Archive for the ‘Crispr’ Category

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

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

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

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

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.

See more here:

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

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.

Visit link:

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

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.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

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.

See the original post here:

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

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.

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

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

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

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)

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

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

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

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

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

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

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

By 2040, there will be 9 billion people in the world. Thats like adding another China onto todays global population, said Professor Sophien Kamoun of the Sainsbury Laboratory in Norwich, UK.

Prof. Kamoun is one of a growing number of food scientists trying to figure out how to feed the world. As an expert in plant pathogens such asPhytophthora infestans the fungus-like microbe responsible for potato blight he wants to make crops more resistant to disease.

Potato blight sparked the Irish famine in the 19th century, causing a million people to starve to death and another million migrants to flee. European farmers now keep the fungus in check by using pesticides. However, in regions without access to chemical sprays, it continues to wipe out enough potatoes to feed hundreds of millions of people every year.

Potato blight is still a problem, said Prof. Kamoun. In Europe, we use 12 chemical sprays per season to manage the pathogen that causes blight, but other parts of the world cannot afford this.

Plants try to fight off the pathogens that cause disease but these are continuously changing to evade detection by the plants immune system.

Arms race

In nature, every time a plant gets a little better at fighting off infection, pathogens adapt to evade their defences. Now biologists are getting involved in the fight.

Its essentially an arms race between plants and pathogens, said Prof. Kamoun. We want to turn it into an arms race between biotechnologists and pathogens by generating new defences in the lab.

If we think of the genome as text, CRISPR is a word processor that allows us to change just a letter or two.

Prof. Sophien Kamoun, Sainsbury Laboratory, UK

Five years ago, Prof. Kamoun embarked on a project called NGRB, funded by the EU's European Research Council. The plan was to find a way to make potatoes more resistant to infection using advanced plant-breeding techniques.

Then serendipity struck. In the early stages of the project, scientists in another lab discovered a ground-breaking gene-editing technique known as CRISPR-Cas which allows scientists to delete or add genes at will. As well as having potential medical applications in humans, this powerful tool is unlocking new approaches to perfecting plants.

If we think of the genome as text, CRISPR is a word processor that allows us to change just a letter or two, explained Prof. Kamoun. The precision that this allows makes CRISPR the ultimate in genetic editing. Its really beautiful.

One of the simplest ways to use CRISPR to improve plants is to remove a gene that makes them vulnerable to infection. This alone can make potatoes more resilient, helping to meet the worlds growing demand for food.

The resulting crop looks and tastes just the same as any other potato. Prof. Kamoun says that potatoes which are missing a gene or two should not be viewed in the same way as genetically modified foods which sometimes contain genes introduced from another species. Its a very important technical difference but not all regulators have updated their rules to make this distinction.

Potatoes are not the only food crops that can be improved by CRISPR-Cas. Prof. Kamoun is now working on a project that aims to protect wheat from wheat blast a fungal disease decimating yields in Bangladesh and spreading in Asia.

Looking ahead, CRISPR will be used to improve the quality and nutritional value of wheat, rice, potatoes and vegetables. It could even be used to remove genes that cause allergic reactions in people with tomato or wheat intolerance.

If we can remove allergens, consumers may soon see hypoallergenic tomatoes on supermarket shelves, Prof. Kamoun said. Its a very exciting technology.

While targeting disease in this way could be a game changer for global food security in the years ahead, experts believe other approaches to plant breeding will continue to have a role. Understanding meiosis a type of cell division that can reshuffle genes to improve plants can help farmers and the agribusiness sector select for hardier crops, according to Professor Chris Franklin of the University of Birmingham, UK.

He leads the COMREC project, which trains young scientists to understand and manipulate meiosis in plants. The project applies the wealth of knowledge generated by leaders in the field to tackle the pressing problem of feeding a hungry world.

COMREC has begun to translate fundamental research into (applications in) key crop species such as cereals, brassicas and tomato, said Prof. Franklin. Close links with plant-breeding companies have provided important insight into the specific challenges confronted by the breeders.

Elite crops

There may be untapped potential in this approach to plant breeding: most of the genes naturally reshuffled during meiosis in cereal crops are at the far ends of chromosomes genes in the middle of chromosomes are rarely reshuffled, limiting the scope for new crop variations.

COMRECs academic and industry partners hope to understand why this is so that they can find a way to shuffle the genes in the middle of chromosomes too. And the food industry is keen to produce new elite varieties that are better adapted to confront the challenges arising from climate change, says Prof. Franklin.

A number of genes have now been identified that can make this reshuffling relatively more frequent, he said. CRISPR-Cas provides a way to modify the corresponding genes in crop species, helping to translate this basic research to target crops.

