Comparative genome analysis of Wolbachia strain wAu

BACKGROUND: Wolbachia intracellular bacteria can manipulate the reproduction of their arthropod hosts, including inducing sterility between populations known as cytoplasmic incompatibility (CI). Certain strains have been identified that are unable to induce or rescue CI, including wAu from Drosophila. Genome sequencing and comparison with CI-inducing related strain wMel was undertaken in order to better understand the molecular basis of the phenotype. RESULTS: Although the genomes were broadly similar, several rearrangements were identified, particularly in the prophage regions. Many orthologous genes contained single nucleotide polymorphisms (SNPs) between the two strains, but a subset containing major differences that would likely cause inactivation in wAu were identified, including the absence of the wMel ortholog of a gene recently identified as a CI candidate in a proteomic study. The comparative analyses also focused on a family of transcriptional regulator genes implicated in CI in previous work, and revealed numerous differences between the strains, including those that would have major effects on predicted function. CONCLUSIONS: The study provides support for existing candidates and novel genes that may be involved in CI, and provides a basis for further functional studies to examine the molecular basis of the phenotype

BamView: visualizing and interpretation of next-generation sequencing read alignments.

So-called next-generation sequencing (NGS) has provided the ability to sequence on a massive scale at low cost, enabling biologists to perform powerful experiments and gain insight into biological processes. BamView has been developed to visualize and analyse sequence reads from NGS platforms, which have been aligned to a reference sequence. It is a desktop application for browsing the aligned or mapped reads [Ruffalo, M, LaFramboise, T, Koyutürk, M. Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics 2011;27:2790-6] at different levels of magnification, from nucleotide level, where the base qualities can be seen, to genome or chromosome level where overall coverage is shown. To enable in-depth investigation of NGS data, various views are provided that can be configured to highlight interesting aspects of the data. Multiple read alignment files can be overlaid to compare results from different experiments, and filters can be applied to facilitate the interpretation of the aligned reads. As well as being a standalone application it can be used as an integrated part of the Artemis genome browser, BamView allows the user to study NGS data in the context of the sequence and annotation of the reference genome. Single nucleotide polymorphism (SNP) density and candidate SNP sites can be highlighted and investigated, and read-pair information can be used to discover large structural insertions and deletions. The application will also calculate simple analyses of the read mapping, including reporting the read counts and reads per kilobase per million mapped reads (RPKM) for genes selected by the user

Circlator: automated circularization of genome assemblies using long sequencing reads

The assembly of DNA sequence data is undergoing a renaissance thanks to emerging technologies capable of producing reads tens of kilobases long. Assembling complete bacterial and small eukaryotic genomes is now possible, but the final step of circularizing sequences remains unsolved. Here we present Circlator, the first tool to automate assembly circularization and produce accurate linear representations of circular sequences. Using Pacific Biosciences and Oxford Nanopore data, Circlator correctly circularized 26 of 27 circularizable sequences, comprising 11 chromosomes and 12 plasmids from bacteria, the apicoplast and mitochondrion of Plasmodium falciparum and a human mitochondrion. Circlator is available at http://sanger-pathogens.github.io/circlator/

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

Evolutionary diversification of an ancient gene family (rhs) through C-terminal displacement

<p>Abstract</p> <p>Background</p> <p><it>Rhs </it>genes are prominent features of bacterial genomes that have previously been implicated in genomic rearrangements in <it>E. coli</it>. By comparing <it>rhs </it>repertoires across the Enterobacteriaceae, this study provides a robust explanation of <it>rhs </it>diversification and evolution, and a mechanistic model of how <it>rhs </it>diversity is gained and lost.</p> <p>Results</p> <p><it>Rhs </it>genes are ubiquitous and comprise six structurally distinct lineages within the Enterobacteriaceae. There is considerable intergenomic variation in <it>rhs </it>repertoire; for instance, in <it>Salmonella enterica</it>, <it>rhs </it>are restricted to mobile elements, while in <it>Escherichia coli </it>one <it>rhs </it>lineage has diversified through transposition as older lineages have been deleted. Overall, comparative genomics reveals frequent, independent gene gains and losses, as well as occasional lateral gene transfer, in different genera. Furthermore, we demonstrate that Rhs 'core' domains and variable C-termini are evolutionarily decoupled, and propose that <it>rhs </it>diversity is driven by homologous recombination with circular intermediates. Existing C-termini are displaced by laterally acquired alternatives, creating long arrays of dissociated 'tips' that characterize the appearance of <it>rhs </it>loci.</p> <p>Conclusion</p> <p><it>Rhs </it>repertoires are highly dynamic among Enterobacterial genomes, due to repeated gene gains and losses. In contrast, the primary structures of <it>Rhs </it>genes are evolutionarily conserved, indicating that <it>rhs </it>sequence diversity is driven, not by rapid mutation, but by the relatively slow evolution of novel core/tip combinations. Hence, we predict that a large pool of dissociated <it>rhs </it>C-terminal tips exists episomally and these are potentially transmitted across taxonomic boundaries.</p

