molecular markers were proposed for future Ficus species identification. According to the phylogenetic analysis, these ten Ficus species were clustered together and further divided into three clades based on different subgenera. Simultaneously, it also showed the relatedness between Ficus and Morus. Conclusion: The chloroplast genome structure of 10 Ficus species was similar to that of other angiosperms, with a typical four-part structure. Chloroplast genome sizes vary slightly due to expansion and contraction of the IR region. And the variation of noncoding regions of the chloroplast genome is larger than that of coding regions. Phylogenetic analysis showed that these eleven sampled CP genomes were divided into three clades, clustered with species from subgenus Urostigma, Sycomorus, and Ficus, respectively. These results support the Berg classification system, in which the subgenus Ficus was further decomposed into the subgenus Sycomorus. In general, the sequencing and analysis of Ficus plastomes, especially the ones of species with no or limited sequences available yet, contribute to the study of genetic diversity and species evolution of Ficus, while providing useful information for taxonomic and phylogenetic studies of Ficus. [ABSTRACT FROM AUTHOR]

Background: Kelch repeat F-box (KFB) proteins play vital roles in the regulation of multitudinous biochemical and physiological processes in plants, including growth and development, stress response and secondary metabolism. Multiple KFBs have been characterized in various plant species, but the family members and functions have not been systematically identified and analyzed in potato. Results: Genome and transcriptome analyses of StKFB gene family were conducted to dissect the structure, evolution and function of the StKFBs in Solanum tuberosum L. Totally, 44 StKFB members were identified and were classified into 5 groups. The chromosomal localization analysis showed that the 44 StKFB genes were located on 12 chromosomes of potato. Among these genes, two pairs of genes (StKFB15/16 and StKFB40/41) were predicted to be tandemly duplicated genes, and one pair of genes (StKFB15/29) was segmentally duplicated genes. The syntenic analysis showed that the KFBs in potato were closely related to the KFBs in tomato and pepper. Expression profiles of the StKFBs in 13 different tissues and in potato plants with different treatments uncovered distinct spatial expression patterns of these genes and their potential roles in response to various stresses, respectively. Multiple StKFB genes were differentially expressed in yellow- (cultivar 'Jin-16'), red- (cultivar 'Red rose-2') and purple-fleshed (cultivar 'Xisen-8') potato tubers, suggesting that they may play important roles in the regulation of anthocyanin biosynthesis in potato. Conclusions: This study reports the structure, evolution and expression characteristics of the KFB family in potato. These findings pave the way for further investigation of functional mechanisms of StKFBs, and also provide candidate genes for potato genetic improvement. [ABSTRACT FROM AUTHOR]

Background: Polystachya Hook. is a large pantropical orchid genus (c. 240 species) distributed in Africa, southern Asia and the Americas, with the center of diversity in Africa. Previous studies on species of this genus have not obtained the complete chloroplast genomes, structures and variations. Additionally, the phylogenetic position of the genus in the Orchidaceae is still controversial and uncertain. Therefore, in this study, we sequenced the complete plastomes of six Kenya Polystachya species based on genome skimming, subjected them to comparative genomic analysis, and reconstructed the phylogenetic relationships with other Orchidaceae species. Results: The results exhibited that the chloroplast genomes had a typical quadripartite structure with conserved genome arrangement and moderate divergence. The plastomes of the six Polystachya species ranged from 145,484 bp to 149,274 bp in length and had an almost similar GC content of 36.9-37.0%. Gene annotation revealed 106-109 single-copy genes. In addition, 19 genes are duplicated in the inverted regions, and 16 genes each possessd one or more introns. Although no large structural variations were observed among the Polystachya plastomes, about 1 kb inversion was found in Polystachya modesta and all 11 ndh genes in the Polystachya plastomes were lost or pseudogenized. Comparative analysis of the overall sequence identity among six complete chloroplast genomes confirmed that for both coding and non-coding regions in Polystachya, SC regions exhibit higher sequence variation than IRs. Furthermore, there were various amplifications in the IR regions among the six Polystachya species. Most of the protein-coding genes of these species had a high degree of codon preference. We screened out SSRs and found seven relatively highly variable loci. Moreover, 13 genes were discovered with significant positive selection. Phylogenetic analysis showed that the six Polystachya species formed a monophyletic clade and were more closely related to the tribe Vandeae. Phylogenetic relationships of the family Orchidaceae inferred from the 85 chloroplast genome sequences were generally consistent with previous studies and robust. Conclusions: Our study is the initial report of the complete chloroplast genomes of the six Polystachya species, elucidates the structural characteristics of the chloroplast genome of Polystachya, and filters out highly variable sequences that can contribute to the development of DNA markers for use in the study of genetic variability and evolutionary studies in Polystachya. In addition, the phylogenetic results strongly support that the genus of Polystachya is a part of the tribe Vandeae. [ABSTRACT FROM AUTHOR]

