Whole genomeSequencePathogenIsolatesStrainsIdentified genome wideSequencesVirulence factorsDatasetsQuantitative traiRecombinationResistanceSpeciesArtificial chromosomeTranscriptomeSingle lociGenomic lociGenetic lociPolymorphismsProteinMolecularProteinsChromosomeChromosomalPathogenicitySusceptibility genesVivoChromosomesEncodePhylogeneticHorizontalMethylationSynthesisInfectionAnalysesWidespreadHuman leukocyAbsentPathwaysDifficileBacteria isolatedEpigeneticAntibioticLineagesAbstractRNAsCommensalAntimicrobialGeneticsExpressionSNPsCommonlyCore genesRelevant genesCharacterizationToxinAnalysisPopulationsMitochondrialEukaryoticInfectionsPathogenesis
Whole genome8
- We undertook whole genome sequencing of E. faecalis associated with bloodstream infection in the UK and Ireland over more than a decade to determine the population structure and genetic associations with hospital adaptation. (nature.com)
- The first whole-genome sequence of E. faecalis was published in 2003 8 . (nature.com)
- 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)
- Whole-genome sequencing (WGS) of M. tuberculosis and related mycobacteria is now routine, allowing comparisons across time and space. (jci.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)
- Therefore, we established an accurate and rapid whole genome sequencing (WGS) based classification and serotyping algorithm and combined it with the detection of resistance genes. (biomedcentral.com)
- Whole-genome methylation profiling reveals regions associated with painful temporomandibular disorders and active recovery processes. (iasp-pain.org)
- We isolated and whole-genome sequenced up to five colonies of faecal E. coli from 66 asymptomatic children aged three-to-five years in rural Gambia (n = 88 isolates from 21 positive stools). (peerj.com)
Sequence16
- We previously demonstrated that the genome of the C. difficile RT027 strain NCKUH-21 contains a prophage-like DNA sequence, which was found to be markedly similar to that of the φCD38-2 phage. (bvsalud.org)
- Sequence comparison of PR-locus haplotypes finds dramatic structural polymorphisms between PR-locus haplotypes including a large portion of each haplotype being composed of non-homologous sequences resulting in haplotypes differing in size by 66 kb. (pacb.com)
- The ability to sequence large bacterial collections means that the molecular epidemiology and gene content of epidemic and sporadic lineages can now be defined systematically. (nature.com)
- This was inferred from sequence analysis of rrs (16S rRNA) and other genetic loci and suggests that they belong to a novel species. (nih.gov)
- The new isolates formed a distinct clade, which was most closely related to Leptospira borgpetersenii, in multilocus sequence analysis using concatenated sequences of the genes rpoB, recA, fusA, gyrB, leuS and sucA. (nih.gov)
- A high-quality reference sequence for the Brassica napus genome is not yet available, thus studies of specific regions of the Brassica napus genome at sequence level have relied on the analysis of bacterial artificial chromosomes (BACs) or BAC contigs. (biomedcentral.com)
- Initially, we performed Multiple Sequence Alignment (MSA) of all species followed by Position Specific Scoring Matrix (PSSM) for both loci to achieve a percentage of discrimination among species. (biomedcentral.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)
- The annotation of the full genome sequence revealed the absence of genes encoding for a non-flagellar type 3 protein secretion system (NF-T3SS). (assignster.com)
- How many mobile elements, simple sequence repeats, or protein kinases are encoded in the genome? (cshlpress.com)
- Using a recent assembly of the human genome sequence, Stewart Scherer has compiled answers to a broad range of questions about the structure and function of the human genome. (cshlpress.com)
- Analysis of the publicly available genome sequence of Nipponbare near the Pi-z locus revealed numerous SSRs that could be converted into markers. (springer.com)
- Phylogenetic methods which do not rely on multiple sequence alignments are important tools in inferring trees directly from completely sequenced genomes. (biomedcentral.com)
- A relatively obvious approach to phylogenetic analysis of whole genomes is to extract as many genes as possible from the genome sequences, create a multiple sequence alignment from each of the genes and to concatenate all alignments. (biomedcentral.com)
- Difficulties with this approach may arise if orthologous genes cannot be identified with certainty or if the combined sequence length is still too small to give well-resolved trees. (biomedcentral.com)
Pathogen7
- The underlying genetics of matching-allele interactions are unknown even in host-parasite systems with empirical support for coevolution by NFDS, as is the case for the planktonic crustacean Daphnia magna and the bacterial pathogen Pasteuria ramosa. (pacb.com)
- Although the bacterial translocase has been characterized in other intercellular pathogens such as Chlamydia trachomatis and Rickettsia prowazeki, this is the first characterization of an ATP/ADP translocases in an obligate-intracellular plant pathogen and, given the conservation of the ATP uptake mechanism, may represent an evolutionary link between plant and animal pathogens. (usda.gov)
