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ABSTRACT: SummaryA fundamental and unresolved question in fluvial sedimentology concerns the nature of scale invariance and whether it is appropriate to apply data from a single river or outcrop of alluvial sediments to others of a different size. This issue is addressed herein by: (i) examining the similarity in aspects of the morphology of modern braided rivers: (ii) comparing the subsurface facies of three sandy braided rivers of differing scale (30–2000 m channel width), as revealed by ground-penetrating radar (GPR). Measurement of braid-bar shape in 15 rivers, covering four orders of magnitude in spatial scale, demonstrates that a simple index of bar planform shape, the width : length ratio, is scale invariant. Additionally, scour depths at channel confluences are similar in their relative scale across channels of greatly differing size. Comparison of the subsurface sedimentary facies of three sandy braided rivers using GPR demonstrates that sandy braided rivers exhibit a degree of scale invariance, with the ubiquitous occurrence of trough cross-stratification associated with migrating dunes. Significant differences exist in the occurrence of other facies, however, both between rivers and between bars within the same river, most notably in the predominance of either high-angle planar cross-stratification or low-angle stratification. These differences are controlled by a wide range of factors, which may include the discharge regime, local bar and channel topography, anabranch width : depth ratio and the abundance of vegetation. Hence, although rivers and individual bars within the same river may have similar surface planform shapes, their subsurface facies may be very different. A single, universal facies model for sandy braided rivers is thus probably inappropriate and will remain elusive.
03/2009: pages 145 - 158; , ISBN: 9781444304350
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Philip N Ward,
Matthew T G Holden,
James A Leigh,
Nicola Lennard,
Alexandra Bignell,
Andy Barron,
Louise Clark,
Michael A Quail, John Woodward,
Bart G Barrell,
Sharon A Egan,
Terence R Field,
Duncan Maskell,
Michael Kehoe,
Christopher G Dowson,
Neil Chanter,
Adrian M Whatmore,
Stephen D Bentley,
Julian Parkhill
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ABSTRACT: Streptococcus uberis, a Gram positive bacterial pathogen responsible for a significant proportion of bovine mastitis in commercial dairy herds, colonises multiple body sites of the cow including the gut, genital tract and mammary gland. Comparative analysis of the complete genome sequence of S. uberis strain 0140J was undertaken to help elucidate the biology of this effective bovine pathogen.
The genome revealed 1,825 predicted coding sequences (CDSs) of which 62 were identified as pseudogenes or gene fragments. Comparisons with related pyogenic streptococci identified a conserved core (40%) of orthologous CDSs. Intriguingly, S. uberis 0140J displayed a lower number of mobile genetic elements when compared with other pyogenic streptococci, however bacteriophage-derived islands and a putative genomic island were identified. Comparative genomics analysis revealed most similarity to the genomes of Streptococcus agalactiae and Streptococcus equi subsp. zooepidemicus. In contrast, streptococcal orthologs were not identified for 11% of the CDSs, indicating either unique retention of ancestral sequence, or acquisition of sequence from alternative sources. Functions including transport, catabolism, regulation and CDSs encoding cell envelope proteins were over-represented in this unique gene set; a limited array of putative virulence CDSs were identified.
S. uberis utilises nutritional flexibility derived from a diversity of metabolic options to successfully occupy a discrete ecological niche. The features observed in S. uberis are strongly suggestive of an opportunistic pathogen adapted to challenging and changing environmental parameters.
BMC Genomics 02/2009; 10:54. · 4.07 Impact Factor
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Nicholas R Thomson,
Debra J Clayton,
Daniel Windhorst,
Georgios Vernikos,
Susanne Davidson,
Carol Churcher,
Michael A Quail,
Mark Stevens,
Michael A Jones,
Michael Watson, [......],
Karen Mungall,
Mandy Sanders,
Sally Whitehead,
Jose A Chabalgoity,
Duncan Maskell,
Tom Humphrey,
Mark Roberts,
Paul A Barrow,
Gordon Dougan,
Julian Parkhill
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ABSTRACT: We have determined the complete genome sequences of a host-promiscuous Salmonella enterica serovar Enteritidis PT4 isolate P125109 and a chicken-restricted Salmonella enterica serovar Gallinarum isolate 287/91. Genome comparisons between these and other Salmonella isolates indicate that S. Gallinarum 287/91 is a recently evolved descendent of S. Enteritidis. Significantly, the genome of S. Gallinarum has undergone extensive degradation through deletion and pseudogene formation. Comparison of the pseudogenes in S. Gallinarum with those identified previously in other host-adapted bacteria reveals the loss of many common functional traits and provides insights into possible mechanisms of host and tissue adaptation. We propose that experimental analysis in chickens and mice of S. Enteritidis-harboring mutations in functional homologs of the pseudogenes present in S. Gallinarum could provide an experimentally tractable route toward unraveling the genetic basis of host adaptation in S. enterica.
