• We describe whole-genome sequences of 2 A. capra strains from metagenomic sequencing of purified erythrocytes from infected goats in China. (cdc.gov)
  • Neanderthal and Denisovan genomes show human-like sequences at both loci, corroborating estimates that the initial pseudogenization events occurred in the common ancestral population of these hominins. (elsevierpure.com)
  • Complete Genome Sequences of Four Macrolide-Resistant Nondiphtheritic Corynebacterium Isolates. (cdc.gov)
  • This report describes the complete genome sequences of four isolates of the nondiphtheritic Corynebacterium (NDC) species Corynebacterium pseudodiphtheriticum and Corynebacterium propinquum, recovered during investigation of a large diphtheria outbreak in Bangladesh. (cdc.gov)
  • genomes were assessed by alignment with the publicly available fully annotated genome sequences of L. casei, L. paracasei, L. rhamnosus, and L. zeae. (unimol.it)
  • There are other duplicated genes in the identified BAC sequences, suggesting that these genomic regions exhibit a high rate of tandem duplication. (inra.fr)
  • This study confirms that the latest generation of DNA sequencing technologies can be applied during high priority public health events, and laboratories need to prepare for this inevitability and assess how to properly analyze and interpret whole genome sequences in the context of molecular epidemiology. (biomedcentral.com)
  • MIRU-VNTR analysis, on the other hand, uses mini-satellite sequences (tandem repeats of 10-100 nucleotides) dispersed at multiple loci in the bacterial genome. (frontiersin.org)
  • Exchanges and losses of the Pa Loc DNA have also occurred, via long homologous recombination events involving flanking chromosomal sequences. (whiterose.ac.uk)
  • To resolve phylogenetic relationships among ries of bacterial clonal complexes by using concatenated isolates, we sequenced 68 isolates from Europe and North sequences of housekeeping genes when within-loci and America at 1 chromosomal locus (16S-23S ribosomal RNA between-loci recombinations are infrequent ( 5 ). (cdc.gov)
  • The genetic homogeneity of ospC -A isolates was confi rmed agent, Borrelia burgdorferi , a spirochete that parasitizes by sequences at 6 additional chromosomal housekeeping vertebrates, is transmitted by hard-bodied ticks through- loci ( gap, alr, glpA, xylB, ackA, and tgt ). (cdc.gov)
  • Sequences shared by a subset of genomes are referred as dispensable and they represent variable features. (biomedcentral.com)
  • Core genes are often under strong evolutionary selection, thus their sequences are transmitted almost without any alteration. (biomedcentral.com)
  • The amount of variations affecting dispensable genes varies and the similarity between homologous sequences tends to decrease according to their phylogenetic distance. (biomedcentral.com)
  • When closely related organisms are analyzed, reasonable thresholds on sequences similarity are applied to recognize gene families. (biomedcentral.com)
  • The geno-mic component is a DNA loci containing short frag-ments of targeted nucleic acid sequences (spacers) inter-spaced by short repeated sequences (repeats). (pjmonline.org)
  • 0.5) selected from among all common variants discovered in genome sequences in this population. (biomedcentral.com)
  • Here, we sequenced 43 H. cinaedi- or H. canicola -like strains isolated from humans, hamsters, rats and dogs and collected 81 genome sequences of H. cinaedi , H. canicola and other enterohepatic Helicobacter strains from public databases. (microbiologyresearch.org)
  • We also developed a method to systematically search for H. cinaedi sequences in large metagenome data sets based on the results of genome comparison. (microbiologyresearch.org)
  • The genomes of the 2 A. capra strains contained comparable G+C content and numbers of pseudogenes with intraerythrocytic Anaplasma species. (cdc.gov)
  • If the bacterial species is identified, antibiotic therapy will be adapted to antibiotic susceptibility. (bvsalud.org)
  • Here we utilized whole-genome sequencing (WGS) to characterize recovered isolates of C. diphtheriae and two co-circulating non-diphtheritic Corynebacterium (NDC) species - C. pseudodiphtheriticum and C. propinquum. (cdc.gov)
  • These bacterial species comprise commercial probiotics with the widest use among consumers and strains naturally occurring in GIT and in fermented food. (unimol.it)
  • Forty-nine of these genes were found to be absent in some strains or species. (unimol.it)
  • Abstract CRISPR/Cas systems have been widely used for genome engineering in many plant species, while their potentials have remained largely untapped in fruit crops, particularly in pear, due to the high levels of genomic heterozygosity and difficulties in tissue culture and stable transformation. (nsf.gov)
  • We showed that the PHF7 gene, which is highly expressed in the rooster testis, is a highly duplicated gene family in the chicken genome, and this phenomenon probably concerns other bird species. (inra.fr)
  • Here, we describe the structure of these genes, their expression in rainbow trout tissues and their phylogenetic relationship to similar genes in mammals, birds and other fish species. (usda.gov)
  • The genes are 95% similar to one another and also appear in other salmonid species including Atlantic salmon and Coho salmon. (usda.gov)
