High-Quality Draft Genome Sequence of Vagococcus lutrae Strain LBD1, Isolated from the Largemouth Bass Micropterus salmoides

Vagococci are usually isolated from marine hosts and occasionally from endodontic infections. Using 16S rRNA gene comparison, the closest relatives are members of the genera Enterococcus and Carnobacterium. A draft sequence of Vagococcus lutrae was generated to clarify the relationship of Vagococcus to these and other related low-G+C Gram-positive bacteria

Elucidation of Beta-Oxidation Pathways in Ralstonia Eutropha H16 by Examination of Global Gene Expression

Ralstonia eutropha H16 is capable of growth and polyhydroxyalkanoate production on plant oils and fatty acids. However, little is known about the triacylglycerol and fatty acid degradation pathways of this bacterium. We compare whole-cell gene expression levels of R. eutropha H16 during growth and polyhydroxyalkanoate production on trioleate and fructose. Trioleate is a triacylglycerol that serves as a model for plant oils. Among the genes of note, two potential fatty acid β-oxidation operons and two putative lipase genes were shown to be upregulated in trioleate cultures. The genes of the glyoxylate bypass also exhibit increased expression during growth on trioleate. We observed that single β-oxidation operon deletion mutants of R. eutropha could grow using palm oil or crude palm kernel oil as the sole carbon source, regardless of which operon was present in the genome, but a double mutant was unable to grow under these conditions. A lipase deletion mutant did not exhibit a growth defect in emulsified oil cultures but did exhibit a phenotype in cultures containing nonemulsified oil. Mutants of the glyoxylate shunt gene for isocitrate lyase were able to grow in the presence of oils, while a malate synthase (aceB) deletion mutant grew more slowly than wild type. Gene expression under polyhydroxyalkanoate storage conditions was also examined. Many findings of this analysis confirm results from previous studies by our group and others. This work represents the first examination of global gene expression involving triacylglycerol and fatty acid catabolism genes in R. eutropha.Malaysia-MIT Biotechnology Partnership Programm

Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii

We acknowledge the Broad Institute Sequencing Platform and Imperial College London for generating the DNA sequence described here (and R265 Illumina sequences described previously [4]). We thank Sinéad Chapman for coordinating sequencing at the Broad Institute and Margaret Priest for assistance in submitting assemblies to NCBI. This project was supported by the National Human Genome Research Institute, grant no. U54HG003067. R.A.F. is supported by the Wellcome Trust. R.C.M. is supported by the Lister Institute for Preventive Medicine, the Medical Research Council UK, and the European Research Council.Peer reviewedPublisher PD

Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop

Improvements in DNA sequencing technologies portend a new era in virology and could possibly lead to a giant leap in our understanding of viral evolution and ecology. Yet, as viral genome sequences begin to fill the world’s biological databases, it is critically important to recognize that the scientific promise of this era is dependent on consistent and comprehensive genome annotation. With this in mind, the NCBI Genome Annotation Workshop recently hosted a study group tasked with developing sequence, function, and metadata annotation standards for viral genomes. This report describes the issues involved in viral genome annotation and reviews policy recommendations presented at the NCBI Annotation Workshop

Comparative Genomics of Recent Shiga Toxin-Producing Escherichia coli O104:H4: Short-Term Evolution of an Emerging Pathogen

The large outbreak of diarrhea and hemolytic uremic syndrome (HUS) caused by Shiga toxin-producing Escherichia coli O104:H4 in Europe from May to July 2011 highlighted the potential of a rarely identified E. coli serogroup to cause severe disease. Prior to the outbreak, there were very few reports of disease caused by this pathogen and thus little known of its diversity and evolution. The identification of cases of HUS caused by E. coli O104:H4 in France and Turkey after the outbreak and with no clear epidemiological links raises questions about whether these sporadic cases are derived from the outbreak. Here, we report genome sequences of five independent isolates from these cases and results of a comparative analysis with historical and 2011 outbreak isolates. These analyses revealed that the five isolates are not derived from the outbreak strain; however, they are more closely related to the outbreak strain and each other than to isolates identified prior to the 2011 outbreak. Over the short time scale represented by these closely related organisms, the majority of genome variation is found within their mobile genetic elements: none of the nine O104:H4 isolates compared here contain the same set of plasmids, and their prophages and genomic islands also differ. Moreover, the presence of closely related HUS-associated E. coli O104:H4 isolates supports the contention that fully virulent O104:H4 isolates are widespread and emphasizes the possibility of future food-borne E. coli O104:H4 outbreaks

Genomics of Loa loa, a Wolbachia-free filarial parasite of humans

Loa loa, the African eyeworm, is a major filarial pathogen of humans. Unlike most filariae, Loa loa does not contain the obligate intracellular Wolbachia endosymbiont. We describe the 91.4 Mb genome of Loa loa, and the genome of the related filarial parasite Wuchereria bancrofti, and predict 14,907 Loa loa genes based on microfilarial RNA sequencing. By comparing these genomes to that of another filarial parasite, Brugia malayi, and to several other nematode genomes, we demonstrate synteny among filariae but not with non-parasitic nematodes. The Loa loa genome encodes many immunologically relevant genes, as well as protein kinases targeted by drugs currently approved for humans. Despite lacking Wolbachia, Loa loa shows no new metabolic synthesis or transport capabilities compared to other filariae. These results suggest that the role played by Wolbachia in filarial biology is more subtle than previously thought and reveal marked differences between parasitic and non-parasitic nematodes

Quantitative MRI evaluation of articular cartilage in patients with meniscus tear

PurposeThe aim of this study was to assess quantitatively articular cartilage volume, thickness, and T2 value alterations in meniscus tear patients.Materials and methodsThe study included 32 patients with meniscus tears (17 females, 15 males; mean age: 40.16 ± 11.85 years) and 24 healthy controls (12 females; 12 males; mean age: 36 ± 9.14 years). All subjects were examined by 3 T magnetic resonance imaging (MRI) with 3D dual-echo steady-state (DESS) and T2 mapping images. All patients underwent diagnostic arthroscopy and treatment. Cartilage thickness, cartilage volume and T2 values of 21 subregions of knee cartilage were measured using the prototype KneeCaP software (version 2.1; Siemens Healthcare, Erlangen, Germany). Mann-Whitney-U tests were utilized to determine if there were any significant differences among subregional articular cartilage volume, thickness and T2 value between patients with meniscus tear and the control group.ResultsThe articular cartilage T2 values in all subregions of the femur and tibia in the meniscus tear group were significantly higher (p< 0.05) than in the healthy control group. The cartilage thickness of the femoral condyle medial, femur trochlea, femur condyle lateral central, tibia plateau medial anterior and patella facet medial inferior in the meniscus tear group were slightly higher than in the control group (p< 0.05). In the femur trochlea medial, patella facet medial inferior, tibia plateau lateral posterior and tibia plateau lateral central, there were significant differences in relative cartilage volume percentage between the meniscus tear group and the healthy control group (p< 0.05). Nineteen patients had no cartilage abnormalities (Grade 0) in the meniscus tear group, as confirmed by arthroscopic surgery, and their T2 values in most subregions were significantly higher (p< 0.05) than those of the healthy control group.ConclusionThe difference in articular cartilage indexes between patients with meniscus tears and healthy people without such tears can be detected by using quantitative MRI. Quantitative T2 values enable early and sensitive detection of early cartilage lesions

Genome analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38–39 Mb genomes include 11,860–14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared t