Archive for the ‘Crispr’ Category

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.

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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.

Continued here:

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

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

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

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

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

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

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

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.

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

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

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

Philippe Huguen/AFP/Getty

A gene mutation that made tomatoes easier to harvest has been identified.

From their giant fruits to compact plant size, todays tomatoes have been sculpted by thousands of years of breeding. But mutations linked to prized traits including one that made them easier to harvest yield an undesirable plant when combined, geneticists have found1.

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 plants a 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 hand a 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 patterns2. 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 in Cell on 18 May, is responsible for the jointless trait1.

The other gene favours the formation of a large green cap of leaf-like structures on top of the fruit a 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 flowers including 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.

See original here:

Fixing the tomato: CRISPR edits correct plant-breeding snafu - Nature.com

May 18, 2017 by Gary Finnegan, From Horizon Researchers in Norwich, UK, are hoping to make crops more resistant to disease. Credit: Kamoun Lab @ TSL

As the world's population rises, scientists want to edit the genes of potatoes and wheat to help them fight plant diseases that cause famine.

By 2040, there will be 9 billion people in the world. "That's like adding another China onto today's 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 as Phytophthora 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 plant's 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.

"It's 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."

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. It's 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 world's 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. "It's 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. "It's 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.

COMREC's 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."

Explore further: US approves 3 types of genetically engineered potatoes (Update)

More information: Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease by Vladimir Nekrasov, Brian Staskawicz, Detlef Weigel, Jonathan D G Jones & Sophien Kamoun in Nature Biotechnology 31, 691693 (2013). DOI: 10.1038/nbt.2655

Involvement of the Cohesin Cofactor PDS5 (SPO76) During Meiosis and DNA Repair in Arabidopsis thaliana by Mnica Pradillo, Alexander Knoll, Cecilia Oliver, Javier Varas, Eduardo Corredor, Holger Puchta and Juan L. Santos in Front. Plant Sci., 01 December 2015 . DOI: 10.3389/fpls.2015.01034

Three types of potatoes genetically engineered to resist the pathogen that caused the Irish potato famine are safe for the environment and safe to eat, federal officials have announced.

Scientists on Monday said they have found a gene to help protect potatoes from a blight that unleashed a devastating famine in Ireland in the 19th century.

Growing crops with stacks of two or more resistance genes from closely related species, introduced into the crop via for instance genetic engineering, combined with the simultaneous introduction of resistance management, ...

A team of scientists from The Sainsbury Laboratory (TSL) and The Genome Analysis Centre (TGAC) have developed a new method to accelerate isolation of plant disease resistance genes. The team have also identified a brand new ...

When you pick up the perfect apple in the supermarket it's easy to forget that plants get sick just like we do. A more realistic view might come from a walk outside during summer: try to find a leaf without a speck, spot ...

We all know that animals have an immune system - but plants have systems to fight infection too. Plant cells have receptor proteins which bind with parts of a pathogen. These receptor proteins are located on the surface of ...

(Phys.org)A pair of researchers from Stanford University has studied the energy used by a type of small parrot as it hops from branch to branch during foraging. As they note in their paper uploaded to the open access site ...

A new Oxford University collaboration revealing the world's prime insect predation hotspots, achieved its landmark findings using an unusual aid: plasticine 'dummy caterpillars.'

Breeding in plants and animals typically involves straightforward addition. As beneficial new traits are discoveredlike resistance to drought or larger fruitsthey are added to existing prized varieties, delivered via ...

After decades of research aiming to understand how DNA is organized in human cells, scientists at the Gladstone Institutes have shed new light on this mysterious field by discovering how a key protein helps control gene organization.

Researchers have successfully developed a novel method that allows for increased disease resistance in rice without decreasing yield. A team at Duke University, working in collaboration with scientists at Huazhong Agricultural ...

University of Chicago psychology professor Leslie Kay and her research group set out to resolve a 15-year-old scientific dispute about how rats process odors. What they found not only settles that argument, it suggests an ...

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Can CRISPR feed the world? - Phys.org - Phys.Org

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Spiny grass and scraggly pines creep amid the arts-and-crafts buildings of the Asilomar Conference Grounds, 100 acres of dune where California's Monterey Peninsula hammerheads into the Pacific. It's a rugged landscape, designed to inspire people to contemplate their evolving place on Earth. So it was natural that 140 scientists gathered here in 1975 for an unprecedented conference.

