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Can Gene Editing Cure Prion Diseases? | Insights from Cyworthy

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DNA molecules are essential carriers of genetic information, including partner molecules. RNA encodes the building blocks of life, specifically amino acids. Together, DNA, RNA, and amino acids form larger structures known as genes, which make up the genetic code for proteins that perform vital functions or contribute to other significant biomolecules.

Occasionally, the RNA within a gene may contain defects that can severely impact protein functionality. Such misfolded proteins, which can lead to fatal diseases, are known as prions. Researchers are optimistic that advancements in RNA editing technology, such as CRISPR, could provide treatment for prion diseases.

The possibility of this treatment has been known since scientists first identified bacteria using natural gene editing methods to combat viruses. Recently, medical researchers from institutions such as Harvard University, the Massachusetts Institute of Technology, and Case Western University conducted a pilot study to explore CRISPR’s effectiveness against prion diseases. The research team aimed to identify defective RNA regions within the genome and modify the corresponding genes. This process involved pinpointing the start and stop codons crucial for gene expression.

In laboratory experiments, scientists collected RNA from mice infected with human prion diseases. Utilizing CRISPR technology, they modified the defective RNA at the molecular level by inserting new start and stop codons to prevent replication. They employed sgRNA designed to produce non-functional proteins. Three versions of the sgRNA were tested: sgRNA, F-sgRNA, and F+E-sgRNA.

The researchers administered a medically approved vector, specifically an adeno-associated virus loaded with modified sgRNA, into mice infected with prion disease. They hypothesized that successful intervention would halt prion replication and prevent related disorders.

To evaluate this, scientists used two groups of mice, one experimental group receiving the modified sgRNAs and a control group receiving none. At ages 6 to 9 weeks, both groups were injected with various strains of human prion disease. Subsequently, only the experimental group was treated with sgRNA between 7 to 10 weeks old.

The mice were monitored for 92 to 95 weeks, recording behavioral changes, weight fluctuation, and lifespan. Post-experiment, researchers compared the health outcomes of both groups to determine the efficacy of the treatment. The findings were promising: treated mice exhibited nearly a 60% increase in lifespan compared to their control counterparts.

To assess the experiment’s success, researchers euthanized the mice post-study and analyzed their brains. They were particularly concerned with ensuring that the edited RNA targeted the proper genes, avoiding off-target editing that could lead to unpredictable outcomes. A thorough examination for possible side effects and abnormalities not linked to prion activity was conducted.

Additionally, they assessed the prion activity to confirm the impact of CRISPR on the targeted RNA strand, focusing on prion protein levels in mice. They observed that treated mice had prion protein levels 4% to 40% lower than those in the control group, with the F+E-sgRNA treatment yielding a 43% reduction in prion levels.

The research team concluded that CRISPR gene editing holds potential for combating prion diseases in mice. However, the significant off-target editing observed could present risks in human applications due to possible adverse effects. The researchers recommend future investigations continue using rodent models until more precise editing techniques are developed. Nevertheless, these results symbolize a meaningful advance toward potential treatments for prion ailments in humans.

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Source: sciworthy.com

CRISPR: Revolutionizing Genetic Code Editing – The Most Innovative Idea of the Century

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New Scientist: Your source for the latest in science news and long-form articles from expert journalists covering advancements in science, technology, health, and environmental issues.

“The pain was like being struck by lightning and being hit by a freight train at the same time,” shared Victoria Gray. New Scientist reflects on her journey: “Everything has changed for me now.”

Gray once endured debilitating symptoms of sickle cell disease, but in 2019, she found hope through CRISPR gene editing, a pioneering technology enabling precise modifications of DNA. By 2023, this groundbreaking treatment was officially recognized as the first approved CRISPR therapy.

Currently, hundreds of clinical trials are exploring CRISPR-based therapies. Discover the ongoing trials that signify just the beginning of CRISPR’s potential. This revolutionary tool is poised to treat a wide range of diseases beyond just genetic disorders. For example, a single CRISPR dose may drastically lower cholesterol levels, significantly reducing heart attack and stroke risk.

