Wednesday, January 13, 2010


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Researchers may now reliably use genetics data to tell a person's ancestry -- what percent of an African-American's genome stems from Europe, for example, and what percent comes from Africa.

The technique detailed in a new study not only allows researchers to compare 300,000 common DNA landmarks in the diverse genetic heritage of humans, but also provides insights into "the personal genetic history of individuals and the journey individual segments of their genomes have taken, particularly those individuals with rich and diverse genetic heritage, such as African-Americans," said Carlos Bustamante, a Cornell population geneticist who co-led the study, which is published in the Dec. 21 issue of Proceedings of the National Academy of Sciences.

The study focused primarily on the genetic structure of West African populations, as previous genetic and historical studies suggested that the region was the source for most of the ancestry of present-day African-Americans. The results suggested clear and discernible genetic differences among some of the West African populations, whereas others appear to be nearly indistinguishable even when comparing more than 300,000 genetic markers. The researchers note that a larger sample size would likely reveal further diversity among these populations.

Of the 365 African-Americans in the study, the researchers found that the degree of West African ancestry in the individuals ranged from 1 to 99 percent. This wide variation has significant implications for using genetic information to personalize drug treatments and assessing disease risk. The median proportion of European ancestry in the African-Americans was 18.5 percent, with large variation among individuals.

The research, whose first author is Katarzyna Bryc, a graduate student in Bustamante's lab, could have implications for personalized ancestry reconstructions, personalized medicine, more effective drug treatments and for developing more effective methods to map genetic risk factors for such common diseases as hypertension, diabetes and prostate cancer.

The research team, led by Bustamante and Sarah Tishkoff, a geneticist at the University of Pennsylvania, collected and analyzed genotype data from the 365 African-Americans as well as 203 individuals from 12 West African populations and 400 Europeans from 42 countries.

The data revealed complex genomic diversity among African and African-American populations and deep historical, cultural, geographic and linguistic impacts on gene flow among populations, Bustamante said.

For example, among its many findings, the researchers found that the X-chromosomes of African-Americans had a higher proportion of African ancestry than the autosomes, consistent with the pattern of gene flow where mothers were more frequently of African ancestry than fathers, who were either of African or European ancestry.

Analyzing patterns of population structure and individual ancestry in Africans and African-Americans is critical for undertaking medical genomic studies on a global scale, the researchers noted. There is also strong reason to believe that high-density genotype data from African and African-American populations may pinpoint more precisely the geographic origin of African ancestry in African Americans, the researchers said.

(Photo: Sarah Tishkoff/Univ. of Pennsylvania)

Cornell University


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Antibiotic resistance in the natural environment is rising despite tighter controls over our use of antibiotics in medicine and agriculture, Newcastle University scientists have found.

Bacterial DNA extracted from soil samples collected between 1940 and 2008 has revealed a rise in background levels of antibiotic resistant genes.

Newcastle University’s Professor David Graham, who led the research, said the findings suggest an emerging threat to public and environmental health in the future.

“Over the last few decades there has been growing concern about increasing antibiotic resistance and the threat it poses to our health, which is best evidenced by MRSA,” explained Professor Graham, who is based in the School of Civil Engineering and Geosciences at Newcastle University.

“Despite increasingly stringent controls on our use of antibiotics, the background level of antibiotic resistant genes, which are markers for potential resistance, continues to rise in soils.”

“This increases the chances of a resistant gene in a harmless bacteria being passed onto a disease-causing pathogen, such as a MRSA, with obvious consequences.”

Published online in the academic journal Environmental Science and Technology, the report uses data taken from five sites in the Netherlands.

The team found that 78 per cent of genes from four classes of antibiotics showed increasing levels since 1940 – despite continued efforts to reduce environmental levels.

Professor Graham said the next step would be to analyse soil samples from other parts of the world, although he expects to see similar results.

He adds: “The big question is that with more stringent European regulations and greater emphasis on conservative antibiotic use in agriculture and medicine, why are antibiotic resistant gene levels still rising?”

“Whatever the cause, this rise suggests an ever increasing risk of resistant genes being passed from environmental organisms to organisms of greater health concern.”

Professor Graham contends that more complementary studies are desperately needed between environmental and public health researchers to determine whether this increasing ‘pool’ of resistance is actually contributing to harmful bacteria, such as MRSA.

Newcastle University


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Stopping male mosquitoes from sealing their sperm inside females with a 'mating plug' could prevent mosquitoes from reproducing, and offer a potential new way to combat malaria, say scientists publishing new results in PLoS Biology on 22 December.

The new study focuses on the species of mosquito primarily responsible for the transmission of malaria in Africa, known as Anopheles gambiae. These mosquitoes mate only once in their lifetime, which means that disrupting the reproductive process offers a good way of dramatically reducing populations of them in Africa.

When they mate, the male transfers sperm to the female and then afterwards transfers a coagulated mass of proteins and seminal fluids known as a mating plug. This plug is not found in any other species of mosquito and until now, very little has been known about what it is for and the role it plays in An. gambiae reproduction.