Background: Despite having a high mortality rate, Asian studies about the characteristics of adult listeriosis are limited. We investigated the incidence of listeriosis per admissions, associated factors, and rate of mortality in listeriosis, compared with non-listeriosis. Methods: We recorded the incidence of listeriosis per 10,000 admissions and conducted a case–control study from January 1, 2010, to December 31, 2019, at Tokyo Medical University Hospital (TMUH) in Japan. Cases were defined as adult with listeriosis that was bacteremia due to L. monocytogenes. Controls, defined as adult with non-listeriosis bacteremia due to other pathogens, were matched by age and clinical department to cases. We analyzed differences in seasonality, including warm season (defined as the period from May to October), medication including steroids, laboratory findings, and mortality. The odds ratio and p value between the cases group and control group were calculated using a chi-square test and Fisher's exact test. Results: The incidence of listeriosis per 10,000 admissions to TMUH was 0.51. Eleven patients, excluding one neonate, were included in the case group. Twenty-six patients, excluding one patient because of contamination and one patient because of insufficient medical record, were included in the control group. Listeriosis onset was associated with the warm season (90.9% vs. 53.8%; p = 0.033), steroid use (54.5% vs. 19.2%; p = 0.042), and a lower ratio of neutrophils to lymphocytes (9.46 vs. 18.44; p = 0.015). The 30-day mortality rate of listeriosis was similar to non-listeriosis (18.3% vs. 19.2%; p = 0.619). Conclusion: The incidence of listeriosis per admissions in this study was similar to that in other Asian countries. Factors associated with listeriosis were the warm season, steroid use, and a lower ratio of neutrophils to lymphocytes. Additionally, the 30-day mortality rate was similarly high in both the listeriosis and non-listeriosis groups. [ABSTRACT FROM AUTHOR]

Background: Despite having a high mortality rate, Asian studies about the characteristics of adult listeriosis are limited. We investigated the incidence of listeriosis per admissions, associated factors, and rate of mortality in listeriosis, compared with non-listeriosis.Methods: We recorded the incidence of listeriosis per 10,000 admissions and conducted a case-control study from January 1, 2010, to December 31, 2019, at Tokyo Medical University Hospital (TMUH) in Japan. Cases were defined as adult with listeriosis that was bacteremia due to L. monocytogenes. Controls, defined as adult with non-listeriosis bacteremia due to other pathogens, were matched by age and clinical department to cases. We analyzed differences in seasonality, including warm season (defined as the period from May to October), medication including steroids, laboratory findings, and mortality. The odds ratio and p value between the cases group and control group were calculated using a chi-square test and Fisher's exact test.Results: The incidence of listeriosis per 10,000 admissions to TMUH was 0.51. Eleven patients, excluding one neonate, were included in the case group. Twenty-six patients, excluding one patient because of contamination and one patient because of insufficient medical record, were included in the control group. Listeriosis onset was associated with the warm season (90.9% vs. 53.8%; p = 0.033), steroid use (54.5% vs. 19.2%; p = 0.042), and a lower ratio of neutrophils to lymphocytes (9.46 vs. 18.44; p = 0.015). The 30-day mortality rate of listeriosis was similar to non-listeriosis (18.3% vs. 19.2%; p = 0.619).Conclusion: The incidence of listeriosis per admissions in this study was similar to that in other Asian countries. Factors associated with listeriosis were the warm season, steroid use, and a lower ratio of neutrophils to lymphocytes. Additionally, the 30-day mortality rate was similarly high in both the listeriosis and non-listeriosis groups. [ABSTRACT FROM AUTHOR]

Coronary heart disease (CHD) is a common ischaemic heart disease whose pathological mechanism has not been fully elucidated. Single target drugs, such as antiplatelet aggregation, coronary artery dilation and lipid-lowering medicines, can relieve some symptoms clinically but cannot effectively prevent and treat CHD. Accumulating evidence has revealed that alterations in GM composition, diversity, and richness are associated with the risk of CHD. The metabolites of the gut microbiota (GM), including trimethylamine N-oxide (TMAO), short-chain fatty acids (SCFAs) and bile acids (BAs), affect human physiology by activating numerous signalling pathways. Due to the advantage of multiple components and multiple targets, traditional Chinese medicine (TCM) can intervene in CHD by regulating the composition of the GM, reducing TMAO, increasing SCFAs and other CHD interventions. We have searched PubMed, Web of science, Google Scholar Science Direct, and China National Knowledge Infrastructure (CNKI), with the use of the keywords "gut microbiota, gut flora, traditional Chinese medicine, herbal medicine, coronary heart disease". This review investigated the relationship between GM and CHD, as well as the intervention of TCM in CHD and GM, and aims to provide valuable insights for the treatments of CHD by TCM. [ABSTRACT FROM AUTHOR]

The human microbiome is defined as the microorganisms that reside in or on the human body, such as bacteria, viruses, fungi, and protozoa, and their genomes. The human microbiome participates in the modulation of human metabolism by influencing several intricate pathways. The association between specific bacteria or viruses and the efficacy of cancer treatments and the occurrence of treatment-related toxicity in cancer patients has been reported. However, the understanding of the interaction between the host microbiome and the cancer treatment response is limited, and the microbiome potentially plays a greater role in the treatment of cancer than reported to date. Here, we provide a thorough review of the potential role of the gut and locally resident bacterial microbiota in modulating responses to different cancer therapeutics to demonstrate the association between the gut or locally resident bacterial microbiota and cancer therapy. Probable mechanisms, such as metabolism, the immune response and the translocation of microbiome constituents, are discussed to promote future research into the association between the microbiome and other types of cancer. We conclude that the interaction between the host immune system and the microbiome may be the basis of the role of the microbiome in cancer therapies. Future research on the association between host immunity and the microbiome may improve the efficacy of several cancer treatments and provide insights into the cause of treatment-related side effects. [ABSTRACT FROM AUTHOR]

