A framework for human microbiome research

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies

Th2 cells are essential for modulation of vascular repair by allogeneic endothelial cells

Author Manuscript 2011 April 1.Background: Endothelial cells (ECs) embedded within 3-dimensional matrices (MEEC) control lumenal inflammation and intimal hyperplasia when placed in the vascular adventitia. Matrix embedding alters endothelial immunogenicity in vitro. T-helper (Th) cell-driven host immunity is an impediment of allogeneic grafts. We aimed to identify if modulation of Th balance would affect immune compatibility and endothelial regulation of vascular repair in vivo. Methods: Pigs (n = 4/group) underwent carotid artery balloon injury and were left untreated (Group 1) or received perivascular porcine MEEC implants (Group 2), 12 days of cyclosporine A (CsA; Group 3), or MEEC and CsA (Group 4). Host immune reactivity was analyzed after 28 and 90 days. Results: MEEC treatment induced formation of EC-specific immunoglobulin (Ig) G1 antibodies (41 ± 6 mean fluorescence intensity [MFI]) and differentiation of host splenocytes into Th2, but not Th1, cytokine-producing cells (interleukin [IL]-4, 242 ± 102; IL-10, 273 ± 114 number of spots). Concomitant CsA therapy reduced IgG1 antibody frequency (25 ± 2 MFI; p < 0.02) and Th2-cytokine producing splenocytes upon MEEC treatment (IL-4, 157 ± 19; IL-10, 124 ± 26 number of spots; p < 0.05). MEECs inhibited luminal occlusion 28 and 90 days after balloon injury (12 ± 7%) vs untreated controls (68 ± 14%; p < 0.001) but to a lesser extent with concomitant CsA treatment (34 ± 13%; p < 0.02 vs Group 2). Conclusions: MEECs do not induce a significant Th1-driven immune response but do enhance differentiation of splenocytes into cells producing Th2 cytokine. Reduction in this Th2 response reduces the vasoregulatory effects of allogeneic ECs after injury

Evaluation of the cutaneous microbiome in psoriasis

Psoriasis, a highly prevalent disease of humans of unknown cause, is a chronic inflammatory disorder primarily involving skin, with distinctive clinical characteristics. With the newly developed tools that facilitate microbiome research, it now is possible to assess whether the cutaneous microbiome plays a role in the pathogenesis of this disorder. Preliminary data from our studies suggest that the cutaneous microbiome in psoriasis is complex and possibly different from normal. To deal with this complexity, we propose to examine the cutaneous microbiome in relation to psoriasis with explorations at several taxonomic and informatic levels. Our overall objective is to examine how changes in the normal cutaneous microbiome contributes to the pathogenesis of psoriasis. Since causality is complex and often difficult to prove, our overall hypothesis is that there are alterations in the cutaneous microbiome in areas of skin affected by psoriasis in comparison with the range observed in clinically unaffected areas, or in healthy persons. We also hypothesize that the characteristics of the microbiome may affect clinical responses to the immunomodulatory agents used to treat psoriasis. An alternative hypothesis is that effective treatment of psoriasis with systemic immunomodulatory agents will not substantially affect the disordered microbial ecosystem. Such observations would provide evidence for the roles of the microbiota in this disorder. Since an important consideration in microbiome research is the optimal level (e.g. phylum, genus, species, strain, gene) at which to examine a scientific question, and we are not yet certain what are the optimal levels for psoriasis, this also will be examined. Our studies of psoriasis should allow development of both approaches and tools that will have general utility for microbiome research. To test our hypothesis, we propose the following specific aims: 1. To understand the cutaneous microbiome species composition overlaying psoriatic lesions; 2. To investigate differences in metagenome content for psoriatic lesions compared to normal skin; 3. To identify differences in the transcriptional profiles of the microbiome and the host between normal skin and psoriatic lesions using high-throughput sequencing; and 4. To estimate the effects of systemic immunomodulatory therapy for psoriasis on microbiome composition. In total, these studies should help us understand the role of the microbiome in psoriasis pathogenesis

RNA Sequencing-Based Genome Reannotation of the Dermatophyte Arthroderma benhamiae and Characterization of Its Secretome and Whole Gene Expression Profile during Infection.

