Biology and Genetics Links

Discussion in 'Biology & Genetics' started by S.A.M., Jun 6, 2007.

  1. S.A.M. uniquely dreadful Valued Senior Member

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    Human Genetic Variation:
    2007 Breakthrough of the Year

    On 21 December 2007, Science unveiled its Breakthrough of the Year for 2007 -- the realization that DNA differs from person to person much more than researchers had suspected. That conceptual advance, driven by results from several fields, may transform medicine, but could also threaten personal privacy.

    In this video presentation, featuring Science news writer Liz Pennisi, Francis Collins of the National Institutes of Health, and David Altshuler of the Harvard/MIT Broad Institute, we offer a look at the past year's discoveries in human genetic variation and their implications. For more on this and other top science stories for 2007, follow the link below.

    http://www.sciencemag.org/sciext/btoy2007/video/bt_video.html
     
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  3. Avatar smoking revolver Valued Senior Member

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    The first 30,000 pages have been unveiled of a vast encyclopedia which aims to catalogue every one of our planet's 1.8 million species.

    The Encyclopedia of Life (EOL) - described as the "ultimate field guide" - is to encompass all six kingdoms of life, and even viruses - which many researchers do not consider to be living organisms.

    http://www.eol.org
    http://news.bbc.co.uk/2/hi/science/nature/7263134.stm
     
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  5. S.A.M. uniquely dreadful Valued Senior Member

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  7. Vkothii Banned Banned

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  8. S.A.M. uniquely dreadful Valued Senior Member

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  9. S.A.M. uniquely dreadful Valued Senior Member

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    Next Bio

    http://www.nextbio.com/b/home/home.nb

    A great resource for those studying gene and disease.

    You can refine data and literature by parameters to quickly find the type of information you need
     
  10. synthesizer-patel Sweep the leg Johnny! Valued Senior Member

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  11. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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  12. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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  13. S.A.M. uniquely dreadful Valued Senior Member

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  14. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    Thanks. I have only spent a few minutes here but it is a great learning center. - I will send hours there (I do not know if that means I will not need to ask you and CharonZ more or less.)
     
  15. Hercules Rockefeller Beatings will continue until morale improves. Moderator

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  16. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    This seems informative, perhaps important, but clearly is self promotional by gene-tools. (I wonder if when that is discounted, is "morpholino" an important advance, or just an alternative.)

    Here is the title and abstract:
    Morpholino, siRNA, and S-DNA Compared: Impact of Structure and Mechanism of Action on Off-Target Effects and Sequence Specificity
    by James E. Summerton, Manager & Owner, GENE TOOLS, LLC, One Summerton Way, Philomath, Oregon 97370, USA

    Abstract: Generally a gene knockdown agent should achieve high sequence specificity and should lack off-target effects (non-antisense
    effects due to interactions with structures other than gene transcripts). Three major gene knockdown types are compared with respect to offtarget
    effects and sequence specificities: 1) phosphorothioate-linked DNA (S-DNA); 2) short interfering RNA (siRNA); and, 3) Morpholino.

    S-DNAs cause multiple off-target effects, largely because their backbone sulfurs bind to many different proteins. S-DNAs also achieve poor
    sequence specificity because S-DNA/RNA duplexes as short as 7 base-pairs are cleaved by RNase H.

    siRNAs cause several off-target effects, but improved designs may soon avoid such effects. siRNAs also provide only limited sequence
    specificity because their short guide sequences largely determine which gene transcripts will be blocked or cleaved, and those guide sequences
    appear to recognize insufficient sequence information to uniquely target a selected gene transcript. This specificity limitation is inherent in
    their mechanism of action and so probably cannot be greatly improved.

    Morpholinos are virtually free of off-target effects - probably because they cannot interact electrostatically with proteins. Morpholinos also
    achieve exquisite sequence specificity - in large part because they must bind at least about 14 to 15 contiguous bases to block a gene transcript,
    and this constitutes sufficient sequence information to uniquely target a selected gene transcript. Because of their freedom from off-target
    effects, exquisite sequence specificity, complete stability in biological systems, and highly predictable targeting, Morpholinos dominate the
    most demanding of all gene knockdown applications, studies in developing embryos.