Background: Understanding the genetic diversity in endangered species that occur inforest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population are unknown due to lack of efficient molecular markers. Results: In this study, we employed Illumina HiSeq™ 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). Raw reads total of 23,741,783 was obtained and then assembled, from which the generated unigenes were 89,271 (average length = 598.3191 nt). The 31,686 unigenes were annotated in different databases i.e. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Nucleotide Collection (NR/NT) and Swiss-Prot for functional annotation. Further, 11,343 EST-SSRs were detected. From 7774 primer pairs, 101 were selected for polymorphism validation, in which; 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used for population structure and diversity analyses. The obtained results revealed high levels of genetic diversity in populations, the average observed and expected heterozygosity were HO = 0.422 and HE = 0.479, respectively. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of the bottleneck in all populations. Genetic differentiation between populations was moderate (FST = 0.133) and indicating slightly high level of gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. Our results shows two genetic clusters related to geographical distances. Conclusion: Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species. [ABSTRACT FROM AUTHOR]

Background: Vespa velutina, one of the most aggressive and fearful wasps in China, can cause grievous allergies and toxic reactions, leading to organ failure and even death. However, there is little evidence on molecular data regarding wasps. Therefore, we aimed to provide an insight into the transcripts expressed in the venom gland of wasps. Results: In our study, high-throughput RNA sequencing was performed using the venom glands of four wasp species. First, the mitochondrial cytochrome C oxidase submit I (COI) barcoding and the neighbor joining (NJ) tree were used to validate the unique identity and lineage of each individual species. After sequencing, a total of 127,630 contigs were generated and 98,716 coding domain sequences (CDS) were predicted from the four species. The Gene ontology (GO) enrichment analysis of unigenes revealed their functional role in important biological processes (BP), molecular functions (MF) and cellular components (CC). In addition, c-type, p1 type, p2 type and p3 type were the most commonly found simple sequence repeat (SSR) types in the four species of wasp transcriptome. There were differences in the distribution of SSRs and single nucleotide polymorphisms (SNPs) among the four wasp species. Conclusions: The transcriptome data generated in this study will improve our understanding on bioactive proteins and venom-related genes in wasp venom gland and provide a basis for pests control and other applications. To our knowledge, this is the first study on the identification of large-scale genomic data and the discovery of microsatellite markers from V. tropica ducalis and V. analis fabricius. [ABSTRACT FROM AUTHOR]

Background: Most lactobacilli found in animal intestines are generally non-motile, but there are few exceptions. Our previous work showed that Lactobacillus agilis BKN88, which is a highly motile strain originating from a chicken, takes advantage of motility in gut colonization in murine models, and thus motile lactobacilli likely have unique ecological characteristics conferred by motility. However, the ecology and habitat of gut-derived motile lactobacilli are still rarely understood. In addition, the limited availability of motile Lactobacillus isolates is one of the major obstacles for further studies. To gain insight into the ecology and habitat of the motile lactobacilli, we established a routinely applicable detection method for motile lactobacilli using PCR and subsequent selective isolation in semi-solid MRS medium for the collection of additional motile lactobacilli from animal feces. Results: We applied the PCR detection using motile lactobacilli-specific primers, based on the motor switch protein gene (fliG) of flagella, to 120 animal feces, followed by selective isolation performed using 45 animal feces. As a result, motile lactobacilli were detected in 44 animal feces. In the selective isolation, 29 isolates of L. agilis and 2 isolates of L. ruminis were obtained from 8 animal species. Conclusions: These results indicated that motile lactobacilli are distributed in different animal species. Moreover, phylogenetic analysis of the L. agilis isolates suggests co-evolution with the host, and adaptation to a particular environmental niche. [ABSTRACT FROM AUTHOR]

Background: Grass carp (Ctenopharyngodon idellus) are important species in Asian aquaculture. A draft genome for grass carp has already been published in 2015. However, there is still a requirement for a suitable genetic linkage map to arrange scaffolds on chromosomal frameworks. QTL analysis is a powerful tool to detect key locations for quantitative traits, especially in aquaculture. There no growth related QTLs of grass carp have been published yet. Even the growth trait is one of the focuses in grass carp culture. Results: In this study, a pair of distantly related parent grass carps and their 100 six-month-old full-sib offspring were used to construct a high-density genetic map with 6429 single nucleotide polymorphisms (SNPs) by 2b-RAD technology. The total length of the consensus map is 5553.43 cM with the average marker interval of 1.92 cM. The map has a good collinearity with both the grass carp draft genome and the zebrafish genome, and it assembled 89.91% of the draft genome to a chromosomal level. Additionally, according to the growth-related traits of progenies, 30 quantitative trait loci (QTLs), including 7 for body weight, 9 for body length, 5 for body height and 9 for total length, were identified in 16 locations on 5 linkage groups. The phenotypic variance explained for these QTLs varies from 13.4 to 21.6%. Finally, 17 genes located in these regions were considered to be growth-related because they either had functional mutations predicted from the resequencing data of the parents. Conclusion: A high density genetic linkage map of grass carp was built and it assembled the draft genome to a chromosomal level. Thirty growth related QTLs were detected. After the cross analysis of Parents resequencing data, 17 candidate genes were obtained for further researches. [ABSTRACT FROM AUTHOR]

