Bio Saga Blog - A Chronicle of Life Sciences & Informatics

Background Methods of determining whether or not any particular HIV-1 sequence stems - completely or in part - from some unknown HIV-1 subtype are important for the design of vaccines and molecular detection systems, as well as for epidemiological monitoring. Nevertheless, a single algorithm only, the Branching Index (BI), has been developed for this task so far. Moving along the genome of a query sequence in a sliding window, the BI computes a ratio quantifying how closely the query sequence clusters with a subtype clade. In its current version, however, the BI does not provide predicted boundaries of unknown fragments. Results We have developed  Unknown Subtype Finder  (USF), an algorithm based on a probabilistic model, which automatically determines which parts of an input sequence originate from a subtype yet unknown. The underlying model is based on a simple profile hidden Markov model (pHMM) for each  known  subtype and an additional pHMM for an  unknown...

A group of leading HIV experts call for the exploration of a new approach to treating HIV – one that could ultimately help eradicate the virus– through a collaboration involving academia, industry, government and patient advocates. This new approach to HIV treatment is discussed in a perspective article published in the March 6, 2009 issue of Science . The article, provocatively titled, “The Challenge of a Cure for HIV Infection,” is authored by three academics, Doug Richman, UCSD; David Margolis, UNC; Warner Greene, UCSF; one community advocate, the late Martin Delaney, Project Inform; and two industry scientist leaders Daria Hazuda, Merck; Roger Pomerantz, Tibotec. This diverse group came together to set a goal for the next era in HIV therapeutics – drug free remission – and assemble a coordinated initiative to identify potential interventions and a clinical assessment to reach this goal. The initiative, which the authors coined a “collaboratory,” aims to accelerate the progress of...

Combination antiretroviral therapy (ART) is frequently initiated in resource-limited countries when patients are being treated for tuberculosis. Co-administration of ART and anti-tubercular therapy may be complicated by shared toxicity or adverse drug interactions, according to background information in the article. Rifampicin-based anti-tubercular therapy reduces the plasma concentrations of the antiretroviral agents efavirenz and nevirapine. The virological consequences of these interactions are not well known. Do you want to know more? Be a part of the XTractor community. XTractor is the first of its kind - Literature alert service , that provides manually curated and annotated sentences for the Keywords of user preference. XTractor maps the extracted entities (genes, processes, drugs, diseases etc) to multiple ontologies and enables customized report generation. With XTractor the sentences are categorized into biological significant relationships and it also provides the user w...

Dr. Ronald Collman talks about exciting new discoveries on HIV, the virus that has taken 25 million lives. Dr. Ronald Collman , professor of medicine in microbiology, virus/cell/molecular core director, Penn Center for AIDS Research, University of Pennsylvania.He describes the molecular structure, pathology, and with great insight, the incredible discoveries that might just help us conquer HIV. Listen to the Original audio source

A protein related to heart disease and Alzheimer's is found to be a factor in HIV. The apolipoprotein (apo) E4 isoform has been implicated in neurodegeneration in Alzheimer's disease, cardiovascular disease, and stroke. Now, investigators at the Gladstone Institutes, the University of California, San Francisco, the University of Texas Health Science Center at San Antonio, and the Infectious Disease Clinical Research Program, Uniformed Services University, Bethesda, Maryland have shown that this troubling protein is a risk factor for AIDS progression rates and promotes entry of HIV into cells. Do you want to read more?