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New Chinese Plant Wants to Clone 1 Million Cows Annually

New Chinese Plant Wants to Clone 1 Million Cows Annually | Amazing Science | Scoop.it
The world’s largest cloning plant is expected to clone 1 million cattle annually and is currently under construction in China.

 

Imagine one million identical cows marching shoulder to shoulder and rib to rib down a path to the slaughterhouse. Imagine one million identical cows getting the same idea simultaneously to turn around and storm the cloning plant that created them. Somewhere in between is what probably will happen when the world’s largest cloning plant, currently under construction in China, goes into full operation in early 2016.


Plant where 1 million cows will be cloned annually

The $31 million plant is being built in Tianjin (160 km (100 miles) from Beijing) by BoyaLife, a three-year-old biotech firm specializing in stem cell and regenerative medicine, biological products, drug innovation and hereditary diseases research. The plan for the 14,000 square meter (150,000 sq. ft.) plant is to produce 100,000 cloned cattle embryos the first year and ramp quickly up to a million annually to satisfy China’s rapidly-growing demand for beef.

 

In addition to cattle, the company will clone pet dogs, police dogs, racehorses and “non-human primates,” with the somewhat altruistic goal of being the first to someday clone endangered pandas.

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NIH: Over 1,000 genome and human genetics videos released

NIH: Over 1,000 genome and human genetics videos released | Amazing Science | Scoop.it

A full listing of videos featuring the science, research, programs and staff of the National Human Genome Research Institute, as well as researchers and scientists from around the world.

Many of these videos were created and produced by Genome Productions, a part of the Communications and Public Liaison Branch of the National Human Genome Research Institute. All government-produced video and audio clips are in the public domain and may be freely distributed and copied, but, as a courtesy, it is requested that the National Human Genome Research Institute be given an appropriate acknowledgement: Courtesy: National Human Genome Research Institute.
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Genome editing comes of age

Genome editing comes of age | Amazing Science | Scoop.it

Genome editing harnesses programmable nucleases to cut and paste genetic information in a targeted manner in living cells and organisms. Methods include the development of programmable nucleases, including zinc finger nucleases (ZFNs), TAL (transcription-activator-like) effector nucleases (TALENs) and CRISPR (cluster of regularly interspaced palindromic repeats)–Cas9 (CRISPR-associated protein 9) RNA-guided endonucleases (RGENs). Key advances that set the foundation for the rapid and widespread implementation of CRISPR–Cas9 genome editing approaches that has revolutionized the field.


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While there may be many corrective and beneficial uses for gene editing, there are few scarier prospects of science-gone-wrong.

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Scientists cut “Gordian knot” in the human genome

Scientists cut “Gordian knot” in the human genome | Amazing Science | Scoop.it

Females have two X chromosomes in each of their cells. Fully unfolded, each copy is two inches long. One of these two X chromosomes is inactive – its genes are turned off. This copy folds into a structure called the Barr body, a mysterious configuration that was discovered in 1949. Recently, scientists have shown that the Barr body contains massive superloops bringing DNA sequences at opposite ends of the chromosome together inside the nucleus of a cell.

 

Now, a team of scientists at Baylor College of Medicine, Florida State University and the Broad Institute of MIT and Harvard has determined which part of the DNA code is responsible for these superloops and has shown that it is possible to use this information to change the structure of the Barr body as a whole. The report, which sheds light on female development in mammals, appears today in Proceedings of the National Academy of Sciences. “X inactivation is fundamentally important for female development,” said Dr. Miriam Huntley, co-first author on the study. “Without it, females would generate too much of every gene product of the X chromosome.”

 

Huntley recently received her Ph.D. at Harvard University, where she worked with co-senior author Dr. Erez Lieberman Aiden, assistant professor of molecular and human genetics, a McNair scholar and director of the Center for Genome Architecture at Baylor. In earlier work, Huntley and her colleagues in the Aiden lab created the first genome-wide map of loops – positions where the genome folds back on itself in the nucleus of a cell and points that lie far apart along the contour of a chromosome come together in 3-D.

 

In the process, they demonstrated that the Barr body – the inactive X chromosome that is present in females – contains superloops, structures that have no analog in men. “The typical loop in a male genome spans about 200,000 letters of the DNA code. If fully stretched out, it would be about three thousandths of an inch long. But the loops in the Barr body can span as many as 77 million DNA letters – an inch of DNA,” said Huntley. “We call these giant structures superloops.”

 

Independently, the laboratory of Dr. Brian Chadwick at Florida State University had been studying X inactivation with a different set of techniques. “We had found that the human inactive X was organized into at least two different types of silent DNA that alternated along the chromosome. At one of the intersections was a strange DNA element called DXZ4, where a single sequence repeated, over and over again, for hundreds of thousands of letters,” said Chadwick, co-senior author of the new study. “I've always been fascinated with what the purpose of this repeat was. Other large repeats in our genome perform structural roles, such as the centromeres and telomeres. I was convinced that the role of DXZ4 was just waiting to be discovered.”


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Game of Genomes: An epic quest to crack the mysteries of our DNA

Game of Genomes: An epic quest to crack the mysteries of our DNA | Amazing Science | Scoop.it
It took hundreds of scientists — and about $3 billion — to assemble the first human genome sequence in 2001. Since then, the cost of DNA sequencing has crashed, while the accuracy has skyrocketed. Scientists have now sequenced the genomes of an estimated 150,000 people.