- Our primary model system is the human bacterial pathogen Haemophilus influenzae , an important agent of ear infections (otitis media) in children, as well as lung infections associated with chronic respiratory conditions. (drexel.edu)
- As a pathogen, E. coli are the most frequent causes of bacterial infections, including urinary tract infections, diarrheal disease, and other clinical infections such as neonatal meningitis, pneumonia and bacteremia. (eurekaselect.com)
- Borrelia burgdorferi , an emerging bacterial pathogen, is maintained in nature by transmission from one vertebrate host to another by ticks. (cdc.gov)
- By means of DNA sequencing of a large sample collection of the pathogen from across the United States, we studied the gene for the bacterium's highly diverse OspC protein, protective immunity against which develops in animals. (cdc.gov)
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, England, United Kingdom of Great Britain and Northern Ireland. (who.int)
Isolates12
- Before the current study, US B. pertussis isolates from 1935-1999 were characterized by pulsed-field gel electrophoresis ( 4 ), and a subset of isolates was analyzed for 2 genes, prn and ptxS1 ( 5 ). (cdc.gov)
- To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the "classical" antiqua biovar, strains Antiqua and Nepal516. (asm.org)
- Putative virulence and antibiotic resistance genes were over-represented in L1, L2 and L3 isolates combined, versus the remainder. (nature.com)
- The isolates were affiliated to 23 genera representing 8 different suborders based on nearly full length 16S rRNA gene sequencing. (uni-wuerzburg.de)
- Using Polymerase Chain Reactions (PCR) and Sanger DNA sequencing, we discovered CRISPRs in additional bacterial isolates of the same species of Bordetella. (ntu.edu.sg)
- Results: Here we describe a novel Type II-C CRISPR and its associated genes-cas1, cas2, and cas9-in several isolates of a newly discovered Bordetella species. (ntu.edu.sg)
- Analysis of average nucleotide identity and genome-to-genome distances, which have recently been proposed as reliable substitutes for classical DNA-DNA hybridization, further confirmed that these isolates should be classified as representatives of a novel species. (nih.gov)
- We report the finding of one novel inversion site for which we demonstrate the inversion potential and quantify inversion proportions during exponential and stationary growth in both historic and modern isolates of the same ribotype. (nih.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)
- 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)
- Several isolates encode putative virulence factors commonly found in Enteropathogenic and Enteroaggregative E. coli, and 53% of the isolates encode resistance to three or more classes of antimicrobials. (peerj.com)
Strains17
- We found 453 single nucleotide polymorphisms in protein-coding regions, which were used to assess the evolutionary relationships of these Y. pestis strains. (asm.org)
- A group of strains representing species of the genus Leptospira, isolated from patients with leptospirosis in Mayotte (Indian Ocean), were previously found to be considerably divergent from other known species of the genus Leptospira. (nih.gov)
- Draft genomes of the strains were also analysed to study the DNA relatedness with other species of the genus Leptospira. (nih.gov)
- however, individual strains vary in their virulence potential due to the presence of mobile accessory genes. (biomedcentral.com)
- Concerningly, iuc has also been reported in MDR strains in the hospital setting, where it was associated with increased mortality, highlighting the need to understand, detect and track the mobility of these virulence loci in the K . pneumoniae population. (biomedcentral.com)
- This study provides a framework for identifying and tracking these important virulence loci, which will be important for genomic surveillance efforts including monitoring for the emergence of hypervirulent MDR K . pneumoniae strains. (biomedcentral.com)
- 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)
- 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)
- We show that phase-variable loci are widespread with some sites being present in virtually all analyzed strains. (nih.gov)
- The relative contribution of recombination events in the generation of new categories of pathogenic E. coli varies among the E. coli population, and it is represented by the wide variety of mobile elements found in different diarrheal strains (e.g. pathogenicity islands, phages, transposons, pathoadaptive mutations, etc). (eurekaselect.com)
- In addition, we sequenced 99 ospC flanking sequences from different lineages and compared the complete cp26 sequences of 11 strains as well as the cp26 bbb02 loci of 56 samples. (cdc.gov)
- Over time, OspC genes were transferred between strains through recombinations involving the whole or parts of the gene and one or both flanks. (cdc.gov)