They were worried about what people called recombinant DNA, the manipulation of the source code of life. It had been just 22 years since James Watson, Francis Crick, and Rosalind Franklin described what DNA wasdeoxyribonucleic acid, four different structures called bases stuck to a backbone of sugar and phosphate, in sequences thousands of bases long. DNA is what genes are made of, and genes are the basis of heredity.

Preeminent genetic researchers like David Baltimore, then at MIT, went to Asilomar to grapple with the implications of being able to decrypt and reorder genes. It was a God-like powerto plug genes from one living thing into another. Used wisely, it had the potential to save millions of lives. But the scientists also knew their creations might slip out of their control. They wanted to consider what ought to be off-limits.

By 1975, other fields of sciencelike physicswere subject to broad restrictions. Hardly anyone was allowed to work on atomic bombs, say. But biology was different. Biologists still let the winding road of research guide their steps. On occasion, regulatory bodies had acted retrospectivelyafter Nuremberg, Tuskegee, and the human radiation experiments, external enforcement entities had told biologists they weren't allowed to do that bad thing again. Asilomar, though, was about establishing prospective guidelines, a remarkably open and forward-thinking move.

At the end of the meeting, Baltimore and four other molecular biologists stayed up all night writing a consensus statement. They laid out ways to isolate potentially dangerous experiments and determined that cloning or otherwise messing with dangerous pathogens should be off-limits. A few attendees fretted about the idea of modifications of the human germ linechanges that would be passed on from one generation to the nextbut most thought that was so far off as to be unrealistic. Engineering microbes was hard enough. The rules the Asilomar scientists hoped biology would follow didn't look much further ahead than ideas and proposals already on their desks.

Earlier this year, Baltimore joined 17 other researchers for another California conference, this one at the Carneros Inn in Napa Valley. It was a feeling of dj vu, Baltimore says. There he was again, gathered with some of the smartest scientists on earth to talk about the implications of genome engineering.

The stakes, however, have changed. Everyone at the Napa meeting had access to a gene-editing technique called Crispr-Cas9. The first term is an acronym for clustered regularly interspaced short palindromic repeats, a description of the genetic basis of the method; Cas9 is the name of a protein that makes it work. Technical details aside, Crispr-Cas9 makes it easy, cheap, and fast to move genes aroundany genes, in any living thing, from bacteria to people. These are monumental moments in the history of biomedical research, Baltimore says. They don't happen every day.

Using the three-year-old technique, researchers have already reversed mutations that cause blindness, stopped cancer cells from multiplying, and made cells impervious to the virus that causes AIDS. Agronomists have rendered wheat invulnerable to killer fungi like powdery mildew, hinting at engineered staple crops that can feed a population of 9 billion on an ever-warmer planet. Bioengineers have used Crispr to alter the DNA of yeast so that it consumes plant matter and excretes ethanol, promising an end to reliance on petrochemicals. Startups devoted to Crispr have launched. International pharmaceutical and agricultural companies have spun up Crispr R&D. Two of the most powerful universities in the US are engaged in a vicious war over the basic patent. Depending on what kind of person you are, Crispr makes you see a gleaming world of the future, a Nobel medallion, or dollar signs.

The technique is revolutionary, and like all revolutions, it's perilous. Crispr goes well beyond anything the Asilomar conference discussed. It could at last allow genetics researchers to conjure everything anyone has ever worried they woulddesigner babies, invasive mutants, species-specific bioweapons, and a dozen other apocalyptic sci-fi tropes. It brings with it all-new rules for the practice of research in the life sciences. But no one knows what the rules areor who will be the first to break them.

In a way, humans were genetic engineers long before anyone knew what a gene was. They could give living things new traitssweeter kernels of corn, flatter bulldog facesthrough selective breeding. But it took time, and it didn't always pan out. By the 1930s refining nature got faster. Scientists bombarded seeds and insect eggs with x-rays, causing mutations to scatter through genomes like shrapnel. If one of hundreds of irradiated plants or insects grew up with the traits scientists desired, they bred it and tossed the rest. That's where red grapefruits came from, and most barley for modern beer.

Genome modification has become less of a crapshoot. In 2002, molecular biologists learned to delete or replace specific genes using enzymes called zinc-finger nucleases; the next-generation technique used enzymes named TALENs.

