The Many Uses of CRISPR: Scientists Tell All

What do infectious diseases, T-cells, tomatoes, heart failure, sickle cell anemia and sorghum harvests have in common?

#cancer, #cereals, #crispr-dna, #genetic-engineering, #heart, #research, #sickle-cell-anemia, #tomatoes

CRISPR, 10 Years On: Learning to Rewrite the Code of Life

The gene-editing technology has led to innovations in medicine, evolution and agriculture — and raised profound ethical questions about altering human DNA.

#biology-and-biochemistry, #broad-institute, #clinical-trials, #crispr-dna, #dna-deoxyribonucleic-acid, #doudna-jennifer-a, #ethics-and-official-misconduct, #genetic-engineering, #genetics-and-heredity, #he-jiankui, #nobel-prizes, #science-and-technology, #university-of-california, #your-feed-health, #your-feed-science

Pig heart transplant failure: Doctors detail everything that went wrong

Image of long arrays of cells stained pink.

Enlarge / Much of the heart is composed of muscle cells like the ones shown here. (credit: Ed Reschke)

Earlier this year, news broke of the first experimental xenotransplantation: A human patient with heart disease received a heart from a pig that had been genetically engineered to avoid rejection. While initially successful, the experiment ended two months later when the transplant failed, leading to the death of the patient. At the time, the team didn’t disclose any details regarding what went wrong. But this week saw the publication of a research paper that goes through everything that happened to prepare for the transplant and the weeks following.

Critically, this includes the eventual failure of the transplant, which was triggered by the death of many of the muscle cells in the transplanted heart. But the reason for that death isn’t clear, and the typical signs of rejection by the immune system weren’t present. So, we’re going to have to wait a while to understand what went wrong.

A solid start

Overall, the paper paints a picture of organ recipient David Bennett as a patient who was on the verge of death when the transplant took place. He was an obvious candidate for a heart transplant and was only kept alive through the use of a device that helped oxygenate his blood outside his body. But the patient had what the researchers refer to as “poor adherence to treatment,” which led four different transplant programs to deny him a human heart transplant. At that point, he and his family agreed to participate in the experimental xenotransplant program.

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#genetic-engineering, #medicine, #science, #transplants, #xenotransplant

Signs of an Animal Virus Discovered in Man Who Received a Pig’s Heart

The patient showed no sign of rejecting the genetically modified organ, but suffered numerous complications.

#cytomegalovirus, #genetic-engineering, #maryland, #pigs, #surgery-and-surgeons, #transplants, #university-of-maryland, #your-feed-science

The Search for a Model Octopus That Won’t Die After Laying Its Eggs

A lab in Massachusetts may have finally found an eight-armed cephalopod that can serve as a model organism and assist scientific research.

#animal-abuse-rights-and-welfare, #animal-behavior, #animal-cognition, #brain, #genetic-engineering, #genetics-and-heredity, #laboratories-and-scientific-equipment, #marine-biological-laboratory, #octopus, #research, #your-feed-animals, #your-feed-science

Patient in Groundbreaking Heart Transplant Dies

David Bennett Sr. had received a heart from a genetically modified pig, a procedure that may yet offer hope to millions of Americans needing transplants.

#genetic-engineering, #heart, #kidneys, #pigs, #surgery-and-surgeons, #transplants, #university-of-maryland-medical-center, #your-feed-science

The genetic engineering behind pig-to-human transplants

Image of young pigs in a plastic container.

Enlarge / Cloned piglets that are engineered to be useful for organ transplants to humans. (credit: Getty Images / Staff)

Last week, when we reported on the first pig-to-human heart transplant, we complained that the commercial company behind the operation wasn’t more forthcoming about the genetic engineering that converted the pig into a viable donor.

We now know much more about porcine genetic engineering thanks to a new paper covering a different, more cautious test procedure. The work described in the paper is a transplant of pig kidneys into a brain-dead recipient and is meant to pave the way for trials in viable humans. The publication that describes the work contains extensive details on the genetic engineering used to ensure that the pig tissue would survive in a human host.

A test case

According to The New York Times, the recipient was rendered brain-dead by a motorcycle accident. He had signed up as an organ donor and was kept alive while his organs were screened; his next of kin gave informed consent to his body’s use in the experimental procedure.

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#biology, #genetic-engineering, #medicine, #organ-transplants, #science, #xenotransplants

Kidneys From a Genetically Altered Pig Are Implanted in a Brain-Dead Patient

Surgeons at the University of Alabama at Birmingham said they hoped to start clinical trials with kidney patients later this year.

#american-journal-of-transplantation, #genetic-engineering, #kidneys, #pigs, #surgery-and-surgeons, #transplants, #university-of-alabama-at-birmingham, #your-feed-science

Patient in Groundbreaking Pig Heart Transplant Has a Criminal Record

David Bennett Sr. was involved in a serious assault nearly 35 years ago, court records show.

#assaults, #genetic-engineering, #maryland, #murders-attempted-murders-and-homicides, #transplants, #university-of-maryland-medical-center, #your-feed-science

Patient in Groundbreaking Heart Transplant Has a Criminal Record

David Bennett Sr. was involved in a serious assault nearly 35 years ago, court records show.

#assaults, #genetic-engineering, #maryland, #murders-attempted-murders-and-homicides, #transplants, #university-of-maryland-medical-center, #your-feed-science

In a First, Man Receives a Heart From a Genetically Altered Pig

The breakthrough may lead one day to new supplies of animal organs for transplant into human patients.