- These genes were identified using a comparative genome analysis of 215 strains belonging to ten human-related Haemophilus (sub)species (training dataset). (biomedcentral.com)
- In particular, H. influenzae serotype b (Hib) strains were one of the major causes of bacterial meningitis in children worldwide until the introduction of an effective conjugate vaccine [ 6 , 7 ]. (biomedcentral.com)
Identified genome wide1
- We identified genome wide SNPs that influence the gene expression of stimulated monocytes (so called expression quantitative trait loci, eQTL) that allow the identification of genes whose expression is influenced by specific genotypes. (ukbiobank.ac.uk)
Sequences4
- The nucleotide sequences of maturaseK ( matK ) and ribulose-1, 5-bisphosphate carboxylase ( rbcL ) marker loci are commonly used in plant species identification. (biomedcentral.com)
- 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)
- What Is the Size Distribution of snRNA Genes and Related Sequences in the Genome? (cshlpress.com)
- MTase methylates specific DNA sequences (recognition sites) in the host genome. (biomedcentral.com)
Virulence factors3
- The long-term goal of this research is to apply statistical genomic approaches developed by human geneticists to the identification of bacterial virulence factors that contribute to disease in natural populations. (drexel.edu)
- C. jejuni does not possess classical virulence factors observed in bacterial enteropathogens such as enterotoxigenic Escherichia coli and Salmonella spp. (assignster.com)
- This finding has raised an intriguing question: Does C. jejuni sense, inject and secrete putative virulence factors into host cells? (assignster.com)
Datasets4
- In order to generate molecular signatures, we used matK and rbcL loci datasets, which encompass 125 plant species in 52 genera reported by the CBOL plant working group. (biomedcentral.com)
- 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)
- Resistance genes were detected in 16 out of 262 datasets from the German cohort. (biomedcentral.com)
- Such datasets can be analysed using the same phylogenetic inference tools as single loci datasets. (biomedcentral.com)
Quantitative trai1
- A major quantitative trait loci (QTL) conditioning common bacterial blight (CBB) resistance in common bean (Phaseolus vulgaris L.) lines HR45 and HR67 was derived from XAN159, a resistant line obtained from an interspecific cross between common bean lines and the tepary bean (P. acutifolius L.) line PI319443. (tamu.edu)
Recombination4
- The high divergence of PR-locus haplotypes suggest a history of multiple, diverse and repeated instances of structural mutation events and restricted recombination. (pacb.com)
- Furthermore, AtRAD54, which performs an important role in the homologous recombination repair pathway, was involved in the pairing of homologous loci with γ-irradiation. (nature.com)
- We found that AtRAD54, which performs an important role in the homologous recombination (HR) repair pathway, was involved in the approach of two homologous loci under γ-irradiation. (nature.com)
- Intragenic recombination among ospC genes is known, but the extent to which recombination extended beyond the ospC locus itself is undefined. (cdc.gov)
Resistance20
- Negative frequency-dependent selection (NFDS) is an evolutionary mechanism suggested to govern host-parasite coevolution and the maintenance of genetic diversity at host resistance loci, such as the vertebrate MHC and R-genes in plants. (pacb.com)
- We fine-map one locus associated with D. magna resistance to P. ramosa and genetically characterize two haplotypes of the Pasteuria resistance (PR-) locus using de novo genome and transcriptome sequencing. (pacb.com)
- Moreover, in natural populations, we find that the PR-locus polymorphism is associated with variation in resistance to different P. ramosa genotypes, pointing to the PR-locus polymorphism as being responsible for the matching-allele interactions that have been previously described for this system. (pacb.com)
- Figure 3: Prevalence of virulence and antibiotic resistance genes in the dominant lineages (L1-L3, n = 89) and remainder ( n = 79). (nature.com)
- Newer work is using the same approach to map the genes responsible for natural variation in other pathogenesis traits, including resistance to human complement-mediated killing, as well as investigating the possibility of identifying genes involved in in vivo pathogenesis in an animal model of otitis media. (drexel.edu)
- The antimicrobial resistance (AMR) and/or virulence determinants possessed by the associated bacteria are generally found on mobile genetic elements (MGEs) that transmit between K . pneumoniae cells via horizontal gene transfer (HGT) [ 4 ]. (biomedcentral.com)
- In addition, the presence of antibiotic resistance genes within the German dataset was evaluated with SRST2 and correlated with results of traditional phenotyping assays. (biomedcentral.com)
- Pi-z is a disease resistance gene that has been effectively used to combat a broad-spectrum of races of the rice blast fungus Magnaporthe grisea . (springer.com)
