Chemically evolved bacteria

“European scientists have created an Escherichia coli strain with a separate genome using chlorinated DNA. The genome should be unable to transfer back into unmodified bacteria, leading to what the researchers call a ‘genetic firewall’.”

First arsenic, now chlorine. In my grad school days, we were studying DNA-protein interactions by modifying specific atoms on the DNA. With this bacteria, it would be interesting to see how the overall biochemistry and enzymatic changes. Opens up a whole new way of studying biochemistry.

And I’d really like to know how they set up their continuous culture system.

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Probiotics In Future May Be Prescribed For Your Neurological Well-Being – Medical News Today

“The study was led by Professor Mark Lyte and has been published recently in BioEssays. The researchers have proposed that neuroactive compounds if delivered via neurochemical-producing probiotics could help improve a host’s gastrointestinal and psychological health. These probiotics could be prepared for delivery of the compound using a unifying process of microbial endocrinology.”This paper proposes a new field of microbial endocrinology, where microbiology meets neuroscience,” said Lyte.”

I’ve seen a few papers talking about immunoregulation by gut bacteria. Here’s a report on neuroregulation. Pretty cool.

[via @microbeworld]

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Navy probe descends on bacteria power | SmartPlanet

“The U.S. Navy has enlisted some very tiny sailors to fuel their latest research vessel. Microorganisms are descending into the sea, enabling unmanned pods to gather data beneath the surface. Weeks later, (perhaps even years researchers say), the craft could emerge via power it had generated on board. No batteries required—just bacteria.”

This is cool.

[via @microbeworld]

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Rediscovered glowing mushroom could shed light on bioluminescence (Wired UK)

“Researchers believe that fungi make light just as the firefly does, using a chemical mix of a compound called luciferin and an enzyme luciferase. However, scientists haven’t yet identified the luciferin and luciferase in fungi which glow at all times rather than in bursts as fireflies do”

Dang. When I read this title, I was hoping it was some symbiotic bacteria that was glowing and there’d be some cool story as to how the fungi take up the bacteria. Alas, the fungi produces its own glow. But then, quite interesting that its done with luciferase, like fireflies. A quick look at Luciferase in Wikipedia <> shows that luciferase is found in quite divergent organisms.

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“DIYbio: hackspaces, open source & f*ck yeah ethics” a proposed SXSW session

I’ve done it. I’ve submitted a proposal to SXSW.

Alas, I was only able to submit one, despite all the ideas I had (anyone going to submit others, want to coordinate?)

I can edit this until 05 August, then I guess the voting begins. Next step for me is to determine if it’s a panel or solo or what. I don’t think I represent a typical DIYbiologist enough to go solo, so hence my preference for leading a panel with some of you hot-shots (you know who you are).

See current proposal below (with comments):

Title: DIYbio: hackspaces, open source & f*ck yeah ethics
Event: SXSW Interactive 2012
Organizer: Charlie Schick
Description: Humanity has been messing with biology for millennia. In the last 50 years, the tools have advanced to where we can design new remixes of organisms to make things for us, such as fuel, drugs, and the fresh smell of rain. What’s more, the open source and hackspace tinkering culture of the tech world has spilled over to create a nascent and vibrant community of do-it-yourself biologists. this session bring you up to speed with what DIYbio is, how you can get involved, and what are the resources available. [CS: Obviously I need to flesh this out. If this is a panel, I have a list of folks I’d like to be on it to represent the community (see supporting material below). If this is a workshop, then it’ll be a about tinkering.]
Questions answered:

1. What is DIYbio?
2. How can I get involved in DIYbio?
3. What are the resrouces I can access – info and instruction, space, pepole, events?
4. What is the future of making things thorugh biology?
5. Why is this important to the SXSWi crowd?

Level: Beginner
Supporting material:,,,
Category: Emerging Technology / Mobile [CS: Best category I could find. Not sure why mobile is still considered “emerging”.]
Tags: diybio, hackerspaces, science

And, hat tip to @100ideas and the folks from the DIYbio Continental Congress for the “f*ck yeah ethics” in the title.

[cross-posted to]

anti-mega at Interesting 2011

“The nature of the day was participatory, so instead of doing a presentation on stage (as I did at Interesting 2007), this time I attempted to get all 200ish people in the room trying, making and tasting things. By-the-by, this is also one of the hardest things I’ve done in years – scaling to 200 people took an awful amount of thinking and prep. Apologies if I’ve seemed scatty in the last few weeks.”

Always something fun and interesting from this guy. He’s a practical microbiologist too!

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The Dirty 11: Panel Names Pathogens That Pose Biggest Security Risk for Research – ScienceInsider

“A United States federal panel of scientists and security experts has identified 11 microorganisms that it wants designated as Tier 1 select agents, a new category of biological agents that would be subject to higher security standards than other pathogens and toxins used in biomedical research. The category would include anthrax, Ebola, Variola major and Variola minor, the Marburg virus, the virus that causes foot and mouth disease, and bacterial strains that produce the botulinum neurotoxin. At the same time, the panel has recommended dropping 19 pathogens and six toxins from the broader list of 82 agents that are currently governed by the select agent program.”

Fine by me. I’d never want to work with any of these in any case. And the “practical” uses aren’t necessarily the kinds of things I want to be practical with. Though, as with botox, what might we learn about medicine and biological mechanisms from these deadly bugs and viruses that might actually help us?

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ScienceShot: Why Wallabies Don’t Pass Methane Gas – ScienceNOW

“When cows digest food, they produce methane, a potent greenhouse gas, but when kangaroos chow down, their digestive tract is relatively methane-free. The difference comes down to one group of bacteria, new research suggests.”

How will this be applied to cattle to cut down on methane generation? Also (a question I have because I don’t have access to the paper), are there energy, efficiency, or source material requirement differences between a succinate- or methane-producing bugs? There might be reasons why wallabies have one and cows have the other.

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Bill Gates Funds Human Waste To Biofuel Project In Ghana | Fast Company

“Developing countries lack both clean water and clean energy sources. By converting soiled water into energy and clean water, a new project could wipe away both problems.”

Every since an organic waste conference I attended a few months ago, I’ve had anaerobic digestors on the mind – for farm, for municipal waste to energy, even for small-scale home systems. Decomposition of poop is an ancient process and we’re just ignoring it and pissing away the benefits. In a smaller and smarter planet, we’re going to have to take more control of the whole organics process – from food, to distribution, to waste, to energy and fertilizer. [I sense a new brainwave coming on…]

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Gut bacteria in Japanese people borrowed sushi-digesting genes from ocean bacteria | Discover Magazine

“Nori is, by far, the most likely source of bacteria with porphyran-digesting genes. It’s the only food that humans eat that contains any porphyrans and until recently, Japanese chefs didn’t cook nori before eating it. Any bacteria that lingered on the green fronds weren’t killed before they could mingle with gut bacteria like B.plebius. Ruth Ley, who works on microbiomes, says, “People have been saying that gut microbes can pick up genes from environmental microbes but it’s never been demonstrated as beautifully as in this paper.””

Japanese gut bacteria picking up genes from marine bacteria that live on seaweed. This blew my mind, but I am not surprised. We do know that there can be rapid gene changes in humans (ADH, lactase), why shouldn’t there be rapid changes in our fellow microbiomes? Very interesting implications with respect to therapy and diets.

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