The Unusual Language That Linguists Thought Couldn’t Exist                  

Julie Sedivy, 09/22/14

Languages, like human bodies, come in a variety of shapes -- but only to a point. Just as people don’t sprout multiple heads, languages tend to veer away from certain forms that might spring from an imaginative mind. For example, one core property of human languages is known as duality of patterning: meaningful linguistic units (such as words) break down into smaller meaningless units (sounds), so that the words sap, pass, and asp involve different combinations of the same sounds, even though their meanings are completely unrelated.

It’s not hard to imagine that things could have been otherwise. In principle, we could have a language in which sounds relate holistically to their meanings -- a high-pitched yowl might mean “finger,” a guttural purr might mean “dark,” a yodel might mean “broccoli,” and so on. But there are stark advantages to duality of patterning. Try inventing a lexicon of tens of thousands of distinct noises, all of which are easily distinguished, and you will probably find yourself wishing you could simply re-use a few snippets of sound in varying arrangements.

As noted by Elizabeth Svoboda in the current issue of Nautilus, the dominant thinking until fairly recently was that universal linguistic properties reflect genetic predispositions. Under this view, duality of patterning is much like an opposable thumb: It evolved within our species because it was advantageous, and now exists as part of our genetic heritage. We are born expecting language to have duality of patterning.

What to make, then, of the recent discovery of a language whose words are not made from smaller, meaningless units? Al-Sayyid Bedouin Sign Language (ABSL) is a new sign language emerging in a village with high rates of inherited deafness in Israel’s Negev Desert. According to a report led by Wendy Sandler of the University of Haifa, words in this language correspond to holistic gestures, much like the imaginary sound-based language described above, even though ABSL has a sizable vocabulary.

To linguists, this is akin to finding a planet on which matter is made up of molecules that don’t decompose into atoms. ABSL contrasts sharply with other sign languages like American Sign Language (ASL), which creates words by re-combining a small collection of gestural elements such as hand shapes, movements, and hand positions.

ABSL provides fodder for researchers who reject the idea that there’s a genetic basis for the similarities found across languages. Instead, they argue, languages share certain properties because they all have to solve similar problems of communication under similar pressures, pressures that reflect the limits of human abilities to learn, remember, produce, and perceive information. The challenge, then, is to explain why ABSL is an outlier -- if duality of patterning is the optimal solution to the problem of creating a large but manageable collection of words, why hasn’t ABSL made use of it?

One possible explanation is that the vocabulary of ABSL hasn’t yet reached a critical mass that would force it into a more combinatorial system for word-creation. This doesn’t look like the full story though. In a study by Tessa Verhoef of the University of Amsterdam, people tried to reproduce a mere 12 sounds of a “language” produced on a slide whistle. Each person’s attempts to replicate the language served as the new version of the language to be learned by the next subject, so that each new learner represented a “generation” in the life of the language. Over just 10 “generations,” learners began to change the original sounds to involve combined sequences of smaller sound patterns. The later iterations of the language were easier to learn than the original holistic sounds, suggesting there’s a learning advantage to breaking down even a very small number of complex sounds into smaller ingredients. In some cases, at least, duality of patterning kicks in at a surprisingly small number of “words.”

The signs of ABSL, though, may be easier to learn because many of them are concretely related to the things they symbolize -- for example, the sign for “lemon” resembles the motion of squeezing a lemon. Another lab study led by Gareth Roberts of Yeshiva University found that both large vocabularies and abstract (as opposed to concrete) symbols encouraged the birth of duality of patterning in artificial languages. Concreteness may be easier to achieve in a gestural language than an auditory one, simply because you can illustrate more ideas using your hands than by making sounds with your mouth.

Researchers don’t yet have a clear answer for why ABSL looks as it does, but systematic lab studies may help solve this puzzle, as may the evolution of ABSL itself; Sandler and her colleagues see hints that ABSL is on the cusp of evolving a more combinatorial system. This intriguing language and the research it inspires may eventually tell us something profound about how languages emerge from the human mind, and why so many of them share some important similarities.

