Bio Saga Blog - A Chronicle of Life Sciences & Informatics

Inching toward the  Dawn of the GATTACA era ! , making up history as we went along.  A group of researchers will use a $2.5 million federal grant to study the ethical and legal implications of providing genetic research results to the relatives of people who donated samples to biobanks, Mayo Clinic said today. The grant from the National Cancer Institute and the National Human Genome Research Institute will fund researchers at Mayo, the University of California, San Francisco, and the University of Minnesota who will study what families prefer, will analyze the legal and ethical issues, and propose recommendations for best practices policies. "Substantial debate surrounds the question of whether researchers have an ethical obligation to return individual research results to genetic relatives of patients, especially when the patient has died, and incidental findings have potential health or reproductive importance for kin," Gloria Petersen, the Purvis and Roberta ...

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...

Avesthagen launches commercial Whole Genome Scanning Bringing Personalized Genomics to your doorstep. Avesthagen will use Affymetrix technology to decipher the association between single nucleotide polymorphisms (SNPs)/ mutation and predisposition to the disease. The DNA chip used by Avesthagen for whole genome scanning features more than 1.8 million markers of genetic variation that include SNPs as well as probes for copy number variation (CNV). A whole genome scan of an individual would provide information to understand his/her own genetic make-up that would lead to an increased awareness about the predisposition to a disease(s). The diseases, which are offered by Avesthagen, include major types of cancer, cardiovascular diseases, diabetes, schizophrenia, Alzheimer’s, asthma, anemia, arthritis and others. The technology platform at Avesthagen is able to interrogate the genetic markers (SNPs and CNVs) across an individual’s genome...

This is no Sci-Fi but reel to real! Yes we can in deed program the DNA for real Now!  Bioinformatics scientists have built two logic gates for what they hope will become a new programming language for drug design as well as chemical and agricultural product engineering. The accomplishment seems hardly noteworthy except that these logic gates are made of E. coli. The two computational switches are based on two strains of the common bacterium. Researchers are now working to assemble them to perform computations. This genetic programming software would resemble any other programming language, says Kevin Clancy, senior staff scientist for bioinformatics at Life Technologies Corp. The Carlsbad, CA, company is funding the work, which is being done by researchers at the UC San Francisco School of Pharmacy. Life Tech plans to commercialize the technology. The software would convert instructions into a DNA sequence to be inserted into a bacterial, yeast or mammal cell. "It allows you ...

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 , ...

Courtesy: Dr Raghava &  Bioclues PubDNA Finder is an online repository to link PubMed Central manuscripts to the sequences of nucleic acids appearing in them. It extends the search capabilities provided by PubMed Central by enabling researchers to perform advanced searches involving sequences of nucleic acids. This includes, among other features, (1) searching for papers mentioning one or more specific sequences of nucleic acids and (2) retrieving the genetic sequences appearing in different articles. These additional query capabilities are provided by a searchable index that was created by using the full text of the 176672 papers available at PubMed Central at the time of writing and the sequences of nucleic acids appearing in them. To automatically  extract the genetic sequences occurring in each paper an original method has been developed. The database is updated monthly by automatically connecting to the PubMed Central FTP site to retrieve and index...

CLC Bio today said that it, along with partners Ion Torrent Systems and Aarhus University Hospital, have received a $2 million grant from the Danish National Advanced Technology Foundation to support a molecular diagnostics collaboration. Under the three-year alliance, the partners aim to develop and integrated hardware and software solution for molecular diagnostics that will utilize high-throughput sequencing. According to CLC Bio, the partners aim to provide faster and more precise DNA-based diagnostics. Earlier this year, Ion Torrent unveiled its Personal Genome Machine, an electronic sequencer last week that reads DNA on a semiconductor chip by measuring the release of hydrogen ions as nucleotides get incorporated by DNA polymerase. The PGM sequencer is a desktop instrument that will cost only $50,000. The Ion PGM sequencer does a single run in about an hour or two. The collaboration will lead to an IT solution that can be used for molecular diagnostics research and for clinical ...