  • The amino acid sequence homology of the rainbow trout il1rl1 genes are highly related to Atlantic and Coho salmon (~94%) but relatively low (22-26%) with avian and mammalian species. (usda.gov)
  • and 16 were "novel" essential genes with no homologs reported to have an essential role in other bacterial species. (biomedcentral.com)
  • This system is present in most archaeal species and approxi-mately half of all bacterial species. (pjmonline.org)
  • The HLA complex is the human version of the major histocompatibility complex (MHC), a gene family that occurs in many species. (medlineplus.gov)
  • Results of phylogenetic reconstruction and virulence-related gene contents of the recovered NDC isolates indicated they were likely commensal organisms, though 80.4%(45/56) were not susceptible to erythromycin, and most showed high minimum inhibition concentrations against azithromycin. (cdc.gov)
  • These results demonstrate the high resolution with which WGS can aid molecular investigation of diphtheria outbreaks, through the quantification of bacterial genetic relatedness, as well as the detection of virulence factors and antibiotic resistance markers among case isolates. (cdc.gov)
  • High-throughput pyrosequencing of two L. monocytogenes isolates was used to rapidly provide the genome sequence of the primary outbreak strain and to investigate the extent of genetic diversity associated with a change of a single restriction enzyme fragment during PFGE. (biomedcentral.com)
  • Notably, these two isolates were found to harbor a 50 kbp putative mobile genomic island encoding translocation and efflux functions that has not been observed in other Listeria genomes. (biomedcentral.com)
  • Phylogenetic analyses and annotation of the regions spanning the Pa Loc were performed using C. difficile population-representative genomes chosen from a collection of 1,693 toxigenic (Pa Loc present) and non toxigenic (Pa Loc absent) isolates. (whiterose.ac.uk)
  • Since the A. marginale genome sequence was reported in 2005 ( 22 ), a total of 24 A. marginale genomes ( 23 ), 32 A. phagocytophilum genomes ( 24 , 25 ), 1 A. centrale genome ( 26 ), 2 A. ovis genomes ( 27 ), and 1 A. platys genome ( 28 ) have been sequenced and deposited in GenBank. (cdc.gov)
  • Whole genome sequence comparison of these populations revealed that more than 45% of the substituted mutations occurred in only five loci for the evolved populations. (bvsalud.org)
  • Gene duplications increase genetic and phenotypic diversity and occur in complex genomic regions that are still difficult to sequence and assemble. (inra.fr)
  • Nucleotide sequence homology between the three genes is >95% and each predicted protein contains three IG/IG-like domains, a transmembrane region and a TIR domain. (usda.gov)
  • Here we obtained a well-resolved polymorphism type of intergenic spacer (IGS) sequence phylogeny of B. burgdorferi sensu stricto clonal complexes (corresponding to the ospC- A and -B groups) is associated by using multilocus sequence typing at housekeeping loci with hematogenous dissemination in patients with early as well as loci under adaptive evolution. (cdc.gov)
  • The genome sequence of Barbarea vulgaris facilitates the study of ecological biochemistry. (pacb.com)
  • Here we report a draft genome sequence of the G-type, and re-sequencing of the P-type for comparison. (pacb.com)
  • Draft genome sequence of Micromonospora sp. (pacb.com)
  • Complete genome sequence of Kosakonia oryzae type strain Ola 51(T). (pacb.com)
  • Here we summarize the features of the strain Ola 51(T) and describe its complete genome sequence. (pacb.com)
  • This study re-analyzed, using multi-locus sequence typing (MLST) and whole genome sequence with single nucleotide polymorphism analysis (WGS-SNP), 52 strains which had been identified as Enterobacter sakazakii as according to the convention at the time of isolation. (biomedcentral.com)
  • A complementary RNA sequence that binds to a naturally occurring (sense) mRNA molecule, thus blocking its translation. (genomicglossaries.com)
  • Highly specific and effective gene silencing of any disease can be achieved by an accurate knowledge of the target mRNA sequence and rational design of its complementary antisense agents for the downregulation of its protein message. (genomicglossaries.com)
  • the complete genome sequence of Mycobacterium tuberculosis continues to provide an invaluable resource to understand tuberculosis (TB), the leading cause of global infectious disease mortality. (jci.org)
  • While the genome sequence was already transformative at the time, the past 25 years of progress have substantially increased its impact on TB taxonomy, drug discovery, resistance mechanisms, epidemiology, vaccine development, and pathogenesis. (jci.org)
  • Paralogy is linked to sequence duplication within the same genome. (biomedcentral.com)
  • We collected draft genome sequence data and associated metadata data on 76 N. gonorrhoeae strains from around the globe and searched for known determinants of antibiotics resistance within the strains. (peerj.com)
  • Both TALEN and CRISPR are chimeric endonucleases that initiate double-strand break (DSB) formation at virtually any target sequence in genomes, leading to mutagenesis. (genecopoeia.com)
  • Using this method, we successfully identified multiple HCCM complex-containing human faecal metagenome samples and obtained the sequence information covering almost the entire genome of each strain. (microbiologyresearch.org)
  • The 2 A. capra strains had 54 unique genes. (cdc.gov)