The authors of today's study, led by Imperial College London, have shown for the first time that the mating plug is essential for ensuring that sperm is correctly retained in the female's sperm storage organ, from where she can fertilise eggs over the course of her lifetime. Without the mating plug, sperm is not stored correctly, and fertilisation cannot occur.

In Imperial's mosquito labs, the scientists showed it was possible to prevent the formation of the plug in males, and that this stopped them successfully reproducing with females.

Lead author Dr Flaminia Catteruccia, from Imperial's Department of Life Sciences, explains the significance of their discovery:

"We have shown that the male mating plug is not a simple barrier to insemination from rival males, as has been previously suggested. Instead, we discovered that the plug plays an important role in allowing the female to successfully store sperm in the correct way inside her, and as such is vital for successful reproduction.

"Removing or interfering with the mating plug renders copulation ineffective. This discovery could be used to develop new ways of controlling populations of An. gambiae mosquitoes, to limit the spread of malaria."

Dr Catteruccia and her colleagues analysed the composition of the protein-rich mating plug and discovered that it is formed when an enzyme called Transglutaminase interacts with other proteins in the male mosquito's seminal fluid. This interaction causes the seminal fluids to coagulate into a gelatinous solid mass.

When the research team knocked out this enzyme in male mosquitoes in the lab, the fluids failed to coagulate and form the plug. Furthermore, when these males, lacking the key protein and therefore the plug, mated with females, reproduction was not successful.

Dr Catteruccia concludes: "If in the future we can develop an inhibitor that prevents the coagulating enzyme doing its job inside male An. gambiae mosquitoes in such a way that can be deployed easily in the field – for example in the form of a spray as it is done with insecticides – then we could effectively induce sterility in female mosquitoes in the wild. This could provide a new way of limiting the population of this species of mosquito, and could be one more weapon in the arsenal against malaria."

(Photo: ICL)

Imperial College London


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Prior research studies have suggested that the so-called hunger hormone ghrelin, which the body produces when it’s hungry, might act on the brain to trigger this behavior. New research in mice by UT Southwestern Medical Center scientists suggest that ghrelin might also work in the brain to make some people keep eating “pleasurable” foods when they’re already full.

“What we show is that there may be situations where we are driven to seek out and eat very rewarding foods, even if we’re full, for no other reason than our brain tells us to,” said Dr. Jeffrey Zigman, assistant professor of internal medicine and psychiatry at UT Southwestern and co-senior author of the study appearing online and in a future edition of Biological Psychiatry.

Scientists previously have linked increased levels of ghrelin to intensifying the rewarding or pleasurable feelings one gets from cocaine or alcohol. Dr. Zigman said his team speculated that ghrelin might also increase specific rewarding aspects of eating.

Rewards, he said, generally can be defined as things that make us feel better.

“They give us sensory pleasure, and they motivate us to work to obtain them,” he said. “They also help us reorganize our memory so that we remember how to get them.”

Dr. Mario Perello, postdoctoral researcher in internal medicine and lead author of the current study, said the idea was to determine “why someone who is stuffed from lunch still eats – and wants to eat – that high-calorie dessert.”

For this study, the researchers conducted two standard behavioral tests. In the first, they evaluated whether mice that were fully sated preferred a room where they had previously found high-fat food over one that had only offered regular bland chow. They found that when mice in this situation were administered ghrelin, they strongly preferred the room that had been paired with the high-fat diet. Mice without ghrelin showed no preference.

“We think the ghrelin prompted the mice to pursue the high-fat chow because they remembered how much they enjoyed it,” Dr. Perello said. “It didn’t matter that the room was now empty; they still associated it with something pleasurable.”

The researchers also found that blocking the action of ghrelin, which is normally secreted into the bloodstream upon fasting or caloric restriction, prevented the mice from spending as much time in the room they associated with the high-fat food.

For the second test, the team observed how long mice would continue to poke their noses into a hole in order to receive a pellet of high-fat food. “The animals that didn’t receive ghrelin gave up much sooner than the ones that did receive ghrelin,” Dr. Zigman said.

Humans and mice share the same type of brain-cell connections and hormones, as well as similar architectures in the so-called “pleasure centers” of the brain. In addition, the behavior of the mice in this study is consistent with pleasure- or reward-seeking behavior seen in other animal studies of addiction, Dr. Zigman said.

The next step, Dr. Perello said, is to determine which neural circuits in the brain regulate ghrelin’s actions.

(Photo: UTSMC)

UT Southwestern Medical Center


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A facial expression can state a lot. A nod indicates understanding, a frown may say: "Please explain that again!" Scientists from the Max Planck Institute for Biological Cybernetics discovered that we are able to classify an expression much better when it moves naturally rather than when it is "frozen" in a photograph. In order to gain the advantage of dynamic information, we need to see the expression moving for at least 100 milliseconds. If the video sequence is shorter, our brain is less capable of interpreting the facial motion. Some expressions rely on changes in head orientation, for example, a nod or a shake of the head, others on the complex deformation of facial parts, such as wrinkling our nose to signalize disgust or a frown.