Genome Research 07/2008; 18(10):1624-37. · 13.61 Impact Factor
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Mohammed Sebaihia,
Andrew Preston,
Duncan J Maskell,
Holly Kuzmiak,
Terry D Connell,
Natalie D King,
Paul E Orndorff,
David M Miyamoto,
Nicholas R Thomson,
David Harris,
Arlette Goble,
Angela Lord,
Lee Murphy,
Michael A Quail,
Simon Rutter,
Robert Squares,
Steven Squares, John Woodward,
Julian Parkhill,
Louise M Temple
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ABSTRACT: Bordetella avium is a pathogen of poultry and is phylogenetically distinct from Bordetella bronchiseptica, Bordetella pertussis, and Bordetella parapertussis, which are other species in the Bordetella genus that infect mammals. In order to understand the evolutionary relatedness of Bordetella species and further the understanding of pathogenesis, we obtained the complete genome sequence of B. avium strain 197N, a pathogenic strain that has been extensively studied. With 3,732,255 base pairs of DNA and 3,417 predicted coding sequences, it has the smallest genome and gene complement of the sequenced bordetellae. In this study, the presence or absence of previously reported virulence factors from B. avium was confirmed, and the genetic bases for growth characteristics were elucidated. Over 1,100 genes present in B. avium but not in B. bronchiseptica were identified, and most were predicted to encode surface or secreted proteins that are likely to define an organism adapted to the avian rather than the mammalian respiratory tracts. These include genes coding for the synthesis of a polysaccharide capsule, hemagglutinins, a type I secretion system adjacent to two very large genes for secreted proteins, and unique genes for both lipopolysaccharide and fimbrial biogenesis. Three apparently complete prophages are also present. The BvgAS virulence regulatory system appears to have polymorphisms at a poly(C) tract that is involved in phase variation in other bordetellae. A number of putative iron-regulated outer membrane proteins were predicted from the sequence, and this regulation was confirmed experimentally for five of these.
Journal of Bacteriology 09/2006; 188(16):6002-15. · 3.83 Impact Factor
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William C. Nierman,
Arnab Pain,
Michael J. Anderson,
Jennifer R. Wortman,
H. Stanley Kim,
Javier Arroyo,
Matthew Berriman,
Keietsu Abe,
David B. Archer,
Clara Bermejo, [......],
Owen White, John Woodward,
Jae-Hyuk Yu,
Claire Fraser,
James E. Galagan,
Kiyoshi Asai,
Masayuki Machida,
Neil Hall,
Bart Barrell,
David W. Denning
Nature 01/2006; 439(7075):502-502. · 36.28 Impact Factor
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William C Nierman,
Arnab Pain,
Michael J Anderson,
Jennifer R Wortman,
H Stanley Kim,
Javier Arroyo,
Matthew Berriman,
Keietsu Abe,
David B Archer,
Clara Bermejo, [......],
Owen White, John Woodward,
Jae-Hyuk Yu,
Claire Fraser,
James E Galagan,
Kiyoshi Asai,
Masayuki Machida,
Neil Hall,
Bart Barrell,
David W Denning
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ABSTRACT: Aspergillus fumigatus is exceptional among microorganisms in being both a primary and opportunistic pathogen as well as a major allergen. Its conidia production is prolific, and so human respiratory tract exposure is almost constant. A. fumigatus is isolated from human habitats and vegetable compost heaps. In immunocompromised individuals, the incidence of invasive infection can be as high as 50% and the mortality rate is often about 50% (ref. 2). The interaction of A. fumigatus and other airborne fungi with the immune system is increasingly linked to severe asthma and sinusitis. Although the burden of invasive disease caused by A. fumigatus is substantial, the basic biology of the organism is mostly obscure. Here we show the complete 29.4-megabase genome sequence of the clinical isolate Af293, which consists of eight chromosomes containing 9,926 predicted genes. Microarray analysis revealed temperature-dependent expression of distinct sets of genes, as well as 700 A. fumigatus genes not present or significantly diverged in the closely related sexual species Neosartorya fischeri, many of which may have roles in the pathogenicity phenotype. The Af293 genome sequence provides an unparalleled resource for the future understanding of this remarkable fungus.
