Tag Archives: University of California at Davis (UC Davis)

Is your smart TV or your car spying on you?

Simple answer: Yes.

Smart television sets (TVs)

A December 10, 2024 Universidad Carlos III de Madrid press release (also on EurekAlert) offers details about the data collected by smart TVs,

A scientific team from Universidad Carlos III de Madrid (UC3M), in collaboration with University College London (England) and the University of California, Davis (USA), has found that smart TVs send viewing data to their servers. This allows brands to generate detailed profiles of consumers’ habits and tailor advertisements based on their behaviour.

The research revealed that this technology captures screenshots or audio to identify the content displayed on the screen using Automatic Content Recognition (ACR) technology. This data is then periodically sent to specific servers, even when the TV is used as an external screen or connected to a laptop.

“Automatic Content Recognition works like a kind of visual Shazam, taking screenshots or audio to create a viewer profile based on their content consumption habits. This technology enables manufacturers’ platforms to profile users accurately, much like the internet does,” explains one of the study’s authors, Patricia Callejo, a professor in UC3M’s Department of Telematics Engineering and a fellow at the UC3M-Santander Big Data Institute. “In any case, this tracking—regardless of the usage mode—raises serious privacy concerns, especially when the TV is used solely as a monitor.”

The findings, presented in November [2024] at the Internet Measurement Conference (IMC) 2024, highlight the frequency with which these screenshots are transmitted to the servers of the brands analysed: Samsung and LG. Specifically, the research showed that Samsung TVs sent this information every minute, while LG devices did so every 15 seconds. “This gives us an idea of the intensity of the monitoring and shows that smart TV platforms collect large volumes of data on users, regardless of how they consume content—whether through traditional TV viewing or devices connected via HDMI, like laptops or gaming consoles,” Callejo emphasises.

To test the ability of TVs to block ACR tracking, the research team experimented with various privacy settings on smart TVs. The results demonstrated that, while users can voluntarily block the transmission of this data to servers, the default setting is for TVs to perform ACR. “The problem is that not all users are aware of this,” adds Callejo, who considers this lack of transparency in initial settings concerning. “Moreover, many users don’t know how to change the settings, meaning these devices function by default as tracking mechanisms for their activity.”

This research opens up new avenues for studying the tracking capabilities of cloud-connected devices that communicate with each other (commonly known as the Internet of Things, or IoT). It also suggests that manufacturers and regulators must urgently address the challenges that these new devices will present in the near future.

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

Watching TV with the Second-Party: A First Look at Automatic Content Recognition Tracking in Smart TVs by Gianluca Anselmi, Yash Vekaria, Alexander D’Souza, Patricia Callejo, Anna Maria Mandalari, Zubair Shafiq. IMC ’24: Proceedings of the 2024 ACM on Internet Measurement Conference Pages 622 – 634 DOI: https://doi.org/10.1145/3646547.3689013 Published: 04 November 2024

This paper is open access.

Cars

This was on the Canadian Broadcasting Corporation’s (CBC) Day Six radio programme and the segment is embedded in a January 19, 2025 article by Philip Drost, Note: A link has been removed,

When a Tesla Cybertruck exploded outside Trump International Hotel in Las Vegas on New Year’s Day [2025], authorities were quickly able to gather information, crediting Elon Musk and Tesla for sending them info about the car and its driver. 

But for some, it’s alarming to discover that kind of information is so readily available.

“Most carmakers are selling drivers’ personal information. That’s something that we know based on their privacy policies,” Zoë MacDonald, a writer and researcher focussing on online privacy and digital rights, told Day 6 host Brent Bambury.

The Las Vegas Metropolitan Police Department said the Tesla CEO was able to provide key details about the truck’s driver, who authorities believe died by self-inflicted gun wound at the scene, and its movement leading up to the destination. 

With that data, they were able to determine that the explosives came from a device in the truck, not the vehicle itself.  

“We have now confirmed that the explosion was caused by very large fireworks and/or a bomb carried in the bed of the rented Cybertruck and is unrelated to the vehicle itself,” Musk wrote on X following the explosion.

To privacy experts, it’s another example of how your personal information can be used in ways you may not be aware of. And while this kind of data can useful in an investigation, it’s by no means the only way companies use the information.  