Dermatophytes are the most common agents of superficial mycoses in humans and animals. The aim of the present investigation was to systematically identify the extracellular, possibly secreted, proteins that are putative virulence factors and antigenic molecules of dermatophytes. A complete gene expression profile of Arthroderma benhamiae was obtained during infection of its natural host (guinea pig) using RNA sequencing (RNA-seq) technology. This profile was completed with those of the fungus cultivated in vitro in two media containing either keratin or soy meal protein as the sole source of nitrogen and in Sabouraud medium. More than 60% of transcripts deduced from RNA-seq data differ from those previously deposited for A. benhamiae. Using these RNA-seq data along with an automatic gene annotation procedure, followed by manual curation, we produced a new annotation of the A. benhamiae genome. This annotation comprised 7,405 coding sequences (CDSs), among which only 2,662 were identical to the currently available annotation, 383 were newly identified, and 15 secreted proteins were manually corrected. The expression profile of genes encoding proteins with a signal peptide in infected guinea pigs was found to be very different from that during in vitro growth when using keratin as the substrate. Especially, the sets of the 12 most highly expressed genes encoding proteases with a signal sequence had only the putative vacuolar aspartic protease gene PEP2 in common, during infection and in keratin medium. The most upregulated gene encoding a secreted protease during infection was that encoding subtilisin SUB6, which is a known major allergen in the related dermatophyte Trichophyton rubrum. IMPORTANCE Dermatophytoses (ringworm, jock itch, athlete's foot, and nail infections) are the most common fungal infections, but their virulence mechanisms are poorly understood. Combining transcriptomic data obtained from growth under various culture conditions with data obtained during infection led to a significantly improved genome annotation. About 65% of the protein-encoding genes predicted with our protocol did not match the existing annotation for A. benhamiae. Comparing gene expression during infection on guinea pigs with keratin degradation in vitro, which is supposed to mimic the host environment, revealed the critical importance of using real in vivo conditions for investigating virulence mechanisms. The analysis of genes expressed in vivo, encoding cell surface and secreted proteins, particularly proteases, led to the identification of new allergen and virulence factor candidates

Simvastatin inhibits TLR8 signaling in primary human monocytes and spontaneous TNF production from rheumatoid synovial membrane cultures

Simvastatin has been shown to have anti-inflammatory effects that are independent of its serum cholesterol lowering action, but the mechanisms by which these anti-inflammatory effects are mediated have not been elucidated. To explore the mechanism involved, the effect of simvastatin on Toll-like receptor (TLR) signalling in primary human monocytes was investigated. A short pre-treatment with simvastatin dose-dependently inhibited the production of tumor necrosis factor-α (TNF) in response to TLR8 (but not TLRs 2, 4, or 5) activation. Statins are known inhibitors of the cholesterol biosynthetic pathway, but intriguingly TLR8 inhibition could not be reversed by addition of mevalonate or geranylgeranyl pyrophosphate; downstream products of cholesterol biosynthesis. TLR8 signalling was examined in HEK 293 cells stably expressing TLR8, where simvastatin inhibited IKKα/β phosphorylation and subsequent NF-κB activation without affecting the pathway to AP-1. Since simvastatin has been reported to have anti-inflammatory effects in RA patients and TLR8 signalling contributes to TNF production in human RA synovial tissue in culture, simvastatin was tested in these cultures. Simvastatin significantly inhibited the spontaneous release of TNF in this model which was not reversed by mevalonate. Together, these results demonstrate a hitherto unrecognized mechanism of simvastatin inhibition of TLR8 signalling that may in part explain its beneficial anti-inflammatory effects

Technological Innovations and Consumer Needs: An Analysis of Mobile Communications Market

Technology, consumer needs, mobile communication, Japa

Supercapacitors Based on c‐ Type Cytochromes Using Conductive Nanostructured Networks of Living Bacteria

