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Archive for the ‘Crispr’ Category

Trump Pulls US From Climate Agreement, CRISPR Human Trials, And A NASA Sun Orbiter – Science Friday

Skip to content On November 4 2016, the Eiffel Tower was illuminated in green to celebrate the entry into the Paris Agreement. Credit: U.S. Department of State

This week, President Trump pulled the U.S. from the Paris Climate Agreement, which 195 countries had signed in 2015, pledging to reduce greenhouse emissions. Trump said that the agreement imposed draconian financial burdens on the U.S. and that he would negotiate for a deal that is fair. Maggie Koerth-Baker, senior science reporter at Fivethirtyeight.com, fills us in on the announcement. Plus, she talks about new CRISPR clinical trials, and NASAs Parker Probe Plus, a mission to explore the sun.

[What happens if the U.S. leaves the Paris climate deal?]

Maggie Koerth-Baker

Maggie Koerth-Baker is a senior science reporter with FiveThirtyEight.com.Shes based inMinneapolis, Minnesota.

Alexa Lim is a producer for Science Friday. Her favorite stories involve space, sound, and strange animal discoveries.

One way is fast and dramatic. The other is slower and leaves wiggle room.

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Trump Pulls US From Climate Agreement, CRISPR Human Trials, And A NASA Sun Orbiter - Science Friday

CRISPR Gene Drives May Not Be As Effective As Once Hoped – Technology Networks

Michael J. Wade. Credit: James Brosher, IU Communications

Researchers are exploring the use of the revolutionary gene-editing tool CRISPR-Cas9 to fight human disease and agricultural blight. But a study from Indiana University has found several challenges to the method's use in saving lives and crops.

The research, reported today in the journal Science Advances, combines advanced genetic and statistical analyses to show how certain genetic and behavioral qualities in disease-carrying insects, like mosquitoes, make these species resistant to genetic manipulation.

This resistance could complicate attempts to use CRISPR-Cas9 in the fight against malaria -- a deadly mosquito-borne disease that threatens over 3 billion people worldwide -- or crop blights such as the western corn rootworm, an invasive species that costs the U.S. about $1 billion in lost crops each year.

The discovery of the CRISPR-Cas9 system -- or simply "CRISPR" -- in the early 2010s introduced an unprecedented level of accuracy in genetic editing. Scientists can use the method to design highly precise genetic "scissors" that snip out and replace specific parts of the genome with sequences of their choosing. Two English scientists were the first to show the method could spread infertility in disease-carrying mosquitoes in late 2015.

"We found that small genetic variation within species -- as well as many insects' tendency to inbreed -- can seriously impact the effectiveness of attempts to reduce their numbers using CRISPR technology," said Michael J. Wade, Distinguished Professor of Biology at IU Bloomington. "Although rare, these naturally occurring genetic variants resistant to CRISPR are enough to halt attempts at population control using genetic technology, quickly returning wild populations to their earlier, 'pre-CRISPR' numbers."

This means costly and time-consuming efforts to introduce genes that could control insect populations -- such as a trait that causes female mosquitoes to lay fewer eggs -- would disappear in a few months. This is because male mosquitoes -- used to transmit new genes since they don't bite -- only live about 10 days.

The protective effect of naturally occurring genetic variation is strong enough to overcome the use of "gene drives" based on CRISPR-based technology -- unless a gene drive is matched to the genetic background of a specific target population, Wade added. Gene drives refer to genes that spread at a rate of nearly 90 percent -- significantly higher than the normal 50 percent chance of inherence that occurs in sexually reproducing organisms.

Wade, an expert in "selfish genes" that function similarly to gene drives due to their "super-Darwinian" ability to rapidly spread throughout a population, teamed up with colleagues at IU -- including Gabriel E. Zentner, an expert in CRISPR-based genetic tools and assistant professor in the Department of Biology -- to explore the effectiveness of CRISPR-based population control in flour beetles, a species estimated to destroy 20 percent of the world's grain after harvest.

The team designed CRISPR-based interventions that targeted three segments in the genome of the flour beetle from four parts of the world: India, Spain, Peru and Indiana. They then analyzed the DNA of all four varieties of beetle and found naturally occurring variants in the targeted gene sequence, the presence of which would impact the effectiveness of the CRISPR-based technology.

The analysis revealed genetic variation in all four species at nearly every analyzed DNA segment, including a variance rate as high as 28 percent in the Peruvian beetles. Significantly, Wade's statistical analysis found that a genetic variation rate as low as 1 percent -- combined with a rate of inbreeding typical to mosquitos in the wild -- was enough to eliminate any CRISPR-based population-control methods in six generations.

The results suggest that a careful analysis of genetic variation in the target population must precede efforts to control disease-carrying insects using CRISPR technology. They also suggest that the unintended spread of modified genes across the globe is highly unlikely since typical levels of genetic variation place a natural roadblock on spread between regions or species.

"Based on this study, anyone trying to reduce insect populations through this method should conduct a thorough genetic analysis of the target gene region to assess variation rates," Wade said. "This will help predict the effectiveness of the method, as well as provide insight into ways to circumvent natural genetic variation through the use of Cas9 variants with an altered sequence specificity."

This article has been republished frommaterialsprovided by Indiana University. Note: material may have been edited for length and content. For further information, please contact the cited source.

Reference

Drury, D. W., Dapper, A. L., Siniard, D. J., Zentner, G. E., & Wade, M. J. (2017). CRISPR/Cas9 gene drives in genetically variable and nonrandomly mating wild populations. Science Advances, 3(5), e1601910.

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CRISPR Gene Drives May Not Be As Effective As Once Hoped - Technology Networks

A World First CRISPR Trial Will Edit Genes Inside the Human Body – Futurism

In Brief The CRISPR process will be used inside the human body for the first time on July 15th to combat HPV, which impacts millions of people worldwide. And this is just one of a huge amount of proposed CRISPR studies occurring soon. Uninvasive CRISPR

A new CRISPR trial, which hopes to eliminate thehuman papillomavirus (HPV), is set to be the first to attempt to use thetechnique inside the human body. In the non-invasive treatment, scientists will apply a gel that carries the necessary DNA coding for the CRISPR machinery to the cervixes of 60 women between the ages of 18 and 50. The team aims to disable the tumor growth mechanism in HPV cells.

The trial stands in contradistinction to the usual CRISPR method of extracting cells and re-injecting them into the affected area; although it will still use the Cas9 enzyme (which acts as a pair of molecular scissors) and guiding RNA that is typical of the process.

20 trials are set to begin in the rest of 2017 and early 2018. Most of the research will occur in China, and will focus on disabling cancers PD-1 gene that fools the human immune system into not attacking the cells. Different trials are focusing on different types of cancer including breast, bladder, esophageal, kidney, and prostate cancers.

The study, if it succeeds, will be promising for sufferers of HPV and act as a milestone in the CRISPR process. Although HPV is not necessarily cancerous, it cancause cervical cancer. In the U.S. alone, there are more than 3 million new infections every year.Although there is a vaccine for the virus, currently, once you have it you can never get rid of it.

More generally, the CRISPR process could be nothing short of a miracle: if it passes all medical tests it wouldnt just make medicine a whole new kettle of fish, it would reinvent the kettleand the fish, for almost any field. It is cheaper than other gene editing therapies, and could potentially save millions of lives by curing diseases we can only deal with therapeutically like cancer, diabetes and cystic-fibrosis. Crops could be altered more effectively using the process. Drugs and materials that were never possible before could be pioneered.

