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Category Archives: Transhuman News

The Surprisingly Early Settlement of the Tibetan Plateau – Scientific American

Posted: February 14, 2017 at 10:51 am

Genetic analysis suggests that humans have continuously inhabited the Tibetan Plateau as far back as the last ice age.

The first humans who ventured onto the Tibetan Plateau, often called the roof of the world, faced one of the most brutal environments our species has ever confronted. At an average elevation of more than 4,500 meters, it is a cold and arid place with half the oxygen present at sea level. Although scientists had long thought no one set foot on the plateau until 15,000 years ago, new genetic and archaeological data indicate that this event may have taken place much earlierpossibly as far back as 62,000 years ago, in the middle of the last ice age. A better understanding of the history of migration and population growth in the region could help unravel the mysteries of Tibetans' origin and offer clues as to how humans have adapted to low-oxygen conditions at high altitudes.

As reported in a recent study in the American Journal of Human Genetics, researchers got a better grasp of the plateau's settlement history by sequencing the entire genomes of 38 ethnic Tibetans and comparing the results with the genomic sequences of other ethnic groups. It has revealed a complex patchwork of prehistoric migration, says Shuhua Xu, a population geneticist at the Chinese Academy of Sciences' Shanghai Institutes for Biological Sciences. A big surprise was the antiquity of Tibetan-specific DNA sequences, Xu says. They can be traced back to ancestors 62,000 to 38,000 years ago, possibly representing the earliest colonization of the plateau.

As an ice age tightened its grip after that first migration, genetic mixing between Tibetans and non-Tibetans ground to a halt for tens of thousands of yearssuggesting that movement into Tibet dropped to a minimum. The migration routes were probably cut off by ice sheets, Xu says. It was simply too harsh even for the toughest hunter-gatherers. But about 15,000 to 9,000 years agoafter the so-called last glacial maximum (LGM), when the ice age was at its harshest and Earth's ice cover had reached its peakthousands flocked to Tibet en masse. It's the most significant wave of migration that shaped the modern Tibetan gene pool, Xu says. This meshes well with several independent lines of evidence showing that Tibetans began to acquire genetic mutations that protected them from hypoxia 12,800 to 8,000 years ago.

Xu's team was the first to sequence the entire Tibetan genome, and the resolution is really impressive, says archaeologist Mark Aldenderfer of the University of California, Merced, who was not involved in the research. The study, he adds, provides fine details of how different populations from various directions may have combined their genes to ultimately create the people that we call Tibetans. It shows that 94 percent of the present-day Tibetan genetic makeup came from modern humanspossibly those who ventured into Tibet in the second wave of migrationand the rest came from extinct hominins. The modern part of the Tibetan genome reflects a mixed genetic heritage, sharing 82 percent similarity with East Asians, 11 percent with Central Asians and 6 percent with South Asians.

In addition, Xu's team identified a Tibetan-specific DNA segment that is highly homologous to the genome of the Ust'-lshim Man (modern humans living in Siberia 45,000 years ago) and several extinct human species, including Neandertals, Denisovans and unknown groups. The segment contains eight genes, one of which is known to be crucial for high-altitude adaptation. Xu suspects that a hybrid of all these species may have been the common ancestor of the pre-LGM population on the plateau.

The study also reveals a startling genetic continuity since the plateau was first colonized. This suggests that Tibet has always been populatedeven during the toughest times as far as climate was concerned, Xu says. That idea contradicts the commonly held notion that early plateau dwellers would have been eliminated during harsh climate intervals, including the LGM, says David Zhang, a geographer at the University of Hong Kong, who was not involved in Xu's work. Aldenderfer and others contend that parts of the plateau could have provided a refuge for people to survive the ice age. There were plenty of places for [those early populations] to live where local conditions weren't that bad, such as the big river valleys on the plateau, he says.

Also supporting the antiquity of the peopling of Tibet is a study presented at the 33rd International Geographical Congress last summer in Beijing, where a team unveiled the plateau's earliest archaeological evidence of human presencedating to 39,000 to 31,000 years ago. The site, rich with stone tools and animal remains, lies on the bank of the Salween River in the southeastern Tibetan Plateau.

Different lines of evidence are now converging to point to much earlier and much more persistent human occupation of the plateau than previously thought, Aldenderfer says. But he notes that pieces are still missing from the puzzle: More excavations are required to close those gaps.

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The Surprisingly Early Settlement of the Tibetan Plateau - Scientific American

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Progression of HIV triggered by each patient’s genes – Genetic Literacy Project

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Scientists have long observed important differences in the rate of disease progression among individuals infected with HIV. It is now well established that the disease progresses faster in people with a higher viral load the amount of genetic material from the virus found in their blood.

