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Search Results: 1 - 10 of 326367 matches for " Georgios S. Vernikos "
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Genetic flux over time in the Salmonella lineage
Georgios S Vernikos, Nicholas R Thomson, Julian Parkhill
Genome Biology , 2007, DOI: 10.1186/gb-2007-8-6-r100
Abstract: From a whole-genome comparative analysis of eleven Salmonella, three Escherichia coli and one Shigella strain, we inferred the relative time of insertion of putative horizontally acquired (PHA) genes in three Salmonella strains on different branches of the S. enterica phylogenetic tree. Compositional analysis suggests that most of the PHA genes are still undergoing an amelioration process and shows a clear correlation between time of insertion and the level of amelioration.The results show that older insertions include almost all functional classes. However, very recent horizontal transfer events in the Salmonella lineage involve primarily prophage elements that are shared only between very recently diverged lineages; despite this, the prophage sequence composition is close to that of the host, indicating that host adaptation, rather than amelioration, is likely to be the source of the compositional similarity. Almost half of the PHA genes were acquired at the base of the Salmonella lineage, whereas nearly three-quarters are shared between most S. enterica subspecies. The numerical distribution of PHA genes in the Salmonella tree topology correlates well with the divergence of the major Salmonella species, highlighting the major impact of horizontal transfer on the evolution of the salmonellae.The divergence of Salmonella and Escherichia coli lineages from their common ancestor has been estimated to have occurred approximately 100-140 million years (Myr) ago [1,2]. Using models of amelioration to estimate the time of horizontal gene transfer (HGT) events it has been previously shown [3] that the entire E. coli chromosome contains more than 600 kb of horizontally transferred, protein-coding DNA. The same authors estimated the HGT rate to be 31 kb per million years, which is close to the point mutation frequency. Under this assumption the E. coli and Salmonella enterica lineages have each gained and lost more than 3 megabases (Mb) of novel DNA since their divergence.D
Identification, variation and transcription of pneumococcal repeat sequences
Nicholas J Croucher, Georgios S Vernikos, Julian Parkhill, Stephen D Bentley
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-120
Abstract: Analysis of the genome of S. pneumoniae ATCC 700669 revealed the presence of a third repeat family, which we have named SPRITE. All three repeats are present at a reduced density in the genome of the closely related species S. mitis. However, they are almost entirely absent from all other streptococci, although a set of elements related to the pneumococcal BOX repeat was identified in the zoonotic pathogen S. suis. In conjunction with information regarding their distribution within the pneumococcal chromosome, this suggests that it is unlikely that these repeats are specialised sequences performing a particular role for the host, but rather that they constitute parasitic elements. However, comparing insertion sites between pneumococcal sequences indicates that they appear to transpose at a much lower rate than IS elements. Some large BOX elements in S. pneumoniae were found to encode open reading frames on both strands of the genome, whilst another was found to form a composite RNA structure with two T box riboswitches. In multiple cases, such BOX elements were demonstrated as being expressed using directional RNA-seq and RT-PCR.BOX, RUP and SPRITE repeats appear to have proliferated extensively throughout the pneumococcal chromosome during the species' past, but novel insertions are currently occurring at a relatively slow rate. Through their extensive secondary structures, they seem likely to affect the expression of genes with which they are co-transcribed. Software for annotation of these repeats is freely available from ftp://ftp.sanger.ac.uk/pub/pathogens/strep_repeats/ webcite.Small interspersed repeats, spatially separated genomic regions of similar sequence typically < 200 bp in length, are frequently found in bacterial chromosomes [1]. These can be classified as either 'simple', when consisting of a single repeated unit, or 'composite', when comprised of a combination of different subsequences arranged in particular patterns [2]. For example, a number of e
GeneViTo: Visualizing gene-product functional and structural features in genomic datasets
Georgios S Vernikos, Christos G Gkogkas, Vasilis J Promponas, Stavros J Hamodrakas
BMC Bioinformatics , 2003, DOI: 10.1186/1471-2105-4-53
