Draft genome sequence of the Streptococcus pneumoniae Avery strain A66

We have used HiSeq 2000 technology to generate a draft genome sequence of Streptococcus pneumoniae strain A66. This is a common study strain used in investigations of pneumococcal bacterium-host interactions and was used in the seminal genetic studies of Avery et al

An Interpretation of Late Quaternary Glacial Flow Indicators in the Baie des Chaleurs Region, Northern New Brunswick

A sequence of late Quaternary geologic events in northern New Brunswick is determined from striation analysis derived from published data, open file reports, and field research conducted by the authors since 1985. These data are integrated with clast provenance and clast fabric trend analysis, as well as information from other studies in the surrounding area. South of the Baie des Chaleurs, a complicated Late Wisconsinan glacial history is preserved in the form of erosive features including nailhead striae, miniature crag-and-tails, and various scars, striations, and fractures. The rarity of sedimentary deposits and datable materials precludes simple stratigraphie interpretation. Based on over 1,000 striation sites, we conclude four major phases of glacial flow affected the area during the Late Wisconsinan: 1) an early flow to the southeast which reflects local Appalachian ice; 2) a second phase of glacial flow to the east indicating a Laurentide ice influence in western New Brunswick; 3) a third phase of glacial flow to the north-northeast, which may represent ice response to drawdown in the Baie des Chaleurs; and 4) a final multidirectional flow indicating localized ice response during the last stages of Late Wisconsinan glaciation. The absence of Canadian Shield erratics in northern New Brunswick is explained in terms of ice streaming along the St. Lawrence channel beneath a southward-flowing Laurentide Ice Sheet. Basal ice debris (including Shield erratics) was apparently truncated and removed by the obliquely flowing ice stream, leaving relatively clean ice in the Ice Sheet as it entered Gaspésie and ultimately New Brunswick.On a déterminé la séquence des événements géologiques du Quaternaire supérieur survenus dans le nord du Nouveau-Brunswick à partir de l'analyse des stries tirée de diverses sources. Au sud de la baie des Chaleurs, l'évolution glaciaire complexe du Wisconsinien supérieur peut être retracée à partir des formes d'érosion glaciaire dont les clouures, les crag-and-tails miniatures, les cicatrices de toutes sortes, les stries et les fractures. La rareté des sédiments et des matériaux pouvant être datés excluent toute interprétation fondée sur la stratigraphie. En s'appuyant sur plus de 1000 sites de stries, on croit que la région a connu quatre épisodes glaciaires pendant le Wisconsinien supérieur: 1 ) le premier mouvement, de faible importance, s'est fait vers le SE en provenance des Appalaches; 2) le deuxième écoulement glaciaire vers PE démontre la force des glaces laurentidiennes au nord du Nouveau-Brunswick; 3) le troisième mouvement glaciaire vers le NNE pourrait être une réaction à l'affaissement qui s'est produit dans la baie des Chaleurs; 4) le dernier mouvement multidirectionnel s'est fait à partir de calottes localisées pendant les derniers stades de la glaciation wisconsinienne. On explique l'absence des blocs erratiques dans le nord du Nouveau-Brunswick par un écoulement des glaces le long du chenal laurentien interrompant l'Inlandsis laurentidien s'écoulant vers le sud. Les débris glaciaires de fond (y compris les blocs erratiques du Bouclier) ont apparemment été tronqués et enlevés par un courant glaciaire oblique, épurant ainsi la glace qui pénétrait en Gaspésie, puis au Nouveau-Brunswick.Een Interpretatie van Laat-glaciale Ijsbewegingsindicaties in de Chaleur Bay Regio, Noord New Brunswick. De Kwartair geologische kartering van noord New Brunswick begon met de studies van Robert Chalmers aan het einde van de 19e eeuw. Sindsdien zijn verschillende pogingen gedaan om de glaciale geschiedenis van dit gebied te ontravelen en uiteindelijk zijn Chalmers ideeen herontdekt en aangepast aan moderne theorien en modellen van glaciale processen en isostasie. De afwezigheid van stratigrafische secties en de aanwezigheid van vêle glaciale erosieve en morphologische vormen heeft geleid tot de ontwikkeling van een "erosie-stratigrafie ". Deze informatie wordt gesteund door till lithologische en ges-teente orientatie studies. Het resultaat van dit gedetailleerde karterings project is de her-kenning van 4 verschillende ijs-bewegingen. Datering van deze gebeurtenissen is een probleem vanwege een gebrek aan dateer-bare materialen. Een eerste zuidoostelijke ijsbeweging is geregistreerd in het oostelijke deel van het gebied en in de Chaleur Coastal Plain. De tweede en sterkste gebeurtenis geeft een oostwaartse ijsbeweging te zien, die waarschijnlijk gedurende het gehele Wisconsinan (Weichselien) en mogelijk het gehele Pleistoceen van belang kan zijn geweest. Een derde ijsbeweging is in noord-oostelijke richt-ing in de Baie des Chaleurs. In een latere fase, lokale ijsbewegingen vonden plaats in verschillende richtingen vanaf de hooglanden en mogelijk vanuit Baie des Chaleurs. Er is een poging gedaan deze gebeurtenissen in een régionale context te plaatsen, waarin de interactie van de Laurentide Ice Sheet met het Appalachian Ice Complex en het concept van een Laurentian ijsstroomkanaal centraal staan