[This study]is the first to investigate the relative impacts of human and viral genetics on viral load, within one group of patients.

[The researchers]found that genetic differences between HIV strains accounted for 29% of the contrasts in viral load between patients. Human genetic variation on the other hand, explains 8.4%. Together, human and viral genetics explained a third of viral load variation.

These findings suggest that the patients genetics trigger genetic mutations in the HIV virus as it multiplies inside them, thus influencing the clinical course of HIV infection.

Our study improves our understanding of HIV pathogenesis. This is an important step the better you know your enemy, the more equipped you are to fight it and fight against the disease, said [Jacques Fellay, director of the study bycole Polytechnique Fdrale de Lausanne in Switzerland.]

[The study can be found here.]

The GLP aggregated and excerpted this blog/article to reflect the diversity of news, opinion, and analysis. Read full, original post:Patients and virus genetics account for a third of HIV viral load

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Progression of HIV triggered by each patient's genes - Genetic Literacy Project

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Studies point way to precision therapies for common class of genetic disorders – HealthCanal.com (press release) (blog)

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Although not widely known, RASopathies are among the most common genetic disorders, affecting approximately one child out of 1,000. RASopathies are caused by mutations within the RAS pathway, a biochemical system cells use to transmit information from their exterior to their interior.

Two Princeton University studies are opening important new windows into understanding an untreatable group of common genetic disorders known as RASopathies that affect approximately one child out of 1,000 and are characterized by distinct facial features, developmental delays, cognitive impairment and heart problems. The researchers observed in zebrafish and fruit fly embryos how cancer-related mutations in the RAS pathway a biochemical system cells use to transmit information from their exterior to their interior caused severe deformations. Fruit-fly embryos (above) showed how signals at the early stage of development (red in top photo) activate genes (purple in middle photo) and pattern structures in the fly larva (bottom photo.) (Photo courtesy of Stanislav Shvartsman, Department of Chemical and Biological Engineering)

Human development is very complex and its amazing that it goes right so often. However, there are certain cases where it does not, as with RASopathies, said Granton Jindal, co-lead author of the two studies. Both Jindal and the other co-lead author, Yogesh Goyal, are graduate students in theDepartment of Chemical and Biological Engineeringand theLewis-Sigler Institute for Integrative Genomics (LSI). Jindal and Goyal do their thesis research in the lab ofStanislav Shvartsman, professor of chemical and biological engineering and LSI.

Our new studies are helping to explain the mechanisms underlying these disorders, Jindal said.

These studies were published this year, one in the Proceedings of the National Academy of Sciences (PNAS) and the other in Nature Genetics online. The researchers made the discoveries in zebrafish and fruit flies animals commonly used as simplified models of human genetics and Jindal and Goyals specialties, respectively. Due to the evolutionary similarities in the RAS pathway across diverse species, changes in this pathway would also be similar. Thus, it is likely that significant parts of findings in animals would apply to humans as well, although further research is needed to confirm this.

The first paper published Jan. 3in PNAS presented a way to rank the severity of different mutations involved in RASopathies. The researchers introduced 16 mutations one at a time in developing zebrafish embryos. As each organism developed, clear differences in the embryos shapes became evident, revealing the strength of each mutation. The same mutant proteins produced similarly varying degrees of defects in fruit flies. Some of the mutations the researchers tested were already known to be involved in human cancers. The researchers noted that these cancer-related mutations caused more severe deformations in the embryos, aligning with the medical communitys ongoing efforts to adapt anti-cancer compounds to treat RASopathies.

Until now, there was no systematic way of comparing different mutation severities for RASopathies effectively, Goyal said.

Jindal added, This study is an important step for personalized medicine in determining a diagnosis to a first approximation. The study therefore suggested a path forward to human diagnostic advances, potentially enabling health care professionals to offer better diagnoses and inform caretakers about patients disease progression.

The study went further and examined the use of an experimental cancer-fighting drug being investigated as a possible way to treat RASopathies. The researchers demonstrated that the amount of medication necessary to correct the developmental defects in the zebrafish embryos corresponded with the mutations severity more severe mutations required higher dosages.

The more recent paper, published online by Nature Genetics Feb. 6, reports an unexpected twist in treatment approach to some RASopathies. Like all cellular pathways, the RAS pathway is a series of molecular interactions that changes a cells condition. Conventional wisdom has held that RASopathies are triggered by overactive RAS pathways, which a biologist would call excessive signaling.

