electric bacteria

Bacteria on the surface of an electrode

Scientists have taught bacteria to feed on electricity. Because the bacteria feed on iron, they were well suited for this kind of study. From Popular Science:

Researchers at the University of Minnesota, St. Paul, have coaxed a species of bacteria into trading their usual diet of partially-oxidized iron for a small current of electricity–a trick that may eventually make the microorganisms useful producers of biofuels.

The bacterium involved in the study was Mariprofundus ferrooxydans, a species that makes its home around hydrothermal vents on the seafloor. Like other iron-oxidizing bacteria, M. ferrooxydans relies on a form of soluble iron, called ferrous iron, or Fe(II), as a source of the electrons it needs to breathe. When plenty of oxygen is present, ferrous iron readily gives up its extra electron to the oxygen, to become the more stable Fe(III), or ferric iron–the kind of iron oxide we know of as rust. But in lower-oxygen environments, M. ferrooxydans’ can do oxygen’s job for it, thereby gaining energy from the extra electron.

In their experiment, the researchers deposited some M. ferrooxydans onto the surface of an electrode, which was tuned to release electrons at the same energy level that Fe(II) would provide. To get the organisms started in their new habitat, the scientists also added some of the bacterium’s natural food–Fe(II)–to the mix.

After letting the microbes multiply over the surface of the electrode for four weeks, they scraped some away and started a new colony on an electrode with no Fe(II) around. Amazingly, the bacteria continued to thrive, even after some were transplanted onward to a third electrode. Some nutrients were still provided to this colony, the study noted, but in amounts much too small to support the bacterium’s apparent growth.

nanoparticles can improve battery performance

A new nanoparticle material may be useful in improving battery energy storage and lifetime. From Scientific American:

According to their paper in Nature Communications (published January 8^*), researchers from Stanford University and the SLAC National Accelerator Laboratory a new material described as a “sulfur-TiO2 yolk-shell nanoarchitecture with internal void space for long-cycle lithium-sulphur batteries.” This material can be used in the cathode of lithium-ion batteries to overcome a key obstacle that has stumped scientists for the past two decades.

This result – a fivefold increase in the amount of energy that can be stored in the battery (per unit of sulfur) plus a long life material that could revolutionize the rechargeable battery market.

According to Stanford’s Yi Cui, a researcher on the project that developed this material:

“After 1,000 charge/discharge cycles, our yolk-shell sulfur cathode had retained about 70 percent of its energy-storage capacity. This is the highest performing sulfur cathode in the world, as far as we know…Even without optimizing the design, this cathode cycle life is already on par with commercial performance. This is a very important achievement for the future of rechargeable batteries.”

computers and reciprocity

How do we relate to computers? You would think its a silly question but a researcher is interested in just that. He wanted to know if a computer helped us complete a task would we be more likely to help the computer than they would a computer that hadn’t done anything for him. What he found was interesting. We are more likely to help the computer that didn’t help us. From NPR:

So they placed a series of people in a room with two computers. The people were told that the computer they were sitting at could answer any question they asked. In half of the experiments, the computer was incredibly helpful. Half the time, the computer did a terrible job.

After about 20 minutes of questioning, a screen appeared explaining that the computer was trying to improve its performance. The humans were then asked to do a very tedious task that involved matching colors for the computer. Now, sometimes the screen requesting help would appear on the computer the human had been using; sometimes the help request appeared on the screen of the computer across the aisle.

“Now, if these were people [and not computers],” Nass says, “we would expect that if I just helped you and then I asked you for help, you would feel obligated to help me a great deal. But if I just helped you and someone else asked you to help, you would feel less obligated to help them.”

What the study demonstrated was that people do in fact obey the rule of reciprocity when it comes to computers. When the first computer was helpful to people, they helped it way more on the boring task than the other computer in the room. They reciprocated.

“But when the computer didn’t help them, they actually did more color matching for the computer across the room than the computer they worked with, teaching the computer [they worked with] a lesson for not being helpful,” says Nass.

This is only the beginning of what he investigated. More here.

dna data storage

DNA, RNA and their bases

In the January 23rd edition of Nature a team of scientists report using DNA to store poems, a picture and a recorded speech. From Science News:

Led by Nick Goldman, researchers from the European Bioinformatics Institute in England began by converting the five files into bits (technically, “trits” — they used a triplet code comprising zero, one and two). Then they translated that code into one made of As, Cs, Gs and Ts, the “letters” of DNA. So TAGAT replaces the “T” that begins line two of Shakespeare’s sonnet 18: “Thou art more lovely and more temperate.”  The team also incorporated a way to index the data — sort of a DNA version of the Dewey Decimal System — and an error correction code to keep the data clean.

Then the researchers sent their code to the instrumentation company Agilent Technologies in Santa Clara, Calif. There scientists read the code and used it to build millions upon millions of DNA molecules, which they sent back to the researchers via FedEx in a test tube inside a cardboard box.

When the test tube, about the size of a pinkie finger, arrived, Goldman and his colleagues sequenced the DNA, the same way researchers read the DNA of organisms, reconstructing the original files. The translation from data to DNA and back was free of errors, says Goldman.

DNA storage offers the potential of holding vastly more data in a smaller amount of space. It might also potentially be cheaper as the cost of DNA synthesis and sequencing continues to become less costly.

dogs, wolves and carbs

Domesticated dog breeds evolved long ago from the wolf. In a study published in Nature, researchers examined differences in the genomes of modern domesticated breeds and wolves and made some interesting discoveries. They expected differences in the nervous systems since the species behave differently. They also found many differences in genes effecting metabolism, especially digestion of carbohydrates. Domesticated breeds digest starches much better than wolves.  From Science News:

The new study focuses on genetic differences between 60 dogs representing 14 breeds and 12 wolves from around the world. Those changes, the researchers reasoned, could identify genes that were important in separating dogs from wolves.