  • The remaining genes were conserved and covered almost all the functions considered, indicating that all strains of the genus may exert some probiotic effects. (unimol.it)
  • Among the variable loci, a taurine utilization operon and a α-L-fucosidase were examined for the presence/absence in 26 strains isolated from infant feces by PCR-based tests. (unimol.it)
  • depends on a conserved set of genes but variable genetic factors, whose role is only in part elucidated, are more numerous and can explain the enhanced probiotic characteristics for some strains. (unimol.it)
  • High-throughput genome sequencing provided a more detailed real-time assessment of genetic traits characteristic of the outbreak strains than could be achieved with routine subtyping methods. (biomedcentral.com)
  • Genome sequencing of multiple R. solanacearum strains has identified both unique and shared genetic traits influencing their evolution and ability to colonize plant hosts. (pacb.com)
  • High levels of recombination could confound studies of the gonococcal populations, especially if the studies are based on few genetic loci within strains as compared to the entire genomes. (peerj.com)
  • Toxin-antitoxin genes are often inherited through horizontal gene transfer and are associated with pathogenic bacteria, having been found on plasmids conferring antibiotic resistance and virulence. (wikipedia.org)
  • mazEF, a toxin-antitoxin locus found in E. coli and other bacteria, was proposed to induce programmed cell death in response to starvation, specifically a lack of amino acids. (wikipedia.org)
  • Our understanding of the ecology of oral microbes surged thanks to the Human Microbiome Project (HMP) [ 20 ], which generated extensive sequencing data from 9 oral sites sampled from 200 healthy individuals and over 300 reference genomes for bacteria isolated from the human oral cavity. (biomedcentral.com)
  • In the present study, we reconstructed large phage genomes from freshwater lakes known to contain bacteria that oxidize methane. (nature.com)
  • Bacteriophages (phages), viruses that infect and replicate within bacteria, are important in both natural and human microbiomes because they prey on bacterial hosts, mediate horizontal gene transfer, alter host metabolism and redistribute bacterially derived compounds via host cell lysis 1 . (nature.com)
  • Scientists observed this phenomenon occurring in bacteria, and some attempted to adapt and utilize this system to our advantage. (medium.com)
  • This study also identified 43 growth-impairing inserts carrying multiple loci targeting 105 genes, of which 25 have homologs reported as essential in other bacteria. (biomedcentral.com)
  • In fact, quantitative trait locus (QTL) approaches have successfully identified variation in candidate host genes that influence the RA of specific bacteria not only in Drosophila and mice but also in humans [ 22 ]. (biomedcentral.com)
  • However, phages mutate in an effort to bypass these defenses: a mutation in the region of the phage genome corresponding to, say, a blue spacer means that the phage can attack and escape the defense of bacteria with blue spacers (fuzzy green circle), but not bacteria with green, orange or pink spacers (red X inside a circle). (elifesciences.org)
  • Further experiments showed that compared to bacteria grown in liquid culture, bacterial cells in the resistant colonies had often acquired multiple spacers and were able to fight off phages with other mutations ( Figure 1 , right). (elifesciences.org)
  • If the immune system recognizes the peptides as foreign (such as viral or bacterial peptides), it triggers a response to attack the invading viruses or bacteria. (medlineplus.gov)
  • Both Siglecs can also be engaged by two potentially lethal sialylated bacterial pathogens of newborns and infants, agents with a potential impact on reproductive fitness. (elsevierpure.com)
  • They commonly occur as food spoilage agents and opportunistic pathogens and are widely used as versatile cell factories. (nature.com)
  • Targeting of novel essential pathways is expected to play an important role in the discovery of new antibacterial agents against bacterial pathogens, such as Pseudomonas aeruginosa , that are difficult to control because of their ability to develop resistance, often multiple, to all current classes of clinical antibiotics. (biomedcentral.com)
  • Since little is known about the distribution of genetic traits for adhesion capacity, polysaccharide production, biofilm formation, and utilization of substrates critically important for survival in GIT, which influence probiotic characteristics, a list of genetic determinants possibly involved in such functions was created by a search for specific genes involved in the above aspects in the genome of the extensively characterized probiotic L. rhamnosus GG. (unimol.it)
  • Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes. (genomicglossaries.com)
  • The Dupuis lab develops statistical approaches to identify specific genes or genetic variants that influence complex phenotypes through their associated quantitative traits, which are traits that can be measured numerically, such as height or blood pressure in humans, and seed size or oil content in plants. (bu.edu)
  • Although A. capra has been extensively detected in ticks and animal hosts worldwide, no genome of the emerging pathogen has been determined so far, which has hindered us from better understanding its genetic features and pathogenesis. (cdc.gov)
