In the dreams of crime scene investigators, no doubt, they can feed a piece of hair into a machine and see a reconstruction of what the owner looks like. There’s a hint of that fantasy in the news that Dutch scientists have developed a test intended help police tell from a crime scene DNA sample the color of a suspect’s eyes. This information is gleaned from examining six single nucleotide polymorphisms, small genetic markers that are used in DNA fingerprinting, and could potentially help steer investigations when there are few other leads on a suspect and there is no match in police DNA databases. But the test, which can tell whether someone has blue, brown, or indeterminate (which encompasses green, hazel, grey, etc.) eyes with an average of 94% accuracy, doesn’t seem to have been tested outside of Europe, which raises questions about how well it would work in populations with greater diversity. It’s also a little hard to feature how you could bring this information to bear in a vacuum of other details—you’d want to avoid hauling someone in just because they looked suspicious and have the same eye color as the readout for the perp. At the moment, the test is not accurate enough to be introduced as evidence in court, which could be a bad thing or a good thing…depending on how many Philip K. Dick novels you’ve read.
Image courtesy of wetwebwork / flickr
What’s the News: We’ve long had signs that when it comes to inheritance, DNA isn’t the be-all, end-all. Trees that have the exact same genes but were raised in different greenhouses behave differently. Worms with genes that impart long life can pass on that longevity to their progeny—even if they don’t pass on the genes. Both of these phenomena, we’ve discovered, come from epigenetic changes in tags attached to DNA that control whether genes get expressed.
But every now and then we get a whiff of other possible routes for inheritance, even stranger than that. A new paper in Cell reports that worms whose grandparents had the ability to fight viruses using a fleet of tiny RNA molecules retain these molecules even when they don’t have the genes for them. They can pass these molecules down for more than a hundred generations.
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Sequencing the DNA in a scoop of dirt can tell scientists what creatures are living nearby, a new study using soil from safari parks shows, and the amount of DNA present can even tell how many individuals of each species there are, which could allow field biologists to get preliminary surveys of species. But though the team managed to identify nearly all the species they had expected in the parks, from wildebeest to elephants, they are still addressing how to take samples that accurately represent the area’s biodiversity—one would have to avoid elephant latrines or wildebeest sleeping areas, for instance—and there is the additional problem that rare or small creatures, like insects, might easily be missed. That said, it’s still an unusual and interesting way to take a look at an area’s inhabitants without actually tracking them down.
Read more at Scientific American.
Image courtesy of malcyzk / flickr
What’s the News: One of biologists’ favorite fantasies is a doctor who can fit inside a cell. This tiny physician, likely a device built from DNA, would make diagnoses by sensing molecules floating around the body that are signatures of certain diseases and would then release the appropriate drug.
While that vision is still a long way off, scientists have taken a significant step in that direction with a system that detects problems at several levels of cells’ machinery.
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Diagram of the new DNA circuit
What’s the News: Researchers have built the most complex DNA-based computer yet, a circuit of 130 strands of DNA that can compute the square root of numbers up to 15. The system, reported today in Science, is made of biological logic gates, which do computations using DNA strands’ natural propensity to zip and unzip. This new method is easily adapted for different calculations and can be automated, meaning it could be used to build much larger circuits.
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What’s the News: Researchers have known for decades that what a woman eats during her pregnancy can impact her child’s weight later in life. Now, a new study shows a possible mechanism for how mom’s diet affects baby’s weight: Epigenetic changes—changes that can increase or decrease the expression of a particular gene but don’t alter the genetic sequence—to a gene involved in fat metabolism can be passed from mother to child during pregnancy.
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The bacterium called Neisseria gonorrhoeae is what gives humans the sexually transmitted infection gonorrhea. And it also takes something: human DNA. Northwestern University researchers report in the journal mBio that they’ve found pieces of human DNA in samples of the bacteria.
Gonorrhea is one of very few diseases exclusive to our species, and is one of the oldest recorded diseases in human history. An ancient disease that resembles gonorrhea’s symptoms is even described in the Bible, according to Hank Seifert, senior author of a paper on the gene transfer. [Popular Science]
Seifert and colleague Mark Anderson looked at 14 different samples of N. gonorrhoeae. Three of them possessed the chunk of human DNA. And they only saw it in the gonorrhea bacteria:
The pair looked for the same human DNA fragment in the genetically related bacterium Neisseria menigitidis, known to cause meningitis. “We screened many isolates and it wasn’t present,” says Seifert. That means the transfer to N. gonorrhoeae must have occurred since the two bacterial species diverged around 200,000 years ago. [New Scientist]
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As more hospitals have begun using DNA testing to analyze babies with birth defects, doctors have occasionally discovered that a family’s little bundle of joy is also a product of incest. Since this is a new dilemma brought on by the spread of technology, doctors are now debating how to handle these incest surprises.
