Circulating microbial RNA and health

© 2015, Nature Publishing Group. All rights reserved. Measurement of health indicators in the blood is a commonly performed diagnostic procedure. Two blood studies one involving extended observations on the health of an individual by integrative Personal Omics Profiling (iPOP), and the other tracking the impact of Left Ventricular Assist Device (LVAD) placement on nine heart failure patients were examined for the association of change in health status with change in microbial RNA species. Decrease in RNA expression ratios of human to bacteria and viruses accompanying deteriorated conditions was evident in both studies. Despite large between-subject variations in bacterial composition before LVAD implantation among all the patients, on day 180 after the implantation they manifested apparent between-subject bacterial similarity. In the iPOP study three periods, namely, pre-respiratory syncytial virus (RSV) infection with normal blood glucose level, RSV infection with normal blood glucose level, and post-RSV infection with high blood glucose level could be defined. The upsurge of Enterobacteria phage PhiX 174 sensu lato and Escherichia coli gene expression, in which membrane transporters, membrane receptors for environment signalling, carbohydrate catabolic genes and carbohydrate-active enzymes were enriched only throughout the second period, which suggests a potentially overlooked microbial response to or modulation of the host blood glucose level.Link_to_subscribed_fulltex

The association between Yang-Deficient Constitution and clinical outcome of highly active antiretroviral therapy on people living with HIV

Objective. To determine the association between Yang-Deficient Constitution and the clinical outcomes of HIV/AIDS patients who have initiated highly active antiretroviral therapy (HAART). Method. A total of 197 antiretroviral-naive adults who initiated HAART between 2009 and 2011 were recruited. The participants were asked to complete a questionnaire twice to assess their Yang-Deficient Constitution status before HAART. During the study, signs and symptoms and CD4 or CD8 T cell counts were recorded. Routine blood and biochemical tests were conducted. For the patients who were found to have infections, pathologic examination was performed. Statistical test of association of clinical attributes and demographic factors with Yang-Deficient Constitution was conducted. Result. Good test-retest reliability was observed for Yang-Deficient Constitution scoring. The median Yang-Deficient Constitution score of 142 eligible participants was 25. Female (score = 32.14, P < 0.05), hepatotoxicity (32.14, P < 0.1), nephrotoxicity (37.50, P < 0.1), total number of adverse events (P < 0.1), and mortality (39.29, P < 0.05) were associated with Yang-Deficient Consitution, while annual changes or nadir values of CD4 or CD8 T lymphocytes, and newly acquired infections after starting HAART were not. Mortality was also associated with total number of adverse events (P < 0.05), hepatotoxicity (P < 0.05), and nephrotoxicity (P < 0.05). Conclusion. Yang-Deficient Constitution score has a potential to be developed as a predictor for early HIV-related mortality and side effects. The interrelation and underlying mechanisms should be further investigated for evidence-based design of a more appropriate treatment strategy. © 2013 Yuwen Cen et al.Link_to_subscribed_fulltex

The draft genome, transcriptome, and microbiome of Dermatophagoides farinae reveal a broad spectrum of dust mite allergens

© 2014 The Authors. Published by Elsevier Inc. Background A sequenced house dust mite (HDM) genome would advance our understanding of HDM allergens, a common cause of human allergies. Objective We sought to produce an annotated Dermatophagoides farinae draft genome and develop a combined genomic-transcriptomic-proteomic approach for elucidation of HDM allergens. Methods A D farinae draft genome and transcriptome were assembled with high-throughput sequencing, accommodating microbiome sequences. The allergen gene structures were validated by means of Sanger sequencing. The mite's microbiome composition was determined, and the predominant genus was validated immunohistochemically. The allergenicity of a ubiquinol-cytochrome c reductase binding protein homologue was evaluated with immunoblotting, immunosorbent assays, and skin prick tests. Results The full gene structures of 20 canonical allergens and 7 noncanonical allergen homologues were produced. A novel major allergen, ubiquinol-cytochrome c reductase binding protein-like protein, was found and designated Der f 24. All 40 sera samples from patients with mite allergy had IgE antibodies against rDer f 24. Of 10 patients tested, 5 had positive skin reactions. The predominant bacterial genus among 100 identified species was Enterobacter (63.4%). An intron was found in the 13.8-kDa D farinae bacteriolytic enzyme gene, indicating that it is of HDM origin. The Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed a phototransduction pathway in D farinae, as well as thiamine and amino acid synthesis pathways, which is suggestive of an endosymbiotic relationship between D farinae and its microbiome. Conclusion An HDM genome draft produced from genomic, transcriptomic, and proteomic experiments revealed allergen genes and a diverse endosymbiotic microbiome, providing a tool for further identification and characterization of HDM allergens and development of diagnostics and immunotherapeutic vaccines.Link_to_subscribed_fulltex

Involvement of gut microbiome in human health and disease: brief overview, knowledge gaps and research opportunities

Abstract The commensal, symbiotic, and pathogenic microbial community which resides inside our body and on our skin (the human microbiome) can perturb host energy metabolism and immunity, and thus significantly influence development of a variety of human diseases. Therefore, the field has attracted unprecedented attention in the last decade. Although a large amount of data has been generated, there are still many unanswered questions and no universal agreements on how microbiome affects human health have been agreed upon. Consequently, this review was written to provide an updated overview of the rapidly expanding field, with a focus on revealing knowledge gaps and research opportunities. Specifically, the review covered animal physiology, optimal microbiome standard, health intervention by manipulating microbiome, knowledge base building by text mining, microbiota community structure and its implications in human diseases and health monitoring by analyzing microbiome in the blood. The review should enhance interest in conducting novel microbiota investigations that will further improve health and therapy

