Dovdox

When I was in graduate school, some colleagues once served a round of drinks in 50mL conical centrifuge tubes. If only someone had dipped a pipet into one of those shots, we might have beaten these guys to publication:

Researchers from [the University of Guelph's] Biodiversity Institute of Ontario (BIO) have discovered that mescal itself contains the DNA of the agave butterfly caterpillar — the famously tasty “worm” that many avoid consuming. Their findings will appear in the March issue of BioTechniques, which is available online now.

Tequila with worm

Grossed out yet? Well, they followed the party trick with a practical application, as described in their open-access article in BioTechniques:

We then successfully amplified and sequenced DNA from the 95% ethanol preservative of 70 freshly collected specimens and 7 archival specimens 7–10 years old. These results suggest that DNA extraction is a superfluous step in many protocols and that preservative ethanol can be used as a source of genetic material for non-invasive sampling or when no tissue specimen is left for further DNA analyses.

Instead of doing a tedious, time-consuming DNA extraction on an alcohol-preserved specimen, one can simply pull out some of the alcohol. Combined with new molecular identification techniques, that could save a lot of time and money in entomology labs. It might turn a few people off tequila, though.

In a new twist on the elegant sterile insect technique, researchers have now made a strain of Aedes aegypti mosquitoes where the females can’t fly. As the accompanying press release explains:

UCI researchers and colleagues from Oxitec Ltd. and the University of Oxford created the new breed. Flightless females are expected to die quickly in the wild, curtailing the number of mosquitoes and reducing – or even eliminating – dengue transmission. Males of the strain can fly but do not bite or convey disease.

When genetically altered male mosquitoes mate with wild females and pass on their genes, females of the next generation are unable to fly. Scientists estimate that if released, the new breed could sustainably suppress the native mosquito population in six to nine months. The approach offers a safe, efficient alternative to harmful insecticides.

Mosquito on a mirror. Image by Schristia.

Because the flightless phenotype only affects females, and the males remain fertile, the selective pressure against it should be pretty mild. These bugs should also be a lot easier to breed than strains with inducible sterility; as long as they’re in captivity getting free blood meals and protection from predators, the females should be able to mate and reproduce just fine.

Aedes aegypti is a major vector for Dengue fever, a nasty virus which infects upwards of 50 million people a year, so if this strategy works in the field, it could be a huge boon to public health. It could be even bigger news if they do the same thing with Anopheles, which transmits the ninth leading cause of death worldwide.

The original paper is open access, for those who want the details.

The apparent success of an HIV vaccine trial last year, after years of failures in the field, was a huge surprise to most virologists (including me). Now it looks like the vaccine regimen’s effect may have been only temporary:

An AIDS vaccine that appears to have worked at least partly in Thailand may only temporarily protect patients, with the effects starting to wane after a year or so, researchers reported on Thursday. That may explain why results of the experimental vaccine have been so difficult to interpret, said Dr. Nelson Michael, a colonel at the Walter Reed Army Research Institute of Research in Maryland, who helped lead the trial. Michael’s team is trying to find out how or why it might have worked. They surprised the world last September when they showed the experimental vaccine cut the risk of infection by 31 percent over three years.

That certainly isn’t what anyone wanted to hear, but against the backdrop of HIV vaccine research, it’s not entirely bad news. Even brief, weak protection is better than any previous vaccine has done against this virus, so it still looks like Michael and his colleagues are onto something. Fortunately, they’re now organizing a large follow-up study to analyze blood samples from the vaccinated volunteers. If they can find biological changes that correlate with protection, or “correlates of immunity,” then that could form the basis for a new round of vaccine development. I wish them luck. They’ll need it.

Lab-on-a-chip devices are a hot topic these days, and more and more researchers are finding cheap ways to make these tiny devices (see my earlier posts on these cool tools for background). Now, some Australian scientists have taken the process into the arts and crafts department:

This paper describes a new and simple concept for fabricating low-cost, low-volume, easy-to-use microfluidic devices using threads. A thread can transport liquid via capillary wicking without the need of a barrier; as it is stainable, it is also a desirable material for displaying colorimetric results. When used in sewing, threads have 3D passageways in sewed materials. The wicking property and flexibility of thread make it particularly suitable to fabricate 3D microfluidic devices. Threads can also be used with other materials (e.g., paper) to make microfluidic devices for rapid qualitative or semiquantitative analysis. These thread-based and thread-paper-based devices have potential applications in human health diagnostics, environmental monitoring, and food safety analysis, and are particularly appropriate for the developing world or remote areas, because of their relatively low fabrication costs.

They’re not kidding about the low fabrication costs. In the paper, they stitched some simple “devices” out of ordinary cotton thread and paper. They did “de-wax” the thread in a vacuum plasma reactor, which most folks probably don’t have sitting around, but there could be other ways of accomplishing that step. The other limitation is that the threads average 244µm in diameter, which is a good bit fatter than the features in a typical commercial lab chip. Maybe we could call these “millifluidic” devices instead of “microfluidic.”

