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paulalbert
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Posted: Wed Sep 2nd, 2009 07:10 |
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There are a number of human microbiome pilot projects in the works. Note that none of these studies don't go beyond surfaces in contact with the extern environment:
• $560,000 to New York University for a study of the skin microbiome and psoriasis;
• $1 million to Virginia Commonwealth University to study changes in the vaginal microbiome and associated environmental factors, diseases, and a woman's genetics;
• $820,000 to Indiana University Purdue University at Indianapolis to collect and characterize samples from an ethnically diverse group of male adolescents in order to understand the male urethral microbes and its relation to puberty, sexual activity, and sexually transmitted disease;
• $2 million to the University of Maryland School Medicine, Baltimore, with $1 million going to a study of the gut microbiome and obesity among the Amish that may inform knowledge of human genetic variation on the composition of the microbiome, and $1 million to understand the relationship between inflammatory bowel disease, Crohn's disease, the intestinal microbiome, and bacterial proteins by studying pairs of twins with and without disease;
• $980,000 to Washington University School of Medicine to analyze the intestinal microbiome and Crohn's disease;
• $990,000 to the University of California, Los Angeles, to examine the association between the skin microbiome and acne;
• $1 million to the New York University School of Medicine to sample the oral cavity, esophagus, and stomach to study the microbes in these sites and esophageal cancer;
• $980,000 to the University of Maryland's School of Medicine, Baltimore, to study how microbes are involved in risk of bacterial vaginosis;
• $400,000 to NHGRI Senior Investigator Julie Segre to study skin and nose microbiomes of subjects with atopic dermatitis; $950,000 to Washington University School of Medicine to study the immune system and the viral microbiome in children who are healthy and those who are sick with sudden high fevers;
• $1 million to Washington University School of Medicine to study the intestinal microbiome and the development of necrotizing enterocolitis, which can damage the intestine in premature infants;
• $750,000 to Baylor College of Medicine to examine the intestinal microbiome and any possible connections with irritable bowel syndrome;
• $1.1 million to the University of Pennsylvania School of Medicine, Philadelphia, to study a treatment of inflammatory bowel disease;
• $1 million to the University of Michigan to study inflammations related to a colon replacement pouch used in some ulcerative colitis cases
Full article here:
http://www.genomeweb.com/nih-awards-42m-more-human-microbiome-studies
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Diag CFS 6.03 / sympt since 9.02 / exercise, food intol, sleep prob / 1,25D: 16, 4.06; 1,25D:27, 25D:26 7.04; 1,25D:43, 25D:6 6.05; 1,25D:17, 25D:8 8.05; / MP: 7.04 / Ph. 3 / Bacteriality
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shegeek
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Posted: Wed Sep 2nd, 2009 14:55 |
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Interesting...I wonder if these grants are part of the stimulus project.
I also notice that the NIH has a new director, i.e. Zerhouni is gone (according to Wikipedia, he stepped down in October to take a position at KAUST).
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FMS,IBS,osteoarthritis,osteopenia, hypertension/ 1,25D/25D=45/44 (10/04), 44/13 (1/05), 36/8 (7/05)
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paulalbert
Research Team
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Posted: Wed Sep 2nd, 2009 15:45 |
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Hi Shegeek,
At least some of these projects are from stimulus funds. I'm not sure if all are.
The new head of the NIH is Francis Collins, who appears to be the world's #1 cheerleader for the potential of finding the cause of human disease in our genome:
http://scienceblogs.com/geneticfuture/2009/08/how_big_does_big_genetics_need.php
Do an in-page search here for Collins:
http://mpkb.mp-dev.com/doku.php/home:pathogenesis:alternate_models:genetic_predisposition
You gotta love that kind of optimism!
Paul
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Diag CFS 6.03 / sympt since 9.02 / exercise, food intol, sleep prob / 1,25D: 16, 4.06; 1,25D:27, 25D:26 7.04; 1,25D:43, 25D:6 6.05; 1,25D:17, 25D:8 8.05; / MP: 7.04 / Ph. 3 / Bacteriality
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Martin78
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Posted: Wed Sep 2nd, 2009 19:33 |
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Paul:
"Note that none of these studies don't go beyond surfaces in contact with the extern environment:"
I dont understand, do you mean: none of these studies go beyond? (doubble negative??)
br
Martin
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Sallie Q
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Posted: Wed Sep 2nd, 2009 20:47 |
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whoopee, Paul
with a bit of luck 3 mil. of that ~12 mil. may actually turn up something that could possibly further prevention (MP) rather than simply satisfy scientific curiosity. (I am a failed scientist, so I in no way mean to knock scientific curiosity) 
In case it doesn't jump out at gentle reader, I refer to 2mil.Maryland plus 1mil.Washington (on premmies)
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paulalbert
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Posted: Thu Sep 3rd, 2009 01:01 |
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Martin,
Oops, I wrote that too fast. What I mean is that some researchers, even in metagenomics believe that the body is like a fortress and that while bacteria may accumulate on external surfaces like the mouth and the GI tract, they are less willing to concede there are substantial quantities in the kidneys, liver, brain, etc.