- Although DNA markers have been reported for selection of the Pi2(t) and Pi-z resistance genes at the Pi-z locus, markers that are more tightly linked to the Pi-z locus would benefit rapid and effective cultivar development. (springer.com)
- Three SSRs on rice PAC AP005659 were found to be very tightly linked to the Pi-z locus, with one marker, AP5659-3, co-segregating with the Pi-z resistance reaction. (springer.com)
- The Pi-z factor conferring resistance to two races of blast was mapped to a 57 kb region on the physical map of Nipponbare in a location where the Pi2(t) gene was physically mapped. (springer.com)
- Two SSR marker haplotypes were unique for cultivars carrying the Pi-z gene, which indicates these markers are useful for selection of resistance genes at the Pi-z locus in rice germplasm. (springer.com)
- AlbaTraDIS automatically identified all well characterised Triclosan resistance genes, including the primary target, fabI . (biorxiv.org)
- 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)
- Four molecular markers tightly linked to this QTL have been identified suitable for marker assisted selection and physical mapping of the resistance gene. (tamu.edu)
- Tn6218 elements were Tn916-related but non conjugative and occasionally contained genes conferring resistance to clinically relevant antibiotics. (whiterose.ac.uk)
- Thus, resident E. coli in these children may constitute reservoirs of virulence- and resistance-associated genes. (peerj.com)
- 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)
- Antimicrobial resistance occurs through different mechanisms, which include spontaneous (natural) genetic mutations and horizontal transfer of resistant genes through deoxyribonucleic acid (DNA). (who.int)
- This report presents the status of AMR in Africa by analysing the main types of resistance and the underlying genes where possible. (who.int)
Species14
- Here we present the analysis of the genome of this enigmatic and important model organism and compare it with closely related species. (duke.edu)
- 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)
- The CRISPR-cas locus, which is absent in all other Bordetella species, has a significantly lower GC-content than the genome-wide average, suggesting acquisition of this locus via horizontal gene transfer from a currently unknown source. (ntu.edu.sg)
- The CRISPR array is transcribed and processed into mature CRISPR RNAs (crRNA), some of which have homology to prophages found in closely related species B. hinzii. (ntu.edu.sg)
- The extant diploid Brassica species, such as Brassica rapa , Brassica oleracea and Brassica nigra are therefore characterised by a complex genome structure. (biomedcentral.com)
- Taking the evolutionary history of the Brassica species into account, every single-copy gene in Arabidopsis thaliana should be present in three copies in the diploid Brassica species, in Brassica napus as much as six copies should be found. (biomedcentral.com)
- DNA barcoding is widely used and most efficient approach that facilitates rapid and accurate identification of plant species based on the short standardized segment of the genome. (biomedcentral.com)
- It mainly involves discrimination of species through standardized molecular marker gene and is gaining support from the taxonomists as well. (biomedcentral.com)
- However, the two loci ribulose-1,5-bisphosphate Carboxylase ( rbcL ) and maturase K ( matK ) gene regions are widely used in plant barcoding studies for phylogenetic analyses or species identification [ 10 , 11 ]. (biomedcentral.com)
- Seven chloroplast loci have been tested for plant species identification by The Consortium for the Barcode of Life (CBOL) Plant Working Group, where the suitability of matK and rbcL loci as a barcode was showed [ 12 ]. (biomedcentral.com)
- 13 ] studied a total of 20 species belonging to the family Zingiberaceae from India by using nine plastids and two nuclear loci and reported that matK and rbcL aids in the determination of 15 species (75%) into monophyletic groups. (biomedcentral.com)
- Who would consider seriously a phylogeny of vertebrates drawn from a comparison of myoglobin [a single polypeptide chain molecule found in the muscles of vertebrates] of some species and hemoglobin from others? (icr.org)
- Also, this study adds significantly to the number of commensal E. coli genomes, a group that has been traditionally underrepresented in the sequencing of this species. (peerj.com)
- The HLA complex is the human version of the major histocompatibility complex (MHC), a gene family that occurs in many species. (medlineplus.gov)
Artificial chromosome2
- Efficient screening of bacterial artificial chromosome (BAC) libraries with polymerase chain reaction (PCR)-based markers is feasible provided that a multidimensional pooling strategy is implemented. (biomedcentral.com)
- A bacterial artificial chromosome (BAC) library was constructed from high molecular weight DNA of HR45 and is composed of 33,024 clones. (tamu.edu)
Transcriptome2
- Complemented with extensive transcriptome data, we define approximately 31,000 gene loci, providing unexpected insights into early eukaryote evolution. (duke.edu)