Still, it’s a very cool idea, and it could have some unusual applications. Now if you’ll excuse me, I have to go stitch up a salmonella-detecting dish cloth.

Sometimes it’s easy to tell when a paper has been published in a British journal:

Frying meat on a gas hob may be more harmful to health than using an electric hob, because of the type of fumes it produces, suggests research published ahead of print in Occupational and Environmental Medicine. Professional chefs and cooks may be particularly at risk.

At this point, I have to pause and thank Wikipedia for helping me through the rest of this post. A hob, you see, is the British term for a stovetop. Or the target in a game of quoits. Or a male ferret. Now that we’ve cleared that up, let’s see how this particular quoits game is going:

The research team simulated the conditions found in a typical Western European restaurant kitchen, frying 17 pieces of steak, weighing 400 g each, for 15 minutes.

Mmm, steak.

They used either margarine or two different brands of soya bean oil to cook the steak on gas and electric hobs. The margarine contained a blend of soya bean, rapeseed, coconut and palm oils as well as vitamins A and D, but no hydrogenated fats.

Blech, margarine!

They measured the amount of PAH, aldehydes, and total particulate matter produced in the breathing zone of the cook. Napthalene – a banned chemical contained in traditional mothballs – was the only PAH detected and ranged from 0.15 to 0.27 ug/m3 air in 16 of the 17 meat samples. The highest levels were produced when frying with margarine on the gas hob. Higher aldehydes were produced during the frying of all the samples, while mutagenic aldehydes were produced for most samples. Overall levels ranged from undetectable to 61.80 µg/m³ air, but the highest levels were found when frying on the gas hob, irrespective of the type of fat used.

Take-home lesson: gas is worse than electric, if you’re concerned about the pollutants your steak generates. All of these levels are well below occupational safety thresholds, though, so what we really have here is a case where improved detection technology is finding “toxins” at levels that might not be any concern at all. Still, I’m going to stay on the safe side and grill my steaks. I never trusted that ferret anyway.

I’m sure this will be an interesting and informative talk. I just wish he could have put together a title without abusing the jargon of another field:

Dr. Francis Collins, director of the National Institutes of Health and recipient of the nation’s highest scientific honors, will address the National Press Club at a February 26 Speaker Luncheon. Topic of his talk will be “A New Era of Quantum Leaps in Biomedical Research.” The luncheon was originally scheduled for December, but postponed because of snow.

Once again, for those in the bleacher seats: the word “quantum” is a term of art in physics and chemistry, but it has been widely abused in lay usage. It means the smallest possible change in energy level. Electrons make quantum leaps to higher orbitals in an atom, because they can’t occupy intermediate energy levels. It’s like switching the TV from channel 2 to channel 3 – you can’t put it on channel 2.5, so the smallest possible change is the one you make. If it were even possible to make a quantum leap in biomedical research, it wouldn’t be something to brag about – it would be the smallest possible unit of progress.

Then again, if Collins is going to talk about the tendency of risk-averse study sections to fund incremental projects in narrowly-defined fields, rather than innovative efforts that cross disciplines, his title might be appropriate. But it’s still not something to brag about.

via PR Newswire for Journalists :: All Releases.

The Obama administration has announced the launch of a new website with troves of freely accessible data from across the government. The site includes major releases of several new datasets that agencies used to charge money for, as well as some that were simply unavailable to the general public. In addition, they appear to have collected direct links to a huge amount of information that was already online but hard to find, hidden behind the quirky site structures of individual agencies.

Even if you don’t need historical maps of mangrove habitats in the Southeast or detailed statistics on cancer incidence and population, it’s worth checking out the site just to get a feel for what’s now available. They certainly haven’t released everything about everything, but this is definitely a big step in the right direction.

Got data?

A paper in the latest issue of Cell Metabolism seems to promise a new generation of fat-loss drugs. The researchers knocked out sarcolemmal ATP-sensitive potassium (K_ATP) channels in mice, causing the animals’ muscles to burn more energy. As a result, the mice were thinner:

Inefficient fuel metabolism in K_ATP channel-deficient striated muscles reduced glycogen and fat body depots, promoting a lean phenotype. The propensity to lesser body weight imposed by K_ATPchannel deficit persisted under a high-fat diet, yet obesity restriction was achieved at the cost of compromised physical endurance. Thus, sarcolemmal K_ATP channels govern muscle energy economy, and their downregulation in a tissue-specific manner could present an antiobesity strategy by rendering muscle increasingly thermogenic at rest and less fuel efficient during exercise.

