ResearchPad - Microbiology https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Comparative Sequence Analysis of Historic and Current Porcine Rotavirus C Strains and Their Pathogenesis in 3-Day-Old and 3-Week-Old Piglets]]> https://www.researchpad.co/product?articleinfo=N82b3c98b-f78f-41b7-bfdc-1afe48213022 <![CDATA[In silico Prediction of Virus-Host Interactions for Marine Bacteroidetes With the Use of Metagenome-Assembled Genomes]]> https://www.researchpad.co/product?articleinfo=N30daefba-d176-4012-a742-922f7c4cde19

Bacteroidetes is one of the most abundant heterotrophic bacterial taxa in the ocean and play crucial roles in recycling phytoplankton-derived organic matter. Viruses of Bacteroidetes are also expected to have an important role in the regulation of host communities. However, knowledge on marine Bacteroidetes viruses is biased toward cultured viruses from a few species, mainly fish pathogens or Bacteroidetes not abundant in marine environments. In this study, we investigated the recently reported 1,811 marine viral genomes to identify putative Bacteroidetes viruses using various in silico host prediction techniques. Notably, we used microbial metagenome-assembled genomes (MAGs) to augment the marine Bacteroidetes reference genomic data. The examined viral genomes and MAGs were derived from simultaneously collected samples. Using nucleotide sequence similarity-based host prediction methods, we detected 31 putative Bacteroidetes viral genomes. The MAG-based method substantially enhanced the predictions (26 viruses) when compared with the method that is solely based on the reference genomes from NCBI RefSeq (7 viruses). Previously unrecognized genus-level groups of Bacteroidetes viruses were detected only by the MAG-based method. We also developed a host prediction method based on the proportion of Bacteroidetes homologs in viral genomes, which detected 321 putative Bacteroidetes virus genomes including 81 that were newly recognized as Bacteroidetes virus genomes. The majority of putative Bacteroidetes viruses were detected based on the proportion of Bacteroidetes homologs in both RefSeq and MAGs; however, some were detected in only one of the two datasets. Putative Bacteroidetes virus lineages included not only relatives of known viruses but also those phylogenetically distant from the cultured viruses, such as marine Far-T4 like viruses known to be widespread in aquatic environments. Our MAG and protein homology-based host prediction approaches enhanced the existing knowledge on the diversity of Bacteroidetes viruses and their potential interaction with their hosts in marine environments.

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<![CDATA[Proteolysis of Gingival Keratinocyte Cell Surface Proteins by Gingipains Secreted From Porphyromonas gingivalis – Proteomic Insights Into Mechanisms Behind Tissue Damage in the Diseased Gingiva]]> https://www.researchpad.co/product?articleinfo=N846558cc-79c5-47b2-8817-74347f916eea

Porphyromonas gingivalis, the main etiologic agent of periodontitis, secretes cysteine proteases named gingipains. HRgpA and RgpB gingipains have Arg-specificity, while Kgp gingipain is Lys-specific. Together they can cleave an array of proteins and importantly contribute to the development of periodontitis. In this study we focused on gingipain-exerted proteolysis at the cell surface of human gingival epithelial cells [telomerase immortalized gingival keratinocytes (TIGK)] in order to better understand the molecular mechanisms behind tissue destruction in periodontitis. Using mass spectrometry, we investigated the whole sheddome/degradome of TIGK cell surface proteins by P. gingivalis strains differing in gingipain expression and by purified gingipains, and performed the first global proteomic analysis of gignpain proteolysis at the membrane. Incubation of TIGK cells with P. gingivalis resulted in massive degradation of proteins already at low multiplicity of infection, whereas incubating cells with purified gingipains resulted in more discrete patterns, indicative of a combination of complete degradation and shedding of membrane proteins. Most of the identified gingipain substrates were molecules involved in adhesion, suggesting that gingipains may cause tissue damage through cleavage of cell contacts, resulting in cell detachment and rounding, and consequently leading to anoikis. However, HRgpA and RgpB gingipains differ in their mechanism of action. While RgpB rapidly degraded the proteins, HRgpA exhibited a much slower proteolysis indicative of ectodomain shedding, as demonstrated for the transferrin receptor protein 1 (TFRC). These results reveal a molecular underpinning to P. gingivalis-induced tissue destruction and enhance our knowledge of the role of P. gingivalis proteases in the pathobiology of periodontitis. Proteomics data are available via ProteomeXchange with identifier PXD015679.

