• gene
  • Approximately 450-500 bp internal fragments of each gene are used, as these can be accurately sequenced on both strands using an automated DNA sequencer. (wikipedia.org)
  • In the data collection step, definitive identification of variation is obtained by nucleotide sequence determination of gene fragments. (wikipedia.org)
  • Particular attention was placed on the analysis of genes involved in biofilm formation and quorum sensing, type IV secretion, flagellum synthesis and motility, lipopolysacharide synthesis, and on the gene xacPNP, which codes for a natriuretic protein. (ufl.edu)
  • Traditional PCR typing schemes classify SCC mec by targeting and identifying the individual mec and ccr gene complex types, but require the use of many primer sets and multiple individual PCR experiments. (jove.com)
  • Mutation analysis of xopAF indicates that the gene contributes to Xcaw growth in Mexican lime but does not contribute to the limited host range of Xcaw. (biomedcentral.com)
  • RNA-Seq analysis was conducted to compare the expression profiles of Xcaw12879 and XccA306 in Nutrient Broth (NB) medium and XVM2 medium, which induces hrp gene expression. (biomedcentral.com)
  • Cronobacter
  • The genome of one strain of Cronobacter sakazakii (BAA-894) has been sequenced and annotated. (wikipedia.org)
  • 2008). "Cronobacter gen. nov., a new genus to accommodate the biogroups of Enterobacter sakazakii, and proposal of Cronobacter sakazakii gen. nov. comb. (wikipedia.org)
  • allele
  • In the data analysis step, all unique sequences are assigned allele numbers and combined into an allelic profile and assigned a sequence type (ST). If new alleles and STs are found, they are stored in the database after verification. (wikipedia.org)
  • bioinformatic
  • A huge set of data is produced during the sequencing and identification process so bioinformatic techniques are used to arrange, manage, analyze and merge all of the biological data. (wikipedia.org)
  • This work will be carried out using available DNA sequence data and a bioinformatic approach. (uio.no)
  • methods
  • Various typing methods have been developed for B. quintana, but these tend to be limited by poor resolution and, in the case of gel-based methods, a lack of portability. (jove.com)
  • evolutionary
  • The emerging phylogenetic structure for the genus outlined in this study can be used to guide isolate selection for future population genomics and evolutionary studies in this important acidophile model. (frontiersin.org)
  • polymorphism
  • psbV and clpC in IRb are highly conserved whereas their counterparts in IRa exhibit three lineage-associated types of structural polymorphism via duplication or disruption of whole or partial genes. (biomedcentral.com)
  • Other tools, including multilocus sequence analysis and amplified fragment-length polymorphism, have been used for classification within clades. (wikipedia.org)
  • comprises
  • The four orders of the Betaproteobactera are sub-divided into families: Burkholderiales (type order) comprises the families Burkholderiacae (type family), Alcaliginaceae, Commamonadaceae, Oxalobacteraceae and Stutterellaceae. (wikipedia.org)
  • Both heterotrophs and photoheterotrophs are found along with some facultative autotrophs.Neisseriales comprises the families Neisseriaceae (type family) and Chromobacteriaceae. (wikipedia.org)
  • Most organisms are heterotrophs with some facultative methylotrophs and chemolithoheterotrophs.Nitrosomonadales comprises the families Nitrosomonadaceae (type family), Methylophilacae, Thiobacillaceae, Sterolibacteriacae, Spirillaceae and Gallionellaceae. (wikipedia.org)
  • Most organisms are chemolithoautotrophs with some methylotrophs and heterotrophsRhodocyclales comprises the families Rhodocyclaceae (type family), Azonexaceae and Zoogloeaceae. (wikipedia.org)
  • multiple loci
  • While the variability of certain VNTRs has brought up questions regarding their suitability for strain typing 7,8,9 , the emerging data suggest that analyzing multiple loci, which are diverse in their stability, can be used as a valuable epidemiological tool. (jove.com)
  • Bordetella
  • Some members of the Betaproteobacteria can cause disease in various eukaryotic organisms, including in humans, such as members of the genus Neisseria: N. gonorrhoeae and N. meninngitides being primary examples, which cause gonorrhea and meningitis respectively, as well as Bordetella pertussis which causes whooping cough. (wikipedia.org)
  • diversity
  • Morphological analysis of all of these phages by electron microscopy revealed a broad diversity with different members of the order Caudovirales, including the families Siphoviridae, Myoviridae, and Podoviridae. (jove.com)
  • Results obtained indicate that there is still considerable unexplored diversity within this genus. (frontiersin.org)
  • differences
  • Sequences that differ at even a single nucleotide are assigned as different alleles and no weighting is given to take into account the number of nucleotide differences between alleles, as we cannot distinguish whether differences at multiple nucleotide sites are a result of multiple point mutations or a single recombinational exchange. (wikipedia.org)
  • restriction
  • Molecular characterisation by DNA restriction analysis revealed that all phages contain linear double-stranded DNA. (jove.com)
  • chromosome
  • Staphylococcal Cassette Chromosome mec (SCC mec ) typing is a very important molecular tool for understanding the epidemiology and clonal strain relatedness of methicillin-resistant Staphylococcus aureus (MRSA), particularly with the emerging outbreaks of community-associated MRSA (CA-MRSA) occurring on a worldwide basis. (jove.com)
  • citri
  • citri, whose genome sequence was made available in 2002. (ufl.edu)
  • citri strain 306 (XccA306) is a type A (Asiatic) strain with a wide host range, whereas its variant X. citri subsp. (biomedcentral.com)
  • study
  • We also present the first expanded study on bacteriophages of the genus Achromobacter that has been so far a blank slate with respect to phage research. (jove.com)
  • Multiple locus VNTR analysis (MLVA) 10 has been used to study leprosy evolution and transmission in several countries including China 11,12 , Malawi 8 , the Philippines 10,13 , and Brazil 14 . (jove.com)
  • commonly
  • To strike the balance between the acceptable identification power, time and cost for the strain typing, about seven to eight house-keeping genes are commonly used in the laboratories. (wikipedia.org)
  • data
  • This includes the creation of fluorescent phages, infection of the cells, imaging under the microscope and data analysis. (jove.com)
  • plasmid
  • A crude phage lysate is first obtained by inducing a lysogen of the gpD-EYFP (Enhanced Yellow Fluorescent Protein) phage, harboring a plasmid expressing wild type gpD. (jove.com)