Julie Sedivy teaches at the University of Calgary. She is the author of Language in Mind: An Introduction to Psycholinguistics and the co-author of Sold on Language: How Advertisers Talk to You and What This Says About You.

The documentary Voices From El-Sayed considered what would happen to the village when children living there started receiving cochlear implants. (請至原網頁觀賞影片)

http://nautil.us/blog/the-unusual-language-that-linguists-thought-couldnt-exist

Mutagens and Multivitamins

Not one to shy away from controversy, Bruce Ames has pitted himself against industry groups, environmentalists, and his peers through his work identifying DNA mutagens. And he’s not done yet.

Megan Scudellari, 06/01/14

On an otherwise ordinary day in 1964, Bruce Ames picked up a box of potato chips and read the list of ingredients. A biochemist at the National Institutes of Health (NIH) in Bethesda, Maryland, Ames spent his days studying mutations in strains of Salmonella, so it wasn’t unusual that he began to wonder if any of the preservatives or chemicals on that long list of ingredients might mutate DNA. Ames decided to use his Salmonella to try to detect genetic damage caused by chemicals. “I figured the world needed some quick, easy test to detect mutagens,” says Ames.

Ames had hundreds of strains of S. typhimurium with mutations in the genes required to produce histidine, a standard amino acid for making proteins. These strains could not grow without the addition of histidine. When millions of bacteria were placed in media lacking the amino acid, however, a few would spontaneously mutate, produce histidine again, and survive as a colony. Ames figured if he added a chemical, such as a potato-chip preservative, to the Salmonella strains, and the chemical increased the number of surviving colonies, it was a mutagen.

Ames began tinkering with the test as a hobby. Then, in 1967, when he moved to the University of California, Berkeley, he got some undergraduates to help him develop the assay further. They added rat liver homogenate to the Salmonella as an approximation of mammalian metabolism, which activates many chemicals whose mutagenic action couldn’t be detected by the bacteria alone, and the “Ames test” was born -- a simple, inexpensive method for detecting DNA mutagens. Ames immediately put the assay to work: he tested 174 suspected cancer-causing chemicals for the ability to mutate DNA, using a range of concentrations up to the level toxic to the bacteria -- and a whopping 90 percent of them were mutagens. It was some of the first evidence that carcinogens mutate DNA.

“Like a lot of hobbies, it slowly took over my life,” says Ames. Over the years, he grew and gave away thousands of samples of the bacteria to other laboratories, and today the Ames test is still used in academic and industrial laboratories worldwide.

His work on mutagens subsequently drew Ames’s interest to cancer prevention, then age-related diseases, then nutrition. A recipient of the National Medal of Science from President Bill Clinton, Ames has published more than 550 papers and is one of the most-cited scientists across all fields.

Here, Ames takes us on a whirlwind tour of his career, from studies of hair dye and children’s pajamas to the defense of pesticide use and vitamins.

Ames the Academic

(omitted, 略)

To dye for. In 1973, after moving to Berkeley, he published details of the Ames test and put it to use straightaway. “I used to teach an undergraduate lab at Berkeley, and I told my students to go bring something in to test. And you know students, what do they test but marijuana and birth control pills and things like that? But one day a student brought in his girlfriend’s hair dye, and it was screamingly mutagenic. So I sent one of my technicians out to the drug store to buy $100 worth of hair dyes. All the permanent hair dyes were mutagenic because they contained aromatic amines, which are often carcinogens. We published a paper on it, and I sent a copy to all the hair-dye companies in the world and said, ‘You guys need to start thinking about this.’ They eventually developed hair dyes that aren’t mutagenic.”

Cataloging cancer. Ames’s team subsequently showed that cigarette smoke was mutagenic, as was the main flame retardant used in children’s pajamas, a chemical called tris-BP. “I didn’t want to put my kids in these pajamas, so we bought their pajamas in Europe when we were there,” he says. Around the same time, Ames became interested in animal cancer tests. “I wanted to look at the relationship between mutagens and carcinogens in animal tests. No one had ever systematized that.” Ames applied for a federal grant to create a database of the potency of rodent carcinogens, but was turned down flat. “They said I didn’t know any pathology or statistics and I wasn’t the right person to do it. But we wanted to do it, and no one else was doing it, so we did it.”

