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11.
Ussery DW 《Genome biology》2006,7(10):237-4
A 'better' Escherichia coli K-12 genome has recently been engineered in which about 15% of the genome has been removed by planned deletions. Comparison with related bacterial genomes that have undergone a natural reduction in size suggests that there is plenty of scope for yet more deletions. 相似文献
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Dawn Field Peter Sterk Renzo Kottmann J. Wim De Smet Linda Amaral-Zettler Guy Cochrane James R. Cole Neil Davies Peter Dawyndt George M. Garrity Jack A. Gilbert Frank Oliver Gl?ckner Lynette Hirschman Hans-Peter Klenk Rob Knight Nikos Kyrpides Folker Meyer Ilene Karsch-Mizrachi Norman Morrison Robert Robbins Inigo San Gil Susanna Sansone Lynn Schriml Tatiana Tatusova Dave Ussery Pelin Yilmaz Owen White John Wooley Gregory Caporaso 《Standards in genomic sciences》2014,9(3):599-601
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The complete genome sequence and analysis of the epsilonproteobacterium Arcobacter butzleri 总被引:1,自引:0,他引:1
Miller WG Parker CT Rubenfield M Mendz GL Wösten MM Ussery DW Stolz JF Binnewies TT Hallin PF Wang G Malek JA Rogosin A Stanker LH Mandrell RE 《PloS one》2007,2(12):e1358
Background
Arcobacter butzleri is a member of the epsilon subdivision of the Proteobacteria and a close taxonomic relative of established pathogens, such as Campylobacter jejuni and Helicobacter pylori. Here we present the complete genome sequence of the human clinical isolate, A. butzleri strain RM4018.Methodology/Principal Findings
Arcobacter butzleri is a member of the Campylobacteraceae, but the majority of its proteome is most similar to those of Sulfuromonas denitrificans and Wolinella succinogenes, both members of the Helicobacteraceae, and those of the deep-sea vent Epsilonproteobacteria Sulfurovum and Nitratiruptor. In addition, many of the genes and pathways described here, e.g. those involved in signal transduction and sulfur metabolism, have been identified previously within the epsilon subdivision only in S. denitrificans, W. succinogenes, Sulfurovum, and/or Nitratiruptor, or are unique to the subdivision. In addition, the analyses indicated also that a substantial proportion of the A. butzleri genome is devoted to growth and survival under diverse environmental conditions, with a large number of respiration-associated proteins, signal transduction and chemotaxis proteins and proteins involved in DNA repair and adaptation. To investigate the genomic diversity of A. butzleri strains, we constructed an A. butzleri DNA microarray comprising 2238 genes from strain RM4018. Comparative genomic indexing analysis of 12 additional A. butzleri strains identified both the core genes of A. butzleri and intraspecies hypervariable regions, where <70% of the genes were present in at least two strains.Conclusion/Significance
The presence of pathways and loci associated often with non-host-associated organisms, as well as genes associated with virulence, suggests that A. butzleri is a free-living, water-borne organism that might be classified rightfully as an emerging pathogen. The genome sequence and analyses presented in this study are an important first step in understanding the physiology and genetics of this organism, which constitutes a bridge between the environment and mammalian hosts. 相似文献17.
