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World Community Grid Forums
Category: Completed Research
Forum: Human Proteome Folding
Thread: HPF update |
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Thread Status: Active Total posts in this thread: 13
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Hi agian from ISB. The latest status image is up. 85% done. It's making me
----------------------------------------wonder .... what if we do a few more work units than we planned, so that we can get to 110%? Just like those deodorant commercials where a football coach gives you an emotioanl account of how he works hard and expects his deoderant to work hard too, that extra 10% of deoderant makes anti-odor which is BO made of anti-matter!... At that point we could say things like "you work hard and you expect your grid to give 110%! thats why WCG is protein activated, to keep your genome free of unannotated domains!". In any case it looks like were on track to have the database populated on schedule. Here is the link to the new status image: http://www.worldcommunitygrid.org/images/rbonneau/HPFStatus200509077l7v6o4e.jpg [Edit 1 times, last edit by Former Member at Sep 9, 2005 6:49:17 PM] |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
 Added: The DNA analysers are turning out more genetic data every month. So what species are you considering, Dr. Bonneau? Something else I have been wondering about. Right now, we know so little about cell biology that any new knowledge has to be considered valuable. Still, I have wondered if the protein structure predictions we produce are good enough to produce a list of proteins in a species such as malaria, that are very different from any of the proteins naturally found in the human body. Are our predictions good enough to help select a list of possible drug targets? mycrofth [Edit 1 times, last edit by Former Member at Sep 9, 2005 6:22:21 PM] |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
answer part 1:
what genomes: This project is devoted primarily to the human proteome and understanding the human proteome by predicting the structure of proteins of unknown function in the human proteome. We are also, however, folding the proteins of unknown function in over 60 other complete genomes that we feel have an important impact on human quality of life. I list below a sampling of the other genomes we’re exploring as part of the proteome folding project on the worldcommunitygrid. I’ll give a sentence or two about each of them, but each organism has a lot of reasons for furthor study. I could give you the full list, but these represent a good mix. In general there are 4 categories of proteins we’re folding (all important for improving people’s health and/or quality of life): 1. Human proteins: Priority 1 for this project. Contribute to the understand the human proteome with structure prediction. 2. Human pathogens: understanding these nasty guys contributes to our efforts to knocking them out. 3. Environmental: More and more we are realizing that the living things in any ecosystem have methods for responding to pollution and other human influences in ways that lead us to believe that bioremediation of toxic waste sites is on the horizon. Understanding bugs/bacteria and archeaeon involved in the environment is the first step. 4. Model systems: These are organisms that are studied in the lab because they are safe, easy to work with and easy to manipulate. Much of what we understand about genetics and biology at large comes from studying these organisms. Now for a few examples of non human proteomes on the grid: (if you don’t see a genome/proteome listed here it doesn’t mean we’re not folding it, just that I’m sick of typing ... over 60 complete genomes were processed as part of this project) Bacillus anthracis str_Sterne ----------------------------------- A relative of a soil bacterium (so environmental) and a possible bioterorism agent (so a pathogen). There are a lot of reasons to better understand this bacteria. Bifidobacterium longum: ----------------------------------- see: http://www.genomenewsnetwork.org/articles/10_02/bifido.shtml this bacteria is important for having a healthy intestine. More and more researchers are realizing the importance of your intestinal flora in health. Deinococcus radiodurans ----------------------------------- a radiation-resistant bacterium see: http://science.nasa.gov/newhome/headlines/ast14dec99_1.htm Desulfovibrio vulgaris ----------------------------------- sulfate-reducing bacterium. Important for understanding the environment and bioremediation. Escherichia coli K12 ----------------------------------- E coli is one of the best studied model organisms. It is a major bacteria in our guts, and it has some strains that are pathogens. 3 very good reasons to do all we can to understand this bug. see: http://en.wikipedia.org/wiki/Escherichia_coli Helicobacter pylori ----------------------------------- This bug is a cause of several ailments of the stomach including ulcers and possibly stomach cancer. Lactobacillus johnsonii ----------------------------------- probiotic intestinal bacterium Listeria monocytogenes ----------------------------------- pathogen: causes Listeriosis, a serious infection caused by eating food contaminated with the bacterium Mycobacterium leprae ----------------------------------- Mycobacterium leprae is the causative agent of the disease, leprosy, also known as Hanson's Disease. The bacterium was discovered in 1873 Mycobacterium tuberculosis ----------------------------------- Mycobacterium tuberculosis is the etiologic agent of tuberculosis in humans. Tuberculosis is on the rise in the 1st world and still a big problem in the developing world. Tuberculosis (TB) is the leading cause of death in the world from a single infectious disease. The disease affects 1.7 billion people/year which is equal to one-third of the entire world population. We must do all we can to understand this bacteria. Mycoplasma genitalium: ----------------------------------- Human pathogen (a Gram-positive parasitic bacterium). one of the smallest genomes (so its interesting to see how it can live with so few genes). Prochlorococcus marinus ----------------------------------- see: http://www.genoscope.cns.fr/externe/English/Projets/Projet_DR/DR.html Important for the environment and the global carbon cycle. from the site where they first sequenced this bug: The marine cyanobacteria from the Prochlorococcus genus are the smallest photosynthetic organisms known; they are also the most