Tag Archives: Robert Sanders

Greater mortality for the CRISPR twins Lulu and Nana?

Every time I think this CRISPR (clustered regularly interspaced short palindromic repeats) story is winding down, something new happens. The latest (I think) is in a June 3, 2019 news item on ScienceDaily,

A genetic mutation that a Chinese scientist attempted to create in twin babies born last year, ostensibly to help them fend off HIV infection, is also associated with a 21% increase in mortality in later life, according to an analysis by University of California, Berkeley, scientists.

The researchers scanned more than 400,000 genomes and associated health records contained in a British database, UK Biobank, and found that people who had two mutated copies of the gene had a significantly higher death rate between ages 41 and 78 than those with one or no copies.

Sarah Zhang’s June 3, 2019 article for The Atlantic provides an overview of the situation before exploring the current controversy,

In the 1990s, virologists in New York learned of a genetic mutation that would become one of the most famous ever discovered. They found it in a man who could not be infected with HIV. He turned out to be missing just 32 letters in a gene called CCR5, and remarkably, it was enough to make him resistant to the virus killing so many others. About 1 percent of people of European descent carry two copies of this mutation, now known as CCR5-Δ32.

In 2018, a Chinese scientist named He Jiankui made the mutation infamous when he attempted to use CRISPR to edit CCR5-Δ32 (pronounced “CCR5-delta-32”) into human embryos. He chose this mutation, he said, because the babies’ father was HIV-positive, and he wanted to make the resulting twin girls resistant to the virus. CCR5-Δ32 is also, after all, one of the most studied mutations.

He’s work immediately provoked outrage among scientists, who knew enough to know how much they did not know about the risks of altering CCR5. And now a new study suggests that CCR5-Δ32 is indeed harmful overall.

The girls’ CCR5 genes were altered, according to data He presented, but they do not exactly match the 32-letter deletion; it’s unclear whether either of them is actually resistant to HIV. Even if they were unable to get HIV, a body of research already suggested that CCR5-Δ32 made people more vulnerable to the flu and West Nile virus. A “good” mutation in the context of HIV can be “bad” in another context. No one knew, exactly, the net effect of a CCR5-Δ32 mutation.

For some reason, Zhang makes no mention of the possibly enhanced cognitive abilities that the twins may have as a consequence of the gene editing assuming that He Jiankui successfully edited the genes. (To my knowledge, the results and data have not been released for review by colleagues.)

Regardless, Zhang’s article provides a handy overview and update.

For anyone who’s interested in more detail about this latest research into mortality and CCR5, there’s a June 3, 2019 University of California at Berkeley news release (also on EurekAlert) by Robert Sanders, which also originated the ScienceDaily news item, details the latest research,

Previous studies have associated two mutated copies of the gene, CCR5, with a fourfold increase in the death rate after influenza infection, and the higher overall mortality rate may reflect this greater susceptibility to death from the flu. But the researchers say there could be any number of explanations, since the protein that CCR5 codes for, and which no longer works in those having the mutation in both copies of the gene, is involved in many body functions.

“Beyond the many ethical issues involved with the CRISPR babies, the fact is that, right now, with current knowledge, it is still very dangerous to try to introduce mutations without knowing the full effect of what those mutations do,” said Rasmus Nielsen, a UC Berkeley professor of integrative biology. “In this case, it is probably not a mutation that most people would want to have. You are actually, on average, worse off having it.”

“Because one gene could affect multiple traits, and because, depending on the environment, the effects of a mutation could be quite different, I think there can be many uncertainties and unknown effects in any germline editing,” said postdoctoral fellow Xinzhu “April” Wei.
Wei is first author and Nielsen is senior author of a paper describing the research that will appear online on Monday, June 3, in the journal Nature Medicine.

Mutation prevents HIV infection

The gene CCR5 codes for a protein that, among other things, sits on the surface of immune cells and helps some strains of HIV, including the most common ones, to enter and infect them. Jiankui He, the Chinese scientist who last November shocked the world by announcing he had experimented with CCR5 on at least two babies, said he wanted to introduce a mutation in the gene that would prevent this. Naturally-occurring mutations that disable the protein are rare in Asians, but a mutation found in about 11% of Northern Europeans protects them against HIV infection.

The genetic mutation, ∆32 (Delta 32), refers to a missing 32-base-pair segment in the CCR5 gene. This mutation interferes with the localization on the cell surface of the protein for which CCR5 codes, thwarting HIV binding and infection. He was unable to duplicate the natural mutation, but appears to have generated a similar deletion that would also inactivate the protein. One of the twin babies reportedly had one copy of CCR5 modified by CRISPR-Cas9 gene editing, while the other baby had both copies edited.

