Category Archives: Genome

Citified nonfarmers worry that corns germplasm is shrinking into a narrow genetic spectrum. To them, all corn looks the same and is controlled by corporate agriculture. And now the truth: Fear not.

Maize is grown around the world, and its genetics are highly adaptable to changing uses and environments. Thats the latest finding of new and much more detailed genome research, published online recently in Nature.

Our new genome for maize shows how incredibly flexible this plant is, a characteristic that directly follows from the way its genome is organized, explains Doreen Ware, USDA genetic researcher at New Yorks Cold Spring Harbor Laboratory. She led scientists at seven academic institutions and several genome technology companies in the gene mapping project.

The plants genomic DNA sequencing in its 10 chromosomes is very large and has a far wider phenotypic plasticity i.e., the potential range in its ability to adapt than even the human genome, she adds. That helps us understand why maize, and not some other plant, is today the most productive and widely grown crop in the world.

This flexibility helps explain why this plant species has been so successful since its adaptation by agriculturalists thousands of years ago. It also bodes well for its ability to grow in new places as Earths climate changes, and for increasing the plants productivity and global environmental sustainability.

Which genes are activated or silenced determines what the total set of genes enables a plant to do, Ware says. This new genome map is bringing to light how the plants genes are regulated in different individuals across the species.

By assembling a highly accurate and very detailed reference genome for the B73 maize line, then comparing it with genome maps for maize individuals from two W22 and Ki11lines grown in different climates, the sequencing team arrived at an astonishing realization.

Maize individuals are much, much less alike at the genome level than people are, points out Ware. The genome maps of two people will each match the reference human genome at around 98% of genome positions. Humans are virtually identical, in genome terms.

But weve found that two maize individuals from the W22 and Ki11 lines each align with our new reference genome for B73 maize only 35%, on average. Their genome organization is incredibly different!

This difference between maize individuals reflects not only of changes in the sequence of the genes themselves, but also where and when genes are expressed, and at what levels, explains Yinping Jiao, another Cold Springs researcher. He developed the first reference genome for maize in 2009, but acknowledges that its now outdated technology that yielded a genome text more akin to a speed-reading version than one fit for close reading.

A boon for corn breeders Current mapping technology sheds much more light on how those genes are regulated. Because of its amazing phenotypic plasticity, concludes Ware, so many more combinations are available to this plant. What does this mean to breeding? It means we have a very large variation in the regulatory component of most of the plants genes. They have lots of adaptability beyond what we see them doing now. That has huge implications for growing maize as the population increases and climate undergoes major change in the period immediately ahead of us.

The new genomes resolution of spaces between genes makes it possible to read detailed histories from the texts of genomes from different maize individuals. Consider, for instance, the impact of transposons bits of DNA that jump around in genomes. This can now be assessed with specificity not previously possible.

When transposons jump into a position within a gene, the gene can be compromised entirely, adds Ware. Other times, whether a transposon has hopped into a position just before or after a gene can determine when and how much it is expressed.

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Corn to remain 'king' of tomorrow's crops - American Agriculturist

June 16, 2017 Cancer cell during cell division. Credit: National Institutes of Health

Liver cancer has the second-highest worldwide cancer mortality, and yet there are limited therapeutic options to manage the disease. To learn more about the genetic causes of this cancer, and to identify potential new therapeutic targets for HCC, a nation-wide team of genomics researchers co-led by David Wheeler, Director of Cancer Genomics and Professor in the Human Genome Sequencing Center (HGSC) at Baylor College of Medicine, and Lewis Roberts, Professor of Medicine at the Mayo Clinic, analyzed 363 liver cancer cases from all over the world gathering genome mutations, epigenetic alteration through DNA methylation, RNA expression and protein expression. The research appears in Cell.

Part of the larger Cancer Genome Atlas project (TCGA), this work represents the first large scale, multi-platform analysis of HCC looking at numerous dimensions of the tumor. "There have been large-cohort studies in liver cancer in the past, but they have been limited mainly to one aspect of the tumor, genome mutation. By looking at a wide variety of the tumor's molecular characteristics we get substantially deeper insights into the operation of the cancer cell at the molecular level," Wheeler said.

The research team made a number of interesting associations, including uncovering a major role of the sonic hedgehog pathway. Through a combination of p53 mutation, DNA methylation and viral integrations, this pathway becomes aberrantly activated. The sonic hedgehog pathway, the role of which had not been full appreciated in liver cancer previously, is activated in nearly half of the samples analyzed in this study.

