Bio Saga Blog - A Chronicle of Life Sciences & Informatics

This is really getting interesting, BioSaga is making history as we keep blogging! The  GATTACA SAGA ! is coming to an reality! The Race has just begun! today for  Olympian Genes; tomorrow may be for a pianist with pair of hands with 6 fingers each!  There is now no limt to the human imagination there could be a new profession  as GENE ARCHITECT or a GENOME SCULPTOR!  Beginning in 2015, Uzbekistan says it will incorporate genetic testing into its search for Olympic athletes, the Atlantic reports. Rustam Muhamedov from Uzbekistan's Institute of Bioorganic Chemistry's genetics laboratory notes that he and his colleagues have been studying the genes of Uzbek athletes and are working on developing a set of 50 genes to determine what sport a child is best suited for. "Developed countries throughout the world like the United States, China, and European countries are researching the human genome and have discovered genes that define a...

O ne more story in our very own GATTACA SAGA ! Patient advocacy groups Global Genes and Swan USA announced on Tuesday a program to provide whole-exome sequencing to patients with rare diseases who cannot afford such services. Beginning March 1, Global Genes and Swan USA will provide funding for the whole-exome sequencing of about 30 undiagnosed patients in order to identify the genetic bases of their ailments. Parabase Genomics and the UCLA Clinical Genomics Center were selected as the first clinical genomic sequencing providers for the pilot project. Global Genes is a rare and genetic disease patient advocacy group, and Swan USA provides support to families of children living with diseases and syndromes that have yet to be named. According to them, a genomic test costs between $3,500 and $5,000. The financing for the program was raised through a donor-directed fund launched in September, and additional funding is underway in order to expand the program to include more undia...

Following Roche's disclosure last week that it will shut down 454 Life Sciences and stop supporting 454 sequencing instruments by 2016, customers are making plans to move their sequencing over to other platforms, if they have not done so already. While Illumina, Life Tech's Ion Torrent, and Pacific Biosciences are eager to step in to fill the void, some customers say aspects of 454's technology cannot be replaced by other platforms at this point. Also, those customers who have started to use 454 for routine clinical applications need to revalidate their assays on a new platform. Roche said last week that it will close down 454, which is based in Branford, Conn., and lay off about 100 employees over the next three years ( GWDN 10/15/2013 ). By mid-2016, it will stop supporting the 454 sequencing platforms, the GS FLX+ and the GS Junior. Roche's decision to pull the plug on 454 came to light less than a month after the company announced a deal with Pacific Bios...

BIBI automates DNA sequence analysis for bacterial identification in the clinical field. BIBI relies on the use of BLAST and CLUSTAL W programs applied to different subsets of sequences extracted from GenBank. These sequences are filtered and stored in a new database, which is adapted to bacterial identification. For further details refer : http://umr5558-sud-str1.univ-lyon1.fr/ lebibi/lebibi.cgi

SHORT TERM TRAINING COURSE on COMPUTER APPLICATIONS IN GENOMICS & PROTEOMICS 02-03 March, 2012 At Bioinformatics Centre Department of Agricultural Biotechnology CSK HP Agricultural University Palampur- 176 062 (HP) SPONSORED BY Department of Biotechnology(DBT) Government of India, New Delhi THEME Genomes of several plants and organisms have been sequenced, thereby resulting in the accumulation of large amount of sequence data in databases. The ‘omics’ technologies such as genomics, transcriptomics, proteomics, metabolomics and phenomics, etc., are all resulting in the generation of large data sets. The outcome from all these technologies is central to the improvement of genomes of economically important crops, microbes and animals. The processing of enormous biological information generated by these novel technologies requires fast and high capacity computational and storage media. Retrieval of sequence information and analysis need sophisticated programmes which can be distribu...

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 ...

Abstract Whole genome amplification by the multiple displacement amplification (MDA) method allows sequencing of DNA from single cells of bacteria that cannot be cultured. Assembling a genome is challenging, however, because MDA generates highly nonuniform coverage of the genome. Here we describe an algorithm tailored for short-read data from single cells that improves assembly through the use of a progressively increasing coverage cutoff. Assembly of reads from single  Escherichia coli  and  Staphylococcus aureus  cells captures >91% of genes within contigs, approaching the 95% captured from an assembly based on many  E. coli  cells. We apply this method to assemble a genome from a single cell of an uncultivated SAR324 clade of Deltaproteobacteria, a cosmopolitan bacterial lineage in the global ocean. Metabolic reconstruction suggests that SAR324 is aerobic, motile and chemotaxic. Our approach enables acquisition of genome assemblies for individual uncu...

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...

The National Institute of Neurological Disorders and Stroke is considering how next-generation genome sequencing (NGS) will be applied in studies of neurological disorders, and is asking researchers in this area for information about how they plan to use the latest sequencing tools and genomic data in their work. To find out how researchers aim to use next-gen whole genome sequencing (WGS), and what the needs are for sequencing, data storage, analysis, and annotation services, NINDS has released a new request for information seeking feedback from the extramural research community. NINDS will use this feedback to inform and complement its efforts to assess the current and future whole genome sequencing needs of researchers studying a wide range of neurologic disease, and conducting basic research into the nervous system, the genetics of the brain, cognition, brain plasticity, neural signaling, learning, memory, motor control, and other areas.

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...

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 , ...