However, it is still extremely nascent technology, and many fear that there could also be a host of unexpected consequences. Recently, it has been found that it causes hundreds of unexpected mutations in DNA. While these concerns are valid, more research is necessary. Which is why the upcoming studies over the next few years are so vital to the future of our health.

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A World First CRISPR Trial Will Edit Genes Inside the Human Body - Futurism

I bio-engineered glowing beer and it hasn’t killed me (yet) – Engadget – Engadget

Bacteria genomes have repeating sequences of DNA with bits of other DNA sandwiched between them. These are the "clustered regularly interspaced short palindromic repeats" that give CRISPR its name. What scientists eventually discovered is that those sequences of unique DNA, in between the repeating bits, matched the DNA of viruses. Basically, it's a gallery of Bacteria's Most Wanted.

A set of enzymes called CRISPR-associated proteins, or Cas for short, looks for these bits of DNA as a way to identify danger when an intruder is detected. When a virus is spotted, the proteins act like assassins, snipping out those offending bits of DNA, rendering the virus harmless. More important, it turns out, you can basically train these Cas proteins to look for any sequence of DNA you want. Then they can replace it with another piece of genetic code.

This all sounds pretty complicated, but you can actually do it in your kitchen with a $160 kit from a company called The Odin. The particular kit I used includes everything you need to make baking or brewing yeast glow green under a black light.

To start, I prepared a whole bunch of agar plates -- petri dishes filled with a nutrient-rich gel for the yeast to grow on. Then I had to wake up my dried French Saison yeast with a little bit of water and "streak" the little guys out on the plates and put aside for about 24 hours to let them grow.

Once the yeast was healthy and I had full cultures, it was time to prep them for their transformation. I introduced them to a solution of chemicals and salts that weakened the cell walls so that our new DNA can enter more easily. Then it was time to introduce the plasmid (a small molecule of DNA) carrying the genes I want the yeast to adopt. The genetic code introduced in this case tells the yeast to produce green fluorescent protein, which is what causes it to glow. Basically, we're tricking the yeast into thinking the DNA we introduced is its own so that it makes the Cas proteins that will cut out the parts we want to replace.

Once it's all combined, the mixture gets incubated in a warm water bath for about an hour, before adding nutrients to the solution and putting the whole thing back in a warm-water bath for another four hours. This gives the yeast time to recover and replicate the DNA that will make it fluoresce. Then it's time to streak the modified yeast on some new agar plates and wait again for them to grow into thriving colonies.

A few days later, I had yeast that glowed green under a black light.

Now, a petri dish worth of yeast isn't nearly enough to brew a beer with. So I had to make a starter -- a weak proto-beer on which the yeast can feast and build its strength. Eventually, I had a 1 liter Erlenmeyer flask filled with fluorescent French Saison yeast.

Brewing beer itself is pretty straightforward but here's the TL;DR version of how it works: Grains, such as barley, are steeped in hot water to extract their sugars. This creates a liquid called wort, which is then boiled to sterilize it, break down and remove unwanted proteins, and extract flavors from additives like hops -- the little green cones that deliver all that lovely beer flavor and aroma.

Then the wort is cooled and the yeast is added, and it becomes a waiting game. The yeast eats away at the sugar, converting it to carbon dioxide and delicious, delicious alcohol.

The results of my grand experiment were successful ... ish.

The yeast certainly glowed and the first couple of samples pulled from the fermenter did as well. But, as the beer settled and the yeast dropped out of my brew, the glow became fainter and fainter. By the end, it was a pale glimmer rather than a blinding glare.

At the end of the day, my glowing beer was a strange novelty; it's merely meant to show off the power and simplicity of CRISPR. It's a technology that could one day lead to a cure for diseases like sickle cell or AIDS, or be used to breed drought-resistant plants. But that's still a ways off. Right now, CRISPR is in its infancy, so I'll just have to settle for yeast that can brew unique-looking (if not particularly unique-tasting) beer.

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I bio-engineered glowing beer and it hasn't killed me (yet) - Engadget - Engadget

Scientists have used CRISPR to slow the spread of cancer cells … – ScienceAlert

CRISPR-Cas9 is the gene editing tool that promised to change the world.

In the short time since its discovery, it has snipped HIVout of human immune cells, sparked a biomedical race between the US and China to work towardbioengineered humans, and now scientists have used CRISPR-Cas9 to slow the spread of cancer.

Every living cell goes through a reproduction cycle, known as the 'cell cycle' a sequence of events that result in cell growth and division.

When this cycle gets out of hand, it becomes a serious and life-threatening problem.Once a cell becomes cancerous it will divide without stopping and quickly invade surrounding the tissue.

And trying to stop cancer is no easy feat. Scientists have used a range of approaches to try to stop it from forming and spreading.

A previous study has turned the body's own immune systemagainst cancer cells, and another team of researchers has created an artificial organthat can pump out cancer-fighting T-cells.

We've even worked out a way to cause particularly aggressiveforms of cancer to self-destruct.

In the latest study, scientists from the University of Rochester have interrupted the cell cycle by targeting a protein responsible for preparing the cell for division, called Tudor-SN.

Tudor-SN influences the cell cycle by controlling microRNA, which are the molecules that fine tune the expression of thousands of genes.

"We know that Tudor-SN is more abundant in cancer cells than healthy cells, and our study suggests that targeting this protein could inhibit fast-growing cancer cells," says lead researcher,Reyad A. Elbarbary.

When Tudor-SN was removed from human cells, using CRISPR-Cas9, the level of microRNAs increases.

With more microRNAs in the mix, it slows down the genes that encourage cell growth. With these genes hindered, the cell transitions slowly to the cell division phase of the cell cycle.

The researchers used this approach to slow the growth of kidney and cervical cancer cells.

"Because cancer cells have a faulty cell cycle, pursuing factors involved in the cell cycle is a promising avenue for cancer treatment," said Lynne E. Maquat, senior researcher on the paper.

The next step for the research is to work out how Tudor-SN functions in combination with other molecules and proteins. That way, scientists may be able to identify the most appropriate drugs to target it.

While the researchers admit that they have a long way to go before we see this technology being used in humans, any new approach that could provide a cure to the millions ofpeople living with cancer is always welcome.

The findings have been reported in Science.

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Scientists have used CRISPR to slow the spread of cancer cells ... - ScienceAlert

CRISPR stocks sank on news the gene editing tool can veer off target. But that’s hardly news – STAT

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CRISPR stocks sank on news the gene editing tool can veer off target. But that's hardly news - STAT

Unraveling The Controversy Over The CRISPR Mutations Study – Fast Company

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.

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Unraveling The Controversy Over The CRISPR Mutations Study - Fast Company

Increasing Wheat Yields with CRISPR – Technology Networks

Associate biology and microbiology professor Wanlong Li assesses the growth of two-week-old wheat seedlings. Credit: South Dakota State University

Larger, heavier wheat kernelsthats how associate professor Wanlong Li of the SDSU Department of Biology and Microbiology seeks to increase wheat production. Through a three-year, $930,000 U.S. Department of Agriculture grant, Li is collaborating with Bing Yang, an associate professor in genetics, development and cell biology at Iowa State, to increase wheat grain size and weight using a precise gene-editing tool known as CRISPR/Cas9.

South Dakota State is one of seven universities nationwide to receive funding to develop new wheat varieties as part of the National Institute of Food and Agricultures International Wheat Yield Partnership (IWYP) Program. The program supports the G20s Wheat Initiative, which seeks to enhance the genetics related to yield and develop varieties adapted to different regions and environmental conditions.

The goal of IWYP, which was formed in 2014, is to increase wheat yields by 50 percent in 20 years. Currently, the yearly yield gain is less than1 percent, but to meet the IWYP goal wheat yields must increase 1.7 percent per year. Its a quantum leap, he said. We need a lot of work to reach this.