Yet the procedures were expensive and complicated. They only worked on organisms whose molecular innards had been thoroughly dissectedlike mice or fruit flies. Genome engineers went on the hunt for something better.

Scientists have used it to render wheat invulnerable to killer fungi. Such crops could feed billions of people.

As it happened, the people who found it weren't genome engineers at all. They were basic researchers, trying to unravel the origin of life by sequencing the genomes of ancient bacteria and microbes called Archaea (as in archaic), descendants of the first life on Earth. Deep amid the bases, the As, Ts, Gs, and Cs that made up those DNA sequences, microbiologists noticed recurring segments that were the same back to front and front to backpalindromes. The researchers didn't know what these segments did, but they knew they were weird. In a branding exercise only scientists could love, they named these clusters of repeating palindromes Crispr.

Then, in 2005, a microbiologist named Rodolphe Barrangou, working at a Danish food company called Danisco, spotted some of those same palindromic repeats in Streptococcus thermophilus, the bacteria that the company uses to make yogurt and cheese. Barrangou and his colleagues discovered that the unidentified stretches of DNA between Crispr's palindromes matched sequences from viruses that had infected their S. thermophilus colonies. Like most living things, bacteria get attacked by virusesin this case they're called bacteriophages, or phages for short. Barrangou's team went on to show that the segments served an important role in the bacteria's defense against the phages, a sort of immunological memory. If a phage infected a microbe whose Crispr carried its fingerprint, the bacteria could recognize the phage and fight back. Barrangou and his colleagues realized they could save their company some money by selecting S. thermophilus species with Crispr sequences that resisted common dairy viruses.

As more researchers sequenced more bacteria, they found Crisprs again and againhalf of all bacteria had them. Most Archaea did too. And even stranger, some of Crispr's sequences didn't encode the eventual manufacture of a protein, as is typical of a gene, but instead led to RNAsingle-stranded genetic material. (DNA, of course, is double-stranded.)

That pointed to a new hypothesis. Most present-day animals and plants defend themselves against viruses with structures made out of RNA. So a few researchers started to wonder if Crispr was a primordial immune system. Among the people working on that idea was Jill Banfield, a geomicrobiologist at UC Berkeley, who had found Crispr sequences in microbes she collected from acidic, 110-degree water from the defunct Iron Mountain Mine in Shasta County, California. But to figure out if she was right, she needed help.

Luckily, one of the country's best-known RNA experts, a biochemist named Jennifer Doudna, worked on the other side of campus in an office with a view of the Bay and San Francisco's skyline. It certainly wasn't what Doudna had imagined for herself as a girl growing up on the Big Island of Hawaii. She simply liked math and chemistryan affinity that took her to Harvard and then to a postdoc at the University of Colorado. That's where she made her initial important discoveries, revealing the three-dimensional structure of complex RNA molecules that could, like enzymes, catalyze chemical reactions.

The mine bacteria piqued Doudna's curiosity, but when Doudna pried Crispr apart, she didn't see anything to suggest the bacterial immune system was related to the one plants and animals use. Still, she thought the system might be adapted for diagnostic tests.

Banfield wasn't the only person to ask Doudna for help with a Crispr project. In 2011, Doudna was at an American Society for Microbiology meeting in San Juan, Puerto Rico, when an intense, dark-haired French scientist asked her if she wouldn't mind stepping outside the conference hall for a chat. This was Emmanuelle Charpentier, a microbiologist at Umea University in Sweden.

As they wandered through the alleyways of old San Juan, Charpentier explained that one of Crispr's associated proteins, named Csn1, appeared to be extraordinary. It seemed to search for specific DNA sequences in viruses and cut them apart like a microscopic multitool. Charpentier asked Doudna to help her figure out how it worked. Somehow the way she said it, I literallyI can almost feel it nowI had this chill down my back, Doudna says. When she said the mysterious Csn1 I just had this feeling, there is going to be something good here.

Back in Sweden, Charpentier kept a colony of Streptococcus pyogenes in a biohazard chamber. Few people want S. pyogenes anywhere near them. It can cause strep throat and necrotizing fasciitisflesh-eating disease. But it was the bug Charpentier worked with, and it was in S. pyogenes that she had found that mysterious yet mighty protein, now renamed Cas9. Charpentier swabbed her colony, purified its DNA, and FedExed a sample to Doudna.

