Category Archives: Transhuman News

The mummified body of Minirdis, a 14-year-old Egyptian boy, and his burial mask, pictured at the Field Museum in Chicago in 2014 after researchers opened the coffin for the first time.

AP

Modern Egyptians have more DNA from sub-Saharan Africa than mummies entombed in their country, according to the first genome data on mummies.

The findings are helping researchers gauge the impact of history on Egyptians' genetics.

The international team of researchers analyzed DNA from 151 mummies from the archaeological site of Abusir el-Meleq. The site is along the Nile River in Middle Egypt. The mummies date from about 1400 B.C. to 400 A.D.

Genetic studies of ancient Egyptian mummies are rare due to a number of issues.

"The hot Egyptian climate, the high humidity levels in many tombs and some of the chemicals used in mummification techniques contribute to DNA degradation and are thought to make the long-term survival of DNA in Egyptian mummies unlikely," said study senior author Johannes Krause. He is director at the Max Planck Institute for the Science of Human History in Germany.

13 Photos

California museum exhibit displays pets preserved for all time in ancient Egypt

This team's success in extracting and analyzing nuclear DNA from mummies is a breakthrough that opens the door to further direct study of mummified remains in order to get a better understanding of Egypt's population history, the study authors explained in an institute news release.

The researchers' goal was to find out if ancient Egyptian populations were affected at the genetic level by foreign conquest and domination during the time period in the study.

According to study co-lead author Verena Schuenemann, of the University of Tuebingen, Germany, the research team "wanted to test if the conquest of Alexander the Great and other foreign powers has left a genetic imprint on the ancient Egyptian population."

Wolfgang Haak, group leader at the Max Planck Institute, said, "The genetics of the Abusir el-Meleq community did not undergo any major shifts during the 1,300-year timespan we studied, suggesting that the population remained genetically relatively unaffected by foreign conquest and rule."

Modern Egyptians share about eight percent more ancestry on the nuclear level with sub-Saharan African populations than with ancient Egyptians, the investigators found.

Stephan Schiffels, also at the Max Planck Institute, concluded that the finding "suggests that an increase in sub-Saharan African gene flow into Egypt occurred within the last 1,500 years."

The study was published May 30 in the journalNature Communications.

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The first genome data from ancient Egyptian mummies is in - CBS News

Researchers have finished the first full genome map of the threatened Mojave desert tortoise (Gopherus agassizii), also known as Agassizs desert tortoise.

Kenro Kusumi with Arizona State Universitys School of Life Sciences said the team hopes the data will aid conservation efforts, fill in blanks in the reptiles evolutionary history and perhaps offer clues to improving human health and longevity.

For diseases, were certainly interested in what makes them susceptible, the connection we study this in humans, too between their diet and their environment and their stresses, and their ability to fight off diseases," said Kusumi.

The research was published May 31 in PLOS ONE.

Mojave desert tortoises face threats from various quarters. Invasive grasses like red brome can stunt their early growth and may reduce their resistance to illnesses including upper respiratory tract disease (URTD), which afflicts the nose, nasal sinuses and trachea of some of the creatures. Humans threaten their survival by destroying habitat and building power lines, which provide new perches for predatory ravens.

Its a new habitat for the ravens. Its great for them, but its bad for baby tortoises, which they like to look at and then swoop down and eat, said Kusumi.

Based on comparisons with other existing reptile genomes, the study found changes in Mojave desert tortoise genes that regulate shell development, longevity and water conservation.

They also found that, among three desert tortoises (Mojave desert tortoise, Sonoran desert tortoise and Goodes Thornscrub tortoise), evolutionary forces seem to have differentiated protein sequences related to circadian rhythm the daily cycle of physiological and behavioral processes and the innate immune system.

The U.S. Fish and Wildlife Service listed the Mojave population that is located north and west of the Colorado River as threatened in 1990. Nevertheless, its numbers declined by about 50 percent from 2004 to 2013.

Understanding genetic variation and responses could help wildlife managers better grasp how disease and inbreeding affect the reptiles. Kusumi said it could also help scientist understand how the creatures adapt to their environs by isolating genes related to withstanding ultraviolet radiation and controlling urine volume.