Humans consume more than 500 million tons of wheat per year, according to Li. However, United States wheat production is decreasing, because farmers can make more money growing other crops. He hopes that increasing the yield potential will make wheat more profitable.

First, the researchers will identify genes that control grain size and weight in bread wheat using the rice genome as a model.

The CRISPR editing tool allows the researchers to knockout each negatively regulating gene and thus study its function, according to Li. CRISPR is both fast and precise, he added. It can produce very accurate mutations.

This technique will be used to create 30 constructs that target 20 genes that negatively impact wheat grain size and weight. From these, the University of California Davis Plant Transformation Facility, through a service contract, will produce 150 first-generation transgenic plants and the SDSU researchers will then identify which ones yield larger seeds. One graduate student and a research assistant will work on the project.

The end products are not genetically modified organisms, Li emphasized. When we transfer one of the CRISPR genes to wheat, its transgenic. That then produces a mutation in a different genomic region. When the plants are then self-pollinated or backcrossed, the transgene and the mutation are separated.

The researchers then screen the plants to select those that carry the desired mutations. This is null transgenic, Li said, noting USDA has approved this process in other organisms. Yang used this technique to develop bacterial blight-resistant rice.

As part of the project, the researchers will also transfer the mutations into durum wheat. Ultimately, these yield-increasing mutations, along with the markers to identify the traits, can be transferred to spring and winter wheat.

This article has been republished frommaterialsprovided by South Dakota State University. Note: material may have been edited for length and content. For further information, please contact the cited source.

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Increasing Wheat Yields with CRISPR - Technology Networks

CRISPR controversy raises questions about gene-editing technique – Joplin Globe

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 news with 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 changes more than 1,600 per mouse in 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.

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 therapies Editas Medicine, Intellia Therapeutics and Crispr Therapeutics all 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 mutations more 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.

Unusual methods were used, https://twitter.com/LluisMontoliu/status/869705549453119489">tweeted Lluis Montoliu, who runs a lab at the Spanish National Centre for Biotechnology that specializes in editing mice genes using CRISPR. He believes the authors used suboptimal molecular components in their injected CRISPR therapies specifically a plasmid that causes cells to produce too much Cas9 enzyme likely leading to the off-target effects they observed.

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 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.

This article was originally published on The Conversation. Read the original article.

Ian Haydon does not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and has disclosed no relevant affiliations beyond the academic appointment above.

See the original post here:

CRISPR controversy raises questions about gene-editing technique - Joplin Globe

That’s the way the CRISPR crumbles – Nature.com

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.

Link:

That's the way the CRISPR crumbles - Nature.com

CRISPR controversy raises questions about gene-editing technique – The Conversation US

Laboratory mice are among the first animals to have their diseases treated by CRISPR.

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 news with 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 changes more than 1,600 per mouse in 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.

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 therapies Editas Medicine, Intellia Therapeutics and Crispr Therapeutics all 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 mutations more 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.

Unusual methods were used, tweeted Lluis Montoliu, who runs a lab at the Spanish National Centre for Biotechnology that specializes in editing mice genes using CRISPR. He believes the authors used suboptimal molecular components in their injected CRISPR therapies specifically a plasmid that causes cells to produce too much Cas9 enzyme likely leading to the off-target effects they observed.

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 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.

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CRISPR controversy raises questions about gene-editing technique - The Conversation US

CRISPR’s Next Target: Wheat Kernels – Laboratory Equipment – Laboratory Equipment

While were most enamored with CRISPRs ability to edit human genomes, the powerful tool is not selectiveit can edit other genomes as well. In one such study, researchers are using CRISPR to expand the size and weight of wheat kernels in the hope of increasing overall wheat yield.

Although humans consume more than 500 million tons of wheat per year, overall production is decreasing as farmers continue to move toward crops that are more profitable. Increasing yield is one way to ensure wheat becomes a desirable, profitable crop again. But, that takes some genetic manipulation.

Fundamentally, this can be achieved by improving wheats photosynthesis. For example, wheat uses less than 1 percent of sunlight to produce the parts we eat, compared to maizes 4 percent efficiency and sugarcanes 8 percent efficiency. Even increasing wheats photosynthetic efficiency from 1 percent to 1.5 percent would allow farmers to increase their yields on the same amount of land, using no more water, fertilizer or other inputs.

Through a new Department of Agriculture grant and working with the International Wheat Yield Partnership Program, South Dakota State Universitys Wanlong Li and Iowa States Bing Yang seek to apply CRISPR to wheats photosynthesis problem.

First, the researchers will identify the genes that control grain size and weight in bread wheat using a rice genome model. Then, they will use CRISPR to edit out each negatively regulating genewhich will serve the two-fold purpose of removing it from the genome, as well as having it available to study.

Li and Yang will create 30 constructs that target 20 negative genes. Partners from the University of California Davis Plant Transformation Facility will then produce 150 first-generation plants for the researchers to study. When all is said and done, the researchers should be able to identify which mutations yield larger seedsand thus, increased yields.

One of the benefits of this process is the end product will not be considered genetically modified organisms.

When we transfer one of the CRISPR genes to wheat, its transgenic. That then produces a mutation in a different genomic region. When the plants are then self-pollinated or backcrossed, the transgene and the mutation are separated, Li explained. This is null transgenic.

In fact, the USDA has approved this technique in other organisms, and Yang has already utilized it in unrelated research to develop bacterial blight-resistant rice.

Ultimately, these yield-increasing mutations, along with the markers to identify the traits, can be transferred to other varieties of wheat, such as durum, spring and winter wheat.

South Dakota State University is one of seven universities nationwide to receive funding to develop new wheat varieties as part of the National Institute of Food and Agricultures International Wheat Yield Partnership Program. Lis focus on CRISPR and photosynthesis efficiency is just one approach to the problem. Other research projects from the organization include: testing genes to boost spike development; optimizing canopy architecture to increase carbon capture and conserve nitrogen; and using selected genes from other species to increase biomass and yield, among others.

A distinguishing feature of the International Wheat Yield Partnership Program is its huba massive parcel of land in Mexico that is used for the evaluation of innovations, and subsequent development pipeline.

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CRISPR's Next Target: Wheat Kernels - Laboratory Equipment - Laboratory Equipment

CRISPR Gene-Editing Can Cause Hundreds of Unexpected … – ScienceAlert

It's been hailed as one of the most potentially transformative inventions in modern medicine, bringing the prospect of designer babies closer than any other technology to date, but CRISPR-Cas9 could be riskier than we thought.

The technology that could spark a gene-editing revolution has been caught introducing hundreds of unintended mutations into the genome, and with scientistsalready testing it in humans, it's set off some serious alarm bells.

"We feel it's critical that the scientific community consider the potential hazards of all off-target mutations caused by CRISPR, including single nucleotide mutations and mutations in non-coding regions of the genome," says Stephen Tsang from the Columbia University Medical Centre.

Tsang and his team have conducted the first whole-genome screening of a living organism that's undergone CRISPR gene-editing to discover that unwanted mutations can crop up in areas that are totally unrelated to the targeted genes.

These mutations have likely been missed by previous studies because they've been using computer algorithms that are designed to identify and scan areas on the genome that are most likely to be affected, based on what's been edited.

"These predictive algorithms seem to do a good job when CRISPR is performed in cells or tissues in a dish, but whole genome sequencing has not been employed to look for all off-target effects in living animals," says one of the team, Alexander Bassuk from the University of Iowa.