Working together, Charpentiers and Doudnas teams found that Crispr made two short strands of RNA and that Cas9 latched onto them. The sequence of the RNA strands corresponded to stretches of viral DNA and could home in on those segments like a genetic GPS. And when the Crispr-Cas9 complex arrives at its destination, Cas9 does something almost magical: It changes shape, grasping the DNA and slicing it with a precise molecular scalpel.

Jennifer Doudna did early work on Crispr. Photo by: Bryan Derballa

Heres whats important: Once theyd taken that mechanism apart, Doudnas postdoc, Martin Jinek, combined the two strands of RNA into one fragmentguide RNAthat Jinek could program. He could make guide RNA with whatever genetic letters he wanted; not just from viruses but from, as far as they could tell, anything. In test tubes, the combination of Jineks guide RNA and the Cas9 protein proved to be a programmable machine for DNA cutting. Compared to TALENs and zinc-finger nucleases, this was like trading in rusty scissors for a computer-controlled laser cutter. I remember running into a few of my colleagues at Berkeley and saying we have this fantastic result, and I think its going to be really exciting for genome engineering. But I dont think they quite got it, Doudna says. They kind of humored me, saying, Oh, yeah, thats nice.

On June 28, 2012, Doudnas team published its results in Science. In the paper and in an earlier corresponding patent application, they suggest their technology could be a tool for genome engineering. It was elegant and cheap. A grad student could do it.

The finding got noticed. In the 10 years preceding 2012, 200 papers mentioned Crispr. By 2014 that number had more than tripled. Doudna and Charpentier were each recently awarded the $3 million 2015 Breakthrough Prize. Time magazine listed the duo among the 100 most influential people in the world. Nobody was just humoring Doudna anymore.

Most Wednesday afternoons, Feng Zhang, a molecular biologist at the Broad Institute of MIT and Harvard, scans the contents of Science as soon as they are posted online. In 2012, he was working with Crispr-Cas9 too. So when he saw Doudna and Charpentier's paper, did he think he'd been scooped? Not at all. I didn't feel anything, Zhang says. Our goal was to do genome editing, and this paper didn't do it. Doudna's team had cut DNA floating in a test tube, but to Zhang, if you weren't working with human cells, you were just screwing around.

That kind of seriousness is typical for Zhang. At 11, he moved from China to Des Moines, Iowa, with his parents, who are engineersone computer, one electrical. When he was 16, he got an internship at the gene therapy research institute at Iowa Methodist hospital. By the time he graduated high school he'd won multiple science awards, including third place in the Intel Science Talent Search.

When Doudna talks about her career, she dwells on her mentors; Zhang lists his personal accomplishments, starting with those high school prizes. Doudna seems intuitive and has a hands-off management style. Zhang pushes. We scheduled a video chat at 9:15 pm, and he warned me that we'd be talking data for a couple of hours. Power-nap first, he said.

If new genes that wipe out malaria also make mosquitoes go extinct, what will bats eat?

Zhang got his job at the Broad in 2011, when he was 29. Soon after starting there, he heard a speaker at a scientific advisory board meeting mention Crispr. I was bored, Zhang says, so as the researcher spoke, I just Googled it. Then he went to Miami for an epigenetics conference, but he hardly left his hotel room. Instead Zhang spent his time reading papers on Crispr and filling his notebook with sketches on ways to get Crispr and Cas9 into the human genome. That was an extremely exciting weekend, he says, smiling.

Just before Doudna's team published its discovery in Science, Zhang applied for a federal grant to study Crispr-Cas9 as a tool for genome editing. Doudna's publication shifted him into hyperspeed. He knew it would prompt others to test Crispr on genomes. And Zhang wanted to be first.

Even Doudna, for all of her equanimity, had rushed to report her finding, though she hadn't shown the system working in human cells. Frankly, when you have a result that is exciting, she says, one does not wait to publish it.

In January 2013, Zhang's team published a paper in Science showing how Crispr-Cas9 edits genes in human and mouse cells. In the same issue, Harvard geneticist George Church edited human cells with Crispr too. Doudna's team reported success in human cells that month as well, though Zhang is quick to assert that his approach cuts and repairs DNA better.

That detail matters because Zhang had asked the Broad Institute and MIT, where he holds a joint appointment, to file for a patent on his behalf. Doudna had filed her patent applicationwhich was public informationseven months earlier. But the attorney filing for Zhang checked a box on the application marked accelerate and paid a fee, usually somewhere between $2,000 and $4,000. A series of emails followed between agents at the US Patent and Trademark Office and the Broad's patent attorneys, who argued that their claim was distinct.