Geneticist Arthur Beaudet at Baylor College of Medicine addressed the issue yesterday in an article in the medical journal The Lancet. The genetic test, the single nucleotide polymorphism-based array, helps doctors identify missing genes (and can therefore help explain a child’s birth defect or disability)–but it also identifies swaths of identical DNA that a child may have inherited from two closely related parents.
In the few months that Baylor has been performing these detailed genetic tests, there have been fewer than 10 cases of consanguinity — the phenomenon of inheriting the same gene variations from two closely related people, said Dr. Arthur L. Beaudet, chairman of Baylor’s department of molecular and human genetics. However, wider use of such testing in children with disabilities is expected to identify additional cases of incestuous parentage. [ABC News]
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Considering the huge numbers of species that have had their DNA sequenced in the wake of the genomics revolution, it might be surprising that scientists are so excited about a tiny freshwater crustacean. But this one is special: The genome of the water flea contains a staggering 30,907 genes—the most ever seen in an animal, and about 8,000 more than humans have.
Daphnia has a large number of never-before seen genes…. “More than one-third of Daphnia‘s genes are undocumented in any other organism — in other words, they are completely new to science,” said Don Gilbert, coauthor and Department of Biology scientist at IU Bloomington. [Discovery News]
According John Colbourne, coauthor of the study in Science, those never-before-seen genes are not dead weight, but rather some of the most important in the crustacean’s genome for responding to changes in its environment.
Not all of the crustacean’s genes are active at any given time. Rather, a large portion of them are switched on or off with changes in the flea’s environment. They are “more or less environment-specific,” Colbourne says. Although they are “coding for the same proteins, they’re being expressed differently depending on what environmental stresses you expose the animal to.” [Scientific American]
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Welcome to the family of critters with sequenced genomes, orangutans. In Nature this week, scientists unveil the draft DNA sequencing of our great ape cousins—the only great apes that live exclusively in Asia.
The researchers assembled the draft genome of the female Sumatran orangutan (Pongo abelii) using a whole-genome “shotgun” strategy, an old-fashioned approach that cost about $20 million. In addition, the researchers gathered sequence data from five wild Sumatran orangutans and five Bornean orangutans (Pongo pygmaeus) using a faster and thousandfold cheaper next-generation platform. [LiveScience]
What did scientists find in there? For one thing, orangutans share about 97 percent of the their genome with humans, compared to the 99 percent we famously share with chimpanzees. The two orangutan species—inhabiting the Indonesian islands of Borneo and Sumatra—diverged about 400,000 years ago, lead author Devin Locke says. That’s much more recently than scientists had thought.
They also discovered that over the last 15 million years, orangutan DNA changed at a different rate than either ours or chimps’. Orangutans have undergone fewer mutations of the DNA, have a lower gene turnover rate, and have fewer duplicated DNA segments.
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Putting on clothing to protect our woefully hair-deficient bodies is one of the key moments in the history of becoming human. Just when our species took this step, however, is open to a fair amount of guesswork—scientists can’t exactly dig up fossilized parkas and trousers. But what scientists can do is determine roughly when two species diverged, and that has made all the difference: Using the lice that have traveled with people for thousands of years, a team has tracked the time that humans first became dedicated followers of fashion—perhaps as long as 170,000 years ago.
The key to the study by David Reed and colleagues, which appears in Molecular Biology And Evolution, is that there are two kinds of lice that hang around humans: the head lice that live on our scalp, and the body lice that live in our clothes. At one point in the past these two shared a common ancestor, Reed reasoned, and the body lice would have split off and become a separate group once they had human clothing in which to live.
So if we can figure out when they arrived at the scene, we’d have a minimum age on clothes. Thanks to modern molecular techniques, we can compare the genomes of these two lice and come up with that date. For the curious, a “Bayesian coalescent modeling approach” tells us that we were going clothed at least 83,000 years ago, and maybe as far back as 170,000 years. [Ars Technica]
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However far-fetched some of their science has been, the barrage of forensic science TV shows during the last decade has ingrained into people the idea that even the most cautious criminals (we’re looking at you here, Dexter) leave something of themselves behind at the scene of the crime. And thanks to the march of genetic science and sequencing, those bits of someone can tell more and more about them. Even their hair.