But inactivating a protein found in all humans and most animals is likely to have negative effects, Nielsen said, especially when done to both copies of the gene — a so-called homozygous mutation

“Here is a functional protein that we know has an effect in the organism, and it is well-conserved among many different species, so it is likely that a mutation that destroys the protein is, on average, not good for you,” he said. “Otherwise, evolutionary mechanisms would have destroyed that protein a long time ago.”

After He’s experiment became public, Nielsen and Wei, who study current genetic variation to understand the origin of human, animal and plant traits, decided to investigate the effect of the CCR5-∆32 mutation using data from UK Biobank. The database houses genomic information on a half million U.K. citizens that is linked to their medical records. The genomic information is much like that acquired by Ancestry.com and 23andMe: details on nearly a million individual variations in the genetic sequence, so-called single nucleotide polymorphisms (SNPs).

Two independent measures indicated a higher mortality rate for those with two mutated genes. Fewer people than expected with two mutations enrolled in the database, indicating that they had died at a higher rate than the general population. And fewer than expected survived from ages 40 to 78.

“Both the proportions before enrollment and the survivorship after enrollment tell the same story, which is that you have lower survivability or higher mortality if you have two copies of the mutation,” Nielsen said. “There is simply a deficiency of individuals with two copies.”

Because the ∆32 mutation is relatively common in Northern Europeans, it must have been favored by natural selection at some point, Nielsen said, though probably not to protect against HIV, since the virus has circulated among humans only since the 1980s.

Wei said that some evidence links the mutation to increased survival after stroke and protection against smallpox and flaviviruses, a group that includes the dengue, Zika and West Nile viruses.

Despite these possible benefits, the potential unintended effects of creating genetic mutations, in both adult somatic cells and in embryonic, germline cells, argue for caution, the researchers said.

“I think there are a lot of things that are unknown at the current stage about genes’ functions,” Wei said. “The CRISPR technology is far too dangerous to use right now for germline editing.”

Here’s a link to and a citation for the latest paper,

CCR5-∆32 is deleterious in the homozygous state in humans by Xinzhu Wei & Rasmus Nielsen. Nature Medicine (2019) DOI: https://doi.org/10.1038/s41591-019-0459-6 Published 03 June 2019

This paper is behind a paywall.

For those who have an insatiable appetite for detail, there’s my November 28, 2018 posting which covers what happened when the CRISPR twins, Lulu and Nana, was first announced, along with a few updates to January 23, 2019. The May 17, 2019 posting covers the news of possible cognitive advantages for the CCR5-Δ32 gene-edited twins and explores some of the social implications.

It’s a very ‘carbony’ time: graphene jacket, graphene-skinned airplane, and schwarzite

In August 2018, I been stumbled across several stories about graphene-based products and a new form of carbon.

Graphene jacket

The company producing this jacket has as its goal “… creating bionic clothing that is both bulletproof and intelligent.” Well, ‘bionic‘ means biologically-inspired engineering and ‘intelligent‘ usually means there’s some kind of computing capability in the product. This jacket, which is the first step towards the company’s goal, is not bionic, bulletproof, or intelligent. Nonetheless, it represents a very interesting science experiment in which you, the consumer, are part of step two in the company’s R&D (research and development).

Onto Vollebak’s graphene jacket,

Courtesy: Vollebak

From an August 14, 2018 article by Jesus Diaz for Fast Company,

Graphene is the thinnest possible form of graphite, which you can find in your everyday pencil. It’s purely bi-dimensional, a single layer of carbon atoms that has unbelievable properties that have long threatened to revolutionize everything from aerospace engineering to medicine. …

Despite its immense promise, graphene still hasn’t found much use in consumer products, thanks to the fact that it’s hard to manipulate and manufacture in industrial quantities. The process of developing Vollebak’s jacket, according to the company’s cofounders, brothers Steve and Nick Tidball, took years of intensive research, during which the company worked with the same material scientists who built Michael Phelps’ 2008 Olympic Speedo swimsuit (which was famously banned for shattering records at the event).

The jacket is made out of a two-sided material, which the company invented during the extensive R&D process. The graphene side looks gunmetal gray, while the flipside appears matte black. To create it, the scientists turned raw graphite into something called graphene “nanoplatelets,” which are stacks of graphene that were then blended with polyurethane to create a membrane. That, in turn, is bonded to nylon to form the other side of the material, which Vollebak says alters the properties of the nylon itself. “Adding graphene to the nylon fundamentally changes its mechanical and chemical properties–a nylon fabric that couldn’t naturally conduct heat or energy, for instance, now can,” the company claims.