“This is unfortunately not surprising that they have this data,” said David Choffnes, executive director of the Cybersecurity and Privacy Institute at Northeastern University in Boston.

“When you see it all together and know that a company has that information and continues at any point in time to hand it over to law enforcement, then you start to be a little uncomfortable, even if — in this case — it was a good thing for society.”

CBC News reached out to Tesla for comment but did not hear back before publication. 

I found this to be eye-opening, Note: A link has been removed,

MacDonald says the privacy concerns are a byproduct of all the technology new cars come with these days, including microphones, cameras, and sensors. The app that often accompanies a new car is collecting your information, too, she says.

The former writer for the Mozilla Foundation worked on a report in 2023 that examined vehicle privacy policies. For that study, MacDonald sifted through privacy policies from auto manufacturers. And she says the findings were staggering.

Most shocking of all is the information the car can learn from you, MacDonald says. It’s not just when you gas up or start your engine. Your vehicle can learn your sexual activity, disability status, and even your religious beliefs [emphasis mine].

MacDonald says it’s unclear how they car companies do this, because the information in the policies are so vague.

It can also collect biometric data, such as facial geometric features, iris scans, and fingerprints [emphasis mine].

This extends far past the driver. MacDonald says she read one privacy policy that required drivers to read out a statement every time someone entered the vehicle, to make them aware of the data the car collects, something that seems unlikely to go down before your Uber ride.

If that doesn’t bother you, then this might, Note: A link has been removed,

And car companies aren’t just keeping that information to themselves.

Confronted with these types of privacy concerns, many people simply say they have nothing to hide, Choffnes says. But when money is involved, they change their tune. 

According to an investigation from the New York Times in March of 2024, General Motors shared information on how people drive their cars with data brokers that create risk profiles for the insurance industry, which resulted in people’s insurance premiums going up [emphases mine]. General Motors has since said it has stopped sharing those details [emphasis mine].

“The issue with these kinds of services is that it’s not clear that it is being done in a correct or fair way, and that those costs are actually unfair to consumers,” said Choffnes. 

For example, if you make a hard stop to avoid an accident because of something the car in front of you did, the vehicle could register it as poor driving.

Drost’s January 19, 2025 article notes that the US Federal Trade Commission has proposed a five year moratorium to prevent General Motors from selling geolocation and driver behavior data to consumer report agencies. In the meantime,

“Cars are a privacy nightmare. And that is not a problem that Canadian consumers can solve or should solve or should have the burden to try to solve for themselves,” said MacDonald.

If you have the time, read Drost’s January 19, 2025 article and/or listen to the embedded radio segment.

Cellulose nanofibrils for slow-release fertilizer

An October 17, 2022 news item on phys.org highlights nanocellulose research from Brazil, Note: A link has been removed,

A research team affiliated with the Laboratory of Polymeric Materials and Biosorbents at the Federal University of São Carlos (UFSCar) in Araras, São Paulo state, Brazil, has produced and is testing cellulose-based materials for enhanced-efficiency fertilizers to improve the supply of nutrients to crops and reduce the release of non-biodegradable chemicals [forever chemicals] into the ecosystem.

The studies were led by Roselena Faez, a professor at the Center for Agricultural Sciences (CCA-UFSCar). The findings have recently been reported in two publications. One is an article published in Carbohydrate Polymers, with Débora França as first author. Here [keep scrolling down] the researchers describe how they used modified nanocellulose to discharge the nutrients contained in fertilizer into the soil slowly and in a controlled manner, given that nitrogen, phosphorus and potassium are highly soluble.

Caption: The first and third photos show the paper made from phosphorylated sugarcane cellulose. The second shows the 3D structure of the material comprising cellulose and nutrient. The fourth shows the microparticles in powder form and after molding into tablets. Credit: Lucas Luiz Messa/Débora França

An October 19, 2022 Fundação de Amparo à Pesquisa do Estado de São Paulo [FAPESP] press release (also on EurekAlert but published October 17, 2022) by Karina Ninni, originated the phys.org news item. The researchers explain (Note: Links have been removed),

“Potassium is rapidly washed away by rain because of its high ion mobility. It’s the hardest to release in a controlled manner. Nitrogen can be obtained from various sources, such as nitrates, ammonia and urea, but plants get the nitrogen they need most easily from nitrate, which is also easily washed away and doesn’t remain in the soil for long. Phosphorus [as phosphate] is a very large ion and less mobile than the other macronutrients,” said Faez, who coordinates the Polymeric Materials and Biosorbents Research Group at UFSCar Araras.