Despite this sequencing explosion, very few of the people who have their genomes sequenced get their hands on their own genomes. And those few people typically only get a highly filtered report.
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“Zombie” HIV RNA might cause ongoing damage

“Zombie” HIV RNA might cause ongoing damage | Amazing Science | Scoop.it

When HIV infects a cell, it inserts its own DNA into the host’s chromosomes. In people whose disease is well-controlled by medication, the majority of affected cells contain a busted HIV genome, with mutations or deletions, that can’t make any more viruses. These have been considered “junk” by most scientists, says study author Hiromi Imamichi, a virologist at NIAID. Imamichi thinks they’re more like “zombies”—dead, but still able to do damage.

 

Using blood samples from a repository at the National Institutes of Health Clinical Center in Bethesda, Imamichi checked for HIV DNA and RNA in cells from nine patients. For people whose disease was poorly controlled, with plenty of detectable virus in their blood, most of the HIV genomes in their cells were intact. But in those whose disease was well-managed, most of the HIV genomes were shortened due to missing pieces. Nonetheless, even in the people with HIV under control, their cells were producing defective RNAs from the truncated HIV genomes. Though flawed, those RNAs contained sequences that could, theoretically, be used to make protein. For example, in some cases different HIV genes were glued together, potentially encoding chimeric proteins.

 

The authors provide “quite convincing evidence” that cells with defective HIV genomes make HIV RNA, says Mathias Lichterfeld, a translational immunologist and infectious disease physician at Brigham and Women’s Hospital in Boston, who was not involved in the study. What remains to be shown is whether those RNAs do then make warped, mismatched HIV proteins. It wasn’t possible to find such proteins in the blood samples, since any amount made by the small cell populations would be undetectable, Lane says. But he and Imamichi are now trying to prove defective HIV genomes make protein both in vitro and in vivo.

 

If those proteins do exist, Lane believes “they’re probably causing some kind of immune activation.” That would explain why even in people whose HIV is kept in check, antibodies to HIV proteins and inflammation persist. The defective proteins might “distract” the immune system from the truly dangerous viruses, Lichterfeld speculates. The authors plan to study whether the presence of defective HIV RNAs correlates with higher immune activity in patients.

 

Lichterfeld thinks it might be possible to block production of the defective HIV RNAs. Knocking out these zombies would likely improve the outlook for patients, by eliminating a cause for inflammation, Lichterfeld says, and Lane suspects such a therapeutic could be a key piece of an eventual cure.

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Kataegis, gene Mutation “Hotspots” Linked to Better Breast Cancer Outcomes

Kataegis, gene Mutation “Hotspots” Linked to Better Breast Cancer Outcomes | Amazing Science | Scoop.it

Kataegis is a recently discovered phenomenon in which multiple mutations cluster in a few hotspots in a genome. The anomaly was previously found in some cancers, but it has been unclear what role kataegis plays in tumor development and patient outcomes. Using a database of human tumor genomic data, researchers at the University of California San Diego School of Medicine and Moores Cancer Center have discovered that kataegis is actually a positive marker in breast cancer — patients with these mutation hotspots have less invasive tumors and better prognoses.

 

The study, published June 30 in Cell Reports, also suggests kataegis status could help doctors determine the treatment options that might work best for patients with the mutation pattern. “We don’t know what causes kataegis, and before this study not much was known about its functional importance at the molecular or clinical level,” said senior author Kelly Frazer, PhD, professor of pediatrics and director of the Institute for Genomic Medicine at UC San Diego School of Medicine and Moores Cancer Center. “We’ve now found that kataegis is associated with a good prognosis for patients with breast cancer.”

 

Kataegis occurs in approximately 55 percent of breast cancers. To determine the role of this phenomenon in patient outcomes, Frazer and her team studied human breast cancer data available from The Cancer Genome Atlas (TCGA), the National Institutes of Health’s database of genomic information from more than 15,000 human tumors representing many cancer types. The Frazer team established the kataegis status of 97 breast tumors and then paired this information with patient data, such as age at diagnosis, treatment and outcome. They also looked at an additional 412 human breast cancers for which they predicted kataegis status.

 

The researchers found several different clinical factors associated with kataegis. These mutation hotspots were more common in breast cancer patients diagnosed at a later age, and patients with HER2-positive and high-grade tumors.

What’s more, the presence of kataegis was a marker for good prognosis. Kataegis on chromosome 17 and 22 in particular were associated with low tumor invasiveness. And finally, although causes of death for patients in the TCGA database are not known, patients without kataegis tended to die younger (median age 47 years old) than patients with kataegis (median age 78 years old).

 

In a finding that helps explain kataegis’ beneficial effect, the researchers noted that genes located near kataegis hotspots were less likely to behave abnormally than genes located further away in the genome. 

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Tweaked deep sequencing technique allows for profiling microRNA

Tweaked deep sequencing technique allows for profiling microRNA | Amazing Science | Scoop.it

MicroRNA (miRNA) are cellular fragments of RNA that in some organisms prevent the production of certain proteins. They have been found to be expressed in tissues of some non-mammals and in some embryos prior to pre-implantation. Little is known about their function in mammals, however, though prior research had found them to exist in oocytes (ovarian cells that lead to the development of an ovum) and early embryos. Prior efforts to deep sequence them in mammals has proved to be extremely challenging due to the numbers of them that must be processed, thus scientists still do not know what role they may play in embryo development, if any. In this new effort, the researchers report that they have found a way to tweak the cDNA library construction method for small RNAs resulting in a need for only 10 nanograms of RNA for doing a deep sequence, and because of that, were able to profile samples of both mouse oocytes and early embryos.