The Nature Genetics study, however, found that some RASopathies could result from insufficient signaling along the RAS pathway in certain regions of the body. This means that drugs intended to treat RASopathies by tamping down RAS pathway signaling might actually make certain defects worse.

To our knowledge, our study is the first to find lower signaling levels that correspond to a RASopathy disease, Goyal said. Drugs under development are primarily RAS-pathway inhibitors aimed at reducing the higher activity, so maybe we need to design drugs that only target specific affected tissues, or investigate alternative, novel treatment options.

The Nature Genetics study also found that RAS pathway mutations cause defects by changing the timing and specific locations of embryonic development. For example, in normal fruit fly cells, the RAS pathway only turns on when certain natural cues are received from outside the cell. In the mutant cells, however, the RAS pathway in certain parts of fly embryo abnormally activated before these cues were received. This early activation disturbed the delicate process of embryonic development. The researchers found similar behavior in zebrafish cells.

Our integrative approach has allowed us to make enormous progress in understanding RASopathies, some of which have just been identified in the last couple of decades, Shvartsman said. With continued steps forward in both basic and applied science, as weve shown with our new publications, we hope to develop new ideas for understanding and treatment of a large class of developmental defects.

Princeton co-authors of the two papers includeTrudi Schpbach, the Henry Fairfield Osborn Professor of Biology and professor ofmolecular biology, andRebecca Burdine, an associate professor of molecular biology, as well as co-advisers to Goyal and Jindal; Alan Futran, a former graduate student in the Department of Chemical and Biological Engineering and LSI; graduate student Eyan Yeung of the Department of Molecular Biology and LSI; Jos Pelliccia, a graduate student in the Department of Molecular Biology; seniors in molecular biology Iason Kountouridis and Kei Yamaya; and Courtney Balgobin Class of 2015.

Bruce Gelb, a pediatric cardiologist specializing in cardiovascular genetics and the director of the Mindich Child Health and Development Institute at the Mount Sinai School of Medicine in New York, described the two new studies as wonderful in advancing the understanding of altered biology in RASopathies and developing a framework for comparing mutation strengths, bringing effective treatments significantly closer.

At this time, most of the issues that arise from the RASopathies are either addressed symptomatically or cannot be addressed, Gelb said. The work [these researchers] are undertaking could lead to true therapies for the underlying problem.

The paper, In vivo severity ranking of Ras pathway mutations associated with developmental disorders, was published Jan. 3 in the Proceedings of the National Academy of Sciences. The paper, Divergent effects of intrinsically active MEK variants on developmental Ras signaling, was published on Feb. 6 in Nature Genetics online. The research for both papers was supported in part by the National Institutes of Health and the National Science Foundation.

Media contact: Steven Schultz, 609-258-3617, sschultz@princeton.edu

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Finding our way around DNA — ScienceDaily – Science Daily

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Finding our way around DNA -- ScienceDaily
Science Daily
A new tool has been developed that maps functional areas of the genome to better understand disease.

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Biotech’s Next Big Catalyst Could Be Synthetic DNA – ETF Daily News (blog)

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February 14, 2017 9:21am NASDAQ:IBB

From Jon Markman: It really is a brave new world. Not long ago, a group of prominent scientists announced plans for a project to create synthetic human DNA from scratch.

That seems appropriate for Valentines Day. If you dont like your lover, one day you might just be able to design a new one.

The project will be led by synthetic biologists Jef Boeke, of the Langone Medical Center at New York University, and George Church, of Harvard Medical School. And it will take up where the previous project to read the human genome ended.

In 2003, the Human Genome Project (HGP) was completed. It was supposed to open the door to countless new treatments and cures for illnesses that had plagued humans for centuries. It didnt quite work out that way. It seems understanding the relationship between genes and illness is more complex than scientists originally thought.

The Human Genome Project-write (HGP-write), as the name implies, will attempt to synthetically write human DNA code. The idea is that writing and understanding genetic code made from scratch will help scientists learn more about those complex gene relationships.

And while creating the building blocks for human life in a lab may seem like science fiction, there is some precedent.

In 2010, scientists at the J. Craig Venter Institute created bacteria controlled by a synthetic genome, effectively turning code back into life. HGP-write will be like that experiment, only on a much bigger scale.

Writing DNA is tedious and expensive work. It involves precisely manipulating tiny amounts of chemicals and a DNA molecule.

These chemicals are sugary building blocks designated A, T, C and G and they must be added in the correct amounts and the proper order hundreds of times to change the structure of DNA.

Boeke and Church believe completing HGP-write will shrink development costs for DNA fabrication by a factor of one thousand. If true, that could actually lead to all of the revolutionary treatments promised by the original Human Genome Project. Yet, pesky ethical questions remain.