We dont really know where the genetic treasure in the gold mine is. Where is the diversity that would allow the tortoise, as a species, to survive changes? said Kusumi.

A clearer picture of Mojave desert tortoises genetics and biodiversity could also improve management of reproduction and maintenance of habitat corridors, particularly under conditions of climate change. It would also help nail down the species geographical range, which overlaps with the Sonoran desert tortoise, aka Morafka's desert tortoise (Gopherus morafkai). The two desert tortoises sometimes mix boundaries and interbreed.

Were trying to answer, based on using the genome, where is the Mojave desert tortoise? Because we actually dont know exactly where that boundary is right now, said Kusumi.

Mojave desert tortoises live 40-50 years in the wild and more than 100 years in captivity. Dark green, with brown and yellow accents, they have rounded shells, stubby hind legs and flat front limbs built for digging. They occur in western Arizona, southern Nevada, Southern California and southwestern Utah. Kusumi said genetics could also offer clues as to how the species can live in such a diverse range of environments.

If you moved one from, say, Las Vegas to Southern California, it probably wouldnt do very well, because thats not the environment that its genome is making it suited for," he said. "So, within that species, wed love to know the genetic instructions that make a tortoise better suited for one place versus another.

See the article here:
Team Maps Genome of Mojave Desert Tortoise - AZPM - Arizona Public Media

Jennifer A. Doudna & Samuel H. Sternberg Houghton Mifflin: 2017. ISBN: 9780544716940

Buy this book: US UK Japan

Graeme Mitchell/Redux/Eyevine

Jennifer Doudna helped to uncover the CRISPRCas gene-editing system.

The prospect of a memoir from Jennifer Doudna, a key player in the CRISPR story, quickens the pulse. And A Crack in Creation does indeed deliver a welcome perspective on the revolutionary genome-editing technique that puts the power of evolution into human hands, with many anecdotes and details that only those close to her may have known. Yet it does not provide the probing introspection, the nuanced ethical analysis, the moral counterpoint that we CRISPR junkies crave.

After the race for discovery comes the battle for control of the discovery narrative. The stakes for the CRISPRCas system are extraordinarily high. In February, the US Patent and Trademark Office ruled against Doudna and the University of California, Berkeley. It found that a patent on the application of CRISPR to eukaryotic cells filed by Feng Zhang of the Broad Institute of MIT and Harvard in Cambridge, Massachusetts did not interfere with Berkeley's more sweeping patent on genetic engineering with CRISPR.

Although that battle is over, the war rages on. Berkeley has already appealed against the decision; meanwhile, the European Patent Office has ruled in favour of Doudna and Berkeley. Doubtless there are many more patents to milk out of this versatile system. And then there's the fistful of 66-millimetre gold medals they give out in Stockholm each year.

So far, the Broad Institute has controlled the CRISPR narrative. Rich in funds and talent, the Broad melds sleek, high-tech sexiness with a sense of East Coast, old-money privilege. Last year, institute director Eric Lander published a now-infamous piece entitled 'The heroes of CRISPR' (E.Lander Cell 164, 1828; 2016). It adopted a tone of magnanimity, crediting Lithuanian biochemist Virginijus Siksnys with observing early on that his findings pave the way for engineering of universal programmable RNA-guided DNA endonucleases, and Doudna and her CRISPR co-discoverer Emmanuelle Charpentier with noting the potential to exploit the system for RNA-programmable genome editing.

Lander's clear implication was that they were laying the groundwork; Zhang's group got CRISPR over the finish line. To many of us, such tactics made Team Broad look like the villains of CRISPR.

Doudna's book was a chance to deliver a righteous knockout blow. Instead, we get a counter-narrative just as constructed as Lander's article. It is written entirely in the first person; co-author Samuel Sternberg, a former student in the Doudna lab, barely surfaces.

