the effects of bad science


A new epidemic of measles has broken out in Wales. Vaccination rates fell after a paper linking the vaccine to autism was published in the 1998. The paper was later proven to be fraudulent. NPR reports:

More than 1,200 people have come down with measles so far this year, following nearly 2,000 cases in 2012. Many of the cases have been in Wales.

Childhood vaccination rates plummeted in Great Britain after a 1998 paper by Dr. Andrew Wakefield claimed that the vaccine for measles, mumps and rubella had caused autism in a dozen children. That study has since been proven , but it fueled fears about vaccine safety in Great Britain and the United States.

“This is the legacy of the Wakefield scare,” Dr. David Elliman, spokesman for the Royal College of Pediatrics and Child Health, told The Associated Press.

Most of the measles cases have been in children and teenagers between the ages of 10 and 18, according to British health officials. In that age group, vaccination rates dropped below 50 percent in some parts of England after the Wakefield paper was published.

fighting tuberculosis with rats

Image from NPR. Abdullah Mchumvu trains African giant pouched rats in Morogoro, Tanzania

Tuberculosis still kills 1.4 million people a year, mostly in the developing world. So it is still beneficial to create new diagnostic techniques, especially when they can be used in rural communities. NPR recently reported on a team of scientists who train African giant pouch rats to sniff out the bacterium in patients’ sputum:

The team trains the critters with a Pavlovian click-and-reward approach. When the rats are just a few weeks old, technicians teach the animals to associate a click sound with a small bite of mashed bananas and a special pellet of food. The next step is to link the scent of TB with the reward.

A trained rat can correctly pick out a TB sample about two-thirds of the time, Beyene says. The rate increases to about 80 percent when two or three animals are put on the task.

The rats aren’t as good as a trained pathologist in the U.S. with a microscope, but they get better results than many clinicians working in rural Africa can achieve, Beyene says. “In an African setting, the sensitivity of the microscopy ranges between 30 to 40 percent,” he explains.

So far APOPO only has around 32 rats in their TB program.

Currently the rats are being used to verify positive test results obtained from microscopic samples.

creating oligodendrocytes


Popular Science covers two papers that appear in Nature Biotechnology on the topic of creating new brain cells. Researchers have developed a method to take skin cells from mice and rats and turn them into oligodendrocytes, which are the type of cells damaged by multiple sclerosis and other disorders.

From Popular Science:

The type of cell that the researchers made is a young, immature version of an oligodendrocyte. Oligodendrocytes normally wrap the nerve fibers of the brain and spinal cord in a protective coating called myelin. With certain diseases, though, people lose that coating or suffer damage to it, which can lead to severe symptoms, such as losing control of the arms and legs.

One major idea researchers have for curing such diseases is adding myelin back by transplanting young, immature oligodendrocytes into the patient. The cells are then supposed to mature and wrap themselves around exposed nerve fibers they find. (Older, more mature oligodendrocytes don’t seem as prone to finding and sheathing exposed nerve fibers.) The idea has worked in lab animals genetically engineered to not have myelin—wohoo!—but there’s a drawback. Until now, researchers generally made oligodendrocytes from stem cells taken from embryos. That’s fine for mice and rats, but it’s difficult to harvest and grow enough embryonic human stem cells for transplants in people.

HIV testing by DVD

A recent paper in Lab on a Chip describes using a DVD player as a diagnostic tool. The researchers convert the optical drive into a laser scanning device that can count the number of CD4+ cells. From Phys Org:

Aman Russom, senior lecturer at the School of Biotechnology at KTH Royal Institute of Technology in Stockholm, says that his research team converted a commercial DVD drive into a laser scanning microscope that can analyse blood and perform cellular imaging with one-micrometre resolution. The breakthrough creates the possibility of an inexpensive and simple-to-use tool that could have far-reaching benefits in health care in the developing world.
“With an ordinary DVD player, we have created a cheap analytical tool for DNA, RNA, proteins and even entire cells,” says Russom. The so-called “Lab-on-DVD” technology makes it possible to complete an HIV test in just a few minutes, he says.
In a proof of concept demonstration, the researchers collected cell-type CD4 + from blood and visualized it using the DVD reader technology. Enumeration of these cells using flow cytometry is now standard in HIV testing, but the practice has been limited in developing countries.
HIV testing currently uses flow cytometry, which requires expensive equipment. If the DVD technique proves reliable, HIV testing can be done much more cheaply.

the see through brain

A mouse brain imaged using the CLARITY technique.