While still in its infancy regarding safety, there’s optimism that CRISPR could eventually be routinely employed to modify children’s genomes, potentially reducing their risk of common diseases.

Additionally, CRISPR is set to revolutionize agriculture, facilitating the creation of crops and livestock that resist diseases, thrive in warmer climates, and are optimized for human consumption.

Given its transformative capabilities, CRISPR is arguably one of the most groundbreaking innovations of the 21st century. Its strength lies in correcting genetic “misspellings.” This involves precisely positioning the gene-editing tool within the genome, akin to placing a cursor in a lengthy document, before making modifications.

Microbes utilize this genetic editing mechanism in their defense against other microbes. Before 2012, researchers identified various natural gene-editing proteins, each limited to targeting a single location in the genome. Altering the target sequence required redesigning the protein’s DNA-binding section, a process that was time-consuming.

However, scientists discovered that bacteria have developed a diverse range of gene-editing proteins that bind to RNA—a close relative of DNA—allowing faster sequence matching. Producing RNA takes mere days instead of years.

In 2012, Jennifer Doudna and her team at the University of California, Berkeley, along with Emmanuelle Charpentier from the Max Planck Institute for Infection Biology, revealed the mechanics of one such gene-editing protein, CRISPR Cas9. By simply adding a “guide RNA” in a specific format, they could target any desired sequence.

Today, thousands of variants of CRISPR are in use for diverse applications, all relying on guide RNA targeting. This paradigm-shifting technology earned Doudna and Charpentier the Nobel Prize in 2020.

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Source: www.newscientist.com

Grafting Technology Could Facilitate Gene Editing Across Diverse Plant Species

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Coffee trees can be propagated by grafting the shoots onto the rootstock of another plant

Sirichai Asawarapsakul/Getty Images

The time-honored method of grafting plants may hold contemporary relevance. This technique allows genetic modifications in species that are typically challenging or unfeasible to alter.

“Though it’s still in its formative stages, this technology shows immense promise,” says Hugo Logo from the University of Pisa, Italy.

Enhancing the yield and nutritional content of crops is vital to address the significant damages caused by farming practices and curbing skyrocketing food prices amid a rising global population and climate change’s impact on production. Utilizing CRISPR gene editing for precise enhancements is the most efficient approach.

However, plants present unique challenges due to their rigid cell walls, necessitating a cautious approach to gene editing. Traditional methods of plant genetic engineering involve techniques like biolistics, which shoot DNA-coated particles into plant cells, alongside employing naturally occurring genetically altered microorganisms like Agrobacterium.

These techniques typically require generating entire plants from modified cells, which is often impractical for various species, including trees such as cocoa, coffee, sunflower, cassava, avocado, etc.

Even if this method functions well, there lies another significant hurdle. When gene editing induces subtle mutations analogous to those that frequently occur in nature, regulatory bodies in certain regions may classify these plants as standard varieties, allowing them to proceed without the extensive and costly examinations required for conventional genetically modified crops. In contrast, biolistic and Agrobacterium-mediated methods often incorporate extra DNA into the plant’s genome, thus necessitating full regulatory scrutiny.

Researchers are exploring ways to refine plants without introducing superfluous DNA segments into the genome. One possibility involves utilizing viruses to deliver RNA carrying parts of the CRISPR toolkit to plant cells. However, a challenge arises since the Cas9 protein, widely used in gene editing, is substantial, making it difficult for most viruses to accommodate RNA that encodes it.

In 2023, Friedrich Kragler at the Max Planck Institute for Molecular Plant Physiology, Germany, unveiled an innovative approach. He discovered that plant roots generate a specific type of RNA capable of moving throughout the plant and infiltrating cells in the shoots and leaves.

His team modified plants to produce RNA encoding two essential components of CRISPR: a Cas protein for editing and a guide RNA that directs the editing process. They then grafted shoots from unaltered plants onto the roots of the engineered plants, demonstrating that some of the shoots and seeds underwent gene editing.