"We have a very active liver cancer community here at Baylor, so we had a great opportunity to work with them and benefit from their insights into liver cancer," Wheeler said. Among the many critical functions of the liver, hepatocytes expend a lot of energy in the production of albumin and urea. It was fascinating to realize how the liver cancer cell shuts these functions off, to its own purpose of tumor growth and cell division.

"Intriguingly, we found that the urea cycle enzyme carbamyl phosphate synthase is downregulated by hypermethylation, while cytoplasmic carbamyl phosphate synthase II is upregulated," said Karl-Dimiter Bissig, Assistant Professor of Molecular and Cellular Biology at Baylor and co-author of the study. "This might be explained by the anabolic needs of liver cancer, reprogramming glutamine pathways to favor pyrimidine production potentially facilitating DNA replication, which is beneficial to the cancer cell."

"Albumin and apolipoprotein B are unexpected members on the list of genes mutated in liver cancer. Although neither has any obvious connection to cancer, both are at the top of the list of products that the liver secretes into the blood as part of its ordinary functions," explained Dr. David Moore, professor of molecular and cellular biology at Baylor. "For the cancer cell, this secretion is a significant loss of raw materials, amino acids and lipids that could be used for growth. We proposed that mutation of these genes would give the cancer cells a growth advantage by preventing this expensive loss."

Multiple data platforms coupled with clinical data allowed the researchers to correlate the molecular findings with clinical attributes of the tumor, leading to insights into the roles of its molecules and genes to help design new therapies and identify prognostic implications that have the potential to influence HCC clinical management and survivorship.

"This is outstanding research analyzing a cancer that's increasing in frequency, especially in Texas. Notably, the observation of gene expression signatures that forecast patient outcome, which we validate in external cohorts, is a remarkable achievement of the study. The results have the potential to mark a turning point in the treatment of this cancer," said Dr. Richard Gibbs, director of the HGSC at Baylor. The HGSC was also the DNA sequence production Center for the project.

Wheeler says they expect the data produced by this TCGA study to lead to new avenues for therapy in this difficult cancer for years to come. "There are inhibitors currently under development for the sonic hedgehog pathway, and our results suggest that those inhibitors, if they pass into phase one clinical trials, could be applied in liver cancer patients, since the pathway is frequently activated in these patients," added Wheeler.

Explore further: Study identifies a role for the metabolism regulator PPAR-gamma in liver cancer

More information: Adrian Ally et al. Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma, Cell (2017). DOI: 10.1016/j.cell.2017.05.046

Journal reference: Cell

Provided by: Baylor College of Medicine

Liver cancers are a major cause of cancer-related deaths. Large-scale genetic analyses have associated liver cancer with dysregulation of numerous molecular pathways, but disruptions in insulin signaling pathways appear to ...

A protein that typically helps keep cells organized and on task becomes a tumor suppressor in the face of liver cancer, scientists say.

Scientists may have discovered a significant new diagnostic marker for liver cancer, according to a paper published in the April 18 online issue of Nature Cell Biology.

University of Hawai'i Cancer Center researchers developed a computational algorithm to analyze "Big Data" obtained from tumor samples to better understand and treat cancer.

A genomic analysis of 37 patients with Szary syndrome, a rare form of T-cell lymphoma that affects the skin and causes large numbers of atypical T-lymphocytes (an immune system disease) to circulate, reveals mutations in ...

Personalized therapies can potentially improve the outcomes of patients with lung cancer, but how to best design such an approach is not always clear. A team of scientists from Baylor College of Medicine and the University ...

Liver cancer has the second-highest worldwide cancer mortality, and yet there are limited therapeutic options to manage the disease. To learn more about the genetic causes of this cancer, and to identify potential new therapeutic ...

Scientists have discovered a new cellular pathway that can promote and support the growth of cancer cells. In a mouse model of melanoma, blocking this pathway resulted in reduction of tumor growth. The study, which appears ...

On Earth, research into antibody-drug conjugates to treat cancer has been around a while. The research presents a problem, though, because Earth-based laboratories aren't able to mimic the shape of the cancer cell within ...

For nearly two decades researchers have sought a way to target an estrogen receptor in the hope they could improve breast cancer survival, but an article published today in Nature Communications contends that the effort may ...

Researchers at University of Pittsburgh School of Medicine and UPMC have discovered a clue that could unlock the potential of immunotherapy drugs to successfully treat more cancers. The findings, published in Cell, were made ...