Parenting style and behavior as longitudinal predictors of adolescent alcohol use

OBJECTIVE: Adolescent alcohol use is a serious problem in Australia and other nations. Longitudinal data on family predictors are valuable to guide parental education efforts. The present study tested Baumrind\u27s proposal that parenting styles are direct predictors of adolescent alcohol use. METHOD: Latent class modeling was used to investigate adolescent perceptions of parenting styles and multivariate regression to examine their predictive effect on the development of adolescent alcohol use. The data set comprised 2,081 secondary school students (55.9% female) from metropolitan Melbourne, Australia, who completed three waves of annual longitudinal data starting in 2004. RESULTS: Baumrind\u27s parenting styles were significant predictors in unadjusted analyses, but these effects were not maintained in multivariate models that also included parenting behavior dimensions. CONCLUSIONS: Family influences on the development of adolescent alcohol use appear to operate more directly through specific family management behaviors rather than through more global parenting styles

Risk of imported Ebola virus disease in China

© 2014 Elsevier Ltd. Background More than 600,000 annual arrivals from Africa, 1.4 billion population and developing health care systems render China at non-negligible risk of imported Ebola virus disease (EVD). Method According to the natural history of EVD, we constructed a deterministic SEIR model. Three published EVD outbreaks in Africa were enrolled to calculate the basic reproduction number (R0) of EVD. Scenarios representing unreported and reported (with n weeks delay) imported EVD in China were simulated to evaluate the effectiveness of interventions assumed to be implemented in different periods of the outbreaks. Results Based on previous Africa outbreak incidence datasets, our mathematical model predicted the basic reproduction number of EVD in the range of 1.53-3.54. Adopting EVD prevalence at 0.04-0.16% from the same datasets and estimated missing information and monitoring rates at 1-10%, a total of 6-194 imported cases were predicted. Be a single case left unidentified/unreported, total attack rate was predicted to reach 60.19%-96.74%. Curve fitting results showed that earlier intervention benefits in exponential and linear decrease in prevalence and duration of outbreak respectively. Conclusion Based on past outbreak experience in China, there is a need to implement an internet-based surveillance and monitoring system in order to reinforce health policy, track suspected cases and protect the general public by timely interventions.Link_to_subscribed_fulltex

Evidence-Based interventions of Norovirus outbreaks in China

Abstract Background In resource-limited settings where laboratory capacity is limited and response strategy is non-specific, delayed or inappropriate intervention against outbreaks of Norovirus (NoV) are common. Here we report interventions of two norovirus outbreaks, which highlight the importance of evidence-based modeling and assessment to identify infection sources and formulate effective response strategies. Methods Spatiotemporal scanning, mathematical and random walk modeling predicted the modes of transmission in the two incidents, which were supported by laboratory results and intervention outcomes. Results Simulation results indicated that contaminated water was 14 to 500 fold more infectious than infected individuals. Asymptomatic individuals were not effective transmitters. School closure for up to a week still could not contain the outbreak unless the duration was extended to 10 or more days. The total attack rates (TARs) for waterborne NoV outbreaks reported in China (n = 3, median = 4.37) were significantly (p < 0.05) lower than worldwide (n = 14, median = 41.34). The low TARs are likely due to the high number of the affected population. Conclusions We found that school closure alone could not contain Norovirus outbreaks. Overlooked personal hygiene may serve as a hotbed for infectious disease transmission. Our results reveal that evidence-based investigations can facilitate timely interventions of Norovirus transmission

Insights into intercontinental spread of Zika virus

<div><p>The epidemic of Zika virus (ZIKV) infection in South America has led to World Health Organization’s declaration of a Public Health Emergency of International Concern. To further inform effective public health policy, an understanding of ZIKV’s transmission mechanisms is crucial. To characterize the intercontinental transmission of ZIKV, we compiled and analyzed more than 250 gene sequences together with their sequence-related geographic and temporal information, sampled across 27 countries spanning from 1947 to 2016. After filtering and selecting appropriate sequences, extensive phylogenetic analyses were performed. Although phylogeographic reconstruction supported the transmission route of the virus in Africa, South-eastern Asia, Oceania and Latin America, we discovered that the Eastern Africa origin of ZIKV was disputable. On a molecular level, purifying selection was found to be largely responsible for the evolution of non-structural protein 5 and envelope protein E. Our dataset and ancestral sequences reconstruction analysis captured previously unidentified amino acid changes during evolution. Finally, based on the estimation of the time to the most recent common ancestors for the non-structural protein 5 gene, we hypothesized potential specific historic events that occurred in the 1940s and might have facilitated the spread of Zika virus from Africa to South-eastern Asia. Our findings provide new insights into the transmission characteristics of ZIKV, while further genetic and serologic studies are warranted to support the design of tailored prevention strategies.</p></div

Zika virus (ZIKV) population dynamics of genetic diversity over time.

<p>The effective estimated population size of virus is shown on y-axis. X-axis shows the time before 2016. The colored area corresponds to the credibility interval based on 95% highest HPD. Mean and median values for relative genetic diversity (y-axis) together with credibility intervals were plotted through time (x-axis). (A) NS5 by African lineage (B) NS5 by South Pacific Rim lineage (C) NS5 (D) ENV (E) NS1 (F) NS3.</p