In order to examine to what extent we are able to recognize - based on facial expressions - the mood of a person with whom we are interacting, the scientists showed participants pictures of humans with various different expressions. Among them were simple, emotional expressions, such as "happy" and "sad", but also more complex ones such as agreement, confusion, or surprise, which are usually used to emphasize or modify statements in a conversation. In order to investigate whether these expressions are recognized more easily in motion or in static pictures, a short video sequence was shown to the participants. The video recordings began at a neutral expression, showed an emotion, and ended at the last frame before the face started to head back to a neutral expression. The frame used in the static conditions was the last, so-called ‘peak’ frame of each dynamic sequence. The participants were then asked to identify the expressions based on the shown sequence or single frame.

In further experiments, the video sequences were converted to a series of photographs that was shown to the participants. Nevertheless, the expressions were still recognized more accurately in the video sequence. This showed that the dynamic advantage is not due to the presence of multiple images, but that some form of dynamic information is being used. In order to figure the degree to which facial expression recognition relies on natural movement, the frames were presented as a movie, but in a random order. Comparisons of the performance in this scrambled condition to the original video sequence shows that the recognition rates were still higher in the original than in the scrambled version. The chronological direction is of importance as well. If the video sequences are temporally reversed, they are again identified less accurately. Finally, the more temporal information we receive, the better we are able to recognize expressions - at least up to 100 milliseconds. The results show that neither pictures, nor motion alone are of importance, but that we need a combination of the correct temporal sequence and the correct facial motion to reliably interpret facial expressions.

"Facial expressions, like gestures and body motion, are a dynamic phenomenon and need to be investigated with the help of video sequences in order to get a better understanding of the dynamic information that is being processed", says Dr. Christian Wallraven, co-author of the study. "Our results also have implications for the area of computer animation, since its goal is to create artificial avatars and facial animations that are able to communicate realistically and believably", says the physicist and perception scientist.

(Photo: MPI für biologische Kybernetik / Christian Wallraven)

Max Planck Institute


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It may seem a small consolation from either point of view, but a new study has affirmed that patients with cancer are less likely to develop Alzheimer's disease, and patients with Alzheimer's disease are less likely to get cancer.

"There were still people who had both Alzheimer's and cancer, but it was significantly less common than we would expect," says lead author Catherine M. Roe, Ph.D., research instructor in neurology at Washington University School of Medicine in St. Louis. "If there truly is an inverse association, it gives us one more way of finding out what's going wrong in both cancer and Alzheimer's, and that could lead us to new ways to treat either condition."

Hints of a disconnect between cancers and neurological disorders have been building for years. The effect was first noticed in patients with Parkinson's disease, who get cancer less often; later studies have suggested that multiple sclerosis sufferers may have fewer tumors, and that Down syndrome patients who live to middle age or older have reduced incidence of cancer.

Six years ago, Maria Behrens, M.D., then a postdoctoral fellow at Washington University's Alzheimer's Disease Research Center (ADRC), noticed that few nursing home patients in her native Chile seemed to have cancer. Roe, Behrens and their colleagues conducted a study using data from research volunteers at the ADRC and found that people with Alzheimer's disease were slower to develop cancer in the future.

For the new study, scientists followed 3,020 people aged 65 and older enrolled in the Cardiovascular Health Study, a National Heart, Lung, and Blood Institute Study that gathered extensive health data on its participants. ADRC researchers monitored the subjects for an average of five years to see if they developed dementia and for an average of eight years to see if they were hospitalized for cancer. As the study began, 164 patients already had Alzheimer's, and 522 patients had been diagnosed with cancer.
During the study, 478 people developed dementia, and 376 developed invasive cancer. Those who had Alzheimer's disease at the start of the study were 69 percent less likely to be hospitalized for cancer treatment than those who did not have Alzheimer's when the study began. Caucasian people who had cancer as the study began had 43 percent less risk of developing Alzheimer's disease. The latter finding, however, was not apparent in minority groups.

To make sure that doctors or caregivers treating Alzheimer's patients weren't just too overwhelmed to notice the start of cancer, researchers also monitored cancer incidence in patients with vascular dementia. Scientists think this condition is caused by lack of blood to the brain.

"If the decreased chance of cancer diagnosis was simply due to the fact that physicians don't notice cancer in people with dementia, the decrease should have shown up for both the Alzheimer's patients and those with vascular dementia," Roe says. "But the drop in cancer risk was only seen in those with Alzheimer's."

Could Alzheimer's be killing patients before they can be diagnosed with cancer? Roe says epidemiologists have analytical techniques to adjust for such deaths. She also notes that patients with vascular dementia tended to die sooner than patients with Alzheimer's, yet they still had a higher risk of cancer than patients with Alzheimer's.

Roe cautions that the study was based on cancer hospitalization data, meaning that cases of benign, inoperable or otherwise untreated cancers could not be considered. She and her colleagues plan to study a larger patient population to see if Alzheimer's disease changes risks of specific types of tumors, and if certain types of cancers have larger or smaller effects on Alzheimer's risk.

Washington University School of Medicine in St. Louis




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