Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads.

As metagenomic studies move to increasing numbers of samples, communities like the human gut may benefit more from the assembly of abundant microbes in many samples, rather than the exhaustive assembly of fewer samples. We term this approach leaderboard metagenome sequencing. To explore protocol optimization for leaderboard metagenomics in real samples, we introduce a benchmark of library prep and sequencing using internal references generated by synthetic long-read technology, allowing us to evaluate high-throughput library preparation methods against gold-standard reference genomes derived from the samples themselves. We introduce a low-cost protocol for high-throughput library preparation and sequencing

Independent Domestication of Two Old World Cotton Species

Domesticated cotton species provide raw material for the majority of the world\u27s textile industry. Two independent domestication events have been identified in allopolyploid cotton, one in Upland cotton ( Gossypium hirsutum L.) and the other to Egyptian cotton ( Gossypium barbadense L.). However, two diploid cotton species, Gossypium arboreum L. and Gossypium herbaceum L., have been cultivated for several millennia, but their status as independent domesticates has long been in question. Using genome resequencing data, we estimated the global abundance of various repetitive DNAs. We demonstrate that, despite negligible divergence in genome size, the two domesticated diploid cotton species contain different, but compensatory, repeat content and have thus experienced cryptic alterations in repeat abundance despite equivalence in genome size. Evidence of independent origin is bolstered by estimates of divergence times based on molecular evolutionary analysis of f7,000 orthologous genes, for which synonymous substitution rates suggest that G. arboreum and G. herbaceum last shared a common ancestor approximately 0.4–2.5 Ma. These data are incompatible with a shared domestication history during the emergence of agriculture and lead to the conclusion that G. arboreum and G. herbaceum were each domesticated independently

HIV vaccine: it may take two to tango, but no party time yet

A press conference on Thursday September 24 in Bangkok, Thailand, released data that an experimental vaccine provided mild protection against HIV-1 infection. This is the first positive signal of any degree of vaccine efficacy in humans, more than a quarter-century after scientists discovered the virus that causes AIDS. The research was conducted by a team including Thai researchers, the U.S. Army and the U.S. National Institutes of Health. The RV144 Phase III clinical trial, which began in 2003, had been disparaged by many critics as a waste of time and money because each of the two components had been shown to produce no benefit as individual vaccines and because the scientific rationales behind the immunogens were just wrong. It was nevertheless speculated that using them together in the prime-boost scenario could be more effective, with the aim to induce heightened CD4+ cellular immune responses against the viral Envelope protein. This optimism seems to have been validated. In fact, this would not be the first time that the discovery of an effective vaccine relied as much on serendipity as opposed to scientific rationale. On the other hand, many questions remain about the RV144 trial, and these issues will be addressed in this editorial

A theory-based approach to understanding condom errors and problems reported by men attending an STI clinic

The official published version can be accessed from the link below - Copyright @ 2008 Springer VerlagWe employed the information–motivation–behavioral skills (IMB) model to guide an investigation of correlates for correct condom use among 278 adult (18–35 years old) male clients attending a sexually transmitted infection (STI) clinic. An anonymous questionnaire aided by a CD-recording of the questions was administered. Linear Structural Relations Program was used to conduct path analyses of the hypothesized IMB model. Parameter estimates showed that while information did not directly affect behavioral skills, it did have a direct (negative) effect on condom use errors. Motivation had a significant direct (positive) effect on behavioral skills and a significant indirect (positive) effect on condom use errors through behavioral skills. Behavioral skills had a direct (negative) effect on condom use errors. Among men attending a public STI clinic, these findings suggest brief, clinic-based, safer sex programs for men who have sex with women should incorporate activities to convey correct condom use information, instill motivation to use condoms correctly, and directly enhance men’s behavioral skills for correct use of condoms

The Global Ant Genomics Alliance (GAGA)

Peer reviewe

Immunization for HIV-1 Broadly Neutralizing Antibodies in Human Ig Knockin Mice

A subset of individuals infected with HIV-1 develops broadly neutralizing antibodies (bNAbs) that can prevent infection, but it has not yet been possible to elicit these antibodies by immunization. To systematically explore how immunization might be tailored to produce them, we generated mice expressing the predicted germline or mature heavy chains of a potent bNAb to the CD4 binding site (CD4bs) on the HIV-1 envelope glycoprotein (Env). Immunogens specifically designed to activate B cells bearing germline antibodies are required to initiate immune responses, but they do not elicit bNAbs. In contrast, native-like Env trimers fail to activate B cells expressing germline antibodies but elicit bNAbs by selecting for a restricted group of light chains bearing specific somatic mutations that enhance neutralizing activity. The data suggest that vaccination to elicit anti-HIV-1 antibodies will require immunization with a succession of related immunogens

Institutional capacity for health systems research in East and Central African Schools of Public Health: strengthening human and financial resources

BACKGROUND: Despite its importance in providing evidence for health-related policy and decision-making, an insufficient amount of health systems research (HSR) is conducted in low-income countries (LICs). Schools of public health (SPHs) are key stakeholders in HSR. This paper, one in a series of four, examines human and financial resources capacities, policies and organizational support for HSR in seven Africa Hub SPHs in East and Central Africa. METHODS: Capacity assessment done included document analysis to establish staff numbers, qualifications and publications; self-assessment using a tool developed to capture individual perceptions on the capacity for HSR and institutional dialogues. Key informant interviews (KIIs) were held with Deans from each SPH and Ministry of Health and non-governmental officials, focusing on perceptions on capacity of SPHs to engage in HSR, access to funding, and organizational support for HSR. RESULTS: A total of 123 people participated in the self-assessment and 73 KIIs were conducted. Except for the National University of Rwanda and the University of Nairobi SPH, most respondents expressed confidence in the adequacy of staffing levels and HSR-related skills at their SPH. However, most of the researchers operate at individual level with low outputs. The average number of HSR-related publications was only <1 to 3 per staff member over a 6-year period with most of the publications in international journals. There is dependency on external funding for HSR, except for Rwanda, where there was little government funding. We also found that officials from the Ministries of Health often formulate policy based on data generated through ad hoc technical reviews and consultancies, despite their questionable quality. CONCLUSIONS: There exists adequate skilled staff for HSR in the SPHs. However, HSR conducted by individuals, fuelled by Ministries’ of Health tendency to engage individual researchers, undermines institutional capacity. This study underscores the need to form effective multidisciplinary teams to enhance research of immediate and local relevance. Capacity strengthening in the SPH needs to focus on knowledge translation and communication of findings to relevant audiences. Advocacy is needed to influence respective governments to allocate adequate funding for HSR to avoid donor dependency that distorts local research agenda.DFI