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Can CRISPR feed the world? | Horizon: the EU Research ... - Horizon magazine

This week we went back to one of our favourite biotech hubs in the UK: Cambridge. Here, a young startup called Nemesis Bioscience is working on new treatment strategies to fight antimicrobial resistance based on CRISPR-Cas9.

Mission: Nemesis strategy is different from that of most companies in the antibiotic resistance space. Instead of developing new antibiotics to kill bacteria, the biotech aims to switch off resistance mechanisms and thereby resurrect antibiotic susceptibility. The Cybergenetics technologies use bacteriophages to deliver programmable RNA-guided endonucleases into the bacteria.

The nuclease can then inactivate antibiotic resistance genes and restore antibiotic activity. Nemesis first nuclease is directed against 8 families of beta-lactamases and is thereby able to inactivate resistance to beta-lactam antibiotics.

Comment: By targeting resistance genes directly, the biotech believes it is able to offset the natural selection pressure, which would eventually result in resistance to new antibiotic drugs. Swiss Bioversys is testing a similar approach, although the biotechs platform is based on small molecules.

Also, Nemesis technology represents yet another exciting therapeutic application of the CRISPR-Cas9 system. Because the endonuclease is delivered using bacteriophages, it is specifically targeted to bacteria, and not mammalian cells. Thereby, the technology overcomes the risk of off-target effects, which are currently limiting the therapeutic use of CRISPR.

Images via shutterstock.com / e X p o s e and nemesisbio.com

Merken

Continued here:

This UK Biotech uses CRISPR-Cas9 To Fight Bacterial Resistance - Labiotech.eu (blog)

What is CRISPR-Cas9?

CRISPR-Cas9 is a genome editing tool thats able to cut DNA in a targeted fashion, allowing scientists to accurately edit the building blocks of life.

It was actually first observed in the 1980s as part of single-celled bacterias defence mechanisms, which ensure that the cells are able to remove unwanted intruders. Scientists have found that, by adapting the technology, they are able to target genome sequences with unprecedented speed, precision and accuracy.

Picture CRISPR-Cas9 as like a find and replace search in a computer document, only instead of words, youre editing genetic sequences.

Accurately modifying DNA is a scientific holy grail, and the potential is enormous. It could be used to eradicate diseases even hereditary ones such as cystic fibrosis, sickle-cell anemia and Huntington's could become a thing of the past.

The name CRISPR is an acronym for the less catchy clustered regularly interspaced short palindromic repeats. The Cas part refers to CRISPR associated.

CRISPR is part of certain bacterias naturally occurring defences. When a bacteria detects an invading virus, it is able to copy and blend segments of the foreign DNA into its own genome around CRISPR.

The next time the virus is spotted, CRISPR has an exact copy of the genome sequence to look out for, which is where the Cas protein comes in: it can cut the DNA up, and disable unwanted genes with incredible accuracy.

Or, as Carl Zimmer explains: As the CRISPR region fills with virus DNA, it becomes a molecular most-wanted gallery, representing the enemies the microbe has encountered. The microbe can then use this viral DNA to turn Cas enzymes into precision-guided weapons. The microbe copies the genetic material in each spacer into an RNA molecule. Cas enzymes then take up one of the RNA molecules and cradle it. Together, the viral RNA and the Cas enzymes drift through the cell. If they encounter genetic material from a virus that matches the CRISPR RNA, the RNA latches on tightly. The Cas enzymes then chop the DNA in two, preventing the virus from replicating.

In 2012, scientists from the University of California, Berkeley, published a groundbreaking paper showing they were able to reprogramme the CRISPR-Cas immune system to edit genes at will. CRISPR-Cas9 uses a specific Cas protein and a hybrid RNA that can identify and edit any gene sequence. The possibilities are huge.

In short, CRISPR lists the DNA sequences to target, and then Cas9 does the cutting. Scientists just need to programme CRISPR with the right code, and Cas9 does the rest.

This could also apply to faulty genes sections currently causing problems could be removed with CRISPR-Cas9, and then replaced with healthy genetic code, theoretically solving the problem.

CRISPR is cutting edge technology, but while its true that its use has massively accelerated in recent years thanks to the above discovery, scientists have actually been aware of it in bacteria since the 1980s. Pubmed lists 5,775 papers discussing CRISPR but 5,575 of those have been in the three years since the UC Berkeley paper, and the number has jumped from 2,071 when I first wrote this article back in October 2015.

CRISPR-Cas9 isnt the first genomic editor, but it has a number of upsides that make it both simpler and far more efficient.

Firstly, CRISPR-Cas9 can edit multiple genes at once, whereas other genome editors such as zinc finger nuclease (ZFN) or transcription activator-like effector nucleases (TALENs) require painstaking modification of a single gene at a time. Its also quicker and cheaper, as you might expect.