#baltimore-md, #cloning, #genetic-engineering, #genetics-and-heredity, #heart, #kidneys, #pigs, #surgery-and-surgeons, #transplants, #university-of-maryland-medical-center, #your-feed-science

This Ink Is Alive and Made Entirely of Microbes

Scientists have created a bacterial ink that reproduces itself and can be 3D-printed into living architecture.

#3-d-printers, #e-coli-bacteria, #genetic-engineering, #microbiology, #nature-communications-journal, #polymers, #sustainable-living, #synthetic-biology, #your-feed-science

In a First, Surgeons Attached a Pig Kidney to a Human — and It Worked

A kidney grown in a genetically altered pig seemed to function normally, potentially a new source for desperately needed transplant organs.

#genetic-engineering, #kidneys, #new-york-university-langone-health, #organ-donation, #pigs, #research, #surgery-and-surgeons, #transplants, #your-feed-science

How Biology is Getting a Technological Makeover

The story of Ginkgo Bioworks shows the challenges and progress in the emerging field of synthetic biology.

#biotechnology-and-bioengineering, #computers-and-the-internet, #genetic-engineering, #ginkgo-bioworks-inc, #laboratories-and-scientific-equipment, #start-ups, #synthetic-biology, #venture-capital

Pioneering Gene Therapy Freed Her of Sickle Cell. Is a Cure at Hand?

Such treatments are extraordinarily promising and costly. Will the Biden administration commit to spending that could speed clinical trial results?

#clinical-trials, #drugs-pharmaceuticals, #genetic-engineering, #genetics-and-heredity, #race-and-ethnicity, #research, #sickle-cell-anemia

A New Company With a Wild Mission: Bring Back the Woolly Mammoth

With $15 million in private funding, Colossal aims to bring thousands of woolly mammoths back to Siberia. Some scientists are deeply skeptical that will happen.

#church-george-m, #cloning, #elephants, #endangered-and-extinct-species, #genetic-engineering, #genetics-and-heredity, #mammoths-animals, #paleontology, #your-feed-science

Should we care about the lives of our kids’ kids’ kids’ kids’…

We live during a time of live, real-time culture. Telecasts, spontaneous tweetstorms, on-the-scene streams, rapid-response analysis, war rooms, Clubhouses, vlogging. We have to interact with the here and now, feel that frisson of action. It’s a compulsion: we’re enraptured by the dangers that are terrorizing whole segments of the planet.

Just this past month, we saw Hurricane Ida strike New Orleans and the Eastern Seaboard, with some of the fiercest winds in the Gulf of Mexico since Hurricane Katrina. In Kabul, daily videos and streams show up-to-the-minute horrors of a country in the throes of chaos. Dangers are omnipresent. Intersect these pulses to the amygdala with the penchant for live coverage, and the alchemy is our modern media.

Yet, watching live events is not living, and it cannot substitute for introspection of both our own condition and the health of the world around us. The dangers that sprawl across today’s headlines and chyrons are often not the dangers we should be spending our time thinking about. That divergence between real-time risks and real risks has gotten wider over time — and arguably humanity has never been closer to the precipice of true disaster even as we are subsumed by disasters that will barely last a screen scroll on our phones.

Toby Ord, in his prophetic book The Precipice, argues that we aren’t seeing the existential risks that can realistically extinguish human life and flourishing. So he has delivered a rigorous guide and compass to help irrational humans understand what risks truly matter — and which we need to accept and move on.

Ord’s canvas is cosmic, dating from the birth of the universe to tens of billions of years into the future. Humanity is but the smallest blip in the universal timeline, and the extreme wealth and advancement of our civilization dates to only a few decades of contemporary life. Yet, what progress we have made so quickly, and what progress we are on course to continue in the millennia ahead!

All that potential could be destroyed though if certain risks today aren’t considered and ameliorated. The same human progress that has delivered so much beauty and improvement has also democratized tools for immense destruction, including destructiveness that could eliminate humanity or “merely” lead to civilizational collapse. Among Ord’s top concerns are climate change, nuclear winter, designer pandemics, artificial general intelligence and more.

There are plenty of books on existential risks. What makes The Precipice unique is its forging in the ardent rationality of the effective altruism movement, of which Ord is one of its many leaders. This is not a superlative dystopic analysis of everything that can go wrong in the coming centuries, but rather a coldly calculated comparison of risks and where society should invest its finite resources. Asteroids are horrific but at this point, well-studied and deeply unlikely. Generalized AI is much more open to terrifying outcomes, particularly when we extend our analysis into the decades and centuries.

While the book walks through various types of risks from natural to anthropogenic to future hypothetical ones, Ord’s main goal is to get humanity to take a step back and consider how we can incorporate the lives of billions — maybe even trillions — of future beings into our calculations on risk. The decisions we make today don’t just affect ourselves or our children, but potentially thousands of generations of our descendants as well, not to mention the other beings that call Earth home. In short, he’s asking the reader for a bold leap to see the world in geological and astronomical time, rather than in real-time.

It’s a mission that’s stunning, audacious, delirious and enervating at times, and occasionally all at the same time. Ord knows that objections will come from nearly every corner, and half the book’s heft is made up of appendices and footnotes to deflect arrows from critics while further deepening the understanding of the curious reader or specialist. If you allow yourself to be submerged in the philosophy and the rigorous mental architecture required to think through long-termism and existential risks, The Precipice really can lead to an awakening of just how precarious most of our lives are, and just how interwoven to the past and future we are.

Humanity is on The Precipice, but so are individuals. Each of us is on the edge of understanding, but can we make the leap? And should we?