Background: Previously, 3% of the human genome has been annotated as simple sequence repeats (SSRs), similar to the proportion annotated as protein coding. The origin of much of the genome is not well annotated, however, and some of the unidentified regions are likely to be ancient SSR-derived regions not identified by current methods. The identification of these regions is complicated because SSRs appear to evolve through complex cycles of expansion and contraction, often interrupted by mutations that alter both the repeated motif and mutation rate. We applied an empirical, kmer-based, approach to identify genome regions that are likely derived from SSRs. Results: The sequences flanking annotated SSRs are enriched for similar sequences and for SSRs with similar motifs, suggesting that the evolutionary remains of SSR activity abound in regions near obvious SSRs. Using our previously described P-clouds approach, we identified 'SSR-clouds', groups of similar kmers (or 'oligos') that are enriched near a training set of unbroken SSR loci, and then used the SSR-clouds to detect likely SSR-derived regions throughout the genome. Conclusions: Our analysis indicates that the amount of likely SSR-derived sequence in the human genome is 6.77%, over twice as much as previous estimates, including millions of newly identified ancient SSR-derived loci. SSR-clouds identified poly-A sequences adjacent to transposable element termini in over 74% of the oldest class of Alu (roughly, AluJ), validating the sensitivity of the approach. Poly-A's annotated by SSR-clouds also had a length distribution that was more consistent with their poly-A origins, with mean about 35 bp even in older Alus. This work demonstrates that the high sensitivity provided by SSR-Clouds improves the detection of SSR-derived regions and will enable deeper analysis of how decaying repeats contribute to genome structure. [ABSTRACT FROM AUTHOR]

Background: Impaired fertility in cattle limits the efficiency of livestock production systems. Unraveling the genetic architecture of fertility traits would facilitate their improvement by selection. In this study, we characterized SNP chip haplotypes at QTL blocks then used whole-genome sequencing to fine map genomic regions associated with reproduction in a population of Nellore (Bos indicus) heifers. Methods: The dataset comprised of 1337 heifers genotyped using a GeneSeek® Genomic Profiler panel (74677 SNPs), representing the daughters from 78 sires. After performing marker quality control, 64800 SNPs were retained. Haplotypes carried by each sire at six previously identified QTL on BTAs 5, 14 and 18 for heifer pregnancy and BTAs 8, 11 and 22 for antral follicle count were constructed using findhap software. The significance of the contrasts between the effects of every two paternally-inherited haplotype alleles were used to identify sires that were heterozygous at each QTL. Whole-genome sequencing data localized to the haplotypes from six sires and 20 other ancestors were used to identify sequence variants that were concordant with the haplotype contrasts. Enrichment analyses were applied to these variants using KEGG and MeSH libraries. Results: A total of six (BTA 5), six (BTA 14) and five (BTA 18) sires were heterozygous for heifer pregnancy QTL whereas six (BTA 8), fourteen (BTA 11), and five (BTA 22) sires were heterozygous for number of antral follicles' QTL. Due to inadequate representation of many haplotype alleles in the sequenced animals, fine mapping analysis could only be reliably performed for the QTL on BTA 5 and 14, which had 641 and 3733 concordant candidate sequence variants, respectively. The KEGG "Circadian rhythm" and "Neurotrophin signaling pathway" were significantly associated with the genes in the QTL on BTA 5 whereas 32 MeSH terms were associated with the QTL on BTA 14. Among the concordant sequence variants, 0.2% and 0.3% were classified as missense variants for BTAs 5 and 14, respectively, highlighting the genes MTERF2, RTMB, ENSBTAG00000037306 (miRNA), ENSBTAG00000040351, PRKDC, and RGS20. The potential causal mutations found in the present study were associated with biological processes such as oocyte maturation, embryo development, placenta development and response to reproductive hormones. Conclusions: The identification of heterozygous sires by positionally phasing SNP chip data and contrasting haplotype effects for previously detected QTL can be used for fine mapping to identify potential causal mutations and candidate genes. Genomic variants on genes MTERF2, RTBC, miRNA ENSBTAG00000037306, ENSBTAG00000040351, PRKDC, and RGS20, which are known to have influence on reproductive biological processes, were detected. [ABSTRACT FROM AUTHOR]