These are heightened by Churchs own colorful and controversial history. In his 2012 book, Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves, he wrote about a world where humans with genomes made in the lab become immune to all viruses. According to Church this could be done simply by removing the host material from our genes that viruses need to replicate. And thats just a start. Hes been vocal about his efforts to resurrect the wooly mammoth now that perfectly preserved DNA material from the prehistoric beast has been recovered. Church is also using CRISPR, a gene editing tool he helped develop, to alter pig genes so that their organs can be transplanted into humans. As for humans, hes not shy about his cradle-to-grave outlook.

Hes aggressively in favor of gene editing to avoid potential birth defects and hes working with gene therapies to reverse the aging process. It doesnt help that when hes pressed about ethics, he demurs to comparisons to the industrial revolution. This type of talk often lands scientists in hot water. And Church has been cooked so many times that he should have developed a rubbery exterior by now. Hell need it.

It should take $100 million and ten years to create the human genome from scratch. If the project is successful, scientists say theyll restrict potential use cases to the petri dish to avoid ethical considerations. Thats not exactly Mary Shelleys Frankenstein but it is one giant step closer to Aldous Huxleys Brave New World.

As is often the case in biotech, the most reliable investment for investors in this space will be the proverbial picks and shovels: The makers of lab equipment and disposables, like Becton Dickinson and Co. (BDX), Teleflex Inc. (TFX) and Cantel Medical Corp. (CMD).

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Biotech's Next Big Catalyst Could Be Synthetic DNA - ETF Daily News (blog)

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McGovern: DA fighting for twin’s DNA test to be accepted in trial – Boston Herald

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New twin-splitting technology is being put to the test for the first time ever in a Hub courtroom this week, and Suffolk prosecutors hope the new-age science can finally help solve a pair of rapes that occurred nearly 15 years ago.

An old DNA test couldnt separate the chief suspect in the case, Dwayne McNair, from his identical twin brother, Dwight McNair. That issue put Suffolk District Attorney Daniel F. Conley in a tight spot, and in 2014 he temporarily dropped charges stemming from a pair of 2004 rapes so he could see if a new test developed in Germany would work.

Prosecutors say it did, and that it conclusively shows that Dwayne McNairs DNA was in a condom he allegedly used during the crime. That potentially damning piece of evidence only exists because a quick-thinking woman McNair is accused of raping kept the condom and brought it to authorities.

Dwayne McNair was eventually re-indicted, and now Conleys office must prove that the test is worthy of being used in a Massachusetts court.

After going through the extensive methodology used by Germany-based Eurofins Scientific to differentiate the McNair twins yesterday, Suffolk prosecutor David Deakin asked his expert how likely it is that Dwights DNA was found.

The scenario is extremely unlikely, said Dr. Burkhard Rolf, head of DNA services Eurofins.

But Robert Tobin, Dwayne McNairs defense attorney, went on the offensive, arguing that the science is relatively new, completely untested by other scientists and has never been considered in any courtroom anywhere.

This has never been entered into evidence in any court in the whole world, right? Tobin asked.

Not yet, Rolf said.

The $120,000 test is vital to the rape case, and if Superior Court Judge Linda Giles allows a jury to consider its results, it would be akin to an admission. Thats why a line of experts are expected to testify about the merits and faults of the test in the coming days.

It has not been accepted in the forensic community, has it? Tobin asked Rolf.

What does accepted mean? Rolf responded. It has not been performed very often, but that doesnt mean it hasnt been accepted.

The test has been published in one peer-reviewed journal, and according to Rolf no one has debunked the science.

But there is no clear answer as to whether Massachusetts will break the mold and allow this science into court.

Its an interesting experiment, Tobin said, his arms full of files as he left the courtroom. Its just not ready for prime time.

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McGovern: DA fighting for twin's DNA test to be accepted in trial - Boston Herald

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Looking at Sardinian DNA for genetic clues to an island’sand … – Phys.Org

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February 13, 2017 DNA double helix. Credit: public domain

Sardinia sits at a crossroads in the Mediterranean Sea, the second largest island next to Sicily. Surrounded by sparkling turquoise waters, this Mediterranean jewel lies northwest of the toe of the Italian peninsula boot, about 350 kilometers due west of Rome.

For evolutionary biologists, islands are often intriguing, geographically isolated pockets with unique populations that can be ripe for exploration.

Now, in a new study appearing in the advanced online edition of Molecular Biology and Evolution an international team led by geneticist Anna Olivieri from the University of Pavia tackles a highly interesting question: what were the origins of the Sardinian population in the context of European prehistory and ancient human migrations?

