Bio Saga Headlines

Bio Saga

Friday, April 30, 2010

JGI-Led Team Sequences Frog Genome

A team of researchers led by investigators at the Department of Energy's Joint Genome Institute reported online today in Science that they have sequenced the first amphibian genome: that of the Western clawed frog Xenopus tropicalis.

The international research team used shotgun sequencing to generate a draft version of the X. tropicalis genome, which they then compared with the human and chicken genomes. In the process, they found more than 20,000 protein-coding genes in the frog genome, as well as regions of synteny with humans and chickens, and a slew of transposable element sequences.

And because amphibians diverged from the amniote lineage leading to mammals, birds, and reptiles some 360 million years ago, senior author Daniel Rokhsar, a researcher affiliated with JGI and the University of California at Berkeley, and his co-authors explained, information in the X. tropicalis genome is helping to reconstruct features found in the shared ancestor of these animals and uncovering clues about vertebrate evolution in general.

The African clawed frog X. laevis is commonly used as a laboratory model for studying everything from cell biology to vertebrate embryonic development. But genetic studies of X. laevis have been complicated by the frog's large, duplicated genome.

To bypass this problem, the team decided to first tackle the genome of a related frog species, X. tropicalis, which has a diploid genome that's roughly half the size of the X. laevis genome.

"It will be tremendous to have a high quality sequence of X. tropicalis upon which to build the X. laevis sequence," co-author Richard Harland, a researcher with UC Berkeley's Center for Integrative Genomics, said in a statement.

The team used shotgun sequencing to sequence the roughly 1.7 billion base genome of a female frog from a Nigerian, X. tropicalis inbred line, generating sequence that covered the genome about 7.6 times.

Their subsequent analysis of the genome turned up between 20,000 and 21,000 protein-coding genes. Around 1,700 of these appear to be orthologs of genes previously implicated in human disease, representing some 79 percent of known disease genes.

Among the gene families that appear to be expanded in the genome are an olfactory receptor family found specifically in tetrapods, a protocadherin family, and pheremone and bitter taste receptor families.

The X. tropicalis genome also contained large stretches of synteny with both human and chicken chromosomes, which the team used to help pin down lineage specific fusions and breakpoints.

The researchers used this synteny — along with markers from the frog's genetic map — to arrange scaffolds on the frog's linkage map.

Comparisons between the frog, human, and chicken genomes also provided new clues about amniote and vertebrate evolution. For example, the team estimated that human chromosomes harbor around 22 fusion events and 21 breakage events — far more than the four fusions and single break identified in the chicken genome.

And the researchers concluded that the amniote ancestor likely had 23 or 24 chromosomes — about double the number of chromosomes thought to have existed in vertebrate and eumetazoan ancestors.

"Both the vertebrate and eumetazoan ancestors have been suggested to have had about a dozen large chromosomes," they wrote. "The current analysis indicates that the amniote ancestor had twice as many, suggesting substantial chromosome breakage on the amniotic stem."

The frog genome is also replete with transposable elements, which made up more than a third of the genome sequence, the researchers noted. But whereas most other vertebrate genomes assessed so far contain mainly retrotransposons, nearly three-quarters of the transposable elements in the frog genome are DNA transposons.

Along with its potential for improving researchers' understanding of evolutionary biology, the genome sequence is already providing information about specific processes previously studied in Xenopus, including development and immune system function.

In addition, those involved in the study highlighted the usefulness of the X. tropicalis genome for genetically characterizing the more complex and commonly used model organism X. laevis. Some members of the X. tropicalis genome sequencing team have reportedly applied for a National Institutes of Health grant to facilitate sequencing of the X. laevis genome.

"Given the utility of the frog as a genetic and developmental biology system and the large and increasing amounts of cDNA sequence from the pseudo-tetrapoloid X. laevis, the X. tropicalis reference sequence is well poised to advance our understanding of genome and proteome evolution in general, and vertebrate evolution in particular," the researchers concluded.

PubMed Canada to Store Government-Funded Studies

Canada has started a national online archive that will house papers and data coming from government-funded research, and will be funded by the Canadian Institutes of Health Research.

Modeled on the National Institutes of Health's PubMed Central, the PubMed Central Canada resource was launched to provide Canadians with a free and open national digital repository of peer-reviewed health and life sciences literature, including research funded by CIHR.

PMC Canada was developed through a partnership between the National Research Council's Canada Institute for Scientific and Technical Information (NRC-CISTI), which will build the infrastructure and manage the repository, the US National Library of Medicine, and CIHR.

The resource supports the Policy on Access to Research Outputs, which requires that CIHR grant recipients make their peer-reviewed publications freely accessible online within six months after they are published.

"The global movement to provide barrier-free access to research is gaining strength and with good reason, said Ian Graham, CIHR's VP of Knowledge Translation, in a statement.

"Having desktop access to a searchable, permanent and freely accessible archive of Canadian health research will serve as a valuable resource for researchers, enabling them to translate that knowledge into solutions to important health issues," NRC-CISTI Director General Pam Bjornson added.