Here the rigor and tenacity of the argument proves a bit more elusive. There isn’t much of a transition available from our live, reality-based daily philosophy to one predicated on seeing existential risks in all the work that we do. You either observe the existential risks and attempt to mitigate them, or you don’t (or worse, you see them and give up on protecting humanity’s fate). As Ord points out, that doesn’t always mean sacrifice — some technologies can lower our existential risk, which means that we should accelerate their development as quickly as possible.

Yet, in a complicated world filled with the daily crises and trauma of people whose pained visages are etched into our smartphone displays, it’s challenging to set aside that emotional input for the deductive and reductive frameworks presented here. In this, the criticism isn’t so much on the book as on the wider field of effective altruism, which attempts to rationalize assistance even as it effaces often the single greatest compulsion for humans to help one another: the emotional connection they feel to another being. The Precipice delivers a logical ethical framework for the already converted, but only offers modest guidance to persuade anyone outside the tribe to join in its momentum.

That’s a shame, because the book’s message is indeed prophetic. Published on March 24, 2020, it discusses pandemics, gain-of-function research, and the risks of modern virology — issues that have migrated from obscure academic journals to the front pages. There really are existential risks, and we really do need to confront them.

As the last year has shown, however, even well-known and dangerous risks like pandemics are difficult for governments to build up capacity to handle. Few humans can spend their entire lives moored to phenomenon that happen once in 100,000 years, and few safety cultures can remain robust to the slow degradation of vigilance that accompanies any defense that never gets used.

The Precipice provides an important and deeply thought-provoking framework for thinking about the risks to our future. Yet, it’s lack of engagement with the social means that it will have little influence on how to slake our obsession for the risks right before us. Long-termism is hard, and TikTok is always a tap away.

The Precipice: Existential Risk and the Future of Humanity by Toby Ord
Hachette, 2020, 480 pages

See Also

#book-review, #book-reviews-climate-change, #climate-change, #disaster-response, #existential-risk, #genetic-engineering, #policy

Engineering a second genetic code in parallel with the normal one

A cartoon of the process that translates the genetic code in DNA into a protein.

Enlarge / A cartoon of the process that translates the genetic code in DNA into a protein. (credit: BSIP / Getty Images)

All living things on Earth use a version of the same genetic code. Every cell makes proteins using the same 20 amino acids. Ribosomes, the protein-making machinery within cells, read the genetic code from a messenger RNA molecule to determine which amino acid to put next into the particular protein they are building.

This code is universal, which is why the ribosomes in our cells can read a piece of viral messenger RNA and make a functional viral protein from it. There are plenty of other amino acids, though. While life does not generally use them, scientists have been incorporating these into proteins. Now, researchers have figured out a way to greatly expand the genetic code, allowing widespread incorporation of these non-biological amino acids. They accomplish this by running a second set of everything—proteins and RNAs—needed to translate the genetic code.

A system apart

Non-canonical amino acids can serve a number of functions. They can act as labels so a researcher’s particular protein of interest can more easily be tracked within cells. They can help to regulate a protein’s function, allowing researchers to activate and inactivate it at a specific time and place of their choosing and then observe the downstream effects. If enough of these non-canonical amino acids are strung together, the resulting proteins would constitute an entirely new class of biopolymers that might carry out functions that traditional proteins cannot—for research, therapeutic, or other purposes.

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#biology, #genetic-code, #genetic-engineering, #science

Caught in the Crossfire Over Covid’s Origins

Alina Chan suggested last year that the coronavirus was “pre-adapted” to humans. Critical reaction was swift and harsh.

#alina-chan, #broad-institute, #cambridge-mass, #content-type-personal-profile, #coronavirus-2019-ncov, #disease-rates, #genetic-engineering, #rumors-and-misinformation, #your-feed-science

Hear top VCs Albert Wegner, Jenny Rooke, and Shilpi Kumar talk green bets at the Extreme Tech Challenge finals

This year, TechCrunch is proudly hosting the Extreme Tech Challenge Global Finals on July 22. The event is among the world’s largest purpose-driven startup competitions that are aiming to solve global challenges based on the United Nations’ 17 sustainability goals.

If you want to catch an array of innovative startups across a range of categories, all of them showcasing what they’re building, you won’t want to miss our must-see pitch-off competition.

You can also catch feature panels hosted by TechCrunch editors, including one of the most highly anticipated discussions of the event, a talk on “going green” with guest speakers Shilpi Kumar, Jenny Rooke, and Albert Wenger, all of whom are actively investing in climate startups that are targeting big opportunities

Shilpi Kumar is a partner with Urban Us, an investment platform focused on urban tech and climate solutions. She previously led go-to-market and early sales efforts at Filament, a startup focused on deploying secure wireless networks for connected physical assets. As an investor, Shilpi has also focused on hardware, mobility, energy, IoT, and robotics, having worked previously for VTF Capital, First Round Capital, and Village Global.

Jenny Rooke is the founder and managing director of Genoa Ventures, but Rooke has been deploying capital into innovative life sciences opportunities for years, including at Fidelity Biosciences and later the Gates Foundation, where she helped managed more than $250 million in funding, funneling some of that capital into genetic engineering, diagnostics, and synthetic biology startups. Rooke began independently investing under the brand 5 Prime Ventures, ultimately establishing among the largest life sciences syndicates on AngelList before launching Genoa.

