Pause for more than just station identification

I am Charlie Schick (see my about page here). This blog has been paused for the time being. Go read my thought stream at molecularist.com.

I set up this blog to focus on things microbiological. While practical microbiology has been a growing interest, it is by no means my only one. Hence, while I thought I’d be able to feed this blog with it’s own content, it’s really become a subset of my main long-term blog at molecularist.com. Over there, I’ll tag post with practical microbiology, but you can also look at such tag like bacteria, fungi, and microbiology, too.

I suppose I’ll return here some day. But for now, with how things have been going here, it’s best to put this into hibernation until I can properly feed it.

Cheers.

PS I also have an associated Twitter stream: @usefulbugs. That, too, will go silent for now. You can keep following me at @molecularist.

Image by rick

“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: http://diybio.org, http://genspace.org/, https://www.facebook.com/BioCurious, http://openpcr.org/
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 molecularist.com]

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.

Read this article…

Trillium toasts to local ingredients, tastes – BostonHerald.com

“A Brookline home brewer cleared a major hurdle this week on the way to opening a brewery of “farmhouse”-style beer in Fort Point. “It’s not a come-and-have-pints-all-night type place, it’s a come-and-have-a-sampler type place,” said Trillium Brewing Co. owner Jean-Claude Tetrault, 34. Trillium, which will have a storefront with a small tasting bar, scored a zoning variance Tuesday that allows for the manufacturing of beer on the site. Tetrault will apply for state and federal licensing in the next few weeks.”

This is indeed a nice story. Looking forward to having a few of their beers.

[via @IDBoston]

Read this article…

PLoS ONE: The Gut as Reservoir of Antibiotic Resistance: Microbial Diversity of Tetracycline Resistance in Mother and Infant

“These findings reinforce the notion that the human GIT is currently a relevant environment for the spread of antibiotic resistances, even in the case of young infants that solely ingest maternal milk. Further analyses involving more mother-infant pairs will be required in order to establish whether the trends observed in this case study describe the general relationship between mother and infant antibiotic resistomes.”

This is really interesting. To me, mother-child form one closely tied ecosystem, so it’s not surprising that bacteria take advantage of that to move locations or capture resistance genes from other bugs. What’s good about a report like this is that it once again reinforces the need to re-evaluate the flow of organisms and information in the human-microbial ecosystem and implications for medicine and health.

Read this article…

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]

Read this article…

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]

Read this article…

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 <http://en.wikipedia.org/wiki/Luciferase> shows that luciferase is found in quite divergent organisms.

Read this article…

Predicting a Human Gut Microbiota’s Response to Diet in Gnotobiotic Mice

“A model community of 10 sequenced human gut bacteria was introduced into gnotobiotic mice, and changes in species abundance and microbial gene expression were measured in response to randomized perturbations of four defined ingredients in the host diet. From the responses, we developed a statistical model that predicted over 60% of the variation in species abundance evoked by diet perturbations, and we were able to identify which factors in the diet best explained changes seen for each community member. The approach is generally applicable, as shown by a follow-up study involving diets containing various mixtures of pureed human baby foods.”

Another great report I can’t read at the moment (no subscription). This sounds like a nice analysis of something everyone has been seeing. Looking to see effect of other diets, beyond the baby food tested.

Read this article…

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!

Read this article…