Nature 01/2006; 438(7071):1151-6. · 36.28 Impact Factor
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Arnab Pain,
Hubert Renauld,
Matthew Berriman,
Lee Murphy,
Corin A Yeats,
William Weir,
Arnaud Kerhornou,
Martin Aslett,
Richard Bishop,
Christiane Bouchier, [......],
Alan R Walker, John Woodward,
Dirk A E Dobbelaere,
Gordon Langsley,
Marie-Adele Rajandream,
Declan McKeever,
Brian Shiels,
Andrew Tait,
Bart Barrell,
Neil Hall
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ABSTRACT: Theileria annulata and T. parva are closely related protozoan parasites that cause lymphoproliferative diseases of cattle. We sequenced the genome of T. annulata and compared it with that of T. parva to understand the mechanisms underlying transformation and tropism. Despite high conservation of gene sequences and synteny, the analysis reveals unequally expanded gene families and species-specific genes. We also identify divergent families of putative secreted polypeptides that may reduce immune recognition, candidate regulators of host-cell transformation, and a Theileria-specific protein domain [frequently associated in Theileria (FAINT)] present in a large number of secreted proteins.
Science 08/2005; 309(5731):131-3. · 31.20 Impact Factor
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Matthew Berriman,
Elodie Ghedin,
Christiane Hertz-Fowler,
Gaëlle Blandin,
Hubert Renauld,
Daniella C Bartholomeu,
Nicola J Lennard,
Elisabet Caler,
Nancy E Hamlin,
Brian Haas, [......],
Elisabetta Ullu,
J David Barry,
Alan H Fairlamb,
Fred Opperdoes,
Barclay G Barrell,
John E Donelson,
Neil Hall,
Claire M Fraser,
Sara E Melville,
Najib M El-Sayed
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ABSTRACT: African trypanosomes cause human sleeping sickness and livestock trypanosomiasis in sub-Saharan Africa. We present the sequence and analysis of the 11 megabase-sized chromosomes of Trypanosoma brucei. The 26-megabase genome contains 9068 predicted genes, including approximately 900 pseudogenes and approximately 1700 T. brucei-specific genes. Large subtelomeric arrays contain an archive of 806 variant surface glycoprotein (VSG) genes used by the parasite to evade the mammalian immune system. Most VSG genes are pseudogenes, which may be used to generate expressed mosaic genes by ectopic recombination. Comparisons of the cytoskeleton and endocytic trafficking systems with those of humans and other eukaryotic organisms reveal major differences. A comparison of metabolic pathways encoded by the genomes of T. brucei, T. cruzi, and Leishmania major reveals the least overall metabolic capability in T. brucei and the greatest in L. major. Horizontal transfer of genes of bacterial origin has contributed to some of the metabolic differences in these parasites, and a number of novel potential drug targets have been identified.
Science 08/2005; 309(5733):416-22. · 31.20 Impact Factor
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Alasdair C Ivens,
Christopher S Peacock,
Elizabeth A Worthey,
Lee Murphy,
Gautam Aggarwal,
Matthew Berriman,
Ellen Sisk,
Marie-Adele Rajandream,
Ellen Adlem,
Rita Aert, [......],
Tim Warren,
Holger Wedler, John Woodward,
Shiguo Zhou,
Wolfgang Zimmermann,
Deborah F Smith,
Jenefer M Blackwell,
Kenneth D Stuart,
Bart Barrell,
Peter J Myler
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ABSTRACT: Leishmania species cause a spectrum of human diseases in tropical and subtropical regions of the world. We have sequenced the 36 chromosomes of the 32.8-megabase haploid genome of Leishmania major (Friedlin strain) and predict 911 RNA genes, 39 pseudogenes, and 8272 protein-coding genes, of which 36% can be ascribed a putative function. These include genes involved in host-pathogen interactions, such as proteolytic enzymes, and extensive machinery for synthesis of complex surface glycoconjugates. The organization of protein-coding genes into long, strand-specific, polycistronic clusters and lack of general transcription factors in the L. major, Trypanosoma brucei, and Trypanosoma cruzi (Tritryp) genomes suggest that the mechanisms regulating RNA polymerase II-directed transcription are distinct from those operating in other eukaryotes, although the trypanosomatids appear capable of chromatin remodeling. Abundant RNA-binding proteins are encoded in the Tritryp genomes, consistent with active posttranscriptional regulation of gene expression.