Controlled-release products are available on the market, she added, but most are made of synthetic polymers, which are non-biodegradable. “Fertilizer grains are about the size of grains of coarse sea salt. To make sure the nutrients are released slowly, they’re coated with layers of polymer that last about two months each, so the manufacturer applies two, three or four coats, according to the desired length of time for controlled release,” Faez explained, noting that the polymers in question are plastics and remain in the soil, eventually degrading into microparticles that last virtually forever.

The researchers at UFSCar developed an entirely different product in which the chemical reaction between the modified nanocellulose and mineral salts keeps the nutrients in the soil. “We focused on the worst problems, which are nitrate and potassium. The material we developed is totally biodegradable and releases these nutrients at about the same slow rate as the available synthetic materials,” Faez said.

The nanocellulose was obtained from pure cellulose donated by a paper factory. The nanofibrils were functionalized with positive and negative charges to enhance polymer-nutrient interaction. “Because the salts are also made up of positively or negatively charged particles and highly soluble, we hypothesized that negatively charged nanocellulose would react with positive ions in the salts, while positively charged nanocellulose would interact with negative ions, reducing the solubility of the salts. This proved to be the case, and the group succeeded in modulating nutrient release in accordance with the type of particle in the material,” França said.

Evaluation in soil

The group fabricated the product in the form of tablets and evaluated its performance in terms of nutrient release into the soil. Evaluation of release into water is the usual method, and water is a very different system from soil. This part of the research was conducted in partnership with Claudinei Fonseca Souza, a professor at CCA-UFSCar’s Department of Natural Resources and Environmental Protection in Araras.

“We evaluated nutrient release into the soil and biodegradation of the material at the site for 100 days. But we deliberately used very poor soil with little organic matter, because this enables us to see the physical effects of release more easily,” Faez said.

The researchers used two techniques to obtain tablets: atomization and spray drying to encapsulate the nutrients with the nanocellulose, followed by heat processing of the resulting powder, which was pressed in a mold. This work was completed with the help of colleagues at the Cellulose and Wood Materials Laboratory belonging to EMPA (Swiss Federal Laboratories for Materials Science and Technology) and in collaboration with UFSCar’s Water, Soil and Environment Engineering Research Group, led by Souza. França performed the cellulose modifications at EMPA while on an internship there with support from FAPESP. She was also supported by a doctoral scholarship in Brazil.

Self-fertilization

The second recent article by the group was published in Industrial Crops and Products, with chemist Lucas Luiz Messa as first author. The goal of the study was to extract cellulose from sugarcane bagasse and modify it with a surface negative charge by phosphorylation (addition of a phosphorus group) to allow controlled release of potassium. In theory, delivery of plant nutrition would be slowed by cellulose phosphorylation, which would create surface anionic charges that would bind to macronutrient and micronutrient cations. 

The group prepared three types of structure with the phosphorylated cellulose: oven-dried paper-like film; spray-dried powder; and freeze-dried porous bulk similar to polystyrene foam. Freeze drying, or lyophilization, was seen to leave nutrients in the voids left by water removal. 

“Technologically speaking, the paper-like structure was the best material we produced for controlled delivery of nutrients. Several products can be created using this paper,” Faez said.

The results obtained in the research led by Messa enabled the group to develop small propagation pots for seedling cultivation. When this material degrades, the phosphorus it contains is released. According to Faez, cellulose phosphorylation is cheap, and the cost of the end product is relatively low. “It’s more or less BRL 0.27 per gram of paper produced. The propagation pot must be about 1 gram. Unit cost is therefore about BRL 0.30 in terms of laboratory costs,” she said.