Abstract: GeneViTo is a JAVA-based computer application that serves as a workbench for genome-wide analysis through visual interaction. The application deals with various experimental information concerning both DNA and protein sequences (derived from public sequence databases or proprietary data sources) and meta-data obtained by various prediction algorithms, classification schemes or user-defined features. Interaction with a Graphical User Interface (GUI) allows easy extraction of genomic and proteomic data referring to the sequence itself, sequence features, or general structural and functional features. Emphasis is laid on the potential comparison between annotation and prediction data in order to offer a supplement to the provided information, especially in cases of "poor" annotation, or an evaluation of available predictions. Moreover, desired information can be output in high quality JPEG image files for further elaboration and scientific use. A compilation of properly formatted GeneViTo input data for demonstration is available to interested readers for two completely sequenced prokaryotes, Chlamydia trachomatis and Methanococcus jannaschii.GeneViTo offers an inspectional view of genomic functional elements, concerning data stemming both from database annotation and analysis tools for an overall analysis of existing genomes. The application is compatible with Linux or Windows ME-2000-XP operating systems, provided that the appropriate Java Runtime Environment is already installed in the system.The impressive progress in Molecular Biology, enhanced by the development of rapid genome sequencing technologies, led to an exponential growth of the number of available DNA/protein sequences deposited in public databases. Between the early 90's, when the Human Genome Project began, and 1996 the complete genome sequences of 5 unicellular organisms had been determined. By the time of this writing (September 2003) 160 genomes (including the Human Genome) have been completely seq
Independent evolution of the core and accessory gene sets in the genus Neisseria: insights gained from the genome of Neisseria lactamica isolate 020-06
Julia S Bennett, Stephen D Bentley, Georgios S Vernikos, Michael A Quail, Inna Cherevach, Brian White, Julian Parkhill, Martin CJ Maiden
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-652
Abstract: Non-pathogenic N. lactamica exhibits very similar population structure and levels of diversity to the meningococcus, whilst gonococci are essentially recent descendents of a single clone. All three species share a common core gene set estimated to comprise around 1190 CDSs, corresponding to about 60% of the genome. However, some of the nucleotide sequence diversity within this core genome is particular to each group, indicating that cross-species recombination is rare in this shared core gene set. Other than the meningococcal cps region, which encodes the polysaccharide capsule, relatively few members of the large accessory gene pool are exclusive to one species group, and cross-species recombination within this accessory genome is frequent.The three Neisseria species groups represent coherent biological and genetic groupings which appear to be maintained by low rates of inter-species horizontal genetic exchange within the core genome. There is extensive evidence for exchange among positively selected genes and the accessory genome and some evidence of hitch-hiking of housekeeping genes with other loci. It is not possible to define a 'pathogenome' for this group of organisms and the disease causing phenotypes are therefore likely to be complex, polygenic, and different among the various disease-associated phenotypes observed.Comparison of the genomes of related bacteria that exhibit distinct pathogenic phenotypes can identify the genetic traits required for invasion and elucidate key steps in the evolution of virulence. The genus Neisseria, which comprises Gram negative oxidase positive diplococci that colonise the mucosa of humans and animals, provides an excellent model for this type of study as it includes species that are never or rarely pathogenic and two human pathogens of global significance, Neisseria meningitidis (the meningococcus) and Neisseria gonorrhoeae (the gonococcus) [1]. Neisseria lactamica is closely related to the pathogenic Neisseria [2,3] and,
A Common Genomic Framework for a Diverse Assembly of Plasmids in the Symbiotic Nitrogen Fixing Bacteria
Lisa C. Crossman, Santiago Castillo-Ramírez, Craig McAnnula, Luis Lozano, Georgios S. Vernikos, José L. Acosta, Zara F. Ghazoui, Ismael Hernández-González, Georgina Meakin, Alan W. Walker, Michael F. Hynes, J. Peter W. Young, J. Allan Downie, David Romero, Andrew W. B. Johnston, Guillermo Dávila, Julian Parkhill, Víctor González
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0002567
Abstract: This work centres on the genomic comparisons of two closely-related nitrogen-fixing symbiotic bacteria, Rhizobium leguminosarum biovar viciae 3841 and Rhizobium etli CFN42. These strains maintain a stable genomic core that is also common to other rhizobia species plus a very variable and significant accessory component. The chromosomes are highly syntenic, whereas plasmids are related by fewer syntenic blocks and have mosaic structures. The pairs of plasmids p42f-pRL12, p42e-pRL11 and p42b-pRL9 as well large parts of p42c with pRL10 are shown to be similar, whereas the symbiotic plasmids (p42d and pRL10) are structurally unrelated and seem to follow distinct evolutionary paths. Even though purifying selection is acting on the whole genome, the accessory component is evolving more rapidly. This component is constituted largely for proteins for transport of diverse metabolites and elements of external origin. The present analysis allows us to conclude that a heterogeneous and quickly diversifying group of plasmids co-exists in a common genomic framework.
