Bio Saga Blog - A Chronicle of Life Sciences & Informatics

https://youtu.be/10oQMHadGos

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...

By considering sequence data for individuals assessed through the 1000 Genomes Project, a team led by researchers from Yale University and Wellcome Trust Sanger Institute came up with a computational method for prioritizing potential disease culprits — including those in non-protein-coding parts of the genome. As they reported online today in Science , the researchers sifted through SNP profiles in coding and non-coding sequences in 1,092 genomes, focusing on functionally annotated areas. With the help of information from the ENCODE project, mutation databases, and other data sources, they narrowed in on sequences that seem especially sensitive to change. The group tapped these mutation-sensitive sites to develop an approach called FunSeq, which proved useful for uncovering new apparent driver mutations using sequences from around 90 cancer genomes. These included almost 100 driver candidates in non-coding sequences, according to study authors, who noted that FunSeq is expected...

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...

Kevin McKernan's company Medicinal Genomics announced that it has a draft assembly of the marijuana genome , reports Bloomberg. The data is to be posted to the Amazon EC2 cloud. According to Nature's News blog , the Cannabis sativa genome is estimated to be about 400 million bases, or three times that of Arabidopsis thaliana . McKernan, who was previously at Life Technologies, started Medicinal Genomics "to find ways to maximize the cannabis plant's therapeutic benefits and minimize its psychoactive effects," Bloomberg says. "This is the beginning of a more scientific approach to the genetics of the species," adds Richard Gibbs from Baylor College of Medicine. "This is not really about marijuana; it's about pharmacology." And, as Nature's News blog notes, the pot samples were prepared for sequencing at a lab in Amsterdam.

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...

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?

Researchers from the International Citrus Genomics Consortium announced this weekend at the Plant and Animal Genome (PAG) XIX conference in San Diego, California the availability of the sequence assembly and annotation of the first citrus genomes, the sweet orange ( Citrus sinensis ) and the Clementine mandarin ( Citrus clementina ). The sweet orange genome was sequenced and analyzed in joint collaboration between the University of Florida, DOE Joint Genome Institute, the Georgia Institute of Technology and  454 Life Sciences , a Roche Company, using the high-throughput  GS FLX System . Funded in part by the Florida Citrus Production Research Advisory Council, a citrus grower industry organization, the project is expected to assist geneticists and breeders improve these important fruit crops. The assembled and annotated genomes have been added to the publicly available database Phytozome.net, a project of the DOE JGI and the Center for Integrative Genomes. Grown in more than...

Practical Course - European Molecular Biology Organization Bioinformatics & Comparative Genome Analyses 27 June - 09 July, 2011 |Institute Pasteur | Paris | France About the Practical Course In the context of large-scale genome comparisons, the main objectives of this general purpose practical course are to strengthen capacities of students in Bioinformatics and data analyses skills by introducing reviews on advanced fundamental algorithms used in Bioinformatics and their applications in genome studies.     Theoretical presentations will be followed by practical sessions, so that the same speaker will ensure links between theory and practice. Reviews on each suggested topic will include their corresponding research perspectives, aiming at helping young scientists to gain insights into ongoing research in this domain.  The course topics will include theoretical and practical aspects in: large-scale genome comparisons, evolutionary analyses, sequence and g...

This something really interesting to PPI, Systems biology  and molecular networks people, I just recently came across, Cellular processes and pathways, whose deregulation may contribute to the development of cancers, are often represented as cascades of proteins transmitting a signal from the cell surface to the nucleus. However, recent functional genomic experiments have identified thousands of interactions for the signalling canonical proteins, challenging the traditional view of pathways as independent functional entities. Combining information from pathway databases and interaction networks obtained from functional genomic experiments is therefore a promising strategy to obtain more robust pathway and process representations, facilitating the study of cancer-related pathways.  Results: We present a methodology for extending pre-defined protein sets representing cellular pathways and processes by mapping them onto a protein-protein interaction network, and extending them t...

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 , ...

Here is the climax of the stories  Life Technologies to Acquire Ion Torrent for up to $725M  and  The Argument Continues - Blue Ray or HD, Intel or AMD and now Illumina or Life Tech?   Life Technologies has completed its acquisition of Ion Torrent for $375 million in cash and stock.  The total value of the deal could rise by another $350 million if certain technical and time-based milestones are met through 2012. The acquisition adds Ion Torrent's semiconductor chip-based sequencing platform, which measures the release of hydrogen ions as nucleotides get incorporated by DNA polymerase. Unlike other existing second-generation sequencers, it does not require lasers, cameras, or labels.  The first system based on the technology is the Personal Genome Machine sequencer, which will be launched in the fourth quarter of this year. Life Technologies said that the transaction is expected to be $.02 dilutive to its earnings per share in 2010, neutral in 2011, and ac...

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...