Daily Archives: December 12, 2014

PUBLIC RELEASE DATE:

11-Dec-2014

Contact: Glenna Picton picton@bcm.edu 713-798-4710 Baylor College of Medicine @bcmhouston

EMBARGOED for release Thursday, Dec. 11, 2014, at 12 p.m. ET

HOUSTON - (Dec. 11, 2014) - The ancient Japanese art of origami is based on the idea that nearly any design - a crane, an insect, a samurai warrior - can be made by taking the same blank sheet of paper and folding it in different ways.

The human body faces a similar problem. The genome inside every cell of the body is identical, but the body needs each cell to be different -an immune cell fights off infection; a cone cell helps the eye detect light; the heart's myocytes must beat endlessly.

Appearing online this week in the journal Cell, researchers at Baylor College of Medicine, Rice University, the Broad Institute of MIT and Harvard, and Harvard University describe the results of a five-year effort to map, in unprecedented detail, how the 2-meter long human genome folds inside the nucleus of a cell. Their results show that the cell-- like a microscopic origamist - modulates its function by folding the genome into an almost limitless variety of shapes.

A centerpiece of the new study is the first reliable catalog of loops spanning the entire human genome. For decades, scientists have examined the regions in the close vicinity of a gene to understand how it is regulated. But as the genome folds, sequences far from a gene loop back and come in contact with those nearby elements.

Looping has been a blind spot for modern biology. "For over a century, scientists have known that DNA forms loops inside of cells, and that knowing where the loops are is incredibly important," said co-first author Suhas Rao, a researcher at the Center for Genome Architecture at Baylor. "But mapping the positions of all those loops was long thought to be an insurmountable challenge."

The researchers showed that the 3 billion DNA letters of the human genome are partitioned into roughly 10,000 loops, a surprisingly small number. (Prior work on loops had suggested that the genome contains over a million.)

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Scientists map the human loop-ome, revealing a new form of genetic regulation

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Newswise (SALT LAKE CITY) Examination of DNA from 21 primate species from squirrel monkeys to humans exposes an evolutionary war against infectious bacteria over iron that circulates in the hosts bloodstream. Supported by experimental evidence, these findings, published in Science on Dec. 12, demonstrate the vital importance of an increasingly appreciated defensive strategy called nutritional immunity.

Weve known about nutritional immunity for 40 years, says Matthew Barber, Ph.D., first author and postdoctoral fellow in human genetics at the University of Utah. What this study shows us is that over the last 40 million years of primate evolution, this battle for iron between bacteria and primates has been a determining factor in our survival as a species. The study also models an approach for uncovering reservoirs of genetic resistance to bacterial infections, knowledge that could be used to confront emerging diseases.

Following infection, the familiar sneezing, runny nose, and inflammation are all part of the immune systems attempts to rid the body of hostile invaders. Lesser known is a separate defense against invasive microbes, called nutritional immunity, that quietly takes place under our skin. This defense mechanism starves infectious bacteria by hiding circulating iron, an essential nutrient it needs for survival. The protein that transports iron in the blood, transferrin, tucks the trace metal safely out of reach.

Clever as it sounds, the ploy is not enough to keep invaders at bay. Several bacterial pathogens - including those that cause meningitis, gonorrhea, and sepsis - have developed a weapon, transferrin binding protein (TbpA), that latches onto transferrin and steal its iron. Though scientists have known of the offensive strategy, they failed to realize how pivotal the battle over iron has been in the conflict between host and pathogen.

Interactions between host and pathogen are transient and temporary, says senior author Nels Elde, Ph.D., assistant professor of human genetics at the University of Utah. It took casting a wide net across all of primate genetic diversity to capture the significance.

Just as details of a struggle can be gleaned from battle scars, Barber and Elde reconstructed this evolutionary conflict by documenting when and where changes in transferrin and TbpA have occurred over millennia. They examined the DNA of transferrin in 21 species from the primate family tree, and of TbpA from dozens of bacterial strains. The majority of accumulated changes in transferrin and TbpA cluster around a single region of contact between the two proteins, highlighting it as a site of evolutionary conflict between host and pathogen. The authors then used these genetic observations as a guide to perform experiments, which showed changes in TbpA enable the protein to grasp hold of transferrin, and that recent changes in transferrin allow it to evade TbpA.

Up to 25 percent of people in the worlds populations have a small alteration in the transferrin gene, which prevents recognition by several infectious bacteria, the most recent sign of this long battle. Up until this study no one had come up with a functional explanation for why this variation occurs at an appreciable frequency in human populations, says Elde. We now know that it is a consequence of the pathogens we and our ancestors faced over millions of years.

Understanding the strategies that underlie natural defense mechanisms, including nutritional immunity, could inform new approaches to combatting antibiotic-resistant bacteria and emerging diseases. By examining the natural conflicts that have played out for millions of years, we can determine what has worked, and apply them in new situations, says Elde.

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Human DNA Shows Traces of 40 Million-Year Battle For Survival Between Primate and Pathogen

Media reports about behavioural genetics unintentionally induce unfounded beliefs, therefore going against the educational purpose of scientific reporting, writes the University of Montreals Alexandre Morin-Chass, following his study of 1,500 Americans. Among other things, we wanted to know if the public understood (or misunderstood) popular science articles about a new research field, genopolitics, and whether this popularization indeed helped people have an informed opinion on human genetics, Morin-Chass explained.