 

To tweak the construction method, the researchers optimized the 5' and 3' adaptor ligation and PCR amplification steps, which allowed for drastically reducing the amount of RNA needed. To test their ideas they performed the tweaking on 293 human embryonic kidney cells. Once they had the technique developed, they switched to testing mice oocytes and early embryos to learn more about the role of miRNA in mammal embryo development. They report that they were able to trace the processes surrounding miRNA as it moved from fertilization to early embryonic development—which was the first time that had ever been done. Furthermore, they found that the role miRNA played was suppressed as initial cell division was occurring—though it was not clear why that occurred—but later it was reactivated, perhaps as part of the process of regulating zygotic genetic growth factors.

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How Neanderthal DNA Helps Humanity: A Map of Ancient Genes

How Neanderthal DNA Helps Humanity: A Map of Ancient Genes | Amazing Science | Scoop.it

Neanderthals and Denisovans would have been a good source of helpful DNA for our ancestors. They had lived in Europe and Asia for hundreds of thousands of years — enough time to adjust to the cold climate, weak sun and local microbes. “What better way to quickly adapt than to pick up a gene variant from a population that had probably already been there for 300,000 years?” Akey said. Indeed, the Neanderthal and Denisovan genes with the greatest signs of selection in the modern human genome “largely have to do with how humans interact with the environment,” he said.

 

To find these adaptive segments, scientists search the genomes of contemporary humans for regions of archaic DNA that are either more common or longer than expected. Over time, useless pieces of Neanderthal DNA — those that don’t help the carrier — are likely to be lost. And long sections of archaic DNA are likely to be split into smaller segments unless there is selective pressure to keep them intact.

 

In 2014, two groups, one led by Akey and the other by David Reich, a geneticist at Harvard Medical School, independently published genetic maps that charted where in our genomes Neanderthal DNA is most likely to be found. To Akey’s surprise, both maps found that the most common adaptive Neanderthal-derived genes are those linked to skin and hair growth. One of the most striking examples is a gene called BNC2, which is linked to skin pigmentation and freckling in Europeans. Nearly 70 percent of Europeans carry the Neanderthal version.

 

Scientists surmise that BNC2 and other skin genes helped modern humans adapt to northern climates, but it’s not clear exactly how. Skin can have many functions, any one of which might have been helpful. “Maybe skin pigmentation, or wound healing, or pathogen defense, or how much water loss you have in an environment, making you more or less susceptible to dehydration,” Akey said. “So many potential things could be driving this — we don’t know what differences were most important.”

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Gene editing creates hornless cattle

Gene editing creates hornless cattle | Amazing Science | Scoop.it
Alison L. Van Eenennaam, PhD, a geneticist and cooperative extension specialist also at UC-Davis, is working with the Minnesota-based company Recombinetics on, among other things, a project that has produced some of the Holstein dairy cattle that lack horns by editing one allele to match another found in Angus cattle.

“We’ve still got a dairy cow with all the good dairy genetics,” she said. “We’ve just gone in and tweaked a little snippet of DNA at the gene that makes horns and made it so it’s the variant for Angus, which doesn’t grow horns.”
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The race to create super-crops

The race to create super-crops | Amazing Science | Scoop.it
Old-fashioned breeding techniques are bearing more fruit than genetic engineering in developing hyper-efficient plants.

 

Big corporations such as DuPont Pioneer in Johnston, Iowa, have spent more than a decadedeveloping improved crops through genetic engineering, and some companies say that their transgenic varieties look promising in field trials. But there are still no fertilizer-frugal transgenic crops on the market, and several agricultural organizations around the globe are reviewing their biotechnology initiatives in this area.

 

Plant biologist Allen Good of the University of Alberta in Edmonton, Canada, spent years working with companies to develop genetically modified (GM) crops that require little fertilizer, but he says that this approach has not been as fruitful as conventional techniques. The problem is that there are so many genes involved in nutrient uptake and use — and environmental variations alter how they are expressed.

 

“Nutrient efficiency was supposed to be one of those traits with broad applicability that could make companies lots of money. But they haven't developed the way we thought,” says Good.

 

Despite the scientific and breeding challenges, some researchers say that all strategies must be explored to develop crops that are less nutrient needy. With the global population heading towards 10 billion people by 2050, frugal crops could be essential to feed the planet. “There is a huge worldwide potential for these traits to help increase food production and sustainable development,” says Matin Qaim, an agricultural economist at the University of Göttingen in Germany.


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Shedding light on the 'dark matter' of the genome

Shedding light on the 'dark matter' of the genome | Amazing Science | Scoop.it

What used to be dismissed by many as "junk DNA" is back with a vengeance as growing data points to the importance of non-coding RNAs (ncRNAs)—genome's messages that do not code for proteins—in development and disease formation. But our progress in understanding these molecules has been slow because of the lack of technologies that allow the systematic mapping of their functions.

 

Now, Professor Benjamin Blencowe's team at the University of Toronto's Donnelly Centre, including lead authors Eesha Sharma and Tim Sterne-Weiler, have developed a method, described in May 19, 2016 issue of Molecular Cell, that enables scientists to explore in depth what ncRNAs do in human cells. The study is published on the same day with two other papers in Molecular Cell and Cell, respectively, from Dr. Yue Wan's group at the Genome Institute of Singapore and Dr. Howard Chang's group at Stanford University in California, who developed similar methods to study RNAs in different organisms.