Although ZFN and TALENs can recognise longer gene sequences than CRISPR-Cas9, custom proteins have to be created each time and its an inexact science, involving the creation of several variants before the winning combination is found.

On top of that, scientists tend to use ZFN and TALENs with organisms scientists know extremely well such as mice, rats and fruit flies. CRISPR-Cas9 should work with every organism ever evolved. Yes, including humans.

Yes, in China. Using human embryos sourced from a fertility clinic, scientists tried to use CRISPR-Cas9 to edit a gene that causes beta thalassemia in every cell. It should be noted that the donor embryos used were non-viable, and could not have resulted in a live birth.

In any case, it failed, and failed quite badly: 86 embryos were injected, and after 48 hours and around eight cells grown, 71 survived, and 54 of those were genetically tested. Just 28 had been successfully spliced, and very few contained the genetic material the researchers intended. If you want to do it in normal embryos, you need to be close to 100%, lead researcher Jungiu Huang told Nature. Thats why we stopped. We still think its too immature.

On top of that, its extremely likely more undocumented damage was done. As the New York Times explains: The Chinese researchers point out that in their experiment gene editing almost certainly caused more extensive damage than they documented; they did not examine the entire genomes of the embryo cells.

As you might imagine, it caused a huge amount of controversy in the scientific community.

In November 2016, another grouip of Chinese scientists became the first to use CRISPR-Cas9 on an adult human, injecting a lung cancer sufferer with the patient's immune cells modified by CRISPR to disable the PD-1 protein, theoretically making the patient's body fight back against the cancer. Results are still yet to be reported. The first American trial of CRISPR in humans is due to take place at the University of Pennsylvania later this year again with cancer.

Even though the Chinese scientists used embryos that were not going to develop into life, there are real ethical concerns about experimenting on human embryos indeed, just a month before the Chinese research was published, a group of American scientists urged the world not to do so.

Part of this comes down to how immature the technology is remember that its only been in active use since 2012, and it would be astonishing if it was fully matured at this point. Scientists warned that it was too misunderstood and dangerous to use on humans at this point, and the Chinese research certainly vindicates this concern. Even if it worked flawlessly, there are concerns that unforeseen consequences could occur over generations.

But, even if it were 100% safe and successful, there are other ethical concerns: while nobody argues that we should hold back the potential of wiping out killer genetic diseases such as Huntingtons and cystic fibrosis, CRISPR-Cas9 potentially offers the opportunity to change anything about a person. As long as the genetic sequence is identified, in theory, it can be edited.

Its one thing to remove life-impacting diseases before birth its quite another for parents to be able to design their babies to be stronger, faster or better looking. Even if you accept that this is something people should be allowed to do, the chances are this would be heavily commercialised, ensuring only the rich could afford all the extra life advantages this would afford, massively affecting inequality.

Of course, these ethical questions are a million miles away when the only recorded embryonic human experiment was such a high-profile set-back. However, CRISPR-Cas9 is now showing extremely promising results in smaller tests.

Examples include HIV infection prevention in human cells, curing genetic mouse diseases and a pair of monkeys born with targeted mutations. As Wired says, it "kills HIV and eats Zika like Pac-man," with hopes that cancer could be the next disease in its sights.

Yes. Stem cell researchers in the UK sought permission to modify human embryos in an attempt to understand early human development, and reduce the likelihood of miscarriage. In February 2016, theHuman Fertilisation and Embryology Authority (HFEA) granted permission.

As mentioned previously, Cas9 can only recognise genetic sequences of around 20 bases long, meaning that longer sequences cannot be targeted.

More significantly, the enzyme still sometimes cuts in the wrong place. Figuring out why this is will be a significant breakthrough in itself fixing it will be even bigger.

Then, of course, theres the issue that CRISPR didnt work terribly well in human embryos. Scientists need to discover what went wrong there, and what the difference is between the success in single cells and the more patchy results with embryos.

That isnt a simple question to answer. Its subject to an ongoing patent battle surprisingly, given CRISPR is naturally occurring in certain bacteria.

Technology Review explains that, although CRISPR-Cas9 was first described in Science in 2012 by Jennifer Doudna from UC Berkeley, Feng Zhang from the Broad Institute won a patent on the technique by submitting lab notebooks proving hed invented it first.

First to file patent rights means that this should be granted to Doudna, but the decision could have been decided based on first to invent rules, which would have favoured Zhang. In the end, the case was resolved in February 2017, when the US Patent Trial and Appeal Board resolved that UC Berkeley would be granted the patent for the use of CRISPR-Cas9 in any living cell, while Broad would get it in any eukaryotic cell which is to say cells in plants and animals.

