BOL: All site news

Accelerating Biology 2014:The Next Wave (18-22 February, 2014)

MineshJ — Mon, 30 Sep 2013 01:36:42 -0500

New advances in biology are being made at a rapidly increasing pace, largely due to new technologies and a large amount of automation. The advent of Next Generation Sequencing (NGS) technology has brought in a new dimension to understand the molecular basis of a living organism. The Next Generation Sequencing technology enables sequencing of hundreds of genomes at an extremely rapid rate and at a significantly lower cost. The availability of hundreds of genomes in a short time is expected to revolutionize area of life sciences. A number of new methods like de-novo sequencing, resequencing, transcriptomics etc. are emerging in the Next Generation Sequencing area. These technologies have a tremendous applications is various areas of Human Health, Agriculture, Livestock and Environment.

The pace of sequencing is leading to a data overload and therefore the ability to analyze is much beyond the existing computing capabilities. This tsunami of data has led to a sea change in the storage and computing requirements. In order to gear up to tackle these challenges most biologists are adopting the use of cyberinfrastructure. Cyberinfrastructure is a combination of data resources, high-speed networks and high performance computing resources that bring people, information and computational resources together to perform science in this information driven world.

The last few decades have witnessed the evolution of biology from what used to be a purely experimental field, to a high end computational domain, where unrelenting computational power is required to decipher pieces of data generated through high throughput techniques into blocks of information that will help to answer many mysteries of life. To be able to generate knowledge from the oceans of genomic data, enabling technologies like High Performance Computing, Grid Computing and Cloud Computing are the latest weapons in the hands of the modern biologist.

This symposium intends to bring together researchers in various domains of human health, agriculture, livestock and environment who are using advanced computational biology tools to solve scientific problems in their respective domains.

More at Accelerating Biology 2013:The Next Wave (20-22 February, 2013) , CDAC, Pune.

Role of microbes in forensic science

Rahul Agarwal — Sun, 29 Sep 2013 10:07:20 -0500

"Studies on decomposing mice suggest that the microbial content of a corpse can offer clues as to how old a body is and the approximate time that death occurred."

Read more: http://www.digitaljournal.com/article/359185#ixzz2gIJFVHRo

http://www.colorado.edu/news/releases/2013/09/24/new-cu-boulder-led-study-finds-%E2%80%98microbial-clock%E2%80%99-may-help-determine-time

Paper:

http://www.elifesciences.org/wp-content/uploads/2013/09/eLife.01104_INPRESS.pdf

OSDDlinux : Computational resources for drug discovery

Archana Malhotra — Sun, 22 Sep 2013 13:15:58 -0500

Open Source Drug Discovery (OSDD), a mission to provide affordable drugs for poors, is in the process of creating an in silico plateform for designing, discovering and simulating drugs. OSDD have initiate number of projects to support in silico drug discovery, including OSDDlinux and computational resources for drug discovery (CRDD).

The main purpose of OSDDLinux is to provide an in silico platform for computer-aided drug design. This is a collection and compilation of large number of software and web services which will be directly or indirectly useful for researches working in the field of drug design/discovery. Overall objective of OSDDlinux is to promote open source in drug discovery, crowdsourcing and network based collobrations. Following are major features of OSDDlinux ...

Find more @ http://osddlinux.osdd.net/index.php

Tigers genome sequenced

Rahul Agarwal — Tue, 17 Sep 2013 16:48:24 -0500

Fifteen scientists led by Dr Jong Bhak of Genome Research Foundation, South Korea, decoded as many as 3 billion nucleotides (organic molecules that form the basic building blocks of nucleic acids, such as DNA). They identified 20,000 genes related to various functions of the tiger.

The biggest and perhaps most fearsome of the world's big cats, the tiger, shares 95.6 percent of its DNA with humans' cute and furry companions, domestic cats.

The new research showed that big cats have genetic mutations that enabled them to be carnivores. The team also identified mutations that allow snow leopards to thrive at high altitudes.

Reference:

http://www.nbcnews.com/science/your-cat-ferocious-tigers-share-lot-95-6-percent-their-4B11182690

http://timesofindia.indiatimes.com/home/environment/flora-fauna/Gene-mapping-of-tiger-completed/articleshow/22671681.cms

Paper:

http://www.nature.com/ncomms/2013/130917/ncomms3433/full/ncomms3433.html

New Vaccine Clears AIDS-Causing Virus in Monkeys

Jit — Tue, 17 Sep 2013 10:57:08 -0500

A newly developed vaccine has the ability to completely kill simian immunodeficiency virus (SIV) in non-human primates, according to scientists at Oregon Health & Science University’s Vaccine and Gene Therapy Institute.