The company says that it’s reversible so you can enjoy graphene’s properties in different ways as the material interacts with either your skin or the world around you. “As physicists at the Max Planck Institute revealed, graphene challenges the fundamental laws of heat conduction, which means your jacket will not only conduct the heat from your body around itself to equalize your skin temperature and increase it, but the jacket can also theoretically store an unlimited amount of heat, which means it can work like a radiator,” Tidball explains.

He means it literally. You can leave the jacket out in the sun, or on another source of warmth, as it absorbs heat. Then, the company explains on its website, “If you then turn it inside out and wear the graphene next to your skin, it acts like a radiator, retaining its heat and spreading it around your body. The effect can be visibly demonstrated by placing your hand on the fabric, taking it away and then shooting the jacket with a thermal imaging camera. The heat of the handprint stays long after the hand has left.”

There’s a lot more to the article although it does feature some hype and I’m not sure I believe Diaz’s claim (August 14, 2018 article) that ‘graphene-based’ hair dye is perfectly safe ( Note: A link has been removed),

Graphene is the thinnest possible form of graphite, which you can find in your everyday pencil. It’s purely bi-dimensional, a single layer of carbon atoms that has unbelievable properties that will one day revolutionize everything from aerospace engineering to medicine. Its diverse uses are seemingly endless: It can stop a bullet if you add enough layers. It can change the color of your hair with no adverse effects. [emphasis mine] It can turn the walls of your home into a giant fire detector. “It’s so strong and so stretchy that the fibers of a spider web coated in graphene could catch a falling plane,” as Vollebak puts it in its marketing materials.

Not unless things have changed greatly since March 2018. My August 2, 2018 posting featured the graphene-based hair dye announcement from March 2018 and a cautionary note from Dr. Andrew Maynard (scroll down ab out 50% of the way for a longer excerpt of Maynard’s comments),

Northwestern University’s press release proudly announced, “Graphene finds new application as nontoxic, anti-static hair dye.” The announcement spawned headlines like “Enough with the toxic hair dyes. We could use graphene instead,” and “’Miracle material’ graphene used to create the ultimate hair dye.”

From these headlines, you might be forgiven for getting the idea that the safety of graphene-based hair dyes is a done deal. Yet having studied the potential health and environmental impacts of engineered nanomaterials for more years than I care to remember, I find such overly optimistic pronouncements worrying – especially when they’re not backed up by clear evidence.

These studies need to be approached with care, as the precise risks of graphene exposure will depend on how the material is used, how exposure occurs and how much of it is encountered. Yet there’s sufficient evidence to suggest that this substance should be used with caution – especially where there’s a high chance of exposure or that it could be released into the environment.

The full text of Dr. Maynard’s comments about graphene hair dyes and risk can be found here.

Bearing in mind  that graphene-based hair dye is an entirely different class of product from the jacket, I wouldn’t necessarily dismiss risks; I would like to know what kind of risk assessment and safety testing has been done. Due to their understandable enthusiasm, the brothers Tidball have focused all their marketing on the benefits and the opportunity for the consumer to test their product (from graphene jacket product webpage),

While it’s completely invisible and only a single atom thick, graphene is the lightest, strongest, most conductive material ever discovered, and has the same potential to change life on Earth as stone, bronze and iron once did. But it remains difficult to work with, extremely expensive to produce at scale, and lives mostly in pioneering research labs. So following in the footsteps of the scientists who discovered it through their own highly speculative experiments, we’re releasing graphene-coated jackets into the world as experimental prototypes. Our aim is to open up our R&D and accelerate discovery by getting graphene out of the lab and into the field so that we can harness the collective power of early adopters as a test group. No-one yet knows the true limits of what graphene can do, so the first edition of the Graphene Jacket is fully reversible with one side coated in graphene and the other side not. If you’d like to take part in the next stage of this supermaterial’s history, the experiment is now open. You can now buy it, test it and tell us about it. [emphasis mine]

How maverick experiments won the Nobel Prize

While graphene’s existence was first theorised in the 1940s, it wasn’t until 2004 that two maverick scientists, Andre Geim and Konstantin Novoselov, were able to isolate and test it. Through highly speculative and unfunded experimentation known as their ‘Friday night experiments,’ they peeled layer after layer off a shaving of graphite using Scotch tape until they produced a sample of graphene just one atom thick. After similarly leftfield thinking won Geim the 2000 Ig Nobel prize for levitating frogs using magnets, the pair won the Nobel prize in 2010 for the isolation of graphene.

Should you be interested, in beta-testing the jacket, it will cost you $695 (presumably USD); order here. One last thing, Vollebak is based in the UK.