Women with breast cancer have long faced complicated choices about the best course of treatment.

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Genomic analysis of liver cancer reveals unexpected genetic players - Medical Xpress

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Genome-wide association studies search through huge groups of people to find DNA variants linked to diseases or traits.

Compare the genomes of enough people with and without a disease, and genetic variants linked to the malady should pop out. So runs the philosophy behind genome-wide association studies (GWAS), which researchers have used for over a decade to find genetic ties to diseases such as schizophrenia and rheumatoid arthritis. But a provocative analysis now calls the future of that strategy into question and raises doubts about whether funders should pour more money into these experiments.

GWAS are fast expanding to encompass hundreds of thousands even millions of patients (see 'The genome-wide tide'). But biologists are likely to find that larger studies turn up more and more genetic variants or 'hits' that have minuscule influences on disease, says Jonathan Pritchard, a geneticist at Stanford University in California. It seems likely, he argues, that common illnesses could be linked by GWAS to hundreds of thousands of DNA variants: potentially, to every single DNA region that happens to be active in a tissue involved in a disease.

In a paper published in Cell on 15 June1, Pritchard and two other geneticists suggest that many GWAS hits have no specific biological relevance to disease and wouldnt serve as good drug targets. Rather, these 'peripheral' variants probably act through complex biochemical regulatory networks to influence the activity of a few core genes that are more directly connected to an illness.

The implicit assumption of GWAS has been that when you find hits, they should be directly involved in the disease youre studying, he says. When you start to think that all of the expressed genes in a tissue can matter, it becomes untenable that theres a simple biological story for each one.

Many geneticists say they think Pritchard's view could be correct and that he articulates widely-held concerns about the difficulty of interpreting GWAS findings because of gaps in understanding about biochemical networks. I think its pretty plausible, says Joe Pickrell, a human geneticist at the New York Genome Center in New York City. We might not actually be learning anything hugely interesting until we understand how these networks are connected.

Rather than more and bigger GWAS, researchers and funders should devote their efforts to mapping regulatory networks in cells, Pritchard argues. Biologists that aim to link genes with diseases, he says, should focus on identifying the mutations that directly cause disorders; some of these variants are so rare that they aren't picked up in GWAS.

GWAS experiments have identified some genes that contribute to the risk of developing conditions such as obesity, but they have also thrown up plenty of vexing problems. Most of the hits found in GWAS dont seem to encode genes that make proteins, so it is hard to interpret their connection to a disease or trait. And even for traits that are known to be highly heritable suggesting that they have a large genetic influence the cumulative influence of all the DNA variants spotted by GWAS doesnt fully explain the variation seen between people. A 2014 study of 250,000 people, for example, identified nearly 700 DNA variants linked to height: but together, they explain only about 16% of differences in height across a population2.

In the Cell paper, Pritchards team re-analysed the data from the 2014 study. The researchers estimate that as many as 100,000 single-letter DNA variants can influence a persons height, but each one has a minuscule impact; on average just about one-tenth of a millimetre. These variants tend to lie in regions that do not themselves encode genes but which influence the activity of regions that do.

The researchers also re-analysed data from GWAS of schizophrenia, rheumatoid arthritis and Crohns disease. They found GWAS hits in DNA regions that are expressed in the particular cells relevant to the disease: neurons for schizophrenia, and immune cells for the two autoimmune diseases. But regions of DNA active in many types of body tissue were just as likely to be hits as those that were active only in neurons or immune cells, the team found. That lends credence to the idea that large GWAS are simply picking up most of the DNA variants that have an influence on gene regulation, and that happen to be active in broad functions of disease-relevant cells, rather than in particular activities linked to illness.

This doesnt mean that researchers should stop carrying out GWAS studies, some geneticists say. Although GWAS hits might be peripheral to a disease, identifying more of them enables scientists to knit together the biological networks implicated in a disease and understand how they interact, says Mark McCarthy, a human geneticist at the University of Oxford, UK, who is working on a GWAS of type 2 diabetes involving around 1 million participants. Those of us who do ever bigger GWAS, we dont just simply crank the handle, he says. Were motivated by lots of biological insights coming out of GWAS.

And Joel Hirschhorn, a human geneticist at Children's Hospital Boston, says that not all hits uncovered by very large GWAS are peripheral. The 2014 height study, which Hirschhorn co-led, uncovered an association to an important growth factor that wasn't picked up in a smaller GWAS study of height, he points out.

