Category Archives: agriculture

Congratulations to winners of 2020 Nobel Prize for Chemistry: Dr. Emmanuelle Charpentier & Dr. Jennifer A. Doudna (CRISPR-cas9)

It’s possible there’s a more dramatic development in the field of contemporary gene-editing but it’s indisputable that CRISPR (clustered regularly interspaced short palindromic repeats) -cas9 (CRISPR-associated 9 [protein]) ranks very highly indeed.

The technique, first discovered (or developed) in 2012, has brought recognition in the form of the 2020 Nobel Prize for Chemistry to CRISPR’s two discoverers, Emanuelle Charpentier and Jennifer Doudna.

An October 7, 2020 news item on phys.org announces the news,

The Nobel Prize in chemistry went to two researchers Wednesday [October 7, 2020] for a gene-editing tool that has revolutionized science by providing a way to alter DNA, the code of life—technology already being used to try to cure a host of diseases and raise better crops and livestock.

Emmanuelle Charpentier of France and Jennifer A. Doudna of the United States won for developing CRISPR-cas9, a very simple technique for cutting a gene at a specific spot, allowing scientists to operate on flaws that are the root cause of many diseases.

“There is enormous power in this genetic tool,” said Claes Gustafsson, chair of the Nobel Committee for Chemistry.

More than 100 clinical trials are underway to study using CRISPR to treat diseases, and “many are very promising,” according to Victor Dzau, president of the [US] National Academy of Medicine.

“My greatest hope is that it’s used for good, to uncover new mysteries in biology and to benefit humankind,” said Doudna, who is affiliated with the University of California, Berkeley, and is paid by the Howard Hughes Medical Institute, which also supports The Associated Press’ Health and Science Department.

The prize-winning work has opened the door to some thorny ethical issues: When editing is done after birth, the alterations are confined to that person. Scientists fear CRISPR will be misused to make “designer babies” by altering eggs, embryos or sperm—changes that can be passed on to future generations.

Unusually for phys.org, this October 7, 2020 news item is not a simple press/news release reproduced in its entirety but a good overview of the researchers’ accomplishments and a discussion of some of the issues associated with CRISPR along with the press release at the end.

I have covered some CRISPR issues here including intellectual property (see my March 15, 2017 posting titled, “CRISPR patent decision: Harvard’s and MIT’s Broad Institute victorious—for now‘) and designer babies (as exemplified by the situation with Dr. He Jiankui; see my July 28, 2020 post titled, “July 2020 update on Dr. He Jiankui (the CRISPR twins) situation” for more details about it).

An October 7, 2020 article by Michael Grothaus for Fast Company provides a business perspective (Note: A link has been removed),

Needless to say, research by the two scientists awarded the Nobel Prize in Chemistry today has the potential to change the course of humanity. And with that potential comes lots of VC money and companies vying for patents on techniques and therapies derived from Charpentier’s and Doudna’s research.

One such company is Doudna’s Editas Medicine [according to my search, the only company associated with Doudna is Mammoth Biosciences, which she co-founded], while others include Caribou Biosciences, Intellia Therapeutics, and Casebia Therapeutics. Given the world-changing applications—and the amount of revenue such CRISPR therapies could bring in—it’s no wonder that such rivalry is often heated (and in some cases has led to lawsuits over the technology and its patents).

As Doudna explained in her book, A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution, cowritten by Samuel H. Sternberg …, “… —but we could also have woolly mammoths, winged lizards, and unicorns.” And as for that last part, she made clear, “No, I am not kidding.”

Everybody makes mistakes and the reference to Editas Medicine is the only error I spotted. You can find out more about Mammoth Biosciences here and while Dr. Doudna’s comment, “My greatest hope is that it’s used for good, to uncover new mysteries in biology and to benefit humankind,” is laudable it would seem she wishes to profit from the discovery. Mammoth Biosciences is a for-profit company as can be seen at the end of the Mammoth Biosciences’ October 7, 2020 congratulatory news release,

About Mammoth Biosciences

Mammoth Biosciences is harnessing the diversity of nature to power the next-generation of CRISPR products. Through the discovery and development of novel CRISPR systems, the company is enabling the full potential of its platform to read and write the code of life. By leveraging its internal research and development and exclusive licensing to patents related to Cas12, Cas13, Cas14 and Casɸ, Mammoth Biosciences can provide enhanced diagnostics and genome editing for life science research, healthcare, agriculture, biodefense and more. Based in San Francisco, Mammoth Biosciences is co-founded by CRISPR pioneer Jennifer Doudna and Trevor Martin, Janice Chen, and Lucas Harrington. The firm is backed by top institutional investors [emphasis mine] including Decheng, Mayfield, NFX, and 8VC, and leading individual investors including Brook Byers, Tim Cook, and Jeff Huber.