Big dose of controversy. Using that database, the still-active Carcinogenic Potency Database, Ames and his collaborator Lois Gold “got into a number of controversies,” he says. “Half of the chemicals tested, whether natural or synthetic, in the standard assay at the maximum tolerated dose were carcinogens. That made us suspicious; something was fishy.” They argued that the huge dose, not the chemical formulation itself, was responsible for inflammation, cell death, and cell proliferation. Their conclusions -- that animal cancer tests do not provide a good assessment of low-dose cancer risk -- “got all the scientists that had spent their lives doing these [animal cancer] tests angry at us,” says Ames.

Rankling ranking. In 1987, Ames and Gold ranked natural and synthetic pesticides and found that cancer risks from traces of pesticide residues on fruits and vegetables are minuscule compared with the cancer-causing potential of some natural chemicals in plants. “We wrote a review pointing out that every plant has a hundred or so toxic chemicals -- nature’s pesticides -- to kill off insects, animals, and other predators, and that we were getting 10,000 times more of them than [of] man-made pesticides. Still, everybody is buying expensive organic food,” says Ames. “It’s the new religion. We won the scientific battle but we lost the public-relations battle.” For that work and more, arguing that traces of synthetic chemicals are not a cancer risk, Ames and Gold have been criticized as being in the pocket of the pesticide industry, despite never accepting money, consulting with industry companies, or testifying in trials.

Ames the Analyst

Big break. In 1989, cytogeneticist Jim MacGregor spent a sabbatical year in Ames’s lab at Berkeley. “Before he came to the lab, he was looking at radiation breaking chromosomes in precursors of mouse red blood cells, and one day all his control mice were full of chromosome breaks. It turned out the company that sold him the vitamin mix for the mice had left out folic acid, and a lack of folic acid breaks chromosomes just like radiation does. MacGregor started looking in people, and he found a guy who had 20 times the level of chromosome breaks as everyone else. The guy ate a pretty poor diet without a lot of veggies, so he was folic-acid deficient.” Ames was already familiar with folic acid: Herschel Mitchell, Ames’s graduate mentor, discovered folic acid by isolating it from four tons of spinach. “Around 10 percent of the US population and half the poor were folic-acid deficient, so I said, ‘I’m getting into this area.’ Nutrition is a muddy field, but I like getting into muddy fields.” A few years later, Ames and his team determined that folate deficiency results in the massive incorporation of uracil, an RNA chemical base, into DNA, leading to chromosome breaks after excision by a repair enzyme.

Damaging diet. “From there, I became interested in all the essential vitamins and minerals. There are about 30 of them, and according to recommended dietary allowances from the USDA, almost everyone in the population is low in one or more. So I started looking to see if you get DNA damage from a vitamin or mineral deficiency.” Beginning at Berkeley and continuing at Children’s Hospital Oakland Research Institute (CHORI), which Ames joined in 2000, he and his lab found many examples of this phenomenon: iron deficiency causes neuron decay and mitochondrial DNA damage, for example, and zinc deficiency damages DNA and disables tumor suppressor p53. But Ames still didn’t know how such deficiencies could directly damage DNA.

Winners and losers. “Then one day I had this epiphany: When you run out of a vitamin or mineral, which happened all the time throughout evolution, maybe nature rations what it has.” In 2006, Ames proposed the triage theory -- that natural selection has developed a rationing response to shortages of micronutrients (vitamins and minerals). When cells run out of a vitamin or mineral, that scarce micronutrient is allotted to proteins essential for short-term survival. Proteins needed for long-term health, including those that protect DNA, lose out and become disabled. With Joyce McCann at CHORI, Ames has demonstrated this rationing is present in cells short on vitamin K and selenium: essential proteins incorporate the micronutrients, and nonessential proteins are disabled or lost. “This suggests you’re paying a price any time you get a little low on any vitamin or mineral,” says Ames.