The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants
Lisa C Crossman, Virginia C Gould, J Maxwell Dow, Georgios S Vernikos, Aki Okazaki, Mohammed Sebaihia, David Saunders, Claire Arrowsmith, Tim Carver, Nicholas Peters, Ellen Adlem, Arnaud Kerhornou, Angela Lord, Lee Murphy, Katharine Seeger, Robert Squares, Simon Rutter, Michael A Quail, Mari-Adele Rajandream, David Harris, Carol Churcher, Stephen D Bentley, Julian Parkhill, Nicholas R Thomson, Matthew B Avison
Genome Biology , 2008, DOI: 10.1186/gb-2008-9-4-r74
Abstract: The genome of the bacteremia-associated isolate S. maltophilia K279a is 4,851,126 bp and of high G+C content. The sequence reveals an organism with a remarkable capacity for drug and heavy metal resistance. In addition to a number of genes conferring resistance to antimicrobial drugs of different classes via alternative mechanisms, nine resistance-nodulation-division (RND)-type putative antimicrobial efflux systems are present. Functional genomic analysis confirms a role in drug resistance for several of the novel RND efflux pumps. S. maltophilia possesses potentially mobile regions of DNA and encodes a number of pili and fimbriae likely to be involved in adhesion and biofilm formation that may also contribute to increased antimicrobial drug resistance.The panoply of antimicrobial drug resistance genes and mobile genetic elements found suggests that the organism can act as a reservoir of antimicrobial drug resistance determinants in a clinical environment, which is an issue of considerable concern.The rise of antimicrobial drug resistance in bacteria is one of the biggest threats to healthcare provision in the developed world. Few new antimicrobial drugs are undergoing clinical trials, and almost none are effective against Gram-negative multi-drug resistant (MDR) pathogens [1]. A return to the pre-antibiotic era is a possibility, and for some infections is the current reality [2].Antimicrobial resistance in historically common pathogens is usually either acquired on a mobile genetic element or results from a mutation [3]. However, some opportunistic pathogens are intrinsically resistant to the actions of a number of antimicrobial classes. These tend to be of environmental origin, and their intrinsic drug resistance determinants either provide resistance to antibiotics produced by competitors, or represent broad-spectrum methods for removing toxic compounds or waste products that, by chance, protect against antimicrobials [3,4]. It is known that established opportuni
Liquid Column Deformation and Particle Size Distribution in Gas Atomization  [PDF]
Georgios S. E. Antipas
Materials Sciences and Applications (MSA) , 2011, DOI: 10.4236/msa.2011.22012
Abstract: A water-gas flow injected by a close coupled atomizer was studied via High Speed Photography and Phase Doppler Anemometry. The formation of a wave disturbance on the surface of the water column was confirmed. The flow converged within an area approximately 3 mm in diameter, independent of atomization conditions. The particle size distribution across the spray suggested a trend of decreasing particle sizes and particle velocities with increasing distance from the spray axis of symmetry.