Last but not least, Albert Wenger, has been a managing partner at Union Square Ventures for more than 13 years. Before joining USV, Albert was the president of through the company’s sale to Yahoo and an angel investor, including writing early checks to Etsy and Tumblr. He previously founded or co-founded several companies, including a management consulting firm and an early hosted data analytics company. Among his investments today is goTenna, a company trying to advance universal access to connectivity by building a scalable mobile mesh network.

Sustainability is the key to our planet’s future and our survival, but it’s also going to be incredibly lucrative and a major piece of our world economy. Hear from these seasoned investors about how VCs and startups alike are thinking about Greentech and how that will evolve in the coming years.

Join us on July 22 to find out how the most innovative startups are working to solve some of the world’s biggest problems. And best of all, tickets are free — book yours today!

#albert-wenger, #angel-investor, #angellist, #energy, #etsy, #fidelity-biosciences, #filament, #finance, #first-round-capital, #gates-foundation, #genetic-engineering, #gotenna, #investment, #managing-partner, #money, #president, #prime-ventures, #startup-company, #tc, #techcrunch, #tumblr, #union-square-ventures, #united-nations, #village-global, #yahoo

The Warnings About the Coronavirus That Were Ignored

Even if the coronavirus did not emerge from a lab, the groundwork for a potential disaster had been laid for years, and learning its lessons is essential to preventing others.

#bats, #china, #coronavirus-2019-ncov, #coronavirus-risks-and-safety-concerns, #daszak-peter, #genetic-engineering, #laboratories-and-scientific-equipment, #sars-severe-acute-respiratory-syndrome, #shi-zhengli, #wildlife-trade-and-poaching, #wuhan-china

Researchers rewire the genetics of E. coli, make it virus-proof

Image of a woman holding bacterial plates.

Enlarge / On the outside, these heavily engineered bacteria look no different from their normal peers. (credit: Raphael Gaillarde / Getty Images)

Many of the fundamental features of life don’t necessarily have to be the way they are. Chance plays a major role in evolution, and there are alternate paths that were never explored, simply because whatever evolved previously happened to be good enough. One instance is the genetic code, which converts the information carried by our DNA into the specific sequence of amino acids that form proteins. There are scores of potential amino acids, many of which can form spontaneously. But most life uses a genetic code that relies on just 20 of them.

Over the past couple of decades, researchers have shown that it doesn’t have to be that way. If you supply bacteria with the right enzyme and an alternative amino acid, they can use it. But bacteria won’t use the enzyme and amino acid very efficiently, as all the existing genetic code slots are already in use.

Now, researchers have managed to edit bacteria’s genetic code to free up a few new slots. They then filled those slots with unnatural amino acids, allowing the bacteria to produce proteins that would never be found in nature. One side effect of the reprogramming? No viruses could replicate in the modified bacteria.

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#amino-acids, #biology, #genetic-code, #genetic-engineering, #genetics, #science, #synthetic-biology

Blind Man’s Sight Partially Restored with ‘Optogenetics’ Gene Therapy

Using a technique called optogenetics, researchers added light-sensitive proteins to the man’s retina, giving him a blurry view of objects.

#blindness, #brain, #eyes-and-eyesight, #genetic-engineering, #research, #science-and-technology

Living in a World in Which Nature Has Already Lost

In “Second Nature,” Nathaniel Rich offers a tour of the ways humans have both conquered the natural world and been overwhelmed by the unintended consequences.

#biotechnology-and-bioengineering, #books-and-literature, #genetic-engineering, #global-warming, #hazardous-and-toxic-substances, #rich-nathaniel-1980, #second-nature-scenes-from-a-world-remade-book

Should We Edit Our Children’s Genes? Would It Be Cruel Not To?

Walter Isaacson and Ezra Klein discuss the implications of humanity’s awesome, terrifying takeover of evolution.

#crispr-dna, #genetic-engineering, #isaacson-walter

New clinical trial data from Locus Biosciences shows promise in CRISPR-Cas3 technology

Antibiotic resistance is one of the biggest potential threats to global health today. But Locus Biosciences is hoping that their crPhage technology might provide a new solution.

Based in North Carolina’s Research Triangle, the startup recently announced promising phase 1b clinical trial results for their use of CRISPR-Cas3-enhanced bacteriophages as a treatment for urinary tract infections caused by escherichia coli. Led in part by former Patheon executive and current Locus CEO Paul Garofolo, the startup launched in 2015 with the goal of using a less popular application of CRISPR technology to address growing antimicrobial resistance.

CRISPR-Cas3 technology has notably different mechanisms from its more well-known CRISPR-Cas9 counterpart. Where the Cas9 enzyme has the ability to cleanly cut through a piece of DNA like a pair of scissors, Garofolo describes Cas3 more like a Pac-Man, shredding the DNA as it moves along a strand.

“You wouldn’t be able to use it for most of the editing platforms people were after,” he said, noting that meant there wouldn’t be as much competition around Cas3. “So I knew it would be protected for some time, and that we could keep it quiet.”

Garofolo and his team wanted to use CRISPR-Cas3 not to edit harmful bacteria found in the body, but to destroy it. To do this, they took the DNA-shredding mechanism of Cas3 and used it to enhance bacteriophages—viruses that can attack and kill different species of bacteria. Together, co-founder and Chief Scientific Officer Dave Ousterout—who has a Ph.D. in biomedical engineering from Duke—thinks this technology offers an extremely direct and targeted way of killing bacteria.

“We armed the phages with this Cas3 system that attacks E. coli, and that sort of dual mechanism of action is what comes together, essentially, as a really potent way to remove just E. coli,” he said in an interview.