Rogo and his team regard this technique as so promising that they published a paper advocating for its further development. “Grafting enables us to harness the CRISPR system in species like trees and sunflowers,” Rogo states.

A notable advantage of grafting is its ability to unite relatively distantly related plants. For example, a tomato bud can be grafted onto a potato root. Therefore, while genetically engineering sunflower rootstocks for gene editing might not be feasible, it is plausible to engineer closely related plants to form compatible rootstocks.

Once you develop a rootstock that produces the required RNA, it can facilitate gene editing across various plants. “We can utilize the roots to supply Cas9 and editing guides to numerous elite varieties,” asserts Julian Hibbard at Cambridge University.

“Creating genetically modified rootstocks is not overly laborious since they only need to be developed once and can serve multiple species indefinitely,” he notes. Ralph Bock, also affiliated with the Max Planck Institute but not part of Kragler’s team, adds that this efficient method has wide applications.

For instance, only a limited number of grape varieties, such as Chardonnay, can be regenerated from an individual cell, making modification feasible. However, once a gene-edited rootstock is established that offers disease resistance, it will benefit all grape varieties and potentially more.

Rogo also foresees the possibility of integrating the transplant and viral techniques, where the rhizome can deliver the large mRNA of Cas9 while the virus provides the guide RNA. This way, he claims, the same rootstock could carry out various gene edits.

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Source: www.newscientist.com

Gene Editing Could Soon Transform Our Meat: Here’s What It Means

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From hot dogs to crispy bacon, by 2026, many food staples in the US will utilize gene-edited meat. Indeed, the US Food and Drug Administration (FDA) has recently given the green light to the agricultural use of certain genetically enhanced pigs. Other global regulators may soon follow suit.

But should we be concerned? Is this modified pork safe? And what about the ethics of creating these pigs?

Firstly, it’s important to note that not all gene-edited animals are produced in a laboratory setting. Instead, these livestock come from animals whose DNA has been modified early in their development, often conferring advantageous traits starting from a single cell or fertilized egg.

This gene editing isn’t focused on enhancing pork flavor; it’s primarily aimed at safeguarding the pigs from diseases.

For instance, a UK company is currently developing genetic modifications in pigs that render them resistant to Porcine Reproductive and Respiratory Syndrome (PRRS), a virus that significantly weakens the immune system of pigs. PRRS poses a serious threat, leading to the deaths of piglets, miscarriages in pregnant sows, and increased vulnerability to other infections.

Pork is the third most consumed meat in the United States after chicken and beef.

These genetically enhanced pigs are significant particularly because there is currently no effective vaccine for PRRS.

The stakes are high, with efforts to manage PRRS costing the US pork industry about $1.2 billion (£878 million) each year.

When the virus does break through, the implications can be dire. In 2006, a pandemic in China infected over 2 million pigs, resulting in 400,000 deaths.

CRISPR Bacon

How much have these pigs really changed? That’s a valid concern. However, the actual modifications are surprisingly minor.

To combat the PRRS virus, scientists have edited out a portion of the CD163 protein in the pig’s DNA, which the virus uses to invade pig cells.

Pigs with this genetic modification show resistance to nearly all known strains of PRRS, but they are otherwise similar to conventional pigs. Despite initial fears that viruses could evolve to bypass edited proteins, this hasn’t occurred.

Dr. Christine Tait-Burkard, a researcher at the University of Edinburgh’s Roslin Institute, describes the original CD163 protein as “like nine beads on a string,” with only one bead—the fifth one—removed during editing.

This minor alteration is sufficient to block viral infection, she elucidates, while not significantly affecting other protein functions (such as those involved in clearing damaged red blood cells).

Interestingly, the gene rearrangement could also occur naturally in some pigs. “It’s possible there is a pig somewhere in the world resistant to this virus,” Tait-Burkard states. “However, we don’t have the luxury of time for natural breeding, so we must utilize biotechnology to introduce it into our breeding programs.”