We know better, of course.
Paul
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Diag CFS 6.03 / sympt since 9.02 / exercise, food intol, sleep prob / 1,25D: 16, 4.06; 1,25D:27, 25D:26 7.04; 1,25D:43, 25D:6 6.05; 1,25D:17, 25D:8 8.05; / MP: 7.04 / Ph. 3 / Bacteriality
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paulalbert
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Posted: Thu Sep 3rd, 2009 01:05 |
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Sallie,
In my opinion, any of these studies can help. We need to be able to show a consistent pattern across diseases.
Paul
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Diag CFS 6.03 / sympt since 9.02 / exercise, food intol, sleep prob / 1,25D: 16, 4.06; 1,25D:27, 25D:26 7.04; 1,25D:43, 25D:6 6.05; 1,25D:17, 25D:8 8.05; / MP: 7.04 / Ph. 3 / Bacteriality
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Dr Trevor Marshall
Foundation Staff
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Posted: Thu Sep 3rd, 2009 01:10 |
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My perspective is that it is going to be such a huge shock to clinical medicine that the body is not a sterile compartment, that the details of the bugs and location don't matter - many will shout "contamination" (and etc) and remain in complete denial until they retire.
The great physicist, Max Planck, surveying his own career in his Scientific Autobiography, sadly remarked that "a new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it."
and, above all, remember: "Computers are useless. They can only give you answers" - Pablo Picasso
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eClaire
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Posted: Thu Sep 3rd, 2009 07:47 |
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A friend of mine has occasion to see Collins socially (he is from around these parts... an MP member, Zeno, lives in his home town) in an acquaintance sort of way. I've asked her to drop a hint about the role of bacteria and the Marshall Protocol. Now if I could just remember to keep following up with her! 
Claire
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Dr Trevor Marshall
Foundation Staff
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Posted: Thu Sep 3rd, 2009 08:13 |
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Francis Collins is certainly a person whom we need to try and contact. He may well have the intellect to figure out what we have done. He has achieved quite a lot in his scientific career.
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jcwat101
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Posted: Thu Sep 3rd, 2009 15:16 |
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That study that found a lot of organisms in the amniotic fluid ought to have alerted people. I suppose some might consider that to be more of the external part, but one would think that the environment of the fetus is an area that would have been kept pretty sterile. Yet microbes in the amniotic fluid were shown by Relman to be linked to preterm births.
Joyce Waterhouse
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20 yrs with CFS/FM/Lyme/IBS, food sensitivities; 1,25D/25D 8/04:64/11 http://SynergyHN.wordpress.com
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Dr Trevor Marshall
Foundation Staff
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Posted: Thu Sep 3rd, 2009 16:11 |
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The last time I spoke with Dave Relman he was unwilling to talk about human microbiota. He was really unwilling to talk about my own work (far too practical).
About two months ago I sent an email to the professor at UCSD who started the Metagenomics conferences, thanking him for starting off the processes in my brain which finally allowed me to figure out the importance of the concept of a metagenomic microbiota, and move on from our emphasis on L-forms. I received a letter back saying that his group had been actively discouraged from any more thought or study of human data, and to concentrate on coral reefs and soil and stuff like that.
I suspect this is just typical kickback when a paradigm becomes threatened, but it is clear (to me) that the grants peer-review process is being used to slow the process of change in the understanding of the Human microbiome.
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Markt9452
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Posted: Thu Sep 3rd, 2009 17:11 |
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the grants peer-review process is being used to slow the process of change
"The medium is the message"
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Russ
Member*
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Posted: Thu Sep 3rd, 2009 20:43 |
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Dr Trevor Marshall wrote: I suspect this is just typical kickback when a paradigm becomes threatened, but it is clear (to me) that the grants peer-review process is being used to slow the process of change in the understanding of the Human microbiome.
This sort of thing really intrigues me. I'm not asking for comment or answers, because I don't think it does any good to focus on this kind of thing (they'll just label you a conspiracy theorist) but I would really like to be able to understand some day how this works. I mean, does the medical industry know that bacteria cause all these diseases and is doing everything they can to keep the world from finding out? Or is it a little less sinister and they don't know what causes diseases but just feel that their highly profitable system of treating symptoms with drugs is threatened by anything that could possibly lead to a better understanding of disease and eventual cure and so they cover their bases by trying to slow down any research that is leading in this direction. But if it was just the latter, why wouldn't there be just as much crackdown on the study of genes. Do they know this is a deadend? Who exactly is "they"? Again, not asking for answers or comments, just thinking outloud.
