Chromosomal genomes loci genes bacterial. Medical search. Frequent questions

Whole genome sequences of these isolates were determined and analysed to compute bacterial multilocus sequence types and plasmid replicon types, infer phylogenetic relationships, and identify antimicrobial resistance and virulence genes. (biomedcentral.com)
RNA was prepared separately from peripheral blood mononuclear cells (PBMC) and granulocytes to UNC1215 identify differentially expressed genes using whole genome microarrays. (tech-strategy.org)
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)
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)
The availability of Oryza '-omics' resources is increasing, yet the number of whole-genome assemblies for non-AA genome wild species remains low. (nature.com)
Whole-genome assemblies of wild Oryza species will provide new sources of genes and gene variants/haplotypes, enhancing the ability of breeding programs to introduce desirable traits into domestic cultivars. (nature.com)
Genomic view of bipolar disorder revealed by whole genome sequencing in a genetic isolate. (cornell.edu)
The common ancestor of the salmonids experienced a whole genome duplication event, making extant salmonids such as the rainbow trout an excellent model for studying the evolution of tetraploidization and re-diploidization in vertebrates. (biomedcentral.com)
A whole genome duplication event occurred 25 to 100 million years ago in the common ancestor of the salmonids. (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)
There are other duplicated genes in the identified BAC sequences, suggesting that these genomic regions exhibit a high rate of tandem duplication. (inra.fr)
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)
Spa gene: s - signal sequence, E, D, A, B, C sequences encoding IgG-binding domains, X - region which lacks IgG-binding activity and consists of repetitive region (Xr) and C-terminal region (Xc). (cftrpathway.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)
Exchanges and losses of the Pa Loc DNA have also occurred, via long homologous recombination events involving flanking chromosomal sequences. (whiterose.ac.uk)
The majority of sequences grouped in clade A, which was represented by the mrk gene cluster from the genome sequenced K. pneumoniae MGH78578. (biomedcentral.com)
The E. coli and K. pneumoniae mrkABCD gene sequences clustered together in two distinct clades, supporting previous evidence for the occurrence of inter-genera lateral gene transfer. (biomedcentral.com)
In order to enrich the genomic tools already available in this species and provide further insight on the complexity of its genome, we sequenced a large number of rainbow trout BAC-end sequences (BES) and characterized their contents. (biomedcentral.com)
Mutation rates are tricky to measure directly because mutations are identified by examining the phenotypes or DNA sequences of bacterial cultures many generations after the mutations would have happened. (fieldofscience.com)

CRISPR-Cas systems are a new generation of RNA-guided microbial genome engineering tools that allow targeted genome modifications, such as insertions, deletions, and point mutations, to be introduced with greater ease than ever before. (sigmaaldrich.com)
In this article, we present an application of our novel E. coli CRISPR/Cas-mediated Lambda-Red (λ-Red) homologous recombination (HR) vector system, which facilitates gene editing through the homology-directed repair (HDR) of double-stranded DNA breaks (DSBs) created by Cas9 endonuclease, using either ssDNA or dsDNA as an editing template. (sigmaaldrich.com)
Until recently, CRISPR/Cas9-based gene editing methods 5 have been overlooked as a microbial gene editing tool because most bacteria lack endogenous DSB repair systems, rendering Cas9 nuclease cleavage toxic. (sigmaaldrich.com)
This approach is known as 'CRISPR' gene editing. (ufl.edu)
We anticipate that, over the next decade, CRISPR and other gene editing techniques will be used to rapidly develop elite strawberry varieties with improved disease resistance, fruit quality, and other valuable attributes. (ufl.edu)
What is CRISPR gene editing? (ufl.edu)
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is one form of gene editing that can be used to precisely modify a gene of interest without otherwise compromising the favorable traits of an elite variety (Rani et al. (ufl.edu)
By using CRISPR technology, these genes or gene variants can be moved into desirable genetic backgrounds that can be further moved via conventional crossing in later generations. (ufl.edu)
Does CRISPR gene editing = transgenic technology? (ufl.edu)
We published another article about CRISPR gene editing in crop improvement ( https://edis.ifas.ufl.edu/publication/HS1334 ). (ufl.edu)
CRISPR/Cas9-mediated genome editing is a next-generation strategy for genetic modifications, not only for single gene targeting, but also for multiple targeted mutagenesis. (nature.com)
We further demonstrated successful examples of multiple targeting including chromosomal deletions in human cells using the all-in-one CRISPR/Cas9 vectors constructed with our novel system. (nature.com)
Genome editing using clustered regularly-interspaced short palindromic repeats (CRISPR)/Cas9 is an easy and efficient strategy for the generation of gene-modified cells and organisms 1 , 2 . (nature.com)
In addition, the plasmids for the second-step reaction retained the structure of a CRISPR/Cas9 expression vector harboring single gRNA and Cas9 expression cassettes and can therefore be used separately for single gene targeting. (nature.com)
Here, we employ diverse CRISPR/Cas9 genome editing tools to generate a series of targeted lesions within the endogenous cis-regulatory module (CRM) required for kni expression in the L2 vein primordium. (elifesciences.org)
In 2015, researchers reported that they had used components of the CRISPR/Cas9 genome editing system to edit genes so that they could propagate in a "Super-Mendelian" fashion. (elifesciences.org)
Here, the fusion proteins MLL-AF4 (MA4) and AF4-MLL (A4M) were CRISPR/Cas9-genome edited in the AAVS1 locus of HEK293 cells as a model to study MLL fusion-mediated DNA-DSB formation/repair. (ibecbarcelona.eu)