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<![CDATA[Differential effects of ‘resurrecting' Csp pseudoproteases during Clostridioides difficile spore germination]]> https://www.researchpad.co/product?articleinfo=N954927dc-0a13-47d4-ae8c-b5023556ee72

Clostridioides difficile is a spore-forming bacterial pathogen that is the leading cause of hospital-acquired gastroenteritis. C. difficile infections begin when its spore form germinates in the gut upon sensing bile acids. These germinants induce a proteolytic signaling cascade controlled by three members of the subtilisin-like serine protease family, CspA, CspB, and CspC. Notably, even though CspC and CspA are both pseudoproteases, they are nevertheless required to sense germinants and activate the protease, CspB. Thus, CspC and CspA are part of a growing list of pseudoenzymes that play important roles in regulating cellular processes. However, despite their importance, the structural properties of pseudoenzymes that allow them to function as regulators remain poorly understood. Our recently solved crystal structure of CspC revealed that its pseudoactive site residues align closely with the catalytic triad of CspB, suggesting that it might be possible to ‘resurrect' the ancestral protease activity of the CspC and CspA pseudoproteases. Here, we demonstrate that restoring the catalytic triad to these pseudoproteases fails to resurrect their protease activity. We further show that the pseudoactive site substitutions differentially affect the stability and function of the CspC and CspA pseudoproteases: the substitutions destabilized CspC and impaired spore germination without affecting CspA stability or function. Thus, our results surprisingly reveal that the presence of a catalytic triad does not necessarily predict protease activity. Since homologs of C. difficile CspA occasionally carry an intact catalytic triad, our results indicate that bioinformatic predictions of enzyme activity may underestimate pseudoenzymes in rare cases.

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<![CDATA[Bacterial phenotypic heterogeneity in DNA repair and mutagenesis]]> https://www.researchpad.co/product?articleinfo=N2f105e55-6cb3-434f-bf59-4522f3199033

Genetically identical cells frequently exhibit striking heterogeneity in various phenotypic traits such as their morphology, growth rate, or gene expression. Such non-genetic diversity can help clonal bacterial populations overcome transient environmental challenges without compromising genome stability, while genetic change is required for long-term heritable adaptation. At the heart of the balance between genome stability and plasticity are the DNA repair pathways that shield DNA from lesions and reverse errors arising from the imperfect DNA replication machinery. In principle, phenotypic heterogeneity in the expression and activity of DNA repair pathways can modulate mutation rates in single cells and thus be a source of heritable genetic diversity, effectively reversing the genotype-to-phenotype dogma. Long-standing evidence for mutation rate heterogeneity comes from genetics experiments on cell populations, which are now complemented by direct measurements on individual living cells. These measurements are increasingly performed using fluorescence microscopy with a temporal and spatial resolution that enables localising, tracking, and counting proteins with single-molecule sensitivity. In this review, we discuss which molecular processes lead to phenotypic heterogeneity in DNA repair and consider the potential consequences on genome stability and dynamics in bacteria. We further inspect these concepts in the context of DNA damage and mutation induced by antibiotics.