The authors analyzed 3,491 modern, whole mitochondrial DNA genomes from Sardinia (which are only passed down maternally). These were compared with 21 samples of ancient mitogenomes from the island, a large panel of non-Sardinian mitogenomes -and even tzi (the nickname of Europe's oldest natural mummy, the 3,300 BCE-year old "Tyrolean Iceman") -to better understand their origins.

Their findings show Sardinia as an outlier in the general European genetic landscape. Almost 80 percent of modern Sardinian mitogenomes belong to branches that cannot be found anywhere else outside the island. Thus, they were defined as Sardinian-Specific Haplogroups (SSHs) that most likely arose in the island after its initial occupation. Almost all SSHs coalesce in the post-Nuragic, Nuragic and Neolithic-Copper Age periods. However, some rare SSHs display age estimates older than 7,800 years ago, the postulated archeologically-based starting time of the Neolithic in Sardinia.

"Our analyses raise the possibility that several SSHs may have already been present on the island prior to the Neolithic," said prof. Francesco Cucca, from the Institute of Genetic and Biomedical Research (IRGB), at the CNR in Cagliari (Sardinia).

The most plausible candidates would include haplogroups K1a2d and U5b1i1, which together comprise almost 3 percent of modern Sardinians, and possibly others. Such a scenario would not only support archaeological evidence of a Mesolithic occupation of Sardinia, but could also suggest a dual ancestral origin of its first inhabitants. K1a2d is of Late Paleolithic Near Eastern ancestry, whereas U5b1i1 harbours deep ancestral roots in Paleolithic Western Europe.

This work provides evidence that contemporary Sardinians harbour a unique genetic heritage, as a result of their distinct history and relative isolation from the demographic upheavals of continental Europe. Anna Olivieri stresses: "It now seems plausible that human mobility, inter-communication and gene flow around the Mediterranean from Late Glacial times onwards may well have left signatures that survive to this day. Some of these signals are still retained in modern Sardinians."

"Although in the past the stress has often been on the spread of the Neolithic, genetic studies too are beginning to emphasize the complexity and mosaic nature of human ancestry in the Mediterranean, and indeed in Europe more widely," concludes prof. Antonio Torroni, from the University of Pavia. "Future work on ancient DNA should be able to test directly to what extent this more complex model is supported by genetic evidence, and whether our predictions of Mesolithic ancestry in contemporary Sardinians can be sustained."

Explore further: Hair from mummy's clothes provides insights into red deer lineage

More information: Anna Olivieri, et al, Mitogenome Diversity in Sardinians: a Genetic Window onto an Island's Past, Molecular Biology and Evolution (2017). DOI: 10.1093/molbev/msx082

Genetic analysis of Neolithic deer hair from Italian Alps mummy's clothes ties deer population to modern day western European lineage, in contrast to the eastern lineage found in the Italian alps today, according to a study ...

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One look at Sardinia's white-sand beaches and turquoise water would lead you to assume that this part of the world is devoted entirely to idyllic getaways and sun-filled vacations. You'd never guess that the island's population ...

The first ancient human genome from Africa to be sequenced has revealed that a wave of migration back into Africa from Western Eurasia around 3,000 years ago was up to twice as significant as previously thought, and affected ...

(Phys.org)A team of researchers at the Shanghai Institutes for Biological Sciences has found that rhesus monkeys can pass the mirror self-awareness test if they are first taught how mirrors work. In their paper published ...

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Scientists at the University of Wrzburg have generated new insights into the intricate molecular underpinnings of ubiquitin signaling. Their results may provide new avenues for cancer therapy.

The protein that helps the sperm and egg fuse together in sexual reproduction can also fuse regular cells together. Recent findings by a team of biomedical researchers from the Technion-Israel Institute of Technology, Argentina, ...

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An ancient people of Sardinia were once called the Shardana...... as in Shar-DAN-a. They were one of the 'Sea Peoples' that plyed the Mediterranean during the Greek Dark Ages, as were the Danoi or DAN-oi of Mycenea and the Dan-nan-oi or DAN-nan-oi of Thutmose's Egypt and the Israeli Tribe of Dan from Tel-Dor in Israel. All were of the 'Danites' and emanated from Israel about the time of the Exodus in the Torah, about 1500 BCE. There is physical archaeology indicating all of this. For further distant antecedants, one need look at pre-Exodus Hebrews working as slaves in Egypt's 'Valley of Terror'. Cave inscriptions there bear some of first uses of modern alphabet.