But Aravinda Chakravarti, a human geneticist at Johns Hopkins University in Baltimore, Maryland, hopes that the paper will challenge what he terms a cowboy attitude in genomics research that emphasizes collecting ever more genetic associations over understanding the deeper biology behind them. This is a nice paper simply because its going to kick people in the shin, which, as scientists, we need from time to time.

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New concerns raised over value of genome-wide disease studies - Nature.com

Microbes are the workhorses of the natural world. In the soil, they convert the essential elements of life into nutrients that can be absorbed by plants. They break down dead organic matter to release carbon and other critical elements back into the earth and air. And without the billions of microbes in our gut, humans wouldnt even be able to digest food and convert it into usable energy.

Yet despite the critical importance of microbes to life on Earth and their increasing usefulness in energy production, agriculture, and biotechnology we still know very little about how they do what they do. Thats because microbes are the most abundant and diverse life forms on the planet, with an estimated billion or more species, only a few thousands of which have been named and identified.

Now a groundbreaking project from the United States Department of Energy (DOE) is attempting to shine light on the unexplored branches of the tree of life by sequencing large numbers of unknown microbial genomes. The group published a study in Nature Biotechnology this week in which they analyzed 1,003 new genomes that were sequenced from bacterial and archaeal organisms.

This latest batch of microbial genomes not only confirms the tremendous genetic diversity of microbes, but adds to the growing catalog of microbe-produced proteins and enzymes that could one day transform medicine, energy production, genetic engineering, and various other fields.

RELATED:Fungal Genomic Breakthrough Unlocks a Gold Rush of New Drug Discoveries

Nikos Kyrpides leads the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative at the DOEs Joint Genome Institute. He explained that the first 20 years of microbial genome sequencing focused on well-known microorganisms like viruses and pathogenic bacteria. In fact, by 2015, 43 percent of all sequenced bacterial genomes were strains from the same 10 pathogenic species.

But that narrow focus ignored large swaths of the phylogenetic family tree that left entire branches without a single representative genome. Armed with radically faster and more powerful sequencing technology, Kyrpidess group set out to catalog genomes representing the full diversity of microbial life on Earth. In 2009, they published an analysis of the first batch of 56 microbial genomes, in which they identified sequences of microbial DNA that pumped out entirely new proteins and enzymes.

We saw theres an enormous amount of discovery that can be done through the study of microbes for which we dont know anything about, said Kyrpides, who quickly proposed funding for a much larger sequencing effort.

This latest batch of more than 1,000 genomes included 845 singletons the only sequenced representative of their species. Analysis of the genomes also revealed a 10 percent increase in novel protein families.

Jonathan Eisen, an evolutionary biologist at the University of California Davis, helped launch the microbial genome encyclopedia project at the DOE. He said that the value of this open genomic reference library is twofold: first, it provides researchers worldwide with a more accurate catalog of the diversity of life; and second, it identifies new proteins and enzymes that can used for a variety of purposes, from developing new cures for chronic diseases to efficiently generating natural gas from biomass.

RELATED:We Can Now Extract the DNA of Rare Animals Preserved in Museum Jars

Eisen noted that data from the first 56 genomes analyzed in 2009 led to the discovery of new forms of cellulase, the enzyme that breaks down plant material for biofuel production. Researchers also scanned the growing genomic encyclopedia to find novel variants of the Cas9 protein that may improve upon the popular CRISPR gene-editing technology, said Kyrpides.

In its mission to fill the microbial gaps in the tree of life, the DOE team searched high and low for microbes that fell outside of the spotlight. The latest batch of 1,000 bacteria and archaea primitive single-celled organisms without a nucleus or membrane-bound organelles were sampled from extreme environments like oil springs, industrial waste sites, and the funkier corners of the human body.

The effort to sequence unknown microbes has already paid off in some appropriately unexpected ways. Eisen points to a 2015 paper that revealed some key differences between the gut microbes of modern Westerners and those living in the digestive tracts of a hunter-gatherer tribe in Peru. One microbe in particular, Treponema, was present in large numbers in the hunter-gatherers but almost non-existent in folks from Oklahoma. The researchers were able to match the mysterious gut microbes genome with its closest relative, a Treponoma species found in pigs, because it was already in the DOE encyclopedia.