Nutrients for all. In an effort to apply his nutrition discoveries to cancer prevention, Ames helped develop a micronutrient-dense, low-calorie fruit bar, called the CHORI-bar. “The local USDA was making a bar out of excess California fruit, and we said, ‘Hey, can you add some vitamins to that bar?’ They said sure, and now we’ve been collaborating for about 10 years. It tasted terrible when we first made it, but it’s quite tasty now.” And consumption of the bar is showing an association with indicators of good health. In a two-week clinical trial involving 25 individuals, the addition of two CHORI-bars per day to a typical American diet, with no other dietary interventions, raised levels of high-density lipoprotein and improved antioxidant defense.

Hormonal reaction. Ames’s latest work involves nutrient deficiency and brain dysfunction. “It turns out vitamin D is converted into a hormone that controls 900 genes, many in the brain. I have a wonderful new postdoc, Rhonda Patrick, an energetic scholar, who started looking into autism and vitamin D.” It was previously known that individuals with autism often have low levels of vitamin D in the blood, as well as low serotonin, a hormone critical for social behavior, in the brain. Earlier this year, Patrick found a mechanism linking the two: vitamin D hormone activates the enzyme that converts tryptophan to serotonin in the brain. “This is relevant not only to autism but to antisocial behavior and all kinds of psychiatric disease,” says Ames. “The four papers Rhonda is churning out are as important as any that have ever come out of my lab.”

Ames the Advocate

The cost of innovation. “American science is really in trouble. Entitlements are eating up the entire federal budget. It’s the worst I’ve seen in all my 60 years in science. If you’re innovative, it’s the kiss of death. I’ve been doing most of my innovative work through private charity and [out of] my own pocket.”

iVitamins. “I think the future of avoiding the degenerative diseases of aging is not drugs but getting your metabolism and nutrition tuned up. In the future, you will put your finger in a machine and have all the marker proteins in blood analyzed from a finger prick. The machine will say, ‘You’re low on magnesium’ and send a message to your iPhone that you should eat a big plate of spinach or kale every once in a while. Everybody knows their cholesterol number, but in the future they’ll know their magnesium number, vitamin D number, and more.”

Practice what you preach. “I have an Italian wife, so I get a wonderful Mediterranean diet: lots of fish, vegetables, and fruit for dessert. My wife keeps nagging me to get more exercise, but I told her that when I feel like exercise, I run my experiments, I skip my controls, and I jump to conclusions. After I told that joke about 50 times, she said, ‘I’ve heard enough of that damn joke. I’m getting you a personal trainer.’”

Die laughing. “I’m 85, so I don’t know how many more years I have left, as my mitochondria are decaying ever more rapidly. However, I’ve finally figured out what they’re decaying into -- hypochondria. But seriously, my five-year plan is to live to 90. My wife says I should have a 10-year plan instead.”

Greatest Hits

l   Created the Ames test, an assay to determine if a chemical is mutagenic.

l   Demonstrated that most carcinogens are mutagens.

l   Built a comprehensive database of carcinogen potency.

l   Showed that many nutrient deficiencies cause DNA damage and proposed the triage theory as a mechanism by which this occurs.

l   Developed a nutrient-rich fruit bar designed to improve metabolism and prevent age-related disease.

l   Uncovered a mechanism linking vitamin D–deficiency to serotonin synthesis, autism, and brain dysfunction.

Finding the Switch: Researchers Create Roadmap for Gene Expression             

Tracey Peake, News Services, 04/13/14

In a new study, researchers from North Carolina State University, UNC-Chapel Hill and other institutions have taken the first steps toward creating a roadmap that may help scientists narrow down the genetic cause of numerous diseases. Their work also sheds new light on how heredity and environment can affect gene expression.