We analyzed travel-associated clinical isolates of Escherichia coli O104:H4, including 1 from the 2011 German outbreak and 1 from a patient who returned from the Philippines in 2010, by genome sequencing and optical mapping. (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)
High resistance to most of the antibiotics tested was observed among the isolates, five ST25, three ST11, one ST45, and one ST505, which harbored a total of 44 plasmids, many of them predicted to be conjugative and carrying genes conferring resistance to a variety of antibiotic, metals, and disinfectants. (biorxiv.org)
The most abundant carbapenemase gene family in the K. pneumoniae isolates (33/39) was bla OXA-232 , with bla NDM-1 additionally identified in 19 of them. (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)
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)

In total, we found eight completely novel deletions/insertions in the IgG-binding region of the spa-gene plus one deletion that has been reported before [14], in 6110 community and inpatient S. aureus strains from Oxfordshire (Figure 3). (cftrpathway.com)
Thus, although PIGA mutations are established as pathogenetic drivers of PNH, larger deletions of the locus are rare. (annexpublishers.co)
Furthermore, we demonstrate simultaneous multiple targeted mutagenesis and chromosomal deletions mediated by not only Cas9 nuclease, but also Cas9 nickase. (nature.com)

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)
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)
Listeria monocytogenes is a Gram-positive, facultative intracellular bacterial pathogen that can cause severe disease in humans, other mammals and birds [ 1 ]. (biomedcentral.com)
Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, England, United Kingdom of Great Britain and Northern Ireland. (who.int)