Background: Previous study reported that patients who suffered coronary heart disease (CHD) complicated with non-alcoholic fatty liver disease (NAFLD) had worse cardiac function and clinical outcomes than patients with CHD only. Notably, the mechanism is still unclear. This study aimed to investigate the changes and roles of intestinal bacterial microbiota in CHD-NAFLD patients. Methods and results: People were recruited and divided into three groups, including CHD patients (without NAFLD), CHD-NAFLD patients and healthy controls (HCs). Each group contained 24 people. Fecal samples and clinical information were carefully collected. The Illumina sequencing of 16S rRNA was applied to profile the overall structure of the fecal bacterial microbiota and the characteristics of the bacterial microbiota based on the Operational Taxonomic Units. In clinical information, the CHD-NAFLD patients showed an increase in BMI, uric acid and triglyceride. There was a significant reduction in the abundance of Parabacteroides and Collinsella in overall CHD patients (including CHD-NAFLD and CHD patients). The intestinal bacterial microbiota in CHD-NAFLD patients showed an increase in the abundance of Copococcus and Veillonella, and a reduction in the abundance of Parabacteroides, Bacteroides fragilis, Ruminococcus gnavus, Bacteroides dorei, and Bifidobacterium longum subsp infantis. Among them, the abundance of Ruminococcus gnavus and Bacteroides dorei was significantly lower than that in CHD patients. Additionally, BMI positively correlated with the abundance of Copococcus and negatively correlated with the abundance of Bifidobacterium longum subsp infantis. The abundance of Veillonella positively correlated with AST. The abundance of Bacteroides dorei negatively correlated with ALT and AST. It indicates that the abundance of intestinal microbiota was related to the changes in clinical indexes. Conclusions: Changes of intestinal bacterial microbiota in CHD-NAFLD patients may be important factors affecting the degree of metabolic disorder, which may be one of the important reasons for the worse clinical outcome and disease progression in CHD-NAFLD patients than in CHD patients. [ABSTRACT FROM AUTHOR]

Background: Pear (Pyrus spp.) is an economically important temperate fruit tree worldwide. In the past decade, significant progress has been made in pear molecular genetics based on DNA research, but the number of molecular markers is still quite limited, which hardly satisfies the increasing needs of geneticists and breeders. Results: In this study, a total of 156,396 simple sequence repeat (SSR) loci were identified from a genome sequence of Pyrus bretschneideri 'Dangshansuli'. A total of 101,694 pairs of SSR primers were designed from the SSR loci, and 80,415 of the SSR loci were successfully located on 17 linkage groups (LGs). A total of 534 primer pairs were synthesized and preliminarily screened in four pear cultivars, and of these, 332 primer pairs were selected as clear, stable, and polymorphic SSR markers. Eighteen polymorphic SSR markers were randomly selected from the 332 polymorphic SSR markers in order to perform a further analysis of the genetic diversity among 44 pear cultivars. The 14 European pears and their hybrid materials were clustered into one group (European pear group); 29 Asian pear cultivars were clustered into one group (Asian pear group); and the Zangli pear cultivar 'Deqinli' from Yunnan Province, China, was grouped in an independent group, which suggested that the cultivar 'Deqinli' is a distinct and valuable germplasm resource. The population structure analysis partitioned the 44 cultivars into two populations, Pop 1 and Pop 2. Pop 2 was further divided into two subpopulations. Results from the population structure analysis were generally consistent with the results from the UPGMA cluster analysis. Conclusions: The results of the present study showed that the use of next-generating sequencing to develop SSR markers is fast and effective, and the developed SSR markers can be utilized by researchers and breeders for future pear improvement. [ABSTRACT FROM AUTHOR]

Background: Individual organisms are linked to their communities and ecosystems via metabolic activities. Metabolic exchanges and co-dependencies have long been suggested to have a pivotal role in determining community structure. In phloem-feeding insects such metabolic interactions with bacteria enable complementation of their deprived nutrition. The phloem-feeding whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) harbors an obligatory symbiotic bacterium, as well as varying combinations of facultative symbionts. This well-defined bacterial community in B. tabaci serves here as a case study for a comprehensive and systematic survey of metabolic interactions within the bacterial community and their associations with documented occurrences of bacterial combinations. We first reconstructed the metabolic networks of five common B. tabaci symbionts genera (Portiera, Rickettsia, Hamiltonella, Cardinium and Wolbachia), and then used network analysis approaches to predict: (1) species-specific metabolic capacities in a simulated bacteriocyte-like environment; (2) metabolic capacities of the corresponding species' combinations, and (3) dependencies of each species on different media components. Results: The predictions for metabolic capacities of the symbionts in the host environment were in general agreement with previously reported genome analyses, each focused on the single-species level. The analysis suggests several previously un-reported routes for complementary interactions and estimated the dependency of each symbiont in specific host metabolites. No clear association was detected between metabolic co-dependencies and co-occurrence patterns. Conclusions: The analysis generated predictions for testable hypotheses of metabolic exchanges and co-dependencies in bacterial communities and by crossing them with co-occurrence profiles, contextualized interaction patterns into a wider ecological perspective. [ABSTRACT FROM AUTHOR]

Background: Xylella fastidiosa (Xf) is a gram negative bacterium inhabiting the plant vascular system. In most species this bacterium lives as a benign symbiote, but in several agriculturally important plants (e.g. coffee, citrus, grapevine) Xf is pathogenic. Xf has four loci encoding homologues to hemolysin RTX proteins, virulence factors involved in a wide range of plant pathogen interactions. Results: We show that all four genes are expressed during pathogenesis in grapevine. The sequences from these four genes have a complex repetitive structure. At the C-termini, sequence diversity between strains is what would be expected from orthologous genes. However, within strains there is no N-terminal homology, indicating these loci encode RTXs of different functions and/or specificities. More striking is that many of the orthologous loci between strains share this extreme variation at the N-termini. Thus these RTX orthologues are most easily visualized as fusions between the orthologous C–termini and different N-termini. Further, the four genes are found in operons having a peculiar structure with an extensively duplicated module encoding a small protein with homology to the N-terminal region of the full length RTX. Surprisingly, some of these small peptides are most similar not to their corresponding full length RTX, but to the N-termini of RTXs from other Xf strains, and even other remotely related species. Conclusions: These results demonstrate that these genes are expressed in planta during pathogenesis. Their structure suggests extensive evolutionary restructuring through horizontal gene transfers and heterologous recombination mechanisms. The sum of the evidence suggests these repetitive modules are a novel kind of mobile genetic element. [ABSTRACT FROM AUTHOR]

