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At least 379 records · Page 21Linked to original sources
PubMed1999

Genome analysis of several marine, magnetotactic bacterial strains by pulsed-field gel electrophoresis.

The genomic DNA of three strains of marine magnetotactic bacteria, including two facultatively anaerobic vibrios, strains MV-1 and MV-2, and the microaerophilic coccus, strain MC-1, was analyzed by pulsed-field gel electrophoresis (PFGE). Digestion of the genomic DNA of strain MV-1 by the restriction endonucleases AvrII, BamHI, HindIII, NheI, SalI, SfiI, SgfI, SgrAI, and XbaI resulted in a large number of fragments below 400 kb that were difficult to resolve by PFGE. Digestion of MV-1 DNA with NotI and RsrII resulted in no fragments. Treatment of genomic DNA of strains MV-1 and MV-2 with PacI, PmeI, and SpeI yielded a manageable number of fragments (ca. 20) that were relatively easily resolved with PFGE, while PacI and SpeI were effective for strain MC-1. There was no evidence for the presence of plasmids and linear chromosomes in any of the strains, and strains MV-1 and MV-2 appear to contain a single, circular chromosome. Genome sizes of strains MV-1, MV-2, and MC-1 were estimated to be between 3.6 and 3.9 Mb (mean +/- SD; 3.7 +/- 0.2), 3. 3 and 3.7 Mb (3.6 +/- 0.2), and 4.3 and 4.7 Mb (4.5 +/- 0.3), respectively. The restriction fragment patterns of the vibrioid strains MV-1 and MV-2 were extremely similar, suggesting that the strains are closely related.

DNA Restriction Enzymes↗
PubMed2000

Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III.

Genome sequencing projects generate a wealth of information; however, the ultimate goal of such projects is to accelerate the identification of the biological function of genes. This creates a need for comprehensive studies to fill the gap between sequence and function. Here we report the results of a functional genomic screen to identify genes required for cell division in Caenorhabditis elegans. We inhibited the expression of approximately 96% of the approximately 2,300 predicted open reading frames on chromosome III using RNA-mediated interference (RNAi). By using an in vivo time-lapse differential interference contrast microscopy assay, we identified 133 genes (approximately 6%) necessary for distinct cellular processes in early embryos. Our results indicate that these genes represent most of the genes on chromosome III that are required for proper cell division in C. elegans embryos. The complete data set, including sample time-lapse recordings, has been deposited in an open access database. We found that approximately 47% of the genes associated with a differential interference contrast phenotype have clear orthologues in other eukaryotes, indicating that this screen provides putative gene functions for other species as well.

Animals↗
PubMed2002

Molecular cloning and genomic analysis of mouse glucuronyltransferase involved in biosynthesis of the HNK-1 epitope.

cDNA and genomic clones encoding the mouse glucuronyltransferase (GlcAT-P) involved in biosynthesis of the HNK-1 carbohydrate epitope were isolated and the structural organization of the gene was determined. The predicted amino acid sequence of mouse GlcAT-P is 96.2 and 98.2% identical to those of the rat and human enzymes, respectively. Alternatively spliced isoforms of mouse GlcAT-P are present in the brain and encode two proteins that are identical throughout their length except for an additional 13 amino acids in the N-terminal cytoplasmic domain of the major form. The coding region of GlcAT-P is composed of 5 exons spanning approximately 6 kb, and the GlcAT-P gene was mapped to the A4 region of mouse chromosome 9. Upstream of the transcriptional start site, no typical TATA or CCAAT box was found, but binding sites for several known transcription factors including Sp1 and Krox-20 were identified. Transient transfection of luciferase reporter constructs demonstrated that a 207 bp fragment of the 5'-upstream region acts as a strong promoter in PC-12 cells, which express the HNK-1 epitope, but not in COS-1 cells. Thus, this minimal promoter region of GlcAT-P is suggested to be associated with the regulation of HNK-1 expression.

5' Flanking Region↗
PubMed1981

Genome analysis of influenza A virus strains isolated during an epidemic of 1979-1980.

