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Pacific Biosciences of California, Inc. Message Board

paulieme60 5 posts  |  Last Activity: Jul 1, 2014 8:20 PM Member since: Feb 12, 2002
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  • Improving potato genetics using the long read sequencing data
    Expected/Ideal Start Date 01 Aug 2014
    The successful applicant will use and optimise tools for assembling a large plant gene sequences and an entire genome using ultra-long Pacific Bioscience (and as available Nanopore) reads, as well as using shorter Illumina reads to verify and correct the assembly.

    (for link go to IHUB PACB M B)

  • Reply to

    Roche just bought Genia, not good for PACB

    by borgati4 Jun 3, 2014 3:36 PM
    paulieme60 paulieme60 Jun 13, 2014 10:59 PM Flag

    (Quote fom an expert) Nick Loman ‏ ·Jun 12 2014
    "PacBio is a great tech, but shame many can’t tell the conceptual difference between a $700k instrument and a $1000 portable USB sequencer." !!!!!!!!!!!!!!!!

  • "Their technology is interesting in that it uses both a biological nanopore and a polymerase. The polymerase sits atop the nanopore, and a template single molecule of DNA is provided to the polymerase. Single nucleotides are added to the mix and each nucleotide has a “NanoTag” tail. As the polymerase incorporates the nucleotides, the nanopore sucks in the NanoTag, and this event is measured electronically. The polymerase moves on and the nanopore measures the next base etc etc. " "Any guidance on the limits on measurement performance in terms of bases per second? 10bps wouldn’t be practical for anything but small viruses. This is quotes from experts in the field,such Mick Watson!

  • James!Gurtowski!
    5/29/2014 Near perfect de novo assemblies of eukaryotic
    genomes using PacBio long read sequencing! (for link go to IHUB PACB M B)

  • PacBio Blog - Tuesday, May 6, 2014--Retroviral Study Reveals Potential for Influencing HIV Replication
    Scientists from the Icahn School of Medicine at Mount Sinai in New York City and the MRC National Institute for Medical Research in London published a paper using Single Molecule, Real-Time (SMRT®) Sequencing to gain a better understanding of how human endogenous retroviruses may be interacting with HIV infection. They pursued a new avenue of research that could shed light on how to interfere with HIV replication.

    The scientists conducted a study uniquely suited to the extremely long reads provided by the PacBio® platform, noting that this technology was needed to accurately parse the complexity in expression among a specific group of human endogenous retroviruses (HERVs). In this project, the scientists dug deeper into evidence that expression of the endogenous retroviruses that make up almost 5% of the human genome is upregulated when a person is infected with HIV-1. “HIV-1 infection in human cells is equivalent to a co-infection by several retroviruses,” -------------The team found nearly 4,000 HERV-K sequences in these lymphocytes, compared to a previous study from other scientists that found fewer than 1,000 of these sequences in 11 samples. They posit that the higher number seen here reflects the greater sensitivity of PacBio sequencing as well as the difference in cell types analyzed.

    In all, the authors identified more than 30 different transcripts for HERV-K envelopes, including two that produce full-length proteins — one of which was found to incorporate into HIV-1 particles. “These findings imply that some HERV-Ks interact specifically with HIV possibly shaping the properties of the lentivirus,” they write. “Future studies are needed to determine the extent of their influence on the HIV-1 life cycle and whether their expression can be harnessed to hinder HIV-1 replication.”
    (for full story,go to PACB web site, click on blog)

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