Graphene skinned plane

An August 14, 2018 news item (also published as an August 1, 2018 Haydale press release) by Sue Keighley on Azonano heralds a new technology for airplans,

Haydale, (AIM: HAYD), the global advanced materials group, notes the announcement made yesterday from the University of Central Lancashire (UCLAN) about the recent unveiling of the world’s first graphene skinned plane at the internationally renowned Farnborough air show.

The prepreg material, developed by Haydale, has potential value for fuselage and wing surfaces in larger scale aero and space applications especially for the rapidly expanding drone market and, in the longer term, the commercial aerospace sector. By incorporating functionalised nanoparticles into epoxy resins, the electrical conductivity of fibre-reinforced composites has been significantly improved for lightning-strike protection, thereby achieving substantial weight saving and removing some manufacturing complexities.

Before getting to the photo, here’s a definition for pre-preg from its Wikipedia entry (Note: Links have been removed),

Pre-preg is “pre-impregnated” composite fibers where a thermoset polymer matrix material, such as epoxy, or a thermoplastic resin is already present. The fibers often take the form of a weave and the matrix is used to bond them together and to other components during manufacture.

Haydale has supplied graphene enhanced prepreg material for Juno, a three-metre wide graphene-enhanced composite skinned aircraft, that was revealed as part of the ‘Futures Day’ at Farnborough Air Show 2018. [downloaded from https://www.azonano.com/news.aspx?newsID=36298]

A July 31, 2018 University of Central Lancashire (UCLan) press release provides a tiny bit more (pun intended) detail,

The University of Central Lancashire (UCLan) has unveiled the world’s first graphene skinned plane at an internationally renowned air show.

Juno, a three-and-a-half-metre wide graphene skinned aircraft, was revealed on the North West Aerospace Alliance (NWAA) stand as part of the ‘Futures Day’ at Farnborough Air Show 2018.

The University’s aerospace engineering team has worked in partnership with the Sheffield Advanced Manufacturing Research Centre (AMRC), the University of Manchester’s National Graphene Institute (NGI), Haydale Graphene Industries (Haydale) and a range of other businesses to develop the unmanned aerial vehicle (UAV), which also includes graphene batteries and 3D printed parts.

Billy Beggs, UCLan’s Engineering Innovation Manager, said: “The industry reaction to Juno at Farnborough was superb with many positive comments about the work we’re doing. Having Juno at one the world’s biggest air shows demonstrates the great strides we’re making in leading a programme to accelerate the uptake of graphene and other nano-materials into industry.

“The programme supports the objectives of the UK Industrial Strategy and the University’s Engineering Innovation Centre (EIC) to increase industry relevant research and applications linked to key local specialisms. Given that Lancashire represents the fourth largest aerospace cluster in the world, there is perhaps no better place to be developing next generation technologies for the UK aerospace industry.”

Previous graphene developments at UCLan have included the world’s first flight of a graphene skinned wing and the launch of a specially designed graphene-enhanced capsule into near space using high altitude balloons.

UCLan engineering students have been involved in the hands-on project, helping build Juno on the Preston Campus.

Haydale supplied much of the material and all the graphene used in the aircraft. Ray Gibbs, Chief Executive Officer, said: “We are delighted to be part of the project team. Juno has highlighted the capability and benefit of using graphene to meet key issues faced by the market, such as reducing weight to increase range and payload, defeating lightning strike and protecting aircraft skins against ice build-up.”

David Bailey Chief Executive of the North West Aerospace Alliance added: “The North West aerospace cluster contributes over £7 billion to the UK economy, accounting for one quarter of the UK aerospace turnover. It is essential that the sector continues to develop next generation technologies so that it can help the UK retain its competitive advantage. It has been a pleasure to support the Engineering Innovation Centre team at the University in developing the world’s first full graphene skinned aircraft.”

The Juno project team represents the latest phase in a long-term strategic partnership between the University and a range of organisations. The partnership is expected to go from strength to strength following the opening of the £32m EIC facility in February 2019.

The next step is to fly Juno and conduct further tests over the next two months.

Next item, a new carbon material.

Schwarzite

I love watching this gif of a schwarzite,

The three-dimensional cage structure of a schwarzite that was formed inside the pores of a zeolite. (Graphics by Yongjin Lee and Efrem Braun)

An August 13, 2018 news item on Nanowerk announces the new carbon structure,

The discovery of buckyballs [also known as fullerenes, C60, or buckminsterfullerenes] surprised and delighted chemists in the 1980s, nanotubes jazzed physicists in the 1990s, and graphene charged up materials scientists in the 2000s, but one nanoscale carbon structure – a negatively curved surface called a schwarzite – has eluded everyone. Until now.

