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How The Genome Sets its Functional Micro-Architecture

The genes that are involved in the development of the fetus are activated in different tissues and at different times. Their expression is carefully regulated by so-called “enhancer sequences”, which are often located far from their target genes, and requires the DNA molecule to loop around and bring them in close proximity to their target genes. Such 3D changes of the DNA are in turn controlled by other sequences called topologically associating domains (TADs). EPFL scientists have now studied the TADs involved in digit development in the fetus and have gained insights in some of the big questions surrounding them. The work is published in Genome Biology.

Now, a study by the lab of Denis Duboule at EPFL, with their colleagues at the University of Geneva, provides significant insights about TADs and how they organize DNA. “We were looking at DNA architecture and function,” says researcher Pierre Fabre, who led the project. The data indicates that these TADs can host multiple associations between Hoxd  and up to three of their enhancers, and that disrupting the 3D structure of chromatin leads to the remodeling of TAD structure. Additionally, CTCF seems to mediate the gating of long-range DNA contacts in a boundary-selection mechanism. “The building of the recomposed TAD depends on both distinct functional and intrinsic parameters such as the genomic distance,” says Fabre.

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Geneticists Trace Humble Apple’s Exotic Lineage All the Way to the Silk Road

Image result for applesIt is a lunchbox staple so ubiquitous as to have become mundane. But the apple we know today is the fruit of an extraordinary journey, researchers have revealed. Scientists studying the genetics of the humble apple have unpicked how the cultivated species emerged as traders travelled back and forth along the Silk Road– ancient routes running from the far east to the Mediterranean sea. Published in the journal Nature Communications by researchers from the US and China, the study focuses on genetic data from 117 different varieties of apple. These encompassed 24 species ranging from wild apples found in North America and China to domestic apples including ancient, cultivated varieties as well as those found in our supermarkets.

“Our research is the first whole genome level analysis about apples’ evolutionary history,” said Yang Bai, co-author of the research from the Boyce Thompson Institute at Cornell University.

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Kent State Researchers Help Find Pathologic Hallmarks of Alzheimer’s Disease in Aged Chimpanzee Brains

Kent State University researchers analyzed the brains of aged chimpanzees to show pathology similar to the human Alzheimer’s disease brain. This image shows tau-positive neuron (black) in proximity to amyloid deposits within blood vessels (red) in an aged chimpanzee brain.Dementia affects one-third of all people older than 65 years in the United States. The most common cause of dementia is Alzheimer’s disease, a progressive, irreversible brain disease that results in impaired cognitive functioning and other behavioral changes. Humans are considered uniquely susceptible to Alzheimer’s disease, potentially due to genetic differences, changes in brain structure and function during evolution, and an increased lifespan. However, a new study published Aug. 1 in Neurobiology of Aging provides the most extensive evidence of Alzheimer’s disease brain pathology in a primate species to date. Researchers from Kent State University’s College of Arts and Sciences, along with colleagues from the George Washington University, Yerkes National Primate Research Center, Georgia State University, Barrow Neurological Institute and the Icahn School of Medicine at Mount Sinai, found that the brains of aged chimpanzees, our closest living relatives, show pathology similar to the human Alzheimer’s disease brain.

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Restless Development: Bad Sleep May Be Evolutionary Survival Tool, Study Finds

Poor sleep is often regarded as a modern affliction linked to our sedentary lifestyles, electric lighting and smartphones on the bedside table. However, new research suggests that fitful sleep could be an ancient survival mechanism designed to guard against nocturnal threats. The study, which tracked the sleep patterns of a modern-day hunter-gatherer tribe in northern Tanzania, found that frequent night-time waking and differing sleep schedules between the young and old ensured that there was nearly always at least one tribe member awake. “They tell an important part of the human evolutionary story because they live a lifestyle that is the most similar to our hunting and gathering past,” said Alyssa Crittenden, an associate professor of anthropology at the University of Nevada, Las Vegas, and one of the study’s co-authors. “They sleep on the ground and have no synthetic lighting or controlled climate.” Of over 220 total hours of observation, there were just 18 minutes when all adults were sound asleep simultaneously. On average, more than a third of the group was alert, or dozing very lightly, at any given time.

The authors claim that the misalignment of sleep schedules of the young and elderly could be an evolutionary adaptation that kept our ancestors safe when sleeping in mixed-age groups.

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Prelude to Global Extinction: Stanford Biologists Say Disappearance of Species Tells Only Part of the Story of Human Impact on Earth’s Animals

Image result for Bornean gibbonNo bells tolled when the last Catarina pupfish on Earth died. Newspapers didn’t carry the story when the Christmas Island pipistrelle vanished forever.

Two vertebrate species go extinct every year on average, but few people notice, perhaps because the rate seems relatively slow – not a clear and present threat to the natural systems we depend on. This view overlooks trends of extreme decline in animal populations, which tell a more dire story with cascading consequences, according to a new study that provides the first global evaluation of these population trends. “This is the case of a biological annihilation occurring globally, even if the species these populations belong to are still present somewhere on Earth,” said co-author Rodolfo Dirzo, a professor of biology.

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First Big Efforts to Sequence Ancient African DNA Reveal How Early Humans Swept Across the Continent

The study of ancient human DNA has not been an equal opportunity endeavor. Early Europeans and Asians have had portions of their genomes sequenced by the hundreds over the past decade, rewriting Eurasian history in the process. But because genetic material decays rapidly in warm, moist climates, scientists had sequenced the DNA of just one ancient African. Until now.

This week, at the annual meeting of the Society for Molecular Biology & Evolution here, scientists announced that they had partially sequenced 15 ancient African genomes, with representatives from all over sub-Saharan Africa. And another group—whose work is still unpublished—has sequenced seven more ancient humans from South Africa. “[Finding] ancient genomes from Africa is pretty amazing,” says Anna-Sapfo Malaspinas, a population geneticist at the University of Bern, who was not involved in either project.

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Long-Term Sexual Intimidation May Be Widespread in Primate Societies

File:Baboons (3540212876).jpgAfter observing the mating habits of chacma baboons living in the wild over a four-year period, researchers have found that males of the species often use long-term sexual intimidation to control their mates. The findings suggest that this mating strategy has a long history in primates, including humans, and may be widespread across social mammals — especially when males of a species are typically larger than females.

“This study adds to growing evidence that males use coercive tactics to constrain female mating decisions in promiscuous primates, thereby questioning the extent of sexual freedom left for females in such societies and suggesting that sexual intimidation has a long evolutionary history in primates — a taxonomic group that of course includes humans,” says Alice Baniel at the Institute for Advanced Study in Toulouse, France.

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How Frogs Benefited From The Dinosaurs’ Extinction

The asteroid that hit Earth 66 million years ago spelled disaster for the dinosaurs. But scientists say they’ve found one silver lining to the mass extinction — turns out, it was really good for frogs. The resilient animals date back some 200 million years. And in the aftermath of the extinction event, they survived and thrived, taking advantage of an ecological vacuum other animals left behind. About 9 in 10 frog species today evolved from three frog lineages that survived the event, which occurred at the boundary between the Cretaceous and Paleogene periods, according to research published Monday in Proceedings of the National Academy of Science.

What this research shows, Wake says, is that frogs have the proven ability to “[take] advantage of opportunities — in this case [an] ecological vacuum that existed following the mass extinction.”

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