That specificity is something that antibiotics lack. Rather than targeting only harmful bacteria in the body, antibiotics typically wipe out all bacteria they come across. “Every time we take antibiotics, we’re not thinking about all the other parts of us that are impacted by the bacteria that do good things,” said Garofolo. But the precision of Locus Biosciences’ crPhage technology means that only the targeted bacteria would be wiped out, leaving those necessary to the body’s normal function intact.

Beyond offering this more specific approach to treatment of pathogens, or any bacteria-based disease, Garofolo and his team also suspect that their approach will also be extremely safe. Though deadly to bacteria, bacteriophages are typically harmless to humans. The safety of CRISPR in humans is well-established, too.

“That’s our secret sauce,” said Garofolo. “We can build drugs that are more powerful than the antibiotics they’re trying to replace, and they use phage, which is probably one of the world’s safest ways to deliver something into the human body.”

While this new technology could certainly help treat pathogens and infectious diseases, Garofolo hopes that indications in immunology, oncology, and neurology might benefit from it too. “We’re starting to figure out that some bacteria might promote cancer, or inflammation in your gut,” he said. If researchers can identify the bacteria at the root cause of those conditions, Garofolo and Ousterout think the crPhage technology might prove to be an effective treatment.

“If we’re right about that, it’s not just about infections or antimicrobial resistance, but helping people overcome cancer or delay the onset of dementia,” Garofolo said. “It’s changing the way we think about how bacteria really help us live.”

Early Stage is the premier ‘how-to’ event for startup entrepreneurs and investors. You’ll hear first-hand how some of the most successful founders and VCs build their businesses, raise money and manage their portfolios. We’ll cover every aspect of company-building: Fundraising, recruiting, sales, product market fit, PR, marketing and brand building. Each session also has audience participation built-in – there’s ample time included for audience questions and discussion.

#biology, #biotech, #biotechnology, #cancer, #cas-3, #crispr, #enzymes, #genetic-engineering, #health, #life-sciences, #locus-biosciences, #north-carolina, #science, #startups

Book Review: ‘The Code Breaker,’ by Walter Isaacson

In “The Code Breaker,” Walter Isaacson turns to the life and work of Jennifer Doudna, the Nobel-winning scientist who has revolutionized gene editing.

#books-and-literature, #charpentier-emmanuelle-m-1968, #crispr-dna, #doudna-jennifer-a, #genetic-engineering, #genetics-and-heredity, #isaacson-walter, #science-and-technology, #the-code-breaker-jennifer-doudna-gene-editing-and-the-future-of-the-human-race-book

Researchers Halt Trials of Promising Sickle Cell Treatment

Two patients in a gene therapy study developed cancer years after treatment. It is not clear whether the therapy was responsible.

#black-people, #bluebird-bio-inc, #bone-marrow, #busulfan, #clinical-trials, #dna-deoxyribonucleic-acid, #drugs-pharmaceuticals, #genetic-engineering, #leukemia, #national-heart-lung-and-blood-institute, #sickle-cell-anemia

My Wife Was Wary of My Lab-Made Dinner Party. The Faux Whiskey Won Her Over.

A slew of start-ups are engineering faux meats, eggs and dairy products that conjure a future in which we move from farm-to-table to lab-to-table.

#ava-food-labs-inc-endless-west, #biotechnology-and-bioengineering, #diamond-foundry-inc, #eat-just-inc, #food, #genetic-engineering, #graeters-inc, #meat, #perfect-day-inc, #veganism

Tiny Blobs of Brain Cells Could Reveal How Your Mind Differs From a Neanderthal’s

Researchers grew clusters of brain cells in the lab with a gene carried by our ancient ancestors.

#brain, #evolution-biology, #genetic-engineering, #genetics-and-heredity, #monkeys-and-apes, #neanderthal-man, #research, #your-feed-science

A mildly insane idea for disabling the coronavirus

Colorful blobs cluster together like a bunch of grapes.

Enlarge / Diagram of the structure of the virus’ spike protein. (credit: McLellan Lab, University of Texas at Austin)

When the COVID-19 pandemic was first recognized for the threat that it is, researchers scrambled to find anything that might block the virus’ spread. While vaccines have grabbed much of the attention lately, there was also the hope that we could develop a therapy that would block the worst effects of the virus. Most of these have been extremely practical: identify enzymes that are essential for the virus to replicate, and test drugs that block similar enzymes from other viruses. These drugs are designed to be relatively easy to store and administer and, in some cases, have already been tested for safety in humans, making them reasonable choices for getting something ready for use quickly.

But the tools we’ve developed in biotechnology allow us to do some far less practical things, and a paper released today describes how they can be put to use to inactivate SARS-CoV-2. This is in no way a route to a practical therapy, but it does provide a fantastic window into what we can accomplish by manipulating biology.

Throw it in the trash

The whole effort described in the new paper is focused on a simple idea: if you figure out how to wreck one of the virus’ key proteins, it won’t be able to infect anything. And, conveniently, our cells have a system for destroying proteins, since that’s often a useful thing to do. In some cases, the proteins that are destroyed are damaged; in others, the proteins are made and destroyed at elevated paces to allow the cell to respond to changing conditions rapidly. In a few cases, changes in the environment or the activation of signaling pathways can trigger widespread protein destruction, allowing the cell to quickly alter its behavior.

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#biology, #biotechnology, #coronavirus, #genetic-engineering, #science, #spike-protein, #ubiquitin

Crispr Gene Editing Can Cause Unwanted Changes in Human Embryos, Study Finds

Instead of addressing genetic mutations, the Crispr machinery prompted cells to lose entire chromosomes.