If you've somehow missed the CRISPR-Cas9 hype train, we started hearing about it a few years ago, when the technology was already being touted as a"revolution", based on its ability to make specific edits to the DNA of humans, other animals, and plants.

The technique workslike a biological 'cut and paste' tool, where researchers use a protein to seek out a particular gene and cut it out of the genome, replacing it with DNA of their choice - for example, they could swap a defective gene for a healthy one.

And unlike many promising medical inventions, CRISPR has continued to live up to its potential.

In recent years, it's been used to tap into cancer's 'control centre', repair a mutation that causes blindness, treat genetic disease in living animals, and even modify human embryos to figure out what causes infertility and miscarriage.

While there have been signs of 'off-target' mutations occurring in preliminary trials, that hasn't stopped the technology from making its way to humans.

The first clinical trial to use CRISPR in actual subjects now underway in China, and the US and the UK are not far behind.

In fact, some researchers are predicting that it could soon trigger some serious competition between China and the US - a kind of biomedical equivalent of the original Space Race.

"I think this is going to trigger 'Sputnik 2.0', a biomedical duel on progress between China and the United States," Carl June, an immunotherapist from the University of Pennsylvania and a scientific adviser on next year's US CRISPR trial, told Nature late last year.

Now researchers have found evidence that the unwanted mutations brought on by CRISPR in living animals could be a more widespread than we thought.

Tsang and his team sequenced the entire genome of two mice that had undergone CRISPR gene-editing in a previous study, and one healthy control.

They were looking for any mutations linked to the technology, including those that only altered a single nucleotide - molecules that serve as the building blocks of DNA and RNA.

They found that the technique had successfully corrected a gene that causes blindness in the mice, but the two mice that had undergone CRISPR gene-editing had sustained more than 1,500 unintended single-nucleotide mutations, and more than 100 larger deletions and insertions.

"None of these DNA mutations were predicted by computer algorithms that are widely used by researchers to look for off-target effects," the team reports.

You can see the results for the two gene-edited mice below, including the unintended single-nucleotide mutations and larger deletions and insertions in the first two rows:

T. Tsang et. al./Nature Methods

To be clear, the find doesn't necessarily mean that CRISPR is unsuitable for use in humans going forward - more research is now needed to see if these results can be replicated in larger samples, and in humans, rather than mice.

But it's like discovering that a medical treatment could be having potentially serious and long-term side effects - and our tests aren't picking them up.

The researchers are now urging for better screening tests for off-target mutations to be applied to CRISPR research immediately.

"We're still upbeat about CRISPR," says one of the team, Vinit Mahajan from Stanford University.

"We're physicians, and we know that every new therapy has some potential side effects - but we need to be aware of what they are."

The research has been accepted for an upcoming edition ofNature Methods.

Excerpt from:

CRISPR Gene-Editing Can Cause Hundreds of Unexpected ... - ScienceAlert

CRISPR Is Taking Over Science, Breaks Out Of Labs And Invades Schools – EconoTimes

CRISPR.National Human Genome Research Institute (NHGRI)/Wikimedia

Science regularly goes through cycles of fads that regularly embodies particular generations. In the 80s, its climate change and in the 90s, it was the internet. This time, it seems the gene-editing tool CRISPR is starting to steal the spotlight from other sectors in the scientific community and its not exactly hard to see why. It holds the potential to allow for major transformations on the genetic level.

As Futurism notes, CRISPR is basically causing a revolution within the scientific community, particularly in Biology. Being the single most powerful tool for manipulating organisms at a genetic level, it can be used to change the properties of absolutely anything. Little wonder why so many fear the method, with some imagining a future where people walk around with tails and horns.

In any case, CRISPR was awarded the 2015 Breakthrough of the Year award by Science magazine. It also found a cozy home on the pages of numerous prestigious publications, including the New Yorker and even entertainment media like The Hollywood Reporter are getting in on the game. There is even a TV series planned by NBC, which will feature CRISPR and have Jennifer Lopez as the lead.

The revolutionary technique is also starting to make its way outside of laboratories and to middle schools, NPR reports. There are numerous special sessions all over the country where students of all ages are introduced to the wondrous world of genetic manipulation.

This is made possible because, despite its highly effective nature in editing genes, CRISPR is also incredibly cheap. Students can get a kit for only $150 and with that, they can do things like creating a naturally spicy mango or a gerbil that changes colors.

Whats more, scientists are only beginning to scratch the full potential of the tool. In the coming years, biologists will be unleashing CRISPR on some of the worlds deadliest diseases, with some touching on the matter of immortality.

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CRISPR Is Taking Over Science, Breaks Out Of Labs And Invades Schools - EconoTimes

Gene-editing technique scientists hope will cure cancer and all … – The Independent

It has been hailed as a cure for cancer and all forms of inherited disease.

But scientists have now discovered that a system for editing the genes of living creatures can have a potentially dangerous side-effect causing unintended mutations.

Human trials of the Crispr-Cas9 gene-editing technique are already underway in China and are due to start in the US next year.

One of the supposed strengths of the system is that it allows specific sections of the genome to be targeted.

This prompted one expert, Dr Edze Westra, to predict earlier this year that it would be used to cure all inherited diseases, to cure cancers, to restore sight to people by adding, deleting or repairing genes.

Writing in the journal Nature Methods, researchers in the US described how they had used Crispr-Cas9 to restore sight to blind mice.

However, when they then sequenced the entire genome of the animals, they found two had more than 1,500 small mutations and more than 100 larger deletions and insertions of genetic material.

One of the researchers, Professor Stephen Tsang, of Columbia University, said: We feel its critical that the scientific community consider the potential hazards of all off-target mutations caused by Crispr.

Researchers who arent using whole genome sequencing to find off-target effects may be missing potentially important mutations.

We hope our findings will encourage others to use whole-genome sequencing as a method to determine all the off-target effects of their Crispr techniques and study different versions for the safest, most accurate editing.

He added that even a small change even affecting a single nucleotide, the basic building block of DNA could have a huge impact.

Previously, scientists have used a computer algorithm to highlight areas of the genome most likely to have been damaged inadvertently and then examine those sections of DNA alone.

The researchers said these algorithms seem to do a good job when Crispr was used on tissues in the laboratory, but full genome sequencing was required when dealing with live animals.

The mice used in the study had a gene that causes blindness and Crispr was used to correct this.

While hundreds of mutations were discovered none of which were predicted by the algorithms the mice themselves did not appear to be any worse for wear.

And the researchers said they were still confident that gene-editing would be medically useful.

Professor Vinit Mahajan, of Stanford University, who also took part in the research, said: Were still upbeat about Crispr.

Were physicians, and we know that every new therapy has some potential side effects but we need to be aware of what they are.

They are now trying to improve the targeting and cutting techniques used by the Crispr system.

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Gene-editing technique scientists hope will cure cancer and all ... - The Independent

In Just a Few Short Years, CRISPR Has Sparked a Research Revolution – Futurism

In BriefCRISPR is allowing scientists to make great strides in manyfields in the relatively short time it's been in use. Advances havebeen made in medicine, nutrition, biology, and more.

Theres a revolution happening in biology, and its name is CRISPR.

CRISPR (pronounced crisper) is a powerful technique for editing DNA. It has received an enormous amount of attention in the scientific and popular press, largely based on the promise of what this powerful gene editing technology will someday do.

CRISPR was Science magazines 2015 Breakthrough of the Year; its been featured prominently in the New Yorker more than once; and The Hollywood Reporter revealed that Jennifer Lopez will be the executive producer on an upcoming CRISPR-themed NBC bio-crime drama. Not bad for a molecular biology laboratory technique.