Whats important to Eisen is that without the Genomic Encyclopedia of Bacteria and Archaea initiative, there would have been no reference point for Treponoma on the phylogenetic family tree. It demonstrates the value of plucking samples from every inch of the tree of life rather than focusing only on sources and systems that we deem most useful.

Heres this ostensibly really important member of the human microbiome, at least in these hunter-gatherer populations, that was completely missed by the Human Microbiome Project, Eisen said, referring to the National Institutes of Health project to sequence the most important good and bad microbes in the human gut.

RELATED:Methane-Eating Microbes Produce Food for Farmed Animals

Kyrpides recognizes that such a large-scale genome sequencing effort would have been prohibitively expensive and painfully slow even five years ago. But profound improvements in sequencing technology have opened the doors to unfettered exploration of microbial diversity. The key next-generation sequencing platforms used by the DOE group were Illumina and PacBio.

Technological improvements are also revolutionizing the application of this new genomic data, Eisen said. If a bioenergy or biomedicine company wants to experiment with a new protein or enzyme found in the encyclopedia, it no longer has to culture the particular microbe that produces the enzyme or extract and clone its DNA. Thats what the genome encyclopedia is for.

When you know the sequence that produces the protein or enzyme, you can actually order it from a company, said Eisen. You can type in the sequence of the gene youre interested in.

Using synthetic biology, Eisen explained, its possible to make that string of DNA from scratch and plug it into a lab-friendly microbe like yeast or E. coli to start pumping out gobs of the target enzyme for whatever purpose you want.

WATCH:Can Bacteria on Earth Help Us Find Alien Life?

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New Microbial Genomes Help Scientists Fill Gaps in the Tree of Life - Seeker

June 12, 2017

An epigenetic mechanism regulating gene activity has been revealed by a KAUST-led international team of researchers investigating interactions between the human genome and its environment in adult tissues.

Valerio Orlando's lab at KAUST looks at the role of Ezh1, a gene whose function in mature tissues has remained unclear for 25 years. Like its twin Ezh2, Ezh1, along with a partner protein, encodes a protein involved in tagging genes to repress their activity. However, while Ezh2 mutations have been linked to cancer and developmental defects, mice lacking Ezh1 seem to develop normally.

Several years ago, Professor Orlando's group observed Ezh1 attached to the promoter of many genes that are normally switched on. "We saw this prototypical epigenetic repressor sitting on active genes, and our interpretation was that it's there to provide the ability to repress them," said Orlando. Hypothesizing that repression might be useful under stress, the team chemically stressed muscle cells and observed repression only in cells expressing Ezh1. Stress spurred Ezh1 into action, tagging genes with a repressive marker that could later be removed, a reversible response that Orlando calls "cell plasticity": the ability to adapt to a dynamic environment.

A turning point in the conception of Ezh1 came when the team discovered a truncated version of the protein. Many human genes encode several slightly different versions of a protein, known as isoforms, and the researchers realized that an additional band lurking in some images was in fact a shorter isoform of Ezh1.

"Once our eyes were redirected to the short version, we immediately understood a number of things," recalled Orlando. The truncated isoform was in the cytoplasm rather than the nucleus, and the team demonstrated that it acts as an environmental sensor regulating the activity of the full-length protein. Ezh1 needs a partner protein in order to tag genes, but the short isoform binds to the partner, trapping it in the cytoplasm, "like keeping that protein on a leash." In stressed cells, the short isoform is degraded, releasing the partner to join full-length Ezh1 in the nucleus. Once the stress stops, short-Ezh1 once again traps the partner, stopping long-Ezh1 from acting, and the repressive tags are removed.

These findings reveal a new landscape of genetic regulation for researchers to explore, where interactions occur between isoforms of a single gene rather than products of different genes. "This offers a new paradigm for gene regulation, linking the genome with the environment," said Orlando. "It's a very exciting perspective."

Explore further: Thyroid tumor: It takes two to tango

More information: Beatrice Bodega et al. A cytosolic Ezh1 isoform modulates a PRC2?Ezh1 epigenetic adaptive response in postmitotic cells, Nature Structural & Molecular Biology (2017). DOI: 10.1038/nsmb.3392

An analysis of data from five major studies of testicular cancer has identified new genetic locations that could be susceptible to inherited testicular germ cell tumors. The findings, which researchers call a success story ...

Researchers at the University of Birmingham have found that a type of protein could hold the secret to suppressing the growth of breast cancer tumours.

