Strategically examining the full-genome of dengue virus type 3 in clinical isolates reveals its mutation spectra

BACKGROUND: Previous studies presented the quasispecies spectrum of the envelope region of dengue virus type 3 (DENV-3) from either clinical specimens or field-caught mosquitoes. However, the extent of sequence variation among full genomic sequences of DENV within infected individuals remains largely unknown. RESULTS: Instead of arbitrarily choosing one genomic region in this study, the full genomic consensus sequences of six DENV-3 isolates were used to locate four genomic regions that had a higher potential of sequence heterogeneity at capsid-premembrane (C-prM), envelope (E), nonstructural protein 3 (NS3), and NS5. The extentof sequence heterogeneity revealed by clonal sequencing was genomic region-dependent, whereas the NS3 and NS5 had lower sequence heterogeneity than C-prM and E. Interestingly, the Phylogenetic Analysis by Maximum Likelihood program (PAML) analysis supported that the domain III of E region, the most heterogeneous region analyzed, was under the influence of positive selection. CONCLUSION: This study confirmed previous reports that the most heterogeneous region of the dengue viral genome resided at the envelope region, of which the domain III was under positive selection pressure. Further studies will need to address the influence of these mutations on the overall fitness in different hosts (i.e., mosquito and human) during dengue viral transmission

Body Mass Index–Mortality Relationship in Severe Hypoglycemic Patients With Type 2 Diabetes

AbstractBackgroundHypoglycemia is associated with a higher risk of death. This study analyzed various body mass index (BMI) categories and mortalities of severe hypoglycemic patients with type 2 diabetes mellitus (DM) in a hospital emergency department.MethodsThe study included 566 adults with type 2 diabetes who were admitted to 1 medical center in Taiwan between 2008 and 2009 with a diagnosis of severe hypoglycemia. Mortality data, demographics, clinical characteristics and the Charlson’s Comorbidity Index were obtained from the electronic medical records. Patients were stratified into 4 study groups as determined by the National institute of Health (NiH) and World Health organization classification for BMi, and the demographics were compared using the analysis of variance and χ2 test. Kaplan-Meier’s analysis and the Cox proportional-hazards regression model were used for mortality, and adjusted hazard ratios were adjusted for each BMi category among participants.ResultsAfter controlling for other possible confounding variables, BMI <18.5 kg/m2 was independently associated with low survival rates in the Cox regression analysis of the entire cohort of type 2 DM patients who encountered a hypoglycemic event. Compared to patients with normal BMI, the mortality risk was higher (adjusted hazard ratios = 4.9; 95% confidence interval [CI] = 2.4-9.9) in underweight patients. Infection-related causes of death were observed in 101 cases (69.2%) and were the leading cause of death.ConclusionsAn independent association was observed between BMI less than 18.5 kg/m2 and mortality among type 2 DM patient with severe hypoglycemic episode. Deaths were predominantly infection related

WormBase: a multi-species resource for nematode biology and genomics

WormBase (http://www.wormbase.org/) is the central data repository for information about Caenorhabditis elegans and related nematodes. As a model organism database, WormBase extends beyond the genomic sequence, integrating experimental results with extensively annotated views of the genome. The WormBase Consortium continues to expand the biological scope and utility of WormBase with the inclusion of large-scale genomic analyses, through active data and literature curation, through new analysis and visualization tools, and through refinement of the user interface. Over the past year, the nearly complete genomic sequence and comparative analyses of the closely related species Caenorhabditis briggsae have been integrated into WormBase, including gene predictions, ortholog assignments and a new synteny viewer to display the relationships between the two species. Extensive site-wide refinement of the user interface now provides quick access to the most frequently accessed resources and a consistent browsing experience across the site. Unified single-page views now provide complete summaries of commonly accessed entries like genes. These advances continue to increase the utility of WormBase for C.elegans researchers, as well as for those researchers exploring problems in functional and comparative genomics in the context of a powerful genetic system

An Evaluation of the Additive Effect of Natural Herbal Medicine on SARS or SARS-like Infectious Diseases in 2003: A Randomized, Double-blind, and Controlled Pilot Study

Natural herbal medicine (NHM) has been used to control infectious diseases for thousands of years. In view of the possible beneficial effect of NHM on SARS, we conducted this study to examine whether NHM is of any benefit as a supplementary treatment of SARS or SARS-like infectious disease. This was a randomized, double-blind, placebo-controlled trial. Twenty-eight patients fulfilled the WHO inclusion criteria and our exclusion criteria. All enrolled patients received routine western-medicine treatment. Patients were randomly allocated to one of the three supplementary treatment groups: NHM A (Group A, n = 9) NHM B (Group B, n = 9) or placebo (Group C, n = 10). Chest X-ray was done every 1 or 2 days for every patient. Reading radiologists use a standard 0–3 scoring system (0: no infiltration; 1: focal haziness or even small patchy lesion; 2: ground glass picture; 3: lobar consolidation) according to the severity of infiltration in each lung field (three lung fields in both right and left lungs). The main outcome measurements were the improving chest radiographic scores (IRS) and the duration (days) till improvement (DI). One patient from the placebo group passed away. Patients from NHM A took less days before showing improvement (6.7 ± 1.8) compared with placebo group (11.2 ± 4.9), which showed statistical significance (P = 0.04). The cases were too few to be conclusive, the initial observations seem to indicate NHM appears to be safe in non-criticallly ill patients and clinical trials are feasible in the setting of pandemic outbreaks