Biodegradable propagation pots are already available on the market. “But our product has built-in fertilizer, which is a major competitive advantage. Indeed, we’ve filed a patent application,” she said.

The pot is about to be trialed by a flower producer in Holambra, São Paulo state. Several batches produced in the laboratory have been shipped there. Nutrient release has so far been tested only in water. “We call this an accelerated ion release assessment method because it’s faster in water, but even in water we found the release rate to be 40%-50% slower compared with the behavior of the ion in the material and without the material. Even in water, therefore, we succeeded in retaining these ions. We assume delivery will be even slower in the substrate,” she said.

The research was also supported by FAPESP via a Doctoral Scholarship in Brazil and a Research Internship Abroad Scholarship awarded to Messa, and a Regular Research Grant awarded to Faez.

Messa was assisted by a colleague at the University of California Davis (USA), where he worked as a research intern.

About São Paulo Research Foundation (FAPESP)

The São Paulo Research Foundation (FAPESP) is a public institution with the mission of supporting scientific research in all fields of knowledge by awarding scholarships, fellowships and grants to investigators linked with higher education and research institutions in the State of São Paulo, Brazil. FAPESP is aware that the very best research can only be done by working with the best researchers internationally. Therefore, it has established partnerships with funding agencies, higher education, private companies, and research organizations in other countries known for the quality of their research and has been encouraging scientists funded by its grants to further develop their international collaboration. You can learn more about FAPESP at www.fapesp.br/en and visit FAPESP news agency at www.agencia.fapesp.br/en to keep updated with the latest scientific breakthroughs FAPESP helps achieve through its many programs, awards and research centers. You may also subscribe to FAPESP news agency at http://agencia.fapesp.br/subscribe

I have links and citations for both papers mentioned in the press release,

Sugarcane bagasse derived phosphorylated cellulose as substrates for potassium release induced by phosphates surface and drying methods by Lucas Luiz Messa, You-Lo Hsieh, Roselena Faez. Industrial Crops and Products Volume 187, Part A, 1 November 2022, 115350 DOI: https://doi.org/10.1016/j.indcrop.2022.115350 Available online 20 July 2022, Version of Record 20 July 2022

This paper is behind a paywall.

Charged-cellulose nanofibrils as a nutrient carrier in biodegradable polymers for enhanced efficiency fertilizers by Débora França, Gilberto Siqueira, Gustav Nyström, Frank Clemens, Claudinei Fonseca Souza, Roselena Faez. Carbohydrate Polymers Volume 296, 15 November 2022, 119934 DOI: https://doi.org/10.1016/j.carbpol.2022.119934 Available online 1 August 2022, Version of Record 3 August 2022

This paper is behind a paywall.

Science Says 2022 SciArt Contest (Jan. 3 – 31, 2022) for California (US) residents

Science Says is affiliated with the University of California at Davis (UC Davis). Here’s a little more about the UC Davis group from the Science Says homepage,

We are a team of friendly neighborhood scientists passionate about making science accessible to the general public. We aim to cultivate a community of science communicators at UC Davis dedicated to making scientific research accessible, relevant, and interesting to everyone. 

As for the contest, here’s more from the 2022 Science Art Contest webpage,

Jan 3-31, 2022 @ 12:00am – 11:59pm

We want to feature your science art in our second annual science art competition! The intersection of science and art offers a unique opportunity for creative science communication.

To participate in our contest you must:

1. Submit one piece of work considered artistic and creative: beautiful microscopy, field photography, paintings, crafts, etc.

2. The work must be shareable on our social media platforms. We encourage you to include your handle or name in the submitted image.

3. You must live within California to be considered for prizes.

You may compete in one of three categories: UC Davis affiliate (student, staff, faculty), the local Davis/Sacramento area or California. *If out of state, you can submit your work for honorable mention to be featured on our social media and news release, although you can’t be considered for prizes.

Winners will be determined by popular vote via a Google Form offered through our February newsletter, social media and website. Prizes vary depending on the contest selected. For entrants in either the UC Davis affiliate contest or local Davis/Sacramento contest, first prize will receive a cash prize of $75 and second place will receive a cash prize of $50. For entrants in the California contest, first place will receive a cash prize of $50.