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)
We validated nine primer pairs by in silico PCR for their use in screening the chicken bacterial artificial chromosome (BAC) library to produce BAC-derived probes to detect and localise PHF7-like loci by fluorescence in situ hybridisation (FISH). (inra.fr)
Lateral gene transfers resulted in different linkages between the ospC gene and loci of the chromosome or other plasmids. (cdc.gov)
Table 1 provides a summary outline of the gene symbols, chromosomal locations, radiation sensitivity characteristics, immunodeficiencies, chromosome breakage characteristics, and major cancer risk for each of these disorders. (medscape.com)
They described two patients with PNH with an acquired rearrangement of chromosome 12 affecting the HMGA2 gene, which encodes a chromatin remodeling protein, in the PIGA mutant cells [ 12 ]. (annexpublishers.co)
Phenotypic analysis of these ' in locus ' mutations based on both expression of Kni protein and adult wing phenotypes, reveals novel unexpected features of L2-CRM function including evidence for a chromosome pairing-dependent process that promotes transcription. (elifesciences.org)
Chromosome markers such as translocation breakpoints found in patients with abnormal phenotypes were often pivotal in identifying the chromosomal region of interest following which positional cloning methods resulted in the identification and characterization of the gene(s) of interest (Tommerup, 1993). (what-when-how.com)
The sequencing of the zebra finch Taeniopygia guttata genome, in combination with targeted bacterial artificial chromosome (BAC) sequencing, has allowed us to characterize an MHC from a highly divergent and diverse avian lineage, the passerines. (biomedcentral.com)
Die Analyse großer Cosmid- und BAC- (Bacterial Artificial Chromosome) Contigs, welche im Rahmen dieser Arbeit erstellt wurden und die mehr als 1 Mb sowohl des X- als auch des Y-Chromosoms des Platys X. maculatus abdecken, zeigte eine hohe Dichte von Retroelementen und anderen repetitiven Sequenzen, besonders im Bereich des dominanten Onkogens Xmrk und in einer durch das duplizierte Gen ps-criptY gekennzeichneten, Y-spezifischen Region. (uni-wuerzburg.de)

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)
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)
The zebra finch MHC differs markedly from that of the chicken, the only other bird species with a complete genome sequence. (biomedcentral.com)

The Neisseria gonorrhoeae Accessory Genome and Its Association with the Core Genome and Antimicrobial Resistance. (ox.ac.uk)
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)
Antimicrobial resistance occurs through different mechanisms, which include spontaneous (natural) genetic mutations and horizontal transfer of resistant genes through deoxyribonucleic acid (DNA). (who.int)

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)
The effects of these mutations unexpectedly suggested that pairs of chromosomes might be interacting to control the activity of this gene. (elifesciences.org)
Leading up to the publication of the advanced draft assembly of the Human Genome Sequence in 2001, attention switched to the innovative use of fully sequenced clones (principally Bacterial or P1 Artificial Chromosomes, BAC/PACs). (what-when-how.com)
Highly efficient modification of bacterial artificial chromosomes (BACs) using novel shuttle vectors containing the R6Kgamma origin of replication. (cornell.edu)
Cytogenetic (FISH) evidence and the genome assembly itself place core MHC genes on as many as four chromosomes with TAP and Class I genes mapping to different chromosomes. (biomedcentral.com)

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)
We show that phase-variable loci are widespread with some sites being present in virtually all analyzed strains. (nih.gov)
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)
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)
The Cano-eMLST Program: An Approach for the Calculation of Canonical Extended Multi-Locus Sequence Typing, Making Comparison of Genetic Differences Among Bunches of Bacterial Strains. (cdc.gov)
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)
In this study, we characterised the genes encoding type 3 fimbriae from CAUTI strains of Escherichia coli , Klebsiella pneumoniae , Klebsiella oxytoca , Citrobacter koseri and Citrobacter freundii . (biomedcentral.com)
Phylogenetic analysis of the type 3 fimbrial genes ( mrkABCD ) from 39 strains revealed they clustered into five distinct clades (A-E) ranging from one to twenty-three members. (biomedcentral.com)
All of the strains examined caused type 3 fimbriae mediated agglutination of tannic acid treated human erythrocytes despite sequence variation in the mrkD -encoding adhesin gene. (biomedcentral.com)
Further work is now required to substantiate the clade structure reported here by examining more strains as well as other bacterial genera that make type 3 fimbriae and cause CAUTI. (biomedcentral.com)

Three methods including MetaCore analysis for disease and pathway correlations, concordance analysis between array-CGH database and the expression array database, and literature search for copy number variation genes were performed to select novel lung cancer candidate genes. (biomedcentral.com)
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)
Moreover, we showed that the expression of some candidate genes (E2F3, CDKAL1 and Sox4) in the 6p22.3 region is highly correlated with the chromosomal amplification. (oncotarget.com)
Furthermore, comparative genomics through BES can be used for identifying positional candidate genes from QTL mapping studies, aid in future assembly of a reference genome sequence and elucidating sequence content and complexity in the rainbow trout genome. (biomedcentral.com)