    See full paper at:
    http://www.gene-tools.com/files/Summerton2007siRNAcompare_0.pdf

    PS I was planning to post in SAM's "papers to discuse" thread but found this thread first - most with interest probably notice both, so it is here.
     
  17. Jon Moulton Registered Senior Member

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    Morpholinos: advance or alternative?

    Billy T wrote:

    ----------------------

    This seems informative, perhaps important, but clearly is self promotional by gene-tools. (I wonder if when that is discounted, is "morpholino" an important advance, or just an alternative.)

    ----------------------

    I work for Gene Tools, so I suppose this is self-promotional too. But, since no one else answered your rhetorical question, I'll accept your offer.

    Morpholinos work in embryos. siRNA and phosphorothioate oligos either kill embryos or interfere with development, producing misshapen embryos. The difference is the specificity of the knockdowns. Teratogenic effects due to off-target RNA interactions make siRNA and phosphorothioate oligos impractical for embryo work, while Morpholinos are used routinely in embryos (see pubs.gene-tools.com for over 2400 citations to Morpholino work). The same specificity that makes a Morpholino usable in an embryo offers an advantage in other systems, such as cell cultures or adult animals.

    Let me know how I can help.

    - Jon
     
    Last edited: Dec 26, 2008
  18. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    Thanks Jon. Welcome to Sciforum. I hope you will contribute more, and not just lurk. There are several active here who know much more of biology and biotechnology than I do. I find this fast developing field facinating.

    I have stocks of about 35 early stage drug develpers. Most are showing losses now, but occasionally I get lucky. About a year ago, company you surely knew, SRAi (or something like that) was bought by Abbott or Merk (I forget which as the other bought another company I owned with total profit of about $50K for me). Three days ago, TEVA bough BRL (I owned both, but BRL does not exist now). I do not invest in Big Pharma, except generics, like TEVA.

    I go visit many conferences via the internet. These early stage developers are constantly needing financial backers and giving presentations. That is how I learn. I have learned a lot so even if I can only break even in the long run, I will be happy.

    What is the nature of the embryo market? Is it only human embryos or is Gene Tools thinking of livestock, etc.? My first reaction, in ignorance, is that there is not a big target for Gene Tools out there if its only advantage is with embryos.
     
    Last edited by a moderator: Dec 26, 2008
  19. Jon Moulton Registered Senior Member

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    Hi Billy T,

    I apologize for not responding sooner, but a half-year later I noticed your rapid response :bugeye:

    Gene Tools is an odd biotech, because we are making our custom-sequence Morpholinos for the research reagent market. They are used in embryos of zebrafish, frogs, sea urchins, tunicates and other model critters. We also make Vivo-Morpholinos for knockdowns in adult animals. However, we are not aiming at producing a Morpholino pharmaceutical. Instead, AVI BioPharma is in that business (I would post a link but I am not allowed), and they currently have one Morpholino in clinical trial for Duchenne muscular dystrophy and a peptide-Morpholino conjugate in clinical trial though Global Therapeutics (a Cook company) to inhibit cardiac restenosis after balloon angioplasty.

    For more on Morpholinos, see the first sections of this open-access paper:
    Moulton JD, Jiang S. Gene Knockdowns in Adult Animals: PPMOs and Vivo-Morpholinos. Molecules. 2009 Mar 25;14(3):1304-23.
    I would post a link, but I am not allowed. The review article is open-access.