Women in contact with the gay and lesbian community in Sydney: Report of the Sydney Women and Sexual Health (SWASH) Survey 2006, 2008, 2010 and 2012

The Sydney Women and Sexual Health (SWASH) survey is run by a collaboration of ACON and researchers at the University of Sydney (prior to 2009, researchers were based at the University of New South Wales). It was first carried out in 1996, initiated by workers from two ACON projects, Women Partners of Gay and Bisexual Men and the Gay and Lesbian Injecting Drug Use Project, who were faced with a lack of empirical evidence on which to base their intervention work. The survey is regularly revised to reflect the needs of the community and knowledge deficits identified through research literature. Over its lifetime, SWASH has become a comprehensive survey of sexual health and wellbeing, violence, mental health and levels of psychological distress, and a number of other important health issues relevant to lesbian, bisexual and queer (LBQ) women, such as tobacco use, illicit drug use, alcohol consumption, and cancer screening behaviours. Where possible, questions have been used from established national surveys such as the Australian Health Survey, National Drug Strategy Household Survey, Australian Study of Health and Relationships, and Australian Longitudinal Survey of Women’s Health. While research on LBQ women’s health and wellbeing has increased since the birth of the survey, epidemiological data on sexual health, mental health, experiences of abuse and violence and behaviours such as screening, illicit drug use, alcohol and smoking that can leave women vulnerable to adverse health outcomes, is still inconsistent. Moreover, as long as the inclusion of sexuality questions in large epidemiological surveys remains patchy or data is reported only by sexuality and not by sexuality and gender, SWASH provides a unique and important source of health-related information about Australian LBQ women. This report presents results from surveys conducted at the Sydney Gay and Lesbian Mardi Gras Fair Day and other community events and venues during the Sydney Gay and Lesbian Mardi Gras seasons in 2006, 2008, 2010 and 2012

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data.

MOTIVATION: High-throughput sequencing (HTS) technologies have made low-cost sequencing of large numbers of samples commonplace. An explosion in the type, not just number, of sequencing experiments has also taken place including genome re-sequencing, population-scale variation detection, whole transcriptome sequencing and genome-wide analysis of protein-bound nucleic acids. RESULTS: We present Artemis as a tool for integrated visualization and computational analysis of different types of HTS datasets in the context of a reference genome and its corresponding annotation. AVAILABILITY: Artemis is freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute websites: http://www.sanger.ac.uk/resources/software/artemis/

Spatiotemporal co-existence of two Mycobacterium ulcerans clonal complexes in the Offin River Valley of Ghana

In recent years, comparative genome sequence analysis of African Mycobacterium ulcerans strains isolated from Buruli ulcer (BU) lesion specimen has revealed a very limited genetic diversity of closely related isolates and a striking association between genotype and geographical origin of the patients. Here, we compared whole genome sequences of five M. ulcerans strains isolated in 2004 or 2013 from BU lesions of four residents of the Offin river valley with 48 strains isolated between 2002 and 2005 from BU lesions of individuals residing in the Densu river valley of Ghana. While all M. ulcerans isolates from the Densu river valley belonged to the same clonal complex, members of two distinct clonal complexes were found in the Offin river valley over space and time. The Offin strains were closely related to genotypes from either the Densu region or from the Asante Akim North district of Ghana. These results point towards an occasional involvement of a mobile reservoir in the transmission of M. ulcerans, enabling the spread of bacteria across different regions

Co-cultivation and transcriptome sequencing of two co-existing fish pathogens Moritella viscosa and Aliivibrio wodanis

Background: Aliivibrio wodanis and Moritella viscosa have often been isolated concurrently from fish with winterulcer disease. Little is known about the interaction between the two bacterial species and how the presence of one bacterial species affects the behaviour of the other. Results: The impact on bacterial growth in co-culture was investigated in vitro, and the presence of A. wodanis has an inhibitorial effect on M. viscosa. Further, we have sequenced the complete genomes of these two marine Gram-negative species, and have performed transcriptome analysis of the bacterial gene expression levels from in vivo samples. Using bacterial implants in the fish abdomen, we demonstrate that the presence of A. wodanis is altering the gene expression levels of M. viscosa compared to when the bacteria are implanted separately. Conclusions: From expression profiling of the transcriptomes, it is evident that the presence of A. wodanis is altering the global gene expression of M. viscosa. Co-cultivation studies showed that A. wodanis is impeding the growth of M. viscosa, and that the inhibitorial effect is not contact-dependen