- Transcriptome analysis further confirmed that the overexpression of ptrX led to the upregulation of the expression of toxin genes, flagellar genes, and csrA. (bvsalud.org)
Single loci1
- Molecular phylogenies of many taxonomic groups are based on analyses of single loci. (biomedcentral.com)
Genomic loci1
- 26 genomic loci were identified whose haploinsufficiency can modify these CDK8- or CycC-specific phenotypes. (sdbonline.org)
Genetic loci1
- Since 2001, more than 140 genetic loci associated with Crohn disease have been identified in genome-wide association studies (GWAS). (medscape.com)
Polymorphisms2
- Additional evidence of the contribution of NOD2 in CD was demonstrated by a study in which the NOD2 gene was sequenced and additional, rare polymorphisms that increase the risk of the development of CD were identified. (medscape.com)
- In polyploid genomes two classes of SNPs need to be distinguished, polymorphisms between accessions (intragenomic SNPs) and those differentiating between homoeologous genomes (intergenomic SNPs). (biomedcentral.com)
Protein18
- Ubiquitin is a small (8.6 kDa) regulatory protein found in most tissues of eukaryotic organisms, i.e., it is found ubiquitously. (wikipedia.org)
- A heat-stable polypeptide present in these extracts, ATP-dependent proteolysis factor 1 (APF-1), was found to become covalently attached to the model protein substrate lysozyme in an ATP- and Mg2+-dependent process. (wikipedia.org)
- also called CARD15 [caspase recruitment domain-containing protein 15]) as the first susceptibility gene for Crohn disease (CD) . (medscape.com)
- NOD2 was identified as an intracellular protein in the proinflammatory nuclear factor kappa B (NFkB) pathway, and the leucine-rich repeat was identified as a receptor for bacterial products (now known to be muramyl dipeptide). (medscape.com)
- The protein product of the translocase gene demonstrated characteristics typical for members in this family of proteins, including 12 transmembrane helices and an isoelectric point of 9.4. (usda.gov)
- They cloned the HIS4 locus, yeast's best candidate for an operon and showed that it in fact encoded a single multifunctional protein, rather than multiple proteins under common regulation. (genestogenomes.org)
- 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)
- 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)
- PDMs represent a new resource of protein families and candidate genes implicated in microbial plant biomass degradation. (biomedcentral.com)
- Hemoglobin is an iron-containing oxygen-transport protein found in red blood cells. (icr.org)
- One of the few antigens against which mammals develop protective immunity is the highly polymorphic OspC protein, encoded by the ospC gene on the cp26 plasmid. (cdc.gov)
- Each SEDS gene is invariably linked with a cognate class B high-molecular weight penicillin-binding protein (HMW PBP) gene. (swan.ac.uk)
- Analysis of secondary metabolite gene and protein expression profiles in Streptomyces coelicolor grown under environmental conditions. (swan.ac.uk)
- How Many Protein-coding Genes Are Present in the Genome? (cshlpress.com)
- Does Exon Number Correlate with Gene Size or Protein Size? (cshlpress.com)
- How Many Protein Kinases Are Encoded in the Genome? (cshlpress.com)
- The HLA-DRB1 gene provides instructions for making a protein that plays a critical role in the immune system. (medlineplus.gov)
- The protein produced from the HLA-DRB1 gene, called the beta chain, attaches (binds) to another protein called the alpha chain, which is produced from the HLA-DRA gene. (medlineplus.gov)
Molecular3
- 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)
- Microbial genome sequencing provides the opportunity to gain a detailed understanding of the molecular basis for hospital adaptation. (nature.com)
- When Fink's career began, the discovery of DNA and the molecular biology revolution had changed little about the study of yeast genetics because there was no method to introduce DNA into a yeast cell, a critical step for tinkering with genes in vivo . (genestogenomes.org)
Proteins9
- UBA52 and RPS27A genes code for a single copy of ubiquitin fused to the ribosomal proteins L40 and S27a, respectively. (wikipedia.org)
- The UBB and UBC genes code for polyubiquitin precursor proteins. (wikipedia.org)
- We describe extensive use of histidine kinase-based two-component systems and tyrosine kinase signaling, the presence of bacterial and plant type photoreceptors (phytochromes, cryptochrome, and phototropin) and of plant-type pentatricopeptide repeat proteins, as well as metabolic pathways, and a cell cycle control system typically found in more complex eukaryotes. (duke.edu)
- We screened three φNCKUH-21 genes encoding DNA-binding proteins to check their effects on PaLoc genes expression. (bvsalud.org)
- 10% transformation frequency), which reside in genes undergoing strong diversifying selection that encode large membrane proteins, likely as an immune invasion tactic. (drexel.edu)
- The rodA and ftsW genes encode polytopic membrane proteins that are essential for bacterial cell elongation and division, respectively. (swan.ac.uk)