Brain research has been getting lots of press since President Barack Obama announced his BRAIN initiative to map the human brain. Earlier this week, Nature published a paper by a group of Stanford researchers or a new technique called CLARITY. This technique allows the researchers to make whole organs transparent. They can then use different chemical compounds to label and highlight specific cells or features of the organ. They were able to demonstrate on brain tissue. From Popular Science:

Making these images is an eight-day process. The Stanford researchers started by infusing a mouse brain with a hydrogel solution. They then put the gel and brain into an incubator to set. (Like making Jell-O! Except that the setting, in this case, required a higher temperature rather than a lower one.)

The set gel bound to and physically supported most of the things in the brain. The gel didn’t bind to lipids, or fats, in the brain, however. Such fat is opaque and surrounds each cell. When researchers extracted this unbound fat, they were left with a clear view of everything else, frozen in place. For example, proteins that were originally embedded in cell membranes and the little spines that come off of neurons both remained.

At this point, the researchers could add different molecules to color the parts of the brain they want to study and look at the whole thing under a light microscope.

hooked leaves kill bedbugs

The New York Times covers this paper on how bean leaves help fight bedbug infestations. The leaves in question have tiny hooks that trap the bedbugs’ legs as they crawl over them. Using these leaves are a common folk remedy for getting rid of bedbugs in Eastern Europe. From the New York Times :

The first task was to determine exactly how the hooks — the technical name is trichomes — worked. The process was viewed through an electron microscope, Dr. Loudon said. “The foot comes down onto the surface, but as it’s lifting up, it’s catching on these hooks,” she said. “The point is pointing down. So all of their legs get impaled.”

“And as soon as one leg gets caught,” she added, “they are rapidly moving legs around and try to get away on the surface. That’s when they get multiply impaled.”

On the natural leaves, bugs were snagged, on average, after six steps, or locomotory cycles. (In one cycle, each of the insect’s six legs moves once.) Once stuck, they tried to free themselves, but they usually ended up just flailing in place around the impaled limb.

vitamin d holds up under scrutiny

Vitamin D

Six studies confirm the health benefits of vitamin D

We often see headlines mentioning a chemical or vitamin has astonishing new health benefits, only to have those claims fall apart under more thorough investigation. Vitamin D is looking like it might be an exception. Science News highlights six studies on the vitamin’s health benefits:

  • An analysis of 24 clinical trials in children finds that kids getting vitamin D supplements had a 47 percent reduced risk of dental caries, researchers report in Nutrition Reviews.

  • A study of 242 healthy adults getting daily calcium supplements shows that those who also took modest vitamin D supplements of 800 IU per day saw their blood pressure decrease. Their top blood pressure number fell by 10 points on average after a year and their bottom BP number fell by four points. Writing in Nutritional Influences on Bone Health, the researchers also report that the vitamin D folks saw their heart rate decline from 74 to 70 beats per minute. The calcium-only group saw no improvement on average.

  • A 28-year study in which Danish scientists monitored the health of nearly 10,000 people finds that those who developed a tobacco-related cancer during that time had vitamin D levels at the study outset of 14.8 nanograms per milliliter of blood on average, compared with 16.4 ng/ml on average for everyone else. That report shows up in Clinical Chemistry.

  • BMJ reports in a review of 31 studies that pregnant women with vitamin D levels of less than 30 ng/ml had an increased risk of developing a complication such as preeclampsia or gestational diabetes.

  • Low vitamin D levels may hamper metabolism in blacks. A study in Nutrition Research finds that adult blacks averaged vitamin D of only 14.6 6 ng/ml compared with 25.6 ng/ml on average in whites. Blacks were also more likely to have insulin resistance, a condition in which cells fail to use the hormone insulin efficiently to process glucose. But when researchers compared groups with similar vitamin D levels, the differences in insulin resistance disappeared. That suggests that the higher burden of insulin resistance in blacks is at least in part the result of low vitamin D, they conclude.

