Daily Archives: March 4, 2017

March 3, 2017 The shaggy megafauna that roamed Siberia and North America together with our ancestors captivate the imagination, but now it looks like theyre giving us a practical lesson in genetics that could help inform conservation efforts.

Scientists compared the DNA of two mammoths: a member of a dwindling island population with an individual from the booming herds of the more distant past. Their findings, published Thursday in the journal PLOS Genetics, provided some of the first concrete proof of the genetic theories describing how population size affects genetic fitness. Genomic meltdown may have doomed the last herd of mammoths, a conclusion that on its face suggests dire consequences for modern endangered species, but that could also offer valuable insight into how to best keep today's rarest creatures from crossing the threshold into extinction.

The furry beasts ruled the tundra for over a million years until climate change turned grasslands into forests and hungry humans arrived on the scene. These pressures caused the mainland population to go extinct about 10,000 years ago, but two pockets managed to survive millenniums longer.

Two arctic islands became their last refuge, with populations surviving on St. Paul island until a lack of fresh water did them in 5,600 years ago, leaving the species to make their final stand on the remote Wrangel Island, where they stuck it out for another 1,600 years.

Researchers compared the DNA of a 4,300-year-old Wrangel Island specimen with that of a 45,000-year-old mainland mammoth. Genomic diversity measures suggest that the mainland individual was part of a breeding population 43 times larger than the 300 remaining island mammoths.

They found that the island genome was damaged compared to that of the mainland mammoth, suggesting that the lack of diversity in the breeding pool may have led to a breakdown in the integrity of the gene pool.As a result, many island mammoths may have had poor senses of smell, and a new coat as the stiff hairs that protected individuals from the cold became soft and shiny. The mighty woolly mammoth became a satin mammoth.

Experts cant be sure that these genetic changes caused the Wrangel population to die out, but Dr. Rogers finds the timing highly suspicious. "We found these bad mutations were accumulating in the mammoth genome right before they went extinct," she told the BBC.

This result contradicts a 2012 paper, which found that while the genetic diversity did indeed drop after the shrinking population became isolated, it continued at a reduced but stable level for thousands of years, until some other cause drove the final nail into the coffin. "I'm personally leaning towards environmental change," co-author Love Dalen, of the Swedish Museum of Natural History, told the BBC at the time.

Regardless of what ended the Wrangel Island mammoths, the study has great significance in the field of genetics, where genome evolution theory has long predicted that damaging mutations should pile up in small populations of organisms.

"The mathematical theories that have been developed said that [individuals in small populations] should accumulate bad mutations because natural selection should become very inefficient," Rogers explained to the BBC.

The problem was that this accumulation takes a long time, making it difficult to confirm the theory by observing the change as it happens within a single species.

But the mammoth made just such an empirical observation possible.

This is probably the best evidence I can think of for the rapid genomic decay of island populations, Hendrik Poinar, an evolutionary geneticist at McMaster University who was not involved in the study, told The New York Times.

The confirmation may have serious consequences for efforts to prevent modern species from going the way of the mammoth.

This is a very novel result," Dr. Dalen, who published the DNA sequences this study was based on, told the BBC. "If this holds up when more mammoth genomes, as well as genomes from other species, are analysed, it will have very important implications for conservation biology."

The paper identifies Asiatic cheetahs (fewer than 100 individuals), pandas (1600 individuals living in highly fragmented territories), and mountain gorillas (300 individuals) as examples of small populations in danger of suffering the same genomic meltdown as the mammoths.

Saving such species may be challenging, because once genes get deleted, its difficult to see how genomes could recover quickly, the authors write. With small effective population sizes, adaptation through both new mutation and standing variation may be severely limited.

Their work suggests the existence of a population point of no return, after which a species may never recover, no matter what careful protections are afforded to the endangered individuals.

But there's a silver lining. A better understanding of the challenges facing small populations can help focus conservation efforts, and direct where limited funds should be best spent. Concentrating resources on preserving vulnerable species before their numbers dwindle could be a more cost-effective strategy than large expenditures on groups that have already suffered a great loss of genetic diversity.

"So if you can prevent these organisms ever being threatened or endangered then that will do a lot more to help prevent this type of genomic meltdown compared to if you have a small population and then bring it back up to larger numbers, because it will still bear those signatures of this genomic meltdown," Rogers explained to the BBC.

Simply put, an ounce of prevention may be worth a pound of cure.