University of California, Berkeley [UC Berkeley], chemists have proved that three carbon structures recently created by scientists in South Korea and Japan are in fact the long-sought schwarzites, which researchers predict will have unique electrical and storage properties like those now being discovered in buckminsterfullerenes (buckyballs or fullerenes for short), nanotubes and graphene.

An August 13, 2018 UC Berkeley news release by Robert Sanders, which originated the news item, describes how the Berkeley scientists and the members of their international  collaboration from Germany, Switzerland, Russia, and Italy, have contributed to the current state of schwarzite research,

The new structures were built inside the pores of zeolites, crystalline forms of silicon dioxide – sand – more commonly used as water softeners in laundry detergents and to catalytically crack petroleum into gasoline. Called zeolite-templated carbons (ZTC), the structures were being investigated for possible interesting properties, though the creators were unaware of their identity as schwarzites, which theoretical chemists have worked on for decades.

Based on this theoretical work, chemists predict that schwarzites will have unique electronic, magnetic and optical properties that would make them useful as supercapacitors, battery electrodes and catalysts, and with large internal spaces ideal for gas storage and separation.

UC Berkeley postdoctoral fellow Efrem Braun and his colleagues identified these ZTC materials as schwarzites based of their negative curvature, and developed a way to predict which zeolites can be used to make schwarzites and which can’t.

“We now have the recipe for how to make these structures, which is important because, if we can make them, we can explore their behavior, which we are working hard to do now,” said Berend Smit, an adjunct professor of chemical and biomolecular engineering at UC Berkeley and an expert on porous materials such as zeolites and metal-organic frameworks.

Smit, the paper’s corresponding author, Braun and their colleagues in Switzerland, China, Germany, Italy and Russia will report their discovery this week in the journal Proceedings of the National Academy of Sciences. Smit is also a faculty scientist at Lawrence Berkeley National Laboratory.

Playing with carbon

Diamond and graphite are well-known three-dimensional crystalline arrangements of pure carbon, but carbon atoms can also form two-dimensional “crystals” — hexagonal arrangements patterned like chicken wire. Graphene is one such arrangement: a flat sheet of carbon atoms that is not only the strongest material on Earth, but also has a high electrical conductivity that makes it a promising component of electronic devices.

schwarzite carbon cage

The cage structure of a schwarzite that was formed inside the pores of a zeolite. The zeolite is subsequently dissolved to release the new material. (Graphics by Yongjin Lee and Efrem Braun)

Graphene sheets can be wadded up to form soccer ball-shaped fullerenes – spherical carbon cages that can store molecules and are being used today to deliver drugs and genes into the body. Rolling graphene into a cylinder yields fullerenes called nanotubes, which are being explored today as highly conductive wires in electronics and storage vessels for gases like hydrogen and carbon dioxide. All of these are submicroscopic, 10,000 times smaller than the width of a human hair.

To date, however, only positively curved fullerenes and graphene, which has zero curvature, have been synthesized, feats rewarded by Nobel Prizes in 1996 and 2010, respectively.

In the 1880s, German physicist Hermann Schwarz investigated negatively curved structures that resemble soap-bubble surfaces, and when theoretical work on carbon cage molecules ramped up in the 1990s, Schwarz’s name became attached to the hypothetical negatively curved carbon sheets.

“The experimental validation of schwarzites thus completes the triumvirate of possible curvatures to graphene; positively curved, flat, and now negatively curved,” Braun added.

Minimize me

Like soap bubbles on wire frames, schwarzites are topologically minimal surfaces. When made inside a zeolite, a vapor of carbon-containing molecules is injected, allowing the carbon to assemble into a two-dimensional graphene-like sheet lining the walls of the pores in the zeolite. The surface is stretched tautly to minimize its area, which makes all the surfaces curve negatively, like a saddle. The zeolite is then dissolved, leaving behind the schwarzite.

soap bubble schwarzite structure

A computer-rendered negatively curved soap bubble that exhibits the geometry of a carbon schwarzite. (Felix Knöppel image)

“These negatively-curved carbons have been very hard to synthesize on their own, but it turns out that you can grow the carbon film catalytically at the surface of a zeolite,” Braun said. “But the schwarzites synthesized to date have been made by choosing zeolite templates through trial and error. We provide very simple instructions you can follow to rationally make schwarzites and we show that, by choosing the right zeolite, you can tune schwarzites to optimize the properties you want.”

Researchers should be able to pack unusually large amounts of electrical charge into schwarzites, which would make them better capacitors than conventional ones used today in electronics. Their large interior volume would also allow storage of atoms and molecules, which is also being explored with fullerenes and nanotubes. And their large surface area, equivalent to the surface areas of the zeolites they’re grown in, could make them as versatile as zeolites for catalyzing reactions in the petroleum and natural gas industries.