A University of Colorado Cancer Center study published today in Nature Communications shows that metastatic breast cancer cells signal neighboring cells in ways that allow otherwise anchored cells to metastasize. The work ...

Tumor suppressor genes protect cells from malignant transformation. If they are turned off as a result of chemical modifications in DNA, called epigenetic labels, this contributes to the development of cancer. As opposed ...

Testing for large numbers of genetic changes can identify men with over a 10-fold increased risk of testicular cancer, a new study shows.

Cancer stem cells, which fuel the growth of fatal tumours, can be knocked out by a one-two combination of antibiotics and Vitamin C in a new experimental strategy, published by researchers at the University of Salford, UK.

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Lecturer and sports genetics expert of the Department of Medical Biology and Genetics at Marmara University Korkut Ulucan has created the genome map of 10,000 successful athletes and provided the details of the National Sports Genome project designed to reveal the successful sportsmen of the future.

The project began five years ago and it was so successful that the team, led by Ulucan, saw the International Sports Genome project become a registered brand. The main target of the project is to gain doping-free sporting successes and to offer training models depending on the genome map of individuals. Providing information on the process behind the project's implementation, Ulucan said: "The clubs and federations that support us analyze samples of saliva and blood collected as part of our research. We examine the unique genetic parameters of individuals and learn their specific needs in terms of exercise, as well as check preexisting conditions regarding possible illness and are able to measure their endurance levels. I hope that this discovery will become a national policy."

When asked which branches of sports will be affected by the developments, Ulucan said that the genetic parameters of the project are still being discovered, while asserting that they have already created the genetic profiles of 1,000 athletes predominantly in football but also of those who compete in basketball, swimming, volleyball, wind surfing, cycling, tennis and mono-pallet swimming, all of which make up 25 percent of national athletes.

The remaining test subjects, according to Ulucan, include professionals and infrastructure sportsmen as well as members of leading football clubs. Ulucan and his team are also considering expanding the scope of their research to include wrestling and fighting.

Ulucan has already carried out genetic mapping for a number of famous football players in Turkey: "We have a former player from Galatasary who allowed us to generate his genome map when he was still in the system. Now we have generated the map of the Beikta players. We have also examined how they should exercise and their sports psychology. These athletes are the future of tomorrow's teams and we are working to develop infrastructure that will allow entire teams to undergo genome mapping. Tomorrow's Gkhan Gnl, Sosa and Brazilian Givanildo Vieira de Souza (known as "the Hulk" among football lovers) are coming," said Ulucan. He also added that he considers Emre Belzolu as one of the best footballers of Turkey, asserting that if he can conduct genome mapping on players like Belzolu, he can offer a similar exercise model to children who can train effectively to become successful athletes as well. "It's all up to the trainee and their families," added Ulucan.

Yet, he also pointed out that when it comes to genome and DNA mapping, sportsmen and women could be a little intimidated as they may worry that they could lose the support of their teams. Instead, Ulucan says they tell them that they are analyzing how they can raise generations to be as successful as these sportsmen.

"We hope that we will be able to create super Olympic individuals in the future. DNA research is already ongoing; soon science may be able to alter the genetic makeup of individuals. After determining which genes contribute to athletic talent, we can use this information to create more Olympic sportsmen; scientific researchers are already exploring this," he said.

The data that have been collected to date indicate that there are certain differences in great athletes compared to the world populace percentage-wise; yet, there are more sprinter sportsmen and women in the genome map when compared to the literature. Ulucan said that there are more sprinters; those who are on the verge of making a breakthrough and that the short-distance and endurance gene are more leading. "For example; Turks perform well in short-distance running and swimming. Wind surfers and mono-pallet swimmers have more strength and endurance genes. We have also come across anxiety problems in sportsmen, which we did not expect," said Ulucan.

Characteristics of successful athletes

Associate Proffessor Korkut Ulucan in the lab.

- Footballers: sprinter-focused, highly devoted individuals with higher anxiety levels compared to the average person

- Basketball players: explosive power in terms of strength, slightly elevated anxiety levels

- Cyclists: higher levels of Vitamin D reported in the bloodstream, higher metabolism, prone to increased endurance levels

- Mono-pallet swimmers: high endurance levels with optimal tendencies for increased endurance levels

- Tennis players: slightly higher rate of lactose intolerance among players compared to general population, more prone to gluten sensitivity

- Wind surfers: higher endurance parameters compared to average population

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Genome project promises super olympic athletes - Daily Sabah

The Jerusalem Post

Sunflower genome code cracked by team that included Tel Hai researcher The Jerusalem Post The sunflower genome is composed of approximately 3.5 billion bases and is larger than the human genome, which is composed of about 3.2 billion bases. Some 85% of the genome consists of identical sections that make identification and separation ...