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<![CDATA[Expanding our understanding of the role polyprotein conformation plays in the coronavirus life cycle]]> https://www.researchpad.co/product?articleinfo=Ndd1d4bd1-8616-4e5e-bb2c-6a55dee0b94d

Coronavirus are the causative agents in many globally concerning respiratory disease outbreaks such as severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS) and coronavirus disease-2019 (COVID-19). It is therefore important that we improve our understanding of how the molecular components of the virus facilitate the viral life cycle. These details will allow for the design of effective interventions. Krichel and coauthors in their article in the Biochemical Journal provide molecular details of how the viral polyprotein (nsp7–10) produced from the positive single stranded RNA genome, is cleaved to form proteins that are part of the replication/transcription complex. The authors highlight the impact the polyprotein conformation has on the cleavage efficiency of the main protease (Mpro) and hence the order of release of non-structural proteins 7–10 (nsp7–10) of the SARS-CoV. Cleavage order is important in controlling viral processes and seems to have relevance in terms of the protein–protein complexes formed. The authors made use of mass spectrometry to advance our understanding of the mechanism by which coronaviruses control nsp 7, 8, 9 and 10 production in the virus life cycle.

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<![CDATA[Data showing differential expression of Monocyte chemoattractant protein-1 in response to symptomatic and asymptomatic T. vaginalis infection]]> https://www.researchpad.co/product?articleinfo=Nbb59ccb4-75d4-4bd3-aada-07c8f7d0c4a3

Trichomoniasis is caused by Trichomonas vaginalis (a protozoan parasite). About 80% of the infected cases remain asymptomatic [1]. The differential response of showing symptoms or no symptoms is not yet explored. However, some studies gave us some insights on the pathogenesis of trichomonas and also about host defense mechanism. Host secretes pro-inflammatory cytokines and chemokines to evade infection. Monocyte chemoattractant protein-1 (MCP-1/CCL2) is a strong chemoattractant of monocytes, NK-cells and T-lymphocytes. Many reports have shown high MCP-1 levels during trichomonas infection [2], [3], [4], [5] in human prostate stromal myofibroblast cells (WPMY-1), HeLa cells, vaginal epithelial cells (VECs) but levels in response to symptomatic and asymptomatic isolates is not yet reported. In this article, we have reported MCP-1 levels in the vaginal washes and serum samples of BALB/c mouse infected with symptomatic and asymptomatic T. vaginalis isolates for different time points. We found higher levels of MCP-1 in vaginal washes of symptomatic group on 2nd day post infection (dpi) than control uninfected group. While on 4th dpi and 14th dpi, higher levels of MCP-1 in vaginal washes was observed in asymptomatic group as compared to control group. However, significant level of MCP-1 was observed in asymptomatic group on 14th dpi as compared to symptomatic group in vaginal washes. We have also observed significantly higher levels of MCP-1 in the serum samples of symptomatic group on 2nd, 4th and 14th dpi as compared to control group. A higher level of MCP-1 was found at all the time points in serum samples of asymptomatic group as compared to control group. Interestingly, a significant higher level of MCP-1 was found in the serum samples of BALB/c mice in asymptomatic as compared to symptomatic group. The MCP-1 levels in both vaginal washes and serum were significantly higher in asymptomatic group at later time points.

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<![CDATA[Bacteriophages to Control Campylobacter in Commercially Farmed Broiler Chickens, in Australia]]> https://www.researchpad.co/product?articleinfo=N38aa5067-c4df-4b1a-9a8a-2d48279527a4

This study describes the development and use of bacteriophage cocktails to control Campylobacter in broiler chickens, in a commercial setting, in Queensland Australia, following the birds from farm to the processing plant. The components of the bacteriophage cocktails were selected to be effective against the maximum number of Campylobacter jejuni and Campylobacter coli isolates encountered on SE Queensland farms. Farms were identified that had suitable Campylobacter target populations and phage were undetectable 1 week prior to the intended treatment. Cocktails of phages were administered at 47 days of age. Groups of study birds were slaughtered the following day, on-farm, at the end of flock transport to the plant, and at processing (approximately 28 h post-treatment). On Farm A, the phage treatment significantly reduced Campylobacter levels in the ceca at the farm in the range of 1–3 log10 CFU/g (p = 0.007), compared to mock treated controls. However, individual birds sampled on farm (1/10) or following transport (2/10) exhibited high cecal Campylobacter counts with low phage titers, suggesting that treatment periods > 24 h may be required to ensure phage replication for effective biocontrol in vivo. At the time of the trial the control birds in Farm B were phage positive despite having been negative one week earlier. There was no significant difference in the cecal Campylobacter counts between the treatment and control groups following treatment but a fall of 1.7 log10 CFU/g was observed from that determined from birds collected the previous week (p = 0.0004). Campylobacter isolates from both farms retained sensitivity to the treatment phages. These trials demonstrated bacteriophages sourced from Queensland farms have the potential to reduce intestinal Campylobacter levels in market ready broiler chickens.