Background: Household contacts of cholera patients have a 100 times higher risk of developing a cholera infection than the general population. To compare the genetic relatedness of clinical and water source Vibrio cholerae isolates from cholera patients' households across three outbreaks, we analyzed these isolates using whole-genome-sequencing (WGS) and multilocus variable-number tandem-repeat analysis (MLVA). Results: The WGS analyses revealed that 80% of households had source water isolates that were more closely related to clinical isolates from the same household than to any other isolates. While in another 20% of households an isolate from a person was more closely related to clinical isolates from another household than to source water isolates from their own household. The mean pairwise differences in single nucleotide-variant (SNV) counts for isolates from the same household were significantly lower than those for different households (2.4 vs. 7.7 p < 0.0001), and isolates from the same outbreak had significantly fewer mean pairwise differences compared to isolates from different outbreaks (mean: 6.2 vs. 8.0, p < 0.0001). Based on MLVA in outbreak 1, we observed that the majority of households had clinical isolates with MLVA genotypes related to other clinical isolates and unrelated to water source isolates from the same household. While in outbreak 3, there were different MLVA genotypes between households, however within the majority of households, the clinical and water source isolates had the same MLVA genotypes. The beginning of outbreak 2 resembled outbreak 1 and the latter part resembled outbreak 3. We validated our use of MLVA by comparing it to WGS. Isolates with the identical MLVA genotype had significantly fewer mean pairwise SNV differences than those isolates with different MLVA genotypes (mean: 4.8 vs. 7.7, p < 0.0001). Furthermore, consistent with WGS results, the number of pairwise differences in the five MLVA loci for isolates within the same household was significantly lower than isolates from different households (mean: 1.6 vs. 3.0, p < 0.0001). Conclusion: These results suggest that transmission patterns for cholera are a combination of person-to-person and water-to-person cholera transmission with the proportions of the two modes varying within and between outbreaks. [ABSTRACT FROM AUTHOR]

Tea (Camellia sinensis, (L.) Kuntze) is considered as most popular drink across the world and it is widely consumed beverage for its several health-benefit characteristics. These positive traits primarily rely on its regulatory networks of different metabolic pathways. Development of microsatellite markers from the conserved genomic regions are being worthwhile for reviewing the genetic diversity of closely related species or self-pollinated species. Although several SSR markers have been reported, in tea, the trait-specific Simple Sequence Repeat (SSR) markers, leading to be useful in marker assisted breeding technique, are yet to be identified. Micro RNAs are short, non-coding RNA molecules, involved in post transcriptional mode of gene regulation and thus effects on related phenotype. Present study deals with identification of the microsatellite motifs within the reported and predicted miRNA precursors that are effectively followed by designing of primers from SSR flanking regions in order to PCR validation. In addition to the earlier reports, two new miRNAs are predicting here from tea expressed tag sequence database. Furthermore, 18 SSR motifs are found to be in 13 of all 33 predicted miRNAs. Trinucleotide motifs are most abundant among all followed by dinucleotides. Since, miRNA based SSR markers are evidenced to have significant role on genetic fingerprinting study, these outcomes would pave the way in developing novel markers for tagging tea specific agronomic traits as well as substantiating non-conventional breeding program. [ABSTRACT FROM AUTHOR]

Background: Early blight, caused by the fungus Alternaria solani, occurs on potato mainly in the south-eastern part of Sweden, but also in other parts of the country. The aim of this study was to investigate the genetic diversity of A. solani populations from different potato growing regions in south-eastern Sweden using AFLP marker analysis. In addition, the cultured isolates were examined for substitutions in the gene encoding cytochrome b, associated with loss of sensitivity against QoI fungicides. Results: Nei's gene diversity index for the Swedish populations of A. solani revealed a gene diversity of up to 0.20. Also genetic differentiation was observed among populations of A. solani from different locations in south-eastern Sweden. The mitochondrial genotype of the isolates of A. solani was determined and both known genotypes, GI (genotype 1) and GII (genotype 2), were found among the isolates. The occurrence of the F129L substitution associated with a loss of sensitivity to strobilurins was confirmed among the GII isolates. In vitro conidial germination tests verified that isolates containing the F129L substitution had reduced sensitivity to azoxystrobin and, at a lower extent, to pyraclostrobin. Conclusions: Genetic diversity was relatively high among isolates of A. solani in south-eastern part of Sweden. F129L substitutions, leading to reduced sensitivity to strobilurins, have been established in field populations, which may have implications for the future efficacy of QoI fungicides. [ABSTRACT FROM AUTHOR]