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Sunflower genome code cracked by team that included Tel Hai researcher - The Jerusalem Post

Matthew Cabe Staff Writer @DP_MatthewCabe

Significant news for the Mojave Desert in recent weeks emanated from separate sections of the scientific world.

Out in Mojave, California, on May 31, the worlds largest all-composite plane ever built rolled out of its Mojave Air and Space Port hangar for the first time.

Dubbed Stratolaunch, the dual-fuselage plane weighs approximately 250 tons unfueled, stands 50 feet tall and boasts a record-setting wingspan (385 feet) thats 25 feet longer than a football field. Its powered by six Boeing 747 engines.

Before Stratolaunchs gargantuan reveal, several weeks were spent removing the fabrication infrastructure and three-story scaffolding around the plane. Crews then rested the planes full weight on 28 wheels.

Stratolaunch belongs to billionaire Paul Allen, the Microsoft co-founder who owns the Seattle Seahawks and is currently Forbes' 42nd richest person in the world. In 2011, Allen founded Stratolaunch Systems with the goal of making access to space more convenient, reliable and routine.

The purpose of Stratolaunch the plane, then, is to launch satellite-carrying rockets into space at a reduced cost. Allens company partnered with the Virginia-based Orbital ATK, which will provide the rockets capable of carrying the 1,000-pound satellites. Stratolaunch will drop the rockets from about 35,000 feet.

The main cost-effective benefit of an air launch such as this, the company said, is an ability to avoid the limitations of fixed launch sites that can be impacted by weather, air traffic and ship traffic on ocean ranges.

According to the Associated Press, all this will translate into new ways to beam the Internet all across the globe, which in turn will provide better communication.

In the interim, Stratolaunch CEO Jean Floyd said the company will conduct numerous tests in the coming weeks at the Mojave hangar while keeping the plane on track for a launch demonstration in 2019.

On the same day Stratolaunch rolled out of its hangar, researchers from Arizona State Universitys School of Life Sciences made headlines by decoding the Mojave Desert tortoises genome. Their findings were published in the scientific journal PLOS ONE.

Such a breakthrough could help our reptilian neighbor survive an increasing number of threats, according to Science Daily.

Those threats include natural predators, invasive grasses also a threat to the beloved Joshua tree an upper respiratory disease and human activity. All have contributed to the decline of the Mojave Desert tortoise.

But the researchers, led by Marc Tollis, believe the tortoises now decoded genome i.e. a complete set of its DNA will provide a launchpad for further study into areas like disease resistance.

Tollis, as quoted in Science Daily: We don't know how the tortoise is handling the fact that it's also being threatened by an upper respiratory disease," said Tollis. "Decoding this genome will help us catalog which tortoise genes are evolving quickly enough to help them overcome this threat.

Other advantages include deeper dives into how the Mojave tortoise is adapting to its changing desert environment and the diversity of its hybridization with its sister species, the Sonoran Desert tortoise.

The goal is to increase conservation efforts for the Mojave tortoise, which is listed as threatened under the U.S. Endangered Species Act, by posing new questions in light of the decoded genome.

Inevitably, though, the simplest answer already exists. It came up during a chat I had in 2016 with Ed LaRue, a former U.S. Bureau of Land Management biologist and tortoise counter with nearly 30 years experience.

I asked Ed what can be done to combat the significant population reductions numbers decreased 50 percent between 2004 and 2012 alone among Mojave tortoises.

(People) go out to the desert and see a tortoise and think it would be cool in their backyard, Ed said. So to encourage people to understand that they are wild and endangered and don't belong in backyards.

Interpretation: leave the tortoises alone. Maybe look toward the desert skies instead.

You might just spot a giant in two years' time.

Matthew Cabe can be reached at MCabe@VVDailyPress.com or at 760-951-6254. Follow him on Twitter @DP_MatthewCabe.

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This Desert Life: A massive plane, a decoded genome - VVdailypress.com

Download PDF Sequence search: A DNA-editing tool helps scientists find functions for the more than 98 percent of the genome that doesn't include genes.