Pinpointing the genetic causes of common diseases is not easy, as multiple genes may be involved with a disease. Moreover, disease-causing variants in DNA often do not act directly, but by activating nearby genes. To add to the complexity, genetic activation is not like a simple on/off switch on a light, but behaves more like a “dimmer switch” – some people may have a particular gene turned all the way up, while others have it only turned halfway on, completely off, or somewhere in between. And different factors, like DNA or the environment, play a role in the dimmer switch’s setting.

According to Fred Wright, NC State professor of statistics and biological sciences, director of NC State’s Bioinformatics Center and co-first author of the study, “Everyone has the same set of genes. It’s difficult to determine which genes are heritable, or controlled by your DNA, versus those that may be affected by the environment. Teasing out the difference between heredity and environment is key to narrowing the field when you’re looking for a genetic relationship to a particular disease.”

Wright, with co-first author Patrick Sullivan, Distinguished Professor of Genetics and Psychiatry at UNC-Chapel Hill and director of the Center for Psychiatric Genomics, and national and international colleagues, analyzed blood sample data from 2,752 adult twins (both identical and fraternal) from the Netherlands Twin Register and an additional 1,895 participants from the Netherlands Study of Depression and Anxiety. For all 20,000 individual genes, they determined whether those genes were heritable – controlled by the DNA “dimmer switch” – or largely affected by environment.

“Identical twins have identical DNA,” Wright explains, “so if a gene is heritable, its expression will be more similar in identical twins than in fraternal twins. This process allowed us to create a database of heritable genes, which we could then compare with genes that have been implicated in disease risk. We saw that heritable genes are more likely to be associated with disease – something that can help other researchers determine which genes to focus on in future studies.”

The study appears online April 13 in Nature Genetics.

“This is by far the largest twin study of gene expression ever published, enabling us to make a roadmap of genes versus environment,” Sullivan says, adding that the study measured relationships with disease more precisely than had been previously possible, and uncovered important connections to recent human evolution and genetic influence in disease.

The Netherlands Twin Register has followed twin pairs for over 25 years and in collaboration with the longitudinal Netherlands Study of Depression and Anxiety established a resource for genetic and expression studies. Professor Dorret Boomsma, who started the twin register, says, “in addition to the fundamental insights into genetic regulation and disease, the results provide valuable information on causal pathways. The study shows that the twin design remains a key tool for genetic discovery.”

Blood samples from the Netherlands were processed by the NIMH Center for Collaborative Genomics Research on Mental Disorders at Rutgers University. NC State research scholar Yi-Hui Zhou and associate professor of statistics Jung-Ying Tzeng contributed to the work. Funding for the study included grants from the National Institute of Mental Health and other NIH Institutes, the Gillings Innovation Lab, the Netherlands Organization for Scientific Research, the Center for Medical Systems Biology, Biobanking and Biomolecular Resources Research Infrastructure, and the European Science Foundation and European Research Council.

Note to editors: Abstract of the paper follows.

“Heritability and genomics of gene expression in peripheral blood”

DOI:10.1038/ng.2951

Authors: Fred A.Wright, NC State University; Patrick F. Sullivan, UNC-Chapel Hill, et al

Published: Online April 13, 2014 in Nature Genetics

Abstract: We assessed gene expression profiles in 2,752 twins, using a classic twin design to quantify expression heritability and quantitative trait loci (eQTLs) in peripheral blood. The most highly heritable genes (~777) were grouped into distinct expression clusters, enriched in gene-poor regions, associated with specific gene function or ontology classes, and strongly associated with disease designation. The design enabled a comparison of twin-based heritability to estimates based on dizygotic identity-by-descent sharing and distant genetic relatedness. Consideration of sampling variation suggests that previous heritability estimates have been upwardly biased. Genotyping of 2,494 twins enabled powerful identification of eQTLs, which we further examined in a replication set of 1,895 unrelated subjects. A large number of local eQTLs (6,988) met replication criteria, whereas a relatively small number of distant eQTLs (165) met quality control and replication standards. Our results provide a new resource toward understanding the genetic control of transcription.

http://news.ncsu.edu/releases/wrightnatgen/

Scientists publish 'navigation maps' for human genome

Kate Kelland, 03/26/14

LONDON (Reuters) - A large international team of scientists has built the clearest picture yet of how human genes are regulated in the vast array of cell types in the body - work that should help researchers target genes linked to disease.

