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New Guide For Finding Genes Linked With Behavior

Scientists interested in finding specific genes that influence the behavior of humans and animals have a new tool, thanks to a two-year research effort aimed at describing how to apply the latest techniques of molecular genomics to the study of complex behavior.  “There’s a really steep learning curve when you get into genomics, and if you’re starting from a place of very little knowledge, it’s incredibly intimidating,” said Sarah Bengston, a Rice University behavioral ecologist and lead author of a new review article about genomic tools for behavioral scientists. “I am the person who needed this paper,” said Bengston, a Huxley Faculty Fellow in Ecology and Evolutionary Biology in Rice’s Department of BioSciences. “I needed a novice-level introduction to how genomic tools could help me answer research questions. For example, was my experimental setup an appropriate system to use for genomic sequencing or any kind of molecular techniques? I couldn’t find that kind of reference, so I worked with a group of really smart people to write one.”

The article, which appears online this week in Nature Ecology and Evolution, is designed to guide behavioral scientists from any discipline with specific recommendations about whether genomics tools are appropriate for their research, and if so, which tools are likely to best work in their labs.

Read the full article here.

Received An At-Home DNA Test As A Holiday Gift? Proceed With Caution

If you or a family member received a consumer genetic testing kit as a holiday gift, you probably weren’t alone. Sales of at-home DNA testing kits reportedly soared in 2017, as people sought clues to their ancestry or future health. Some genetic-testing companies encouraged the purchase of kits as holiday gifts — even offering free gift wrapping. However, the results from at-home DNA tests are proving problematic for some people, even as the tests’ growing popularity helps to raise public awareness of the link between one’s genetic make-up and their health. “We’ve definitely seen a steady increase in at-home genetic tests and an uptick recently, in part because of the new trend to give these tests as a family gift,” said Wayne Grody, director of the UCLA Molecular Diagnostic Laboratories and Clinical Genomics Center and a professor of pathology, human genetics and pediatrics at the Geffen School of Medicine at UCLA. “Our genetic clinic gets an increasing number of calls from people who either don’t understand the results or are upset and seeking someone to explain the findings to them.”

Grody notes that at-home DNA tests differ significantly from the much more comprehensive and scientifically rigorous genetic testing that is performed at UCLA’s genomics center. At the center, people undergo a comprehensive analysis and diagnostic interpretation of their entire protein-encoding genome, involving some 20,000 genes, to potentially locate the single DNA change responsible for a person’s disorder. Grody sees some value in the at-home DNA tests. From his experience, he has seen a small number of cases in which use of the tests has led to a quicker diagnosis of a medical condition than would otherwise have happened. “Also these at-home tests have provided a kind of education and stimulation of interest about DNA among people who didn’t have a genetics background in school or who had forgotten it,” he said.

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Flower Or Flesh? Genetics Explain Mosquito Preference

Image result for mosquitoImagine a world in which mosquitoes choose blossoms over blood. Nice, right? There already exists a mosquito species called Wyeomyia smithii in which most of the bugs refuse blood meals in favor of sweet floral nectar. And new research is helping to explain the evolutionary genetics of the switch from blood sucker to flower fanatic. The researchers, including co-lead author David Denlinger of The Ohio State University, expect that all of the mosquitoes in the species once relied on blood for nourishment and that over time, some evolved to prefer plants. He suspects that the majority of the species moved away from blood meals because of the associated risks – risks that include the aggravated patio-sitting human. “Blood meals come at a cost. A person could swat you – even do you in,” Denlinger said. On top of that, the warm meal is a stressor on the mosquito’s body and can contain agents that are toxic to the bug. “If you could survive without taking all those risks, there could be some evolutionary advantages,” Denlinger said.

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DNA Reveals That Silky Anteaters Are Seven Species

The silky anteater (Cyclopes didactylus) has previously been recognized to be a single species divided into several sub-species. But a new genetic analysis, published in the Zoological Journal of the Linnean Society, suggests that this enigmatic mammal is not one species, but seven separate ones. Lead author Dr. Flávia Miranda, a researcher with the Universidade Federal de Minas Gerais, Brazil, and co-authors analyzed 33 samples of DNA and examined more than 280 specimens of this rare mammal in museums worldwide. “We examined a total of 287 specimens of Cyclopes, including skins and skulls, housed in 20 natural history collections and 33 samples for molecular analyses,” they said. “Based on evidence provided by molecular phylogenetics using mitochondrial and nuclear DNA, allied with coalescent species delimitation analyses, diagnostic characters of the skull, color patterns and structures of pelage, we suggest that the genus Cyclopes comprises at least seven species.”