The new approach involves the use of cytomegalovirus, or CMV, a common virus already carried by a large percentage of the population. Dr Picker and his colleagues discovered that pairing CMV with SIV had a unique effect.

Research finding provide compelling evidence for progressive clearance of a pathogenic lentiviral infection, and suggest that some lentiviral reservoirs may be susceptible to the continuous effector memory T-cell-mediated immune surveillance elicited and maintained by cytomegalovirus vectors.

Reference:

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12519.html

http://www.bbc.co.uk/news/science-environment-24051860

Image Source: ucsf.edu

Upcoming R Webinar

Jitendra Narayan — Wed, 11 Sep 2013 10:30:16 -0500

This webinar will describe an R based approach to considerably speed GWAS computation time on a notebook book computer.

More http://www.extension.org/pages/68354/upcoming-webinar:-fast-semi-parallel-linear-and-logistic-regression-for-genome-wide-association-studi#.UjCL9azyPqV

A fast package to parse BLAST

Jitendra Narayan — Tue, 10 Sep 2013 16:58:56 -0500

In current era, we are handling huge amount of genomics data, and analysing it to make some biological sense out of it. Large-scale sequence studies requiring BLAST-based analysis produce huge amounts of data to be parsed. There are several BLAST parsers are available, but they are often missing some important features, such as keeping all information from the raw BLAST output, allowing direct access to single results, and performing logical operations over them.

Massimiliano Orsini and Simone Carcangiu develope a new and fast fast package "BlaSTorage" to parse and store BLAST results. BlaSTorage shows comparable speed of more basic parser written in compiled languages as C++ and can be easily integrated into web applications or software pipelines.

Find more @ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3571973/

http://biowiki.crs4.it/biowiki/MassimilianoOrsini

Fourth Branch of Life

Jitendra Narayan — Mon, 09 Sep 2013 21:48:37 -0500

Scientist have found the biggest viruses known, pandoraviruses which opened up entirely /completely... new questions questions and raise objections to in science. It even suggesting a fourth domain of life.

The new visrus are about one micron—a thousandth of a millimeter—in length, the newfound genus Pandoravirus dwarfs other viruses, which range in size from about 50 nanometers up to 100 nanometers. A genus is a taxonomic ranking between species and family.

Find more at @ http://www.nature.com/scitable/blog/viruses101/newly_found_pandoraviruses_hint_at

http://news.nationalgeographic.co.uk/news/2013/07/130718-viruses-pandoraviruses-science-biology-evolution/

RCSB PDB Sept'13 Release

Jitendra Narayan — Thu, 05 Sep 2013 15:07:48 -0500

RCSB PDB Sept'13 Release offers following new features:

- New tools to search for drugs and drug targets
- Improved interface for 3D visualisation using Jmol/JSmol
- An update to the representation of protein symmetry and stoichiometry.
- Improvements when performing sequence searches.

Reference

http://www.rcsb.org/pdb/static.do?p=general_information/whats_new.jsp?b=1308

Vaccination can be dangerous sometimes !!!

Jit — Thu, 05 Sep 2013 14:54:40 -0500

It is always believed that vaccination is permanent cure from specific diseases, but recent finding suggest something else. A group of scientist led by Surender Khurana discover that Pigs vaccinated against H1N2 influenza were more vulnerable to the rarer H1N1 strain. Which open a new area of discussion, and may give some vaccine developers pause.

The study/research recently published in Science Translational Medicine journal shows, a vaccine for H1N2 spurred pigs to produce antibodies that bound the cap and the stem of that virus’s haemagglutinin. But some of those antibodies also targeted the stem of H1N1’s haemagglutinin protein, helping that virus fuse to cell membranes. That made H1N1 more efficient at infecting pigs and causing disease.

This study suggests a role for fusion-enhancing anti-HA2 antibodies in VAERD, in the absence of receptor-blocking virus-neutralizing antibodies.

Reference:

http://www.nature.com/news/flu-vaccine-backfires-in-pigs-1.13621#/b1

http://stm.sciencemag.org/content/5/200/200ra114