Submit Here

Submissions open the first week of January and close on January 31, 2022. Voting begins February 2, 2022 and ends February 16, 2022. Winners will be announced by social media and a special news release on our website and contacted via email on February 23, 2022. Prizes will be awarded by March 4, 2022.

H/t to Raymond K. Nakamura for his retweet of the competition announcement by the Science Says team on Twitter.

Art/Sci or SciArt?

It depends on who’s talking. An artist will say art/sci or art/science and a scientist will say sciart. The focus, or pride of place, of course, being placed on the speaker’s primary interest.

“transforming a plant is still an art” even with CRISPR

“Plus ça change, plus c’est la même chose (the more things change, the more things stay the same), is an old French expression that came to mind when I stumbled across two stories about genetic manipulation of food-producing plants.

The first story involves CRISPR (clustered regularly interspersed short palindromic repeats) gene editing and the second involves more ancient ways to manipulate plant genetics.

Getting ‘CRISPR’d’ plant cells to grow into plants

Plants often don’t grow from cells after researchers alter their genomes. Using a new technology, a team coaxed wheat (above) and other crops to more readily produce genome-edited healthy adult plants. Credit: Juan Debernardi

An October 13, 2020 news item on phys.org announces research about getting better results after a plant’s genome has been altered,

Researchers know how to make precise genetic changes within the genomes of crops, but the transformed cells often refuse to grow into plants. One team has devised a new solution.

Scientists who want to improve crops face a dilemma: it can be difficult to grow plants from cells after you’ve tweaked their genomes.

A new tool helps ease this process by coaxing the transformed cells, including those modified with the gene-editing system CRISPR-Cas9, to regenerate new plants. Howard Hughes Medical Institute Research Specialist Juan M. Debernardi and Investigator Jorge Dubcovsky, together with David Tricoli at the University of California, Davis [UC Davis] Plant Transformation Facility, Javier Palatnik from Argentina, and colleagues at the John Innes Center [UK], collaborated on the work. The team reports the technology, developed in wheat and tested in other crops, October 12, 2020, in the journal Nature Biotechnology.

An October 12, 2020 Howard Hughes Medical Institute (HHMI) news release, which originated the news item, provides more detail,

“The problem is that transforming a plant is still an art [emphasis mine],” Dubcovsky says. The success rate is often low – depending on the crop being modified, 100 attempts may yield only a handful of green shoots that can turn into full-grown plants. The rest fail to produce new plants and die. Now, however, “we have reduced this barrier,” says Dubcovsky, a plant geneticist at UC Davis. Using two genes that already control development in many plants, his team dramatically increased the formation of shoots in modified wheat, rice, citrus, and other crops.

Although UC Davis has a pending patent for commercial applications, Dubcovsky says the technique is available to any researcher who wants to use it for research, at no charge. A number of plant breeding companies have also expressed interested in licensing it. “Now people are trying it in multiple crops,” he says.

Humans have worked to improve plants since the dawn of agriculture, selecting wild grasses to produce cultivated maize and wheat, for example. Nowadays, though, CRISPR has given researchers the ability to make changes to the genome with surgical precision. They have used it to create wheat plants with larger grains, generate resistance to fungal infection, design novel tomato plant architectures, and engineer other traits in new plant varieties.

But the process isn’t easy. Scientists start out with plant cells or pieces of tissue, into which they introduce the CRISPR machinery and a small guide to the specific genes they’d like to edit. They must then entice the modified cells into forming a young plant. Most don’t sprout – a problem scientists are still working to understand.

They have tried to find work-arounds, including boosting the expression of certain genes that control early stages of plant development. While this approach has had some success, it can lead to twisted, stunted, sterile plants if not managed properly.Dubcovsky and his colleagues looked at two other growth-promoting genes, GRF and GIF, that work together in young tissues or organs of plants ranging from moss to fruit trees. The team put these genes side-by-side, like a couple holding hands, before adding them to plant cells. “If you go to a dance, you need to find your partner,” Dubcovsky says. “Here, you are tied with a rope to your partner.”