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<![CDATA[Quantifying antibiotic impact on within-patient dynamics of extended-spectrum beta-lactamase resistance]]> https://www.researchpad.co/product?articleinfo=N7ecc8fa1-20b8-4271-9018-7ac9004c16bc

Antibiotic-induced perturbation of the human gut flora is expected to play an important role in mediating the relationship between antibiotic use and the population prevalence of antibiotic resistance in bacteria, but little is known about how antibiotics affect within-host resistance dynamics. Here we develop a data-driven model of the within-host dynamics of extended-spectrum beta-lactamase (ESBL) producing Enterobacteriaceae. We use blaCTX-M (the most widespread ESBL gene family) and 16S rRNA (a proxy for bacterial load) abundance data from 833 rectal swabs from 133 ESBL-positive patients followed up in a prospective cohort study in three European hospitals. We find that cefuroxime and ceftriaxone are associated with increased blaCTX-M abundance during treatment (21% and 10% daily increase, respectively), while treatment with meropenem, piperacillin-tazobactam, and oral ciprofloxacin is associated with decreased blaCTX-M (8% daily decrease for all). The model predicts that typical antibiotic exposures can have substantial long-term effects on blaCTX-M carriage duration.

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<![CDATA[Global phenotypic profiling identifies a conserved actinobacterial cofactor for a bifunctional PBP-type cell wall synthase]]> https://www.researchpad.co/product?articleinfo=Nefdb3229-e9b1-4d1b-9ce4-a316915871d7

Members of the Corynebacterineae suborder of Actinobacteria have a unique cell surface architecture and, unlike most well-studied bacteria, grow by tip-extension. To investigate the distinct morphogenic mechanisms shared by these organisms, we performed a genome-wide phenotypic profiling analysis using Corynebacterium glutamicum as a model. A high-density transposon mutagenized library was challenged with a panel of antibiotics and other stresses. The fitness of mutants in each gene under each condition was then assessed by transposon-sequencing. Clustering of the resulting phenotypic fingerprints revealed a role for several genes of previously unknown function in surface biogenesis. Further analysis identified CofA (Cgp_0016) as an interaction partner of the peptidoglycan synthase PBP1a that promotes its stable accumulation at sites of polar growth. The related Mycobacterium tuberculosis proteins were also found to interact, highlighting the utility of our dataset for uncovering conserved principles of morphogenesis for this clinically relevant bacterial suborder.

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<![CDATA[Driving polar growth]]> https://www.researchpad.co/product?articleinfo=Nb5f2fb1c-910a-4289-9d7a-1266ceac5116

Profiling the phenotype of 200,000 mutants revealed a new cofactor that may help a group of rod-shaped bacteria elongate and grow.

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<![CDATA[Draft whole-genome sequence of Brevibacterium casei strain isolated from a bloodstream infection]]> https://www.researchpad.co/product?articleinfo=N2a648919-e4b2-486d-a619-a8a1e283d8c7