Images: Petra B Fritz, VeeDunn, NIH Image Gallery, and Steve Jurvetson used under Creative Commons

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What is CRISPR-Cas9, and will it change the world? | Alphr - Alphr

From their giant fruits to compact plant size, todays tomatoes have been sculpted by thousands of years of breeding. But mutations linked to prized traitsincluding one that made them easier to harvestyield an undesirable plant when combined, geneticists have found.

It is a rare example of a gene harnessed during domestication that later hampered crop improvement efforts, says geneticist Zachary Lippman of Cold Spring Harbor Laboratory in New York. After identifying the mutations, he and his colleagues used CRISPR gene editing to engineer more productive plantsa strategy that plant breeders are eager to adopt.

Its pretty exciting, says Rod Wing, a plant geneticist at the University of Arizona in Tucson. The approach can be applied to crop improvement, not just in tomato, but in all crops.

Lippman knows his way around a tomato farm. As a teenager, he spent his summers picking the fruit by handa chore he hated. Rotten tomatoes. The smell lasts all day long, he says. I would always pray for rain on tomato-harvest day.

But years later, his interest in the genetics that control a plants shape led him back to tomato fields, to untangle the genetic changes that breeders had unknowingly made.

In the 1950s, researchers found a new trait in a wild tomato relative growing in the Galpagos Islands: it lacked the swollen part of the stem called the joint.

Joints are weak regions of the stem that allow fruit to drop off the plant. Wild plants benefit from dropping fruit because it helps seed dispersal. But with the advent of mechanical tomato pickers, farmers wanted their fruit to stay on the plant. Breeders rushed to incorporate the jointless trait into their tomatoes.

This new trait came with a downside. When it was crossed into existing tomato breeds, the resulting plants had flower-bearing branches that produced many extra branches and looked like a broom, terminating in a host of flowers. The flowers were a drain on plant resources, diminishing the number of fruits it produced. Breeders selected for other genetic variants that overrode this defect. But decades later, Lippman's team went looking for the genes behind this phenomenon.

They had previously screened a collection of 4,193 varieties of tomato, looking for those with unusual branching patterns. From that collection, they tracked down variants of two genes that, together, caused extreme branching similar to what plant breeders had seen. One of the two genes, the team reports in a paper published online inCellon 18 May, is responsible for the jointless trait.

The other gene favours the formation of a large green cap of leaf-like structures on top of the fruita trait that was selected for thousands of years ago, in the early days of tomato domestication. The benefits of this trait are unclear, Lippman says, but it may have helped to support heavier fruits.

With these genes uncovered, his team used CRISPRCas9 editing to eliminate their activity, as well as that of a third gene that also affects flower number, in various combinations. This generated a range of plant architectures, from long, spindly flower-bearing branches to bushy, cauliflower-like bunches of flowersincluding some with improved yields.

The findings should help to quell lingering doubts among plant breeders that negative interactions between desirable genetic traits are a force to be reckoned with, says Andrew Paterson, a plant breeder at the University of Georgia in Athens. The idea has been controversial, he says, because the effects have been difficult to detect statistically.

Lippmans team is now working with plant breeders to use gene editing to develop tomatoes with branches and flowers optimized for the size of the fruit. Plants with larger fruit, for example, may have better yields if they have fewer flowering branches than those with smaller fruit.

We really are tapping into basic knowledge and applying it to agriculture, he says. And ironically, it happens to be in the crop that I least liked harvesting on the farm.

This article is reproduced with permission and wasfirst publishedon May 18, 2017.

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Fixing the Tomato: CRISPR Edits Correct Plant-Breeding Snafu ... - Scientific American

Precision editing DNA allows for some amazing applications.

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.

See more here:

Beyond just promise, CRISPR is delivering in the lab today - The Conversation US

Precision editing DNA allows for some amazing applications. Ian Haydon, CC BY-ND

Ian Haydon, University of Washington

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.

Two of the CRISPR co-inventors, Emmanuelle Charpentier (middle-left) and Jennifer Doudna (middle-right), rubbing elbows with celebs after receiving the 2015 Breakthrough Prize in Life Sciences. Breakthrough Prize Foundation, CC BY-ND

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).

Feng Zhang, another co-inventor of CRISPR technology, discussing its safety and ethical ramifications. AP Photo/Susan Walsh

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.

White Agaricus bisporus mushrooms with no browning are more visually appealing. Olha Afanasieva/Shutterstock.com

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.

Ian Haydon, Doctoral Student in Biochemistry, University of Washington

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

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Gene-editing tool 'CRISPR' gaining massive attention - KMOV.com