abundant photosynthetic organisms in the oceans, and therefore on the planet. With a size of less than one micrometer (diameter between 0.5 and .07 micrometer), these prokaryotic cells were not noticed until the end of the 1980s, although the existence of photosynthetic organisms of the order of one micron in size (picophytoplankton) has been known since 1979. Salmonella typhi Ty2 ----------------------------------- Causes typhoid fever, a life-threatening illness that is still a big problem in the developing world. Shewanella oneidensis ----------------------------------- Known as a heavy metal breather, this bug can tolerate lots of heavy metals, and even A very metabolically versatile bacterium in the environment utilizing a diversity of electron acceptors (nitrite, nitrate, thiosulfate, iron, manganese, uranium). That right this thing can grow and use Uranium instead of oxygen. Streptococcus pneumoniae ----------------------------------- Human pathogen. Synechocystis PCC6803 ----------------------------------- An important photosynthetic bacterial in the environment. Yersinia pestis: ----------------------------------- also known as plague, this bug is very nasty and has an important place in history. Yeast (Bakers and Brewers): ----------------------------------- Two of the most well studied organisms. These little fungi have produced a huge wealth of biological info, and will continue to do so for years to come. A lot of what we know about our own cellular biology comes from studying yeast. Malari ------- Again, a very big problem in the developing world. |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
answer part two:
Function (what it is all about -- good question by the way). can we get function from Rosetta structure predictions. We've shown it many times in many ways, all in peer-reviewed settings. this is a new result, but the short answer is that in the last few years we have found that we can get a whole bunch of info from structure predictions. you can't go from function to drug (there is no silver bullet). But knowing the function or structure of a couple more thousand domains in malaria will help the people working on it. a few current specific efforts include: 1. annotation of canser biomarkers: proteins that show up as highly expressed in tumors ... what do they do? knowing thier function and structure is essential to piecing together what is going on in cancer cells (cells that have deviated quite a bit from normal cell program). 2. vacine dev: it helps quite a bit just to know what parts of the protein are on the surface to attempt to find imunogenic proteins/peptides. there are a lot of other ways we can use this info ... i typed this so fast i hurt one of my fingers, so: check out: http://genomebiology.com/2004/5/8/r52/abstract for references and an overall less rushed responce (better spelling no doubt as well). thanks again for asking a question about the science. |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Thank you Dr Bonneau. I would like to say more but words fail me; a very impressive response. I shall no doubt be up half the night reading through the links you provided above - fascinating stuff that makes me wish I had paid a little more attention whilst still at school . . . .
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Thank you Dr Bonneau. I would like to say more but words fail me; a very impressive response. I shall no doubt be up half the night reading through the links you provided above - fascinating stuff that makes me wish I had paid a little more attention whilst still at school . . . . Im in total agreement--Thanks so much for your help and others in this area!!!--And also thanks for taking your valuable time to try to teach us or should say inform us [Edit 1 times, last edit by Former Member at Sep 10, 2005 12:35:31 PM] |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
nice open replies, well appreciated.
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msim
Cruncher Joined: Dec 31, 2004 Post Count: 20 Status: Offline Project Badges: 
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Hi agian from ISB. The latest status image is up. 85% done. It's making me wonder .... what if we do a few more work units than we planned, so that we can get to 110%? Nah, you shouldn't do more work than originally intended. It's very helpful for PR work and motivating the public, if you haven't already noticed, to provide data that can reference points of completion, give credit where credit is due, etc. People like to feel like they're a part of something -- that their efforts contributed to something and made a difference. If you say "yay we're done 100%" it makes it that much clearer and makes people more proud that they've contributed, gives you a clear chance and point at which to celebrate (and possibly get more publicity,etc.) In addition, as is the benefit to distributed and parallel computing projects -- a key point is in breaking up large problems into smaller components. You make things more manageable, more understandable, etc. In addition -- say if you have a project that is specifically dedicated to analyzing one problem or another -- be it the malaria genome, leprosy, TB, etc. you create a project which can have a whole new public face and can and WILL solicit new members of the public, government agencies, new audiences in new countries, etc. Lets face it -- the people and organizations that deal with these issues or in countries significantly plagued by some of these diseases would be more motivated to contribute to efforts targetted towards these very specific and limited goals. Also, you reduce risk that a project can turn into BAD pr, by people saying (or feeling) that they were misled and used to analyze things they didn't actually sign up for. What if someone were to say "I was used to mathematically analyze 'a possible bioterrorism agent'"? Or what if someone is legally or morally restricted from having anything whatsoever to do with such a thing? Given, their concerns could be unfounded, or based on an incorrect layman's understanding of what is implied, but then again, research can be misued, or have unintended consequences. |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Where can I find the HPF data statistics as to how much of the total project has been completed. I would never have been able to find that graph if it wasn't posted in this thread. Am I overlooking a link to where this information is being viewed?
Thanks, Brian |
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