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DNA reveals mammoth secret - Christian Science Monitor

A daily digest of IT news, curated from blogs, forums and news sites around the web each morning. We highlight the key commentary and demystify the real story.

Computerworld | Mar 3, 2017 5:11 AM PT

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Humans create a lot of digital data. And figuring out the best way to store it is a challenge.

Well, researchers think they may have started to solve that problem, by figuring out an efficient way to store digital data: on DNA. But how does it work?

In IT Blogwatch, we get our science caps on.

So what exactly is going on? Eva Botkin-Kowacki has some background:

But how do you store digital data on DNA? Robert Service has the details:

But how exactly does it work? Charles Choi fills us in:

So what did the scientists store on the DNA strands? We let the Columbia University give us the official line:

How exactly did the researchers store the information on the DNA? And how did they then read it again? Brooks Hays has that info:

And what are the benefits of storing data this way? Ed Yong is in the know:

This isn't the first time this has been done, though, right? Vlad Dudau has some background:

Is there a downside to all this? Alyssa Navarro has a reality check:

So what does this all mean? Stuart Ponder has an "ah-ha" moment:

Rebecca Linke is a Senior Associate Editor at Computerworld who writes about social media and personal technology. She also helps manage Computerworld's Facebook and Google+ pages.

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DNA: The hard drive of the future - Computerworld

Science Daily

Computer operating system and short movie stored on DNA: New ... Science Daily An algorithm designed for streaming video on a cellphone can unlock DNA's nearly full storage potential by squeezing more information into its four base ... and more »

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Computer operating system and short movie stored on DNA: New ... - Science Daily

In Brief

CRISPR-Cas9 is the most advanced and efficient gene editing tool we have. Its uses, however, have been largely limited to silencing protein-coding genes in the DNA. This leaves out whats called the DNA dark matter the non-coding DNA that covers about 99 percent of our genetic code. A study published in the journal PLOS Computational Biology may soon change this.

The new technique, developed by a team of researchers led by Carlos Pulido, is a software pipeline called CRISPETa.Its based ona breakthrough tool (which uses CRISPR-Cas9) called DECKO. The tool was recently developed by the Johson lab, and was specifically designed for deleting those piecesof non-coding DNA. DECKO employs two sgRNAs as molecular scissors that snip out a piece of DNA. While the concept might seem simple, designing deletion experiments using DECKO was time consuming due to thee lack of software to createthe required sgRNAs.

This is where CRISPETa comes in. Users can tell CRISPETa which region of DNA they wish to delete. The software then generates a pair of optimized sgRNAs that can be used directly for that experiment. Even better, the software can develop designs at high scale, which would all for future screening experiments as well.

We hope that this new software tool will allow the greatest possible number of researchers to harness the power of CRISPR deletion in their research, Pulido said.

CRISPETa designs have already demonstrated their ability to efficiently delete desired targets in human cells. Ultimately, we expect that CRISPR deletion and other genome engineering tools to lead to a revolution in our ability to understand the genomic basis of disease, particularly in the 99% of DNA that does not encode proteins, researcher Rory Johnson explained. The deletions could also be carried in RNA molecules.

Apart from being used as a basic research tool, CRISPR may even be used in the future as a powerful therapeutic to reverse disease-causing mutations, Johnson added. This is the underlying value of the research: the software could be used to develop CRISPR scissors to delete suspected disease-causing, non-coding DNA. At the very least CRISPETa willimprove our understanding of non-coding DNA, which could lead to the discovery of new disease-causing genes, and aid in the development of potential new drugs with which to treat and maybe even eventually cure them.

Read more:
Scientists Have Created A Way to "Delete" DNA in Living Cells - Futurism

A young company developing technology created at the University of New Mexico (UNM) is on a mission to disrupt the landscape of DNA sequencing.

Armonica Technologies, LLC, is developing a DNA sequencing platform that will sequence a complete human genome in minutes. The companys goal is to make the technology the gold standard for DNA sequencing for precision medicine research applications. Armonica has optioned a portfolio of patented and patent pending technologies from STC.UNM.The technology is called optical nanopore sequencing and uses nanochannels to deliver single DNA molecules through nanopores.Nanopores are very small holes with an internal diameter of 1 nanometer (one billionth of a meter). The nanopores slow down DNA translocation enough to produce massively parallel, single-base resolution using optical techniques.

Heres how nanopore sequencing works: when a nanopore is immersed in conducting fluid, voltage can be applied to produce an electric current. The current is sensitive to the size and shape of the nanopore so that if a DNA strand passes through or near the nanopore, the amount of current changes. The change in the current as the DNA molecule passes through the nanopore represents a reading of the DNA sequence.