In two major studies published in the journal Nature, the consortium mapped how a network of switches, built into human DNA, controls where and when genes are turned on and off.

The three-year long project, called FANTOM5 and led by the RIKEN Center for Life Science Technologies in Japan, involved more than 250 scientists across 20 countries and regions.

"Humans are complex multicellular organisms composed of at least 400 distinct cell types. This beautiful diversity of cell types allow us to see, think, hear, move and fight infection - yet all of this is encoded in the same genome," said Alistair Forrest, scientific coordinator of FANTOM5.

He explained that the difference between cell types comes down to which parts of the genome they use - for instance, brain cells use different genes than liver cells, and therefore work very differently.

"In FANTOM5, we have for the first time systematically investigated exactly what genes are used in virtually all cell types across the human body, and the regions which determine where the genes are read from the genome," he said.

The team studied the largest ever set of cell types and tissues from humans and mice so that they could identify the location of switches within the genome that turn individual genes on or off.

They also mapped where and when the switches are active in different cell types and how they interact with each other.

David Hume, director of the Roslin Institute at Britain's Edinburgh University and one of the lead researchers on the project, used the analogy of an airplane:

"We have made a leap in understanding the function of all of the parts. And we have gone well beyond that - to understanding how they are connected and control the structures that enable flight," he said.

Although there are many years' more research ahead, researchers hope the FANTOM5 work will be a reference atlas to help them navigate the genome and figure out which genes are involved, and how, in a whole range of diseases: from cancer, to diabetes, to blood diseases, to psychiatric conditions.

In a linked study, a Roslin Institute team used information from the atlas to investigate the regulation of an important set of genes required to build muscle and bone.

Another study used the FANTOM5 atlas to look at the regulation of genes in cells of the blood, producing what scientists described as a roadmap of blood cells that will help them pinpoint where and how cancerous tumors start to grow.

"Now that we have these incredibly detailed pictures of each of these cell types, we can now work backwards to compare cancer cells to the cells they came from originally to better understand what may have triggered the cells to malfunction, so we will be better equipped to develop new and more effective therapies," said Forrest.

(Editing by Mark Trevelyan)

http://news.yahoo.com/scientists-publish-navigation-maps-human-genome-180322348--finance.html

Genetic Mutation May Have Allowed Early Humans to Migrate Throughout Africa

ScienceDaily (Sep. 19, 2012) — A genetic mutation that occurred thousands of years ago might be the answer to how early humans were able to move from central Africa and across the continent in what has been called "the great expansion," according to new research from Wake Forest Baptist Medical Center.

By analyzing genetic sequence variation patterns in different populations around the world, three teams of scientists from Wake Forest Baptist, Johns Hopkins University School of Medicine and the University of Washington School of Medicine, Seattle, demonstrated that a critical genetic variant arose in a key gene cluster on chromosome 11, known as the fatty acid desaturase cluster or FADS, more than 85,000 years ago. This variation would have allowed early humans to convert plant-based polyunsaturated fatty acids (PUFAs) to brain PUFAs necessary for increased brain size, complexity and function. The FADS cluster plays a critical role in determining how effectively medium-chain PUFAs found in plants are converted to the long-chain PUFAs found in the brain.

This research is published online today in PLOS ONE.

Archeological and genetic studies suggest that homo sapiens appeared approximately 180,000 years ago, but stayed in one location around bodies of water in central Africa for almost 100,000 years. Senior author Floyd H. "Ski" Chilton, Ph.D., professor of physiology and pharmacology and director of the Center for Botanical Lipids and Inflammatory Disease Prevention at Wake Forest Baptist, and others have hypothesized that this location was critical, in part, because early humans needed large amounts of the long-chain PUFA docosahexaenoic acid (DHA), which is found in shellfish and fish, to support complex brain function.