  • Transfers of a single gene, a complete metabolic pathway 10 , whole chromosomes 11 or even cases of the integration of almost complete genomes from bacterial endosymbionts into their eukaryotic hosts 12 have been described. (nature.com)
  • Ixodes ricinus ticks ( 11 ) and is carried by a large variety of ize genetic variations of natural populations of a bacterial hosts, including birds and small- to medium-sized mam- pathogen ( 1 , 2 ). (cdc.gov)
  • In addition, heterozygous hosts having one wild-type gene and one mutated gene could be mated to obtain homozygous hosts, so that all of the cells would have the appropriate modification. (justia.com)
  • This mechanism of immunity is based on short fragments of foreign DNA incorporated within the hosts genome. (pjmonline.org)
  • Using camalexin biosynthesis genes as an example, we confirmed that these two modifications were co-localized to form bivalent chromatin. (biorxiv.org)
  • Eighty-two gene loci were retrieved and their presence and variability in other Lacticaseibacillus spp. (unimol.it)
  • In presence of phylogenetically distant genomes, due to the variability introduced in gene duplication and transmission, the task of recognizing homologous genes becomes even more difficult. (biomedcentral.com)
  • Gene-nutrient interactions may help explain this variability in response to food that is associated with IBD. (mdpi.com)
  • We selected nine BAC that highlighted nine chromosomal regions for a total of 10 distinct PHF7-like loci on five Gallus gallus chromosomes: Chr1 (three loci), Chr2 (two loci), Chr12 (one locus), Chr19 (one locus) and ChrZ (three loci). (inra.fr)
  • See how the University of Washington used HiFi sequencing to uncover a key finding about ALS and the human genome. (pacb.com)
  • Because of the Human Genome and the HapMap projects, developments in genotyping technology have brought the possibility of identifying associations between specific genetic alterations and common diseases closer to reality. (hindawi.com)
  • The virulence of this bacterium results from the 32 Y pestis chromosomal genes and two Y pestis -specific plasmids, constituting the only new genetic material acquired since its evolution from its predecessor. (medscape.com)
  • Development of asthma is multifactorial and depends on the interactions among multiple susceptibility genes and environmental factors. (msdmanuals.com)
  • Because it cuts through both strands of DNA, the repair process of the DNA segment can introduce dangerous mutations , as the DNA repair systems are likely to insert random insertions or deletions when repairing the genome. (medium.com)
  • For example, even if comprehensive insertion libraries are produced, it is inevitable that some genes, especially the shortest ones, could elude insertion and be spuriously annotated as essential, while transposon insertions that occur at gene ends and do not fully inactivate the function could lead to genes being incorrectly classified as non-essential. (biomedcentral.com)
  • So, the availability of a genomic locus that can accommodate benign insertions that are appropriately expressed is of great utility. (genecopoeia.com)
  • AAV insertions at this locus, also known as AAVS1, do not have any visible phenotype on cells, including primary and immortalized cells, induced pluripotent stem cells (iPSC), and embryonic stem cells. (genecopoeia.com)
  • a software application for rapid large-scale comparative analysis of TraDIS experiments that predicts the impact of transposon insertions on nearby genes. (biorxiv.org)
  • 2013). Two genome editing technologies have emerged recently that exploit bacterial systems for plant pathogenesis or adaptive immunity: TALEN (Transcription Activator-Like Effector Nucleases) and CRISPR (Clustered, Regularly Interspaced, Short Palindromic Repeats), respectively. (genecopoeia.com)
  • Both pangenomic and phylogenomic analyses group tongue-specific clades with other host-associated TM7 genomes. (biomedcentral.com)
  • Phylogenetic analyses suggest these genes arose by tandem duplication but are inconclusive whether these events occurred prior-to or after speciation. (usda.gov)
  • This project involves developing statistical analyses which combine genome wide association results with prior information from "omics" studies (gene variant functionality, gene expression, methylation, metabolomic data, and proteomic data) to determine regions with common or rare genetic variants that are potentially causally associated with traits of interest. (bu.edu)
  • Analyses of published transcriptomes revealed that the Xo1-mediated response is more similar to those mediated by two other NLR resistance genes than it is to the response associated with TALE-specific transcriptional activation of the executor resistance gene Xa23 and that a truncTALE dampens or abolishes activation of defense-associated genes by Xo1. (uea.ac.uk)
  • The Xo1 locus in the heirloom rice variety Carolina Gold Select confers resistance to bacterial leaf streak and bacterial blight, caused by Xanthomonas oryzae pv. (uea.ac.uk)
  • We describe a new computational method for the targeted discovery of functional modules of plant biomass-degrading protein families, based on their co-occurrence patterns across genomes and metagenome datasets, and the strength of association of these modules with the genomes of known degraders. (biomedcentral.com)