In that counter-narrative, Doudna had always been interested in gene editing. Her early work was on RNA enzymes, or ribozymes. She developed an impeccable pedigree, doing her PhD with Jack Szostak at Harvard and a postdoc with Tom Cech at the University of Colorado Boulder, before joining the faculty at Yale University in New Haven, Connecticut. From the mid-1990s, she writes, she was exploring the basic molecular mechanisms that would be able to unlock the full potential of gene editing.

Her work on CRISPR dates to 2006 six years before the key papers were published and a call from Berkeley geomicrobiologist Jillian Banfield. Over coffee, Banfield described the clustered, regularly interspaced, short palindromic repeats that kept popping up in her DNA databases of bacteria and archaea. The sequences were ubiquitous among these prokaryotes, but unique to each species. This realization sent a little shiver of intrigue down my spine, Doudna writes. If CRISPR was so widespread, there was a good chance that nature was using it to do something important. By 2012, she and her co-workers had characterized the natural CRISPR system, harnessed it as a laboratory tool and developed a modified system that was programmable, cheap and easy to use.

The middle of the book reels off the obligatory breathless list of potential uses, generating everything from malaria-free mosquitoes and police dogs with muscles like Vin Diesel to the canonical cure for cancer. Thankfully, Doudna counterweights sensationalism with a sober accounting of the risks and responsibilities of applications such as altering the genomes of entire populations of organisms with 'gene drives'. In 2015, she sustained doubts about CRISPR ever being safe enough for clinical trials, but she has come to embrace editing of the human germ line inheritable DNA modification once it is proved safe.

But the discussion is ultimately unsatisfying. When it is time to grapple with tricky ethical issues, such as human experimentation, she baulks, unspooling instead a series of rhetorical questions. Rather than guiding us through the ethical thickets of precision genetic engineering, or providing a candid, warts-and-all look at one of the great scientists of our time, the book mainly polishes her 'good scientist' image and rationalizes the unfettered self-direction of human evolution, within liberal bounds of safety, efficacy and individual choice.

Rather than dispel the cartoon-character feel of this epic battle, Doudna elaborates on it. She presents us with a persona so flawless that it seems more concealing than revealing. She waves away the bloody patent fight as a disheartening twist in the story, but the entire biomedical world knows that it was much more. As I read A Crack in Creation, I was reminded of Benjamin Franklin's benevolent man, who, he wrote, should allow a few faults in himself, to keep his friends in countenance and, I would add, to give him- or herself more depth.

The narrative often substitutes melodrama for dramatic tension. A conference in Puerto Rico sees Charpentier and Doudna strolling the cobbles of Old San Juan, with Charpentier saying earnestly, I'm sure that by working together we can figure out the activity of what became the Cas enzyme. I felt a shiver of excitement as I contemplated the possibilities of this project, Doudna writes. When first wrestling with the ethical dilemmas of gene editing, she dreams of meeting Adolf Hitler, who demands to know the secrets of her technique. She wakes, of course, freshly determined to ensure that CRISPR is not put to nefarious use.

The larger purpose of A Crack in Creation, clearly, is to show that Doudna is the true hero of CRISPR. And ultimately, despite the book's flaws, I'm convinced. Nominators and the Nobel Committee will need to read this book. But CRISPR binge-watchers like me still await a truly satisfying account one that is insightful, candid and contextualized.

The rest is here:
That's the way the CRISPR crumbles - Nature.com

The Memorial Sloan Kettering Cancer Center (MSK) and Philips will exploit the latters IntelliSpace Genomics platform through their research collaboration to develop new genome analysis methods and informatics approaches for diagnosing pancreatic cancer and aiding personalized therapeutics. The collaboration will employ large-scale next-generation sequencing to generate new insights into the drivers of pancreatic cancer at the single-cell level, with the goal of enabling more precise diagnosis so that patients can be prescribed optimum treatments that target the cause of their disease.

Philips' IntelliSpace Genomics platform has been developed to support the implementation and scaling of informatics-heavy precision medicine research. "Collaborating with MSK and its experts will allow us to take a unique approach to diagnosing and treating this devastating disease, commented Henk van Houten, Ph.D., CTO at Philips. Leveraging the advanced capabilities of the Philips IntelliSpace Genomics solution we can gain new insights into the origin, development, and optimal treatment of pancreatic cancer and share these insights broadly with care providers to help improve outcomes for patients. Our ultimate goal is to translate these findings into more precise diagnostics and therapeutics to battle this devastating disease."

