Bio Saga Blog - A Chronicle of Life Sciences & Informatics

To design cells to spec, researchers still need better tools. MONDAY, JUNE 20, 2011 BY KATHERINE BOURZAC Last July , scientists created the first " synthetic cell ," an organism that's controlled by a chemically synthesized genome edited on a computer and stitched together in the lab. One year later, biologists at the  Fifth Annual Synthetic Biology  conference at Stanford University are still struggling to take the next step in the field. Holding them back are the vagaries of biology itself, and the expense and time needed to get from idea to engineered organism. While the creation of the synthetic cell, at the J. Craig Venter Institute , hints at a future in which synthetic biologists can redesign living cells to perform whatever tasks they dream up, that goal is still distant. Most research has focused on coaxing microbes to perform tasks that are similar to what they already do, such as transforming sugar into fuels using processes and materials that resemble the on...

A thorough discussion about personal genomics — what it means for the average consumer, the health care system, and the research community often raises more questions than it answers. While the public discourse on genetic privacy can be traced back to the days of the Human Genome Project, only recently has a new era been ushered in thanks to the steady decrease in the cost of DNA sequencing with promises of a tailor-made approach to medical treatment and new discoveries from rich genetic data sets. Depending on whom you ask, personal genetic information should either be protected at all costs as personal property or is merely information fit to published online for the whole world to see and contains nothing more revealing about health than, say, the knowledge that someone smokes. That there is such concern over whether genetic information is more vulnerable to attack or misuse than traditional personal health care records may be an unintended consequence of the hype that touted perso...

DNA sequencing’s first attempt at a personal-computer-like console is about to get a whole lot faster. The Ion Torrent Personal Genome Machine (PGM), launched with much fanfare (and  a Forbes cover ) in December, will be 100 times more powerful than it was at launch by the third quarter, according to Life Technologies, the $3 billion life sciences company that makes it. Life Technologies' Personal Genome Machine That means that the PGM will be able to sequence 1 billion letters of DNA code in two hours, making it much more competitive with a rival machine, the MiSeq, developed by Illumina, which now dominates the sequencing business. Perhaps more importantly, this leap would fulfill the promise made by Ion Torrent founder Jonathan Rothberg, who has promised that because his device relies on the same kind of semiconductor factories used to make Xboxes and iPods its performance will be able to improve 10-fold every six months. As he told me last year: “There isn’t a technology that w...

Initiating sequencing of a set of 60 closely related human genomes to identify novel genetic information relevant to cancer, metabolic and neurological disorders. Through this project, Avesthagen intends to establish a direct link between genes, genetics and the disorders themselves.  The study, led by Avesthagen, a life sciences company based in Bangalore, is being carried out in partnership with Genome Enterprise Limited, a subsidiary of The Genome Analysis Centre (TGAC) on the Norwich Research Park..   The TGAC team, specialists in DNA sequencing and bioinformatics, will use the SOLiD™ 4 next generation sequencing platform from Applied Biosystems, part of Life Technologies, to generate draft sequence, and will collaborate with the Avesthagen’s own bioinformatics experts to analyze and interpret the sequence data It is known that many genes on the human chromosomes may be involved during the manifestation of the above disorders. However, the power of present technologies to...

Using genome sequencing and other strategies, researchers from Pennsylvania State University and elsewhere are finding genetic clues that they say may be useful for selecting Tasmanian devils for breeding programs aimed at saving the animals from extinction. The team used Roche 454 technology to do  de novo  sequencing of two Tasmanian devil genomes, Penn State biochemistry and molecular biology researcher Stephan Schuster said during Roche Applied Science workshop at the Plant and Animal Genomes conference this week. By looking at SNP data in the nuclear and mitochondrial genomes of Tasmanian devils, he explained, the team is tracking down informative markers that they believe may be useful for gauging genetic diversity and managing Tasmanian devil populations through more tailored breeding programs. Do you wish to know more?

A team of researchers from the J. Craig Venter Institute has created the first synthetic organellar genome, using a method called isothermal DNA assembly to construct a synthetic mouse mitochondrial genome from hundreds of overlapping oligonucleotides. The work, published online yesterday in   Nature Methods , is the latest in a series of synthetic biology achievements by the group. JCVI researchers reported in  Science  in 2008  that they had put together four Mycoplasma genitalium  quarter genomes in  Escherichia coli  and yeast to create the first synthetic genome, dubbed  M. genitalium  JCVI-1.0. They later tweaked this process, showing that they could assemble the  synthetic  M. genitalium  genome in a single step in yeast. And earlier this year the team took another step toward synthetic life when they made a synthetic  M. mycoides  genome, transplanted it into another bacterial species,  M. capricolum , ...

A team of UK researchers, funded by the Biotechnology and Biological Sciences Research Council (BBSRC), has publicly released the first sequence coverage of the wheat genome. The release is a step towards a fully annotated genome and makes a significant contribution to efforts to support global food security and to increase the competitiveness of UK farming. The genome sequences released comprise five read-throughs of a reference variety of wheat and give scientists and breeders access to 95% of all wheat genes. This is among the largest genome projects undertaken, and the rapid public release of the data is expected to accelerate significantly the use of the information by wheat breeding companies. The team involved Prof Neil Hall and Dr Anthony Hall at the University of Liverpool, Prof Keith Edwards and Dr Gary Barker at the University of Bristol and Prof Mike Bevan at the John Innes Centre, a BBSRC-funded Institute. The genome data released are in a 'raw' format, comprisin...

In a paper appearing in the early, online edition of the Proceedings of the National Academy of Sciences yesterday, an international research team reported that they have sequenced the genome of the human body louse , Pediculus humanus humanus . In the process, the researchers also generated sequence that helped them piece together the genome of a bacterial symbiont residing in the louse. Together, the two genomes are providing clues about louse adaptations to obligate parasitism on the human body. In addition, those involved say the work may ultimately provide insights needed to pave the way for more targeted control measures. "Understanding the genome should ultimately open up doors to better understanding how to deal with louse populations," co-senior author Barry Pittendrigh, an entomologist at the University of Illinois at Urbana-Champaign, told GenomeWeb Daily News .

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 anima...

The first effort to sequence a complete cancer genome has underscored the power of second-generation sequencing while further establishing the lack of a “killer software app” in the field. In the study, published this week in Nature , a team of 48 scientists at the Genome Center of Washington University and elsewhere sequenced a female patient’s acute myeloid leukemia genome and compared it to the genome of her biopsied skin as well as reference genomes to uncover 10 cancer-associated mutations — eight of which were previously unknown. The team used two high-throughput sequencing platforms — the Illumina Genome Analyzer and the Roche/454 FLX platform — and software tools such as Maq, Cross_Match, BLAT, and Decision Tree analysis. The team also did its own scripting and algorithm development in the course of the project, Rick Wilson, director of the Genome Sequencing Center at Washington University School of Medicine, said. The AML sequencing team applied several established soft...