The way I kind of see it would be like the oil tycoons and the oil industry. They make a ton of money on the basis that the world uses oil for energy and that money would be threatened by any competing energy sources. So they would like the inevitable process of the world moving to better cleaner fuels to be delayed as much as it possibly can be. So they use their "experts" and their "studies" and their lobbyists to paint a picture that oil is not really that bad, global warming isn't that big a deal, and these alternative fuel ideas will never work. It's not like they're sitting on the knowledge of some perfect clean and efficient alternative fuel technology that will solve all the world's problems, they just cover their bases by being against anything that has the potential to threaten their profits. Likewise I'm thinking the medical industry makes a ton of money off the current system of treating diseases by prescribing drugs and having a population of "customers" that need to take multiiple drugs throughout their life. Anything that finds
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Dr Trevor Marshall
Foundation Staff
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Posted: Thu Sep 3rd, 2009 21:14 |
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I think it really is very simple. Here is an illustrative anecdote:
In 2003 I contacted Herbert Reynolds, who headed up the NIH / NHLBI Sarcoidosis info and grants programs. I told him that the first twelve months of our SarcInfo study had shown that Sarcoidosis must be caused by an infection, as the antibacterial therapy we were using was having amazing results.
Herbert told me "Look, I have treated hundreds of sarcoidosis patients, and not one of them had any sign of infection. You must be wrong. What's more, I know you are wrong because I gave these patients antibiotics, and none of them ever got any better."
Herbert then withdrew NHLBI support of a grant for a retrospective study which I had applied for. Eventually it was reviewed favorably by a committee from the NIH Institute on Aging. At that point there was no money available. After a discussion with Herbert about 'throwing money down the toilet', or something similar, I broke off discussions with him.
So you can see the problem is not a conspiracy, the problem is that we all have different ways of looking at the world, and some of those models are so colored and invariant that there is little chance that they will ever be changed. After all, Herbert had treated 'hundreds' of sarc patients, which he regarded as plenty to have enabled him to form a clear picture about what the disease was, and what it wasn't.
Herbert Reynolds is credited with having pioneered Bronchoscopy as a diagnosis tool for Sarcoidosis, and his bio would be regarded by NIH as that of a good scientist:
http://en.scientificcommons.org/herbert_y_reynolds
..Trevor..
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Russ
Member*
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Posted: Thu Sep 3rd, 2009 21:41 |
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| That makes sense. They just act so aggressive against any suggestion of bacterial cause of disease and seem so threatened by it that it makes you think there must be something more behind it. But I guess it's enough that they have thought about disease a certain way for a long time, and treated disease in a certain way for a long time, and they just can't deal with the thought they might be wrong. Still, you'd think they'd be open-minded enough to let some of this research go forward even if they are skeptical that it will lead anywhere. I am really looking forward to see how this all shakes out over the next decade.
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Bane
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Posted: Mon Apr 5th, 2010 19:13 |
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Please listen to this? i promise it's worth your while!
Rob Knight - The Microbes That Inhabit Us
http://blip.tv/file/get/Meetthescientist-MTS43RobKnightTheMicrobesThatInhabitUs513.mp3
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Marysue
Foundation Staff
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Posted: Tue Apr 6th, 2010 06:18 |
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Thanks Bane,
I listened to this today--great stuff! I have a few questions but don't want to hijack Paul's thread. Is there another bacteria-related thread where you can post it (or just start another thread)?
Marysue
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MP Apr09 (no breaks)| CFS/FM,infert/endometriosis | hypotension, cardiac IP, chronic muscle/joint pain, neuro symptoms, severe light sensitivity | last 25D=12.5 Sep'11
Marysue on Benicar
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Dr Trevor Marshall
Foundation Staff
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Posted: Tue Apr 6th, 2010 06:22 |
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That was a microbiome-related podcast. Here is as good a place as any to discuss it
..Trevor..
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Marysue
Foundation Staff
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Posted: Tue Apr 6th, 2010 20:09 |
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OK--so here's my first question.
At about 8:05-8:45 in the recording, Rob talks about how if they are 97% identical then we have "approximately a species"....and if it's less than 97%, they are not the same species. I assume here he's talking about analyzing the DNA of several species of bacteria.
Is he talking about bacteria that they can see under a microscope or the ultra tiny L-forms? And how are they able to test a large number of bacteria? Isn't that incredibly time consuming? Or are they just testing a very small sample of cellular material and then extrapolating out to estimate numbers?
Could someone explain how they are able to even distinguish between the types of material they are testing at such a microscopic level?
Perhaps I'm getting a little confused with the idea of bacteria swapping and exchanging DNA material with the human DNA in the cells. Once that happens, how do they distinguish between human cellular material and bacteria produced/swapped material?
Marysue
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