Supercapacitors have attracted interest in energy storage because they have the potential to complement or replace batteries. Here, we report that c ‐type cytochromes, naturally immersed in a living, electrically conductive microbial biofilm, greatly enhance the device capacitance by over two orders of magnitude. We employ genetic engineering, protein unfolding and Nernstian modeling for in vivo demonstration of charge storage capacity of c ‐type cytochromes and perform electrochemical impedance spectroscopy, cyclic voltammetry and charge–discharge cycling to confirm the pseudocapacitive, redox nature of biofilm capacitance. The biofilms also show low self‐discharge and good charge/discharge reversibility. The superior electrochemical performance of the biofilm is related to its high abundance of cytochromes, providing large electron storage capacity, its nanostructured network with metallic‐like conductivity, and its porous architecture with hydrous nature, offering prospects for future low cost and environmentally sustainable energy storage devices. Living supercapacitors: The capacitance of an electrode‐based device can be enhanced 100‐fold using the redox chemistry of c ‐type cytochromes naturally embedded in an electrically conductive network of living bacteria (see picture). This study demonstrates the unique survival strategy by metal‐respiring bacteria when electron acceptors are temporarily unavailable and suggests a novel method for supercapacitive energy storage using self‐renewing microbes.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90083/1/cphc_201100865_sm_miscellaneous_information.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/90083/2/463_ftp.pd

Knowledge, attitudes and practice of condom use among the married women in Mirpur area of Dhaka city, Bangladesh

Background: Condom is an important method of family planning and prevention of sexually transmitted infections. Condom is the only contraceptive method that can protect against both pregnancy and sexually transmitted infections. Unprotected sex leads to many unintended pregnancies and sexually transmitted infections (STIs). The family planning saves lives of women and children and improves the quality of life. This study was aimed to assess the knowledge, attitudes and practice of condom use among the married women in Mirpur area of Dhaka city in Bangladesh.Methods: A descriptive cross-sectional study was conducted among the randomly selected sample of 101 women aged 15-49 years from selected areas of Mirpur in Dhaka city of Bangladesh. Pre-designed and pre-tested questionnaire was used to elicit the required information from the study participants using face to face interview. The collected data was analyzed using SPSS 21.0 version.Results: Only 5.9% of the study participants had ever used condom. Most of the study participants (93.1%) considered a condom as an effective method for birth control and prevention of sexually transmitted infections (10.9%). However, 36.6% of them believed that condom use had some harmful effects. The main reason for condom use among the users was for family planning (83.3%) and the rest (16.7%) mentioned that it was due to STIs prevention and family planning. The condom use was found significantly associated with age, educational level, partner’s educational level, socio-economic status, and perceived risk of STIs.Conclusions: The study revealed that the rate of condom use was very low among the study participants. This might be due to lack of knowledge about proper and effective use of condoms, low perception of risk of STIs, misperception about harmful effects of condoms and the use of other family planning methods by respondents

The influence of technology and demand factors on firm size and industrial structure in the DRAM market -- 1973-1988

The focus of this research is on the impact of the diffusion of innovations in integrated circuit technology on the market structure of that industry and the implications of firm strategy for both further innovation and market structure change. The study examines the effects of sustained product innovation over a fifteen-year-period in the DRAM segment of the integrated circuit industry. Assessments are made on first mover advantages, shape of the diffusion curve, and resource needs in a market characterized by an increasingly complex technology. Comparisons are made along the dimensions of number of firms in the market, continuity of the firms and market concentration.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/30210/1/0000600.pd

Microbiota of De-Novo Pediatric IBD : Increased Faecalibacterium Prausnitzii and Reduced Bacterial Diversity in Crohn's But Not in Ulcerative Colitis

ACKNOWLEDGMENTS We are grateful for the expertise of our sequencing provider NewGene and in particular for the support and help of Dr Jonathan Coxhead.Mrs Karen McIntyre and Dr Dagmar Kastner were invaluable in identifying patients for recruitment in Dundee. Mrs Ann Morrice provided administrative support in Aberdeen. Dr Paul Henderson gave helpful comments on the manuscript. We appreciate the generosity of the families who freely gave their time and samples to make this study possible and the theatre staff of all centers who allowed time for sample collection during busy endoscopy lists.Peer reviewedPublisher PD