“The first challenge that OSDD’s cyber-community assigned itself was to glean more information from the M. tuberculosis genome. It was sequenced in 1998, but researchers had clues to the functions of only a quarter of its 4000 genes. In December 2009, OSDD set out to reannotate all possible genes. Some 500 volunteers got the job done in a mere 4 months. Now OSDD is trying to exploit these data. “The more people you put to work on the problem, the more chances you will have to identify the set of compounds that will likely make it through compound optimization, animal models, preclinical, and, eventually, clinical trials. If you increase your success chances, then your overall costs decrease,” says Marc Marti-Renom of the National Center for Genomic Analysis in Barcelona, Spain.”
FoldIt, GalaxyZoo, now this. Is the next phase of computing networked human computing?
Read this article…
“We report on the remarkable degree of biodiversity in the wine yeast populations naturally present in a small area of Sicily where traditional (non-industrial) winery practices are still in place. Out of more than 900 yeast isolates recovered from late spontaneous fermentations, we detected at least 209 strains. Given that the characteristics of the wines produced were found to be industrially appealing, the study demonstrated the economic potential of preserving the patrimony of Sicilian yeast biodiversity and highlighted the importance of maintaining traditional wine making practices.”
This is a great paper – studying the biodiversity of yeast obtained from traditional wineries; analyzing their genetic and metabolic qualities; and even using a few to make wines.
How fun. How inspiring.
Read this article in PLoS ONE
UPDATE 15mar12: Science wrote a nice review on this article. Ironic though that a publication with closed access articles is writing about an open access article.
“Seeking to spur drug development, Stephen Friend has launched a daring series of initiatives to make biomedical research more open and effective.”
Interesting fellow. He’s a mover and shaker in the bioinformatics “data must be free” crowd. It’s a very good article. Read it.
Read this article…
 A bit of history:
I experienced a huge brain- and world-expanding time during my Nokia Lifeblog years (2004-05). Early on, we paired up with Six Apart (via Marko Ahtisaari and Joi Ito), and I spent a lot of time under Loïc LeMeur’s wing promoting blogging, Six Apart, and Lifeblog, and meeting some of the key movers in the nascent Web 2.0 (thank you, Loïc).
In those days, I pushed for the fusion of web and mobile, started seeing how everything was coming in as streams, and how people started exuding their own lifestreams. The next logical idea was how to bring that together.
In 2006, the poster child was NetVibes. But I though we could do better. Some started talking about personal aggregators, Digital Lifestyle Aggregators, the widgetization of everything.
Morsels:
For me, the sweetspot was to be the one holding all the morsels (He who hold the morsels, holds the experience. “The structure holding the morsels becomes the experience” – Fabio Sergio), a dynamic dashboard where all my social streams come in, where I could mix and match, and then send all the things of note out back into the streams.
This was my original vision of what should have become Ovi.com. Alas, I could point to so many places where the harpoon was sunk and twisted into me (and into those who stayed on), but I had been given a huge wad of cash to do it, and I f-ed it up by not channeling my inner-Jobs and insisting we stay true to vision.
Lesson learned. Enough self-pitying. I had my chance and blew it.
In the time since, I have seen attempts to create similar services, and even some blatant suggestions from some great thinkers as to what was missing in this age of lifestreams (which I thought would be in 2008). But nothing really took hold (though I think Seesmic desktop shows promise).
Bottlenose:
And, lo, on comes a new service. And from a brilliant semantic web guy with a track record of actually coming out with things that I thought approached what I wanted to see.
“Bottlenose is a new social media dashboard for influencers of all stripes. But it’s not just for posting and reading; it helps you filter and manage your networks with semantics and machine learning. It’s all Web-based, written in HTML 5 and Javascript. It does the data crunching on the browser side (for the non-pro users), so you get native performance behind these major operations reading and parsing your stream.”
Read this article from Read Write Web
I signed up and have been checking it out. Of course, I’m sure this is better than whatever I would have built in 2007, given how the Web and mobile world have changed since then. I think one issue that could come to bite is any deviation from the usual UI folks are accustomed to for scanning info and streams. The weirder, the less likely someone will use it without feeling geeky.
In any case, I’m excited to play with it. If you check it out, let me know what you think of it.
One more thing:
I’ve also evolved my thinking since 2007 and think Bottlenose should be a P2P system. Take back the Cloud!
Image from the Read Write article on Bottlenose.
A Global Strategic Business Report
This report analyzes the worldwide markets for Probiotics in US$ Million. The report provides separate comprehensive analytics for the US, Canada, Japan, Europe, Asia-Pacific, Middle East, and Latin America. Annual estimates and forecasts are provided for each region for the period 2007 through 2015. Also, a seven-year historic analysis is provided for these markets. The report profiles 119 companies including many key and niche players such as BioGaia Biologics AB, Chr. Hansen A/S, Danisco A/S, Groupe Danone, Institut Rosell, Lifeway Foods, Inc., Natren, Inc., Nestlé Nutrition, Probi AB, Seven Seas Ireland Ltd., Stonyfield Farm, Valio Ltd., and Yakult Honsha Co., Ltd. Market data and analytics are derived from primary and secondary research. Company profiles are mostly extracted from URL research and reported select online sources.
Alas, too expensive for me to purchase. But if I were really in the business, probably worth it.
Read this article…
“Supplements containing a combination of Lactobacillus salivarius and fructo-oligosaccharide for eight weeks were associated with significant reductions in measures of the severity of eczema, compared with a control group receiving only prebiotics, according to findings published in the British Journal of Dermatology.”
In addition to the usual yogurt bugs, I am starting to see salivarius popping up more frequently. It’s from the mouth, by the way.