CRISPR is not the first molecular tool designed to edit DNA, but it gained its fame because it solves some longstanding problems in the field. First, it is highly specific. When properly set up, the molecular scissors that make up the CRISPR system will snip target DNA only where you want them to. It is also incredibly cheap. Unlike previous gene editing systems which could cost thousands of dollars, a relative novice can purchase a CRISPR toolkit for less than US$50.

Research labs around the world are in the process of turning the hype surrounding the CRISPR technique into real results. Addgene, a nonprofit supplier of scientific reagents, has shipped tens of thousands of CRISPR toolkits to researchers in more than 80 countries, and the scientific literature is now packed with thousands of CRISPR-related publications.

When you give scientists access to powerful tools, they can produce some pretty amazing results.

The most promising (and obvious) applications of gene editing are in medicine. As we learn more about the molecular underpinnings of various diseases, stunning progress has been made in correcting genetic diseases in the laboratory just over the past few years.

Take, for example, muscular dystrophy a complex and devastating family of diseases characterized by the breakdown of a molecular component of muscle called dystrophin. For some types of muscular dystrophy, the cause of the breakdown is understood at the DNA level.

In 2014, researchers at the University of Texas showed that CRISPR could correct mutations associated with muscular dystrophy in isolated fertilized mouse eggs which, after being reimplanted, then grew into healthy mice. By February of this year, a team here at the University of Washington published results of a CRISPR-based gene replacement therapy which largely repaired the effects of Duchenne muscular dystrophy in adult mice. These mice showed significantly improved muscle strength approaching normal levels four months after receiving treatment.

Using CRISPR to correct disease-causing genetic mutations is certainly not a panacea. For starters, many diseases have causes outside the letters of our DNA. And even for diseases that are genetically encoded, making sense of the six billion DNA letters that comprise the human genome is no small task. But here CRISPR is again advancing science; by adding or removing new mutations or even turning whole genes on or off scientists are beginning to probe the basic code of life like never before.

CRISPR is already showing health applications beyond editing the DNA in our cells. A large team out of Harvard and MIT just debuted a CRISPR-based technology that enables precise detection of pathogens like Zika and dengue virus at extremely low cost an estimated $0.61 per sample.

Using their system, the molecular components of CRISPR are dried up and smeared onto a strip of paper. Samples of bodily fluid (blood serum, urine, or saliva) can be applied to these strips in the field and, because they linked CRISPR components to fluorescent particles, the amount of a specific virus in the sample can be quantified based on a visual readout. A sample that glows bright green could indicate a life-threatening dengue virus infection, for instance. The technology can also distinguish between bacterial species (useful for diagnosing infection) and could even determine mutations specific to an individual patients cancer (useful for personalized medicine).

Almost all of CRISPRs advances in improving human health remain in an early, experimental phase. We may not have to wait long to see this technology make its way into actual, living people though; the CEO of the biotech company Editas has announced plans to file paperwork with the Food and Drug Administration for an investigational new drug (a necessary legal step before beginning clinical trials) later this year. The company intends to use CRISPR to correct mutations in a gene associated with the most common cause of inherited childhood blindness.

Physicians and medical researchers are not the only ones interested in making precise changes to DNA. In 2013, agricultural biotechnologists demonstrated that genes in rice and other crops could be modified using CRISPR for instance, to silence a gene associated with susceptibility to bacterial blight. Less than a year later, a different group showed that CRISPR also worked in pigs. In this case, researchers sought to modify a gene related to blood coagulation, as leftover blood can promote bacterial growth in meat.

You wont find CRISPR-modified food in your local grocery store just yet. As with medical applications, agricultural gene editing breakthroughs achieved in the laboratory take time to mature into commercially viable products, which must then be determined to be safe. Here again, though, CRISPR is changing things.

A common perception of what it means to genetically modify a crop involves swapping genes from one organism to another putting a fish gene into a tomato, for example. While this type of genetic modification known as transfection has actually been used, there are other ways to change DNA. CRISPR has the advantage of being much more programmable than previous gene editing technologies, meaning very specific changes can be made in just a few DNA letters.

This precision led Yinong Yang a plant biologist at Penn State to write a letter to the USDA in 2015 seeking clarification on a current research project. He was in the process of modifying an edible white mushroom so it would brown less on the shelf. This could be accomplished, he discovered, by turning down the volume of just one gene.

Yang was doing this work using CRISPR, and because his process did not introduce any foreign DNA into the mushrooms, he wanted to know if the product would be considered a regulated article by the Animal and Plant Health Inspection Service, a division of the U.S. Department of Agriculture tasked with regulating GMOs.

APHIS does not consider CRISPR/Cas9-edited white button mushrooms as described in your October 30, 2015 letter to be regulated, they replied.

Yangs mushrooms were not the first genetically modified crop deemed exempt from current USDA regulation, but they were the first made using CRISPR. The heightened attention that CRISPR has brought to the gene editing field is forcing policymakers in the U.S. and abroad to update some of their thinking around what it means to genetically modify food.

One particularly controversial application of this powerful gene editing technology is the possibility of driving certain species to extinction such as the most lethal animal on Earth, the malaria-causing Anopheles gambiae mosquito. This is, as far as scientists can tell, actually possible, and some serious players like the Bill and Melinda Gates Foundation are already investing in the project. (The BMGF funds The Conversation Africa.)

Most CRISPR applications are not nearly as ethically fraught. Here at the University of Washington, CRISPR is helping researchers understand how embryonic stem cells mature, how DNA can be spatially reorganized inside living cells, and why some frogs can regrow their spinal cords (an ability we humans do not share).

It is safe to say CRISPR is more than just hype. Centuries ago we were writing on clay tablets in this century we will write the stuff of life.

Continued here:

In Just a Few Short Years, CRISPR Has Sparked a Research Revolution - Futurism

How A Gene Editing Tool Went From Labs To A Middle-School Classroom – NPR

Will Shindel prepares for a gene-editing class using the CRISPR tool at a Brooklyn community lab called Genspace. Alan Yu/WHYY hide caption

Will Shindel prepares for a gene-editing class using the CRISPR tool at a Brooklyn community lab called Genspace.

On a Saturday afternoon, 10 students gather at Genspace, a community lab in Brooklyn, to learn how to edit genes.

There's a recent graduate with a master's in plant biology, a high school student who started a synthetic biology club, a medical student, an eighth grader, and someone who works in pharmaceutical advertising.

"This is so cool to learn about; I hadn't studied biology since like ninth grade," says Ruthie Nachmany, one of the class participants. She had studied anthropology, visual arts, and environmental studies in college, but is now a software engineer.

In the 1970s, personal computers emerged from labs and universities and became something each person could have. That made it possible for people like Nachmany to become a professional programmer despite not having studied it in school.

Some compare that democratization of personal computing in the '70s to the current changes in access to genetic engineering tools.

In 2015, the journal Science declared the gene editing tool CRISPR Cas9 the breakthrough of the year. It let scientists make changes in DNA of living cells easier and cheaper than before. Today, the CRISPR tool is no longer something that only researchers do in labs. You can take classes in gene editing at a community lab. You can buy a $150 kit to do it at home. Some middle schoolers are doing it in their science classes.

Genspace lab manager Will Shindel, who teaches the genome-editing class, says his students are usually professionals who want to learn a new career skill or curious everyday people. "They just know that it's this word that everybody's throwing around," Shindel says. "It's either going to lead to the singularity or the apocalypse."

Shindel, a biologist by training, is one of many people now dreaming about and starting synthetic biology projects using the CRISPR tool. With some friends, he is working on genetically engineering a spicy tomato. Some people are trying to make bacteria produce insulin. At Acera, an elementary and middle school in Massachusetts, 13-year-old Abby Pierce recently completed a CRISPR experiment, genetically modifying bacteria so that it could grow in an antibiotic that would have killed it otherwise.