  • From approximately 6.4 million family annotations for 2,884 microbial genomes, and 332 taxonomic bins from 18 metagenomes, we identified 5 functional modules that are distinctive for plant biomass degraders, which we term "plant biomass degradation modules" (PDMs). (biomedcentral.com)
  • On average, 70% of the families of each PDM were found to map to gene clusters in known degraders, which served as an additional confirmation of their functional relationships. (biomedcentral.com)
  • Functional modules of protein families that are involved in different aspects of plant cell wall degradation can be inferred from co-occurrence patterns across (meta-)genomes with a probabilistic topic model. (biomedcentral.com)
  • Taken together, we build a highly efficient CRISPR toolbox for genome editing and gene regulation, paving the way for functional genomics studies as well as molecular breeding in pear. (nsf.gov)
  • These rapid adaptations in fungi provide excellent models for studying general processes of eukaryotic genome evolution, including the functional and ecological impact of horizontal gene transfer 1 and changes in metabolism 2 . (nature.com)
  • Students will help develop tools and workflows to compile annotated libraries of genes and genomes, curate functional associations between genes and microbes in metabolism, and link microbial abundance to host gene/pathway expression and other outcomes. (bu.edu)
  • To map the epigenetic marks on metabolic enzymes, pathways, and domains, we used the genome-wide functional annotations of metabolism we generated previously ( 6 ). (biorxiv.org)
  • As part of an effort to determine the mechanisms behind rainbow trout resistance to BCWD, we have identified for the first time, three interleukin-1 receptor like-1 (il1rl1) genes within a genetic locus associated with disease resistance. (usda.gov)
  • The B. vulgaris genome will promote the study of mechanisms in ecological biochemistry to benefit crop resistance breeding. (pacb.com)
  • Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. (genomicglossaries.com)
  • The discovery of novel essential genes or pathways that have not yet been targeted by clinical antibiotics can underlie the development of alternative effective antibacterials to overcome existing mechanisms of resistance. (biomedcentral.com)
  • Different mechanisms are involved in gene transmission. (biomedcentral.com)
  • Antimicrobial resistance occurs through different mechanisms, which include spontaneous (natural) genetic mutations and horizontal transfer of resistant genes through deoxyribonucleic acid (DNA). (who.int)
  • One of these five fixed mutations affects mae, the first gene of the citrate operon. (bvsalud.org)
  • On the contrary, "horizontal" transmission occurs between genomes of organisms of different lineages, involving one or few genes. (biomedcentral.com)
  • Novel cellulolytic enzymes have been discovered in microbial genomes and metagenomes of microbial communities. (biomedcentral.com)
  • For 15 draft genomes of a cow rumen metagenome, we used cross-referencing to confirmed cellulolytic enzymes to validate that the PDMs identified plant biomass degraders within a complex microbial community. (biomedcentral.com)
  • PDMs represent a new resource of protein families and candidate genes implicated in microbial plant biomass degradation. (biomedcentral.com)
  • Our findings provide evidence of host genetic influences on upper airway microbial composition in humans and implicate mucosal immunity genes in this relationship. (biomedcentral.com)
  • A number of new loci were also implicated in Triclosan resistance and the predicted phenotypes for a selection of these were validated experimentally and results showed high consistency with predictions. (biorxiv.org)
  • Recruiting metagenomic short reads using single-copy core genes, Donati et al. (biomedcentral.com)
  • Genes present in every genome are core genes of the pan-genome and they may be involved in essential living functionalities. (biomedcentral.com)
  • The genome of A. capra was the smallest among members of the genus Anaplasma . (cdc.gov)
  • A toxin-antitoxin system consists of a "toxin" and a corresponding "antitoxin", usually encoded by closely linked genes. (wikipedia.org)
  • for example, chromosomal toxin-antitoxin systems could have evolved to prevent the inheritance of large deletions of the host genome. (wikipedia.org)
  • Toxin-antitoxin systems could prevent harmful large deletions in a bacterial genome, though arguably deletions of large coding regions are fatal to a daughter cell regardless. (wikipedia.org)
  • In Vibrio cholerae, multiple type II toxin-antitoxin systems located in a super-integron were shown to prevent the loss of gene cassettes. (wikipedia.org)
  • Type I toxin-antitoxin (TA) systems are widespread genetic modules in bacterial genomes. (mdpi.com)
  • Abstract CRISPR-Cas12a is a promising genome editing system for targeting AT-rich genomic regions. (nsf.gov)
  • Unrooted phylogenetic trees grouped the il1rl1 genes apart from other genes of the interleukin 1 receptor family and genomic comparisons identify preserved synteny between mammals, birds and salmonids albeit a pseudogene is present in both Atlantic salmon and Coho salmon. (usda.gov)
  • We present PanDelos, a stand alone tool for the discovery of pan-genome contents among phylogenetic distant genomes. (biomedcentral.com)