Despite its low virulence potential and a commensal lifestyle as a member of the human skin microbiota, Brevibacterium casei has been increasingly reported as an opportunistic pathogen, especially in immunocompromised patients. Here, we present the draft genome sequence of the S51 strain isolated from a bloodstream infection. To the best of the authors’ knowledge, this is the first report of the draft genome sequence of the B. casei strain isolated from the clinical infection. The strain was identified using phenotypic and molecular methods and subsequently sequenced using the next-generation sequencing. The draft whole genome was assembled de novo, automatically annotated by Rapid Annotations using Subsystems Technology (RAST) server and scrutinized to predict the presence of virulence, resistance, and stress response proteins. The genome size of the S51 strain was 3,743,532 bp and an average G+C content was 68.3%. The predicted genes included 48 genes involved in resistance to antibiotics (including vancomycin, fluoroquinolones, and beta-lactams) and toxic compounds (heavy metals), 16 genes involved in invasion and intracellular resistance (Mycobacterium virulence operons), and 94 genes involved in stress response (osmotic, oxidative stress, cold and heat shock). ResFinder has indicated the presence of a beta-lactamase, and a phenotypic analysis showed resistance to penicillin. This whole-genome NGS project for the S51strain has been deposited at EMBL/GenBank under the accession no. QNGF00000000.

Electronic supplementary material

The online version of this article (10.1007/s42770-020-00236-x) contains supplementary material, which is available to authorized users.

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<![CDATA[The type IV pilin PilA couples surface attachment and cell-cycle initiation in Caulobacter crescentus]]> https://www.researchpad.co/product?articleinfo=Ndf4b9f7d-0eed-4a07-9f4a-91f96a480897

Significance

Pili are dynamic, long proteinaceous appendages found on the surface of many bacteria to promote adhesion. Here, we provide systems-level findings on a molecular signal transduction pathway that interlinks surface sensing with cell-cycle initiation. We propose that surface attachment induces depolymerization of pili filaments. The concomitant increase in pilin subunits within the inner membrane function as a stimulus to activate the second messenger cyclic di-GMP and trigger cell-cycle initiation. Furthermore, we show that the provision of a 17-amino acid synthetic peptide corresponding to the membrane portion of the pilin subunit mimics surface sensing, activates cell-cycle initiation, and inhibits surface attachment. Thus, synthetic peptide mimetics of pilin represent promising chemotypes to control biofilm formation and treat bacterial infections.

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<![CDATA[A multiproducer microbiome generates chemical diversity in the marine sponge Mycale hentscheli]]> https://www.researchpad.co/product?articleinfo=N09e84a7f-8bd9-43bc-ab75-8afaa59bc07e

Significance

Sponges, one of the oldest extant animal phyla, stand out among marine organisms as sources of structurally diverse bioactive natural products. Previous work on chemically rich sponges identified single “superproducer” symbionts in their microbiomes that generate the majority of the bioactive compounds known from their host. Here, we present a contrasting scenario for the New Zealand sponge Mycale hentscheli in which a multiproducer consortium is the basis of chemical diversity. Other than the known cocktail of cytotoxins, metagenomic and functional data support further chemical diversity originating from various uncultivated bacterial lineages. The results provide a rationale for distinct patterns of chemical variation observed within sponge species and reinforce uncultured microbes as promising source of compounds with therapeutic potential.

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<![CDATA[Infectious KoRV-related retroviruses circulating in Australian bats]]> https://www.researchpad.co/product?articleinfo=Na7bff1f4-2d91-4ce2-88e7-be52c4bf7672

Significance

Bats represent 20% of all mammalian species and are an important reservoir of viruses that infect humans and other mammals. Retroviruses, such as HIV, are among the most important zoonotic viruses infecting humans, although little is known about their circulation in bat populations. We report the first exogenous retrovirus described in bats, the Hervey pteropid gammaretrovirus (HPG), a reproduction-competent retrovirus within northeast Australia. Koala populations are currently in severe decline and at risk from koala retrovirus (KoRV), which is closely related to HPG and whose origins remain unclear. The identification of bats as a source of diverse infectious retroviruses related to KoRV implicates bats as a reservoir of KoRV-related viruses that potentially can be transmitted to other mammalian species.