GENCODE: producing a reference annotation for ENCODE

BACKGROUND: The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results. RESULTS: The GENCODE gene features are divided into eight different categories of which only the first two (known and novel coding sequence) are confidently predicted to be protein-coding genes. 5' rapid amplification of cDNA ends (RACE) and RT-PCR were used to experimentally verify the initial annotation. Of the 420 coding loci tested, 229 RACE products have been sequenced. They supported 5' extensions of 30 loci and new splice variants in 50 loci. In addition, 46 loci without evidence for a coding sequence were validated, consisting of 31 novel and 15 putative transcripts. We assessed the comprehensiveness of the GENCODE annotation by attempting to validate all the predicted exon boundaries outside the GENCODE annotation. Out of 1,215 tested in a subset of the ENCODE regions, 14 novel exon pairs were validated, only two of them in intergenic regions. CONCLUSION: In total, 487 loci, of which 434 are coding, have been annotated as part of the GENCODE reference set available from the UCSC browser. Comparison of GENCODE annotation with RefSeq and ENSEMBL show only 40% of GENCODE exons are contained within the two sets, which is a reflection of the high number of alternative splice forms with unique exons annotated. Over 50% of coding loci have been experimentally verified by 5' RACE for EGASP and the GENCODE collaboration is continuing to refine its annotation of 1% human genome with the aid of experimental validation

The role of Havana and communities in the manual curation of unfinished vertebrate genomes

Manual annotation&#x202d; (&#x202c;the&#x202d; &#x22;&#x202c;museum&#x202d;&#x22; &#x202c;model of annotation&#x202d;) &#x202c;relies on a small group of specialized curators to catalogue and classify genes according to their functional roles.&#x202d; This&#x202c; is both costly and time consuming and therefore is used only for model organisms with sufficient funding.&#x202d; &#x202c;Smaller research communities often have to rely on other models of annotation,&#x202d; &#x202c;mainly automated annotation&#x202d; (&#x202c;the&#x202d; &#x22;&#x202c;factory&#x202d;&#x22; &#x202c;model,&#x202d; &#x202c;e.g.&#x202d; &#x202c;Ensembl&#x202d;)&#x202c;,&#x202d; &#x202c;and the&#x202d; &#x22;&#x202c;jamboree&#x202d;&#x22; &#x202c;model&#x202d; (&#x202c;in which a group of leading biologists from the community and bioinformaticians come together for a short intensive annotation workshop&#x202d;)&#x202c;.&#x202d; &#x202c;At the Wellcome Trust Sanger Institute&#x202d; (&#x202c;WTSI&#x202d;)&#x202c;,&#x202d; &#x202c;the Havana team provides high quality manual annotation of finished vertebrate genome sequences,&#x202d; &#x202c;namely human,&#x202d; &#x202c;mouse and zebrafish.&#x202d; &#x202c;We also perform the curation of specific finished regions such as the MHC in dog,&#x202d; &#x202c;cow and pig,&#x202d; &#x202c;whose whole genomes have been&#x202d; &#x202c;assembled from unfinished BACs or from whole genome shotgun sequences.&#x202d; &#x202c;In addition,&#x202d; &#x202c;we at Havana have also hosted annotation jamborees for the cow&#x202d; (&#x202c;Bos taurus&#x202d;) &#x202c;and pig&#x202d; (&#x202c;Sus scrofa&#x202d;) &#x202c;genomes.&#x202d; &#x202c;During those sessions,&#x202d; &#x202c;the research community had the opportunity to annotate their genes of interest under expert guidance using the custom written publicly available Otterlace annotation system,&#x202d; &#x202c;and the unified manual annotation guidelines.&#x202d; &#x202c;By making use of the tools and skills acquired during the cow and pig jamborees,&#x202d; &#x202c;the delegates can continue annotating their genomes remotely.&#x202d; &#x202c;For the pig genome,&#x202d; &#x202c;a highly contiguous physical map has been generated by an international effort of four laboratories (available in Pre!Ensembl) and&#x202d; &#x202c;is being used as a substrate for the swine genome sequencing project.&#x202d; &#x202c;Upcoming vertebrate genomes will be sequenced to a high depth coverage with the next generation sequencing technologies&#x202d; (&#x202c;e.g.&#x202d; &#x202c;Illumina,&#x202d; &#x202c;454,&#x202d; &#x202c;SOLiD&#x202d;) &#x202c;but will have the drawback of not being manually finished.&#x202d; &#x202c;Manual annotation will be more accurate than the automated predictions at coping with any assembly problems derived from these high coverage but unfinished&#x202d; (&#x202c;or automatic pre-finished&#x202d;) &#x202c;genomes.&#x202d; &#x202c;Once these inherent assembly errors are corrected and the gene structures are accurately identified with manual annotation,&#x202d; &#x202c;the curated genes will be incorporated and merged with the predicted gene models in Ensembl to provide a unified view of the landscape of vertebrate genomes.&#x202d; &#x202c;I will present an introduction to our manual annotation system and our experience using it for annotation jamborees at the WTSI