The editing employs a toolkit known as CRISPR, a Nobel Prize-winning technology that has gained popularity in scientific research for its efficiency, precision, and affordability. The CRISPR tool uses a “guide” sequence to target DNA, employing protein “scissors”—naturally occurring proteins found in bacteria—to make necessary cuts. Minor adjustments, such as those seen in PRRS-resistant pigs, disable particular genes.

A New Norm?

Once they hit grocery store shelves, PRRS-resistant pigs are expected to become the first widely consumed gene-edited animals. However, they are not the first genetically modified products available to consumers.

Hypoallergenic “Gal Safe” Pork, designed for consumers with meat allergies, received approval in 2020. In 2022, the FDA also approved a type of cow known as Smooth cow—a breed enhanced with traits from naturally occurring genetic variants in tropical cows for shorter hair and better heat recovery. Additionally, genetically modified “Aquadvantage” Salmon is available in the US, albeit primarily sold in restaurants.

The situation is more complex across the Atlantic. As it stands, gene-edited foods cannot be marketed in the EU, and legislation for Genetic Technology (Precision Breeding) in the UK lays groundwork for breeding gene-edited crops, but it has not yet been extended to animals.

Even if regulations evolve globally, will consumers be eager to purchase gene-edited sausages and bacon?

The labeling for this new gene-edited pork remains undecided, but Dr. Katie Sanders, a communications specialist at North Carolina State University, suggests that there is greater potential for consumer acceptance compared to traditional genetically modified (GM) foods. This perception stems from the belief that gene-edited products appear more natural.

In the past, genetically modified (GM) crops stirred up fears and headlines focused on “frankenfood.” However, many of these crops were ultimately approved, with most scientists considering them safe for consumption. These GM crops often incorporate foreign genes—like “Bt” corn, which carries genes from the bacterium Bacillus thuringiensis to repel insect pests.

In contrast, the current wave of CRISPR-edited foods only features modifications that could naturally occur within the species. Scientists have not created an entirely new variety of pigs.

Sanders and her colleagues, along with associate professor Jean Parera at Texas A&M University, conducted a national survey of more than 2,000 Americans to gauge attitudes towards CRISPR-edited pork. While results await publication, Sanders notes that respondents generally indicated a likelihood to purchase CRISPR-edited pork.

This trend was especially noted in urban populations (compared to rural ones) and among those with lower educational attainment (as opposed to individuals with degrees).

In 2006, PRRS outbreaks in China affected over 2 million pigs, leading to 400,000 deaths.

When asked how producers can persuade more consumers to adopt gene-edited meat, Parrella emphasized the importance of “responsible use and ethical considerations surrounding CRISPR applications.”

Initial marketing of PRRS-resistant pigs highlights these ethical considerations, demonstrating they have been addressed. A division of the industry, known as The Pig Improvement Company—yes, that’s its actual name—underscores benefits like enhanced animal welfare, reduced antibiotic reliance, and positive environmental effects.

If their messaging resonates, could more gene-edited animals find their way to our dinner tables? Perhaps. Scientists at the Roslin Institute are currently researching edits to combat other livestock diseases, including the bovine diarrhea virus.

However, Tait-Burkard cautions that engineering resistance to specific viruses, like avian influenza, may pose more significant challenges or require edits harmful to animal cells. The proteins they edited for pig PRR resistance are “excellent targets,” but they are challenging to identify.

For traits linked to productivity, such as improved breeding and meat quality, the agricultural sector is already refining efficient breeding techniques to achieve these objectives. As such, it’s unlikely that costly gene editing will be utilized to create “super” meat anytime soon.

Nonetheless, if gene editing can enhance animal protection, minimize antibiotics, and alleviate environmental burdens, it could swiftly transition from novelty to normalcy—provided animal welfare remains uncompromised.

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Source: www.sciencefocus.com

Gene Editing Offers Hope for “Irreversible” Kidney Disease Damage Treatment

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Kidney disease can result in hypertension and infections

Mohammed Haneefa Nizamudeen/Getty Images

Recent animal research suggests that damage caused by the most prevalent hereditary kidney disease may not be as irreversible as previously thought. Researchers are using CRISPR gene editing to potentially reverse certain mutations responsible for the condition.