 

Of the 3 billion letters in the human genome, only two per cent make up the protein-coding genes. The genes are copied, or transcribed, into messenger RNA (mRNA) molecules, which provide templates for building proteins that do most of the work in the cell. Much of the remaining 98 per cent of the genome was initially considered by some as lacking in functional importance. However, large swaths of the non coding genome—between half and three quarters of it—are also copied into RNA.

 

What the resulting ncRNAs might do depends on whom you ask. Some researchers believe that most ncRNAs have no function, that they are just a by-product of the genome's powerful transcription machinery that makes mRNA. However, it is emerging that many ncRNAs have important roles in gene regulation. This view is supported in that some ncRNAs act as carriages for shuttling the mRNAs around the cell, or provide a scaffold for other proteins and RNAs to attach to and do their jobs.

 

But the majority of available data has trickled in piecemeal or through serendipitous discovery. And with emerging evidence that ncRNAs could drive disease progression, such as cancer metastasis, there was a great need for a technology that would allow a systematic functional analysis of ncRNAs.

 

"Up until now, with existing methods, you had to know what you are looking for because they all require you to have some information about the RNA of interest. The power of our method is that you don't need to preselect your candidates, you can see what's occurring globally in cells, and use that information to look at interesting things we have not seen before and how they are affecting biology," says Eesha Sharma, a PhD candidate in Blencowe's group who, along with postdoctoral fellow Tim Sterne-Weiler, co-developed the method.

 

The new tool, called 'LIGR-Seq', captures interactions between different RNA molecules. When two RNA molecules have matching sequences - strings of letters copied from the DNA blueprint - they will stick together like Velcro. The paired RNA structures are then removed from cells and analyzed by state-of-the-art sequencing methods to precisely identify the RNAs that are stuck together. "Most researchers in the life sciences agree that there's an urgent need to understand what ncRNAs do. This technology will open the door to developing a new understanding of ncRNA function," says Blencowe, who is also a professor in the Department of Molecular Genetics.

 

Not having to rely on pre-existing knowledge is one strength of the method that will boost the discovery of RNA pairs that have never been seen before. The other is that scientists can for the first time look at RNA interactions as they occur in living cells, in all their complexity, unlike in the juices of mashed up cells that they had to rely on before. This is a bit like moving on to explore marine biology from collecting shells on the beach to scuba-diving among the coral reefs where the scope for discovery is so much bigger.

ncRNAs come in multiple flavours: there's rRNA, tRNA, snRNA, snoRNA, piRNA, miRNA, and lncRNA, to name a few, where prefixes reflect the RNA's place in the cell or some aspect of its function. But the truth is that no one really knows the extent to which these ncRNAs control what goes on in the cell, nor how they do this. The new technology developed by Blencowe's group has been able to pick up new interactions involving all classes of RNAs and has already revealed some unexpected findings.

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The gene hunters 

The gene hunters  | Amazing Science | Scoop.it

Criss-crossing the globe on a quest for unusual DNA, researchers have discovered a rare mutation that promises insights into both epilepsy and autism — and points to a treatment.


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Catalog of genetic information from 60,000 people reveals unexpected surprises

Catalog of genetic information from 60,000 people reveals unexpected surprises | Amazing Science | Scoop.it

More than one million people have now had their genome sequenced, or its protein-coding regions (the exome). The hope is that this information can be shared and linked to phenotype — specifically, disease — and improve medical care. An obstacle is that only a small fraction of these data are publicly available:

 

 

In an important step, we report this week the first publication from the Exome Aggregation Consortium (ExAC), which has generated the largest catalogue so far of variation in human protein-coding regions. It aggregates sequence data from some 60,000 people. Most importantly, it puts the information in a publicly accessible database that is already a crucial resource (http://exac.broadinstitute.org).

 

There are challenges in sharing such data sets — the project scientists deserve credit for making this one open access. Its scale offers insight into rare genetic variation across populations. It identifies more than 7.4 million (mostly new) variants at high confidence, and documents rare mutations that independently emerged, providing the first estimate of the frequency of their recurrence. And it finds 3,230 genes that show nearly no cases of loss of function. More than two-thirds have not been linked to disease, which points to how much we have yet to understand.

 

The study also raises concern about how genetic variants have been linked to rare disease. The average ExAC participant has some 54 variants previously classified as causal for a rare disorder; many show up at an implausibly high frequency, suggesting that they were incorrectly classified. The authors review evidence for 192 variants reported earlier to cause rare Mendelian disorders and found at a high frequency by ExAC, and uncover support for pathogenicity for only 9. The implications are broad: these variant data already guide diagnoses and treatment (see, E. V. Minikel et al. Sci. Transl. Med. 8, 322ra9; 2016 and R. Walsh et al. Genet. Med. http://dx.doi.org/10.1038/gim.2016.90; 2016).

 

These findings show that researchers and clinicians must carefully evaluate published results on rare genetic disorders. And it demonstrates the need to filter variants seen in sequence data, using the ExAC data set and other reference tools — a practice widely adopted in genomics.

 

The ExAC project plans to grow over the next year to include 120,000 exome and 20,000 whole-genome sequences. It relies on the willingness of large research consortia to cooperate, and highlights the huge value of sharing, aggregation and harmonization of genomic data. This is also true for patient variants — there is a need for databases that provide greater confidence in variant interpretation, such as the US National Center for Biotechnology Information’s ClinVar database.