"This may have kept early humans tethered to the water in central Africa where there was a constant food source of DHA," Chilton said. "There has been considerable debate on how early humans were able to obtain sufficient DHA necessary to maintain brain size and complexity. It's amazing to think we may have uncovered the region of genetic variation that arose about the time that early humans moved out of this central region in what has been called the 'great expansion.'"

Once this trait arose, the study shows that it was under intense selective pressure and thus rapidly spread throughout the population of the entire African continent. "The power of genetics continually impresses me, and I find it remarkable that we can make inferences about things that happened tens of thousands of years ago by studying patterns of genetic variation that exist in contemporary populations," said Joshua M. Akey, Ph.D., lead scientist at the University of Washington.

This conversion meant that early humans didn't have to rely on just one food source, fish, for brain growth and development. This may have been particularly important because the genetic variant arose before organized hunting and fishing could have provided more reliable sources of long-chain PUFAs, Akey said.

To investigate the evolutionary forces shaping patterns of variation in the FADS gene cluster in geographically diverse populations, the researchers analyzed 1,092 individuals representing 15 different human populations that were sequenced as part of the 1000 Genome Project and 1,043 individuals from 52 populations from the Human Genome Diversity Panel database. They focused on the FADS cluster because they knew those genes code for the enzymatic steps in long-chain PUFA synthesis that are the least efficient.

Chilton said the findings were possible because of the collaboration of internationally recognized scientists from three distinct and diverse disciplines -- fatty acid biochemistry (Wake Forest Baptist), statistical genetics (Johns Hopkins) and population genetics (University of Washington). This new information builds on Chilton's 2011 research findings published in BMC Genetics that showed how people of African descent have a much higher frequency of the gene variants that convert plant-based medium-chain omega-6 PUFAs found in cooking oils and processed foods to long-chain PUFAs that cause inflammation. Compared to Caucasians, African Americans in the United States have much higher rates of hypertension, type 2 diabetes, stroke, coronary heart disease and certain types of cancer. "The current observation provides another important clue as to why diverse racial and ethnic populations likely respond differently to the modern western diet," Chilton said.

This research was supported by National Institutes of Health grants, P50 AT002782 and a Clinical and Translational Science Award grant to The Johns Hopkins Medical Institutions. Additional support was received from the Wake Forest Health Sciences Center for Public Health Genomics. Additional support came from the Mary Beryl Patch Turnbull Scholar Program and the MOSAIC initiative of Johns Hopkins University.

Chilton has a financial interest in and is a consultant for Gene Smart Health. His potential conflict of interest is being institutionally managed by Wake Forest Baptist and outside sponsors, as appropriate. No other authors have a conflict of interest.

First author is Rasika Mathias, Sc.D, assistant professor of medicine and epidemiology, Johns Hopkins; contributing authors include Hannah C. Ainsworth and Susan Sergeant, both of Wake Forest Baptist; Wenqing Fu, U of W; Dara G. Torgerson, University of California San Francisco; and Ingo Ruczinski and Kathleen C. Barnes of Johns Hopkins.

The above story is reprinted from materials provided by Wake Forest Baptist Medical Center.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Journal Reference:

1.     Rasika A. Mathias, Wenqing Fu, Joshua M. Akey, Hannah C. Ainsworth, Dara G. Torgerson, Ingo Ruczinski, Susan Sergeant, Kathleen C. Barnes, Floyd H. Chilton. Adaptive Evolution of the FADS Gene Cluster within Africa. PLoS ONE, 2012; 7 (9): e44926 DOI: 10.1371/journal.pone.0044926

http://www.sciencedaily.com/releases/2012/09/120919190100.htm

Genes Help Explain Who Gets Fit

Rachael Rettner, LiveScience Staff Writer, LiveScience.com

When you put in hours at the gym, you expect to get fitter. It turns out, that assumption doesn't hold true for everyone. A new study suggests specific genes may determine, at least in part, how much we really benefit from exercise.