    Again, I apologise for my tardy response. Best wishes, - Jon
     
  20. aswini Registered Member

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    Last edited by a moderator: Aug 6, 2009
  21. holli Registered Member

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    PD Online Research: a new resource for scientific communication

    I wanted to share with you all a new resource for posting questions and getting answers: PD Online Research, a collaborative community for technical discussion and problem-solving in Parkinson’s disease science. PD Online is powered by the Michael J. Fox Foundation for Parkinson's Research - and our goal is to help move your work forward on the road to cure Parkinson's.
    1. Get information from our growing list of resources: a detailed guide to Parkinson's disease science, a database of clinical trials, and coming soon, animal models, genes, and therapeutic targets!
    2. Find answers to your technical questions from our community of experts, from top scientists in the field to grad students and post-docs.
    3. Network with other scientists to find collaborators.
    4. Debate the hot topics in PD science.
    5. Discuss the latest publications from top journals and business and industry news.
    6. Connect with funders to help shape future programs.

    Check it out at pdonlineresearch.org!
     
  22. Hercules Rockefeller Beatings will continue until morale improves. Moderator

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    Need help explaining your genetics work to your extended family? The New York Times published a special section on modern post-gene genetics this past week, helping to make the field of genetic research palatable to even the most scientifically disinclined.

    The section, “Beyond the Gene,” explores current issues in genetics for interested non-scientific readers. The section’s articles focused on the changing concept of the “gene,” silencing genes through RNA interference, and a theory connecting autism and schizophrenia to genetics. The section also included two graphics: one explaining the types of RNA, and the other explaining epigenetics. Articles in the section include:


    Now: The Rest of the Genome
    By Carl Zimmer
    Only 1 percent of the genome is made up of classic genes. Scientists are exploring the other 99 percent and uncovering new secrets and new questions.

    The Promise and Power of RNA
    By Andrew Pollack
    RNA interference, discovered only about 10 years ago, is attracting huge interest for its seeming ability to knock out disease-causing genes.

    In a Novel Theory of Mental Disorders, Parents’ Genes Are in Competition
    By Benedict Carey
    A new theory of brain development would change the way mental disorders like autism and schizophrenia are understood.

    Scientists and Philosophers Find That ‘Gene’ Has a Multitude of Meanings
    By Natalie Angier
    Scientists have learned that the canonical “genes” account for an embarrassingly tiny part of the human genome.

    Graphic: A Bestiary of RNA
    RNA seems to play a powerful role in how genes function.

    Graphic: Mapping the Epigenome
    A diagram of the epigenome, a new way to look at DNA
     
  23. Hercules Rockefeller Beatings will continue until morale improves. Moderator

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    http://www.gmo-compass.org/eng/home/
    Tasked with collecting “objective, science-based information on the use of genetic engineering in the agri-food industry,” GMO Compass is an all-encompassing European-based source of information on these high-tech consumables. With coverage ranging from the latest news (for example, the new blue roses) to an enormous user-searchable database, GMO Compass is surely one of the most significant sites on this subject to appear on the Web. You can learn a lot just by scrolling through its pages. Were you aware, for example, of the great divide between European and the U.S. on GMOs in the food of each country? Did you know that no genetically modified fruits or vegetables are on the market in the EU or that genetically modified tomatoes have disappeared from U.S. stores?

    http://www.micrographia.com/
    It doesn't take an electron microscope to produce beautiful and educational images of tiny life forms. That message is clearly in focus at Micrographia.com, where an eclectic collection of (mostly) microorganisms is on display 24/7. From the movie of a tiny juggling act on the opening page to an expansive set of images sorted biologically, Micrographia wows with its pictures, and there's no shortage of them to be seen. But, there's more at the site than the photos that meet the eye. With interesting articles (“The Microscopy of Inkjet Printing”), editorials, tutorials, microscopy projects, and archives of previous content, Micrographia is a full-service station for light-based microbial delights.

    http://asksci.com/
    There was a time when one had a burning question to be answered and a librarian was consulted, but even at its best, that only worked for general interest topics. Science questions require a more authoritative treatment and that is exactly what the designers of asksci.com have begun to create. Organized recently at the University of California at Irvine by a group of graduate students, AskSci is structured a bit like Digg (www.digg.com) for scientists, with a format focused exclusively on questions and answers. Like Digg, answers can be voted up, providing a sort of immediate peer-review. If, like recent inquirers on the site, you need to know how to troubleshoot a Western blot or what happened at the ICSB 2009 meeting, asksci.com is the place to go.
     

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