Monthly Archives: July 2017

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Genome analysis of ancient people from Africa reveals a complicated migration history for the human species.

Ignored for too long by researchers, ancient humans who lived in Africa thousands of years ago are finally having their genomes studied. Two projects released results this week on the genomes of around 20 individuals, which together reveal that the history of our species on the continent was far more complex than previously thought.

Africas neglect until now by ancient-DNA researchers was largely down to the continents scorching climate. Because heat speeds the deterioration of DNA, scientists have focused on sequencing remains from cooler European sites and Siberian permafrost. The first success in Africa came in 2015 when researchers sequenced the genome of a 4,500-year-old man from Ethiopia who was preserved in a relatively chilly mountainous cave.

But advances in removing contamination and the discovery that a tinyinner ear bone is chock full ofancient DNA has convincedresearchers that the technology is finally ready to grapple withAfricas past.

Stephan Schiffels, a population geneticist at the Max Planck Institute for the Science of Human History, in Jena, Germany, says gaps in the knowledge of sub-Saharan African history are embarrassing especially in light of how much researchers know about ancient peoples in Eurasia. This makes it all the more important to use DNA to uncover Africa's hidden history of human migration, he says.

That is what a team led by Pontus Skoglund and David Reich, population geneticists at Harvard Medical School in Boston, Massachusetts, have now done. In a talk on 3 July at the Society for Molecular Biologys annual meeting in Austin, Texas, Skoglund said his team had examined the genomes of 15 ancient individuals and described detailed analysis of 11 of them who lived as long as 6,000 years ago in eastern and southern Africa.

They showed ancient humans moved around on the continent far more than was appreciated. The genome of a 3,000-year-old individual from Tanzania bore the ancestry of both ancient East African hunter-gatherers and early farmers from the Middle East. That supports past studies that documented a back to Africa migration several thousand years ago: these migrants were closely related to early farmers from the Levant region in the Middle East.

The Tanzanian fossil was found at an archaeological site linked to animal herding, or pastoralism, and some of its genetic signatures have also been found in present-day pastoralists in southern Africa, Skoglund said. This suggests that east Africans brought herding to southern Africa.

The unpublished study from Skoglunds team revealed additional movement. The genome of a 2,000-year-old individual from southern Africa was related to contemporary southern African hunter-gatherers known as the San, as well as to ancient hunter-gatherers the team sequenced from Malawi and Tanzania but not to the current inhabitants of eastern Africa.

The reason for this, Skoglund suggested, is a well-documented migration of Bantu groups from Western Africa, who brought agriculture and distinct language to eastern and southern Africa around 1,000-2,000 years ago. This Bantu expansion seems to have completely replaced local hunter-gatherers. An individual who lived on Tanzanias Zanzibar peninsula 750 year ago, after the migration, shared no ancestry with earlier hunter-gatherers from southern or east Africa.

A separate team, led by Mattias Jakobsson at Uppsala University in Sweden, found evidence for the same migrations in the genome of a boy who lived 2,000 years ago near Balito Bay in South Africa and 6 other ancient southern Africans. Their study1 was posted to the bioRxiv preprint server last month.

Proof of migrations such as the Bantu expansion have been found at archaeological sites, as well as in the DNA of contemporary Africans, says Schiffels. But it is still nice to have direct evidence of these movements, he notes.

Ancient African genomes also have the potential to illuminate much earlier events. Jakobssons team used the Ballito Bay boys genome to infer that Homo sapiens emerged at least 260,000 years ago far earlier than previous genetic studies have suggested. Skoglunds team, meanwhile, used their ancient genomes to help uncover a possible ghost population that diverged from the founding population of H. sapiens before any other African group and later contributed to the genetic make-up of some present-day West Africans.

IainMathieson, a population geneticist at the University of Pennsylvania in Philadelphia,hopes that ancient African DNA can explain our species migration out of Africa, some 50,000-100,000 years ago, by painting a genetic picture of the continents inhabitants around this time.

This might require DNA far older than several thousand years which could mandateanother major technical advance. Analysis of bones thought to be about 300,000 years old from Morocco, attributed to the earliest-known H. sapiens, has so far yielded no usable DNA. "It's early days," for ancient African genomics, says Mathieson, "it really is."

See more here:
Ancient-genome studies grapple with Africa's past - Nature.com

July 6, 2017 Wild Emmer wheat. Credit: Energin .R Technologies 2009 LTD.

A global team of researchers has published the first-ever Wild Emmer wheat genome sequence in Science magazine. Wild Emmer wheat is the original form of nearly all the domesticated wheat in the world, including durum (pasta) and bread wheat. Wild emmer is too low-yielding to be of use to farmers today, but it contains many attractive characteristics that are being used by plant breeders to improve wheat.