Pronunciations in southern Europe and the Levant seem all relative to varying forms of pronunciation of alphabetic or abjadic letters. Russia, as remote as it seems, got much of its culture from ancient Dacia which is where also later on the Kievan' Rus.......Ukraine, got started. The French suffix 'in' has its vowel sounding almost like a flat 'aanh'. These differing vowel pronunciations spread all across cultures from ancient Iberia to Capodoccia to Assyria to Ur across not only distance but also time measured in millennia. The Hebrew's ancient alphabet or 'alef-bet' came from Linear-A script copied into Heiratic in Egypt with its 600 letters whose' difficulty in learning was a purposeful act to prevent the common folk from educating themselves. That those secretive fuedal societies like the Hittites and Egyptian Pharoanics left so little behind seems a tribute to their shared interest in looting their present, uncaring of future progress.

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Team develops tool that maps functional areas of the genome to … – Medical Xpress

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February 13, 2017 A Salk team developed a tool that maps functional areas of the genome to better understand disease. Credit: Salk Institute

Most of us would be lost without Google maps or similar route-guidance technologies. And when those mapping tools include additional data about traffic or weather, we can navigate even more effectively. For scientists who navigate the mammalian genome to better understand genetic causes of disease, combining various types of data sets makes finding their way easier, too.

A team at the Salk Institute has developed a computational algorithm that integrates two different data types to make locating key regions within the genome more precise and accurate than other tools. The method, detailed during the week of February 13, 2017, in Proceedings of the National Academy of Sciences, could help researchers conduct vastly more targeted searches for disease-causing genetic variants in the human genome, such as ones that promote cancer or cause metabolic disorders.

"Most of the variation between individuals is in noncoding regions of the genome," says senior author Joseph Ecker, a Howard Hughes Medical Institute investigator and director of Salk's Genomic Analysis Laboratory. "These regions don't code for proteins, but they still contain genetic variants that cause disease. We just haven't had very effective tools to locate these areas in a variety of tissues and cell typesuntil now."

Only about two percent of our DNA is made up of genes, which code for proteins that keep us healthy and functional. For many years, the other 98 percent was thought to be extraneous "junk." But, as science has developed ever more sophisticated tools to probe the genome, it has become clear that much of that so-called junk has vital regulatory roles. For example, sections of DNA called "enhancers" dictate where and when the gene information is read out.

Increasingly, mutations or disruption in enhancers have been tied to major causes of human disease, but enhancers have been hard to locate within the genome. Clues about them can be found in certain types of experimental data, such as in the binding of proteins that regulate gene activity, chemical modifications of proteins (called histones) that DNA wraps around, or in the presence of chemical compounds called methyl groups in DNA that turn genes on or off (an epigenetic factor called DNA methylation). Typically, computational methods for finding enhancers have relied on histone modification data. But Ecker's new system, called REPTILE (for "regulatory-element prediction based on tissue-specific local epigenomic signatures"), combines histone modification and methylation data to predict which regions of the genome contain enhancers. In the team's experiments, REPTILE proved more accurate at finding enhancers than algorithms that rely on histone modification alone.

"The novelty of this method is that it uses DNA methylation to really narrow down the candidate regulatory sequences suggested by histone modification data," says Yupeng He, a Salk graduate student and first author of the paper. "We were then able to test REPTILE'S predictions in the lab and validate them with experimental data, which gave us a high degree of confidence in the algorithm's ability to find enhancers."

The REPTILE algorithm operates in two general steps: training and prediction. For training, the Salk team taught REPTILE to recognize mammalian enhancers by feeding into the algorithm both the locations of known enhancers as well as genomic areas other than enhancers in the DNA. In the prediction step, the algorithm ran on nine mouse and five human cell lines and tissues whose enhancer regions were unknown and pinpointed the locations of potential enhancers. Finally, the team utilized data from laboratory experiments to test whether the predictions made by REPTILE in the prediction step corresponded to real regulatory regions. Because enhancers increase the activity of target genes, researchers can test the activity of DNA sequences by connecting them to a reporter gene and watching to see whether the supposed target gene ramps up. Using molecular tools, the team engineered mouse embryos so that enhancer activation would trigger the expression of linked reporters, which can be monitored by staining. So, if REPTILE predicted that a specific enhancer was linked to mouse forebrain development, the team was able to look for a staining pattern in the embryo's forebrain region. If they saw it, REPTILE's prediction was considered valid. The Salk team also tested REPTILE's predictions against four other commonly used enhancer-finding algorithms. Overall, REPTILE outperformed each one, finding enhancer regions with greater accuracy (getting closer to them along the DNA strand) and fewer errors (misidentifications). In particular, REPTILE was more successful than the other systems at the invaluable task of finding enhancers in different tissue types than those it was trained on.