Multidrug and carbapenem-resistant K. pneumoniae (CR- Kp ) are considered critical threats to global health and key traffickers of resistance genes to other pathogens. (biorxiv.org)
Highly accurate-single chromosomal complete genomes using IonTorrent and MinION sequencing of clinical pathogens. (cdc.gov)
MHC Class I genes encode surface receptors in most nucleated cell types and facilitate immune responses to intracellular pathogens. (biomedcentral.com)
MHC Class II genes also encode receptors but are restricted to antigen presenting cells of the immune system where they play a role in combating extracellular pathogens. (biomedcentral.com)
Polymorphism at MHC loci facilitates binding of a diversity of pathogens and this evolutionary selection pressure is thought to contribute to the high genetic variation in MHC loci [ 1 ]. (biomedcentral.com)

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)
The candidate will be expected to contribute to this tool development and microbiome research in the lab, by conducting microbiology and molecular biology techniques, including bacterial and bacteriophage manipulation, cloning, protein purification, sequencing, mass spectrometry, and biochemical assays. (ucsf.edu)
Antibiotic-resistant bacteria on personal devices in hospital intensive care units: Molecular approaches to quantifying and describing changes in the bacterial community of personal mobile devices. (cdc.gov)
MHC genes are perhaps the most thoroughly studied example of adaptive molecular evolution, representing a classic example of balancing selection [ 2 - 4 ]. (biomedcentral.com)
Nuclear compartments have diverse roles in regulating gene expression, yet the molecular forces and components that drive compartment formation remain largely unclear. (cipsm.de)

26 genomic loci were identified whose haploinsufficiency can modify these CDK8- or CycC-specific phenotypes. (sdbonline.org)
In Cas9 nuclease-mediated genome editing, we constructed an all-in-one vector expressing Cas9 nuclease and seven gRNAs and targeted seven genomic loci. (nature.com)

Here, we report the first application of single Cas9 nickase (Cas9n) to induce gene insertion at a selected locus in cattle. (biomedcentral.com)
The natural Cas9 protein possesses a nuclease activity and can induce a DNA double-strand break (DSB) in any genomic sequence guided by a gRNA, provided that a protospacer adjacent motif (PAM) sequence exists in the target locus 3 , 4 , 5 . (nature.com)
Since Cas9 has no DNA recognition specificity except for the PAM sequence, simple multiplication of gRNAs along with a common Cas9 protein results in multiplex genome engineering. (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)

Significant associations were found between the prevalence of accessory elements and core genome multi-locus sequence types (cgMLST), consistent with a structured gonococcal population despite frequent horizontal gene transfer (HGT). (ox.ac.uk)

The genetic organization of the clade 3 Pa Loc was unique in containing a stably integrated novel trans poson (designated Tn6218), variants of which were found at multiple chromosomal locations. (whiterose.ac.uk)

Accessory elements showed similar synteny across genomes, indicating either a predisposition for particular genomic locations or ancestral inheritance that are conserved during strain expansion. (ox.ac.uk)
The apparent lack of synteny between TAP and the expressed MHC Class I locus is in fact reminiscent of a pattern seen in some mammalian lineages and may represent convergent evolution. (biomedcentral.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)

RRResearch: Have bacteria evolved gene-specific rates of point mutations? (fieldofscience.com)

Although the resistance mechanisms against this class of antibiotics have not been entirely resolved, resistance against other classes of antibiotics, such as tetracyclines, is known to be mediated through plasmids, which are known gonococcal extra-chromosomal accessory elements. (ox.ac.uk)
Ten plasmids encoding either KPC-2, NDM-1, or NDM-7 carbapenemases were characterized, including novel plasmids with increased resistance gene load and a novel genetic environment for bla KPC-2 gene. (biorxiv.org)
These MGEs, most typically plasmids and integrative and conjugative elements (ICEs), are therefore important constituents of the accessory genome that imbue K . pneumoniae organisms with their distinct HA or CA clinical profiles. (biomedcentral.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)

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)