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Researchers sequence genome of sphinx moth (Manduca sexta)

Researchers sequence genome of sphinx moth (Manduca sexta) | Amazing Science | Scoop.it

An international team of researchers has sequenced the genome of the tobacco (or tomato) hornworm—a caterpillar species used in many research laboratories for studies of insect biology.

 

Professor Gary Blissard of the Boyce Thompson Institute, located at Cornell University, and Professor Michael Kanost of Kansas State University, initiated the study and are co-senior authors on this large international project that included 114 researchers from 50 institutions and 11 countries.

 

The researchers have published their work in a paper titled “Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta” in the journal Insect Biochemistry and Molecular Biology. The scientists have made the genome sequence available to the public through the National Agricultural Library and the National Center for Biotechnology Information (NCBI).

 

“The completion of this project marks a major milestone in the study of insect biochemistry and molecular biology, as Manduca sexta is an important model insect: one that has been studied for its physiology and biochemistry for many decades,” said Blissard. Manduca sexta is susceptible to infection with the Autographa californica (AcNPV) Baculovirus.

 

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How DNA evidence could be a game-changer in monitoring freshwater fish

How DNA evidence could be a game-changer in monitoring freshwater fish | Amazing Science | Scoop.it

Scientists are pioneering a new way of monitoring water species, using techniques more familiar to fans of crime scene TV shows. Water may well be everywhere, but freshwater lake ecosystems are among some of the most vulnerable on Earth. In recent decades, freshwater species have suffered double the rate of decline of land species. And nearly 50% of fresh water lakes, rivers and streams across Europe failed to meet the EU Water Framework Directive, which aimed to achieve “good ecological status” of freshwater in Europe by 2015.

 

Part of the problem is that current tools used to monitor the so called “health" of a lake can be costly, time consuming, inefficient, and in some cases, lethal to the organisms they are sampling. Which is why a new research is pioneering a new way of monitoring water species – using techniques more familiar to fans of crime TV shows.

 

Environmental DNA, also known as eDNA works in the same way as regular DNA testing, but rather than using saliva or hair, samples of water, soil or even air are taken and tested. The method works because every creature in freshwater leaves behind traces of its eDNA as it swims around, shedding minute flakes of skin, eggs, sperm or in the case of plants, pollen or seeds.

 

The majority of eDNA studies so far have focused on detecting single species using highly specific DNA-based procedures which focus on detecting one species at a time. A new study instead used a form of DNA testing called “metabarcoding”. This is where a single region of DNA called a “barcode” is simultaneously sequenced from a whole community of organisms. This enabled a team of scientists now to analyse millions of DNA sequences from water samples, identifying the DNA of a broad range of species and looking at whole communities of organisms – rather than just detecting single species.

 

Metabarcoding of eDNA is a very new technology, and has only been tested in controlled conditions – such as in aquaria – or on a small scale in natural environments. But this technique has the potential to be a game changer for biodiversity monitoring, as it is completely non-invasive and extremely sensitive. It detects more species than established methods, and gives a surprisingly good indication of how abundant they are within the water environment.


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Dr. Stephen Kingsmore Sets Guinness World Records Title for Fastest Genetic Diagnosis

Dr. Stephen Kingsmore Sets Guinness World Records Title for Fastest Genetic Diagnosis | Amazing Science | Scoop.it

Stephen Kingsmore, M.D., D.Sc., president and CEO of Rady Children's Institute for Genomic Medicine at Rady Children's Hospital – San Diego, is the official title holder of the Guinness World Records® designation for fastest genetic diagnosis, which he accomplished by successfully diagnosing critically ill newborns in just 26 hours, as published in the journal Genome Medicine.

 

The feat was made possible by several time-shrinking technologies, including Edico Genome's genomic data-crunching computer chip, DRAGEN, and one of Illumina's high-throughput sequencing instruments. In addition, other parameters of the sequencing process were optimized.

 

Dr. Kingsmore achieved this Guinness World Records title while serving as executive director of Medical Panomics at Children's Mercy Kansas City; he will implement the enabling technologies at the new Rady Children's Institute for Genomic Medicine. Today's celebration in San Diego, often called "the genomics capital of the world," is being held on National DNA Day, which commemorates the completion of the Human Genome Project and the discovery of DNA's double helix.

 

"Diagnosing acutely ill babies is a race against the clock, which is why it's so essential for physicians to have access to technology that will provide answers faster and help set the course of treatment," Dr. Kingsmore said. "My work at Children's Mercy Kansas City that led to this recognition would not have been possible without our key technology partners Edico Genome and Illumina, who share a vision for unraveling mysteries of disease and giving hope to families with ill newborns. I look forward to collaborating with both parties to implement this approach at Rady Children's Institute for Genomic Medicine and ultimately neonatal and pediatric intensive care units across the country."

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Scientist sequence genome of a very abundant ocean microbe

Scientist sequence genome of a very abundant ocean microbe | Amazing Science | Scoop.it

Sea turtles and whales may be the charismatic critters of the sea, but the true kingpins of the ocean make up 98 percent of the ocean’s biomass — and yet individually are too small to see with the naked eye.

 

An almost unknown organism by the name Candidatus Thioglobus autotrophicus, is present in low-oxygen waters around the world and is one of the dominant organisms in these areas — between 40 and 60 percent of all cells in some regions.