  • Very low vitamin D might be linked to suicide risk. An analysis of military service members finds that people who committed suicide appear to have similar vitamin D levels on average compared with those who don’t. But a closer look finds that people with the very lowest levels, less than 15 ng/ml, were roughly twice as likely to commit suicide as people with vitamin D ranging from 17 to 41 ng/ml. That study appears in PLoS One.

red meat linked to cardiovascular disease


Carnitine, found in red meat and some energy drinks, has been linked to cardiovascular disease in a new study.

Consuming lots of red meat has long been thought to increase the chances of developing cardiovascular diseases. Researchers now believe they have evidence that a molecule called carnitine found in red meat is likely a key player in the link between the two. From The New Scientist:

Some bacteria in the intestine use carnitine as an energy source, breaking it down and producing a waste product called trimethylamine (TMA). The liver converts this into another substance, trimethylamine-N-oxide (TMAO), which is excreted in urine.

In mice, high levels of dietary carnitine shifted the types of bacteria present in the gut and increased the volume of TMAO produced tenfold. “Imagine a Petri dish full of bacteria,” says Hazen. “If you start feeding them carnitine, the ones that like carnitine more will reproduce and those that don’t will decrease.”

TMAO levels matter because the substance increases the uptake of “bad” cholesterol and prevents its destruction by macrophages – white blood cells – in artery walls. This causes a build-up of plaque that can lead to atherosclerosis.

In further tests, Hazen’s team found that meat-eaters produced higher levels of TMAO than vegans or vegetarians after they were fed carnitine, suggesting that they had more TMA-producing bacteria in their gut. “I’m not telling people to cut out red meat,” Hazens says. “But cut down the frequency and portion sizes.”

As a check, the researchers looked at the blood levels of carnitine and TMAO in human blood samples and determined whether there was a link to cardiovascular disease. And there was. From Scientific American:

[E]ven when they took l-carnitine supplements, vegans and vegetarians made far less TMAO than meat eaters. Fecal studies showed that meat eaters and non-meat eaters also had very different types of bacteria in their guts. Hazen says that a regular diet of meat probably encourages the growth of bacteria that can turn l-carnitine into TMAO.

To further make the case, researchers checked the levels of l-carnitine in the blood of nearly 2,600 people who were having elective heart check-ups. By itself, the nutrient didn’t seem to make a difference. However, people who had high levels of both l-carnitine and TMAO were prime targets for heart disease, further evidence that it’s the bacterial alchemy — not the l-carnitine alone — that poses the real threat.

The original research is published in Nature Medicine.

some links to get you through the weekend

An observer shows the shell of the western painted turtle

Here are some links to check out if you have some spare time this weekend:

crystal scaffolds

Crystalline sponge with guaiazulene guests (light blue). Image from Nature

Cyrstallographers everywhere will attest to how hard it can be to get some molecules to crystalize. Sometimes, there might not even be enough material there to attempt crystallization. Someone is working on a solution though. C&EN reports that researchers have generated a nanoscale scaffold that captures molecules in pores and allows x-ray crystal data to be collected on samples with as little as 80ng of material. From the magazine:

In X-ray crystallography, X-rays are shot through a single crystal of a compound. How they bounce, or diffract in crystallographic lingo, reveals the structure of the molecule that makes up the crystal. The technique has helped scientists visualize innumerable molecules, including antibiotics, industrial catalysts, and even artificial sweeteners.

A team led by Makoto Fujita, of the University of Tokyo, in Japan, reports it can use porous metal frameworks with large cavities as “crystalline sponges” that soak up guest molecules within their voids, putting the molecules in an ordered array that can be studied via X-ray crystallography (Nature, DOI: 10.1038/nature11990). The technique works on as little as 80 ng of material.

In one example, the researchers used a zinc-based crystalline sponge to soak up just 5 µg of miyakosyne A, a scarce marine natural product with a central methyl group that had defied stereochemical assignment. Using their crystal-free crystallographic technique, the team was able to identify the compound’s stereochemistry.

Check out the full study at Nature.