Polycystic kidney disease (PKD) gradually alters kidney function, leading to debilitating effects. “It was generally believed that correcting the mutations would not change the outcome,” says Michael Kaminski from Berlin University of Medicine.

PKD results in the formation of fluid-filled cysts in the kidneys and liver, leading to organ failure and necessitating dialysis or transplants. Besides organ failure, damage and swelling can lead to other severe issues, including high blood pressure and infections.

The disease typically affects adults, with approximately 12 million individuals globally estimated to be affected. Symptoms may not manifest until the cysts reach significant size in one’s 30s, by which point there may already be extensive damage to the kidneys and liver.

Kaminski’s team has utilized a CRISPR method known as base editing to correct mutations in the PKD1 gene in mice models.

This technique successfully corrected mutations primarily in the liver, resulting in a reduction in both the size and number of cysts post-treatment. Kaminski noted potential improvements in the kidneys as well.

Specifically, Xiaogang Li’s team at Mayo Clinic conducted a similar study using more precise methods targeting the kidneys, indicating a reduction in cyst size and quantity, according to Li.

Both teams employed viral vectors to deliver gene-editing tools, which poses challenges with repeated doses due to immune responses might hinder treatment. “This is a legitimate concern,” Li notes. “However, we’ve observed limited immune responses in our animal models so far.”

Utilizing lipid nanoparticles instead of viral vectors, as seen in mRNA vaccines, could mitigate immune-related issues, but Kaminski warns that these particles may struggle to penetrate deeply into the kidneys through the bloodstream. “I believe that the delivery method using [lipid nanoparticles] might become more feasible through urinary pathways,” he says.

Another limitation is that base editing primarily addresses single-character mutations, rendering it ineffective for individuals with longer mutation sequences. However, Li reports successful outcomes using a technique known as Prime editing.

These findings are poised to be published shortly in scientific journals, with plans for human trials to follow. “After our publication, I aim to organize a small clinical trial,” he states.

The broader implications of this research suggest that if PKD can indeed be reversed, it could ignite more research into this potential therapeutic avenue. Currently, the only approved treatment is tolvaptan, which only slightly slows disease progression and requires significant fluid intake.

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Source: www.newscientist.com

CRISPR gene editing brings us sweeter tomatoes

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Gene editing can make larger tomato varieties sweeter

Paul Maguire/Shutterstock

If you like sweet tomatoes, smaller cherry tomato varieties are the way to go right now. But larger tomato varieties could soon be enhanced for sweetness with the help of CRISPR gene editing.

Jinzhe Zhang of the Chinese Academy of Agricultural Sciences in Beijing said the larger the tomato, the lower the sugar content usually is. Efforts to increase the sweetness of large varieties also had downsides, such as lower yields.

Zhang and colleagues compared different varieties to identify genetic variations that affect sweetness. They discovered two closely related genes called. SlCDPK27 and SlCDPK26 Larger varieties are more active. These genes code for proteins that reduce the levels of sugar-producing enzymes.

When the research team used CRISPR gene editing to disable these genes in a variety called Moneymaker, glucose and fructose levels in the fruit increased by up to 30% without any loss in yield. Taste tests also rated the fruit as sweeter. The only other effect is that the number of species that consumers are likely to prefer will be smaller and smaller.

“We are working with several companies to develop several commercial varieties by knocking out these genes,” Zhang says. “It's still in the early stages.”

In addition to increased sweetness, another potential benefit is that fewer tomatoes are needed to make tomato ketchup with the same sweetness level.

Gene-edited Money Maker tomatoes aren't as sweet as cherry varieties such as Sungold, but they could be made even sweeter, Zhang said. “Many important genes that control sugar are still waiting to be discovered.”

CRISPR-edited tomatoes, which contain high concentrations of a beneficial nutrient called GABA, are already on sale in Japan, the first CRISPR food to be sold, and are sometimes given as seedlings.