- What are the largest genes and proteins? (cshlpress.com)
- This mimicry triggers B- and T-cell immune responses directed against the heart, joints, central nervous system (CNS), skin, and subcutaneous tissues where those proteins are found. (medscape.com)
- MHC class II genes provide instructions for making proteins that are present on the surface of certain immune system cells. (medlineplus.gov)
Chromosome2
- We are now using advanced optical mapping technology to reproduce these maps in the absence of genetic variation, in order to disentangle the role of chromosome structure from the potential for genetic incompatibilities ("speciation genes") skewing our results. (drexel.edu)
- Lateral gene transfers resulted in different linkages between the ospC gene and loci of the chromosome or other plasmids. (cdc.gov)
Chromosomal3
- We have generated high-resolution genome-wide maps of transformation, finding massive variation in rates at different chromosomal loci. (drexel.edu)
- Recent genomic analysis of an epidemic ribotype 027 (RT027) Clostridioides difficile strain revealed the presence of several chromosomal site-specific invertible sites hypothesized to control the expression of adjacent genes in a bimodal on-off mode. (nih.gov)
- 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)
Pathogenicity3
- Evidence suggests that bacteriophages can regulate the expression of the pathogenicity locus (PaLoc) genes of C. difficile. (bvsalud.org)
- In the present study, we investigated the mechanisms underlying the φNCKUH-21-mediated regulation of the pathogenicity and the PaLoc genes expression in the lysogenized C. difficile strain R20291. (bvsalud.org)
- The symptoms of Clostridium difficile infection are caused by toxins expressed from its 19 kb pathogenicity locus (Pa Loc). (whiterose.ac.uk)
Susceptibility genes2
- Development of asthma is multifactorial and depends on the interactions among multiple susceptibility genes and environmental factors. (msdmanuals.com)
- More than 100 asthma susceptibility genes have been reported. (msdmanuals.com)
Vivo2
- This study provides the first genome-wide captures of the dynamics of in vivo AmtR binding events and the regulatory network they define. (frontiersin.org)
- Furthermore, this analyses confirmed the positive roles of CDK9 and Yorkie in regulating Mad-dependent gene expression in vivo. (sdbonline.org)
Chromosomes3
- In addition, inspired by Barbara McClintock's work on jumping genes in maize, Fink and his postdocs discovered that yeast transposable elements, known as Ty elements, move around the chromosomes through retrotransposition via an RNA intermediate. (genestogenomes.org)
- Is Gene Density Uniform Across the Chromosomes? (cshlpress.com)
- Do Gene-rich Chromosomes Have Smaller Genes? (cshlpress.com)
Encode1
- The genomes of Antiqua and Nepal516 are 4.7 Mb and 4.5 Mb and encode 4,138 and 3,956 open reading frames, respectively. (asm.org)
Phylogenetic4
- We are applying a variety of genomic methods to identifying putative virulence genes, including machine learning and phylogenetic correlated evolution methods. (drexel.edu)
- Here, we extend the recently described Genome BLAST Distance Phylogeny (GBDP) strategy to compute phylogenetic trees from all completely sequenced plastid genomes currently available and from a selection of mitochondrial genomes representing the major eukaryotic lineages. (biomedcentral.com)
- δ values are found to be a reliable predictor of phylogenetic accuracy. (biomedcentral.com)
- Nowadays, an increasing number of completely sequenced genomes are available and a growing field of phylogenetic research deals with the question of how to infer reliable phylogenies from this large amount of data to overcome the limitations of single-gene phylogenies. (biomedcentral.com)
Horizontal1
- Specifically, the presence of tyrosine kinases in Acanthamoeba and Physarum as representatives of two distantly related subdivisions of Amoebozoa argues against the later emergence of tyrosine kinase signaling in the opisthokont lineage and also against the acquisition by horizontal gene transfer. (duke.edu)
Methylation7
- Therefore, we assessed associations between occupational exposure to pesticides and genome-wide DNA methylation sites. (bmj.com)
- In addition, we performed genome-wide stratified and interaction analyses by gender, smoking and airway obstruction status, and assessed associations between gene expression and methylation for genome-wide significant CpGs (n=2802). (bmj.com)
- 0.05) associated with differential DNA methylation of 31 CpGs annotated to 29 genes. (bmj.com)
- Conclusions We show for the first time that occupational exposure to pesticides is genome-wide associated with differential DNA methylation. (bmj.com)
- Reasoning that the unexplained heritability may be because of DNA methylation, an epigenetic phenomenon, we measured genome-wide DNA methylation using the Illumina MethylationEPIC platform with blood samples from participants in the Orofacial Pain: Prospective Evaluation and Risk Assessment (OPPERA) study. (iasp-pain.org)
