A spaceship that tastes like Grape-Nuts

This morning, Marketplace Tech Report had a story on a new cellulose-based building material that could be made by genetically engineered bacteria — altered versions of the bacteria that naturally make stuff like kombucha. This tech sounds like it's got a long way to go from laboratory to the real world, but if they can perfect the process and make it large enough quantities, what you'd end up with a strong, inexpensive goop that could be used to build everything from medical dressings, to digital paper, to spaceships. Yes, you could theoretically use this stuff to make rocket casings, according to R. Malcolm Brown, Jr., a professor of cell biology at UT Austin. And if you can build a rocket from this stuff, you could also break the same material back down into an edible, high-fiber foodstuff. Read the rest

Lake Vostok bacteria: It's something new. No, it's not. Yes, it is, maybe.

Let's just play this safe and assume that, until more samples have been collected and detailed DNA analysis has been done, the real answer to the question, "Is bacteria found in Antarctica's Lake Vostok actually new to science or just contamination from the drilling?" is "We don't really know." This is a great example of why making scientific pronouncements from the field, before you've had time to do the really in-depth analysis that goes into writing a peer-reviewed research paper, can be problematic. Right now, you've got different camps of researchers making totally contradictory claims. Who is right is, so far, anybody's guess. Read the rest

"New" bacteria from Lake Vostok is not actually new (or from Lake Vostok)

"You can say anything you want in a press release". Sadly, that sentiment is too true. Turns out, recent reports of the discovery of previously unknown bacteria in samples hauled up from the waters of Antarctica's frozen Lake Vostok have turned out to be premature. The bacteria turned out to be contaminants carried by the drilling and collection apparatus. At Scientific American, Elizabeth Howell talks about this flub in the context of other stories where scientists bypassed peer review and announced findings to the newspapers first. Read the rest

Scientists discover life in Antarctica

“It appears that there lies a large wetland ecosystem under Antarctica’s ice sheet, with an active microbiology.” — There's some really exciting news coming from the land at the bottom of the world. Read the rest

How bad research gets published (and promoted)

In 2010, a group of scientists claimed to have found bacteria that could build its DNA using arsenic, instead of the phosphorous used by the rest of Earth's life forms. Within days, the research behind "arsenic life" was under serious scrutiny and we now know that it was totally wrong. But the work was peer-reviewed. It was sponsored by NASA. How do so many experts make such a big mistake? Dan Vergano at USA Today has an excellent article looking at just that — and it includes the peer review comments that helped the arsenic life paper get published. Though normally secret, Vergano got a hold of them through a Freedom of Information Act request. Read the rest

The future of fuel has gone to sh*%.

Scientists are studying panda poop to learn how to make better biofuels.

Viruses to the rescue

Technology Review's list of 35 Innovators Under 35 includes Timothy Lu, an MIT researcher who is engineering viruses designed to seek out and destroy biofilms — bacterial colonies that stick together on a surface, like bits of pear suspended in the world's most disgusting jell-o salad. Biofilms have been implicated in human disease, especially chronic infections like those that can happen in the urinary tract and inner ear. But the first place Lu's biofilm-eating viruses will likely be put to work is cleaning out ducts in industrial HVAC systems. (Via Carl Zimmer) Read the rest

Bacteriogoraphs of famous scientists in petri dishes

Zachary Copfer is a microbiologist and artist who creates portraits of his favorite scientists from living bacterial emulsions in petri dishes. I find what he wrote here to be inspiring:

When I was an undergraduate perusing a degree in Biology, I found myself utterly mesmerized by what I was learning. Each day’s lecture brought to my attention new insights into the complex systems at work in the world around me. The more I learned, the more mystified I became. Science grew into a way for me to revel in the beauty of the universe. I began to better understand and appreciate my place among all of the other particles floating in space. After obtaining my bachelors degree, I began working as a microbiologist in a commercial lab setting. Quickly I began to lose sight of all that I had found romantic about science. Shortly after this disinfatuation of science, I began an adventure into the field of photography. Photography developed into my new method of inquiry. Everything that I had missed about science I rediscovered in photography. For me, the two seemingly disparate fields of study served the same purpose, a way to explore my connection to everything else around me. As a former microbiologist recently turned visual artist, I seek to create work that is less of an intersection of art and science and more of a genuine fusion of the two.

"Bacteria Portraits, Bacteriogoraphy" (via Smithsonian)

Previously: "Photosensitive bacteria art" Read the rest

You are your bellybutton lint

Last January, at the Science Online conference, I noticed that there was a research group collecting swabs taken from the bellybuttons of scientists, science bloggers, and science journalists. That culture above? It's made from the bellybutton of Anton Zuiker, one of the organizers of that conference.

Beyond personalized petri dishes, what is the point of all this? Turns out, the goal is to learn more about the bacteria that lives on us. Some of the data from analyzing all those bellybutton samples is starting to come back, and it's turning up some interesting facts about the tiny ecological niches on our tummys.

About 18 months ago, researcher in the laboratory of Dr. Dunn, a North Carolina State University professor, came up with an idea to explore the ecology and evolution of daily life and wanted to find a spot on the body that could provide an understanding of the natural skin microbiome. They needed a place that was infrequently disturbed, avoided the scrubbing of daily wash and was common to all humans. There was no better choice than the bellybutton. Dunn and his clan of navel gazers then invited people from two conferences, 60 in total, to swab their bellybuttons and provide him with the samples, which he took back to his lab and cultured. The next several months were spent not only growing the bacteria, but also typing them to identify the species.