Here, the gonococcal accessory genome was characterized using gene-by-gene approaches and its association with the core genome and AMR were assessed. (ox.ac.uk)
In fact, a highly organized genome composition was identified with a strong association between the accessory and core genome. (ox.ac.uk)
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)

2. Can natural transformation be exploited to map pathogenesis genes? (drexel.edu)
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)

Second, fluorescence in situ hybridization was conducted for the region containing the HMGA2 gene in addition to expression analysis, to study the recurrence of changes at this locus. (annexpublishers.co)
Using fluorescence in situ hybridization (FISH) analyses, we evaluated chromosomal 6p22 amplification in a large cohort of bladder cancer patients with complete surgical staging and outcome data. (oncotarget.com)

Here, we examined the genetic diversity, distribution and mobilisation of iuc and iro loci amongst 2503 K . pneumoniae genomes using comparative genomics approaches and developed tools for tracking them via genomic surveillance. (biomedcentral.com)

however, chromosomal accessory genes could also play a role in AMR. (ox.ac.uk)

Stable integration of the Pa Loc is suggested by its single chromosomal location and the clade specificity of its different genetic variants. (whiterose.ac.uk)
The International Oryza Map Alignment Project emphasises its significance as the sole representative of the EE genome clade. (nature.com)
Two of these species ( O. sativa and Oryza glaberrima ), both of which belong to the AA genome clade, were independently domesticated in Asia and Africa, respectively. (nature.com)
To date, the species and cultivars that make up the AA genome clade have provided most of the genetic variation and resources that have led to the success of domesticated rice 4 , while other genome clades have contributed relatively little to domestication. (nature.com)

E. coli , one of the most commonly engineered bacteria, has an active homologous recombination (HR) system, so chromosomal integration can be achieved simply by donating DNAs with homology arms to recombine at a target site. (sigmaaldrich.com)

FOXP2 is a member of the forkhead box family of transcription factors, proteins that regulate gene expression by binding to DNA. (wikipedia.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 mrk gene cluster is similar to other fimbrial operons of the chaperone-usher class in that it contains genes encoding major ( mrkA ) and minor ( mrkF ) subunit proteins as well as chaperone- ( mrkB ), usher- ( mrkC ) and adhesin- ( mrkD ) encoding genes [ 37 , 38 ]. (biomedcentral.com)
Some MHC-linked genes encode proteins that interact with MHC molecules. (biomedcentral.com)

Mutations in FOXP2 are among several (26 genes plus 2 intergenic) loci which correlate to ADHD diagnosis in adults - clinical ADHD is an umbrella label for a heterogeneous group of genetic and neurological phenomena which may result from FOXP2 mutations or other causes. (wikipedia.org)

Identification of regions with copy number aberrations and the genes involved thus offers a basis for better understanding of cancer development [ 6 ]. (biomedcentral.com)

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 comprehensively characterize the gonococcal accessory genome to better understand genome architecture as well as the evolution and mechanisms of AMR in this species. (ox.ac.uk)
This system is present in most archaeal species and approxi-mately half of all bacterial species. (pjmonline.org)
8 provided an update to the OryzaGenome database which includes short-read sequencing data for several non-AA genome Oryza species. (nature.com)

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)
In several ongoing collaborations, we are investigating how the genomes of bacteria isolated from patients with chronic infections change over time. (drexel.edu)
Upon detection of environmental alterations, bacteria adjust their gene expression in order to obtain a phenotype that is suitable for the environment to which they are exposed ( Federle, 2012 ). (frontiersin.org)

Figure 3 Scheme of the rearrangements identified in the IgG-binding domains of spa -gene in samples from Oxfordshire. (cftrpathway.com)
In culture, cells from affected individuals exhibit elevated rates of chromosomal breakage or instability, leading to chromosomal rearrangements. (medscape.com)

We are applying a variety of genomic methods to identifying putative virulence genes, including machine learning and phylogenetic correlated evolution methods. (drexel.edu)
The gonococcal accessory gene pool consisted of 247 genes, which were mainly genes located on large mobile genetic elements, phage associated genes, or genes encoding putative secretion systems. (ox.ac.uk)
A putative regulatory gene ( mrkE ) located upstream of mrkA has been described previously in Klebsiella pneumoniae [ 37 ]. (biomedcentral.com)