"The number of genetic variants in the genome is enormous," says Ecker. "So in terms of finding ones that cause disease, you really want to shine a spotlight on the regions you think are most important and identifying enhancers is a critical step in the process."

Explore further: 'Mysterious' non-protein-coding RNAs play important roles in gene expression

More information: Improved regulatory element prediction based on tissue-specific local epigenomic signatures, PNAS, http://www.pnas.org/cgi/doi/10.1073/pnas.1618353114

In cells, DNA is transcribed into RNAs that provide the molecular recipe for cells to make proteins. Most of the genome is transcribed into RNA, but only a small proportion of RNAs are actually from the protein-coding regions ...

Scientists at the Gladstone Institutes have invented a new way to read and interpret the human genome. The computational method, called TargetFinder, can predict where non-coding DNAthe DNA that does not code for proteinsinteracts ...

The complex process regulating gene expression is often compared to following a recipe. Miss a genetic ingredient, or add it in the wrong order, and you could have a disaster on your hands.

Researchers have shown that when parts of a genome known as enhancers are missing, the heart works abnormally, a finding that bolsters the importance of DNA segments once considered "junk" because they do not code for specific ...

Purdue University and Indiana University School of Medicine scientists were able to force an epigenetic reaction that turns on and off a gene known to determine the fate of the neural stem cells, a finding that could lead ...

Monash University and Danish researchers have discovered a gene in worms that could help break the cycle of overeating and under-exercising that can lead to obesity.

A new study shows how errors in a specific gene can cause growth defects associated with a rare type of dwarfism.

Specific genetic errors that trigger congenital heart disease (CHD) in humans can be reproduced reliably in Drosophila melanogaster - the common fruit fly - an initial step toward personalized therapies for patients in the ...

A newly discovered mutation in the INPP5K gene, which leads to short stature, muscle weakness, intellectual disability, and cataracts, suggests a new type of congenital muscular dystrophy. The research was published in the ...

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Genome Mapping Could Lead to Cheaper and More Abundant Quinoa – Smithsonian

Posted: at 10:50 am

smithsonian.com February 13, 2017 3:09PM

Quinoa is commonly considered the ultimate "superfood." Packed with protein, vitamins and minerals, thisSouth American grain was once revered by the Inca, but its fanbase has grown worldwide. Now, asReuters reports, new research into the genome of the grain shows that it has potential to be even more superand, perhaps, cheaper to produce.

An international team of researchers mapped the genome of quinoa, determining that the grain has 1.3 billion nucleotides (the building blocks of DNA) spread over 18 chromosomes. The hope is that access to the genome will help researchers figure out how to breed more productive strains of quinoa that could be cultivated in food insecure areas of the globe with harsh growing conditions. The research appears this week in the journal Nature.

Having the genome would enable the wider community both to study how this plant does all the amazing things it does, and also use that knowledge of the genome to make much faster and greater improvements in the crop, improvements that really haven't been so easy to do over the past couple of decades, Mark Tester, leader of the project and professor at King Abdullah University of Science and Technology in Saudi Arabia tells Mengqi Sun at The Christian Science Monitor.

Quinoa was an important food crop in the Andes when the Spanish arrived in South America in the 1500s, according toa press release. Because it had religious significance for the Inca, the Spanish forbade the cultivation of quinoa and forced the Inca to grow wheat instead, Reuters reports. As European grains became more prevalent, quinoa, which was not as easy to grow or process, the superfood couldn't keep pace on a global stage.

One reason quinoa has only recently become popular outside the Andesis that the grains are covered by saponins, a bitter tasting substance. That means quinoa needs processing before eating, which raises its cost. On the other hand, it also has the ability to grow at high altitude, in poor soils and even saline conditions, making it an important crop in many parts of the world.

AsRyan F. Mandelbaum at Gizmodo reports,outside of its home range, quinoa is currently seen a high-end specialty food. And prices reflect that, tripling between 2006 and 2013 when the grain's popularity grew overseas. Tester, however, thinks the grain has the potential to be as common and cheap as rice if breeders can produce the right varieties.

[The goal is to] move this crop from its current status as a crop of importance in South America, and a crop of novelty in the West, to become a true commodity in the world, he tells Cici Zhang at Popular Science. Id like to see quinoa changed into a crop that can be grown much more widely and become much cheaper. I want the price to come down by a factor of fiveI want it out of the health food section.