Dubcovsky’s team found that genetically altered wheat, rice, hybrid orange, and other crops produced many more shoots if those experiments included the linked GRF and GIF genes. In experiments with one variety of wheat, the appearance of shoots increased nearly eight-fold. The number of shoots in rice and the hybrid orange, meanwhile, more than doubled and quadrupled, respectively. What’s more, these shoots grew into healthy plants capable of reproducing on their own, with none of the defects that can result when scientists boost other development-controlling genes. That’s because one of the genes is naturally degraded in adult tissues, Dubcovsky says.

Caroline Roper, a plant pathologist at University of California, Riverside who was not involved in the work, plans to use the new technology to study citrus greening, a bacterial disease that kills trees and renders oranges hard and bitter.

To understand how citrus trees can protect themselves, she needs to see how removing certain genes alters their susceptibility to the bacterium — information that could lead to ways to fight the disease. With conventional techniques, it could take at least two years to generate the gene-edited plants she needs. She hopes Dubcovsky’s tool will shorten that timeline.  

“Time is of the essence. The growers, they wanted an answer yesterday, because they’re at the brink of having to abandon cultivating citrus,” she says.

For anyone who noticed the reference to citrus greening in the last paragraphs of this news release, I have more information aboutthe disease and efforts to it in an August 6, 2020 posting.

As for the latest in gene editing and regeneration, here’s a link to and a citation for the paper,

A GRF–GIF chimeric protein improves the regeneration efficiency of transgenic plants by Juan M. Debernardi, David M. Tricoli, Maria F. Ercoli, Sadiye Hayta, Pamela Ronald, Javier F. Palatnik & Jorge Dubcovsky. Nature Biotechnology volume 38, pages 1274–1279(2020) DOI: https://doi.org/10.1038/s41587-020-0703-0 First Published Online: 12 October 2020 Journal Issue Date: November 2020

This paper is behind a paywall.

Ancient farming techniques for engineering crops

I stumbled on this story by Gabriela Serrato Marks for Massive Science almost three years late (it’s a Dec. 5, 2017 article),

There are more than 50 strains of maize, called landraces, grown in Mexico. A landrace is similar to a dog breed: Corgis and Huskies are both dogs, but they were bred to have different traits. Maize domestication worked the same way.

Some landraces of maize can grow in really dry conditions; others grow best in wetter soils. Early maize farmers selectively bred maize landraces that were well-adapted to the conditions on their land, a practice that still continues today in rural areas of Mexico.

If you think this sounds like an early version of genetic engineering, you’d be correct. But nowadays, modern agriculture is moving away from locally adapted strains and traditional farming techniques and toward active gene manipulation. The goal of both traditional landrace development and modern genetic modification has been to create productive, valuable crops, so these two techniques are not necessarily at odds.

But as more farmers converge on similar strains of (potentially genetically modified) seeds instead of developing locally adapted landraces, there are two potential risks: one is losing the cultural legacy of traditional agricultural techniques that have been passed on in families for centuries or even millennia, and another is decreasing crop resilience even as climate variability is increasing.

Mexico is the main importer of US-grown corn, but that imported corn is primarily used to feed livestock. The corn that people eat or use to make tortillas is grown almost entirely in Mexico, which is where landraces come in.

It is a common practice to grow multiple landraces with different traits as an insurance policy against poor growth conditions. The wide range of landraces contains a huge amount of genetic diversity, making it less likely that one adverse event, such as a drought or pest infestation, will wipe out an entire crop. If farmers only grow one type of corn, the whole crop is vulnerable to the same event.

Landraces are also different from most commercially available hybrid strains of corn because they are open pollinating, which means that farmers can save seeds and replant them the next year, saving money and preserving the strain. If a landrace is not grown anymore, its contribution to maize’s genetic diversity is permanently lost.

This diversity was cultivated over generations from maize’s wild cousin, teosinte, by 60 groups of indigenous people in Mexico. Teosinte looks like a skinny, hairier version of maize. It still grows wild in some parts of Central America, but its close relatives have been found, domesticated, at archaeological sites in the region over 9,000 years old. These early maize cobs could easily fit in the palm of your hand – not big enough to be a staple crop that early farmers could depend upon for sustenance. Genetically, they were more similar to wild teosinte than to modern maize.