Background: Chloroplast chaperonin, consisting of multiple subunits, mediates folding of the highly abundant protein Rubisco with the assistance of co-chaperonins. ATP hydrolysis drives the chaperonin allosteric cycle to assist substrate folding and promotes disassembly of chloroplast chaperonin. The ways in which the subunits cooperate during this cycle remain unclear. Results: Here, we report the first crystal structure of Chlamydomonas chloroplast chaperonin homo-oligomer (CPN60β1) at 3.8 Å, which shares structural topology with typical type I chaperonins but with looser compaction, and possesses a larger central cavity, less contact sites and an enlarged ATP binding pocket compared to GroEL. The overall structure of Cpn60 resembles the GroEL allosteric intermediate state. Moreover, two amino acid (aa) residues (G153, G154) conserved among Cpn60s are involved in ATPase activity regulated by co-chaperonins. Domain swapping analysis revealed that the monomeric state of CPN60α is controlled by its equatorial domain. Furthermore, the C-terminal segment (aa 484-547) of CPN60β influenced oligomer disassembly and allosteric rearrangement driven by ATP hydrolysis. The entire equatorial domain and at least one part of the intermediate domain from CPN60α are indispensable for functional cooperation with CPN60β1, and this functional cooperation is strictly dependent on a conserved aa residue (E461) in the CPN60α subunit. Conclusions: The first crystal structure of Chlamydomonas chloroplast chaperonin homo-oligomer (CPN60β1) is reported. The equatorial domain maintained the monomeric state of CPN60α and the C-terminus of CPN60β affected oligomer disassembly driven by ATP. The cooperative roles of CPN60 subunits were also established. [ABSTRACT FROM AUTHOR]

Background: Trichophyton rubrum is a cosmopolitan filamentous fungus that can infect human keratinized tissue (skin, nails and, rarely, hair) and is the major agent of all chronic and recurrent dermatophytoses. The dermatophyte infection process is initiated through the release of arthroconidial adhesin, which binds to the host stratum corneum. The conidia then germinate, and fungal hyphae invade keratinized skin structures through the secretion of proteases. Although arthroconidia play a central role in pathogenesis, little is known about the dormancy and germination of T. rubrum conidia and the initiation of infection. The objective of this study was to evaluate the transcriptional gene expression profile of T. rubrum conidia during growth on keratin- or elastin-containing medium, mimicking superficial and deep dermatophytosis, respectively. Results: A transcriptional profiling analysis was conducted using a custom oligonucleotide-based microarray by comparing T. rubrum conidia grown on elastin and keratin substrates. This comparison shows differences according to protein source used, but consisted of a very small set of genes, which could be attributed to the quiescent status of conidia. The modulated genes were related to the dormancy, survival and germination of conidia, including genes involved in the respiratory chain, signal transduction and lipid metabolism. However, an induction of a great number of proteases occurred when T. rubrum was grown in the presence of keratin such as the subtilisin family of proteases (Sub 1 and Sub 3) and leucine aminopeptidase (Lap 1 and Lap 2). Interestingly, keratin also promoted the up-regulation of a gene encoding an adhesin-like protein with a tandem repeat sequence. In silico analysis showed that the protein contains a domain related to adhesin that may play a role in host-pathogen interactions. The expression of this adhesin-like gene was also induced during the co-culture of T. rubrum with a human keratinocyte cell line, confirming its role in fungal-host interactions. Conclusion: These results contribute to the discovery of new targets involved in the adhesion of conidia and the maintenance of conidial dormancy, which are essential for triggering the process of infection and the chronicity of dermatophytosis. [ABSTRACT FROM AUTHOR]

Fish plays an important role in the human diet, and there is an observed increase in the consumption of fish per capita in Europe. However, intensive growth of industry and agriculture may cause contamination of natural and human-made aquatic environments, and may affect not only the health of fish, but also raise safety concerns with regard to fish used for human consumption. It is well known that fish and fish products are often associated with human diseases. Thus, it is necessary to study the prevalence of pathogens in fish to ensure the safety of fish products and environments. Microbial assessment of fish also gives additional information about the hygienic status of environments, including lakes, rivers, ponds, and fish farms. Detection of pathogenic microorganisms or changes in natural microflora in the water environment could be an important indicator of possible contamination. The aim of this review was to describe and discuss the five most relevant bacterial genera and species linked to aquatic environments- Vibrio spp., Listeria monocytogenes, Yersinia spp., pathogenic Salmonella serovars, and Clostridium botulinum-causing human foodborne diseases. [ABSTRACT FROM AUTHOR]

Background: Low complexity regions (LCRs) are a ubiquitous feature in genomes and yet their evolutionary history and functional roles are unclear. Previous studies have shown contrasting evidence in favor of both neutral and selective mechanisms of evolution for different sets of LCRs suggesting that modes of identification of these regions may play a role in our ability to discern their evolutionary history. To further investigate this issue, we used a multiple threshold approach to identify species-specific profiles of proteome complexity and, by comparing properties of these sets, determine the influence that starting parameters have on evolutionary inferences. Results: We find that, although qualitatively similar, quantitatively each species has a unique LCR profile which represents the frequency of these regions within each genome. Inferences based on these profiles are more accurate in comparative analyses of genome complexity as they allow to determine the relative complexity of multiple genomes as well as the type of repetitiveness that is most common in each. Based on the multiple threshold LCR sets obtained, we identified predominant evolutionary mechanisms at different complexity levels, which show neutral mechanisms acting on highly repetitive LCRs (e.g., homopolymers) and selective forces becoming more important as heterogeneity of the LCRs increases. Conclusions: Our results show how inferences based on LCRs are influenced by the parameters used to identify these regions. Sets of LCRs are heterogeneous aggregates of regions that include homo- and heteropolymers and, as such, evolve according to different mechanisms. LCR profiles provide a new way to investigate genome complexity across species and to determine the driving mechanism of their evolution. [ABSTRACT FROM AUTHOR]

