Tagbacteria

Gut–brain link could shed light on mental health

Nature reports:

Companies selling ‘probiotic’ foods have long claimed that cultivating the right gut bacteria can benefit mental well-being, but neuroscientists have generally been sceptical. Now there is hard evidence linking conditions such as autism and depression to the gut’s microbial residents, known as the microbiome. And neuroscientists are taking notice — not just of the clinical implications but also of what the link could mean for experimental design. […]

The evidence that probiotics affect human behaviour “is minimal to say the least”, Mazmanian acknowledges. Still, he says, a growing number of researchers are starting to look at some mental illnesses through a microbial lens.

Full Story: Nature: Gut–brain link grabs neuroscientists

Previously:

Networks, Bacteria, and the Illusion of Control

Can Bacteria Make You Smarter?

Humans Are Really Just Biomechanical Suit-Cities For Bacteria

Humans Are Really Just Biomechanical Suit-Cities For Bacteria

Archigram's Walking City

“The City Is A Battlesuit For Surviving The Future” Matt Jones wrote in 2009, referencing Archigram‘s Walking City. As I’ve noted before we fill that same role for bacteria.

Food guru Michael Pollan has picked up on the “we’re more bacteria than human” meme and written an long, impressive New York Times article about it. He doesn’t go so far as to bring up the theory that oil is actually the excrement of bacteria that live beneath the earth’s crust, not the decomposed organic matter from the surface, as suggested by Thomas Gold (and apparently some unnamed Russians). If Gould is right then humans are not just city-suits for bacteria, but also a waste disposal system for bacteria. This idea led Reza Negarestani to obliquely postulate that global warming will actually function to make the surface of the earth hot enough for those particular bacteria to live on the surface of the earth as well. Which means we’re doing, like, triple duty for our bacterial masters.

No, Pollan doesn’t go into any of that weird shit. He’s more practical, writing instead about the role that bacteria has in our health. For example, obesity, heart disease and other health issues may depend on what kind of gut bacteria we’re carrying around. This may pose some more challenges for Soylent, the food substitute, because it turns out there’s stuff in food that we don’t digest but feeds our bacteria.

Of course this reminds me of the 90s gene craze (“the obesity gene,” the “addiction gene,” the “wearing white socks with dress shoes gene”) and the 00s neuroanatomy craze. The upside is that a bacteria-focused model of health is less fatalistic than the genetic or neuroanatomical models — you can change your bacteria, you can’t change your genes. But there’s plenty of room for woo and quackery and unfulfilled promises. That’s not lost on bacteria researchers. Pollan writes:

My first reaction to learning all this was to want to do something about it immediately, something to nurture the health of my microbiome. But most of the scientists I interviewed were reluctant to make practical recommendations; it’s too soon, they told me, we don’t know enough yet. Some of this hesitance reflects an understandable abundance of caution. The microbiome researchers don’t want to make the mistake of overpromising, as the genome researchers did. They are also concerned about feeding a gigantic bloom of prebiotic and probiotic quackery and rightly so: probiotics are already being hyped as the new panacea, even though it isn’t at all clear what these supposedly beneficial bacteria do for us or how they do what they do. There is some research suggesting that some probiotics may be effective in a number of ways: modulating the immune system; reducing allergic response; shortening the length and severity of colds in children; relieving diarrhea and irritable bowel symptoms; and improving the function of the epithelium. The problem is that, because the probiotic marketplace is largely unregulated, it’s impossible to know what, if anything, you’re getting when you buy a “probiotic” product. One study tested 14 commercial probiotics and found that only one contained the exact species stated on the label.

That didn’t stop Pollan from seeking out a little bit of practical advise, which mostly consists of: eat a variety of fiber sources, don’t load up too much on processed foods, relax a little about hygiene and eat pre-biotics like kimchi, sauerkraut and yogurt. Your bacterial masters will thank you for it.

Full Story: New York Times Magazine: Some of My Best Friends Are Germs

Cities Of The Future, Built By Drones, Bacteria, And 3-D Printers

generative architecture
Above: generative cities and architecture by Aranda & Lasch

Futurist Chris Arkenberg outlines a possible scenario for urban planning and architecture:

As complex ecosystems, cities are confronting tremendous pressures to seek optimum efficiency with minimal impact in a resource-constrained world. While architecture, urban planning, and sustainability attempt to address the massive resource requirements and outflow of cities, there are signs that a deeper current of biology is working its way into the urban framework.

Innovations emerging across the disciplines of additive manufacturing, synthetic biology, swarm robotics, and architecture suggest a future scenario when buildings may be designed using libraries of biological templates and constructed with biosynthetic materials able to sense and adapt to their conditions. Construction itself may be handled by bacterial printers and swarms of mechanical assemblers.