 

Living things use oxygen for their metabolic activities, but in low-oxygen areas, bacteria and archaea have evolved to “breathe” other elements available in seawater. One of those is a chemical called nitrate which, when respired, produces gaseous nitrogen. That gas escapes to the atmosphere, effectively leaving the ocean and removing valuable nitrogen from the water.

 

The bacteria grown and sequenced by the UW oceanographers have been pegged as playing a big role in removing nitrogen from the ocean, but until now scientists didn’t have a complete picture of how it happened.

 

“We are filling in the gaps by providing a full genome,” said lead author Vega Shah, a UW doctoral student in oceanography. “Now we can talk about both what these organisms can and can’t do.”

 

The research team confirmed the bacteria are contributing to nitrogen loss, but in a different way than expected. More specifically, they are responsible for a key step — converting nitrate to a similar chemical called nitrite — which then goes on to fuel other nitrogen-removal processes. Earlier research had hypothesized that these microbes also produce ammonia, another nitrogen-containing chemical. Instead, the UW team found that the microbes consume ammonia, essentially competing with other organisms for this nitrogen compound that is also important for growth and development.

 

The findings were published July 19, 2016, in the Multidisciplinary Journal of Microbial Ecology, a Nature publication.


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Noncoding RNAs Not So Noncoding

Noncoding RNAs Not So Noncoding | Amazing Science | Scoop.it

In 2002, a group of plant researchers studying legumes at the Max Planck Institute for Plant Breeding Research in Cologne, Germany, discovered that a 679-nucleotide RNA believed to function in a noncoding capacity was in fact a protein-coding messenger RNA (mRNA).1 It had been classified as a long (or large) noncoding RNA (lncRNA) by virtue of being more than 200 nucleotides in length. The RNA, transcribed from a gene called early nodulin 40 (ENOD40), contained short open reading frames (ORFs)—putative protein-coding sequences bookended by start and stop codons—but the ORFs were so short that they had previously been overlooked.

 

When the Cologne collaborators examined the RNA more closely, however, they found that two of the ORFs did indeed encode tiny peptides: one of 12 and one of 24 amino acids. Sampling the legumes confirmed that these micropeptides were made in the plant, where they interacted with a sucrose-synthesizing enzyme.

 

Five years later, another ORF-containing mRNA that had been posing as a lncRNA was discovered inDrosophila.2,3 After performing a screen of fly embryos to find lncRNAs, Yuji Kageyama, then of the National Institute for Basic Biology in Okazaki, Japan, suppressed each transcript’s expression. “Only one showed a clear phenotype,” says Kageyama, now at Kobe University. Because embryos missing this particular RNA lacked certain cuticle features, giving them the appearance of smooth rice grains, the researchers named the RNA “polished rice” (pri).

 

Turning his attention to how the RNA functioned, Kageyama thought he should first rule out the possibility that it encoded proteins. But he couldn’t. “We actually found it was a protein-coding gene,” he says. “It was an accident—we are RNA people!” The pri gene turned out to encode four tiny peptides—three of 11 amino acids and one of 32—that Kageyama and colleagues showed are important for activating a key developmental transcription factor.4

 

Since then, a handful of other lncRNAs have switched to the mRNA ranks after being found to harbor micropeptide-encoding short ORFs (sORFs)—those less than 300 nucleotides in length. And given the vast number of documented lncRNAs—most of which have no known function—the chance of finding others that contain micropeptide codes seems high.

 

Genomes contain countless sORFs, but most do not produce functional proteins. To help identify the true protein-coding needles in the nonsense haystacks, scientists have devised methods and metrics to calculate sORFs’ coding potential based on their sequences and ribosome profiling characteristics.


Ribosome Release Score (RSS): After a ribosome reaches the stop codon of a true protein-coding mRNA, the ribosome’s association with the transcript ceases. The distribution of ribosome-bound fragments for those RNAs would thus show a dramatic reduction following the putative stop codon. (Cell, 154:240-51, 2013)

Fragment Length Organization Similarity Score (FLOSS):This metric distinguishes RNAs that have ribosome profiling fragment sizes clustered tightly in the 30–32 nucleotide range—the size protected by a eukaryotic ribosome—from those that have more varied fragment sizes, which might indicate protection by contaminating nonribosomal proteins. (Cell Rep, 8:1365-79, 2014)

ORF Regression Algorithm for Translation Evaluation of RPFs (ribosome-protected mRNA fragments) (ORF-RATER):This algorithm determines the likelihood that an ORF is translated based on its similarity to known protein-coding ORFs in terms of ribosome-occupancy pattern—that is, the distribution of ribosome profiling fragments across the ORF. For example, true protein-coding ORFs tend to exhibit peaks in the number of fragments at the start and stop codons where ribosomes are built and dismantled, and their fragments show a three-nucleotide periodicity in the expected reading frame—the ribosome appears to jump along three nucleotides (one codon) at a time. (Mol Cell, 60:816-27, 2015)

Phylogenetic Conservation Score of a sORF (PhyloCSF): This metric examines conservation of a sORF across species. (Bioinformatics, 27:i275-i282, 2011)

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The ultimate discovery power of the gene chip is coming to nanotechnology

The ultimate discovery power of the gene chip is coming to nanotechnology | Amazing Science | Scoop.it

The discovery power of the gene chip is coming to nanotechnology, as a Northwestern University research team develops a  tool to rapidly test millions — and perhaps even billions — of different nanoparticles at one time to zero in on the best nanoparticle for a specific use.