Characterization of hepatitis B virus X gene quasispecies complexity in mono-infection and hepatitis delta virus superinfection. (cdc.gov)
The characterization of BES provided insights on the rainbow trout genome. (biomedcentral.com)
The discovery of specific repeat elements will facilitate analyses of sequence content (e.g. for SNPs discovery and for transcriptome characterization) and future genome sequence assemblies. (biomedcentral.com)

Cancer-related genes show racial differences. (biomedcentral.com)
Our analyses of the zebra finch MHC suggest a complex history involving chromosomal fission, gene duplication and translocation in the history of the MHC in birds, and highlight striking differences in MHC structure and organization among avian lineages. (biomedcentral.com)

Phylogeny revealed that the duplications occurred first between chromosomal regions and then inside each region. (inra.fr)

PacBio Iso-Seq data were generated for five distinct tissues to improve the functional annotation of 34,587 protein-coding genes and 42,329 transcripts. (nature.com)

Hannenhalli received his doctorate in computer science from Pennsylvania State University in 1996, where he developed combinatorial algorithms for genome rearrangement problems. (umd.edu)
The most frequent rearrangement of the human MLL gene fuses MLL to AF4 resulting in high-risk infant B-cell acute lymphoblastic leukemia (B-ALL). (ibecbarcelona.eu)

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)
Most of the ST235 genomes formed a distinct lineage from global genomes, thus raising the possibility that they may be unique to the Philippines. (who.int)

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)
A single deletion affecting the PIGA locus was found, but no other relevant or recurrent abnormalities were detected. (annexpublishers.co)
1997). These studies were instrumental in defining the so-called terminal deletion syndromes that are distributed throughout the genome and were found in ~5% patients with idiopathic developmental delay with or without associated congenital abnormalities (de Vries et al. (what-when-how.com)

These findings highlight the potential of visible light-activated photosensitizer for mitigating the dissemination of plasmid-encoded antibiotic resistance genes. (bvsalud.org)

The genome sequence of Barbarea vulgaris facilitates the study of ecological biochemistry. (pacb.com)

1998. A genome-wide search for chromosomal loci linked to mental health wellness in relatives at high risk for bipolar affective disorder among the Old Order Amish. . (cornell.edu)

Matching to known miRNA alignment, a total of 25 known miRNAs were significantly different between them, with 1 up-regulated and 24 down-regulated in the flying matured virgin queens while there were 11 target genes of 19 known miRNA which were expressed differentially between them. (chinaagrisci.com)

The total chromosomal content of a cell involves approximately 105 genes in a specialized macromolecule of deoxyribonucleic acid (DNA). (cdc.gov)

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)
The symptoms of Clostridium difficile infection are caused by toxins expressed from its 19 kb pathogenicity locus (Pa Loc). (whiterose.ac.uk)

Genome-wide DNA demethylation is a unique feature of mammalian development and naïve pluripotent stem cells. (cipsm.de)

used genome editing to make mutations in a stretch of DNA that regulates the gene involved in wing vein formation. (elifesciences.org)
Via positional cloning, we show that mutations in a zebrafish LTCC encoding gene, cav1.3a , underlie the auditory-vestibular defects of gemini ( gem ) circler mutants. (jneurosci.org)

MIRU-VNTR represents one of the most plastic elements within mycobacterial genomes ( 14 , 15 ). (frontiersin.org)