The genome and polypeptides of influenza A virus H3N2 strains isolated during the epidemic of 1979-1980 in the U.S.S.R. and G.D.R. have been analysed. Five varieties of H3N2 strains differing in a number of genes have been found. The isolates of the first group was similar to the A/Texas/1/77 strain in all the genes; the isolates of the second group were similar to the A/Bangkok/1/79 strain in all the genes; the strain representative of the third variety, contained all the genes except gene 4 close to those of the A/Bangkok/1/79 strain; the isolates of the fourth group contained genes 7 and 8 similar to those of the A/Bangkok/1/79 strain while the other genes corresponded to those of no strains under comparison; the viruses of the fifth group contained gene 3 similar to that of A/Moscow/406/76 strain, gene 7 was similar to that of A/Texas/1/77 strain and the other genes differed from all other strains compared. The data obtained indicate that during an influenza epidemic occurring in certain region several influenza virus varieties of the same serotype can circulate simultaneously, differing not only in the antigenic specificity of the haemagglutinin, but also in other genes.

Disease Outbreaks↗
PubMed2006

Sentra: a database of signal transduction proteins for comparative genome analysis.

Sentra (http://compbio.mcs.anl.gov/sentra), a database of signal transduction proteins encoded in completely sequenced prokaryotic genomes, has been updated to reflect recent advances in understanding signal transduction events on a whole-genome scale. Sentra consists of two principal components, a manually curated list of signal transduction proteins in 202 completely sequenced prokaryotic genomes and an automatically generated listing of predicted signaling proteins in 235 sequenced genomes that are awaiting manual curation. In addition to two-component histidine kinases and response regulators, the database now lists manually curated Ser/Thr/Tyr protein kinases and protein phosphatases, as well as adenylate and diguanylate cyclases and c-di-GMP phosphodiesterases, as defined in several recent reviews. All entries in Sentra are extensively annotated with relevant information from public databases (e.g. UniProt, KEGG, PDB and NCBI). Sentra's infrastructure was redesigned to support interactive cross-genome comparisons of signal transduction capabilities of prokaryotic organisms from a taxonomic and phenotypic perspective and in the framework of signal transduction pathways from KEGG. Sentra leverages the PUMA2 system to support interactive analysis and annotation of signal transduction proteins by the users.

Archaeal Proteins↗
PubMed2004

Can whole genome analysis refine the taxonomy of the genus Rhodococcus?

The current systematics of the genus Rhodococcus is unclear, partly because many members were originally included before the application of a polyphasic taxonomic approach, central to which is the acquisition of 16S rRNA sequence data. This has resulted in the reclassification and description of many new species. Hence, the literature is replete with new species names that have not been brought together in an organized and easily interpreted form. This taxonomic confusion has been compounded by assigning many xenobiotic degrading isolates with phylogenetic positions but without formal taxonomic descriptions. In order to provide a framework for a taxonomic approach based on multiple genetic loci, a survey was undertaken of the known genome characteristics of members of the genus Rhodococcus including: (i) genetics of cell envelope biosynthesis; (ii) virulence genes; (iii) gene clusters involved in metabolic degradation and industrially relevant pathways; (iv) genetic analysis tools; (v) rapid identification of bacteria including rhodococci with specific gene RFLPs; (vi) genomic organization of rrn operons. Genes encoding virulence factors have been characterized for Rhodococcus equi and Rhodococcus fascians. Based on peptide signature comparisons deduced from gene sequences for cytochrome P-450, mono- and dioxygenases, alkane degradation, nitrile metabolism, proteasomes and desulfurization, phylogenetic relationships can be deduced for Rhodococcus erythropolis, Rhodococcus globerulus, Rhodococcus ruber and a number of undesignated Rhodococcus spp. that may distinguish the genus Rhodococcus into two further genera. The linear genome topologies that exist in some Rhodococcus species may alter a previously proposed model for the analysis of genomic fingerprinting techniques used in bacterial systematics.

Actinobacteria↗
PubMed2003

Identification of glycosylphosphatidylinositol-anchored proteins in Arabidopsis. A proteomic and genomic analysis.