- Functional characterization of the identified regions found relationships between methylation at these loci and nearby genetic variation contributing to chronic painful TMD and with gene expression of proximal genes. (iasp-pain.org)
- These findings reveal epigenetic contributions to chronic painful TMD through methylation of the genes FMOD, PM20D1, ZNF718, ZFP57, and RNF39, following the development of acute painful TMD. (iasp-pain.org)
Synthesis2
- Genes in the PG0104-PG0121 locus have been shown to be required for K1 capsule synthesis (19, 20). (oscars2019info.com)
- The susceptibility of the spores of sfr and php2 mutants to such a physical and chemical stress implies an important role of these genes in spore wall synthesis. (swan.ac.uk)
Infection3
- Our study contributes to distinguish fungal from bacterial infection and bridges genetic variability and transcriptomic expression. (ukbiobank.ac.uk)
- We have used this method to map an operon involved in intracellular invasion of airway epithelial cells, a trait with implications for chronic infection, bacterial persistence, and trafficking of cells to different body sites. (drexel.edu)
- Little is known about the genomic diversity of Escherichia coli in healthy children from sub-Saharan Africa, even though this is pertinent to understanding bacterial evolution and ecology and their role in infection. (peerj.com)
Analyses2
- Both pangenomic and phylogenomic analyses group tongue-specific clades with other host-associated TM7 genomes. (biomedcentral.com)
- analyses gradually elucidated the perfected genome-scale metabolic map of C. glutamicum , expanding the scope of its application. (frontiersin.org)
Widespread2
- Type I toxin-antitoxin (TA) systems are widespread genetic modules in bacterial genomes. (mdpi.com)
- The avoidance of orthodox Type II R-M system recognition sites in prokaryotic genomes is a widespread phenomenon. (biomedcentral.com)
Human leukocy2
- A genome-wide association study for Hunner-type interstitial cystitis led to amino acid variants in the class II human leukocyte antigen DQ-beta1 and DP-beta1 chain genes. (genomeweb.com)
- The HLA-DRB1 gene is part of a family of genes called the human leukocyte antigen (HLA) complex. (medlineplus.gov)
Absent1
Pathways2
- [ 16 ] This finding is of particular interest because other known CD genes play significant roles within the autophagy pathways, which highlights an evolving phenomenon: although the number of CD-associated genes increases, many of the new genes fall into pathways already identified as important in the development of chronic GI inflammation. (medscape.com)
- Botstein is honored for contributions that include developing methods for defining genetic pathways, mapping genomes, and analyzing gene expression. (genestogenomes.org)
Difficile1
- Clostridioides difficile is a Gram-positive, anaerobic, and spore-forming bacterial member of the human gut microbiome. (bvsalud.org)
Bacteria isolated2
- In several ongoing collaborations, we are investigating how the genomes of bacteria isolated from patients with chronic infections change over time. (drexel.edu)
- 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)
Epigenetic1
- Our lab is interested in the systems biology and evolution of epigenetic switches (bistability) and clocks (oscillators) in gene regulatory networks, two functions that are essential for patterning, cell proliferation, and differentiation in biological systems. (duke.edu)
Antibiotic1
- This pathway, called "natural transformation," is a major mechanism of gene transfer across bacteria and has a profound effect on genome evolution, including spreading antibiotic resistances and other virulence determinants. (drexel.edu)
Lineages1
- The major burden of iuc and iro amongst the genomes analysed was due to two linked lineages ( iuc1 / iro1 74% and iuc2 / iro2 14%), each carried by a distinct non-self-transmissible IncFIB K virulence plasmid type that we designate KpVP-1 and KpVP-2. (biomedcentral.com)
Abstract1
RNAs2
- Which Transfer RNAs Are Present in the Genome? (cshlpress.com)
- Which Genes Host Small Nuclear RNAs and Small Nucleolar RNAs? (cshlpress.com)
Commensal1
- Escherichia coli are Gram-negative bacteria found as normal commensal flora in the gastrointestinal tract. (eurekaselect.com)
Antimicrobial1
- Antimicrobial resistant microorganisms are found in people, animals and the environment and can spread globally. (who.int)
Genetics1
- In 1970 Fink co-founded the influential yeast genetics course at Cold Spring Harbor Laboratory and taught it for 17 years, sharing his knowledge widely through the yeast community. (genestogenomes.org)
Expression8
- One of the index association studies suggests that the mutations have a "loss of function" effect, meaning that after bacterial stimulation, there was reduced NFkB expression. (medscape.com)
- In the ptrX-overexpressing R20291 strain, PtrX influenced the expression of flagellar genes and the sigma factor gene sigD, possibly through an increased flagellar phase ON configuration ratio. (bvsalud.org)
- Fink's work in the budding yeast Saccharomyces cerevisiae led to our deep understanding of gene expression control in eukaryotic metabolism. (genestogenomes.org)
