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Yes, Computing Genetic Ancestors is Super Accurate

Colorfully fluorescing mutated proteins

Remnants of extinct monkeys are hiding inside you, along with those of lizards, jellyfish and other animals. Your DNA is built upon gene fragments from primal ancestors.

Now researchers at the Georgia Institute of Technology have made it more likely that ancestral genes, along with ancestral proteins, can be confidently identified and reconstructed. They have benchmarked a vital tool that would seem nearly impossible to benchmark. The newly won confidence in the tool could also help scientists use ancient gene sequences to synthesize better proteins to battle diseases.

For some 20 years, scientists have used algorithms to compute their way hundreds of millions of years back into the evolutionary past. Starting with present-day gene sequences, they perform what’s called ancestral sequence reconstruction (ASR) to determine past mutations and figure out the genes’ primal forerunners. “With the help of ASR, we can now actually build those ancient genes in the laboratory and express their encoded ancient proteins,” said Eric Gaucher, an associate professor at Georgia Tech’s School of Biological Sciences.

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Zika Reference Strain Sequenced, Will Aid in Diagnosis, Screening

Zika virus to spread to all but 2 countries in the Americas, WHO predictsAn international team of researchers has sequenced a strain of the Zika virus that will be used as a World Health Organization (WHO) reference strain to identify Zika virus infection in the blood, thus making it easier to diagnose the disease. While the reference material will undergo formal WHO review in October, the agency has given the go-ahead for the strain’s use given the urgent need of medical products to diagnose and treat Zika. The sequence is published September 1st in Genome Announcements, a journal of the American Society for Microbiology. “WHO’s go-ahead before it’s expert committee meeting in October reflects the urgent need for researchers and companies to access valid reference material to diagnose Zika virus infection,” said principal investigator Sally Baylis, PhD, senior scientist, Virus Safety section, Paul-Ehrlich-Institut, Langen, Germany. “This will facilitate the development of sensitive, better performing tests to detect Zika in patients.”

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Looking to Saliva to Gain Insight on Evolution

salivaThere’s no need to reinvent the genetic wheel. That’s one lesson of a new study that looks to the saliva of humans, gorillas, orangutans, macaques and African green monkeys for insights into evolution. The research, published on Aug. 25 in Scientific Reports, examined a gene called MUC7 that tells the body how to create a salivary protein of the same name. The protein, which is long and thin, forms the backbone of a bottlebrush-shaped molecule that helps to give spit its slimy, sticky consistency. The study found that within the MUC7 gene, instructions for building important components of the bottlebrush were repeated multiple times in each of the five primate species studied. Gorillas had the fewest copies of this information (4-5), while African green monkeys had the most (11-12). Humans fell somewhere in between, with 5-6. Through an in-depth analysis of MUC7’s evolutionary history, the researchers concluded that having numerous copies of the repeated instructions likely conferred an evolutionary advantage to primates — possibly by enhancing important traits of saliva such as its lubricity and, perhaps even more importantly, its ability to bind to microbes (a capability that may help curb disease).

Evolution can favor the expansion of tried-and-true genetic tools, in addition to the development of totally new ones, says University at Buffalo biologist Omer Gokcumen, who led the study together with Stefan Ruhl, a salivary researcher in UB’s oral biology department. “You don’t always have to invent a new tool,” says Gokcumen, PhD, an assistant professor of biological sciences in UB’s College of Arts and Sciences. “Sometimes, you just need to amplify the tool you already have.”

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DNA Database Brings Scientists Closer to Pinpointing Genes for Disease

Untitled-1Scientists say they are closer to pinning down the genetic causes of inherited diseases ranging from muscular dystrophy to certain types of heart disease after analysing the DNA of more than 60,000 people. Researchers have discovered more than 3,000 genes in which certain mutations are likely to play a role in disease, as well as more than 160 genetic mutations that have previously been linked to inherited conditions – but are in fact harmless. The findings will help to pin down whether genetic mutations seen in a patient are likely to be behind their disease.

The research is the fruit of an international collaboration, dubbed Exac, which pulled together data from around the world to produce the largest ever catalogue of variations in protein-coding regions of DNA, boasting data from 60,706 individuals.