The first set of data is in review, but the results suggest that the bellybutton offers far more to our understanding of life and our journey through it.

Read the rest

What a chronic ear infection looks like

These are images from the inside of two human ears. The ear on the top doesn't get chronic infections. The ear on the bottom does. The difference seems to be the presence of a biofilm—a little colony of bacteria or other microorganisms that build up in a thin layer.

Biofilms happen all over the place in nature. That slime that covers the surface of rocks at the bottom of a river or lake? That's a biofilm. The slick, green coating on the underside of a boat when you pull it out of the water? That's a biofilm, too. And so is the plaque that builds up on your teeth.

In the case of ears, though, biofilms might explain why it's so difficult to treat chronic ear infections—biofilms are not easily killed off by antibiotics. The image above, showing a biofilm-coated ear drum, was captured using a new imaging device that produces pictures from reflected light, the same way ultrasound makes images from reflected sound waves. It's part of a research paper that presents evidence about the role of biofilms in ear infection and long-term hearing loss.

Check out Scientific American for more information

Via Bora Zivkovic

Read the rest

Exploring ancient water

I love it when news lines up almost perfectly with our editorial calendar. Next week, I've got a Science Question from a Toddler feature lined up that will explain how scientists can date reserves of water, and what makes ancient water special.

This week, in Antarctica, a team of Russian scientists made contact with some very ancient water. Yesterday, they drilled through the last of a more than 12,000-foot ice cover and into Lake Vostok, a reserve of liquid water that hasn't had contact with the outside world in 15-34 million years.

These researchers are looking for extremophile bacteria—semi-alien Earthlings that have evolved separately from the rest of their terrestrial kin. Bryan Walsh at Time.com explains:

The hope is that some form of new microbial life might exist within the waters of the lake, which remain liquid despite the cold thanks to heat generated by the pressure of all that ice and geothermal energy rising from the planet’s core. The environment of Lake Vostok is similar to that found on Jupiter’s icy moon of Europa. If life can survive in Lake Vostok, it might just be able to survive on another planetary body.

It’s still going to take the Russian scientists some time to actually take samples from the lake—with the Antarctic winter on its way, they’ll need to leave Vostok Station soon. And there are environmental concerns that the drilling process could contaminate the lake, which is pristine. The researchers used more than 66 tons (60 metric tons) of lubricants and antifreeze in the drilling process—chemicals that would have polluted Lake Vostok had they leaked through the ice, and contaminated any samples.

Read the rest

The world, as mapped by frequency of cholera cases

This really fascinating image comes from a Scientific American guest blog post about the appendix. What does the appendix have to do with cholera? Turns out, the more we study the appendix, the more it appears that this organ—once thought to be useless—is actually a storage system that allows your gut to repopulate itself with beneficial bacteria following a bout with a dramatic, gut-wrenching such as cholera.

This theory makes a lot of sense, but it hasn't been proven yet. The blog post, written by Rob Dunn, tells the story of a couple of studies that seem to add further support to the theory. In one, 11% of people with an appendix had a recurrence of Clostridium difficile infection, while 48% of those without an appendix had a recurrence.

Grendell’s results do not prove Parker is right. Science does not work that way. More tests, even true experiments, need to be done. Maybe there was something else that differed between individuals with and without their appendixes. Maybe the result only applies to the mostly white population Winthrop hospital serves. Maybe the immune system plays a more important or different role than Parker envisions. These “maybes” are part of what make science beautiful — the idea that each question, each test, and each day, lead to more questions. Every good question is a road that goes on forever, diverging and bounding forward, sometimes quickly, other times more slowly, as new paths emerge and some of the old ones run straight into brick walls.

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Instant holiday diet plan

Reduce your consumption of turkey this Thanksgiving by simply reading Maryn McKenna's report on drug-resistant staph bacteria infecting the U.S. meat supply. Read the rest

How yogurt can alter gene expression

Scientists don't actually know how the bacteria in yogurt and other fermented foods help humans digest food easier. But a recent study hit on a possible explanation. Turns out, some probiotics seem to be capable of altering gene expression in our native gut flora.

Jeffrey Gordon, a microbiologist at Washington University in St. Louis, and his team gave a commercially-available probiotic yogurt containing five strains of bacteria to healthy adult volunteers and administered the same five strains to mice that harbored a subset of genetically-characterized human gut microbes. The yogurt bacteria did not significantly alter population structure in any of the entrenched gut microbes, in humans or mice—a result that is not surprising, according to Mills. “To assume that you could eat a yogurt and numerically challenge what’s in your gut is kind of like dumping a gallon of Kool-Aid in your swimming pool and expecting it to change color,” he said.

But RNA sequencing of the human gut microbes in the mice revealed that the probiotic bacteria changed the expression of gut microbe genes encoding key metabolic enzymes, such as those involved in the catabolism of sugars called xylooligosaccharides, which are found in many fruits and vegetables. Mass spectrometry of metabolites in urine, which result from the ramped up metabolic processes in the probiotic-fed mice, confirmed the alterations, and when the researchers ran similar analyses on gut microbes from the human yogurt eaters, they found upregulation of the same genes.

This study won't be the final word on the subject of how probiotics work. Read the rest

Scientists simulate Europa

Researchers at the Universidad de Buenos Aires recreated conditions found on the surface of Jupiter's moon Europa in the lab, and then proved that some Earth organisms are capable of surviving in that extreme environment. At least, for three hours. It's one experiment in a growing body of work aimed at proving that Earth could seed other planets with life. Read the rest