  • We aimed to identify novel essential genes in P. aeruginosa by shotgun antisense screening. (biomedcentral.com)
  • To also target low expressed essential genes, we included some variant steps that were expected to overcome the non-stringent regulation of the promoter carried by the expression vector used for the shotgun antisense libraries. (biomedcentral.com)
  • For the first time in P. aeruginosa , we applied regulated antisense RNA expression and showed the feasibility of this technology for the identification of novel essential genes. (biomedcentral.com)
  • A recent refinement of this approach allows the roles of essential genes in conditional stress survival to be inferred by altering their expression. (biorxiv.org)
  • There are over 300 alleles (one of two or more forms of a gene that produce variations in a given trait) for the hemoglobin gene, part of the globin gene superfamily. (icr.org)
  • Researchers have identified hundreds of different versions (alleles) of the HLA-DRB1 gene, each of which is given a particular number (such as HLA-DRB1 *04:01). (medlineplus.gov)
  • Epistatic interactions are non-additive interactions between alleles, loci, or mutations. (beacon-center.org)
  • Sequencing of the two leading filamentous fungi used in cheese making, P. roqueforti and P. camemberti , and comparison with the penicillin producer P. rubens reveals a 575 kb long genomic island in P. roqueforti -called Wallaby -present as identical fragments at non-homologous loci in P. camemberti and P. rubens . (nature.com)
  • Homologous recombination is employed to inactivate genes, particularly genes associated with MHC antigens. (justia.com)
  • Homology candidate relations are integrated into a global network and groups of homologous genes are extracted by applying a community detection algorithm. (biomedcentral.com)
  • Two genes are homologous if they share a common ancestral gene. (biomedcentral.com)
  • Homologous genes can be distinguished into paralogous, when homology occurs within the same genome, or orthologous, when homology occurs between different genomes. (biomedcentral.com)
  • We call pan-genome content discovery the determination of homologous groups within a collection of genomes. (biomedcentral.com)
  • The variations make the task of recognizing homologous genes difficult, especially when ancestor genomes are no more available. (biomedcentral.com)
  • Furthermore, we used 16S ribosomal RNA gene sequencing to detect associations with different abundances of the gut microbiota with dietary patterns. (uni-frankfurt.de)
  • The recently reported phage genomes range up to 735 kb in length and encode a diversity of genes involved in transcription and translation, as well as genes that may augment host metabolism 2 . (nature.com)
  • Metabolism underpins development and physiology, but little is known about how metabolic genes and pathways are regulated, especially in multicellular organisms. (biorxiv.org)
  • However, the genome-wide epigenetic regulatory landscape of metabolism in plants is not known. (biorxiv.org)
  • For example, genes associated with energy metabolism showed higher expression levels compared to those involved in specialized metabolism (Fig. S1B). (biorxiv.org)
  • Whole-genome transposon-mutagenesis (TM) followed by identification of insertion sites is one of the most practical and frequently used experimental approaches to screen for essential bacterial genes [ 6 - 8 ]. (biomedcentral.com)
  • Pan-genome approaches afford the discovery of homology relations in a set of genomes, by determining how some gene families are distributed among a given set of genomes. (biomedcentral.com)
  • New metabolic engineering approaches have recently been developed to modulate carotenoid content, including the employment of CRISPR technologies for single-base editing and the integration of exogenous genes into specific "safe harbors" in the genome. (frontiersin.org)
  • Methods: The individual taxonomic microbiota composition of fecal samples from 90 NAFLD patients and 21 healthy controls was analyzed using 16S rRNA gene sequencing. (uni-frankfurt.de)
  • A challenge on this field is that of designing fast and adaptive similarity measures in order to find a suitable pan-genome structure of homology relations. (biomedcentral.com)
  • Augmentation of bacterial energy generation by auxiliary metabolic genes has been reported for phages with smaller genomes. (nature.com)
  • Surprisingly, specialized metabolic genes, often involved in defense, were predominantly regulated by two modifications that have opposite effects on gene expression, H3K27me3 (repression) and H3K18ac (activation). (biorxiv.org)
  • To see if there are any interactions between epigenetic modifications across metabolic genes, we computed pairwise Pearson's correlation coefficients between the 16 epigenetic modifications based on their relative abundance at each metabolic gene region. (biorxiv.org)
  • Enrichment of modifications in each metabolic domain, relative to all the genes in the genome, revealed both shared and diverse patterns. (biorxiv.org)
  • In contrast, metabolic genes involved in specialized and hormone metabolic domains, which are generally involved in interactions with biotic and abiotic environmental stimuli, showed distinct patterns with the enrichment of a repression mark H3K27me3 and an activation mark H3K18ac ( Fig. 1B ). (biorxiv.org)