A little more than a year after those human-cell papers came out, Doudna was on her way to work when she got an email telling her that Zhang, the Broad Institute, and MIT had indeed been awarded the patent on Crispr-Cas9 as a method to edit genomes. I was quite surprised, she says, because we had filed our paperwork several months before he had.

The Broad win started a firefight. The University of California amended Doudna's original claim to overlap Zhang's and sent the patent office a 114-page application for an interference proceedinga hearing to determine who owns Crisprthis past April. In Europe, several parties are contesting Zhang's patent on the grounds that it lacks novelty. Zhang points to his grant application as proof that he independently came across the idea. He says he could have done what Doudna's team did in 2012, but he wanted to prove that Crispr worked within human cells. The USPTO may make its decision as soon as the end of the year.

The stakes here are high. Any company that wants to work with anything other than microbes will have to license Zhang's patent; royalties could be worth billions of dollars, and the resulting products could be worth billions more. Just by way of example: In 1983 Columbia University scientists patented a method for introducing foreign DNA into cells, called cotransformation. By the time the patents expired in 2000, they had brought in $790 million in revenue.

It's a testament to Crispr's value that despite the uncertainty over ownership, companies based on the technique keep launching. In 2011 Doudna and a student founded a company, Caribou, based on earlier Crispr patents; the University of California offered Caribou an exclusive license on the patent Doudna expected to get. Caribou uses Crispr to create industrial and research materials, potentially enzymes in laundry detergent and laboratory reagents. To focus on diseasewhere the long-term financial gain of Crispr-Cas9 will undoubtedly lieCaribou spun off another biotech company called Intellia Therapeutics and sublicensed the Crispr-Cas9 rights. Pharma giant Novartis has invested in both startups. In Switzerland, Charpentier cofounded Crispr Therapeutics. And in Cambridge, Massachusetts, Zhang, George Church, and several others founded Editas Medicine, based on licenses on the patent Zhang eventually received.

Thus far the four companies have raised at least $158 million in venture capital.

Any gene typically has just a 5050 chance of getting passed on. Either the offspring gets a copy from Mom or a copy from Dad. But in 1957 biologists found exceptions to that rule, genes that literally manipulated cell division and forced themselves into a larger number of offspring than chance alone would have allowed.

A decade ago, an evolutionary geneticist named Austin Burt proposed a sneaky way to use these selfish genes. He suggested tethering one to a separate geneone that you wanted to propagate through an entire population. If it worked, you'd be able to drive the gene into every individual in a given area. Your gene of interest graduates from public transit to a limousine in a motorcade, speeding through a population in flagrant disregard of heredity's traffic laws. Burt suggested using this gene drive to alter mosquitoes that spread malaria, which kills around a million people every year. It's a good idea. In fact, other researchers are already using other methods to modify mosquitoes to resist the Plasmodium parasite that causes malaria and to be less fertile, reducing their numbers in the wild. But engineered mosquitoes are expensive. If researchers don't keep topping up the mutants, the normals soon recapture control of the ecosystem.

Push those modifications through with a gene drive and the normal mosquitoes wouldn't stand a chance. The problem is, inserting the gene drive into the mosquitoes was impossible. Until Crispr-Cas9 came along.

Emmanuelle Charpentier did early work on Crispr. Photo by: Baerbel Schmidt

Today, behind a set of four locked and sealed doors in a lab at the Harvard School of Public Health, a special set of mosquito larvae of the African species Anopheles gambiae wriggle near the surface of shallow tubs of water. These aren't normal Anopheles, though. The lab is working on using Crispr to insert malaria-resistant gene drives into their genomes. It hasn't worked yet, but if it does well, consider this from the mosquitoes' point of view. This project isn't about reengineering one of them. It's about reengineering them all.

Kevin Esvelt, the evolutionary engineer who initiated the project, knows how serious this work is. The basic process could wipe out any species. Scientists will have to study the mosquitoes for years to make sure that the gene drives can't be passed on to other species of mosquitoes. And they want to know what happens to bats and other insect-eating predators if the drives make mosquitoes extinct. I am responsible for opening a can of worms when it comes to gene drives, Esvelt says, and that is why I try to ensure that scientists are taking precautions and showing themselves to be worthy of the public's trustmaybe we're not, but I want to do my damnedest to try.