Braun modeled ZTC structures computationally using the known structures of zeolites, and worked with topological mathematician Senja Barthel of the École Polytechnique Fédérale de Lausanne in Sion, Switzerland, to determine which of the minimal surfaces the structures resembled.

The team determined that, of the approximately 200 zeolites created to date, only 15 can be used as a template to make schwarzites, and only three of them have been used to date to produce schwarzite ZTCs. Over a million zeolite structures have been predicted, however, so there could be many more possible schwarzite carbon structures made using the zeolite-templating method.

Other co-authors of the paper are Yongjin Lee, Seyed Mohamad Moosavi and Barthel of the École Polytechnique Fédérale de Lausanne, Rocio Mercado of UC Berkeley, Igor Baburin of the Technische Universität Dresden in Germany and Davide Proserpio of the Università degli Studi di Milano in Italy and Samara State Technical University in Russia.

Here’s a link to and a citation for the paper,

Generating carbon schwarzites via zeolite-templating by Efrem Braun, Yongjin Lee, Seyed Mohamad Moosavi, Senja Barthel, Rocio Mercado, Igor A. Baburin, Davide M. Proserpio, and Berend Smit. PNAS August 14, 2018. 201805062; published ahead of print August 14, 2018. https://doi.org/10.1073/pnas.1805062115

This paper appears to be open access.

CRISPR-Cas12a as a new diagnostic tool

Similar to Cas9, Cas12a is has an added feature as noted in this February 15, 2018 news item on ScienceDaily,

Utilizing an unsuspected activity of the CRISPR-Cas12a protein, researchers created a simple diagnostic system called DETECTR to analyze cells, blood, saliva, urine and stool to detect genetic mutations, cancer and antibiotic resistance and also diagnose bacterial and viral infections. The scientists discovered that when Cas12a binds its double-stranded DNA target, it indiscriminately chews up all single-stranded DNA. They then created reporter molecules attached to single-stranded DNA to signal when Cas12a finds its target.

A February 15, 2018 University of California at Berkeley (UC Berkeley) news release by Robert Sanders and which originated the news item, provides more detail and history,

CRISPR-Cas12a, one of the DNA-cutting proteins revolutionizing biology today, has an unexpected side effect that makes it an ideal enzyme for simple, rapid and accurate disease diagnostics.

blood in test tube

(iStock)

Cas12a, discovered in 2015 and originally called Cpf1, is like the well-known Cas9 protein that UC Berkeley’s Jennifer Doudna and colleague Emmanuelle Charpentier turned into a powerful gene-editing tool in 2012.

CRISPR-Cas9 has supercharged biological research in a mere six years, speeding up exploration of the causes of disease and sparking many potential new therapies. Cas12a was a major addition to the gene-cutting toolbox, able to cut double-stranded DNA at places that Cas9 can’t, and, because it leaves ragged edges, perhaps easier to use when inserting a new gene at the DNA cut.

But co-first authors Janice Chen, Enbo Ma and Lucas Harrington in Doudna’s lab discovered that when Cas12a binds and cuts a targeted double-stranded DNA sequence, it unexpectedly unleashes indiscriminate cutting of all single-stranded DNA in a test tube.

Most of the DNA in a cell is in the form of a double-stranded helix, so this is not necessarily a problem for gene-editing applications. But it does allow researchers to use a single-stranded “reporter” molecule with the CRISPR-Cas12a protein, which produces an unambiguous fluorescent signal when Cas12a has found its target.

“We continue to be fascinated by the functions of bacterial CRISPR systems and how mechanistic understanding leads to opportunities for new technologies,” said Doudna, a professor of molecular and cell biology and of chemistry and a Howard Hughes Medical Institute investigator.

DETECTR diagnostics

The new DETECTR system based on CRISPR-Cas12a can analyze cells, blood, saliva, urine and stool to detect genetic mutations, cancer and antibiotic resistance as well as diagnose bacterial and viral infections. Target DNA is amplified by RPA to make it easier for Cas12a to find it and bind, unleashing indiscriminate cutting of single-stranded DNA, including DNA attached to a fluorescent marker (gold star) that tells researchers that Cas12a has found its target.

The UC Berkeley researchers, along with their colleagues at UC San Francisco, will publish their findings Feb. 15 [2018] via the journal Science’s fast-track service, First Release.

