• genomic loci
  • By fusing this dCas9 to eGFP, we and others could show that the CRISPR/Cas9 system can be further expanded to label and trace genomic loci in living cells. (springer.com)
  • Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS et al (2013) Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. (springer.com)
  • The CRISPR-Cas components, Cas9 gene and a designer genome targeting CRISPR guide RNA (gRNA), show robust and specific RNA-guided endonuclease activity at targeted endogenous genomic loci in yeast. (harvard.edu)
  • Sequence
  • However, with the modest exception of Alligator mississippiensis for which there is roughly 2.5 Mb of BAC end sequence [ 9 ] and 26 partially assembled BACs (GenBank, 10/3/2008), little sequence data is available for crocodilian genomes, in part due to a relative lack of high-quality molecular tools for this important clade. (biomedcentral.com)
  • PATRIC Data Release Policy Bacillus Bartonella Borrelia Brucella Burkholderia Campylobacter Chlamydophila Clostridium Coxiella Ehrlichia Escherichia Francisella Helicobacter Lysteria Mycobacterium Rickettsia Salmonella Shigella Staphylococcus Vibrio Yersinia Other Bacteria Protein Family Sorter: Compares protein families across closely related or diverse groups of genomes, visualizes them using interactive heatmaps, and generates multiple sequence alignments and phylogenetic trees for an individual families. (wikipedia.org)
  • Besides a conserved backbone related to pAgK84 of Agrobacterium radiobacter K84, pAMI2 carries a three-gene cluster coding for the protein DmfR, which has sequence similarities to members of the LuxR family of transcription regulators, and two subunits (DmfA1 and DmfA2) of N , N -dimethylformamidase, an enzyme of high substrate specificity that catalyzes the first step in the degradation of DMF. (pubmedcentralcanada.ca)
  • CAAT box (also CAT box) A conserved sequence found within the promoter region of the protein-encoding genes of many eukaryotic organisms. (fao.org)
  • protein
  • The CHM gene was shown to encode a protein related to the MutS protein of Escherichia coli that is involved in mismatch repair and DNA recombination. (pnas.org)
  • Coevolution of mitochondria and chloroplasts has permitted economy of function via protein dual-targeting ( 5 , 6 ), genome capacity and coding have been altered ( 7 ), and the mitochondrial genomes of plants have acquired structural and maintenance features distinct from their animal counterparts. (pnas.org)
  • Corn rootworm-resistant maize line MON88017 was produced using recombinant-DNA techniques to express the cry3Bb1 gene encoding a Coleopteran-specific insecticidal protein from Bacillus thuringiensis (subsp. (cbd.int)
  • The cry3Bb1 gene encodes the insect control protein Cry3Bb1, a delta-endotoxin. (cbd.int)
  • candidate-gene strategy An experimental approach in which knowledge of the biochemistry and/or physiology of a trait is used to draw up a list of genes whose protein products could be involved in the trait. (fao.org)
  • The pan-genome, that is a combined set of 30 sequenced strains, encodes 2,239 protein families (orthologous groups, OGs). (wikipedia.org)
  • Twinkle protein is a mitochondrial protein that in humans is encoded by the C10orf2 gene. (wikipedia.org)
  • plasmid
  • Bacterial toxin-antitoxin (TA) systems are genetic elements, which are encoded by plasmid as well as chromosomal loci. (mdpi.com)
  • Of particular interest is the Ssr8013-Slr8014 system encoded on plasmid pSYSG, which is part of a larger defense island or the pSYSX system Slr6056-Slr6057, which is linked to a bacterial ubiquitin-like system. (mdpi.com)
  • Molecular analyses of MON 88017 confirmed that single copies of the cp4 epsps and cry3Bb1 genes are integrated at a single locus in the corn genome with all expression elements intact and no plasmid bacterial backbone present. (cbd.int)
  • pathogen
  • PATRIC (Pathosystems Resource Integration Center) is the Bacterial Bioinformatics Resource Center, an information system designed to support the biomedical research community's work on bacterial infectious diseases via integration of vital pathogen information with rich data and analysis tools. (wikipedia.org)
  • The genome of this pathogen contains >40 phase variable loci whose expression is regulated by tandem DNA repeat tracts. (bl.uk)
  • cluster