- Yeast transformation allowed the introduction of a DNA molecule from any organism into yeast cells and enabled the manipulation of the expression of those genes. (genestogenomes.org)
- Seven out of 31 CpGs were associated with gene expression levels. (bmj.com)
- By activating the expression of genes whose products are required for metamorphosis, ecdysone and EcR-USP are essential for the reorganization of flies' body plans before emerging from pupal cases as adults. (sdbonline.org)
- 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)
- How Reliable Are Gene Expression-Based and Immunohistochemical Biomarkers Assessed on a Core-Needle Biopsy? (lu.se)
SNPs3
- For these candidate SNPs, our eQTL study can provide the genes that are influenced by them. (ukbiobank.ac.uk)
- This work has a public health impact because it provides new insights in interindividual differences in the immune response and can be used to identify causal genes for candidate SNPs that are associated with a disease. (ukbiobank.ac.uk)
- It is demonstrated that intergenomic SNPs represent a powerful tool for BAC library screening of a polyploid genome. (biomedcentral.com)
Commonly2
- Xylans and β-glucans are homopolysaccharides composed of either xylose or β-1,3, β-1,4-linked D-glucose, respectively, and are commonly found in plant cell walls of grasses. (biomedcentral.com)
- Which genes are commonly associated with genetic diseases? (cshlpress.com)
Core genes1
- Recruiting metagenomic short reads using single-copy core genes, Donati et al. (biomedcentral.com)
Relevant genes1
- Selection for recombinants that acquired the trait, followed by genome-wide profiling of donor-specific allele frequencies, we can rapidly identify the relevant genes. (drexel.edu)
Characterization1
- This study focused on characterization of four SEDS genes [SC02085 (ftsW), SC02607 (sfr), SC03846 (rodA) and SC05302 (rodA2)] and SC02090 (ftsi) and SC02608 ipbp2) [cognate HMW PBP genes ftsWand sfr, respectively]. (swan.ac.uk)
Toxin2
- The carriage of φNCKUH-21 in R20291 cells substantially enhanced toxin production, bacterial motility, biofilm formation, and spore germination in vitro. (bvsalud.org)
- The overexpression of NCKUH-21_03890, annotated as a transcriptional regulator (phage transcriptional regulator X, PtrX), considerably enhanced toxin production, biofilm formation, and bacterial motility of R20291. (bvsalud.org)
Analysis7
- Gene reduction analysis revealed that the gene deletion processes are under selective pressure, and many of the inactivations are probably related to the organism's interaction with its host environment. (asm.org)
- In addition, we established a CRISPR activation (CRISPRa) system for multiplexed gene activation in pear calli for gain-of-function analysis. (nsf.gov)
- Researchers found ancestry-specific risk variants and developed a better polygenic risk score based on a GWAS and subsequent meta-analysis. (genomeweb.com)
- A single translocase encoding gene was identified through an in silico analysis of the recently completed Las genome. (usda.gov)
- Computational analysis of each SEDS gene locus revealed that each gene is a part of specific gene cluster. (swan.ac.uk)
- Since leaving Minnesota, he has focused on bioinformatics, both in industry and in the analysis of the Candida albicans genome. (cshlpress.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)
Populations2
- [ 18 ] Although these studies have been mainly in individuals of European descent, many CD-associated genes are shared with non-European populations. (medscape.com)
- We found that the distributions and frequencies of types of OspC genes differed between populations of B. burgdorferi in the Northeast, the Midwest, and California. (cdc.gov)
Mitochondrial4
- What Is the Base Composition of the Mitochondrial Genome? (cshlpress.com)
- Which Genes Are Present in the Mitochondrial Genome? (cshlpress.com)
- How Are Genes Organized in the Mitochondrial Genome? (cshlpress.com)
- Our results indicate that, at this taxonomic level, plastid genomes are much more valuable for inferring phylogenies than are mitochondrial genomes, and that distances based on breakpoints are of little use. (biomedcentral.com)
Eukaryotic1
- Fink is recognized for the discovery of principles central to genome organization and regulation in eukaryotic cells. (genestogenomes.org)
Infections3
- Blood monocytes are an important part of the innate immune response that cover a wide range of defense mechanisms including phagocytosis or release of cytokines against systemic fungal or bacterial infections. (ukbiobank.ac.uk)
- 3. How do bacterial genomes change during the course of chronic infections? (drexel.edu)
- In particular, gene clusters encoding the biosynthesis of siderophores aerobactin ( iuc ) and salmochelin ( iro ) are associated with invasive disease and are common amongst hypervirulent K . pneumoniae clones that cause severe community-associated infections such as liver abscess and pneumonia. (biomedcentral.com)
Pathogenesis1
- 2. Can natural transformation be exploited to map pathogenesis genes? (drexel.edu)