There is an unmet need in the fast-growing DNA sequencing market, said Armonica President & CEO Scott Goldman. Todays standard genome sequencing approach requires extensive library preparation and creates a massive computational and bioinformatics problem related to reassembling the data set. Armonica will resolve these problems by introducing a sequencing instrument that will not require library preparation and will generate reads of up to 50,000 bases, combined with a parallelism of 1 million. This approach will net 50 billion basesmore than sufficient to sequence the entire human genome in minutes.

The innovative nanopore technology was developed by Distinguished Professor Emeritus Steve Brueck, Research Assistant Professor Yuliya Kuznetsova, and Postdoctoral Fellow Alexander Neumann from UNMs Center for High Technology Materials (CHTM) and Professor Jeremy Edwards from UNM's Department of Chemistry & Chemical Biology, in collaboration with Redondo Optics CEO Edgar Mendoza.

Nanopore sequencing analyzes long DNA strings, with long reads that provide more accurate identification of genome variations, said Brueck. It is an approach, therefore, that leads to a more thorough, faster, and accurate genomic analysis, allowing researchers to substantially improve the ability to make new discoveries. One of the challenges of nanopore sequencing is to improve the resolution to be able to detect single nucleotides (bases).

We believe our nanochannel technology will disrupt the industry because it produces very long reads for higher accuracy, very high parallelism using optical techniques, and high throughput rates for greater processing speed. It will be an affordable tool for researchers, said STC CEO Lisa Kuuttila. This technology portfolio represents a leap in genomic sequencing technology that could be a huge benefit for the DNA sequencing industry, which is experiencing explosive growth. The companys research and development are currently being done at UNMs CHTM, a research center with a global reputation for inventing disruptive nanoscale technologies and providing outstanding scientific expertise and technical support. We are very excited about the technologys potential and believe in the companys vision.

The inventors have successfully demonstrated the viability of the technology and have received a National Institutes of Health Small Business Innovation Research (SBIR) grant to advance development of sequencing instruments for genomic, research and medical facilities.

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Pushing the boundaries of DNA sequencing - UNM Newsroom

TOPEKA - Post-conviction DNA testing usually reserved for murder and rape cases in Kansas will be allowed in a Johnson County robbery case after the Kansas Supreme Court declined to stop it Friday.

Jack LaPointe, 47, was convicted of aggravated robbery and aggravated assault for the Oct. 30, 2000, robbery of a Payless Shoe Source in a Roeland Park strip mall. The robbery, committed with a sawed-off shotgun, yielded $1,000.

LaPointe was sentenced to 245 months in prison for the crime. In 2007, about seven years later, his attorney, Richard Ney, requested DNA testing be completed. Ten years later, the legal dispute continues.

Though a Kansas statute allows for post-conviction DNA testing only in cases of murder and rape, Ney argued his clients long sentence warranted testing. Johnson County District Court Judge Kevin Moriarty agreed and granted DNA testing. Prosecutors appealed to the Kansas Court of Appeals, which upheld the order, and the Kansas Supreme Court, which also upheld the order in an opinion Friday.

The question before the high court was whether the state could challenge Moriartys order, which was not a final order, and stop the DNA testing. The court ruled unanimously that the state fails to persuade us that a final order has been entered and dismissed the prosecutions appeal.

We conclude the state had no statutory right to appeal the (DNA testing) order and the Court of Appeals correctly determined it lacked jurisdiction to hear the merits of the case, wrote Justice Marla Luckert.

The opinion says nothing about LaPointes guilt or innocence but allows for DNA testing that LaPointes defenders believe could exonerate him. A website FreeJackLaPointe.com has been established for that purpose.

Court documents show the states case against LaPointe lacked physical evidence. Some forensic evidence collected at the scene was inconclusive. Hairs found at the scene likely did not come from LaPointe, an expert testified.

A career criminal in FBI custody who testified against LaPointe, claiming they committed the crime together, had 10 prior convictions for dishonesty or false statements. Two witnesses failed to conclusively recognize LaPointe in a photo lineup. Eyewitness reports indicated the robber was slender but LaPointe weighed 240 pounds.

LaPointes girlfriend, who he later married, said he was at home eating Halloween candy with her daughter at the time of the robbery.

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Kansas Supreme Court allows DNA testing in 2000 robbery case - Hutchinson News