The FOXP2 gene region acts as a transcription factor for the forkhead box P2 protein. (wikipedia.org)
Genomic DNA copy number variation is a hallmark of cancer and can lead to alteration in the expression and functions of genes residing within the affected chromosomal region [ 5 ]. (biomedcentral.com)
The 20-bp target region of the gRNA is customized for each gene target of interest. (sigmaaldrich.com)
This revealed no aberration of the chromosomal region containing the HMGA2 gene in the cohort, and HMGA2 expression was surprisingly only detectable in a single case. (annexpublishers.co)
The zebra finch MHC includes multiple Class I and Class II genes, some of which appear to be pseudogenes, and spans a much more extensive genomic region than the chicken MHC, as evidenced by the presence of MHC genes on each of seven BACs spanning 739 kb. (biomedcentral.com)
The major histocompatibility complex ( MHC ) is a gene-dense genomic region within which many genes play a role in vertebrate immune response. (biomedcentral.com)
Therefore, the presence of these genes, along with Class I and Class II genes can be used to define the MHC region. (biomedcentral.com)
In addition to Class I and Class II genes, many of the other genes in the MHC region also play a role in immune response. (biomedcentral.com)
Andere potentielle Gene zeigen Homologien zu den menschlichen Genen CHRNA, CHRND und TMEFF und lassen auf eine syntenische Region zum menschlichen Chromosom 2q schließen. (uni-wuerzburg.de)

Tn6218 elements were Tn916-related but non conjugative and occasionally contained genes conferring resistance to clinically relevant antibiotics. (whiterose.ac.uk)

We compare all five currently sequenced Y. pestis genomes and the corresponding features in Yersinia pseudotuberculosis . (asm.org)

The knirps ( kni ) locus encodes transcription factors required for induction of the L2 wing vein in Drosophila . (elifesciences.org)

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)

These findings enhance our understanding of gonococcal genome architecture and have important implications for gonococcal population biology. (ox.ac.uk)
Genome Biology and Evolution, 6 (1). (whiterose.ac.uk)

Transcription factors affect other regions, and the forkhead box P2 protein has been suggested to also act as a transcription factor for hundreds of genes. (wikipedia.org)

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 M. tuberculosis genome has ushered in a quarter century of substantial clinical and public health advancements. (jci.org)
Subsequent studies have identified a number of genes implicated in the William's contiguous gene phenotype, and in common with many other human microdeletion syndromes, hemizygosity at one or more loci leading to the disruption of expression of dosage-sensitive genes appears to be the principal mutational mechanism underlying the clinical phenotypes. (what-when-how.com)

Gene duplications increase genetic and phenotypic diversity and occur in complex genomic regions that are still difficult to sequence and assemble. (inra.fr)

Oxford Nanopore long reads were combined with Illumina short reads to generate a high-quality ~ 858 Mbp genome assembly within 850 contigs with 46× long read coverage. (nature.com)
Reference-guided scaffolding increased genome contiguity, placing 88.2% of contigs into 12 pseudomolecules. (nature.com)

Conversely, in human children aged 4-5, the gene was found to be 30% more expressed in the Broca's areas of female children. (wikipedia.org)
Conversely, the genome-wide mutational landscape in MLL-rearranged infant B-ALL has been reported silent. (ibecbarcelona.eu)

Organisms2

Chemicals and Drugs1

Analytical, Diagnostic and Therapeutic Techniques and Equipment3

Phenomena and Processes20

Disciplines and Occupations1

Technology, Industry, Agriculture1

Information Science3

Whole genome10

Sequences10

CRISPR17

Isolates7

Deletions3

Pathogen5

Chromosome9

Complete Genome Sequence4

Antimicrobial Resistance3

Chromosomes5

Strains12

Candidate genes4

Pathogens5

Molecular5

Genomic loci2

Cas93

Including resistance1

Multi-locus1

Multiple chromosomal1

Synteny3

Point mutations1

Plasmids4

Activating the expression of ge1

Core genome3

Pathogenesis2

Fluorescence2

Comparative genomics1

Accessory genes1

Clade4

Homologous recombination1

Proteins4

Intergenic1

Aberrations1

Species4

Bacteria3

Rearrangements2

Putative3

Characterization3

Differences2

Phylogeny1

Protein-codin1

Rearrangement2

Distinct2

Deletion3

Resistance genes1

Facilitates1

19981

Target genes1

Deoxyribonucleic acid1

Infection2

Mammalian1

Mutations2

Mycobacterial1

Region9

Conjugative1

Pestis1

Encodes1

Difficile1

Biology2

Transcription1

Clinical3

Phenotypic1

Contigs2

Conversely2