Tomatoes were also the first genetically modified food to be sold commercially. Called Flavr Savr, it was sold in paste form in the United States starting in 1994, but was later discontinued. Since last year, purple GM tomatoes rich in anthocyanins have become available in the United States in fruit and seedling form.

Several countries, including Japan and China, have regulations that make it easier to obtain approval for gene-edited crops compared to other forms of genetic modification, except for conventional breeding. approved by china Last year, the first gene-edited crop was created. Soybeans have high levels of oleic acid.

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Source: www.newscientist.com

‘Refining Bridge Editing: A Potential Improvement Over CRISPR for DNA Modification’

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Bridge editing physically links two DNA strands

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A powerful DNA-editing mechanism discovered in bacteria has the potential to enable much larger genome modifications than are currently possible with CRISPR-based techniques, but it is not yet clear whether it would work in human cells.

Patrick Shue Researchers at the Ark Institute in California call their new genome editing system the “bridge editing” system because it physically links, or bridges, two strands of DNA. “Using this system, we can modify large parts of the genome,” says Su. Su's team has figured out how bacterial “parasitic” DNA sequences naturally replicate using this system and how it can be applied to genome editing.

“We're excited about the possibility of making much broader genome modifications that go far beyond what we can do today with CRISPR,” he says, “and we see this as an important step toward a broader vision for genome design.”

CRISPR gene editing has revolutionized biology since it was introduced in 2012. It is used for a variety of purposes, and the first CRISPR-based therapeutic was approved last year. However, the basic form of CRISPR, which uses the Cas9 protein, is gene disruption rather than gene editing.

A standard CRISPR Cas9 protein has two parts: one part binds to a guide RNA molecule and looks for DNA that matches a specific section of the guide RNA. Custom guide RNAs are easy to create, so CRISPR Cas9 can be “programmed” to look for any part of the genome.

The second part of CRISPR Cas9 is a cutter that cuts the DNA when Cas9 binds to the target site. Once the cell has repaired the damage, Cas9 cuts it again. This action continues until an error is made during repair, resulting in the intended mutation of the target site.

While being able to mutate specific sites is useful, biologists want to make more precise changes, so they are modifying CRISPR proteins to edit DNA directly rather than relying on cellular repair mechanisms. For example, base editors can change one DNA letter to another without cutting the DNA, while prime editors can convert an extra section of guide RNA into DNA and add it to the target site.

These improved versions of CRISPR have the potential to treat a wide range of diseases, with several clinical trials already underway, but to address some diseases, more sophisticated genome modifications are needed. Many teams around the world are working on ways to achieve this. Some have realized that the mechanism by which genetic parasites cut and paste from one part of the genome to another, called IS110 elements, has potential because, like CRISPR, it is RNA-guided, but Hsu's team is the first to fully understand how it works.

The bridge-editing system consists of a so-called recombinase protein that binds to a guide RNA, such as the CRISPR Cas9 protein. What's unique about this system is that the guide RNA specifies two DNA sequences to seek out, not just one, Hsu's team found.

One sequence specifies the target site in the genome to modify, similar to CRISPR, and the other specifies the DNA to change. Using this system, DNA sequences of virtually any length can be added, deleted, or inverted.

There are already ways to do this, but they typically require multiple steps and leave behind a piece of extra DNA called a scar. “Bridge editing leaves virtually no scar,” Hsu says. “It offers an unprecedented level of control in engineering the genome.”

This means that it could be used for more than just replacing faulty genes, he says: It could also be useful for completely remaking the genomes of plants and animals. “What we want to do is go from inserting individual genes to doing chromosome-scale genome engineering,” Su says.

“The findings reported are certainly exciting and the underlying biology is truly surprising.” Steven Tang Bridge editing is being done at Columbia University in New York, but so far it has only been demonstrated to work in bacterial cells or in test tubes. Tang says it remains to be seen whether and to what extent bridge editing will work in complex cells like humans. But even if bridge editing doesn't work in initial tests in human cells, it may be possible to modify the system to work over time.