Esvelt talked all this over with his adviserChurch, who also worked with Zhang. Together they decided to publish their gene-drive idea before it was actually successful. They wanted to lay out their precautionary measures, way beyond five nested doors. Gene drive research, they wrote, should take place in locations where the species of study isn't native, making it less likely that escapees would take root. And they also proposed a way to turn the gene drive off when an engineered individual mated with a wild counterparta genetic sunset clause. Esvelt filed for a patent on Crispr gene drives, partly, he says, to block companies that might not take the same precautions.

Within a year, and without seeing Esvelt's papers, biologists at UC San Diego had used Crispr to insert gene drives into fruit fliesthey called them mutagenic chain reactions. They had done their research in a chamber behind five doors, but the other precautions weren't there.Church said the San Diego researchers had gone a step too farbig talk from a scientist who says he plans to use Crispr to bring back an extinct woolly mammoth by deriving genes from frozen corpses and injecting them into elephant embryos. (Church says tinkering with one woolly mammoth is way less scary than messing with whole populations of rapidly reproducing insects. I'm afraid of everything, he says. I encourage people to be as creative in thinking about the unintended consequences of their work as the intended.)

Ethan Bier, who worked on the San Diego fly study, agrees that gene drives come with risks. But he points out that Esvelt's mosquitoes don't have the genetic barrier Esvelt himself advocates. (To be fair, that would defeat the purpose of a gene drive.) And the ecological barrier, he says, is nonsense. In Boston you have hot and humid summers, so sure, tropical mosquitoes may not be native, but they can certainly survive, Bier says. If a pregnant female got out, she and her progeny could reproduce in a puddle, fly to ships in the Boston Harbor, and get on a boat to Brazil.

These problems don't end with mosquitoes. One of Crispr's strengths is that it works on every living thing. That kind of power makes Doudna feel like she opened Pandora's box. Use Crispr to treat, say, Huntington's diseasea debilitating neurological disorderin the womb, when an embryo is just a ball of cells? Perhaps. But the same method could also possibly alter less medically relevant genes, like the ones that make skin wrinkle. We haven't had the time, as a community, to discuss the ethics and safety, Doudna says, and, frankly, whether there is any real clinical benefit of this versus other ways of dealing with genetic disease.

Researchers in China announced they had used Crispr to edit human embryos.

That's why she convened the meeting in Napa. All the same problems of recombinant DNA that the Asilomar attendees tried to grapple with are still theremore pressing now than ever. And if the scientists don't figure out how to handle them, some other regulatory body might. Few researchers, Baltimore included, want to see Congress making laws about science. Legislation is unforgiving, he says. Once you pass it, it is very hard to undo.

In other words, if biologists don't start thinking about ethics, the taxpayers who fund their research might do the thinking for them.

All of that only matters if every scientist is on board. A month after the Napa conference, researchers at Sun Yat-sen University in Guangzhou, China, announced they had used Crispr to edit human embryos. Specifically they were looking to correct mutations in the gene that causes beta thalassemia, a disorder that interferes with a person's ability to make healthy red blood cells.

The work wasn't successfulCrispr, it turns out, didn't target genes as well in embryos as it does in isolated cells. The Chinese researchers tried to skirt the ethical implications of their work by using nonviable embryos, which is to say they could never have been brought to term. But the work attracted attention. A month later, the US National Academy of Sciences announced that it would create a set of recommendations for scientists, policymakers, and regulatory agencies on when, if ever, embryonic engineering might be permissible. Another National Academy report will focus on gene drives. Though those recommendations don't carry the weight of law, federal funding in part determines what science gets done, and agencies that fund research around the world often abide by the academy's guidelines.

The truth is, most of what scientists want to do with Crispr is not controversial. For example, researchers once had no way to figure out why spiders have the same gene that determines the pattern of veins in the wings of flies. You could sequence the spider and see that the wing gene was in its genome, but all youd know was that it certainly wasnt designing wings. Now, with less than $100, an ordinary arachnologist can snip the wing gene out of a spider embryo and see what happens when that spider matures. If its obviousmaybe its claws fail to formyouve learned that the wing gene must have served a different purpose before insects branched off, evolutionarily, from the ancestor they shared with spiders. Pick your creature, pick your gene, and you can bet someone somewhere is giving it a go.