While "benefit from exercise" can mean plenty of things, from slimming down to boosting one's ability to complete a marathon, the researchers specifically looked at what is called VO2 max, or aerobic capacity. This is a measure of how much blood your heart pumps and how much oxygen your muscles consume when they constrict to, say, move your legs on a treadmill.

Bottom line, VO2 max represents your endurance. And this study, detailed today in the Journal of Applied Physiology, suggests a group of 29 genes could potentially categorize individuals into low, medium and high responders to exercise.

The researchers stress that exercise has benefits, regardless of whether or not a person can improve aerobic capacity. You can still lose weight, and other health factors such as cholesterol levels could benefit.

So-called low responders "may not see an improvement in their tolerance to exercise, or any improvement in their capacity to do the exercise, but their blood levels of cholesterol and lipids may improve quite substantially," said lead researcher Claude Bouchard, of the Pennington Biomedical Research Center in Baton Rouge, La.

What's fitness?

In theory, the more you train, the better your body should get at using oxygen, and your VO2 max should increase. Indeed, elite athletes often have very high VO2 max's compared with average Joe.

However, about 20 years ago, some scientists started to question whether or not the link between training and fitness level was so clearcut. For instance, in the so-called Heritage family study, Bouchard and colleagues had about 500 relatively sedentary individuals train for 20 weeks between 1992 and 1997. Participants' ability to improve their fitness varied greatly lot, despite the fact that all participants rigorously adhered to the same exercise regime.

In that study, some people could increase their VO2 max up to 50 percent, while others saw no change. Since the study involved about 100 families, Bouchard's team could check to see if genetics was at play. Indeed, it was. Genes could account for about half of the difference they were seeing in people's ability to increase their VO2 max.

In other words, a good portion, but not all, of a person's capacity to get more fit was set by their heredity.

The question then became, what genes?

Exercise genes

To find out, Bouchard and his colleagues, who came from 14 different institutions, used data from three separate exercise studies, including the Heritage.

They initially identified, using a novel approach, a set of 29 genes that seemed to predict a person's ability to improve their VO2 max. Then, they examined the individual DNA sequence of those genes, looking for differences in the genetic code. They found a total of 11 DNA differences, or markers, which appeared to be predictive of a person's ability to get fitter.

But these markers don't tell the whole story. Remember, heredity is only thought to account for 50 percent of a person's capacity to improve their fitness. Of this 50 percent, the newly identified genes can only explain about 23 percent of the variation in an individual's ability to be trained to improve VO2 max.

"With this we can identify, with a reasonable degree of precision, who is a low responder [to exercise], an average responder, or a high responder," Bouchard said. "We can begin to rank order people for their ability to be trained before they are trained."

In addition, in the Heritage study, the people who improved their fitness (VO2 max) the most weren't necessarily the ones who improved their blood pressure the most, or lowered their cholesterol. So these factors, which are thought to be indicators for heart disease risk, could be controlled by different genes, Bouchard said.

Real-world implications

While Bouchard feels this study is a big step forward, more work is needed before it can have real-world applications, including finding more genes and then verifying the markers in other populations.

But down the road, the findings may have practical uses. For instance, if someone learns they are a "low responder" to exercise, they know they may need to be more aggressive with their training in order to see an increase in their endurance. It may also help out with job selection, if a job requires a high level of fitness.

While other scientists agree that the work is intriguing, and notable for its unique approach to find and verify genes, they feel more research is needed. "It's helpful to provide some insights, but it clearly leaves a lot of questions," said Paul Gordon, professor at the University of Michigan who specializes in preventive and rehabilitative exercise science.

For example, the actual genes identified in this study were different from those previously found to play a role in the exercise-VO2 max link. And scientists know very little about what these genes really do to cause physical improvements in the body.

"I think the question still remains as to how important these genes are in contributing to the improvements. What is the actual cause and effect that's going on here?" Gordon said.

Furthermore, the study size was small, and Gordon would like to see if the results can be replicated on a larger scale, and among different demographics.

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