  • Alignment and phylogenetic analyses performed to ascertain evolutionary relationships revealed that ABPs cluster into at least six distinct, unrelated families (AbpA, AbpB, and four novel ABPs) with no phylogenetic evidence that one group evolved from another, and no single ancestral gene found within each group. (springer.com)
  • strains
  • Strains with both genes or only hmbR were present at similar frequencies among disease isolates as compared with carriage isolates. (bl.uk)
  • Strains with only hpuAB gene were under-represented among disease isolates, possibly due to the receptor having a high level of immunogenicity or being inefficient in iron acquisition during systemic spread. (bl.uk)
  • virulence
  • An analysis for the distribution, frequency and role of PV of these genes is relevant in determining their virulence association and suitability as a future vaccine candidate. (bl.uk)
  • presented a comprehensive analysis of transcription at single-nucleotide resolution by differential RNA-seq that confirmed the known acid induction of major virulence loci, such as the urease (ure) operon or the cag pathogenicity island (see below). (wikipedia.org)
  • encode
  • Majority of these loci encode OMPs, which are potential targets for host innate and adaptive immune responses. (bl.uk)
  • heterozygous
  • Hemizygous transgenic mice carrying the huα-globin locus on a heterozygous knockout background (huα+/0, muα++/−−) demonstrated complementation of most hematologic parameters. (deepdyve.com)
  • proteins
  • Where possible, key amino acid residues in the above proteins (generally in active sites, effectors binding sites or substrate binding sites) were identified in order to support gene identification. (biomedcentral.com)
  • 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)
  • Rich, interactive visualizations that support analyses such as, a bird's-eye view of the conservation (or lack thereof) of particular genes of interest, discerning how many proteins have the same function within a single genome, and identifying proteins with multiple homologs or paralogs across a set of genomes. (wikipedia.org)
  • The heatmap view is an interactive visualization tool that provides an overview of the distribution of proteins across a selected set of genomes. (wikipedia.org)
  • These include the locus of enterocyte effacement (LEE)-encoded type III secretion system (T3SS), various T3-secreted effector proteins, H7 flagellin, and a number of specific adhesins, including F9 fimbriae and autotransporters. (frontiersin.org)
  • One such mechanism is the production of surface proteins that facilitate adhesive interactions with host and bacterial ligands. (springer.com)
  • Cas9
  • Interestingly, a catalytically dead Cas9 (dCas9) can be employed as a targeted DNA-binding platform to alter gene expression. (springer.com)
  • synthase
  • The cp4 epsps gene encodes for a form of the plant enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) that is highly tolerant to inhibition by glyphosate. (cbd.int)
  • bacteria
  • In the present article we review the differential contribution to the evolution of bacterial genomes that processes such as gene modification, gene acquisition and gene loss may have when bacteria colonize different habitats that present characteristic ecological features. (mdpi.com)
  • To our knowledge, this is the first study to provide insights into the genetic organization and regulation as well as the dissemination in bacteria of genes involved in the enzymatic breakdown of DMF. (pubmedcentralcanada.ca)
  • species
  • These interactions often result in enzymatic activity and/or intra- and inter-species signaling functions that help to maintain a relatively stable collection of bacterial species comprising the oral microbiome. (springer.com)
  • genetic
  • Their presence in direct orientation permits the subdivision of the genome into a collection of molecules, each containing only a portion of the genetic information. (pnas.org)
  • candidate gene A gene whose function suggests that it may be involved in the genetic variation observed for a particular trait, e.g., the gene for growth hormone is a candidate gene for body weight. (fao.org)
  • transient
  • We propose a model accounting specifically for such clustering, and show that indispensability in a genome with frequent gene deletion and insertion leads to the transient clustering of these genes. (biomedcentral.com)
  • organization