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Google Has Released an AI Tool That Makes Sense of Your Genome

Image result for genomeAlmost 15 years after scientists first sequenced the human genome, making sense of the enormous amount of data that encodes human life remains a formidable challenge. But it is also precisely the sort of problem that machine learning excels at. On Monday, Google released a tool called DeepVariant that uses the latest AI techniques to build a more accurate picture of a person’s genome from sequencing data. DeepVariant helps turn high-throughput sequencing readouts into a picture of a full genome. It automatically identifies small insertion and deletion mutations and single-base-pair mutations in sequencing data.

A number of tools exist for interpreting these readouts, including GATK, VarDict, and FreeBayes. However, these software programs typically use simpler statistical and machine-learning approaches to identifying mutations by attempting to rule out read errors. “One of the challenges is in difficult parts of the genome, where each of the [tools] has strengths and weaknesses,” says Brad Chapman, a research scientist at Harvard’s School of Public Health who helped develop DeepVariant. “These difficult regions are increasingly important for clinical sequencing, and it’s important to have multiple methods.”

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Everything Your Biology Teacher Told You About Earlobes Is Wrong

Image result for earlobeMost of us learned in high school biology that genetics can sometimes be incredibly simple. Some physical traits are the result of an easy equation containing a pair of parents’ genes. One trait—blue eyes, for example—results from recessive genes, but only if no dominant gene—the one to thank for brown eyes—shows up to take a stand. Parents each pass on two genes for eye color, or so your teacher probably told you. Depending on the combination, dominant genes can override any recessive genes to create their signature color. Sorry to break it to you, but very few traits actually work this way. Not even the classic example of eye color is actually so simple. With more genetic information available, it’s becoming clear that a number of different genes determine each feature. In a paper out this week in The American Journal of Human Genetics, scientists show that earlobes are no exception.

The researchers studied two different groups to identify those genes. They first recruited 10,000 people, sequenced their DNA, and examined their ears. From that initial set, the researchers spotted just six genes that played a role. But when they added their second group, which included 65,000 people who use the genetic testing company 23andMe (and have agreed to allow their samples to be used for research purposes) that number increased to 49. While the main point of this study is that seemingly simple genetic traits are far more complicated than previously thought, the fact that it took more than 10,000 people to identify those genes is also key. Geneticists often don’t like to perform population studies at such scale, because they are too large to zoom in on any specific details. But that means that we might not be getting the full picture, notes lead author John Shaffer, a geneticist at the University of Pittsburgh. Doing studies that combine small and large data sets could provide the best of both worlds, Shaffer says.

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Chimp Females Who Leave Home Postpone Parenthood

Image result for chimpanzeeWild chimpanzee females in western Tanzania who leave home or are orphaned take roughly three years longer to start a family. The researchers analyzed more than 50 years’ worth of daily records for 36 female chimps born in Gombe National Park. Stored in the Jane Goodall Institute Research Center at Duke University, the records are part of a larger database containing close observations of hundreds of wild chimpanzees, going all the way back to Goodall’s first field notes from the early 1960s. Several factors may contribute to the delay, the researchers said. Having left their family and friends behind, they must jostle for position in the pecking order of a new and unfamiliar group. In contrast, stay-at-home females benefit from better support. Females also started reproducing earlier if their own mothers were around while they were growing up, particularly if their moms were high-ranking — in part because females with high-ranking moms get better access to food.

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CRISPR-Carrying Nanoparticles Edit the Genome

In a new study, MIT researchers have developed nanoparticles that can deliver the CRISPR genome-editing system and specifically modify genes in mice. The team used nanoparticles to carry the CRISPR components, eliminating the need to use viruses for delivery. “What’s really exciting here is that we’ve shown you can make a nanoparticle that can be used to permanently and specifically edit the DNA in the liver of an adult animal,” says Daniel Anderson, an associate professor in MIT’s Department of Chemical Engineering and a member of MIT’s Koch Institute for Integrative Cancer Research and Institute for Medical Engineering and Science (IMES).

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