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WCG Status Update

WCG Post

Bi monthly NEWSLETTER:
[May 25, 2005 5:35:59 PM]

I thought for this bi-montly newsletter I'll focus on something different, the non-human proteins that we're folding on the grid, and the reasons for folding them.

So far we've talked a lot about the human health side of this project, i.e. we've talked about the human proteome and what predicting human protein structures can hope to accomplish.

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.