Exciton coherence lifetimes from electronic structure

We model the coherent energy transfer of an electronic excitation within covalently linked aromatic homodimers from first-principles, to answer whether the usual models of the bath calculated via detailed electronic structure calculations can reproduce the key dynamics. For these systems the timescales of coherent transport are experimentally known from time-dependent polarization anisotropy measurements, and so we can directly assess the whether current techniques might be predictive for this phenomenon. Two choices of electronic basis states are investigated, and their relative merits discussed regarding the predictions of the perturbative model. The coupling of the electronic degrees of freedom to the nuclear degrees of freedom is calculated rather than assumed, and the fluorescence anisotropy decay is directly reproduced. Surprisingly we find that although TDDFT absolute energies are routinely in error by orders of magnitude more than the coupling energy, the coherent transport properties of these dimers can be semi-quantitatively reproduced from first-principles. The directions which must be pursued to yield predictive and reliable prediction of coherent transport are suggested.Comment: 22 pages, 7 figure

DNAPlotter: circular and linear interactive genome visualization

Summary: DNAPlotter is an interactive Java application for generating circular and linear representations of genomes. Making use of the Artemis libraries to provide a user-friendly method of loading in sequence files (EMBL, GenBank, GFF) as well as data from relational databases, it filters features of interest to display on separate user-definable tracks. It can be used to produce publication quality images for papers or web pages

Genomic Analysis of Companion Rabbit Staphylococcus aureus.

In addition to being an important human pathogen, Staphylococcus aureus is able to cause a variety of infections in numerous other host species. While the S. aureus strains causing infection in several of these hosts have been well characterised, this is not the case for companion rabbits (Oryctolagus cuniculus), where little data are available on S. aureus strains from this host. To address this deficiency we have performed antimicrobial susceptibility testing and genome sequencing on a collection of S. aureus isolates from companion rabbits. The findings show a diverse S. aureus population is able to cause infection in this host, and while antimicrobial resistance was uncommon, the isolates possess a range of known and putative virulence factors consistent with a diverse clinical presentation in companion rabbits including severe abscesses. We additionally show that companion rabbit isolates carry polymorphisms within dltB as described as underlying host-adaption of S. aureus to farmed rabbits. The availability of S. aureus genome sequences from companion rabbits provides an important aid to understanding the pathogenesis of disease in this host and in the clinical management and surveillance of these infections.This project was supported by internal funding from the School of Biological, Biomedical and Environmental Sciences, University of Hull (GKP), a Medical Research Council (MRC) Partnership Grant (G1001787/1) (MAH and JP), and the Wellcome Trust, Grant number 098051 (JP).This is the final version of the article. It first appeared from PLOS via http://dx.doi.org/10.1371/journal.pone.015145

Meningococcal genetic variation mechanisms viewed through comparative analysis of Serogroup C strain FAM18