In a recent bioinformatic analysis, we predicted the presence of multiple families of cell surface glycosylphosphatidylinositol (GPI)-anchored proteins (GAPs) in Arabidopsis (G.H.H. Borner, D.J. Sherrier, T.J. Stevens, I.T. Arkin, P. Dupree [2002] Plant Physiol 129: 486-499). A number of publications have since demonstrated the importance of predicted GAPs in diverse physiological processes including root development, cell wall integrity, and adhesion. However, direct experimental evidence for their GPI anchoring is mostly lacking. Here, we present the first, to our knowledge, large-scale proteomic identification of plant GAPs. Triton X-114 phase partitioning and sensitivity to phosphatidylinositol-specific phospholipase C were used to prepare GAP-rich fractions from Arabidopsis callus cells. Two-dimensional fluorescence difference gel electrophoresis and one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis demonstrated the existence of a large number of phospholipase C-sensitive Arabidopsis proteins. Using liquid chromatography-tandem mass spectrometry, 30 GAPs were identified, including six beta-1,3 glucanases, five phytocyanins, four fasciclin-like arabinogalactan proteins, four receptor-like proteins, two Hedgehog-interacting-like proteins, two putative glycerophosphodiesterases, a lipid transfer-like protein, a COBRA-like protein, SKU5, and SKS1. These results validate our previous bioinformatic analysis of the Arabidopsis protein database. Using the confirmed GAPs from the proteomic analysis to train the search algorithm, as well as improved genomic annotation, an updated in silico screen yielded 64 new candidates, raising the total to 248 predicted GAPs in Arabidopsis.

Arabidopsis↗
PubMed2002

[Genome analysis of transgenic homozygous line "Minghui 63-Xa21"].

By using rice SSRP, RAPD and AFLP molecular markers, the genome of rice transgenic line "Minghui 63-Xa21" was analyzed. 32 SSRP primers, 42 RAPD primers and 8 AFLP primers could produce obvious PCR bands in the analysis of at least 12 individual plants selected randomly from "Minghui 63-Xa21" T3 generation. Totally 550 PCR bands, equivalent to 550 genomic sites, were detected. Different individual plants of the transgenic homozygous line displayed almost the same PCR pattern. Compared with the control "Minghui 63", no difference was found in their PCR patterns. This indicated that the introduction of Xa21 into the genome of "Minghui 63" did not change these 550 genome sites and their heredity. Very few variant PCR bands were observed in some individual plants from both "Minghui 63-Xa21" and "Minghui 63". However, the variant percentage was equivalent between the transgenic line and the non-transgenic control line.

Chromosome Mapping↗
PubMed2007

Comparative genomic analysis of the mouse and rat amylase multigene family.

The rat and mouse amylase gene families were characterized using sequence data from the UCSC genome assembly. We found that the rat genome contains one amylase-1 and two amylase-2 genes, lying close to one another on the same chromosome. Detailed analysis revealed at least six additional amylase pseudogenes in the rat genome in the region adjacent to the amylase-2 genes. In contrast, the mouse has one amylase-1 gene and five amylase-2 genes; the latter are tandemly and systematically arranged on the same chromosome and were generated by segmental duplication. Detailed analysis revealed that the mouse has two amylase pseudogenes, located 5' to the five amylase-2 segments. Thus, the amylase genes of mouse and rat tend to be amplified; the sequences of some of them are fixed while others have become pseudogenes during evolution. This is the second report of amylase genomic organization in mammals and the first in the rodents.

Amylases↗
PubMed2025

Genomic analysis of the liverpool epidemic strain of pseudomonas aeruginosa infecting persons with cystic fibrosis reveals likely Canadian origins.

INTRODUCTION: The Liverpool Epidemic Strain (LES) of Pseudomonas aeruginosa is one of several known strains to be transmissible between persons with cystic fibrosis (CF) (pwCF) and the only known strain to have infected large proportions of CF populations on two continents. Despite its prevalence, efforts to understand its spread have proven elusive. METHODS: We leveraged a prospective collection of P. aeruginosa isolates from pwCF attending the Southern Alberta Adult CF clinic from 1986 to 2020 to identify all individuals with LES infection. LES isolates collected every 1-2 years from each pwCF were sequenced and compared with 171 published LES genomes by phylogenetic analysis. RESULTS: Of 395 pwCF screened, ten pwCF infected with the LES were identified, from whom 46 LES isolates were sequenced. The earliest LES isolate was recovered in 1986, ∼2 years earlier than the previously oldest published LES isolate recovered in the UK. Phylogenetic analysis identified a diverse set of isolates at the root of the LES phylogeny that formed four clades, one of which gave rise to a "classic LES" clade. Canadian isolates formed a paraphyletic group that included the root of this clade and out of which the UK LES clade emerged. We estimated the date of the most recent common ancestor (MRCA) of the UK LES clade as 1977. CONCLUSIONS: Our study provides genomic evidence in support of a silent epidemic of LES infection occurring in the late 1970s among pwCF first originating in Canada and being spread to the UK, where transmission markedly accelerated.

Humans↗
PubMed2004

The olfactory receptor universe--from whole genome analysis to structure and evolution.