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Who’s the Daddy? Female Fish Have Novel Way of Finding Reliable Mates

fishFemale fish have a novel way of finding Mr Right when it comes to picking fathers for their offspring, scientists have revealed. Like most other species of fish, female ocellated wrasse release their eggs into the water for fertilization by males, making just who ends up as the daddy something of a lottery. But now researchers have revealed that females are able to influence which males will succeed in fertilizing their eggs. Writing in the journal Nature Communications, a team of researchers from the US say that the female ocellated wrasse is able to sort Mr Nice from Mr Nasty thanks to a substance, known as ovarian fluid, that coats the eggs she has released. While the researchers are still teasing apart just how the ovarian fluid affects the reproductive success of the males, the study suggests that the ovarian fluid could be affecting the velocity and motion of the sperm. In a number of experiments, the researchers took eggs from female fish and either removed the ovarian fluid, left it in place, or removed it and then re-introduced the fluid. Sperm from both types of male were then introduced to the eggs simultaneously, with the fertilized eggs later analyses to determine their paternity. Further experiments introduced the sperm from each type of male separately to explore whether the influence of the ovarian fluid differed between them.

The results revealed that rather than attracting more nesting males, or simply offering an advantage to their sperm, the ovarian fluid appears to remove the numbers advantage for sperm of the sneaker males.

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Finding the Brain’s Generosity Centre

Would you give money to this man?Scientists from Oxford University and UCL have identified part of our brain that helps us learn to be good to others. The discovery could help understanding of conditions like psychopathy where people’s behaviour is extremely antisocial. The researchers were led by Dr Patricia Lockwood, who explained: ‘Prosocial behaviours are social behaviours that benefit other people. They are a fundamental aspect of human interactions, essential for social bonding and cohesion, but very little is currently known about how and why people do things to help others.’ The scientists used a well-understood model of how people learn to maximise good outcomes for themselves and applied this model to understand how people learn to help others. While being scanned in a MRI machine, volunteers had to work out which symbols were more likely to give them, or someone else, a reward. ‘This the first time anyone has shown a particular brain process for learning prosocial behaviours – and a possible link from empathy to learning to help others. By understanding what the brain does when we do things for other people, and individual differences in this ability, we are better placed to understand what is going wrong in those whose psychological conditions are characterised by antisocial disregard for others.’

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The Biggest Issue in Women’s Sports Is About to Come to a Head

Expectations are soaring for 25-year-old South African runner Caster Semenya, who races next week in the 800 meters. She’s favored to clinch a gold medal. She might even shatter the longest-running world record for track and field. And if she does, it could affect much more than the pride of her competitors. A big win for Semenya would likely add fuel to an already-fiery debate about gender and sports, and whether women like her should be allowed to race at all. For decades, the International Association of Athletics Federations (IAAF), the world’s governing body for track and field, has sought to preserve the male-female division in its sport through variations of sex testing—gynecological exams, chromosome tests, or hormone tests to make sure female competitors aren’t actually men trying to pass as women, or intersex women with masculine traits that might give them an unfair boost. Since 2011, sex testing has focused on testosterone. Women like Semenya whose functional levels of the hormone are within “the male range,” or higher than 10 nanomoles per liter of blood, have been barred from international competitions like the Olympics. But not this year. For the first time in more than half a century, female Olympians will not be subject to any form of sex testing in Brazil, which means intersex track athletes will be allowed to compete with their natural testosterone levels.

Now, as scientists struggle to determine how testosterone affects performance, thousands of athletes are converging on Rio de Janeiro for what some have described as a total “free-for-all,” as far as gender boundaries go. If Semenya dominates, will it be fair? What does the science say?


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Where There’s Smoke And A Mutation There May Be An Evolutionary Edge For Humans

Smoke Lab-HubbardA genetic mutation may have helped modern humans adapt to smoke exposure from fires and perhaps sparked an evolutionary advantage over their archaic competitors, including Neandertals, according to a team of researchers. Modern humans are the only primates that carry this genetic mutation that potentially increased tolerance to toxic materials produced by fires for cooking, protection and heating, said Gary Perdew, the John T. and Paige S. Smith Professor in Agricultural Sciences, Penn State. At high concentrations, smoke-derived toxins can increase the risk of respiratory infections. For expectant mothers, exposure to these toxins can increase the chance of low birth weight and infant mortality. “If you’re breathing in smoke, you want to metabolize these hydrophobic compounds and get rid of them, however, you don’t want to metabolize them so rapidly that it overloads your system and causes overt cellular toxicity,” said Perdew.

The researchers used computational and molecular techniques to examine the difference in the genetics of polycyclic aromatic hydrocarbon tolerance between humans and Neandertals. They examined a genomic database of humans, Neandertals and a Denisovan, a hominin more closely related to Neandertals than humans. “We thought the differences in aryl hydrocarbon receptor ligand sensitivity would be about ten-fold, but when we looked at it closely, the differences turned out to be huge,” said Perdew. “Having this mutation made a dramatic difference. It was a hundred-fold to as much of a thousand-fold difference.”

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