Pierce's science teacher, Michael Hirsch, made the argument to get genetic engineering kits for his science students to experiment with in class. "It's going to take molecular bio out of the 'Oh man, cool, they do it in labs' to 'Wait, we can do this in our homes,' " Hirsch says. "We could do things like create pigments, and create flavor extracts, and all of these really nifty things safely and carefully in our kitchens."

New skill set

In fact, the University of Pennsylvania's Orkan Telhan argues, genetic engineering will become an increasingly important skill, like coding has been. Telhan is an associate professor of fine arts and emerging design practices and he worked with a biologist and an engineer on a desktop machine that allows anyone to do genetic engineering experiments, without needing a background in biology.

"Biology is the newest technology that people need to learn," Telhan says. "It's a new skill set everyone should learn because it changes the way you manufacture things, it changes the way we learn, store information, think about the world." As an example of a recent application, Telhan points to an Adidas shoe made from bioengineered fiber, inspired by spider silk.

The comparison between genetic engineering and computing is not new. Two years ago at a conference, MIT Media Lab Director Joi Ito gave a talk called "Why bio is the new digital":

Genspace Lab Manager Will Shindel mixes all the chemicals before class, so the students don't have to make calculations to dilute them during the class. Alan Yu/WHYY hide caption

Genspace Lab Manager Will Shindel mixes all the chemicals before class, so the students don't have to make calculations to dilute them during the class.

"You can now take all of the gene bricks, these little parts of genetic code, categorize them as if they were pieces of code, write software using a computer, stick them in a bacteria, reboot the bacteria and the bacteria just as with computers, usually does what you think it does."

'We need to dig deeper'

Gene editing tools have already started a debate about ethics and safety. Some scientists have warned about not just intentionally harmful uses, but also potential unintended consequences or dangerous mistakes in experimentation.

The German government in March sent out a warning about one kind of CRISPR kit, saying officials found potentially harmful bacteria on two kits they tested, though it's not clear how those bacteria got there. The European Centre for Disease Prevention and Control responded with a statement earlier this month that the risk to people using these kits was low and asked EU member states to review their procedures around these kits.

Earlier, the German Federal Office of Consumer Protection and Food Safety also issued a reminder that depending on the kit, genetic-engineering laws still applied, and doing this work outside of a licensed facility with an expert supervisor could lead to a fine of up to 50,000 euros ($56,000).

In the U.S., then-Director of National Intelligence James Clapper in early 2016 added genome editing to a list related to "weapons of mass destruction and proliferation." But bioengineering experts say overall, the U.S. government agencies have long been monitoring the gene-editing and the DIY bio movement "very proactive in understanding" the field, as Johns Hopkins University biosecurity fellow Justin Pahara puts it.

"There is a lot of effort going into understanding the scope of DIY biology, who can do it, what can be done, what are some of the concerns, how do we mitigate risk," says Pahara, who is also a co-founder of bioengineering-kit company Amino Labs. He says DIY bio, or biohacking, poses little security concern for now, being at a very early stage.

"I would suggest that just all of these discussions, including looking into the past at computing and other technologies, [have] really helped us understand that we need to dig deeper," he says.

More variables

As much as the gene-engineering revolution is being compared to the PC revolution before it, bacteria are not as predictable as computers, says Kristala Prather, associate professor of chemical engineering at MIT. Her team studies how to engineer bacteria so they produce chemicals that can be used for fuel, medications and other things.

"I have a first-year graduate student ... who was lamenting the fact that even though she has cloned genes many times before, it's taking her a little while to get things to work well at my lab," Prather says. "And my response to her is that the same is true for about 80 percent of students who come into my group."

Prather explains that engineering bacteria isn't quite like coding because many more variables are at play.

"One of the common mistakes that people make it to assume all water is just water. The water that comes out of the tap in Cambridge is different than the water that comes out of the tap in New York," she says. "So there are very small things like that that can turn out to make a significant difference."

But Prather who remembers writing programs on a Commodore 64 computer as a 13-year-old is nonetheless excited about the prospect of more people learning about genetic engineering through kits and classes: She says even if all this access does right now is get more people excited about becoming scientists, it's still really valuable.

Alan Yu reports for WHYY's health and science show, The Pulse. This story originally appeared on an episode of its podcast called Do It Yourself.

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How A Gene Editing Tool Went From Labs To A Middle-School Classroom - NPR

Using CRISPR gene editing to slow cancer growth | FierceBiotech – FierceBiotech

The gene editing technology CRISPR/CAS9 is being used to develop a host of new treatments, mostly for genetic diseases. But a team of researchers from the University of Rochester's Center for RNA Biology are investigating whether gene editing can be used for another purpose: to slow the growth of cancer cells.

Although there are many types of cancer, theyre all characterized by the same uncontrollable cell growth. So the University of Rochester team is targeting the cell cycle, which is the series of events that leads to cell growth and division, according to a press release. And theyve zeroed in on a single protein, called Tudor-SN, thats a key element in the preparatory phase of cell division.

Using CRISPR, the scientists eliminated Tudor-SN from cells. Then they observed that those cells were taking much longer to prepare for division.

"We know that Tudor-SN is more abundant in cancer cells than healthy cells, and our study suggests that targeting this protein could inhibit fast-growing cancer cells," said Reyad A. Elbarbary, Ph.D., a research assistant at the University of Rochester and the lead author, in the release.

Elbarbary works in a lab that discovered that Tudor-SN influences the cell cycle by controlling microRNAs, according to the release. When the protein is removed, levels of many types of microRNAs rise, which in turn switches off genes that promote cell growth.

This isnt the first time CRISPR has been proposed in the context of finding new ways to attack cancer. Last year, Facebook and Napster billionaire Sean Parker turned heads when his Parker Institute funded research at the University of Pennsylvania thats focused on editing T cellsimmune cells that usually cant recognize cancer as a foreign invader. The Penn scientists are using CRISPR to edit out genes of T cells in the hopes of enabling the immune system to search out and kill cancer cells.

Eliminating Tudor-SN through gene editing is more about disrupting the very process that results in cancerabnormal cell proliferation. There are already molecules in the clinic that target Tudor-SN, Elbarbary says, making it possible to consider cancer therapies based on this mechanism. The University of Rochester team plans further studies to determine how Tudor-SN works with other proteins so they can best identify drugs that will target cell division.

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Using CRISPR gene editing to slow cancer growth | FierceBiotech - FierceBiotech

Watch This Scientist Brilliantly Explain CRISPR to Everyone from a Child to a Ph.D. – Patheos (blog)

How well can scientists communicate their research to people depending on their level of understanding?

That was the challenge posed to biologist Neville Sanjana, who attempted to explain CRISPR (a kind of gene editing technology) to a child, a teenager, a college student, a graduate student, and a fellow CRISPR expert. Its fascinating to watch him maneuver between them all.

As I wrote when this same kind of communication experiment was done with a neuroscientist, we may not all be scientists, but we often have ideas that we want to get across. How well do we adapt what we say based on the audience? Ive been to plenty of debates on philosophy and read several books about the subject where it felt like everything was way over my head. And there were other books geared to a more knowledgeable audience that never went beyond the 101 level. It was a waste of my time.

All good communicators should be able to explain their ideas with the audience in front of them, meeting them where theyre at.

(via Kottke. Portions of this article were published earlier)

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Watch This Scientist Brilliantly Explain CRISPR to Everyone from a Child to a Ph.D. - Patheos (blog)

CRISPR gene editing puts the brakes on cancer cells – Cosmos

A cancer cell in the process of division. Knocking out the Tudor-SN protein might have stopped things getting this far.