#cell-journal, #chromosomes, #crispr-dna, #dna-deoxyribonucleic-acid, #ethics-and-official-misconduct, #genetic-engineering, #genetics-and-heredity, #mitalipov-shoukhrat, #nobel-prizes, #your-feed-health, #your-feed-science

What’s Special About Bat Viruses? What We Don’t Know Could Hurt Us

The immune systems of bats are weird, but we don’t know how weird, how they got that way or enough about other animals.

#bats, #coronavirus-2019-ncov, #genetic-engineering, #national-science-foundation, #research, #science-journal, #viruses, #your-feed-animals, #your-feed-science

Nobel laureate Jennifer Doudna shares her perspective on COVID-19 and CRISPR

CRISPR co-discoverer Jennifer Doudna was named a Nobel laureate in Chemistry today, sharing the honour with Emmanuelle Charpentier . We had the opportunity to speak to Doudna recently at our TechCrunch Disrupt 2020 event, and she shared her thoughts on CRISPR, and how it can be used to test and potentially treat COVID-19, as well as what it may do for our ability to address future pandemics and healthcare crises.

“It’s really interesting to think about the ability to program CRISPR to be detecting not only the the current coronavirus, but also other viruses,” she explained in the interview in September. “We were already working on a strategy to co-detect influenza and coronavirus, as you know that it’s really important to be able to do that, but also to pivot very quickly to detect new viruses that are emerging. I don’t think any of us think that, you know, viral pandemics are going away – I think this current pandemic is a call to arms, and we have to make sure that scientifically, we’re ready for the next attack by a new virus.”

Much closer to hand, CRISPR has the potential to greatly expand testing capabilities in the near-term, and to do so in ways that could change the pace, frequency and nature of testing. That could translate to very different frontline care and pandemic management, across both healthcare facilities as well as any shared workspaces.

“I think from what I’ve seen that very likely before the end of the year, we’re going to see CRISPR diagnostic tests rolling out,” she said. “Whether they’re in laboratory settings – I think that may be the first format that we see – but also something that we’re working on right now at the Innovative Genomics Institute at Berkeley and UCSF and the Gladstone is a strategy for a point-of-care CRISPR tests, where we have a small device that we envision located in different floors of buildings and institutions and dormitories, where you could do very rapid surveillance-type testing of saliva or swab samples.”

Check out the full interview with Doudna above, which also ranges into the most recent advances in CRISPR science, and where it’s heading next for everything from therapeutics, to crop modification.

#biology, #biotech, #biotechnology, #crispr, #emmanuelle-charpentier, #genetic-engineering, #genomics, #health, #innovative-genomics-institute, #jennifer-doudna, #life-sciences, #nobel-prize, #science, #tc

Nobel Prize in Chemistry Awarded to 2 Scientists for Work on Genome Editing

Emmanuelle Charpentier and Jennifer A. Doudna developed the Crispr tool, which can change the DNA of animals, plants and microorganisms with high precision.

#chemistry, #genetic-engineering, #medicine-and-health, #nobel-prizes, #your-feed-science

Scribe Therapeutics launches a platform for engineering CRISPR-based therapeutics

A new company called Scribe Therapeutics founded by two former members of CRISPR pioneer Jennifer Doudna’s UC Berkely genetics lab (alongside Doudna herself) launched on Tuesday, debuting a platform designed specifically to help develop and engineer new thereapeutics based on CRISPR for addressing specific diseases, with permanent treatments in patients.

Doudna is part of the leadership team behind Scribe, but it’s primarily led by CEO and co-founder Benjamin Oakes, along with VP of Platform Brett T. Staahl. Oakes and Staahl shared time at Doudna’s lab, with Oakes as a student while Staahl was a postdoc. Staahl’s interest was specifically in how gene editing, and CRISPR in particular, could be used to help treat Huntington’s disease – while Oakes, who originally set out to be a practicing medical doctor, realized early on he actually wanted to do more with solving the underlying causes of disease, and changed tack to pursue genome editing.

“I set out on this journey to understand how we could, and how we could best actually solve those underlying problems of disease,” Oakes explained in an interview. That led to him pursuing research in Zinc-Finger Nuclease (ZFN)-based genome editing – a precursor technique to CRISPR that was far less specific and much more work-intensive and time consuming. Doudna’s groundbreaking paper on CRISPR was published in 2012, and Oakes immediately saw the potential, so he joined her lab at Berkeley.

Meanwhile, Staahl was looking at treatment for disorders that specifically lead to neural degeneration – something that had not previously been part of Doudna’s lab’s research prior to him joining.

“He spent several years in the lab, developing strategies for neurons, and really trying to bring that technology to a point where it could be deployed as a real treatment for neurodegenerative disease, with Huntington’s as a model,” Doudna told me. “So Ben and Brett met up, they came from very different backgrounds, they had really different scientific training originally, but they hit it off. And they saw a really exciting opportunity to use the kind of technology development that Ben had been doing, and that he was very keen on continuing, and to focus it on this challenge of neurodegeneration.”

The result is Scribe Therapeutics, which has already raised $20 million in a Series A funding round (plus some small amount of earlier seed financing contributed by the founders) led by Andreessen Horowitz . Scribe has been at work on their solution since 2018, but remained mostly quiet about their progress until Oakes felt confident that what they’re presenting is a real, viable technology that can be used to produce therapeutics now. Representative of that progress, the company is also announcing a new collaboration with large drugmaker Biogen, Inc. to collaborate on CRISPR-based medecines for treating neurological diseases, and specifically Amyotriophic Lateral Sclerosis.