The first phase of PMC Canada includes development of a bilingual interface and help desk and a manuscript submission system. The planned second phase of the repository will incorporate a customized web front-end and enhanced reporting and alerting features for system funders and users.

PMC Canada's future development will be guided by an advisory committee that will include health researchers and other stakeholders.

Global biotech sector posted $3.7 billion profit in 2009

Biotech companies return to profitability

Biotechnology companies worldwide turned a profit last year for the first time since at least 1985 due to reduced spending on research and increased revenue.

Profit in the industry was $3.7 billion, compared with a loss of $1.8 billion in 2008, according to a report Wednesday on biotechnology in the United States, Europe, Canada and Australia by London-based Ernst & Young Global. The company has compiled its report annually for 24 years.

Research and development spending in the U.S. fell 13 percent last year, with about two-thirds of companies cutting those expenses as capital for some grew scarcer, said Glen Giovannetti, leader of Ernst & Young's global biotech unit. Sixty percent of European firms reduced research costs.

At the same time, overall sales increased in the industry, driven primarily by a small number of large companies with well-performing existing products, he said.

"What we don't know is whether it was just fat that was cut or if some of these cutbacks in spending got into the muscle," Giovannetti said. "Unfortunately it could be planting the seeds for a slowdown several years out."

The comparisons exclude Genentech, which was fully purchased by Roche Holding in March 2009 for $44 billion. Roche had already owned part of the company.

Celgene, the maker of the cancer treatment Revlimid, spent $794.8 million on research and development last year, down 15 percent from 2008, the company said in a statement. Sales increased 20 percent to $2.57 billion. Amgen, which bought Seattle-based Immunex in 2002 and is now the maker of Enbrel for arthritis and psoriasis, spent $2.86 billion on research and development in 2009, down 5.5 percent from the previous year.

Some larger companies reduced spending to increase efficiency, while smaller ones had to cut costs as they saw less access to capital, Giovannetti said. Though capital raised last year increased 42 percent from 2008 to $23.2 billion, most went to established companies, he said.

The value of mergers and acquisitions in the U.S., excluding Roche-Genentech, decreased by half to $14.1 billion, according to the report. Three of those transactions had a value of more than $1 billion. In Europe, the value of merger and acquisition deals declined 42 percent to $2.37 billion.

"There have been three mergers of large pharmaceutical companies, including Roche-Genentech," Giovannetti said, citing Pfizer's October acquisition of Wyeth for $64.4 billion and Merck's November purchase of Schering-Plough for $51 billion.

"You have fewer potential buyers, and those companies themselves — from a post-merger integration perspective — are looking at rationalizing their own product pipelines and areas of focus."

Wednesday, April 21, 2010

Jobs@Premas Biotech Gurgaon,INDIA

PREMAS Biotech is a cGMP compliant Contract Research And Manufacturing
Services (CRAMS) organization located in IMT-Manesar, Gurgaon near New
Delhi, India. It is formed on the strong foundation of scientific
expertise and technology development that is dedicated to developing
and providing integrated research solutions in the area of life
science research.

Bioinformatics:

MSc or MS or M.Tech in Life Sciences with specialisation in
Bioinformatics with 0-5 years experience in a similar position.
Proficiency in computer languages and bioinformatic applications is
necessary. Experience in microarray data analysis is desirable.
Please send your resume / response by e mail to: praveen.gupta@premasbiotech.com

many other positions of Life sciences are available at the organisations.
Follow the link for more details on them
http://www.premasbiotech.com/opportunities.aspx

courtesy
naturejobs

Monday, April 5, 2010

SBIR Grant Values to Jump for Phase I and II

The Small Business Administration has decided to raise the amount of Small Business Innovation Research program grants in both phases, with Phase I awards increasing from $100,000 to $150,000, and Phase II awards rising from $750,000 to $1 million.

In 2008, SBA initially considered making the increases in the grants in order to catch up with inflation. Following a comments period and analysis, the administration has decided to implement the increases.

The current award value of $100,000 and $750,000 was originally set in 1992. SBA has the authority to increase the amount of the award every five years.

SBA said in an announcement in the Federal Register that adjusting the threshold of awards up to $150,000 and $1 million "adequately offsets the general effects of inflation, maintains a degree of stability and simplicity to the threshold levels, and continues to provide participating agencies with an appropriate degree of flexibility in award size."

In determining the amount of the increases, SBA used information from the Department of Commerce's Bureau of Economic Analysis, including the Biomedical Research and Development Price Index, the GDP Implicit Price Deflator, and the Satellite R&D Account.

Life Science and Informatics

What is this?
is this a new industry?
or a old wine in a new bottle?

Well Life Sciences and Informatics can be anything form computational biology, all omes and omics, core bioinformatics to curation and literature mining, database creation, in the area of biology, chemistry , bio-chem space.

There are number of companies in India and bangalore is the forefront as a major bio-cluster with 20 to 30 companies in this sphere.

now how good are these companies doing?
how good are they in terms of the international markets and how profitable is their business?
what do they do?
their clients?

These are some interesting things that could be discussed in this blog page...

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