Salmonella bongori Provides Insights into the Evolution of the Salmonellae
Maria Fookes ?,Gunnar N. Schroeder ?,Gemma C. Langridge ?,Carlos J. Blondel,Caterina Mammina,Thomas R. Connor,Helena Seth-Smith,Georgios S. Vernikos,Keith S. Robinson,Mandy Sanders,Nicola K. Petty,Robert A. Kingsley,Andreas J. B?umler,Sean-Paul Nuccio,Inés Contreras,Carlos A. Santiviago,Duncan Maskell,Paul Barrow,Tom Humphrey,Antonino Nastasi,Mark Roberts,Gad Frankel,Julian Parkhill,Gordon Dougan,Nicholas R. Thomson
PLOS Pathogens , 2011, DOI: 10.1371/journal.ppat.1002191
Abstract: The genus Salmonella contains two species, S. bongori and S. enterica. Compared to the well-studied S. enterica there is a marked lack of information regarding the genetic makeup and diversity of S. bongori. S. bongori has been found predominantly associated with cold-blooded animals, but it can infect humans. To define the phylogeny of this species, and compare it to S. enterica, we have sequenced 28 isolates representing most of the known diversity of S. bongori. This cross-species analysis allowed us to confidently differentiate ancestral functions from those acquired following speciation, which include both metabolic and virulence-associated capacities. We show that, although S. bongori inherited a basic set of Salmonella common virulence functions, it has subsequently elaborated on this in a different direction to S. enterica. It is an established feature of S. enterica evolution that the acquisition of the type III secretion systems (T3SS-1 and T3SS-2) has been followed by the sequential acquisition of genes encoding secreted targets, termed effectors proteins. We show that this is also true of S. bongori, which has acquired an array of novel effector proteins (sboA-L). All but two of these effectors have no significant S. enterica homologues and instead are highly similar to those found in enteropathogenic Escherichia coli (EPEC). Remarkably, SboH is found to be a chimeric effector protein, encoded by a fusion of the T3SS-1 effector gene sopA and a gene highly similar to the EPEC effector nleH from enteropathogenic E. coli. We demonstrate that representatives of these new effectors are translocated and that SboH, similarly to NleH, blocks intrinsic apoptotic pathways while being targeted to the mitochondria by the SopA part of the fusion. This work suggests that S. bongori has inherited the ancestral Salmonella virulence gene set, but has adapted by incorporating virulence determinants that resemble those employed by EPEC.
Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens
Mark W Silby, Ana M Cerde?o-Tárraga, Georgios S Vernikos, Stephen R Giddens, Robert W Jackson, Gail M Preston, Xue-Xian Zhang, Christina D Moon, Stefanie M Gehrig, Scott AC Godfrey, Christopher G Knight, Jacob G Malone, Zena Robinson, Andrew J Spiers, Simon Harris, Gregory L Challis, Alice M Yaxley, David Harris, Kathy Seeger, Lee Murphy, Simon Rutter, Rob Squares, Michael A Quail, Elizabeth Saunders, Konstantinos Mavromatis, Thomas S Brettin, Stephen D Bentley, Joanne Hothersall, Elton Stephens, Christopher M Thomas, Julian Parkhill, Stuart B Levy, Paul B Rainey, Nicholas R Thomson
Genome Biology , 2009, DOI: 10.1186/gb-2009-10-5-r51
Abstract: Comparisons of three P. fluorescens genomes (SBW25, Pf0-1, Pf-5) revealed considerable divergence: 61% of genes are shared, the majority located near the replication origin. Phylogenetic and average amino acid identity analyses showed a low overall relationship. A functional screen of SBW25 defined 125 plant-induced genes including a range of functions specific to the plant environment. Orthologues of 83 of these exist in Pf0-1 and Pf-5, with 73 shared by both strains. The P. fluorescens genomes carry numerous complex repetitive DNA sequences, some resembling Miniature Inverted-repeat Transposable Elements (MITEs). In SBW25, repeat density and distribution revealed 'repeat deserts' lacking repeats, covering approximately 40% of the genome.P. fluorescens genomes are highly diverse. Strain-specific regions around the replication terminus suggest genome compartmentalization. The genomic heterogeneity among the three strains is reminiscent of a species complex rather than a single species. That 42% of plant-inducible genes were not shared by all strains reinforces this conclusion and shows that ecological success requires specialized and core functions. The diversity also indicates the significant size of genetic information within the Pseudomonas pan genome.Pseudomonas fluorescens is a physiologically diverse species of opportunistic bacteria (gamma-proteobacteria) found throughout terrestrial habitats. The species contributes greatly to the turnover of organic matter and, while present in soil, is abundant on the surfaces of plant roots and leaves. Of the plant-colonizing strains, some, such as isolates SBW25 and Pf-5, positively affect plant health and nutrition [1-3]. The mechanistic bases of these effects remain unclear, but are known to include the production of plant growth hormones, the suppression of pathogens (especially fungi and oomycetes) detrimental to plant health via competitive and/or allelopathic effects, and the direct elicitation of plant defense res
Spray Forming of al Alloys: experiment and theory
Antipas, Georgios S. E.;
Materials Research , 2012, DOI: 10.1590/S1516-14392012005000007
Abstract: close coupled gas atomization has been studied. pitot tube gas flow measurements support a postulate of transition from an initial sonic to a supersonic and a final sonic state along the convergence region of the jets. predictions of the d50 median diameter utilizing a two phase model for primary and secondary break up correlate strongly with experimental results from he-atomized al alloys by a factor of 0.8216.
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