[] archaeologists also found that the cobs in Honduras, which is outside the natural range of teosinte, were larger than cobs of the same age from the original domestication region in southern Mexico. The scientists think that people in Honduras were able to develop more productive maize landraces because their crops were isolated from wild teosinte.

The size and shape of the ancient cobs from Honduras show that early farmers engineered the maize crop [emphasis mine] to make it more productive. They developed unique landraces that were well adapted to local conditions and successfully cultivated enough maize to support their communities. In many ways, they were early geneticists. [emphasis mine] …

We have a lot to learn from the indigenous farmers who were growing maize 4,000 years ago. Their history provides examples of both environmentally sound genetic modification and effective adaptation to climate variability. [emphases mine] …

Plus ça change …, eh?

The Broad Institute gives us another reason to love CRISPR

More and more, this resembles a public relations campaign. First, CRISPR (clustered regularly interspersed short palindromic repeats) gene editing is going to be helpful with COVID-19 and now it can help us to deal with conservation issues. (See my May 26, 2020 posting about the latest CRISPR doings as of May 7, 2020; included is a brief description of the patent dispute between Broad Institute and UC Berkeley and musings about a public relations campaign.)

A May 21, 2020 news item on ScienceDaily announces how CRISPR could be useful for conservation,

The gene-editing technology CRISPR has been used for a variety of agricultural and public health purposes — from growing disease-resistant crops to, more recently, a diagnostic test for the virus that causes COVID-19. Now a study involving fish that look nearly identical to the endangered Delta smelt finds that CRISPR can be a conservation and resource management tool, as well. The researchers think its ability to rapidly detect and differentiate among species could revolutionize environmental monitoring.

Caption: Longfin smelt can be difficult to differentiate from endangered Delta smelt. Here, a longfin smelt is swabbed for genetic identification through a CRISPR tool called SHERLOCK. Credit: Alisha Goodbla/UC Davis

A May 21, 2020 University of California at Davis (UC Davis) news release (also on EurekAlert) by Kat Kerlin, which originated the news item, provides more detail (Note: A link has been removed),

The study, published in the journal Molecular Ecology Resources, was led by scientists at the University of California, Davis, and the California Department of Water Resources in collaboration with MIT Broad Institute [emphasis mine].

As a proof of concept, it found that the CRISPR-based detection platform SHERLOCK (Specific High-sensitivity Enzymatic Reporter Unlocking) [emphasis mine] was able to genetically distinguish threatened fish species from similar-looking nonnative species in nearly real time, with no need to extract DNA.

“CRISPR can do a lot more than edit genomes,” said co-author Andrea Schreier, an adjunct assistant professor in the UC Davis animal science department. “It can be used for some really cool ecological applications, and we’re just now exploring that.”

WHEN GETTING IT WRONG IS A BIG DEAL

The scientists focused on three fish species of management concern in the San Francisco Estuary: the U.S. threatened and California endangered Delta smelt, the California threatened longfin smelt and the nonnative wakasagi. These three species are notoriously difficult to visually identify, particularly in their younger stages.

Hundreds of thousands of Delta smelt once lived in the Sacramento-San Joaquin Delta before the population crashed in the 1980s. Only a few thousand are estimated to remain in the wild.

“When you’re trying to identify an endangered species, getting it wrong is a big deal,” said lead author Melinda Baerwald, a project scientist at UC Davis at the time the study was conceived and currently an environmental program manager with California Department of Water Resources.

For example, state and federal water pumping projects have to reduce water exports if enough endangered species, like Delta smelt or winter-run chinook salmon, get sucked into the pumps. Rapid identification makes real-time decision making about water operations feasible.

FROM HOURS TO MINUTES

Typically to accurately identify the species, researchers rub a swab over the fish to collect a mucus sample or take a fin clip for a tissue sample. Then they drive or ship it to a lab for a genetic identification test and await the results. Not counting travel time, that can take, at best, about four hours.

SHERLOCK shortens this process from hours to minutes. Researchers can identify the species within about 20 minutes, at remote locations, noninvasively, with no specialized lab equipment. Instead, they use either a handheld fluorescence reader or a flow strip that works much like a pregnancy test — a band on the strip shows if the target species is present.