The European Molecular Biology Laboratory (EMBL) has launched a genomics resource called the European Nucleotide Archive (ENA) that consolidates three DNA and RNA sequence databases. EMBL's European Bioinformatics Institute (EMBL-EBI) will host the ENA resource, which is made up of the EMBL Nucleotide Sequence Database, the European Trace Archive, and the Sequence Read Archive (SRA). The European Trace Archive, formerly maintained at the Wellcome Trust Sanger Institute, contains raw data from electrophoresis-based sequencing machines, while the SRA is a new repository for raw data from next-generation, array-based sequencing platforms. The ENA research team plans to launch new features for the resource over the coming year, including enhancements for the browser, improved interactive submissions tools and organism and project-centered portals into ENA data. "ENA has been designed to provide our users with improved access both to annotated and to raw sequence data through the s...

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...

At JGI, we use whole-genome shotgun sequencing. This is a technique for determining the DNA sequence of a genome by randomly shearing the DNA, sequencing multiple fragments whose sequences overlap, and inferring the original sequence by reassembling the fragments. Three sizes of fragments are sequenced, 2-4 kb (kilobase, or 1000 bases), 8-10 kb, and 40 kb. This explanation follows the procedure for 2-4-kb fragments. Animation of the JGI production sequencing process Do you want to know more?

It is true that the DNA has become vernacular now, blogging previously on the Genome entering the drawing rooms in Dawn of the GATTACA era! found another cute, small and interesting article which relates to this interesting fact on how common a word is the "DNA" now When you care enough to send the very best DNA . After reading it i felt in days to come, well we might have MATTEL come out with a "Francis Crick DNA code-breaker toy" fighting and saving the world and a "Craig Venter" toy challenging him...

Biodesign Institute colleague John Chaput is working to give researchers brand new materials to aid their designs. In an article recently published in the Journal of the American Chemical Society, Chaput and his research team have made the first self-assembled nanostructures composed entirely of glycerol nucleic acid (GNA)—a synthetic analog of DNA. “Everyone in DNA nanotechnology is essentially limited by what they can buy off the shelf,” said Chaput, who is also an ASU assistant professor in the Department of Chemistry and Biochemistry. “We wanted to build synthetic molecules that assembled like DNA, but had additional properties not found in natural DNA.” The DNA helix is made up of just three simple parts: a sugar and a phosphate molecule that form the backbone of the DNA ladder, and one of four nitrogenous bases that make up the rungs. The nitrogenous base pairing rules in the DNA chemical alphabet fold DNA into a variety of useful shapes for nanotechnology, given that "A...

By activating a cancer suppressor gene, a small molecule called nutlin-3a can block cancer cell division, according to researchers at the National Cancer Institute (NCI), part of the National Institutes of Health. This activation of the p53 gene leads to cellular senescence. An opportunity for new genetic mutations occurs each time a cell divides, so limiting the number of cell divisions in a cancer cell inhibits tumor progression. Activation of p53 can suppress tumor growth through more than one mechanism. It can interfere with the cell cycle, prompting a cell with unrepaired DNA damage to commit suicide through a complex signaling pathway called apoptosis. Alternatively, p53 may trigger cellular senescence in response to DNA damage or cellular stress. The expression of p53 is regulated by Mdm2, a protein that is overexpressed in several human cancers. Nutlins are small-molecule ...

For the first time in Britain, researchers at Newcastle University said Tuesday they had created human-animal hybrid embryos, amid a political row over a disputed embryo research bill in parliament. According to the northern English university, the research, which was first presented at a lecture in Tel Aviv on March 25, has yet to be published or verified, with a spokesman for the university telling AFP that the institution "wouldn't claim it to be final at all." The revelation comes with British MPs engaged in a fierce battle over the Human Fertilisation and Embryology Bill, which allows the creation of human-animal hybrid embryos for medical research. Prime Minister Gordon Brown's governing Labour Party conceded in March that its party lawmakers with moral or ethical objections would be allowed to vote against parts of the proposed legislation when it comes before parliament this year. The embryos were created by injecting DNA taken from human skin cells into egg...