 

When materials are miniaturized, their properties — optical, structural, electrical, mechanical and chemical — change, offering new possibilities. But determining what nanoparticle size and composition are best for a given application, such as catalysts, biodiagnostic labels, pharmaceuticals and electronic devices, is a daunting task.

 

“As scientists, we’ve only just begun to investigate what materials can be made on the nanoscale,” said Northwestern’s Chad A. Mirkin, a world leader in nanotechnology research and its application, who led the study. “Screening a million potentially useful nanoparticles, for example, could take several lifetimes. Once optimized, our tool will enable researchers to pick the winner much faster than conventional methods. We have the ultimate discovery tool.”

 

Combinatorial libraries of nanoparticles - more than half never existed on Earth.

 

Using a Northwestern technique that deposits materials on a surface, Mirkin and his team figured out how to make combinatorial libraries of nanoparticles in a controlled way. (A combinatorial library is a collection of systematically varied structures encoded at specific sites on a surface.) Their study was published today (June 24) by the journal Science.

The nanoparticle libraries are much like a gene chip, Mirkin says, where thousands of different spots of DNA are used to identify the presence of a disease or toxin. Thousands of reactions can be done simultaneously, providing results in just a few hours. Similarly, Mirkin and his team’s libraries will enable scientists to rapidly make and screen millions to billions of nanoparticles of different compositions and sizes for desirable physical and chemical properties.

 

“The ability to make libraries of nanoparticles will open a new field of nanocombinatorics, where size — on a scale that matters — and composition become tunable parameters,” Mirkin said. “This is a powerful approach to discovery science.”

Mirkin is the George B. Rathmann Professor of Chemistry in the Weinberg College of Arts and Sciences and founding director of Northwestern’s International Institute for Nanotechnology.

 

Using just five metallic elements — gold, silver, cobalt, copper and nickel — Mirkin and his team developed an array of unique structures by varying every elemental combination. In previous work, the researchers had shown that particle diameter also can be varied deliberately on the 1- to 100-nanometer length scale.

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Genome sequencing helps determine end of tuberculosis outbreak

Genome sequencing helps determine end of tuberculosis outbreak | Amazing Science | Scoop.it

Using genome sequencing, researchers from the University of British Columbia, along with colleagues at the Imperial College in London, now have the ability to determine when a tuberculosis (TB) outbreak is over.

 

The research is the first of its kind to demonstrate that genomic analysis can be used to determine when a TB outbreak has ended—valuable knowledge which can assist public health investigators understand an outbreak’s dynamics and guide a real-time public health response. Genomic analysis involves reading the complete genetic instructions of the pathogens causing a disease, and using that data to infer who might have infected whom. By looking for mutations that are shared between the pathogens taken from different people, researchers can see whose pathogens are most closely related to each other, suggesting potential transmission.

 

“Declaring the end of a TB outbreak is a difficult thing to do,” said senior author Jennifer Gardy, assistant professor in UBC’s school of population and public health and a senior scientist at the British Columbia Centre for Disease Control. “Because the bacterium that causes TB can lie dormant in someone’s lung for months or even years before it causes disease, we had no way of knowing whether a TB case we have just diagnosed was a recent infection – suggesting the outbreak is still going on – or whether the person was infected years ago.”

 

Using mathematical and statistical techniques, the researchers evaluated a TB outbreak that began in May 2008 and were able to determine when each outbreak case was infected. This provided public health officials with a way to determine when disease transmission had stopped and the outbreak had ended. They were able to declare the outbreak over in January 2015, after the data indicated no disease transmission had occurred since mid-2012.

 

“By using a series of techniques from the world of mathematics and statistics, we can come up with an estimated time at which each infection occurred,” explained Gardy. “This information is incredibly useful to the public health officials managing an outbreak. Responding to an outbreak requires a lot of effort and resources, and we need to know when we can step down our response.”

 

“Genomics has been used to monitor infectious disease outbreaks before, but this is the first time it’s ever been possible to declare a complicated outbreak of TB over,” said Gardy. “It really opens up new doors in the world of TB control.”

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Cancer-patient big data can save lives if shared globally

Cancer-patient big data can save lives if shared globally | Amazing Science | Scoop.it

Sharing genetic information from millions of cancer patients around the world could revolutionize cancer prevention and care, according to a paper in Nature Medicine by the Cancer Task Team of the Global Alliance for Genomics and Health (GA4GH). Hospitals, laboratories and research facilities around the world hold huge amounts of this data from cancer patients, but it’s currently held in isolated “silos” that don’t talk to each other, according to GA4GH, a partnership between scientists, clinicians, patients, and the IT and Life Sciences industry, involving more than 400 organizations in over 40 countries. GA4GH intends to provide a common framework for the responsible, voluntary and secure sharing of patients’ clinical and genomic data.

 

“Imagine if we could create a searchable cancer database that allowed doctors to match patients from different parts of the world with suitable clinical trials,” said GA4GH co-chair professor Mark Lawler, a leading cancer expert fromQueen’s University Belfast. “This genetic matchmaking approach would allow us to develop personalized treatments for each individual’s cancer, precisely targeting rogue cells and improving outcomes for patients.

 

“This data sharing presents logistical, technical, and ethical challenges. Our paper highlights these challenges and proposes potential solutions to allow the sharing of data in a timely, responsible and effective manner. We hope this blueprint will be adopted by researchers around the world and enable a unified global approach to unlocking the value of data for enhanced patient care.”