Science 08/2005; 309(5733):436-42. · 31.20 Impact Factor
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Ana M Cerdeño-Tárraga,
Sheila Patrick,
Lisa C Crossman,
Garry Blakely,
Val Abratt,
Nicola Lennard,
Ian Poxton,
Brian Duerden,
Barbara Harris,
Mike A Quail, [......],
Natasha Larke,
Alexandra Line,
Angela Lord,
Halina Norbertczak,
Doug Ormond,
Claire Price,
Ester Rabbinowitsch, John Woodward,
Bart Barrell,
Julian Parkhill
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ABSTRACT: The obligately anaerobic bacterium Bacteroides fragilis, an opportunistic pathogen and inhabitant of the normal human colonic microbiota, exhibits considerable within-strain phase and antigenic variation of surface components. The complete genome sequence has revealed an unusual breadth (in number and in effect) of DNA inversion events that potentially control expression of many different components, including surface and secreted components, regulatory molecules, and restriction-modification proteins. Invertible promoters of two different types (12 group 1 and 11 group 2) were identified. One group has inversion crossover (fix) sites similar to the hix sites of Salmonella typhimurium. There are also four independent intergenic shufflons that potentially alter the expression and function of varied genes. The composition of the 10 different polysaccharide biosynthesis gene clusters identified (7 with associated invertible promoters) suggests a mechanism of synthesis similar to the O-antigen capsules of Escherichia coli.
Science 04/2005; 307(5714):1463-5. · 31.20 Impact Factor
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Arnab Pain, John Woodward,
Michael A Quail,
Michael J Anderson,
Richard Clark,
Matthew Collins,
Nigel Fosker,
Audrey Fraser,
David Harris,
Natasha Larke, [......],
Ester Rabbinowitsch,
Marie-Adele Rajandream,
Steven Salzberg,
David Saunders,
Kathy Seeger,
Sarah Sharp,
Tim Warren,
David W Denning,
Bart Barrell,
Neil Hall
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ABSTRACT: Aspergillus fumigatus is the most ubiquitous opportunistic filamentous fungal pathogen of human. As an initial step toward sequencing the entire genome of A. fumigatus, which is estimated to be approximately 30 Mb in size, we have sequenced a 922 kb region, contained within 16 overlapping bacterial artificial chromosome (BAC) clones. Fifty-four percent of the DNA is predicted to be coding with 341 putative protein coding genes. Functional classification of the proteins showed the presence of a higher proportion of enzymes and membrane transporters when compared to those of Saccharomyces cerevisiae. In addition to the nitrate assimilation gene cluster, the quinate utilisation gene cluster is also present on this 922 kb genomic sequence. We observed large scale synteny between A. fumigatus and Aspergillus nidulans by comparing this sequence to the A. nidulans genetic map of linkage group VIII.
Fungal Genetics and Biology 05/2004; 41(4):443-53. · 3.74 Impact Factor
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Arnab Pain, John Woodward,
Michael A Quail,
Michael J Anderson,
Richard Clark,
Matthew Collins,
Nigel Fosker,
Audrey Fraser,
David Harris,
Natasha Larke, [......],
Ester Rabbinowitsch,
Marie-Adele Rajandream,
Steven Salzberg,
David Saunders,
Kathy Seeger,
Sarah Sharp,
Tim Warren,
David W Denning,
Bart Barrell,
Neil Hall
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ABSTRACT: Aspergillus fumigatus is the most ubiquitous opportunistic filamentous fungal pathogen of human. As an initial step toward sequencing the entire genome of A. fumigatus, which is estimated to be ∼30 Mb in size, we have sequenced a 922 kb region, contained within 16 overlapping bacterial artificial chromosome (BAC) clones. Fifty-four percent of the DNA is predicted to be coding with 341 putative protein coding genes. Functional classification of the proteins showed the presence of a higher proportion of enzymes and membrane transporters when compared to those of Saccharomyces cerevisiae. In addition to the nitrate assimilation gene cluster, the quinate utilisation gene cluster is also present on this 922 kb genomic sequence. We observed large scale synteny between A. fumigatus and Aspergillus nidulans by comparing this sequence to the A. nidulans genetic map of linkage group VIII.
Fungal Genetics and Biology.