Philips and MSK have previously established a research collaboration in the field of radiation oncology. Just yesterday, MSK and Mabvax Therapeutics signed a research agreement to develop chimeric antigen receptor (CAR) T-cellimmunotherapies for pancreatic and small-cell lung cancer.

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Philips, MSK Partner on Genome Analytics for Prostate Cancer Precision Medicine - Genetic Engineering & Biotechnology News

By Ian Haydon 3 minute Read

A new research paper is stirring up controversy among scientists interested in using DNA editing to treat disease.

In a two-page article published in the journal Nature Methods on May 30, a group of six scientists report an alarming number of so-called off-target mutations in mice that underwent an experimental gene repair therapy.

CRISPR, the hot new gene-editing technique thats taken biology by storm, is no stranger to headlines. What is unusual, however, is a scientific article so clearly describing a potentially fatal shortcoming of this promising technology.

The research community is digesting this newswith many experts suggesting flaws with the experiment, not the revolutionary technique.

The research team sought to repair a genetic mutation known to cause a form of blindness in mice. This could be accomplished, they showed, by changing just one DNA letter in the mouse genome.

They were able to successfully correct the targeted mutation in each of the two mice they treated. But they also observed an alarming number of additional DNA changesmore than 1,600 per mousein areas of the genome they did not intend to modify.

The authors attribute these unintended mutations to the experimental CRISPR-based gene-editing therapy they used.

Cas9, the CRISPR enzyme that snips DNA, in contact with its target. [Graph: via rcsb.org]A central promise of CRISPR-based gene editing is its ability to pinpoint particular genes. But if this technology produces dangerous side effects by creating unexpected and unwanted mutations across the genome, that could hamper or even derail many of its applications.Several previous research articles have reported off-target effects of CRISPR, but far fewer than this group found.

The publicly traded biotech companies seeking to commercialize CRISPR-based gene therapiesEditas Medicine, Intellia Therapeutics, and Crispr Therapeuticsall took immediate stock market hits based on the news.

Experts in the field quickly responded.

Either the enzyme is acting at near optimal efficiency or something fishy is going on here, tweeted Matthew Taliaferro, a postdoctoral fellow at MIT who studies gene expression and genetic disease.

The Cas9 enzyme in the CRISPR system is what actually cuts DNA, leading to genetic changes. Unusually high levels of enzyme activity could account for the observed off-target mutationsmore cutting equals more chances for the cell to mutate its DNA. Different labs use slightly different methods to try to ensure the right amount of cuts happen only where intended.

Gatan Burgio, whose laboratory at the Australian National University is working to understand the role that cellular context plays on CRISPR efficiency, believes the papers central claim that CRISPR caused such an alarming number of off-target mutations is not substantiated.

Burgio says there could be a range of reasons for seeing so many unexpected changes in the mice, including problems with accurately detecting DNA variation, the extremely small number of mice used, random events happening after Cas9 acted, or, he concedes, problems with CRISPR itself.

Burgio has been editing the DNA of mice using CRISPR since 2014 and has never seen a comparable level of off-target mutation. He says hes confident that additional research will refute these recent findings.

Although the news of this two-mouse experiment fired up the science-focused parts of the Twittersphere, the issue it raises is not new to the field.

Researchers have known for a few years now that off-target mutations are likely given certain CRISPR protocols. More precise variants of the Cas9 enzyme have been shown to improve targeting in human tissue in the lab.

Researchers have also focused on developing methods to more efficiently locate off-target mutations in the animals they study.

As scientists continue to hone the gene-editing technique, we recognize theres still a way to go before CRISPR will be ready for safe and effective gene therapy in humans.

Ian Haydon is a doctoral student in Biochemistry at the University of Washington. This story originally appeared at The Conversation.

More:
Unraveling The Controversy Over The CRISPR Mutations Study - Fast Company