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<![CDATA[Long-term continuously monocropped peanut significantly changed the abundance and composition of soil bacterial communities]]> https://www.researchpad.co/product?articleinfo=N2b441e4b-bf77-472a-8f83-cfd091e8da1e

Soil sickness is the progressive loss of soil quality due to continuous monocropping. The bacterial populations are critical to sustaining agroecosystems, but their responses to long-term peanut monocropping have not been determined. In this study, based on a previously constructed gradient of continuous monocropped plots, we tracked the detailed feedback responses of soil bacteria to short- and long-term continuous monocropping of four different peanut varieties using high-throughput sequencing techniques. The analyses showed that soil samples from 1- and 2-year monocropped plots were grouped into one class, and samples from the 11- and 12-year plots were grouped into another. Long-term consecutive monocropping could lead to a general loss in bacterial diversity and remarkable changes in bacterial abundance and composition. At the genera level, the dominant genus Bacillus changed in average abundance from 1.49% in short-term monocropping libraries to 2.96% in the long-term libraries. The dominant species Bacillus aryabhattai and Bacillus funiculus and the relatively abundant species Bacillus luciferensis and Bacillus decolorationis all showed increased abundance with long-term monocropping. Additionally, several other taxa at the genus and species level also presented increased abundance with long-term peanut monocropping; however, several taxa showed decreased abundance. Comparing analyses of predicted bacterial community functions showed significant changes at different KEGG pathway levels with long-term peanut monocropping. Combined with our previous study, this study indicated that bacterial communities were obviously influenced by the monocropping period, but less influenced by peanut variety and growth stage. Some bacterial taxa with increased abundance have functions of promoting plant growth or degrading potential soil allelochemicals, and should be closely related with soil remediation and may have potential application to relieve peanut soil sickness. A decrease in diversity and abundance of bacterial communities, especially beneficial communities, and simplification of bacterial community function with long-term peanut monocropping could be the main cause of peanut soil sickness.

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<![CDATA[Impact of Phellinus gilvus mycelia on growth, immunity and fecal microbiota in weaned piglets]]> https://www.researchpad.co/product?articleinfo=N29e6fa4b-e2c8-4f6d-9177-b56d8a78ff78

Background

Antibiotics are the most commonly used growth-promoting additives in pig feed especially for weaned piglets. But in recent years their use has been restricted because of bacterial resistance. Phellinus, a genus of medicinal fungi, is widely used in Asia to treat gastroenteric dysfunction, hemrrhage, and tumors. Phellinus is reported to improve body weight on mice with colitis. Therefore, we hypothesize that it could benefit the health and growth of piglets, and could be used as an alternative to antibiotic. Here, the effect of Phellinus gilvus mycelia (SH) and antibiotic growth promoter (ATB) were investigated on weaned piglets.

Methods

A total of 72 crossbred piglets were randomly assigned to three dietary treatment groups (n = 4 pens per treatment group with six piglets per pen). The control group was fed basal diet; the SH treatment group was fed basal diet containing 5 g/kg SH; the ATB treatment group was feed basal diet containing 75 mg/kg aureomycin and 20 mg/kg kitasamycin. The experiment period was 28 days. Average daily gain (ADG), average daily feed intake (ADFI), and feed intake to gain ratio were calculated. The concentrations of immunoglobulin G (IgG), interleukin-1β (IL-1β), tumor necrosis factor (TNF)-α and myeloperoxidase (MPO) in serum were assessed. Viable plate counts of Escherichia coli in feces were measured. Fecal microbiota was analyzed via the 16S rRNA gene sequencing method.

Results

The ADG (1–28 day) of piglets was significantly higher in SH and ATB treatment groups (P < 0.05) compared to the control, and the ADG did not show significant difference between SH and ATB treatment groups (P > 0.05). Both SH and ATB treatments increased the MPO, IL-1β, and TNF-α levels in serum compared to the control (P < 0.05), but the levels in SH group were all significantly higher than in the ATB group (P < 0.05). Fecal microbiological analysis showed that viable E. coli counts were dramatically decreased by SH and ATB. The 16S rRNA gene sequencing analysis showed that ATB shifted the microbiota structure drastically, and significantly increased the relative abundance of Prevotella, Megasphaera, and Faecalibacterium genera. But SH slightly influenced the microbiota structure, and only increased the relative abundance of Alloprevotella genus.