That deal is valued at $15 million in upfront commitments, with as much as $400 million or more in milestone payouts to follow, as well as royalties attached to any shipping therapeutics that result. Oakes says it’s a testament to the maturity of their platform that they were able to secure this partnership. But Scribe will also be pursuing development of its own therapeutics in-house, while partnering where it makes sense – a strategy Oakes says is in service of addressing the greatest number of possible disease treatments the startup can manage. And while it’s already generating revenue, and Oakes says he’s in no rush to secure additional funding, he does believe that ultimately they will seek out additional investment in order to help ensure they can treat as many potential conditions as possible, as quickly and safely as possible.

As for the fundamental science behind Scribe, their advantage lies in the work they’ve done to adapt a molecule called CRISPR-CasX, which is a bit smaller than Cas9 and not derived from pathogen molecules, both of which make it better-suited to therapeutics. Scribe has spent the past year-and-a-half turning CasX into the basis of a platform that works better than any CRISPR protein that exists for delivery via adeno-associated virus (the current state-of-the-art in gene therapy delivery), as well as engineering it for greater specificity.

“We built Scribe specifically to do that, to build an engineering core focused exclusively on making the most advanced the very best therapeutic genome editing molecules that we could,” Oakes said.

#andreessen-horowitz, #biology, #biotech, #biotechnology, #crispr, #disease, #emerging-technologies, #genetic-engineering, #health, #jennifer-doudna, #life-sciences, #model, #science, #tc, #technology-development

Mammoth Biosciences lands exclusive license to new CRISPR proteins that could boost gene editing precision

CRISPR pioneer Mammoth Biosciences has secured an exclusive license to a new family of CRISPR proteins, from UC Berkeley, which covers R&D and commercialization across all potential fields. This is a significant addition to Mammoth’s intellectual property holdings, since this new family of CRISPR proteins, known as the Casɸ family, is roughly half the size of Cas9, the protein that effectively launched CRISPR to begin with.

In CRISPR, size actually matters quite a lot – the smaller size of Casɸ could help this new protein family excel in areas including the exact precision of gene editing, as well as easing delivery for use in actual living cells, and combining different target edits in a so-called ‘multiplex’ arrangement.

In July, a peer-reviewed paper published in Science detailed the discovery of Casɸ and outlined its potential advantages for use in CRISPR gene editing. Casɸ was discovered in bacteriophages, which is a type of virus that infects and replicates within bacteria – their literal translation is “bacteria eater.”

Increasing accuracy in CRISPR-based genetic editing has been an ongoing goal in the industry, with various approaches conceived and developed to help mitigate what is known as “off-target” activity, or unintended edits and genetic modifications that can occur when using the original Cas9-based editing approaches.

Mammoth Biosciences was founded by CRISPR co-discoverer Jennifer Doudna, and Douda’s lab at UC Berkeley is the source of the new discovery. This definitely helps strengthen its portfolio, and could lead to significant potential upside to the business through eventual commercialization.

#biology, #biotech, #biotechnology, #crispr, #genetic-engineering, #health, #life-sciences, #mammoth-biosciences, #science, #tc, #uc-berkeley

Mammoth Biosciences’s CRISPR-based COVID-19 test receives NIH fundings through RADx program

CRISPR tech startup Mammoth Biosciences is among the companies that revealed backing from the National Institutes of Health (NIH) Rapid Accleration of Diagnostics (RADx) program on Friday. Mammoth received a contract to scale up its CRISPR-based SARS-CoV-2 diagnostic test in order to help address the testing shortages across the U.S.

Mammoth’s CRISPR-based approach could potentially offer a significant solution to current testing bottlenecks, because it’s a very different kind of test when compared to existing methods based on PCR technology. The startup has also enlisted the help of pharma giant GSK to develop and produce a new COVID-19 testing solution, which will be a handheld, disposable test that can offer results in as little as 20 minutes, on site.

While that test is still ind development, the RADx funding received through this funding will be used to scale manufacturing of the company’s DETECTR platform for distribution and use in commercial laboratory settings. This will still offer a “multi-fold increase in testing capacity,” the company says, even though it’s a lab-based solution instead of a point-of-care test like the one it’s seeking to create with GSK.

Already, UCSF has received an Emergency Use Authorization (EUA) from the FDA to use the DETECTR reagent set to test for the presence of SARS-CoV-2, and the startup hopes to be able to extend similar testing capacity to other labs across the U.S.

#articles, #biology, #biotech, #biotechnology, #coronavirus, #covid-19, #crispr, #fda, #genetic-engineering, #health, #mammoth-biosciences, #national-institute-of-health, #science, #startup-company, #tc, #tech-startup, #united-states

A ‘Cure for Heart Disease’? A Single Shot Succeeds in Monkeys

A novel gene-editing experiment seems to have permanently reduced LDL and triglyceride levels in monkeys.

#cholesterol, #genetic-engineering, #genetics-and-heredity, #heart, #international-society-for-stem-cell-research, #kathiresan-sekar, #monkeys-and-apes, #rna-ribonucleic-acid, #triglycerides

I Tried to Grow a Pandemic Garden. My Strawberry Seedling Got a Virus.

Plants can get sick, too.

#agriculture-and-farming, #corn, #flowers-and-plants, #genetic-engineering, #strawberries

Even My Strawberry Seedling Has a Virus

Plants can get sick, too.