Copyright @ 2007 Public Library of ScienceThe bacterium Neisseria meningitidis is commonly found harmlessly colonising the mucosal surfaces of the human nasopharynx. Occasionally strains can invade host tissues causing septicaemia and meningitis, making the bacterium a major cause of morbidity and mortality in both the developed and developing world. The species is known to be diverse in many ways, as a product of its natural transformability and of a range of recombination and mutation-based systems. Previous work on pathogenic Neisseria has identified several mechanisms for the generation of diversity of surface structures, including phase variation based on slippage-like mechanisms and sequence conversion of expressed genes using information from silent loci. Comparison of the genome sequences of two N. meningitidis strains, serogroup B MC58 and serogroup A Z2491, suggested further mechanisms of variation, including C-terminal exchange in specific genes and enhanced localised recombination and variation related to repeat arrays. We have sequenced the genome of N. meningitidis strain FAM18, a representative of the ST-11/ET-37 complex, providing the first genome sequence for the disease-causing serogroup C meningococci; it has 1,976 predicted genes, of which 60 do not have orthologues in the previously sequenced serogroup A or B strains. Through genome comparison with Z2491 and MC58 we have further characterised specific mechanisms of genetic variation in N. meningitidis, describing specialised loci for generation of cell surface protein variants and measuring the association between noncoding repeat arrays and sequence variation in flanking genes. Here we provide a detailed view of novel genetic diversification mechanisms in N. meningitidis. Our analysis provides evidence for the hypothesis that the noncoding repeat arrays in neisserial genomes (neisserial intergenic mosaic elements) provide a crucial mechanism for the generation of surface antigen variants. Such variation will have an impact on the interaction with the host tissues, and understanding these mechanisms is important to aid our understanding of the intimate and complex relationship between the human nasopharynx and the meningococcus.This work was supported by the Wellcome Trust through the Beowulf Genomics Initiative

Bioactive ceramic-reinforced composites for bone augmentation

Biomaterials have been used to repair the human body for millennia, but it is only since the 1970s that man-made composites have been used. Hydroxyapatite (HA)-reinforced polyethylene (PE) is the first of the ‘second-generation’ biomaterials that have been developed to be bioactive rather than bioinert. The mechanical properties have been characterized using quasi-static, fatigue, creep and fracture toughness testing, and these studies have allowed optimization of the production method. The in vitro and in vivo biological properties have been investigated with a range of filler content and have shown that the presence of sufficient bioactive filler leads to a bioactive composite. Finally, the material has been applied clinically, initially in the orbital floor and later in the middle ear. From this initial combination of HA in PE other bioactive ceramic polymer composites have been developed

Detection of livestock-associated meticillin-resistant Staphylococcus aureus CC398 in retail pork, United Kingdom, February 2015

No abstract available

Complete Genome Sequence and Comparative Metabolic Profiling of the Prototypical Enteroaggregative Escherichia coli Strain 042

Background \ud Escherichia coli can experience a multifaceted life, in some cases acting as a commensal while in other cases causing intestinal and/or extraintestinal disease. Several studies suggest enteroaggregative E. coli are the predominant cause of E. coli-mediated diarrhea in the developed world and are second only to Campylobacter sp. as a cause of bacterial-mediated diarrhea. Furthermore, enteroaggregative E. coli are a predominant cause of persistent diarrhea in the developing world where infection has been associated with malnourishment and growth retardation. \ud \ud Methods \ud In this study we determined the complete genomic sequence of E. coli 042, the prototypical member of the enteroaggregative E. coli, which has been shown to cause disease in volunteer studies. We performed genomic and phylogenetic comparisons with other E. coli strains revealing previously uncharacterised virulence factors including a variety of secreted proteins and a capsular polysaccharide biosynthetic locus. In addition, by using Biolog™ Phenotype Microarrays we have provided a full metabolic profiling of E. coli 042 and the non-pathogenic lab strain E. coli K-12. We have highlighted the genetic basis for many of the metabolic differences between E. coli 042 and E. coli K-12. \ud \ud Conclusion \ud This study provides a genetic context for the vast amount of experimental and epidemiological data published thus far and provides a template for future diagnostic and intervention strategies