Patterns of Gene Flow Define Species of Thermophilic Archaea: PLoS Biology

“Patterns of homologous gene flow among genomes of 12 strains from a single hot spring in Kamchatka, Russia, demonstrate higher levels of gene flow within than between two persistent, coexisting groups, demonstrating that these microorganisms fit the biological species concept. Furthermore, rates of gene flow between two species are decreasing over time in a manner consistent with incipient speciation.”

This is a really cool paper analyzing speciation in action. It shows how microbes slowly become less likely to swap genetic information as they differentiate. A key concept, too, is that each species has its own genetic island.

Great stuff.

Read this article…

Influence of Milk-Feeding Type and Genetic Risk of Developing Coeliac Disease on Intestinal Microbiota of Infants: The PROFICEL Study

“This study demonstrates that the milk-feeding type and the HLA-DQ genotype differently influence the bacterial colonization pattern of the newborn intestine during the first 4 months of life and, therefore, could also influence the risk of developing CD in later life. Breast-feeding reduced the genotype-related differences in microbiota composition, which could partly explain the protective role attributed to breast milk in this disorder.”

Interesting study doing two things: 1) showing an effect of genotype on bacterial populations in the gut – and that they are different for those at risk for celiac disease; and, 2) showing a difference between the bacterial populations of breast-fed and formula-fed children, and a possible microbial reason why breast-feeding protects against celiac disease.

Very cool. And scary how it makes such good sense.

Read this article in PLoS ONE.

Crowd-Sourcing Drug Discovery

“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…

Biodiversity of Indigenous Saccharomyces Populations from Old Wineries of South-Eastern Sicily: Preservation and Economic Potential

“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.

Vaccine development: Man vs MRSA : Nature News

“For decades, Robert Daum has studied the havoc wreaked by methicillin-resistant Staphylococcus aureus. Now he thinks he can stop it for good.”

Excellent story of the fight against MRSA by the guy who first made us aware of it.

 

Read this article…

Image from Nature

China’s Sequencing Powerhouse Comes of Age

“With new sequencing centers in Europe and the United States, BGI hopes its growing clout will help deliver the benefits promised by genomics—and revenue to pay off a mounting debt.”

Genomics at a scale only China could do.

Oh, my.

Read this article…

Ecosphere Associates, Inc.: Closed Ecosystem, Self Contained Aquarium

“The Original EcoSphere® is the world’s first totally enclosed ecosystem – a complete, self-contained and self-sustaining miniature world encased in glass. Be wary of inferior and lower quality imitations. Easy to care for, an EcoSphere is an incredible learning tool that can provide powerful insights about life on our own planet… and provide a glimpse of technology that’s shaping the future of space exploration.”

So cool. Will have to get one some day. [via @curisma]

Read this article…

UM Carey Law | Federal Regulation of Probiotics

An Analysis of the Existing Regulatory Framework and Recommendations for Alternative Frameworks

A team of researchers at the University of Maryland Baltimore is studying federal regulation of probiotics under a grant from NIH’s Human Microbiome Project (HMP). A portion of HMP funds were set aside to study the Ethical, Legal, and Social Implications (often referred to as the ELSI issues) of the Project’s scientific goals. The probiotics project is an interdisciplinary collaboration between faculty members from the University of Maryland Schools of Law, Pharmacy and Medicine.

This site is chock-full of info on probiotics policy, regulations, and science. Really good stuff.

Read this article…

Welcome, Bottlenose Intelligent Social Dashboard. What took ya?

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.

PLoS Biology: How Bacteria Turn Fiber into Food

“Now, a new study by Eric Martens, David Bolam, and colleagues has looked into how a pair of the most common species of gut bacteria metabolize polysaccharides, showing that each bacterium is highly specialized. Using a high-throughput system for feeding the bacteria dozens of kinds of carbohydrates, one at a time, and tracking the bacteria’s gene expression, they were able to see how these microbes have tailored themselves to fill specific niches in the gut.”

This is a really good study. For me, a better understanding of the gut metabolic ecology will allow for the development of better probiotics. One interesting finding in this study is that some bug don’t grow well on simple sugar because their sensors are built for complex sugars. Made me think of folks in developed world and what effect eating more simple sugars (high-fructose corn syrup) has on gut flora and any consequential obesity.

Read this article…