Steve Gschmeissner / Getty

Cancer cells are known for their fast and rapacious growth, but a new technique to slow them down may one day offer new treatment options.

Scientists from the US have discovered a protein called Tudor-SN linked to the preparatory phase of cell life when cells prepare to divide and spread.

Using the gene-editing technology CRISPR, the researchers removed the protein, which is more abundant in cancer cells than healthy cells, and found cancer cell growth was effectively delayed.

The research team, led by Reyad Elbarbary and Keita Myoshi from the University of Rochester, in New York, made its findings in a laboratory using cells from kidney and cervical cancers.

While the technique is still far from human trials, the researchers report in the journal Science that their findings could potentially be used as a treatment option.

Thomas Cox from the Garvan Institute of Medical Research in Sydney, who wasnt involved in the study, says there is potential for the technique to boost the effectiveness of some standard therapies by slowing tumour cells down.

The treatment works by hacking into molecules involved in the life cycle of cancerous cells.

Healthy cells go through a cycle of growth, division and death. For cancerous cells, this cycle is faulty and the cells grow abnormally and uncontrollably, infiltrating nearby tissues.

The proteins effect on the cell cycle is a result of its influence on microRNAs the molecules that determine what genes are switched on and when, including the genes that control cell growth.

Plucking out Tudor-SN boosted the number of certain microRNAs that, in turn, prevented the production of proteins responsible for cell growth.

Cox says the process of targeting microRNAs is difficult and technically challenging:

This study is saying: Well, if we cant target microRNAs directly, can we target something regulating them?

MicroRNAs have long been known to be involved in cancer, and recent studies have also looked at the influence of Tudor-SN. What this present research does differently, Cox says, is home in on how these affect the cell cycle.

The next step, he adds, will be testing the treatment in mice.

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CRISPR gene editing puts the brakes on cancer cells - Cosmos

Fine-tuning CRISPR to Create Popular Mouse Models – Technology Networks

CRISPR has built a tremendous amount of excitement in the scientific community since 2013. Though it can be used to create simple gene-disrupted animal models, it is extremely challenging to use it to insert foreign cassettes into genomes to create knock-ins or more complex models such as conditional knockouts.

A team headed by Dr. Channabasavaiah B Gurumurthy (Guru) at the University of Nebraska Medical Center, Omaha, U.S.A., in collaboration with Dr. Masato Ohtsuka, Tokai University, Japan have developed a method they call Easi-CRISPR.

This new technique revolutionizes the speed at which, much-needed, mutant mouse models are created for biomedical research.This work was published in Genome Biology journal on May 17, 2017.

TheEasi-CRISPR method employs long single stranded DNAs as donor cassettes for gene editing via CRISPR, unlike the typically very inefficient double stranded DNA donors commonly used by the scientific community. In addition, the ssDNA donors are combined with newer platforms of CRISPR guide RNAs (that constitute separated crRNA and tracrRNA) and Cas9 protein, together called ctRNP.

During the previous 4 years, many scientists have tried to use CRISPR to create knock-in models, that relied on homology-directed repair (HDR), but many were unsuccessful as their methods were not able to shift the balance from NHEJ to HDR for it to work efficiently. A recent Science Magazine news article captured the frustration of the research community about the limitations of the previously used CRISPR methods.

Gurus and Masatos labs first observed the robustness of ssDNA donors for HDR, in their Easi-CRISPR platform, in the summer of 2016. They posted their preliminary results on the preprint serverbiorXiv,started presenting their data at several conferences so that their method can immediately be available to the scientific community, before their manuscript was peer-reviewed and published in a journal.

Guru said Several independent labs have already been able to use Easi-CRISPR for other genes, thanks to its early online posting on bioRxiv.He added, Hundreds of labs are interested in using the technology we posted another bioRxiv article on this work today that describes detailed step-by-step protocols of Easi-CRISPR, which should help the community further.

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Fine-tuning CRISPR to Create Popular Mouse Models - Technology Networks

Scientists Are Using CRISPR To "Program" Living Cells – Futurism – Futurism

In Brief Scientists from the University of Washington have constructed digital logic gates in living cells. Though they're not the first to do so, the researchers' living circuitry is the largest and most complex of any created thus far. Living Circuits

Thanks to projects like Elon Musks Neuralink, a future in which humankind merges with machinesis on everyones minds. While a brain computer interface (BCI) like the one Musk is proposing would involve making acomputer function as part ofa human body, other researchers are taking an opposite route. Instead of making machines that can imitate biology, theyre looking for ways to make biological systems function more like computers.

One such project is the topic of a study by researchers from the University of Washington (UW)that was justpublished inNature Communications. They have developed a new method of turning cells into computers that process information digitally instead of following their usual macromolecular processes. They did so by building cellular versions of logic gates commonly found in electric circuits.

The team built theirNOR gates, digital logic gates that pass a positive signal only when their two inputs are negative, in the DNA of yeast cells. Each of these cellular NOR gates was made up of three programmable DNA stretches, with two acting as inputs and one as an output. These specific DNA sequences were targeted using CRISPR-Cas9, with the Cas9 proteins serving as the molecular gatekeeper that determined if a certain gate shouldbe active or not.

This UW study isnt the first to buildcircuits in cells, but it is the most extensive one to date, with seven cellular NOR gates in a single eukaryotic cell. This added complexity puts us one step closer to transforming cells into biological computers witha number of potential medical applications.

While implementing simple programs in cells will never rival the speed or accuracy of computation in silicon, genetic programs can interact with the cells environment directly, senior author Eric Klavins explained in a press release. For example, reprogrammed cells in a patient could make targeted, therapeutic decisions in the most relevant tissues, obviating the need for complex diagnostics and broad spectrum approaches to treatment.

If given the ability to hackour biology in this way, we could potentially engineer immune cells to respond to cancer markers or cellular biosensors to diagnose infectious diseases. Essentially, wed have an effectiveway to fight diseases on the cellular level, ushering in a new era in human evolution.

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Scientists Are Using CRISPR To "Program" Living Cells - Futurism - Futurism

Scientists are using gene editing to create the perfect tomato for your salad – Quartz


Quartz
Scientists are using gene editing to create the perfect tomato for your salad
Quartz
In a study published in the journal Cell on May 18, geneticist Zachary Lippman of Cold Spring Harbor Laboratory explains his research team's efforts to fix mutated tomatoes using CRISPR gene editing technology. By identifying the genes associated with ...

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Scientists are using gene editing to create the perfect tomato for your salad - Quartz

How the CRISPR-Cas9 System is Redefining Drug Discovery – Labiotech.eu (blog)

The recent emergence of easily accessible CRISPR-Cas9 technologies is enabling nearly unlimited opportunities for genome editing. Apart from its potential as a therapeutic tool, the system is currently spurring a revolution in drug discovery.

The targets were finding with CRISPR-Cas9 are going to guide the drugs coming out in the 2020s, said Jon Moore, CSO of Horizon Discovery, at a recent event in the UK. Only shortly after the first publication on the new genome engineering system in late 2012, the gene editing company and CRO started to recognize the potential of the new technology.

Around 2013 we started getting interested in CRISPR-Cas9 () and over the next year and a half we went from predominantly generating models using AAV to almost exclusively using CRISPR-Cas9,Chris Lowe, Head of Research Operations at Horizon, told us. Today, the company uses CRISPR across all of its platforms from engineering customized cell lines or animal models to performing functional screens. We can generate hundreds of knock-outmodels a month on a rolling platform. And thats really only possible because of the CRISPR-Cas9 technology. Its pretty much all pervasive, commented Chris.