The hope is that other researchers will use the genome data to find other adaptations that will help scientists breed strains of quinoa for various soils and climates around the world. For example, we discovered mutations which ensure that certain quinoa varieties cannot produce bitter tasting saponins, Robert van Loo, quinoa breeder at Wageningen University in the Netherlands says in the press release. These 'sweet' varieties do not need to be polished to remove the bitter substances, saving some 15 to 20 per cent. With the new knowledge of quinoa DNA, we can quickly and easily select plants that do not produce bitter substances in the breeding process."

Similar projects with other grains have resulted in new varieties of crops in the last decade. The rice genome, for instance, was first publicly released in 2006. Last week, Chinese scientists announced that they were cultivating new varieties of insect and disease resistant rice based on studies of the rice genome.

But Douglas Cook, the director of the Feed the Future Innovation Lab for Climate Resilient Chickpea at the University of California, Davis, cautions that there is no silver bullet when it comes to solving food insecurity, and that developing new strains of quinoa wont be a food revolution all on its own.

Personally, I think it could mean an important part of the solution, but it's not going to be a game changer, he tells Sun. The places where bigger changes are going to occur are in crops that have already had significant investments and that are already mainstayin the human diet.

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Genome Mapping Could Lead to Cheaper and More Abundant Quinoa - Smithsonian

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The battle of the sexes can show us how to live longer, say researchers – Horizon magazine

Posted: at 10:50 am

The battle of the sexes has been raging on earth for millions of years, and its all down to sexual antagonism, the evolutionary genetic variants that are good for one sex but bad for the other.

An obvious one is longevity no matter how advanced medicine becomes, on average women still live longer than men.

It is important to remember that evolution maximises Darwinian fitness rather than longevity, explained Dr Alexei Maklakov, at the Department of Animal Ecology of Uppsala Universitys Evolutionary Biology Centre in Sweden.

He explained that this meant that one sex can live longer than the other.Males and females have very different reproductive strategies, meaning that the trade-off between reproduction and longevity can be optimised differently between the sexes.

Those aged 65 years or over are projected to account for 28.7 % of the EUs population by 2080, compared with 18.9 % in 2015, according to EU data. As the global population ages,it is more important than ever to study this subject.

There is a massive research effort underway to find treatments that can improve the human condition in late life, said Dr Maklakov. However, because of the fundamental biological differences between the sexes, men and women are likely to respond differently to the same treatments.

Because of the fundamental biological differences between the sexes, men and women are likely to respond differently to the same treatments.

Dr Alexei Maklakov, Uppsala University, Sweden

As part of the EU-funded AGINGSEXDIFFproject, he has done tests on roundworms and fruit flies - organisms commonly used by biologists - to look at the factors which affect longevity.

The project also analysed human data to help explain the variation in longevity between species, populations, sexes and individuals.

Dr Maklakov gives the example of female beetles, where longevity is positively associated with fitness, meaning longer-lived females produce more offspring. In male beetles its a different story, successful males invest a lot in early-life reproduction and die young.

The same principle explains how shifts in demographics are giving human females longer average lifespans than males.

In the past, women paid a higher cost than men in terms of longevity for having children. A historical shift to smaller families has therefore increased longevity among women but not among men, Dr Maklakov explains.

The project has helped to explain the link between evolutionary biology and biogerontology the science of why and how we age.

Sex-specific

For biogerontologists, our results imply that lifespan- and healthspan-extending treatments in humans will likely always affect men and women differently, suggesting that we need more research on sex-specific effects of the new treatments, saidDr Maklakov.

Sexual antagonism may also help to explain a longstanding paradox for evolutionary biologists why there is so much genetic variation in many natural populations.

Any gene variants that are good should spread throughout the population, and any bad ones should be lost, said Dr Jessica Abbott at Lund Universitys Department of Biology in Sweden. So why do we see so much variation?

She has selected successive generations of fruit flies and flatworms in a sex-specific manner and is now setting about genetic and genomic analysis of the changes she has observed in the subjects as part of the EU-funded ComplexSex project.

Sexual antagonism can explain how sex chromosomes evolve, how males and females evolve to be different from one another, and how genetic conflicts shape evolution, Dr Abbott adds.

The findings of the ComplexSex project will apply specifically to flatworms and fruit flies, but Dr Abbott believes the broader evolutionary mechanisms the research highlights should be relevant to many species, including humans.

Lots of diseases with a genetic component have different prevalence in men and women. My colleagues and I have speculated that this might be partially due to sexual antagonism, she said.

The better we understand sexual antagonism as a phenomenon, the more we might be able to understand the reasons for these differences between men and women in disease and ageing.

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The battle of the sexes can show us how to live longer, say researchers - Horizon magazine

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