Full Story: Fast Coexist: Cities Of The Future, Built By Drones, Bacteria, And 3-D Printers

This reminds me of the recent sci-fi short story “Crabapple by Lavie Tidhar:

Neighborhoods sprouted around Central Station like weeds. On the outskirts of the old neighborhood, along the Kibbutz Galuyot Road and Siren Road and Sderot Menachem Begin, the old abandoned highways of Tel Aviv, they grew, ringing the immense structure of the spaceport rising high into the sky. Houses sprouted like trees, blooming, adaptoplant weeds feeding on rain and sun, and digging roots into the sandy ground, breaking ancient asphalt. Adaptoplant neighborhoods, seasonal, unstable, sprouting walls and doors and windows, half-open sewers hanging in the air, exposed bamboo pipes, apartments growing over and into each other, growing without order or sense, creating pavements suspended in midair, houses at crazy angles, shacks and huts with half-formed doors, windows like eyes–

In autumn the neighborhoods shed, doors drying, windows shrinking slowly, pipes drooping. Houses fell like leaves to the ground below and the road cleaning machines murmured happily, eating up the shrunken leaves of former residencies. Above ground the tenants of those seasonal buoyant suburbs stepped cautiously, testing the ground with each step taken, to see if it would hold, migrating nervously across the skyline to other, fresher spurts of growth, new adaptoplant blooming delicately, windows opening like fruit–

For more of Arkenberg check out our interview with him. Want to learn to think like he does? Here’s his guest post listing his favorite books on systems thinking.

And for more big, mad ideas about architecture and cities check out:

Paul Laffoley

The Fab Tree Hab

Archigram

Conway’s Game of Life generates a city

Aranda & Lasch’s generative architecture

The Biocurious DIY BioPrinters

Biocurious InkJetBioPrinter

bioprint petri dish

The Biocurious biohacker lab in the San Francisco Bay Area (Sunnyvale, specifically) is working on a couple of DIY bioprinters, InkJetBioPrinter and the HackteriaBot.

They’re built out of old CD-ROM drives, recycled ink cartridges and a open source Arduino boards. So far I think they just print bacteria? From the InkJetBioPrinter page:

We’ve disassembled an abandoned HP 5150 inkjet printer for use as a bioprinter. So far, we’ve pried open some ink cartridges, filles the black cartridge with arabinose, printed the BioCurious logo on filter paper, put the paper on a lawn of pGLO E. coli, and watched our logo light up in GFP!

Check out some pics on our Flickr group here: http://www.flickr.com/groups/bioprinter

Next, we want to start printing live cells, starting with E. coli. We’ll probably print the cells on a sheet of filter material and put it onto an agar plate, or pour a thin, dense layer of agar on a support material, and feed that into the printer directly. We’ll see…

(via H+ Magazine)

Scientists Can Now Rewrite DNA

TAG

MIT and Harvard researchers have developed technologies that could be used to rewrite the genetic code of a living cell, allowing them to make large-scale edits to the cell’s genome. Such technology could enable scientists to design cells that build proteins not found in nature, or engineer bacteria that are resistant to any type of viral infection.

The technology, described in the July 15 issue of Science, can overwrite specific DNA sequences throughout the genome, similar to the find-and-replace function in word-processing programs. Using this approach, the researchers can make hundreds of targeted edits to the genome of E. coli, apparently without disrupting the cells’ function.

MIT News: Scientists unveil tools for rewriting the code of life

(via Richard Yonck)

Bacteria Loves Caffeine Too

Think you live on caffeine? You’re still no match for a newly described bitty bacteria called Pseudomonas putida CBB5. These little guys can feast on pure caffeine all day—and presumably all night—long. And researchers have now located just how they accomplish this arguably admirable feat.

Celebrated and cursed, caffeine is actually an alluring blend of carbon, hydrogen, nitrogen and oxygen, and the clever bacterium uses specialized enzymes as it “breaks caffeine down into carbon dioxide and ammonia,” Ryan Summers, a doctoral researcher in chemical and biochemical engineering at the University of Iowa, said in a prepared statement.

Scientific American: Newly Discovered Bacteria Lives on Caffeine

Did Scientists Discover Bacteria in Meteorites?