#agriculture-and-farming, #corn, #flowers-and-plants, #genetic-engineering, #strawberries

Emerging from stealth, Octant is bringing the tools of synthetic biology to large scale drug discovery

Octant, a company backed by Andreessen Horowitz just now unveiling itself publicly to the world, is using the tools of synthetic biology to buck the latest trends in drug discovery.

As the pharmaceuticals industry turns its attention to precision medicine — the search for ever more tailored treatments for specific diseases using genetic engineering — Octant is using the same technologies to engage in drug discovery and diagnostics on a mass scale.

The company’s technology genetically engineers DNA to act as an identifier for the most common drug receptors inside the human genome. Basically, it’s creating QR codes that can flag and identify how different protein receptors in cells respond to chemicals. These are the biological sensors which help control everything from immune responses to the senses of sight and smell, the firing of neurons; even the release of hormones and communications between cells in the body are regulated.

“Our discovery platform was designed to map and measure the interconnected relationships between chemicals, multiple drug receptor pathways and diseases, enabling us to engineer multi-targeted drugs in a more rational way, across a wide spectrum of targets,” said Sri Kosuri, Octant’s co-founder and chief executive officer, in a statement.

Octant’s work is based on a technology first developed at the University of California Los Angeles by Kosuri and a team of researchers, which slashed the cost of making genetic sequences to $2 per gene from $50 to $100 per gene.

“Our method gives any lab that wants the power to build its own DNA sequences,” Kosuri said in a 2018 statement. “This is the first time that, without a million dollars, an average lab can make 10,000 genes from scratch.”

Joining Kosuri in launching Octant is Ramsey Homsany, a longtime friend of Kosuri’s, and a former executive at Google and Dropbox . Homsany happened to have a background in molecular biology from school, and when Kosuri would talk about the implications of the technology he developed, the two men knew they needed to for a company.

“We use these new tools to know which bar code is going with which construct or genetic variant or pathway that we’re working with [and] all of that fits into a single well,” said Kosuri. “What you can do on top of that is small molecule screening… we can do that with thousands of different wells at a time. So we can build these maps between chemicals and targets and pathways that are essential to drug development.”

Before coming to UCLA, Kosuri had a long history with companies developing products based on synthetic biology on both the coasts. Through some initial work that he’d done in the early days of the biofuel boom in 2007, Kosuri was connected with Flagship Ventures, and the imminent Harvard-based synthetic biologist George Church . He also served as a scientific advisor to Gen9, a company acquired by the multi-billion dollar synthetic biology powerhouse, Ginkgo Bioworks.

“Some of the most valuable drugs in history work on complex sets of drug targets, which is why Octant’s focus on polypharmacology is so compelling,” said Jason Kelly, the co-founder and CEO of Gingko Bioworks, and a member of the Octant board, in a statement. “Octant is engineering a lot of luck and cost out of the drug discovery equation with its novel platform and unique big data biology insights, which will drive the company’s internal development programs as well as potential partnerships.”

The new technology arrives at a unique moment in the industry where pharmaceutical companies are moving to target treatments for diseases that are tied to specific mutations, rather than look at treatments for more common disease problems, said Homsany.

“People are dropping common disease problems,” he said. “The biggest players are dropping these cases and it seems like that just didn’t make sense to us. So we thought about how would a company take these new technologies and apply them in a way that could solve some of this.”

One reason for the industry’s turn away from the big diseases that affect large swaths of the population is that new therapies are emerging to treat these conditions which don’t rely on drugs. While they wouldn’t get into specifics, Octant co-founders are pursuing treatments for what Kosuri said were conditions “in the metabolic space” and in the “neuropsychiatric space”.

Helping them pursue those targets, since Octant is very much a drug development company, is $20 million in financing from investors led by Andreessen Horowitz .

“Drug discovery remains a process of trial and error. Using its deep expertise in synthetic biology, the Octant team has engineered human cells that provide real-time, precise and complete readouts of the complex interactions and effects that drug molecules have within living cells,” said Jorge Conde, general partner at Andreessen Horowitz, and member of the Octant board of directors. “By querying biology at this unprecedented scale, Octant has the potential to systematically create exhaustive maps of drug targets and corresponding, novel treatments for our most intractable diseases.”

#andreessen-horowitz, #articles, #biology, #biotechnology, #chemicals, #dna, #dna-sequencing, #dropbox, #drug-development, #drug-discovery, #emerging-technologies, #executive, #flagship-ventures, #general-partner, #genetic-engineering, #genetics, #george-church, #ginkgo-bioworks, #google, #harvard, #jason-kelly, #jorge-conde, #pharmaceutical, #synthetic-biology, #tc

A Coronavirus Vaccine Project Takes a Page From Gene Therapy

The technique aims to make a person’s cells churn out proteins that will stimulate the body to fight the coronavirus.

#coronavirus-2019-ncov, #fazzalari-emilia, #freeman-mason-w, #genetic-engineering, #grousbeck-wyc, #harvard-university, #massachusetts-eye-and-ear, #massachusetts-general-hospital, #vaccination-and-immunization, #your-feed-healthcare

Can Genetic Engineering Bring Back the American Chestnut?

The tree helped build industrial America before disease wiped out an estimated three billion or more of them. To revive their lost glory, we may need to embrace tinkering with nature.

#agriculture-and-farming, #american-chestnut-foundation, #genetic-engineering, #genetics-and-heredity, #trees-and-shrubs

Are ‘Natural Flavors’ Really Natural?

Food manufacturers add flavorings to a surprising number of basic products, like Breyers Natural Vanilla ice cream.

#cooking-and-cookbooks, #food, #genetic-engineering, #labeling-and-labels-product, #organic-foods-and-products