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Tweaks to the CRISPR gene-editing system allow researchers to identify stretches of DNA that regulate gene expression1. Researchers could use the method to find sequences that control genes tied to autism.

The CRISPR system uses RNA guides to direct the DNA-cleaving enzyme CAS9 to specific spots in the genome. Scientists have used the system to edit, activate and disable genes. But regions that control these genes are hidden in the vast expanse of poorly understood DNA dubbed the dark genome.

The new method, described in the April issue of Nature Biotechnology, involves the use of chemical tags for DNA that activate or deactivate certain sections of the genome. Researchers engineered one version of CAS9 to add an activating tag, and another to add a deactivating tag.

They created two libraries that each contain thousands of guide RNAs. Each of the RNAs targets a DNA segment thought to regulate the expression of a gene or group of related genes. One library is specific for the beta-globin region, which contains genes involved in the production of hemoglobin. The other targets the breast cancer gene HER2.

The researchers loaded each of the guide RNAs into a virus and injected the virus into cultured human cells.

After 14 days in culture, the researchers gauged the expression of HER2 and beta-globin genes in the cells using fluorescent markers on the genes. They used a specialized instrument to sort out the brightest 10 percent and the darkest 10 percent of cells.

The researchers then identified where in the genome the guides had attached, revealing the sequences that regulate the expression of HER2 or beta-globin genes.

The study confirmed known regulatory segments for beta-globin genes and revealed new ones for HER2.

The regulatory segments generally produce subtle changes in gene expression, those that differ from baseline by less than twofold. But several of them working together might produce more dramatic changes, the researchers say.

They also say the method can be scaled up to enable screening of the entire genome, rather than just selected regions.

Original post:
CRISPR hack unearths gems buried in 'dark genome' - Spectrum

June 6, 2017 Apple with apple scab. Credit: Wageningen University

A high quality genome sequence of apple is published in this week's Nature Genetics by an international team of scientists, among which researchers of Wageningen University & Research in the Netherlands. The publication of the sequence facilitates faster and more targeted breeding of new apple varieties with increased disease resistance, improved production traits, and better fruit quality. With this the results support a more sustainable production of apple fruit, both from an environmental and a financial perspective.

The genome sequence was assembled by an international consortium of research institutions from France, Italy, Germany, the Netherlands and South Africa. The high quality of the genome data, indicating over 42 thousand putative genes, is the result of the use of latest sequencing technologies, which generate long stretches of DNA sequences, a very specific apple variety, and the most informative genetic linkage map in apple developed in earlier research.

The genome sequence gives new insights into the organization of the apple genome. Already 93 percent of the 42,000 putative genes have been validated through RNA sequencing. This knowledge is useful for the identification of genes that control a trait of interest and for the development of DNA-based diagnostic tests that can accelerate breeding of new varieties.

The use of a so-called di-haploid apple variety was critical for the success of this study. Apple is an outcrossing species, making its genome heterozygous. Also, apple originated from a hybridization between two different species, which was coupled with a whole genome duplication. As a result, each regular apple variety has up to four variants for each of its DNA sequences. The di-haploid variety used in this study is special as it has only up to two variants of every sequence. This leads to a dramatic complexity reduction, which made it possible to generate a very high quality genome sequence.

The new insights in the apple genome include a clear view on the duplication patterns among the 17 chromosomes of apple. This facilitates the identification of gene copies with similar function. Next, so called 'repetitive regions' have been assembled. These thus far uncharacterized regions of the apple genome may be involved in regulating gene expression. Finally, a new type of repeat sequence was found that may be specific for centromeres, which may lead to new insights in chromosome division and replication.

The research was coordinated by Etienne Bucher of INRA-Angers. Researchers of Wageningen University & Research contributed to the genome sequencing, genome mapping and assembly, applying their experience and skills in bioinformatics and by giving early access to a high quality reference genetic linkage map in apple.

Wageningen University & Research itself develops new apple varieties, which resulted in the top-variety 'Elstar', 'Santana' and the recently released 'Natyra'. The latter two are suited for biological production since these varieties have disease resistances. Additionally, 'Santana' is suitable for consumption by most individuals with a mild apple allergy.

Wageningen will use the new insights in the DNA of the apple in the targeted breeding of new varieties.

Explore further: Sunflower genome sequence to provide roadmap for more resilient crops

More information: High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development, Nature Genetics (2017). nature.com/articles/doi:10.1038/ng.3886

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Apple genome sequence helpful to breeding of new varieties ... - Phys.Org