The study participants first had to read a news article about research on the influence of a gene on one of the following three traits: breast cancer, political ideology (liberal or conservative), or the tendency to go into debt. After reading the article assigned to them, they were then asked to estimate the influence of genetics on various biological (e.g., hair colour, height) or behavioural (e.g., violence, alcoholism) traits on a scale from 0% genetic to 100% genetic. They were told that there were no right or wrong answers. The purpose of the study was simply to examine the interpretation of facts.

The conclusions were troubling, to say the least. Morin-Chass observed that after reading an article published in the British Daily Telegraph in October 2010 about a "gene responsible for liberal ideas, the readers tended to generalize the influence of genetics to other behaviours or social orientations of which there was no mention in the news article (including sexual orientation and intelligence). The same phenomenon was observed among the readers of the other article, originally published in the Scientific American Mind magazine in June 2010, which associated a gene with susceptibility to debt.

However, public misunderstanding is not the only thing to blame for this misinterpretation. Generally, science reporters first goal is to inform the public about scientific developments. However, this practice is not disinterested; some news is purposely written in a manner intended to catch the publics attention with startling results in order to increase or to maintain market shares," Morin-Chass explained.

Genetic research into behaviour is certainly a minefield. It is often associated with other more controversial theoretical work, for example, in sociobiology, which attempts to explain social inequalities using the theory of evolution and the concept of natural selection. In contrast, current trends in research are based on empirical analysis of DNA data.

"Personally, I am in favour of this innovative approach to better understand our world, but I cant argue with the facts: the field is often misunderstood or even disregarded, Morin-Chass said. Some reduce it to its most deterministic form. The danger, which, in my mind, is present, is that scientific research findings could be manipulated for ideological purposes by certain social groups. Hence the importance of making sure the public understands the scope and limitations of such research.

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The above story is based on materials provided by Universit de Montral. Note: Materials may be edited for content and length.

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Current practices in reporting on behavioural genetics can mislead the public

It's not just great minds that think alike. Dozens of the genes involved in the vocal learning that underpins human speech are also active in some songbirds. And knowing this suggests that birds could become a standard model for investigating the genetics of speech production and speech disorders.

Complex language is a uniquely human trait, but vocal learning the ability to pick up new sounds by imitating others is not. Some mammals, including whales, dolphins and elephants, share our ability to learn new vocalisations. So do three groups of birds: the songbirds, parrots and hummingbirds.

The similarities between vocal learning in humans and birds are not just superficial. We know, for instance, that songbirds have specialised vocal learning brain circuits that are similar to those that mediate human speech.

What's more, a decade ago we learned that FOXP2, a gene known to be involved in human language, is also active in "area X" of the songbird brain one of the brain regions involved in those specialised vocal learning circuits.

Andreas Pfenning at the Massachusetts Institute of Technology and his colleagues have now built on these discoveries. They compared maps of genetic activity transcriptomes in brain tissue taken from the zebra finch, budgerigar and Anna's hummingbird, representing the three groups of vocal-learning birds.

They then compared these genetic maps with others taken from birds and primates that can't learn new vocalisations, and with maps taken from the brains of six people who donated tissue to the Allen Brain Institute in Seattle.

Their results showed that FOXP2 is just one of 55 genes that show a similar pattern of activity in the brains of humans and the vocal-learning birds. Those same genes show different patterns of activity in the brains of animals incapable of vocal learning.

"The similarities are beyond one or a handful of genes," says Pfenning. "There are just systematic molecular similarities between song-learning birds and humans."

The findings suggest that songbirds might make ideal animal models for studying the genetics of speech production.

"There's potential for songbirds to be used to study neurodegeneration especially conditions like Huntington's," says Pfenning. Huntington's disease affects the ability to produce complex motor behaviour, such as singing and talking, so experiments with birds might implicate particular genes in the disease.

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Humans and birds share the same singing genes

A pedestrian walks outside a Merck & Co. facility in Summit, New Jersey.

A human trial of an experimental Ebola vaccine recently licensed by Merck & Co. has been suspended until January after four healthy volunteers receiving it experienced mild joint pain, according to a Geneva hospital helping conduct the trial.

As a precautionary measure, the study team has declared a pause in the injections, the hospital said. It added that joint pain after infection or vaccination is a well-documented phenomenon which does not worry specialists. However, it deserves to be carefully studied. The hospital said the vaccine overall has been very well tolerated among the 59 people who have received it in Geneva.

Merck agreed in November to pay NewLink Genetics Corp. NLNK, +0.76% of Ames, Iowa, $30 million for the rights to the vaccine, plus an additional $20 million and royalties on sales if the vaccine meets certain development targets.

Merck MRK, -2.73% , of Whitehouse Station, N.J., said in a statement that it was aware the study had been placed on a temporary hold after transient complaints of joint pain in Geneva. These events have not been reported at any of the other clinical sites, the company added. It is not known at this time whether these events are related to the vaccine or not. We understand the level of vaccine being administered in the trial, which is being conducted at a number of other sites, will proceed using lower doses of the vaccine.

NewLink didnt immediately respond to a request for comment.

An expanded version of this report appears at WSJ.com.

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The Wall Street Journal: Human trial of experimental Merck Ebola vaccine is suspended