Background: Tandem amino acid repeats are characterised by the consecutive recurrence of a single amino acid. They exhibit high rates of length mutations in addition to point mutations and have been proposed to be involved in genetic plasticity. Squamate reptiles (lizards and snakes) diversify in both morphology and physiology. The underlying mechanism is yet to be understood. In a previous phylogenomic analysis of reptiles, the density of tandem repeats in an anole lizard diverged heavily from that of the other reptiles. To gain further insight into the tandem amino acid repeats in squamates, we analysed the repeat content in the green anole (Anolis carolinensis) proteome and compared the amino acid repeats in a large orthologous protein data set from six vertebrates (the Western clawed frog, the green anole, the Chinese softshell turtle, the zebra finch, mouse and human). Results: Our results revealed that the number of amino acid repeats in the green anole exceeded those found in the other five species studied. Species-only repeats were found in high proportion in the green anole but not in the other five species, suggesting that the green anole had gained many amino acid repeats in either the Anolis or the squamate lineage. Since the amino acid repeat containing genes in the green anole were highly enriched in genes related to transcription and development, an important family of developmental genes, i.e., the Hox family, was further studied in a wide collection of squamates. Abundant amino acid repeats were also observed, implying the general high tolerance of amino acid repeats in squamates. A particular enrichment of amino acid repeats was observed in the central class Hox genes that are known to be responsible for defining cervical to lumbar regions. Conclusions: Our study suggests that the abundant amino acid repeats in the green anole, and possibly in other squamates, may play a role in increasing the genetic variability, and contribute to the evolutionary diversity of this clade. [ABSTRACT FROM AUTHOR]

Background: Adaptive processes shape the evolution of genomes and the diverse functions of different genomic regions are likely to have an impact on the trajectory and outcome of this evolution. The main underlying hypothesis of this study is that the evolution of Simple Sequence Repeats (SSRs) is correlated with the evolution of the genomic region in which they are located, resulting in differences of motif size, number of repeats, and levels of polymorphisms. These differences should be clearly detectable when analyzing the frequency and type of SSRs within the genome of a species, when studying populations within a species, and when comparing closely related sister taxa. By coupling a genome-wide SSR survey in the genome of the plant pathogenic fungus Heterobasidion irregulare with an analysis of intra- and interspecific variability of 39 SSR markers in five populations of the two sibling species H. irregulare and H. annosum, we investigated mechanisms of evolution of SSRs. Results: Results showed a clear dominance of trirepeats and a selection against other repeat number, i.e. di- and tetranucleotides, both in regions inside Open Reading Frames (ORFs) and upstream 5' untranslated region (5'UTR). Locus per locus AMOVA showed SSRs both inside ORFs and upstream 5'UTR were more conserved within species compared to SSRs in other genomic regions, suggesting their evolution is constrained by the functions of the regions they are in. Principal coordinates analysis (PCoA) indicated that even if SSRs inside ORFs were less polymorphic than those in intergenic regions, they were more powerful in differentiating species. These findings indicate SSRs evolution undergoes a directional selection pressure comparable to that of the ORFs they interrupt and to that of regions involved in regulatory functions. Conclusions: Our work linked the variation and the type of SSRs with regions upstream 5'UTR, putatively harbouring regulatory elements, and shows that the evolution of SSRs might be affected by their location in the genome. Additionally, this study provides a first glimpse on a possible molecular basis for fast adaptation to the environment mediated by SSRs. [ABSTRACT FROM AUTHOR]

Background: Enteropathogenic Escherichia coli (EPEC) is distinguished mainly by the presence of EPEC adherence factor plasmid (pEAF) in typical EPEC (tEPEC) and its absence in atypical EPEC (aEPEC). The initial adherence to the intestinal mucosa is complex and mediated by adhesins other than bundle-forming pilus, which is not produced by aEPEC. Extracellular matrix (ECM) proteins of eukaryotic cells are commonly recognized by bacterial adhesins. Therefore, binding to ECM proteins may facilitate colonization, invasion and/or signaling by intestinal pathogens. Previous studies from our group demonstrated that aEPEC O26:H11 (strain BA2103) showed high binding activity to fibronectin, not shared by its counterpart, aEPEC O26:HNM. Results: In the present study, using mass spectrometry after fibronectin-associated immunoprecipitation, two proteins, flagellin (50 kDa) and GroEL (52 kDa), were identified and BA2103 binding ability to fibronectin was inhibited in the presence of anti-H11 and anti-GroEL sera, but not by either naïve rabbit or other unrelated sera. It was also observed that the presence of purified flagellin inhibits adhesion of BA2103 to cellular fibronectin in a dose-dependent manner. Additionally, BA2103 GroEL is similar to the same protein of uropathogenic E. coli. Conclusions: Our results suggest that flagellin may play a role in the in vitro interaction of BA2103 with cellular fibronectin, and GroEL can be an accessory protein in this process. [ABSTRACT FROM AUTHOR]