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Scientists Map the Human Metabolome
Cache22x writes "Scientists at the University of Alberta have published the first draft of the Human Metabolome Project, the chemical equivalent of the human genome. In the same spirit as the human genome project, the information has been made freely available to the scientific community and the general public through the project's website. Knowing the makeup of the metabolome will lead to potentially enormous medical advances as clinicians now have a comparative base for analyzing the metabolite levels found in our bodies."
How does cataloging 3,000 body chemicals equate with decoding a gigabyte sized blueprint/factory for cell manufacture?
I come here for the love
metabolome... sounds like a nice deli meat... Isn't that what they use in Italian subs?
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The metabolome hasn't been mapped like the genome has been mapped. i.e. it's not a complete list of metabolic reactions, enzymes and small molecules in a human cell.. it's a database (currently with 2100 metabolites) for the classic biochemical charts that show metabolism networks (like how the citric cycle is connected to amino-acid production). Nonetheless, it's a great idea, and as a BSc graduate from the dept, I'm quite proud.
The metabalone is connect to the ... genome. The genome is connected to the ... chromosome. The chromosome is connected to the ...
I hope, when they die, cartoon characters have to answer for their sins.
Incase you don't know what it is (like I didn't, here is the wikipedia definition:
Metabolome[1] refers to the complete set of small-molecule metabolites (such as metabolic intermediates, hormones and other signalling molecules, and secondary metabolites) to be found within a biological sample, such as a single organism. The word was coined in analogy with transcriptomics and proteomics; like the transcriptome and the proteome, the metabolome is dynamic, changing from second to second. Although the metabolome can be defined readily enough, it is not currently possible to analyse the entire range of metabolites by a single analytical method (see metabolomics). In January 2007 scientists at the University of Alberta finished a draft of the human metabolome. They have catalogued and characterized 2,500 metabolites, 1,200 drugs and 3,500 food components that can be found in the human body.
However, I am still in the dark about why this is required.
I suppose its like organising your stamp collection by number of nobbles around the edge.
liqbase
This complements the genome project. DNA codes are used ultimately to make proteins, enzymes (and other things). Proteins and enzymes are used for metabolic processes in the cell (and other things). In fact, having knowledge of the metabolome is more useful for pharmaceutical and health sciences research than knowledge of the genome. Moreover, these networks are quite complicated and contain many redundancies and inter-relationships, and compiling it in a database makes it easier to see these relationships. The human metabolome is most directly useful in developing pharmaceuticals, but the metabolome databases for other organisms would be very useful as well -- such as Saccharomyces cerevisiae (yeast) and Escherichia coli. For example, in my lab we grow 13C/15N-isotope labeled protein molecules with cloned genes in E. coli, and being able to search a metabolism network database would help us identify small molecules to feed bacteria to get specific labeling patterns.
I think I'm going to need a new dictiolome.
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- - You can't take something off the Internet! That's like trying to take pee out of a swimming pool.
whatever's in my body lets me eat like 6000 calories a day, sit on my ass, and never gain a pound. I don't want people copying that! I better encode my internal chemicals with DRM so people can't decode and copy me.
Google's Super Secret Search Algorithm: SELECT @search_results FROM internet WHERE @search_results = 'good'
Does this project specify which are male or female specific?
The future is epigenetic. The sequence of the genome is a cold, dead thing that does not exist in nature. Nature uses the runtime system of particular cells. The DNA is methylated and the chromatin is modeled (and other as yet undiscovered mechanisms may exist) in a particular runtime configuration for a particular type of cell. These guys seem to be looking at the end products of this runtime configuration. I suspect all those dead areas of "junk" DNA will make much more sense when we stop looking at cold, dead DNA that has been stripped of "life" and start looking at the actual cells as they exists en vivo.
Okay, let me explain for you non-biochemist computer guys what this means. Take a computer, break it down into the smallest possible parts you can. I'm not talking about the hard drive/motherboard/case level. I'm talking about the level of transistors, resistors, ICs, connectors, motors, and the little blue LED that blinks whenever your hard drive spins. Now catalog everything. Keep a record of what you found where, and how many you found (eg, you found a laser in the DVD drive but not in the motherboard). So now you have a parts list, and a good idea of what parts to expect where. If you start finding unexpected things in unexpected places (like a SCSI connector on your video card, or an audio out port on one of your DIMMs), that tells you something is wrong.
Take a look at the database entry for something common like glucose. It's got
Now what's missing is a lot of information about the connections, so technically this isn't really a map (because it's missing relational data), but a catalog. We need to know how each chemical turns into another, and what does the conversion. It's kinda like having a complete parts list for the computer, but not knowing how most of the parts fit together, nor how many volts and amps to run through the wires. Some of these connections we already know. I have a very large poster on my wall illustrating the more common chemical pathways in various organisms. It's not nearly as complete as this catalog in terms of chemicals, but it's got a lot of connections.
The connections are what's really useful. To continue the computer analogy, if you know that the blue LED connects to the hard drive, then if you don't see the blue light blink, then there's probably something wrong with the hard drive. A significant number of drugs aren't active in the form that you take them. They become active when the body (usually in the liver) converts them from the delivery form to the active form. But some people, because of their genetic makeup, convert the drugs differently. They turn them into different metabolites. These metabolites might be totally inactive, or even toxic in some cases. So if you know the connecting system, you can put a drug in, look for what metabolites result, and determine whether or not that person should continue taking the drug.
This seems to open the door to a whole new way of diagnosing problems... more technical, precise and complete than we have had before. In the way that the development of algebraic proofs changed math, so too will this change medicine.
-John Fenley
to make a database of all compounds of a human is a really great idea. from my point of view (master student in biochemistry + infection biology) it's one of the essential in the right direction to increase the understanding of humans!
R D=HMDB00030
;)
:) ... for the non-molecular-biologists: what i mean is something similar to the KEGG onem l
i didn't know about this database till now, so i played around alittle bit and find it usefull, but quite hard to use. the problem is more a technical one. if you for example open the entry of biotin here
http://www.hmdb.ca/scripts/show_card.cgi?METABOCA
you see a huge list of nice links that would maybe interest you (PDB, PubChem, KEGG,...) but there is a quite confusing part of such an entry (that's why i have choosen biotin as example, it is quite well known and a big entry) and that is the overview of the node itself related to the enzymes that make, degrade and modify the node. just listening the pathway names, the kegg maps and the SimCell maps, it may contain all the information needed, but it is not at all userfriendly, if you want to browse the metabolome and go from one node to another somewhere completely different... like you wolud be able to do on the big poster one tends to have. of course, the poster is missing a whole lot of information you have in a digital database, but it is much more userfriendly. you can use your finger to follow pathways
of course the enthusiastic biochemists among us would say, that we already have learned this overview in the textbooks and that you should know them by heart anyway.. but for natures (like me) who are more interested interdisciplinary and want to use this database as a browsable map.
some coding experts should sit together with the biologists to code a clickable SVG rendering map for a visual tour trough the metabolome
http://www.genome.jp/kegg/pathway/map/map00010.ht
but in a more interactive and more modern way (modern way = vector based, clickable, popups presenting links to other DBs and maybe adding color... or am i asking too much? *smile*).
great work - right step in the right direction!
Meta tags blow me...
Perhaps we can put the patient in some sort of bone-crushing centrifuge to separate out the metabolites.
Viper is the preferred editor of the Emacs operating system.
I can only conclude one of two things;
a) Nobody cares about "Canadian Science", unless it is Beer Science.
b) Nobody on Slashdot cares about biological stuff. They only care about stuff stuff.
This issue is a bit more complicated than you think.