Academic and pharmaceutical company labs have begun to develop Crispr-based research tools, such as cancerous miceperfect for testing new chemotherapies. A team at MIT, working with Zhang, used Crispr-Cas9 to create, in just weeks, mice that inevitably get liver cancer. That kind of thing used to take more than a year. Other groups are working on ways to test drugs on cells with single-gene variations to understand why the drugs work in some cases and fail in others. Zhangs lab used the technique to learn which genetic variations make people resistant to a melanoma drug called Vemurafenib. The genes he identified may provide research targets for drug developers.

The real money is in human therapeutics. For example, labs are working on the genetics of so-called elite controllers, people who can be HIV-positive but never develop AIDS. Using Crispr, researchers can knock out a gene called CCR5, which makes a protein that helps usher HIV into cells. Youd essentially make someone an elite controller. Or you could use Crispr to target HIV directly; that begins to look a lot like a cure.

Feng Zhang was awarded the Crispr patent last year. Photo by: Matthew Monteith

Orand this idea is decades away from executionyou could figure out which genes make humans susceptible to HIV overall. Make sure they dont serve other, more vital purposes, and then fix them in an embryo. Itd grow into a person immune to the virus.

But straight-out editing of a human embryo sets off all sorts of alarms, both in terms of ethics and legality. It contravenes the policies of the US National Institutes of Health, and in spirit at least runs counter to the United Nations Universal Declaration on the Human Genome and Human Rights. (Of course, when the US government said it wouldnt fund research on human embryonic stem cells, private entities raised millions of dollars to do it themselves.) Engineered humans are a ways offbut nobody thinks theyre science fiction anymore.

Even if scientists never try to design a baby, the worries those Asilomar attendees had four decades ago now seem even more prescient. The world has changed. Genome editing started with just a few big labs putting in lots of effort, trying something 1,000 times for one or two successes, says Hank Greely, a bioethicist at Stanford. Now its something that someone with a BS and a couple thousand dollars worth of equipment can do. What was impractical is now almost everyday. Thats a big deal.

In 1975 no one was asking whether a genetically modified vegetable should be welcome in the produce aisle. No one was able to test the genes of an unborn baby, or sequence them all. Today swarms of investors are racing to bring genetically engineered creations to market. The idea of Crispr slides almost frictionlessly into modern culture.

In an odd reversal, its the scientists who are showing more fear than the civilians. When I ask Church for his most nightmarish Crispr scenario, he mutters something about weapons and then stops short. He says he hopes to take the specifics of the idea, whatever it is, to his grave. But thousands of other scientists are working on Crispr. Not all of them will be as cautious. You cant stop science from progressing, Jinek says. Science is what it is. Hes right. Science gives people power. And power is unpredictable.

Amy Maxmen (@amymaxmen) writes about science for National Geographic, Newsweek, and other publications. This is her first article for WIRED.

This article appears in the August 2015 issue.

Animation by Anthony Zazzi; Illustrations by Ben Wiseman

See original here:

Easy DNA Editing Will Remake the World. Buckle Up - WIRED

Welcome to the CRISPR-Cas.org webpage. This website is maintained by the Joung Lab at the Massachusetts General Hospital and will provide information and links to resources for those interested in using targetable CRISPR/Cas systems for genome engineering and other applications.

CRISPR/Cas systems are used by various bacteria and archaea to mediate defense against viruses and other foreign nucleic acid. Recent work has shown that Type II CRISPR/Cas systems can be engineered to direct targeted double-stranded DNA breaks in vitro to specific sequences by using a single "guide RNA" with complementarity to the DNA target site and a Cas9 nuclease (Jinek et al., Science 2012). This targetable Cas9-based system also works efficiently in cultured human cells (Mali et al., Science 2013; Cong et al., Science 2013) and in vivo in zebrafish (Hwang and Fu et al., in press) for inducing targeted alterations into endogenous genes.

We hope that the information provided on this webpage will be helpful to those interested in using CRISPR/Cas systems for genome engineering. Note that this webpage is currently under construction and further updates will be posted in the near future. We also welcome suggestions for additional materials about CRISPR/Cas technology not yet listed on these pages.

Read the original post:

CRISPR-Cas.org

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Originally posted here:

What is CRISPR? A Beginner's Guide | Digital Trends

Fruit farmers in the United States have long feared the arrival of harmful citrus tristeza virus to their fields. But now, this devastating pathogen could be their best hope as they battle a much worse disease that is laying waste to citrus crops across the south of the country.