  • Gene clustering plays an important role in the organization of the bacterial chromosome and several mechanisms have been proposed to explain its extent. (biomedcentral.com)
  • However, the controversies raised about the validity of each of these mechanisms remind us that the cause of this gene organization remains an open question. (biomedcentral.com)
  • Isolation
  • To demonstrate the utility of the library in gene isolation, we probed the C. porosus macroarrays with an overgo designed from a C-mos (oocyte maturation factor) partial cDNA. (biomedcentral.com)
  • regulation
  • Klug A (2010) The discovery of zinc fingers and their development for practical applications in gene regulation and genome manipulation. (springer.com)
  • mechanisms
  • Therefore, studies on bacterial evolution are of increasing interest to understand the basic mechanisms of evolution. (mdpi.com)
  • Since they have similar cis-elements and promoter structures, the mechanisms underlying their distinct gene expression and possible applications are discussed. (nih.gov)
  • metabolism
  • The purpose of this study was to perform a genome-wide bioinformatic analysis of key genes encoding metabolism of diverse storage compounds by Rhodococcus jostii RHA1 and to examine its ability to synthesize and accumulate triacylglycerols (TAG), wax esters, polyhydroxyalkanoates (PHA), glycogen and polyphosphate (PolyP). (biomedcentral.com)
  • 6 genes encoding key enzymes for glycogen metabolism, one gene coding for a putative polyphosphate kinase and 3 putative exopolyphosphatase genes. (biomedcentral.com)
  • As demonstrated, this may be of particular use for identifying genes with redundant functions such as adhesion and carbon metabolism. (frontiersin.org)
  • recombination
  • In plants, relative copy number of recombination-derived subgenomic DNA molecules within mitochondria is controlled by nuclear genes, and a genomic shifting process can result in their differential copy number suppression to nearly undetectable levels. (pnas.org)
  • Ectopic recombination results in expressed gene chimeras that cause cytoplasmic male sterility, plant variegation, and other aberrant phenotypes ( 15 , 16 ). (pnas.org)
  • functions
  • During this process, genes within batches coding for coupled functions will have a higher chance of increasing the organism fitness, and thus their own, than uncoupled genes, which would require pre-existence of the interacting partners in the chromosome. (biomedcentral.com)
  • acquisition
  • In addition, we discuss the temporal constraints in the evolution of bacterial genomes, considering bacterial evolution from the perspective of processes of short-sighted evolution and punctual acquisition of evolutionary novelties followed by long stasis periods. (mdpi.com)
  • expression
  • Genome change in wheat observed through the structure and expression of α/β-gliadin genes. (nih.gov)
  • Our studies demonstrate that the huα-globin locus in the 191-kb transgene contains all the necessary elements for the regulated expression of huα-globin in transgenic mice. (deepdyve.com)
  • evolution
  • Particularly relevant in this respect are the studies on the evolution of bacterial pathogens that produce long-lasting chronic infections. (mdpi.com)
  • The BAC library should expedite complete genome sequencing of C. porosus and facilitate detailed analysis of genome evolution within Crocodylia and between crocodilians and diverse amniote lineages including birds, mammals, and other non-avian reptiles. (biomedcentral.com)
  • Agrobacterium
  • kumamotoensis) in order to control infestation with corn root worm, and the cp4 epsps gene from the soil bacterium Agrobacterium ssp. (cbd.int)
  • possible
  • Genome level analyses of a crocodilian would be especially useful in leveraging information from the chicken, and a crocodilian genome would be the best possible outgroup for all genomic work within birds. (biomedcentral.com)
  • Results
  • The results indicate that there are a minimum of 20,000 CR1a/b elements in C. porosus and that their distribution throughout the genome is decidedly non-random. (biomedcentral.com)
  • found
  • In total, twelve α/β-gliadin intact genes and four pseudogenes were found, and retrotransposons or other transposons existed in each BAC clone. (nih.gov)
  • Further, one or both genes were found in an ON state in 96 % of disease and 66 % of carriage isolates. (bl.uk)