The study was led by Dr. Assaf Distelfeld of Tel Aviv University's School of Plant Sciences and Food Security and Institute for Cereal Crops Improvement, in collaboration with several dozen scientists from institutions around the world and an Israel-based company - NRGene, which developed the bioinformatics technology that accelerated the research.

"This research is a synergistic partnership among public and private entities," said Dr. Daniel Chamovitz, Dean of Tel Aviv University's George S. Wise Faculty of Life Sciences, who was also involved in the research. "Ultimately, this research will have a significant impact on global food safety and security."

"Our ability to generate the Wild Emmer wheat genome sequence so rapidly is a huge step forward in genomic research," said Dr. Curtis Pozniak from the University of Saskatchewan, a project team member and Chair of the Canadian Ministry of Agriculture Strategic Research Program. "Wheat accounts for almost 20% of the calories humans consume worldwide, so a strong focus on improving the yield and quality of wheat is essential for our future food supply."

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"From a biological and historical viewpoint, we have created a 'time tunnel' we can use to examine wheat from before the origins of agriculture," said Dr. Distelfeld. "Our comparison to modern wheat has enabled us to identify the genes involved in domestication - the transition from wheat grown in the wild to modern day varieties. While the seeds of wild wheat readily fall off the plant and scatter, a change in two genes meant that in domesticated wheat, the seeds remained attached to the stalk; it is this trait that enabled humans to harvest wheat."

"This new resource allowed us to identify a number of other genes controlling main traits that were selected by early humans during wheat domestication and that served as foundation for developing modern wheat cultivars," said Dr. Eduard Akhunov of Kansas State University. "These genes provide an invaluable resource for empowering future breeding efforts. Wild Emmer is known as a source of novel variation that can help to improve the nutritional quality of grain as well as tolerance to diseases and water-limiting conditions."

"New genomic tools are already being implemented to identify novel genes for wheat production improvement under changing environment," explains Dr. Zvi Peleg of the Hebrew University of Jerusalem, Israel. "While many modern wheat cultivars are susceptible to water stress, Wild Emmer has undergone a long evolutionary history under the drought-prone Mediterranean climate. Thus, utilization of the wild genes in wheat breeding programs promotes producing more yield for less water." "The wheat genome is much more complex than most of the other crops and has agenome four times the size of a human genome." said Dr. Gil Ronen, NRGene's CEO. "Still, the computational technology we developed has allowed us to quickly assemble the very large and complex genome found in Wild Emmer's 14 chromosomes to a standard never achieved before in genomic studies."

For the first time, the sequences of the 14 chromosomes of Wild Emmer wheat are collapsed into a refined order, thanks to additional technology that utilizes DNA and protein links. "It was originally tested in humans and recently demonstrated in barley, both of which have smaller genomes than Wild Emmer wheat," says Dr. Nils Stein, the Head of Genomics of Genetic Resources at Leibniz Institute of Plant Genetics and Crop Plant Research in Germany. "These innovative technologies have changed the game in assembling the large cereal genomes."

"This sequencing approach used for Wild Emmer wheat is unprecedented and has paved the way to sequence durum wheat (the domesticated form of Wild Emmer). Now we can better understand how humanity transformed this wild plant into a modern, high-yielding and high-quality crop," said Dr. Luigi Cattivelli, Head of the CREA Research Centre for Genomics and Bioinformatics (Italy) and coordinator of the International Durum Wheat Genome Sequencing Consortium. "This Wild Emmer wheat sequencing and approach is an invaluable contribution to the entire wheat community to improve and better understand nutritional mechanisms," said Dr. Hikmet Budak, Montana Plant Science Endowed Chair at Montana State University.

"We now have the tools to study crops directly and to make and apply our discoveries more efficiently than ever before," concluded Dr. Distelfeld.

Explore further: A lesson from wheat evolution: From the wild to our spaghetti dish

More information: R. Avni el al., "Wild emmer genome architecture and diversity elucidate wheat evolution and domestication," Science (2017). science.sciencemag.org/cgi/doi 1126/science.aan0032

Journal reference: Science

Provided by: Tel Aviv University

While wheat has been much maligned recently for it's gluten content, and new suspicions casted about as to its nutritional value, scientists have been eager to trace the evolutionary history of wheat to better understand ...

Kansas State University wheat scientists have completed the first study of a chromosome in a tertiary gene pool and have called it a breakthrough in exploring wheat wild relatives for future crop improvement.

Increases in climate variability have placed new emphasis on the need for resilient wheat varieties. Alongside demands for increased resiliency, consumer interest in healthier, more functional foods is growing. Therefore, ...

The German Federal Ministry of Food and Agriculture announced today that it would award 1.5 million Euros to a project aimed at providing a reference sequence for two wheat chromosomes, part of the international effort to ...