The agricultural company Southern Gardens Citrus in Clewiston, Florida, applied to the US Department of Agriculture (USDA) in February for permission to use an engineered version of the citrus tristeza virus (CTV) to attack the bacterium behind citrus greening. This disease has slashed US orange production in half over the past decade, and threatens to destroy the US$3.3-billion industry entirely.

The required public comment period on the application ended last week, and the USDA will now assess the possible environmental effects of the engineered virus.

Field trials of engineered CTV are already under way. If the request is approved, it would be the first time this approach has been used commercially. It could also provide an opportunity to sidestep the regulations and public stigma attached to genetically engineered crops.

Theres a real race on right now to try to save the citrus, says Carolyn Slupsky, a food scientist at the University of California, Davis. This disease is everywhere, and its horrible.

The engineered virus is just one option being explored to tackle citrus greening. Other projects aim to edit the genome of citrus trees using CRISPRCas9 to make them more resistant to the pest, or engineer trees to express defence genes or short RNA molecules that prevent disease transmission. Local growers have also helped to fund an international project that has sequenced citrus trees to hunt for more weapons against citrus greening.

There are great scientific opportunities here, says Bryce Falk, a plant pathologist at the University of California, Davis. We need to take advantage of new technologies.

Citrus greening is caused by species from the candidate bacterial genus Candidatus Liberibacter. Spread by sap-sucking, flying insects called Asian citrus psyllids (Diaphorina citri), the bacteria cause citrus trees to make bitter, misshapen fruits that have green lower halves. The disease is also widely known by its Chinese name, huanglongbing.

The first tree in the United States with symptoms was reported in Miami in 2005. We had the uh-oh moment, says Fred Gmitter, who breeds new citrus varieties at the University of Florida in Lake Alfred.

Some researchers have had accidental success against the disease. Gmitters team released a mandarin variety called Sugarbell just as the outbreak was getting under way. Although those trees have since become infected with C.Liberibacter, farmers are able to reap a reasonable crop of sweet oranges if the plants receive proper pruning and nutrition. But it is difficult to build on that success: why the trees are relatively tolerant of the disease remains a mystery.

For years, Southern Gardens Citrus has been genetically engineering plants to express genes taken from spinach that defend against the disease. The company says that the results of field trials suggest some degree of protection. But this approach will take many years to meet regulatory requirements for marketing a genetically modified crop. And consumers may not take kindly to a fruit or juice that comes from a genetically modified tree.

So Southern Gardens Citrus added a different approach, and began the USDA approval process for engineered CTV in February. Instead of modifying the trees, the company wants to alter the genome of a harmless strain of CTV so that it produces the spinach defence gene. The company intends to graft tree limbs infected with the virus onto trees. In April, the USDA announced it would start work on an environmental impact statement, a process that typically takes about two years and will be needed before the department allows the modified virus to be used commercially.

Because the virus does not alter the fruit, this approach may allow farmers to argue that the oranges are not genetically modified, and so avoid regulation and reduce public doubt.

That is also the goal of separate projects looking for genes that confer disease resistance when switched off. If researchers can find such genes, they could use CRISPR to inactivate them. Nian Wang, a plant pathologist also at the University of Florida, is using this approach to edit orange trees, and hopes to know by 2019 whether they are disease-resistant. Others are using RNA interference in psyllids to switch off genes that allow the insects to transmit the bacteria.

For now, one question dominates: whether the citrus industry will still be alive by the time these solutions make it to the groves. Its an incredibly devastating disease, says Gmitter. Growers needed answers ten years ago.

This article is reproduced with permission and wasfirst publishedon May 16, 2017.

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Geneticists Enlist Engineered Virus and CRISPR to Battle Citrus Disease - Scientific American

TechCrunch

Synthego's genetic toolkit aims to make CRISPR more accessible TechCrunch We hear a lot about the potential and implications of the gene-editing technique CRISPR, but it's not like just anyone can open up an app, pick a gene they don't like, and build the molecular machinery needed to snip it out. That's the goal, though ... Synthego aims to simplify CRISPR editing for genetic researchersEngadget Synthego Offers Free CRISPR Design ToolBio-IT World Synthego First to Offer Over 100000 Genomes in Powerful New CRISPR SoftwareMarketwired (press release) all 5 news articles »

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Synthego's genetic toolkit aims to make CRISPR more accessible - TechCrunch