Of course, a fat-burning pill is the Holy Grail of the pharmaceutical industry, but if I were a drug developer, I’d hold off charging after K_ATP channel inhibitors. That’s because the abstract giveth, but the data taketh away. See, for example, Figure 7 (I don’t want to repost the figure here because Elsevier has been prickly about copyrights in the past, but the paper is open-access, so you can just click the link).

In the graph, note that the knockout mice are indeed less heavy than their wild-type colleagues on the obesity-inducing diet, but the weight curves are exactly the same. They’re both gaining. The experiment ends at 160 days, which means the mice were just hitting middle age.

There’s also the issue of side-effects, which we can practically guarantee in any potential K_ATP channel-targeting drug. The knockout mice had reduced endurance in an exercise test, but I’d bet a beer that’s not their only problem. Previous work has shown that this channel is a critical part of stress responses in both skeletal and cardiac muscle. Even taking a hypothetically perfect K_ATP channel-targeting compound for weight loss would be like popping a zit with a chainsaw: it might work, but is it worth the risk?

I’m not the only scientist skeptical of this approach, either. Greg Cooney, an Associate Professor at the Garvan Institute in Australia – who I’m guessing was a reviewer on the Cell Metabolism paper – just sent out a press release throwing some much-needed cold water on the weight-loss hype. In it, he reiterates the fundamental problem at the root of the obesity pandemic.

“The energy you use in your home can come from a coal-fired power station, hydroelectric power, or a wind turbine. You won’t know which because the end result is electricity. The energy that fuels your body can come from fats, proteins or carbohydrates. You won’t know which because the end result is ATP, or cellular energy,” says Cooney, concluding that “Your body will use the energy it needs and store the leftover fats, proteins or carbohydrates as fat. When you do the sums, it’s ultimately a matter of calories in and calories out.”

So how do you lose weight? Eat less and exercise more. Nobody likes that answer, but continuing to ask the question isn’t going to change it.

In research bound to haunt the nightmares of certain trial lawyers and state legislators, scientists at the University of South Florida have found that long-term cell phone use might actually be good medicine:

“It surprised us to find that cell phone exposure, begun in early adulthood, protects the memory of mice otherwise destined to develop Alzheimer’s symptoms,” said lead author Gary Arendash, PhD, USF Research Professor at the Florida ADRC. “It was even more astonishing that the electromagnetic waves generated by cell phones actually reversed memory impairment in old Alzheimer’s mice.”

Mice were exposed to cell phone signals from a centrally-located antenna.

Arendash’s experiment involved housing wild-type and Alzheimer’s-prone mice in cages placed around an antenna, which emitted signals near cell phone frequencies for two one-hour periods each day over the course of several months. This appears to be the first time anyone has looked at such a chronic, realistic exposure level to the same frequencies used by cellular phones, in a controlled laboratory setting.

That said, the usual caveats apply. Mice are not humans, and the Alzheimer’s mouse model in this study is an inbred strain that mimics many aspects of human dementia, but not all. Also, the experiment wasn’t really set up to detect tumors, which are the real focus of litigators’ and legislators’ ire. While the researchers did not find any visible masses in the brains of dissected mice at the end of the study, the sample size and length of the test weren’t really adequate to assess the animals’ cancer risks.

So using a cell phone might or might not increase your risk for cancer, but it might also prevent or treat Alzheimer’s disease. Choose your poison, but don’t be surprised if it turns out to be nontoxic.

As a microbiologist and drummer, I’ve been fascinated by the recent story from New Hampshire, where a woman appears to have caught gastric anthrax from an animal-hide drum:

State officials are trying to find everyone who attended the drum circle, offering to vaccinate them and hoping to gather information that will explain how one young woman contracted a case of gastrointestinal anthrax a short time after attending the event.

One paragraph, two bizarre medical events: catching B. anthracis from drumming, and getting the weird gastrointestinal form of the disease. While it’s sometimes been used as a cover story for bioweapons accidents (as during the Sverdlovsk incident), actual gastric anthrax is ridiculously rare. A PubMed search returns a whopping 15 hits from the biomedical literature about this form of the disease, and almost all of them are either reviews or basic research papers. You’re probably more likely to get struck by lightning while winning the lottery than to catch gastric anthrax.

Getting this freak disease from a drum head is just … well, there aren’t even words for this level of probability. And the weirdness just keeps coming:

On Thursday, New Hampshire officials confirmed that the strain of anthrax spores found on two drums used at the Dec. 4 drumming circle, as well as on an electrical socket at the United Campus Ministry, matched the anthrax strain that infected the woman. The officials have taken 56 other drums for testing. The woman, who is not a student, brought her own synthetic drum to the circle on Dec. 4.

Got that? She apparently ingested anthrax that must have been on someone else’s drum.

For its part, the CDC offers these tips for drum makers and drummers. They focus on the risk of catching inhalation anthrax from making drums, which is rare, but nowhere near as whack as what just happened in New Hampshire.