 

GA4GH acknowledges that there are security issues, and has created a Security Working Group and a policy paper that documents the standards and implementation practices for protecting the privacy and security of shared genomic and clinical data.

 

Examples of current initiatives for clinico-genomic data-sharing include the U.S.-based Precision Medicine Initiative and the UK’s 100,000 Genomes Project, both of which have cancer as a major focus.

 

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Scientists hold closed meeting to discuss building a human genome from scratch

Scientists hold closed meeting to discuss building a human genome from scratch | Amazing Science | Scoop.it

More than 130 scientists, lawyers, entrepreneurs, and government officials from five continents gathered at Harvard this week for an “exploratory” meeting to discuss the topic of creating genomes from scratch — including, but not limited to, those of humans, said George Church, Harvard geneticist and co-organizer of the meeting.  The meeting was closed to the press, which drew the ire of prominent academics.

 

Synthesizing genomes involves building them from the ground up — chemically combining molecules to create DNA. Similar work by Craig Venter in 2010 created what was hailed as the first synthetic cell, a bacterium with a comparatively small genome.

 

In recent months, Church has been vocal in saying that the much-hyped genome-editing technology called CRISPR, which is only a few years old and which he helped develop, would soon be obsolete. Instead of changing existing genomes through CRISPR, Church has said, scientists could build exactly the genomes they want from scratch, by stringing together off-the-shelf DNA letters.

 

The topic is a heavy one, touching on fundamental philosophical questions of meaning and being. If we can build a synthetic genome — and eventually, a creature — from the ground up, then what does it mean to be human?

 

“This idea is an enormous step for the human species, and it shouldn’t be discussed only behind closed doors,” said Laurie Zoloth, a professor of religious studies, bioethics, and medical humanities at Northwestern University.

 

In response, she co-authored an article with Drew Endy, a bioengineering professor at Stanford University, calling for broader conversations around the research.

 

Church said that the meeting was originally going to be “an open meeting with lots of journalists engaged.” It was supposed to be accompanied by a peer-reviewed article on the topic. But, he said, the journal (which Church declined to identify) wanted the paper to include more information about the ethical, social, and legal components of synthesizing genomes — things that were discussed at the meeting.

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Intron Addition into Genome Detected as an Ultra-rare Event

Intron Addition into Genome Detected as an Ultra-rare Event | Amazing Science | Scoop.it

After nearly a half trillion tries, a rare event was seen that might solve an evolutionary puzzle about noncoding sequences of DNA in genomes and address speciation and the cause of diseases like cancer.

 

For a long time, scientists have known that much of the DNA within any given organism’s genome does not code for functional molecules or protein. However, recent research has found that these genetic sequences, misnamed “junk” DNA in the past, often do have functional significance. These introns are no exception. Now known to play a role in gene expression, introns are the portion of gene sequences that are removed or spliced out of RNA before genes are translated into protein. When eukaryotes first diverged from bacteria, there was a massive invasion of introns into the genome. All living eukaryotes — from yeast to mammals — share this common ancestor, and whereas simple organisms such as yeast have eliminated most of their introns, organisms such as mammals have considerably expanded their intron inventory. Humans have more than 200,000 introns that take up about 40 percent of the genome.

 

In a current paper, Stevens and co-author Sujin Lee, a former graduate student in cellular and molecular biology at UT Austin, used a new reporter assay to directly detect the loss and gain of introns in budding yeast (Saccharomyces cerevisiae). The team tested nearly a half trillion yeast and found only two instances in which an intron was added to a new gene. The proposed mechanism for this addition is a reversal of a splicing reaction.

 

Normally, to make proteins, RNA is read from the instructions in DNA, and the introns are spliced out. But in these two instances, the cell allowed the spliced out introns to make it back into a different RNA and was recombined back into the genome, thus creating a permanent genetic change. These are called intron gains, and if these accumulate over time, they can contribute to the development of new species as well as human disease.

 

“We showed in this project that introns continue to be gained, although infrequently at any point in time,” says Stevens. “But can introns drive evolution? If these sequences give organisms a selective advantage and become fixed in a population, others have shown that it can be a major factor in the creation of new species.”

 

These evolutionary advances come at a cost, however, because diseases such as cancer correlate with the improper removal of introns from RNA. Stevens adds, “We are continuing this work to further understand how this process impacts our genetic history, our future, and the prospects of curing disease.”


Via Integrated DNA Technologies
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Genome Sequencing Reveals Differences Between Giraffes and Ocapi

Genome Sequencing Reveals Differences Between Giraffes and Ocapi | Amazing Science | Scoop.it

Scientists spot mutations that could explain how giraffes became the world’s tallest living mammals.

 

Call it a tall task: researchers have decoded the genomes of the giraffe and its closest relative, the okapi. The sequences, published on May 17 in Nature Communications, reveal clues to the age-old mystery of how the giraffe evolved its unusually long neck and legs.

 

Researchers in the United States and Tanzania analyzed the genetic material of two Masai giraffes (Giraffa camelopardalis tippelskirchi) from the Masai Mara National Reserve in Kenya, one at the Nashville Zoo in Tennessee and an okapi fetus (Okapia johnstoni) from the White Oak Conservation Center in Yulee, Florida.

 

“This is one more wonderful demonstration of the power of comparative genomics to connect the evolution of animal species on this planet to molecular events that we know must underpin the extraordinary diversity of life on this planet,” says David Haussler, director of the Genomics Institute at the University of California, Santa Cruz.

 

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