The researchers developed a diagnostic system they dubbed the DNA Endonuclease Targeted CRISPR Trans Reporter, or DETECTR, for quick and easy point-of-care detection of even small amounts of DNA in clinical samples. It involves adding all reagents in a single reaction: CRISPR-Cas12a and its RNA targeting sequence (guide RNA), fluorescent reporter molecule and an isothermal amplification system called recombinase polymerase amplification (RPA), which is similar to polymerase chain reaction (PCR). When warmed to body temperature, RPA rapidly multiplies the number of copies of the target DNA, boosting the chances Cas12a will find one of them, bind and unleash single-strand DNA cutting, resulting in a fluorescent readout.

The UC Berkeley researchers tested this strategy using patient samples containing human papilloma virus (HPV), in collaboration with Joel Palefsky’s lab at UC San Francisco. Using DETECTR, they were able to demonstrate accurate detection of the “high-risk” HPV types 16 and 18 in samples infected with many different HPV types.

“This protein works as a robust tool to detect DNA from a variety of sources,” Chen said. “We want to push the limits of the technology, which is potentially applicable in any point-of-care diagnostic situation where there is a DNA component, including cancer and infectious disease.”

The indiscriminate cutting of all single-stranded DNA, which the researchers discovered holds true for all related Cas12 molecules, but not Cas9, may have unwanted effects in genome editing applications, but more research is needed on this topic, Chen said. During the transcription of genes, for example, the cell briefly creates single strands of DNA that could accidentally be cut by Cas12a.

The activity of the Cas12 proteins is similar to that of another family of CRISPR enzymes, Cas13a, which chew up RNA after binding to a target RNA sequence. Various teams, including Doudna’s, are developing diagnostic tests using Cas13a that could, for example, detect the RNA genome of HIV.

infographic about DETECTR system

(Infographic by the Howard Hughes Medical Institute)

These new tools have been repurposed from their original role in microbes where they serve as adaptive immune systems to fend off viral infections. In these bacteria, Cas proteins store records of past infections and use these “memories” to identify harmful DNA during infections. Cas12a, the protein used in this study, then cuts the invading DNA, saving the bacteria from being taken over by the virus.

The chance discovery of Cas12a’s unusual behavior highlights the importance of basic research, Chen said, since it came from a basic curiosity about the mechanism Cas12a uses to cleave double-stranded DNA.

“It’s cool that, by going after the question of the cleavage mechanism of this protein, we uncovered what we think is a very powerful technology useful in an array of applications,” Chen said.

Here’s a link to and a citation for the paper,

CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity by Janice S. Chen, Enbo Ma, Lucas B. Harrington, Maria Da Costa, Xinran Tian, Joel M. Palefsky, Jennifer A. Doudna. Science 15 Feb 2018: eaar6245 DOI: 10.1126/science.aar6245

This paper is behind a paywall.

‘Neural dust’ could lead to introduction of electroceuticals

In case anyone is wondering, the woman who’s manipulating a prosthetic arm so she can eat or a drink of coffee probably has a bulky implant/docking station in her head. Right now that bulky implant is the latest and greatest innovation for tetraplegics (aka, quadriplegics) as it frees, to some extent, people who’ve had no independent movement of any kind. By virtue of the juxtaposition of the footage of the woman with the ‘neural dust’ footage, they seem to be suggesting that neural dust might some day accomplish the same type of connection. At this point, hopes for the ‘neural dust’ are more modest.

An Aug. 3, 2016 news item on ScienceDaily announces the ‘neural dust’,

University of California, Berkeley engineers have built the first dust-sized, wireless sensors that can be implanted in the body, bringing closer the day when a Fitbit-like device could monitor internal nerves, muscles or organs in real time.

Because these batteryless sensors could also be used to stimulate nerves and muscles, the technology also opens the door to “electroceuticals” to treat disorders such as epilepsy or to stimulate the immune system or tamp down inflammation.

An Aug. 3, 2016 University of California at Berkeley news release (also on EurekAlert) by Robert Sanders, which originated the news item, explains further and describes the researchers’ hope that one day the neural dust could be used to control implants and prosthetics,

The so-called neural dust, which the team implanted in the muscles and peripheral nerves of rats, is unique in that ultrasound is used both to power and read out the measurements. Ultrasound technology is already well-developed for hospital use, and ultrasound vibrations can penetrate nearly anywhere in the body, unlike radio waves, the researchers say.

“I think the long-term prospects for neural dust are not only within nerves and the brain, but much broader,“ said Michel Maharbiz, an associate professor of electrical engineering and computer sciences and one of the study’s two main authors. “Having access to in-body telemetry has never been possible because there has been no way to put something supertiny superdeep. But now I can take a speck of nothing and park it next to a nerve or organ, your GI tract or a muscle, and read out the data.“

Maharbiz, neuroscientist Jose Carmena, a professor of electrical engineering and computer sciences and a member of the Helen Wills Neuroscience Institute, and their colleagues will report their findings in the August 3 [2016] issue of the journal Neuron.