In a study coming soon to the journal Human Genetics, Manfred Kayser and colleagues identify genetic markers that can predict a person’s hair color.
The researchers studied DNA and hair colour information from hundreds of Europeans. They investigated genes previously known to influence the differences in hair colour. “We identified 13 ‘DNA markers’ from 11 genes that are informative to predict a person’s hair colour,” said Professor Kayser. [BBC News]
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In a remarkable medical feat, researchers used a blood sample from a pregnant woman to work out the entire genome of her unborn fetus. The technique, published in the journal Science Translational Medicine, could provide a safer and less invasive way to check a fetus for fatal genetic mutations.
Currently, determining a fetus’s genome requires either amniocentesis, in which a needle is inserted through the mother’s abdomen into the amniotic sac, or chorionic villus sampling, in which a piece of placenta is removed. But both techniques carry a small risk to the baby, and are reserved for cases when there is an increased risk of genetic defects.
“The major advantage of the technique in this paper is that there’s no risk of miscarriage,” said Dr. Diana W. Bianchi, a reproductive geneticist at Tufts University who called the work a “technological tour de force.” Amniocentesis and CVS testing carry about a 1% risk of miscarriage, she said. [LA Times]
The new technique sequences the fetal genome from fragments present in the mother’s blood. In the late 1990s researchers discovered that fragments of fetal DNA are present in maternal plasma, presumably because the DNA gets broken down and crosses over the placental barrier.
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While a certain bacterium that can thrive in arsenic has dominated the science press this week, the big story in the world at large is on the ongoing WikiLeaks saga. The release of an enormous trove of confidential documents from the U.S. State Department has provoked plenty of fall-out: there’s governmental embarrassment and anger, and WikiLeaks founder Julian Assange is now wanted in Sweden on alleged sex crimes. But we’re most interested in how the never-ending story touches several science and tech stories, some of which have unraveled here on 80beats.
Get That DNA
One embarrassing revelation of the leaked diplomatic cables was that American diplomats were supposed to be part spy; they were asked to try to gather genetic material from foreign governmental officials. Once the cables leaked, the State Department couldn’t exactly deny that this happened, but it now says that these suggestions came from intelligence agencies. And relax—the requests were voluntary.
A senior department official said the requests for DNA, iris scans and other biometric data on foreign government and U.N. diplomats came from American “intelligence community managers.” The official said American diplomats were free to ignore the requests and that virtually all do. [Washington Post]
China Source of Google Hack
Early in 2010 we reported on the large cyber-attack against Google. Though rumors swirled, the Chinese government denied its involvement; the country and the search engine giant went through months of tension before arriving at a truce in the summer. According to WikiLeaks, leaders of the Chinese Communist Party were directly connected to the hack.
China’s Politburo directed the intrusion into Google’s computer systems in that country, a Chinese contact told the American Embassy in Beijing in January, one cable reported. The Google hacking was part of a coordinated campaign of computer sabotage carried out by government operatives, private security experts and Internet outlaws recruited by the Chinese government. [The New York Times]
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The science world is abuzz with news of a strange new life form found in California’s Mono Lake: Researchers report that they’ve discovered a bacterium that can not only thrive in an arsenic-rich environment, it can actually use that arsenic to build its DNA. If the researchers, who published their findings in Science, are correct, then they’ve found a form of life unlike anything we’ve ever seen before.
As you might expect, DISCOVER’s blogs offered plenty of coverage of this exciting news.
At The Loom, Carl Zimmer writes: “Scientists have found a form of life that they claim bends the rules for life as we know it. But they didn’t need to go to another planet to find it. They just had to go to California.”
At Bad Astronomy, Phil Plait explains exactly how the bacteria can make use of arsenic to build their DNA. A few days ago, Phil also took NASA to task for its press release promising news of “an astrobiology finding that will impact the search for evidence of extraterrestrial life,” which fueled wild speculation on whether NASA had found little green men in the solar system.
At Not Exactly Rocket Science, Ed Yong debunks a few of the more breathless accounts. The bacteria do not “belong to a second branch of life on Earth…. They aren’t a parallel branch of life; they’re very much part of the same tree that the rest of us belong to. That doesn’t, however, make them any less extraordinary.”
At Gene Expression, Razib Khan has more thoughts on the wild speculation that preceded the announcement–which he compares to the hype surrounding the unveiling of the Segway.
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