  • A. Correlation analysis reveals four groups of epigenetic marks, activating (red) and repressing (blue), based on their relative abundance on metabolic genes. (biorxiv.org)
  • When grown in an acidic medium supplemented with citrate, a significantly higher bacterial biomass was produced with the evolved populations compared to the parental strain. (bvsalud.org)
  • Now, in eLife, Nora Pyenson and Luciano Marraffini from the Rockefeller University report that the number of spacers each bacterial cell acquires depends on its local environment ( Pyenson and Marraffini, 2020 ). (elifesciences.org)
  • Genome Biology and Evolution, 6 (1). (whiterose.ac.uk)
  • Transposon mutagenesis has been proven to be a powerful tool to identify genes and networks which are involved in survival and fitness under a given condition by simultaneously assaying the fitness of millions of mutants, thereby relating genotype to phenotype and contributing to an understanding of bacterial cell biology. (biorxiv.org)
  • This enables us to identify candidate genes underlying glucosinolate diversity, trichome density, and study the genetics of biochemical variation for glucosinolate and saponins. (pacb.com)
  • At the 25-year anniversary of this accomplishment, we describe how insights gleaned from the M. tuberculosis genome have led to vital tools for TB research, epidemiology, and clinical practice. (jci.org)
  • The increasing accessibility of whole-genome sequencing across research and clinical settings has improved our ability to predict antibacterial susceptibility, to track epidemics at the level of individual outbreaks and wider historical trends, to query the efficacy of the bacille Calmette-Guérin (BCG) vaccine, and to uncover targets for novel antitubercular therapeutics. (jci.org)
  • The M. tuberculosis genome has ushered in a quarter century of substantial clinical and public health advancements. (jci.org)
  • Plague occurs as 3 major clinical events: bubonic plague, septicemic plague, and pneumonic plague. (medscape.com)
  • In addition, we established a CRISPR activation (CRISPRa) system for multiplexed gene activation in pear calli for gain-of-function analysis. (nsf.gov)
  • Cas12a (formerly known as Cpf1), the class II type V CRISPR nuclease, has been widely used for genome editing in mammalian cells and plants due to its distinct characteristics from Cas9. (nsf.gov)
  • CRISPR Locus example. (medium.com)
  • Yes, the CRISPR-Cas9 tool does sound like the ultimate gene-editing tool, at least in theory. (medium.com)
  • Phage populations, however, can also adapt and evade bacterial CRISPR-Cas systems. (elifesciences.org)
  • 90%), and affiliate phylogenetically with, those of coexisting bacterial methanotrophs, including members of Methyloparacoccus , Methylocystis and Methylobacter spp. (nature.com)
  • Respiratory diphtheria is a serious infection caused by toxigenic Corynebacterium diphtheriae, and disease transmission mainly occurs through respiratory droplets. (cdc.gov)
  • Thus, augmentation of bacterial methane oxidation by pmoC-phages during infection could modulate the efflux of this potent greenhouse gas into the environment. (nature.com)
  • The symptoms of Clostridium difficile infection are caused by toxins expressed from its 19 kb pathogenicity locus (Pa Loc). (whiterose.ac.uk)
  • Neisseria gonorrhoeae , a Gram-negative bacterium, causes gonorrhea, the most common bacterial sexually transmitted infection (STIs), causing more than 106 million cases per year globally ( World Health Organization (WHO), 2012 ). (peerj.com)
  • Hence, susceptibility to infection can be characterized by a construct that involves not only gene expression patterns of the host but also that of the microorganism, both of which continue to adapt in response to external stimuli. (hindawi.com)
  • Here, we assemble metagenomes from tongue and dental plaque samples from multiple individuals and reconstruct 790 non-redundant genomes, 43 of which resolve to TM7, a member of the Candidate Phyla Radiation, forming six monophyletic clades that distinctly associate with either plaque or tongue. (biomedcentral.com)
  • Comprehensive genome engineering requires simultaneous targeting of multiple genes at defined locations. (nsf.gov)
  • In order to stay protected, some bacterial cells within the colony acquire multiple spacers (multi-colored bacterial cells) and can fight off various mutant phages. (elifesciences.org)
  • AlbaTraDIS can identify genes which are up or down regulated, or inactivated, between multiple conditions, producing a filtered list of genes for further experimental validation as well as several accompanying data visualisations. (biorxiv.org)
  • Variations in the HLA-DRB1 gene have been associated with an increased risk of developing multiple sclerosis. (medlineplus.gov)
  • In addition, long-read sequencing of one representative XDR ST235 isolate identified an integron carrying multiple resistance genes (including bla VIM-2), with differences in gene composition and synteny from the P. aeruginosa class 1 integrons described previously. (who.int)
  • Both loci also show limited polymorphic diversity, suggesting selection forces predating the origin of modern humans. (elsevierpure.com)
  • Because alternative RNA splicing allows different types of mRNA molecules to be created from a single gene, it generates the diversity of protein function and structure that is essential to complex organisms. (genomicglossaries.com)