A team of Spanish scientists, with the participation of the University of Granada, has carried out the first durum wheat genetic, phenotypic and geographic adaptation study to date. Durum wheat is mostly used for the production ...

The International Wheat Genome Sequencing Consortium (IWGSC) announced today the production of a whole genome assembly of bread wheat, the most widely grown cereal in the world, significantly accelerating global research ...

In butterflies, sex is determined by chromosome differences between males and females. But unlike in humans with the familiar X and Y, in butterflies, it is the females that determine the sex of offspring.

A University of Kentucky plant pathologist is part of an international team of researchers who have uncovered an important link to a disease which left unchecked could prove devastating to wheat. UK College of Agriculture, ...

A global team of researchers has published the first-ever Wild Emmer wheat genome sequence in Science magazine. Wild Emmer wheat is the original form of nearly all the domesticated wheat in the world, including durum (pasta) ...

After 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 ...

Bacteria of the Spiroplasma genus produce toxic, ribosome-inactivating proteins (RIPs) that appear to protect their symbiotic host flies against parasitic wasps, according to new research published in PLOS Pathogens.

Plants and brains are more alike than you might think: Salk scientists discovered that the mathematical rules governing how plants grow are similar to how brain cells sprout connections. The new work, published in Current ...

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Wild wheat genome sequencing provides 'time tunnel' capable of ... - Phys.Org

A new era of genome-based personalised medicine could open up for cancer patients within five years under new plans unveiled by the Government's chief medical adviser.

The "genomics dream" outlined by Professor Dame Sally Davies would see millions of patients having all their DNA tested as genome sequencing becomes as routine as MRI or CT scans.

Ultimately, the future goal is for every cancer patient to have his or her whole genome sequenced, making the procedure as standard as blood tests and biopsies.

People with rare diseases are also expected to benefit from having greater access to the technology, ending the years long "diagnostic odyssey" of multiple tests and visits to different specialists.

Whole genome sequencing involves unscrambling the entire book of genetic instructions that make us what we are, encompassing 3.2 billion "letters" of code.

Research suggests that in 60 per centof cases, the genomes of cancer patients reveal "actionable" data - personal mutations that can shape future treatment.

Tens of thousands of NHS patients have already had their DNA mapped, but the new recommendations set out in Chief Medical Officer Dame Sally's "Generation Genome" report aim to multiply the numbers many times over.

Dame Sally said: "The age of precision medicine is now and the NHS must act fast to keep its place at the forefront of global science .

"This technology has the potential to change medicine forever - but we need all NHS staff, patients and the public to recognise and embrace its huge potential.

"Genomic medicine has huge implications for the understanding and treatment of rare diseases, cancer and infections."

Currently, genetic testing of NHS patients in England is conducted via 25 regional laboratories and a plethora of smaller ones operating along the lines of a "cottage industry", said Dame Sally.

Her chief recommendation is to centralise all the labs and establish a national network providing equal access to the tests across the country.

Within government, a new National Genomics Board would be set up, chaired by a minister, to oversee the expansion and development of genomic services taking into account new advances within the rapidly evolving technology.

Other proposals include offering every existing clinician training in genomics and ensuring their descendants are equipped to practise genomic medicine.

The report also recommends setting up a standing committee of experts to advise on the availability of genetic tests and indications for their use.

Lessons could be learned from the highly successful 100,000 Genomes Project, which has now sequenced more than 31,000 genomes from patients with cancer and rare diseases, said Dame Sally.

Her report calls for a simplified two-stage consent system that draws on the Genomes Project model and makes it easier for patients to get involved in research studies and clinical trials.

Speaking at a news briefing in London, Dame Sally said she hoped to see the new system fully operational within five years.

Part of what made greater access to whole genome sequencing feasible was the rapidly reducing cost of the tests, which has fallen from several thousand pounds to an average 680, she pointed out.

Results from analysis of cancer samples could now be delivered in as little as four weeks.

In the short term, she wanted to see "all appropriate patients" given the opportunity to have their genomes sequenced under the guidance of experts.

Wearable device could help fight brain cancer

Further down the line, she hoped the tests would become routine for every cancer patient.

Dame Sally said: "Yes, my dream is that, in the end, every patient gets their genome done if they've got cancer.

"It's not just their genome but its the cancer itself, and as the cancer changes over time and with treatment it will need redoing.

"But you go at it through what will give a worthwhile actionable result for the patients, and the experts will tell us."

Health Secretary Jeremy Hunt said he welcomed the report, pointing out that the UK had established itself as a world leader in genomics medicine.

He added: "Tens of thousands of patients across the country have already benefited from quicker diagnosis, precise treatment and care, and we will support the NHS to continue its relentless drive to push the boundaries of modern science to benefit even more people."

Press Association

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Every cancer patient could have DNA tested under five-year government plan to cut deaths - The Independent