Olfactory receptors (ORs) constitute the largest gene-family in the vertebrate genome. We have attempted to provide a comprehensive view of the OR universe through diverse tools of bioinformatics and computational biology. Among others, we have constructed the Human Olfactory Receptor Data Exploratorium (HORDE, http://bioportal.weizmann.ac.il/HORDE/) as a free online resource, which integrates information on ORs from different species. We studied the genomic organization of 853 human ORs and divided the repertoire into 135 clusters, accessible through our new cluster viewer feature. An analysis of intact and pseudogenized ORs in different clusters, as well as of OR expression patterns, is provided, relevant to OR transcription control. Coding single nucleotide polymorphisms were integrated; these are to be used for genotype-phenotype correlation studies. HORDE allows a unique opportunity for discerning protein structural and functional information of the individual OR proteins. By applying novel data analysis strategies to the >3000 OR genes of mouse, dog and human within HORDE, we have generated a set of refined rhodopsin-based homology models for ORs. For model improvement, we employed a novel analysis of specific positions along the seven transmembrane helices at which prolines generate helix-breaking kinks. The model shows family-specific structural features, including idiosyncratic kink patterns, which lead to significant differences in the inferred odorant binding site structure. Such analyses form a basis for a comprehensive sequence-based classification of OR proteins in terms of potential odorant binding specificities.

Amino Acid Sequence↗
PubMed1996

Chromosome Microdissection-Based Techniques for Genome Analysis

It is now possible to start at a cytogenetically defined position in any eucaryotic genome and proceed toward isolation and identification of candidate genes known to map to that position, taking advantage of the new PCR amplification technology to produce position-specific DNA. The starting material for this very useful exercise is DNA microdissected from standard cytogenetic preparations. Here we describe techniques for acquiring useful samples of such DNA and strategies for the use of chromosome region-specific DNA for gene discovery projects.

Journal Article↗
PubMed2002

Whole genome analysis of the Epiphyas postvittana nucleopolyhedrovirus.

The nucleotide sequence of the Epiphyas postvittana nucleopolyhedrovirus (EppoMNPV) genome has been determined and analysed. The circular dsDNA genome contains 118584 bp, making it the smallest group I NPV sequenced to date. The genome has a G+C content of 40.7% and encodes 136 predicted open reading frames (ORFs), five homologous repeat regions and one unique repeat region. Of the genome, 92.9% encodes predicted ORFs and 2.2% is in repeat regions; the remaining 4.9% of the genome comprises nonrepeat intergenic regions. EppoMNPV encodes homologues of 126 Orgyia pseudotsugata MNPV (OpMNPV) ORFs and 120 Autographa californica MNPV ORFs, with average identities of 64.7 and 53.5%, respectively. Between the four sequenced group I NPVs, 117 ORFs are conserved, whereas 86 ORFs are conserved between all fully sequenced NPVs. A total of 62 ORFs is present in all baculoviruses sequenced to date, with EppoMNPV lacking a homologue of the superoxide dismutase (sod) gene, which has been found in all other fully sequenced baculoviruses. Whole genome phylogenetic analyses of the ten fully sequenced baculoviruses using the sequences of the 62 shared genes, gene content and gene order data sets confirmed that EppoMNPV clusters tightly with OpMNPV in the group I NPVs. The main variation between EppoMNPV and OpMNPV occurs where extra clusters of genes are present in OpMNPV, with sod occurring in one such cluster. EppoMNPV encodes one truncated baculovirus repeated ORF (bro) gene. The only repeated ORFs are the four iap genes. Eight, randomly distributed, unique ORFs were identified on EppoMNPV, none of which show any significant homology to genes in GenBank.

Animals↗
PubMed1990

Genome analysis of Bradyrhizobium japonicum serocluster 123 field isolates by using field inversion gel electrophoresis.

The genomes of 11 Bradyrhizobium japonicum serocluster 123 field isolates were analyzed by using field inversion gel electrophoresis. Genomic fingerprints produced by digestion of intact genomic DNA in agarose plugs with the rare-cutting restriction enzymes AseI, DraI, SpeI, and XbaI showed that the isolates were genetically diverse. Few (30 to 50%) isolates exhibited the same fingerprint as the USDA serogroup strain with which they are antigenically related. Southern hybridization with a nifHD gene probe to the blotted field inversion electrophoresis gels provided further evidence of the relatedness between members of serogroups 123 and 127.

Colony Count, Microbial↗