  • The A and B clones of Borrelia burgdorferi sensu stric- maintenance of these clonal complexes in natural bacterial to, distinguished by outer surface protein C ( ospC ) gene populations ( 3 , 4 ). (cdc.gov)
  • The population of P. aeruginosa was diverse, with clonal expansions of XDR genomes belonging to MLSTs ST235, ST244, ST309 and ST773. (who.int)
  • However, the identification of relevant genes without known homologs, and the elucidation of the lignocellulolytic pathways and protein complexes for different microorganisms remain challenging. (biomedcentral.com)
  • 0.05) and were enriched for genes in mucosal immunity pathways. (biomedcentral.com)
  • spacer) and 3 plasmid loci ( ospC , dbpA , and BBD14). (cdc.gov)
  • First evidence of bacterial translocation from the intestinal tract as a route of Helicobacter cinaedi bacteremia. (microbiologyresearch.org)
  • Mycobacterial colonies were isolated from a popliteal lymph node aspirate sample and molecular typed by SNPs typing of the genes gyrB and rpsA , the 3′ region of the hsp65 gene and the internal transcribed spacer (ITS), and MIRU-VNTR analysis. (frontiersin.org)
  • MIRU-VNTR represents one of the most plastic elements within mycobacterial genomes ( 14 , 15 ). (frontiersin.org)
  • The presence of a PDM in a genome or taxonomic metagenome bin furthermore allowed us to accurately predict the ability of any particular organism to degrade plant biomass. (biomedcentral.com)
  • They can also be used to predict the plant biomass degradation ability for a genome or taxonomic bin. (biomedcentral.com)
  • Understanding how host genetic variation shapes the microbiome and how the microbiome ultimately functions to modulate host immunity are fundamental questions that are central to fully characterizing the architecture of many common diseases that occur at mucosal surfaces, including those involving the airway. (biomedcentral.com)
  • Most osteoarticular infections (OAI) occur via the hematogenous route, affect children under 5 years of age old, and include osteomyelitis, septic arthritis, osteoarthritis and spondylodiscitis. (bvsalud.org)
  • In addition, pmoC-phage abundance patterns correlate with those of the coexisting bacterial methanotrophs, supporting host-phage relationships. (nature.com)
  • Here, we report the genomic organization and evolution of the three il1rl1 genes (il1rl1 genes 1-3), and use both RNA-seq and gene-specific qPCR methods to quantify expression patterns. (usda.gov)
  • The enrichment patterns of epigenetic modifications were consistent with expression levels of genes involved in each domain under healthy conditions (Fig. S1A). (biorxiv.org)
  • This would be an example of altruism and how bacterial colonies could resemble multicellular organisms. (wikipedia.org)
  • the organisms then only suffers a fitness decrease when both genes are not working properly. (beacon-center.org)
  • In the present study, we searched the unreported phage genomic fragments from this lake for genes involved in methane oxidation. (nature.com)
  • Comparison of the core genome and Pa Loc phylogenies demonstrated aneventful evolutionary history, with distinct Pa Loc variants acquired clade specifically after divergence. (whiterose.ac.uk)
  • Future work is needed to determine whether phage-associated PmoC has similar functions to additional copies of PmoC encoded in bacterial genomes, thus contributing to growth on methane. (nature.com)
  • Transcriptomics data from Lake Rotsee (Switzerland) showed that some phage-associated pmoC genes were highly expressed in situ and, of interest, that the most rapidly growing methanotroph was infected by three pmoC-phages. (nature.com)
  • This system protects the bacterial cell by taking a short length of DNA from the phage and inserting this 'spacer' into its own genome. (elifesciences.org)
  • If the bacterial cell becomes re-infected, the spacer allows the cell to recognize the phage and stop it from replicating by cutting and destroying its DNA. (elifesciences.org)
  • When growing in a liquid environment (left), individual bacterial cells usually acquire a single spacer that targets just one region of the wild-type (WT) phage (shown in grey). (elifesciences.org)
  • In a study on vertebrate globins, Jay Storz and his colleagues wrote, "The retention of the proto- Hb and Mb genes in the ancestor of jawed vertebrates permitted a physiological division of labor between the oxygen-carrier function of Hb [hemoglobin] and the oxygen-storage function of Mb [myoglobin]. (icr.org)
  • In addition, genome editing methodology can be used to introduce transgenes at any locus, including the Rosa26 and AAVS1 Safe Harbor loci. (genecopoeia.com)
  • q = 0.002), a long non-coding RNA that binds to peptidoglycan recognition protein 3 ( PGLYRP3 ) mRNA , a gene encoding a known antimicrobial protein. (biomedcentral.com)
  • We aimed to explore and characterise in the chicken genome the expanding family of the numerous orthologues of the unique mouse Phf7 gene (highly expressed in the testis), observing the fact that this information is unclear and/or variable according to the versions of databases. (inra.fr)
  • qPCR assays specific to Il1rl1 gene-1 or -3, as well as a multi-gene qPCR assay (combined genes 1-3), confirmed that gene-1 is >20 fold more highly expressed than genes-2 and -3 in whole body lysates. (usda.gov)
  • The CAS genes are what produces the enzymes, the Cas enzyme complex and the class 1 Cas protein. (medium.com)