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Source: www.newscientist.com

Making plants blue through gene editing could simplify weed removal by robots

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Changing the color of crops may make it easier to distinguish between target plants and weeds

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Common crops such as wheat and corn could be genetically modified to be brightly colored to make them easier for weeding robots to work with, researchers have suggested.

Weeding reduces the need for herbicides, but the artificial intelligence models that power weeding robots can have trouble distinguishing weeds from crops that are similar in shape and color.

To avoid this problem, Pedro Correia Researchers from the University of Copenhagen in Denmark and their colleagues have suggested that crop genomes could be adapted to express pigments such as anthocyanins, which make blueberries blue, and carotenoids, which make carrots orange.

It is also possible to grow crops with unusually shaped leaves or other traits that are invisible to the naked eye but can be detected by sensors such as those in the infrared spectrum.

Correia said AI's weeding struggles could get worse as wild species adapt to agriculture, taking advantage of their ability to cope with changing climate. This type of new domestication can produce crops that are more environmentally sustainable and higher yielding, but can also be difficult to distinguish from their unchanged ancestors.

“We're trying to change a very small number of genes to increase productivity,” Correia says. “It would be great if he could change one or two more genes to make them more recognizable and to be able to use robots to weed.”

charles fox The University of Lincoln in the UK says there is precedent for intentionally changing the color of crops. Orange carrots were not common until producers selectively bred stable varieties. But he thinks genetic modification is probably not the easiest way to improve the effectiveness of weed-killing robots.

“Other methods would probably be much easier and less controversial because people generally don't like genetic modification,” Fox says. “Sounds like a lot of effort.”

Correia says he's not suggesting creating something new or adding animal genes. The research involves modifying crop genomes to incorporate genes for pigments already produced in other plants. “We're just making some changes to the crop so they can eat it too,” he says. “We'll have to test everything and test for side effects and things like that, but I think it's quite possible.”

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Source: www.newscientist.com

The merger of quantum biology and AI fueled genome editing advancements

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Scientists at Oak Ridge National Laboratory have utilized quantum biology and explainable artificial intelligence to advance CRISPR Cas9 technology for genome editing in microorganisms. This breakthrough has enabled more precise genetic modification of microorganisms, opening up possibilities for the production of renewable fuels and chemicals. The research at Oak Ridge National Laboratory has significantly improved the efficiency of CRISPR Cas9 genome editing in microorganisms and contributed to renewable energy development.

CRISPR is a powerful tool for bioengineering, used to modify the genetic code to improve the performance of organisms or correct mutations. ORNL scientists developed a method to improve the accuracy of the CRISPR Cas9 gene editing tool used to modify microorganisms for the production of renewable fuels and chemicals. They have leveraged their expertise in quantum biology, artificial intelligence, and synthetic biology to achieve this.

To improve the modeling and design of guide RNAs, ORNL scientists sought to better understand what is happening at the most fundamental level in the cell nucleus, where genetic material is stored. They turned to quantum biology to study how electronic structure affects the chemical properties and interactions of nucleotides, such as DNA and RNA.

Furthermore, scientists at ORNL have built an explainable artificial intelligence model called iterated random forest, which has been used to train the model on a dataset of about 50,000 guide RNAs targeting the genome of Escherichia coli. This model has provided important features regarding the nucleotides that allow for better selection of guide RNAs.

Improving the CRISPR Cas9 model provides scientists with a high-throughput pipeline for linking genotype to phenotype in functional genomics. This research will impact efforts at the ORNL-led Center for Bioenergy Innovation (CBI), such as improving bioenergy feedstock plants and bacterial fermentation of biomass.

The results of this research significantly improve the prediction of guide RNAs. This represents an exciting advance toward understanding how avoid ‘mistakes’ and improving the ability to use CRISPR tools to predictively modify the DNA of more organisms. The study was funded by SEED SFA and CBI, part of the DOE Office of Science’s Biological and Environmental Research Program, ORNL’s Laboratory-Directed Research and Development Program, and OLCF and Compute’s High Performance Computing Resources and Data Environment for Science, both supported by the Office of Science.

Source: scitechdaily.com