“Anyone working anywhere could use this tool to quickly come up with a species identification,” Schreier said.

OTHER CRYPTIC CRITTERS

While the three fish species were the only animals tested for this study, the researchers expect the method could be used for other species, though more research is needed to confirm. If so, this sort of onsite, real-time capability may be useful for confirming species at crime scenes, in the animal trade at border crossings, for monitoring poaching, and for other animal and human health applications.

“There are a lot of cryptic species we can’t accurately identify with our naked eye,” Baerwald said. “Our partners at MIT are really interested in pathogen detection for humans. We’re interested in pathogen detection for animals as well as using the tool for other conservation issues.”

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

Rapid and accurate species identification for ecological studies and monitoring using CRISPR‐based SHERLOCK by Melinda R. Baerwald, Alisha M. Goodbla, Raman P. Nagarajan, Jonathan S. Gootenberg, Omar O. Abudayyeh, Feng Zhang, Andrea D. Schreier. Molecular Ecology Resources https://doi.org/10.1111/1755-0998.13186 First published: 12 May 2020

This paper is behind a paywall.

The business of CRISPR

SHERLOCK™, is a trademark for what Sherlock Biosciences calls one of its engineering biology platforms. From the Sherlock Biosciences Technology webpage,

What is SHERLOCK™?

SHERLOCK is an evolution of CRISPR technology, which others use to make precise edits in genetic code. SHERLOCK can detect the unique genetic fingerprints of virtually any DNA or RNA sequence in any organism or pathogen. Developed by our founders and licensed exclusively from the Broad Institute, SHERLOCK is a method for single molecule detection of nucleic acid targets and stands for Specific High Sensitivity Enzymatic Reporter unLOCKing. It works by amplifying genetic sequences and programming a CRISPR molecule to detect the presence of a specific genetic signature in a sample, which can also be quantified. When it finds those signatures, the CRISPR enzyme is activated and releases a robust signal. This signal can be adapted to work on a simple paper strip test, in laboratory equipment, or to provide an electrochemical readout that can be read with a mobile phone.

However, things get a little more confusing when you look at the Broad Institute’s Developing Diagnostics and Treatments webpage,

Ensuring the SHERLOCK diagnostic platform is easily accessible, especially in the developing world, where the need for inexpensive, reliable, field-based diagnostics is the most urgent

SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing) is a CRISPR-based diagnostic tool that is rapid, inexpensive, and highly sensitive, with the potential to have a transformative effect on research and global public health. The SHERLOCK platform can detect viruses, bacteria, or other targets in clinical samples such as urine or blood, and reveal results on a paper strip — without the need for extensive specialized equipment. This technology could potentially be used to aid the response to infectious disease outbreaks, monitor antibiotic resistance, detect cancer, and more. SHERLOCK tools are freely available [emphasis mine] for academic research worldwide, and the Broad Institute’s licensing framework [emphasis mine] ensures that the SHERLOCK diagnostic platform is easily accessible in the developing world, where inexpensive, reliable, field-based diagnostics are urgently needed.

Here’s what I suspect. as stated, the Broad Institute has free SHERLOCK licenses for academic institutions and not-for-profit organizations but Sherlock Biosciences, a Broad Institute spinoff company, is for-profit and has trademarked SHERLOCK for commercial purposes.

Final thoughts

This looks like a relatively subtle campaign to influence public perceptions. Genetic modification or genetic engineering as exemplified by the CRISPR gene editing technique is a force for the good of all. It will help us in our hour of need (COVID-19 pandemic) and it can help us save various species and better manage our resources.

This contrasts greatly with the publicity generated by the CRISPR twins situation where a scientist claimed to have successfully edited the germline for twins, Lulu and Nana. This was done despite a voluntary, worldwide moratorium on germline editing of viable embryos. (Search the terms [either here or on a standard search engine] ‘CRISPR twins’, ‘Lulu and Nana’, and/or ‘He Jiankui’ for details about the scandal.

In addition to presenting CRISPR as beneficial in the short term rather than the distant future, this publicity also subtly positions the Broad Institute as CRISPR’s owner.

Or, maybe I’m wrong. Regardless, I’m watching.