Escherichia coli is an important component of the biosphere and is an ideal model for studies of processes involved in bacterial genome evolution. Sixty-one publically available E. coli and Shigella spp. sequenced genomes are compared, using basic methods to produce phylogenetic and proteomics trees, and to identify the pan- and core genomes of this set of sequenced strains. A hierarchical clustering of variable genes allowed clear separation of the strains into clusters, including known pathotypes; clinically relevant serotypes can also be resolved in this way. In contrast, when in silico MLST was performed, many of the various strains appear jumbled and less well resolved. The predicted pan-genome comprises 15,741 gene families, and only 993 (6%) of the families are represented in every genome, comprising the core genome. The variable or ‘accessory’ genes thus make up more than 90% of the pan-genome and about 80% of a typical genome; some of these variable genes tend to be co-localized on genomic islands. The diversity within the species E. coli, and the overlap in gene content between this and related species, suggests a continuum rather than sharp species borders in this group of Enterobacteriaceae. 相似文献
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Eleven completely sequenced Chlorobi genomes were compared in oligonucleotide usage, gene contents, and synteny. The green sulfur bacteria (GSB) are equipped with a core genome that sustains their anoxygenic phototrophic lifestyle by photosynthesis, sulfur oxidation, and CO2 fixation. Whole-genome gene family and single gene sequence comparisons yielded similar phylogenetic trees of the sequenced chromosomes indicating a concerted vertical evolution of large gene sets. Chromosomal synteny of genes is not preserved in the phylum Chlorobi. The accessory genome is characterized by anomalous oligonucleotide usage and endows the strains with individual features for transport, secretion, cell wall, extracellular constituents, and a few elements of the biosynthetic apparatus. Giant genes are a peculiar feature of the genera Chlorobium and Prosthecochloris. The predicted proteins have a huge molecular weight of 106, and are probably instrumental for the bacteria to generate their own intimate (micro)environment. 相似文献
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Lois DW Arnold 《International breastfeeding journal》2006,1(1):1-8
Background
The past ten years have witnessed a rising trend in the prevalence and duration of breastfeeding in Italy, but breastfeeding rates increase in an unequal way; they are higher in the North of Italy than in the South. The purpose of this study was to describe the experiences, expectations and beliefs of a sample of mothers, and to identify differences, if any, between the North and the South of Italy.Methods
The study was conducted in two regions of Italy, Friuli Venezia Giulia in the Northeast and Basilicata in the South. Two hundred and seventy-nine mothers of infants and children 6 to 23 months of age were interviewed using an 85-item questionnaire including closed and open questions on infant feeding experiences and beliefs, sources of information and support, reasons for intended and actual choices and practices, and some demographic and social variables. Face-to-face interviews were conducted between May 2001 and September 2002. Quantitative and qualitative methods were used for data analysis.Results
The distribution of the mothers by age, education, employment and parity did not differ from that of the general population of the two regions. The reported rates of initiation and duration of breastfeeding were also similar: 95% started breastfeeding, exclusive breastfeeding was 32% at three and 9% at six months, with 64% and 35% of any breastfeeding, respectively. Some differences were reported in the rates of full breastfeeding, reflecting different ages of introduction of non-nutritive fluids. These, as well as nutritive fluids – including infant formula – and complementary foods, were introduced far too early. Advice on infant feeding was generally provided by health professionals and often was not based on up-to-date recommendations. Mothers were generally aware of the advantages of breastfeeding, but at the same time reported problems that they were not able to solve alone or through social and health system support. Most mothers would welcome the support of a peer counsellor. More mothers in Basilicata than in Friuli Venezia Giulia reported difficulties with breastfeeding related to returning to work and were not familiar with their rights on breastfeeding and maternity leave.Conclusion
Programmes for the protection, promotion and support of breastfeeding in these and similar regions of Italy should concentrate on better training of health professionals with regards to lactation management, communication, and counselling skills. The addition of trained peer counsellors could reinforce the work done by the health system and, through community involvement, could help change social prejudice in the mid- and long-term. The differences between regions should be taken into account in formulating these programmes to avoid increasing, and possibly to decrease, the current gaps. 相似文献20.
To predict origins of replication in prokaryotic chromosomes, we analyse the leading and lagging strands of 200 chromosomes for differences in oligomer composition and show that these correlate strongly with taxonomic grouping, lifestyle and molecular details of the replication process. While all bacteria have a preference for Gs over Cs on the leading strand, we discover that the direction of the A/T skew is determined by the polymerase-alpha subunit that replicates the leading strand. The strength of the strand bias varies greatly between both phyla and environments and appears to correlate with growth rate. Finally we observe much greater diversity of skew among archaea than among bacteria. We have developed a program that accurately locates the origins of replication by measuring the differences between leading and lagging strand of all oligonucleotides up to 8 bp in length. The program and results for all publicly available genomes are available from http://www.cbs.dtu.dk/services/GenomeAtlas/suppl/origin. 相似文献