Doesn’t look like it. P.Z. Meyers writes:

Fox News broke the story, which ought to make one immediately suspicious — it’s not an organization noted for scientific acumen. But even worse, the paper claiming the discovery of bacteria fossils in carbonaceous chondrites was published in … the Journal of Cosmology. I’ve mentioned Cosmology before — it isn’t a real science journal at all, but is the ginned-up website of a small group of crank academics obsessed with the idea of Hoyle and Wickramasinghe that life originated in outer space and simply rained down on Earth. It doesn’t exist in print, consists entirely of a crude and ugly website that looks like it was sucked through a wormhole from the 1990s, and publishes lots of empty noise with no substantial editorial restraint. For a while, it seemed to be entirely the domain of a crackpot named Rhawn Joseph who called himself the emeritus professor of something mysteriously called the Brain Research Laboratory, based in the general neighborhood of Northern California (seriously, that was the address: “Northern California”), and self-published all of his pseudo-scientific “publications” on this web site. […]

We’ve actually got to look at the claims and not dismiss them because of their location. […]

Reading the text, my impression is one of excessive padding. It’s a dump of miscellaneous facts about carbonaceous chondrites, not well-honed arguments edited to promote concision or cogency. The figures are annoying; when you skim through them, several will jump out at you as very provocative and looking an awful lot like real bacteria, but then without exception they all turn out to be photos of terrestrial organisms thrown in for reference. The extraterrestrial ‘bacteria’ all look like random mineral squiggles and bumps on a field full of random squiggles and bumps, and apparently, the authors thought some particular squiggle looked sort of like some photo of a bug. This isn’t science, it’s pareidolia. They might as well be analyzing Martian satellite photos for pictures that sorta kinda look like artifacts.

Pharyngula: Did scientists discover bacteria in meteorites?

You can find the paper here if you’d like to check it out for yourself.

Previous coverage of astrobiology can be found here.

Hong Kong Group Building Encrypted Bacterial Data Storage

Chinese University of Hong Kong iGem

Data encryption and storage has always been an important branch of research in computer engineering. In our project, we explored the possibility of harnessing a biological system as an alternative solution for data en/decryption and storage. Using bacteria as the information storage device is not new. However the practicability of previous research is being doubt due to the limited size of information available to be inserted into the bacteria.

We recognized the current barricades in developing a truly useful system and we forecasted the indispensable modules that one would be anticipating when putting fantasy into reality. This year, we have proposed a model that is a true, massively parallel bacterial data storage system.

In addition we have created an encryption module with the R64 Shufflon-Specific Recombinase to further secure the information. Together with the data proof-read/correction and random access modules developed, our expectation is high – we believe this could be an industrial standard in handling large scale data storage in living cells.

Team:Hong Kong-CUHK – 2010.igem.org

(via Wade)

Arsenic-Based Life Possible, But Not Certain

Mono Lake

Boing Boing’s Maggie Koerth-Baker adds a quick dose of realism and clarity to this morning’s NASA announcement:

Not everybody agrees that this research proves the bacteria are capable of replacing phosphate with arsenic. You can read more about that debate in the really nicely done article at Nature News that I’m quoting above.

Also, even if this is proof that phosphate isn’t necessary for life, we still don’t know whether the bacteria in question actually replace their phosphate in the wild. Right now, this is something humans are convincing it to do in a petri dish. That’s why it’s not entirely fair to say that weird life has been discovered—all this paper does (if it stands up to the coming onslaught of scrutiny) is show that weird life is, in fact, possible.

But that’s still a pretty big deal. However you slice it, this is an extremely interesting little bacterium. It isn’t alien. It still has the same basic DNA structure we all know and love. It just might be able to use different chemicals to build that old, familiar structure. And that’s pretty cool on its own.

Also, Mono Lake sounds pretty cool:

A couple of years ago, scientists found bacteria in California’s Mono Lake that used arsenic compounds, rather than water, as an ingredient of photosynthesis. In fact, there’s been a lot of weird life research centered around Mono Lake. Hot, salty, low in oxygen, and high in lots of other useful chemicals, the Lake has been described as a here-and-now model of the old primordial soup.

Boing Boing: Weird life found on Earth—kind of, maybe

Photo by Chris Streeter

NASA Discovers New Life on Earth: Bacteria with Arsenic-Based DNA

Arsenic

Update: Please see this update on how, although this research is significant, it doesn’t necessarily indicate that there is arsenic-based bacteria in the wild.

Evidence that the toxic element arsenic can replace the essential nutrient phosphorus in biomolecules of a naturally occurring bacterium expands the scope of the search for life beyond Earth, according to Arizona State University scientists who are part of a NASA-funded research team reporting findings in the Dec. 2 online Science Express.

It is well established that all known life requires phosphorus, usually in the form of inorganic phosphate. In recent years, however, astrobiologists, including Arizona State University professors Ariel Anbar and Paul Davies, have stepped up conversations about alternative forms of life. […]

Davies has previously speculated that forms of life different from our own, dubbed “weird life,” might even exist side-by-side with known life on Earth, in a sort of “shadow biosphere.” The particular idea that arsenic, which lies directly below phosphorous on the periodic table, might substitute for phosphorus in life on Earth, was proposed by Wolfe-Simon and developed into a collaboration with Davies and Anbar. Their hypothesis was published in January 2009, in a paper titled “Did nature also choose arsenic?” in the International Journal of Astrobiology.

PhysOrg: Deadly arsenic breathes life into organisms

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