The sensors, which the researchers have already shrunk to a 1 millimeter cube – about the size of a large grain of sand – contain a piezoelectric crystal that converts ultrasound vibrations from outside the body into electricity to power a tiny, on-board transistor that is in contact with a nerve or muscle fiber. A voltage spike in the fiber alters the circuit and the vibration of the crystal, which changes the echo detected by the ultrasound receiver, typically the same device that generates the vibrations. The slight change, called backscatter, allows them to determine the voltage.

Motes sprinkled thoughout the body

In their experiment, the UC Berkeley team powered up the passive sensors every 100 microseconds with six 540-nanosecond ultrasound pulses, which gave them a continual, real-time readout. They coated the first-generation motes – 3 millimeters long, 1 millimeter high and 4/5 millimeter thick – with surgical-grade epoxy, but they are currently building motes from biocompatible thin films which would potentially last in the body without degradation for a decade or more.

While the experiments so far have involved the peripheral nervous system and muscles, the neural dust motes could work equally well in the central nervous system and brain to control prosthetics, the researchers say. Today’s implantable electrodes degrade within 1 to 2 years, and all connect to wires that pass through holes in the skull. Wireless sensors – dozens to a hundred – could be sealed in, avoiding infection and unwanted movement of the electrodes.

“The original goal of the neural dust project was to imagine the next generation of brain-machine interfaces, and to make it a viable clinical technology,” said neuroscience graduate student Ryan Neely. “If a paraplegic wants to control a computer or a robotic arm, you would just implant this electrode in the brain and it would last essentially a lifetime.”

In a paper published online in 2013, the researchers estimated that they could shrink the sensors down to a cube 50 microns on a side – about 2 thousandths of an inch, or half the width of a human hair. At that size, the motes could nestle up to just a few nerve axons and continually record their electrical activity.

“The beauty is that now, the sensors are small enough to have a good application in the peripheral nervous system, for bladder control or appetite suppression, for example,“ Carmena said. “The technology is not really there yet to get to the 50-micron target size, which we would need for the brain and central nervous system. Once it’s clinically proven, however, neural dust will just replace wire electrodes. This time, once you close up the brain, you’re done.“

The team is working now to miniaturize the device further, find more biocompatible materials and improve the surface transceiver that sends and receives the ultrasounds, ideally using beam-steering technology to focus the sounds waves on individual motes. They are now building little backpacks for rats to hold the ultrasound transceiver that will record data from implanted motes.

They’re also working to expand the motes’ ability to detect non-electrical signals, such as oxygen or hormone levels.

“The vision is to implant these neural dust motes anywhere in the body, and have a patch over the implanted site send ultrasonic waves to wake up and receive necessary information from the motes for the desired therapy you want,” said Dongjin Seo, a graduate student in electrical engineering and computer sciences. “Eventually you would use multiple implants and one patch that would ping each implant individually, or all simultaneously.”

Ultrasound vs radio

Maharbiz and Carmena conceived of the idea of neural dust about five years ago, but attempts to power an implantable device and read out the data using radio waves were disappointing. Radio attenuates very quickly with distance in tissue, so communicating with devices deep in the body would be difficult without using potentially damaging high-intensity radiation.

Marharbiz hit on the idea of ultrasound, and in 2013 published a paper with Carmena, Seo and their colleagues describing how such a system might work. “Our first study demonstrated that the fundamental physics of ultrasound allowed for very, very small implants that could record and communicate neural data,” said Maharbiz. He and his students have now created that system.

“Ultrasound is much more efficient when you are targeting devices that are on the millimeter scale or smaller and that are embedded deep in the body,” Seo said. “You can get a lot of power into it and a lot more efficient transfer of energy and communication when using ultrasound as opposed to electromagnetic waves, which has been the go-to method for wirelessly transmitting power to miniature implants”

“Now that you have a reliable, minimally invasive neural pickup in your body, the technology could become the driver for a whole gamut of applications, things that today don’t even exist,“ Carmena said.

Here’s a link to and a citation for the team’s latest paper,

Wireless Recording in the Peripheral Nervous System with Ultrasonic Neural Dust by Dongjin Seo, Ryan M. Neely, Konlin Shen, Utkarsh Singhal, Elad Alon, Jan M. Rabaey, Jose M. Carmena. and Michel M. Maharbiz. Neuron Volume 91, Issue 3, p529–539, 3 August 2016 DOI: http://dx.doi.org/10.1016/j.neuron.2016.06.034

This paper appears to be open access.