To date, most of the attention on CRISPR has revolved around its potential as a therapeutic tool and the possibilities of engineering human embryos, crops or life stock. However, it seems like the real revolution right now is taking place in the lab. In 2015 alone, the scientific community published 1,185 publications (corresponding to 3 publications a day!) on the new gene editing system, and scientists have hacked the system to do far more than just cut DNA. CRISPR appears to be emerging as a key tool for drug discovery ranging from target identification and validation to preclinical testing.

RNA-guided Cas9 nucleases, which are derived from microbial adaptive immune systems, are enabling fast and accurate alterations of genomic information in mammalian model systems, including human tissues. While genome editing tools are not entirely new, Chris told us that the benefit of CRISPR really is in the speed and ease with which you can create the reagents necessary to perform gene editing, thereby overcoming many limitations of its predecessors such as zinc-finger nucleases (ZFN) and transcription activator-like effector nucleases (TALENs).

Cas9 makescuts at specific locations along the DNA with help from a short stretch of guide RNA that targets the Cas9 endonuclease to a specific site. By simply changing the guide RNA sequence, Cas9 can be directed to any site within the genome. The synthesis of such short pieces of RNA is way simpler than having to engineer a whole protein to direct it towards a specific DNA sequence.

The resulting double-strand break is then repaired by the cells error-prone DNA repair machinery. That alone is usually enough to knock-out the gene of interest and allows scientists to study what happens to cells or organisms when the protein or gene is shut off. Alternatively, the scientist can provide a piece of new DNA, maybe a new gene, which is then built in at the target site.

The RNA-guided Cas9 nuclease.

CRISPR gives scientists the opportunity to engineer and study virtually all cell types and it has become common practice around the globe. In fact, as the system is incredibly fast and cost-effective, it has enabled scientists, for the first time, to conduct high-throughput knock-out screens to speed up target discovery.

Using retroviral libraries of guide RNAs that target every single gene within the genome, CRISPR can be used to generate thousands of different cell lines at once, each containing a different guide RNA that targets a particular gene.

Principle setup of a CRISPR screen.

Feng Zhangs lab, the first lab that used CRISPR to engineer human cells, made use of such genome-wide screens to address treatment resistance to melanoma. BRAF V600E is a common cancer mutation that is treated by the FDAapproved drug vemurafenib. Yet, the rapidly mutating cancer cells quickly become resistant, and by 24 weeks of treatment, the tumors return.

We thought this might be an opportunity for us to apply a genome-scale library to see what are the geneswhen you either turn them on or turn them offthat would render the tumor cell resistant to vemurafenib, Zhang explained in an article in The Scientist.

Apart from identifying genes that make cells resistant to specific drugs, researchers are using the system toscreen for genes that are essential to the cancer cells, but not normal cells a state referred to assynthetic lethality. Others are using CRISPR screens to search for survival factors of pathogens such as the Zika and Dengue viruses.

Although RNA interference-based screens were widely used beforeCRISPR, the new system has considerable advantages.Most significantly, gene editing will lead to the complete inactivation of a target, compared to the incomplete knockdown seen with RNA interference (RNAi). In addition, confounding off-target effects of siRNA molecules are widely reported. As Chris told us, we are seeingmuch greater reproducibility than what weve seen using RNAi over the years. So thats a big element thats driving the adoption of the CRISPRscreening technique as a complementary technique to the siRNA approaches.

A key to successful drug development isthe availability of suitable model systems to make early drug development decisions. As Friedhelm Bladt, Director of Biomarker Strategy at Bayer, told us, One limitation in drug development is that you test your efficacy in mouse models, sometimes in rats. But these animals react very differently from a human being and they are in some aspects much more robust than human beings would be.

Generating a new disease model used to be a laborious and expensive tasklimited to a few species that came with a good tool kit for genetic manipulation. CRISPR now allows us to generate much better animal models that really reflect the human situation,commented Friedhelm.

Today, CRISPR has been used to engineer a wide range of species including rats, dogs and cynomolgous monkeys, which are all commonly used during preclinical drug discovery. Others are using it to engineer the genome of ferrets, in order to modify their susceptibility to flu infections. These animals are much better suited as influenza transmission models, due to the fact that unlike mice, ferrets sneeze when infected.

Another major advantage is that CRISPR allows tweaking more than one gene at a time, taking into account that most human diseases are not monogenic. Tumors, for example, are very heterogeneous and you usually have a lot of different types of mutations as well asdifferences within thetumor. Modeling that is a huge challenge in animal models, explained Friedhelm. With CRISPR we are able to really introduce aset of mutations or potentially even introduce some heterogeneity in thetumors.

Creating a mouse model with multiple mutations used to take years due to lenghty backcrossing, costing about $20,000 per mutation. With CRISPR, this time has been reduced to months or even weeks.

Apart from serving as a gene editing tool, CRISPR has already been hacked to do much more than that. As Chris explained: I see the CRISPR system not so much as an editing tool but more as a targeting system. It allows us to precisely target tools to specific locations in the genome and this ability is challenging our imagination, allowing the investigation of much more subtle effects on the genome compared to the fairly blunt technique that was brought out a couple of years ago where you just damage the DNA and let it repair.

When the group of Jonathan Weissman at the University of California, San Francisco (UCSF) got hold of CRISPR, the first thing they did was to break the scissors, he explains in a recent Natureinterview. The group mutated the Cas9 protein so that it still bound to the DNA but no longer cut it, allowing the team to turn off genes without changing the DNA sequence.

Then they tethered Cas9 to a protein that activates gene expression. They now had a simple system available that allowed them to turn genes either on or off at their will. Others are using CRISPR to make more subtle modifications to the DNA: by coupling CRISPR to epigenetic modifiers such as histone acetylases, scientists are able to study the direct effect of epigenetic marks, providing a straightforward tool to study how epigenetics can drive disease. These types of alterations can be modified with CRISPR in a much more selective way than it was possible in the past, explained Friedhelm. And there are many more potential applications people have just started to discover these.

Since its appearance in 2012, CRISPR has given rise to a massive number of new tools that are impacting the entire drug discovery process. The system is redefining whats possible in R&D, which is why many biotech and pharma companies have started integrating the technology into their R&D programs.

Novartis recently entered a partnership with Jennifer Doudnas Caribou Biosciences to accessCaribous CRISPR drug screening and validation technologies, while AstraZeneca signed up for four research collaborations to use CRISPR across its entire drug discovery platform. Similarly, German Evotec recently teamed up with Merck to access its CRISPR libraries that are based on a license from the Broad Institute.

As CRISPR Therapeutics CEO Rodger Novak told us at our last Refresh Event, There is probably no larger biotech or pharma company out there anymore, who have their own R&D, who are not using CRISPR. They are all using CRISPR in their labs. Its a very powerful technology, not only for human therapeutics.

Images via shutterstock.com / CHORNYI SERHII / Perception7 / unoL; horizondiscovery.com; igem.org

Merken

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How the CRISPR-Cas9 System is Redefining Drug Discovery - Labiotech.eu (blog)

Will this gene-editing tool cure the diseases of the future? – Sacramento Bee


Sacramento Bee
Will this gene-editing tool cure the diseases of the future?
Sacramento Bee
The most used gene-editing agent is CRISPR-cas 9, a combination of an enzyme that cuts strands of DNA at a specific location and a predesigned RNA sequence that binds to the DNA. Usually, a professionally trained microinjectionist delivers CRISPR-cas9 ...

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Will this gene-editing tool cure the diseases of the future? - Sacramento Bee

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