Conclusion

Our work demonstrated that though SH slightly influenced the microbiota structure, it markedly reduced the fecal E. coli population, and improved growth and innate immunity in piglets. Our finding suggested that SH could be an alternative to ATB in piglet feed.

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<![CDATA[PSGL-1 restricts HIV-1 infectivity by blocking virus particle attachment to target cells]]> https://www.researchpad.co/product?articleinfo=N814338ab-cdf1-46bb-921d-afe4e6c8492e

Significance

PSGL-1 and CD43 are surface glycoproteins expressed on blood CD4 T cells to bind to selectins for T cell tethering, rolling, and migration into inflamed tissues. The PSGL-1 level is greatly up-regulated during inflammation. Here we found that PSGL-1 and CD43 expression inhibits HIV spreading infection. Mechanistically, PSGL-1 blocks the binding of virus particles to target cells. PSGL-1–mediated suppression of virus infectivity extends to another retrovirus—murine leukemia virus—and to influenza A virus. These results further our understanding of virus–host interactions and help elucidate mechanisms by which cellular host factors regulate viral infection and pathogenesis.

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<![CDATA[Coinfinder: detecting significant associations and dissociations in pangenomes]]> https://www.researchpad.co/product?articleinfo=N5b6aa6ad-3805-4584-b068-4ce452f6f591

The accessory genes of prokaryote and eukaryote pangenomes accumulate by horizontal gene transfer, differential gene loss, and the effects of selection and drift. We have developed Coinfinder, a software program that assesses whether sets of homologous genes (gene families) in pangenomes associate or dissociate with each other (i.e. are ‘coincident’) more often than would be expected by chance. Coinfinder employs a user-supplied phylogenetic tree in order to assess the lineage-dependence (i.e. the phylogenetic distribution) of each accessory gene, allowing Coinfinder to focus on coincident gene pairs whose joint presence is not simply because they happened to appear in the same clade, but rather that they tend to appear together more often than expected across the phylogeny. Coinfinder is implemented in C++, Python3 and R and is freely available under the GNU license from https://github.com/fwhelan/coinfinder.

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<![CDATA[An assessment of genome annotation coverage across the bacterial tree of life]]> https://www.researchpad.co/product?articleinfo=Ncb63aa35-dacb-42fa-a1c9-402a3005b91e

Although gene-finding in bacterial genomes is relatively straightforward, the automated assignment of gene function is still challenging, resulting in a vast quantity of hypothetical sequences of unknown function. But how prevalent are hypothetical sequences across bacteria, what proportion of genes in different bacterial genomes remain unannotated, and what factors affect annotation completeness? To address these questions, we surveyed over 27 000 bacterial genomes from the Genome Taxonomy Database, and measured genome annotation completeness as a function of annotation method, taxonomy, genome size, 'research bias' and publication date. Our analysis revealed that 52 and 79 % of the average bacterial proteome could be functionally annotated based on protein and domain-based homology searches, respectively. Annotation coverage using protein homology search varied significantly from as low as 14 % in some species to as high as 98 % in others. We found that taxonomy is a major factor influencing annotation completeness, with distinct trends observed across the microbial tree (e.g. the lowest level of completeness was found in the Patescibacteria lineage). Most lineages showed a significant association between genome size and annotation incompleteness, likely reflecting a greater degree of uncharacterized sequences in 'accessory' proteomes than in 'core' proteomes. Finally, research bias, as measured by publication volume, was also an important factor influencing genome annotation completeness, with early model organisms showing high completeness levels relative to other genomes in their own taxonomic lineages. Our work highlights the disparity in annotation coverage across the bacterial tree of life and emphasizes a need for more experimental characterization of accessory proteomes as well as understudied lineages.

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