Read this article…
“The story of a group of University of Massachusetts students who set out to initiate the construction of the school’s first permaculture garden a year ago is a remarkable one, but it’s only the beginning of a worldwide movement.”
This is really interesting. Small-scale farming was killed by industrial farming to feed huge masses. But could it be that small-scale farming, like it used to be, to feed a local group, say a family or a cafeteria, is making a comeback? That would be cool.
Question: does technology and science help make us better “micro-farmers”?
Read this article…
Image of the garden from the article linked above.
 When I lived in the US in the 90s, it was hard to find live-culture yogurt in supermarkets (you could find them in natural food stores, of course). The only one I could find was Stonyfield yogurt.
When I lived in Finland, not only were there a bunch of live-culture milk products, but there was one in particular “Valio A+” that was specifically recommended for women to balance their flora.
Now back in the US, it’s hard not to find live-culture yogurt, and some are specifically marketed, yes, for women to balance their flora. Furthermore, the use of live bacterial cultures for health purposes, called probiotics, has become mainstream enough that you can find probiotic supplements for children in the supermarket.
What does this mean?
It means that folks are becoming aware of functional foods, of the importance of microorganism in their diet, and that the feeding desire to find a short cut (a pill rather than eating wholesome yogurt) is always a good business.
I’ve been seeking out all these probiotic products to get an idea of what’s out there, what the message is, and, for me, always on the look out for practical use of microbes, I’ve been trying to understand what microorganisms are in fashion.
OK, so the science behind probiotics is still in progress, so I will not go into that right now.
But, going on the premise that yogurt is the gold standard for beneficial live (with microorganisms) food, then my standard for all probiotic products used for digestive health is Stonyfield’s yogurt. Stonyfield’s has 6 bacteria (S thermophilus, L bulgaricus, L acidophilus, Bifidus, L casei, and L rhamnosus). I’d say that most of the products I have seen have one or more of these bugs. There are some proprietary sub-species and I’ve been pleased to see a few products with S salivarius or some other bacteria.
For me, the type, variety, and number of bacteria in a probiotic food or supplement is key. And I think it’s just snake oil if the product only has one bug.
Nonetheless, I think as probiotics go mainstream, buyers will be more astute as to what they are looking for. Also, I hope that new applications show up, beyond gut and vaginal flora health (I can think of a few).
What I do know, is that doctors are starting to suggest probiotics to patients on antibiotics or with digestive issues such as colitis or C diff.*
And that’s great.
Do you eat probiotic foods or take supplements? Send me pics of the ones you see or take! I could/should create a database of products and attach reviews or commentary. Hm…. not another project….
*Ego boost: A gastroenterologist aked me recently what probiotics I recommended. Ha! My first probiotic consulting gig?
 As you know, I’m always looking for practical uses of microbes. One that I stumbled upon a long while back was “transfaunation”, or, seeding one person’s gut with microbes from another’s. Yes, transfering poop microbes from one to another.
Be an adult. Don’t get grossed out. I’ve read some great papers on the process how our guts get colonized after birth. Also, there are some really interesting papers on how our gut microbes (or lack thereof) are involved in various intestinal disorders. And there are some promising papers on how diet affect the bacterial ecology in the gut. [Sorry, I'll link to the papers in a larger gut related set of posts at some point in the future - you can also just search for gut and microbes in my posts.]
Here’s the basic idea. People suffering from the hardy C. diff bacteria are generally prescribed a powerful antibiotic. Problem is, the drugs don’t just kill the invaders; they also wipe out much of the beneficial bacteria in the gut. With these “good” microorganisms out of the way, any C. diff stragglers have a much easier time regrouping for a second bout of illness. If there were some way to respawn the beneficial bacteria in the intestines, such re-infections could be warded off. Some people, like Ruth, turn to expensive probiotic supplements. (At one point she was spending $350 on them every week.) But in certain cases, a patient who has lost nearly all of her good bacteria will find it nearly impossible to get them back. A fecal transplant seems to work as a sort of mega-probiotic, allowing doctors to repopulate a patient’s intestines with the appropriate microorganisms by placing a robust sample directly into her gut.
Slate had a nice article on the subject (quoted above). It’s a serious subject and for many, the only hope to get a better and healthier bacterial gut fauna (hence the term, transfaunation).
My wife’s a vet and she’s not only heard of this procedure, but performed it on animals. It’s not uncommon to jumpstart an animal’s ability to digest grass by grabbing bugs from one animal and putting it in the right place. And, did you know, some animals eat poop on purpose for this very reason – rabbits, capibaras, hamsters, elephants, termites, pandas, koalas, and hippos – to colonize their gut?
And really, folks eat yogurt to populate their gut with good bacteria. Why not poo bacteria as probiotics? I actually think, as we learn more about our gut fauna, this will be come a more accepted course of action for folks with nasty bowel infections, colitis, or inflammatory bowel diseases.
What do you think?
Image of Kristen Paulson’s Anatomy and Guts Embroidery Hoop Art on Etsy (get your own!)
“A team led by Jay Keasling, a bioengineer at the Joint BioEnergy Institute in Emeryville, California, worked to extend the strategy to make more commonly used fuels. They used Escherichia coli, a bacterium into which it’s relatively easy to insert new genes. They started by creating two strains of E. coli, inserting genes for breaking down cellulose in one and genes for breaking down hemicellulose in the other. They then split each of these two strains into three groups and to each group added genes for one of three different metabolic pathways that allow the microbes to make chemical precursors for either gasoline, diesel, or jet fuel.”
Nice step towards making this happen.
Read this article…
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