The researchers determined the genetic makeup of groups of dogs and compared the results to those from wolves, concentrating on parts of the genetic instruction book that differ between the two species. As they had expected, the researchers uncovered differences in many genes relating to the brain. But the search also revealed lots of genes involved in starch digestion and metabolism, and in the use of fats. Dogs, the team found, have more copies than wolves do of the AMY2B gene, which produces an enzyme that breaks starch into easily digestible sugars.

Other genetic variants seem to contribute to dogs’ increased ability to convert a sugar called maltose to glucose, the sugar that cells prefer to burn for energy. Yet other genetic changes improve dogs’ ability to move glucose into their cells. Combined, the tweaks alter dogs’ metabolism so they can get more energy out of a carbohydrate-rich diet than wolves can, the researchers conclude. The scientists confirmed the effect of the genetic variants by identifying biochemical differences in starch metabolism in blood and tissue samples from dogs and wolves.

neanderthals cloning, continued

Tyler Cowen considers reasons why we wouldn’t want to clone neanderthals. There are many ethical questions on how we would deal with the offspring:

Then ask yourself some basic questions about Neanderthals: could they be taught in our schools?  Who would rear the first generation?  Would human parents find this at all rewarding?  Do they have enough impulse control to move freely in human society?  How happy would they be with such a limited number of peers?  What public health issues would be involved and how would we learn about those issues in advance?  What would happen the first time a Neanderthal kills a human child?  Carries and transmits a contagious disease?  By the way, how much resistance would the Neanderthals have to modern diseases?

What kinds of “human rights” would we issue to them?  Would we end up treating them better than lab chimpanzees?  Would they be covered by ACA and have emergency room rights?

We don’t know the answers here, but I would expect to run up against a number of significant fails on these issues and others.

neanderthal cloning

A Neanderthal man

A Harvard professor believes it is possible to bring back the Neanderthal species from extinction. To do so you would need “an adventurous surrogate” as he puts it. The Neanderthals have been extinct for more than 30,000 years, but traces of their DNA remain. George Church, a geneticist, says in theory you should be able to clone the DNA and create an embryo, which can be implanted in a surrogate and brought to term. The ethics of such an experiment are murky, to put it mildly.

More about it here [Der Spiegel] and here [New York Daily News].

berries and heart attacks

Berries

Berries seem to lower womens’ risk of heart attacks. From New York Times Well blog:

Beginning in 1991, researchers at Harvard tracked more than 100,000 women ages 25 to 42 with food-frequency questionnaires every four years through 2009. They recorded 405 fatal and nonfatal heart attacks in them over the period. The study was published last week in the journal Circulation.

After adjusting for many dietary, behavioral and physiological risk factors, the scientists found that compared with those below the 20th percentile in anthocyanin intake, those above the 80th percentile were 32 percent less likely to have a heart attack. Other flavonoids were not significantly associated with reduced risk.

Women who ate more than three servings of blueberries or strawberries a week — the most common anthocyanin-rich foods consumed — had a 34 percent lower risk than those who ate less.

poo transplants

Clostridium difficile.

Count on Ed Yong to keep us updated on the wonderful world of gut bacteria. Today he brings news of clinical trials where fecal transplants are used to ward off infection by C. difficile.  An excerpt is below. Click here for more.

Last week, I wrote about scientists who developed a stool substitute and used it to cure gut infections in two women. This sham poo contained 33 gut bacteria, which were meant to displace the harmful ones that were causing diarrhoea in the patients.

For decades, doctors have been doing the same thing using actual faeces. This unorthodox technique, known as a faecal transplant, has been used to treat over 500 people with recurring infections of the diarrhoea-causing bacteriumClostridium difficile.

The concept is inherently revolting, and many mistake it for pseudoscience. But faecal transplants work. Over 90 percent of patients make a full recovery, far greater than the proportion who responds to conventional antibiotics. (In fact, it may be antibiotics that cause recurring C.difficile infections in the first place, by annihilating the beneficial gut bacteria that normally keep such infections at bay.)

Some might argue that all of this amounts of anecdotal evidence. Faecal transplants have never been tested in a randomised clinical trial – the gold standard of medicine. But that objection no longer applies. The first results from a faecal transplant trial have been published in the New England Journal of Medicine, and they are a resounding vindication for the technique.

those long january mornings

The New York Times has an explanation of why it continues to stay dark in the mornings even after the solstice has passed and the days get longer. It has to do with the intricacies of elliptical orbit and axial tilt.

Earth’s tilt means that every day during the fall, the angle at which we view the Sun changes. It appears farther south and travels a shorter arc across the sky, affecting sunrise and sunset equally, and making the day shorter.

The changes in the solar time follow a different cycle. In the early 1600s, Keplerdiscovered that planets move faster at the part of their orbit that is closest to the sun, the perihelion. For Earth, perihelion comes a little after the winter solstice, so from November on, Earth is accelerating.

That increased speed means we reach the Sun’s maximum a little earlier each day, which pushes solar noon backward against clock time. That shift is amplified because the Sun is traveling a little south each day, while clocks only count its east to west traverse.

Add it all together and you get sunrise and sunset times that are not symmetrical. In the weeks before the winter solstice, sunrise is being pushed later by both the changing angle of the Sun and the slowing of solar time. But sunset is being pushed in both directions — earlier by the Sun’s angle and later by the change in solar time.

Read the whole explanation here.