An October 7, 2029 Nobel Prize press release, which unleashed all this interest in Doudna and Charpentier, notes this,

Prize amount: 10 million Swedish kronor, to be shared equally between the Laureates.

In Canadian money that amount is $1,492,115.03 (as of Oct. 9, 2020 12:40 PDT when I checked a currency converter).

Ordinarily there’d be a mildly caustic comment from me about business opportunities and medical research but this is a time for congratulations to both Dr. Emanuelle Charpentier and Dr. Jennifer Doudna.

Effective treatment for citrus-destroying disease?

Citrus greening is a worldwide problem. A particularly virulent disease that destroys citrus fruit, it’s a problem that is worsening. Before getting to the research from the University of California at Riverside (UCR), here’s more about the disease and how it’s developing from the UCR Huanglongbing, (HLB, Citrus Greening webpage,

The Situation: Citrus huanglongbing (HLB), previously called citrus greening disease, is one of the most destructive diseases of citrus worldwide.  Originally thought to be caused by a virus, it is now known to be caused by unculturable phloem-limited bacteria.  There are three forms of greening that have been described.  The African form produces symptoms only under cool conditions and is transmitted by the African citrus psyllid Trioza erytreae, while the Asian form prefers warmer conditions and is transmitted by the Asian citrus psyllid Diaphorina citri.  Recently a third American form transmitted by the Asian citrus psyllid was discovered in Brazil.  This American form of the disease apparently originated in China.  In North America, the psyllid vector, Diaphorina citri, of HLB is found in Florida, Louisiana, Georgia, South Carolina, Texas and Hawaii, and recently arrived in Southern California from Mexico. HLB is known to occur in Florida Lousiana, South Carolina, Georgia, Cuba, Belize and the Eastern Yucatan of Mexico.  A federal quarantine restricts all movement of citrus and other plants in the family Rutaceae from Asian Citrus Psyllid or HLB-infested areas into California in order to prevent introduction of the disease.

 Damage:  The HLB bacteria can infect most citrus cultivars, species and hybrids and even some citrus relatives.  Leaves of newly infected trees develop a blotchy mottle appearance.  On chronically infected trees, the leaves are small and exhibit asymmetrical blotchy mottling (in contrast to Zinc deficiency that causes symmetrical blotching).  Fruit from HLB-infected trees are small, lopsided, poorly colored, and contain aborted seeds. The juice from affected fruit is low in soluble solids, high in acids and abnormally bitter.  The fruit retains its green color at the navel end when mature, which is the reason for the common name “citrus greening disease.”  This fruit is of no value because of poor size and quality.  There is no cure for the disease and rapid tree removal is critical for prevention of spread.

Economic Impact: HLB is one of the most devastating diseases of citrus and since its discovery in Florida in 2005, citrus acreage in that state has declined significantly.  If the disease were to establish in California, the nursery industry would be required to move all of their production under screenhouses, pesticide treatments for the vector would be instituted resulting in greatly increased pesticide costs (3-6 treatments per year) and indirect costs due to pesticide-induced disruption of integrated pest management programs for other citrus pests.  A costly eradication program would need to be instituted to remove infected trees in order to protect the citrus industry.

Distribution of HLB: In April 2012, after about a week of testing, the California Department of Food and Agriculture (CDFA) removed a pumelo tree with a lemon graft from Hacienda Heights in Los Angeles County after the tree and an Asian citrus psyllid found on the tree both tested positive for Huanglongbing. In 2005, HLB was also found in Florida and it is now known to occur in Louisiana, Georgia, South Carolina, Cuba, Belze and Eastern Mexico.  Worldwide, HLB is also present in China, eastern and southern Africa, the Indian subcontinent, Mauritius, Reunion, the Saudi Arabian peninsula, and southeast Asia.

Research:  Research is focusing on characterization of the bacteria, development of detection methods, and control of the disease and the psyllid.  To date, control of the disease is based on planting HLB-free citrus germplasm, eradication of infected citrus plants, and control of the vector with systemic insecticides.  Countries with HLB learn to manage the disease so that they can still produce citrus.  In California, the best strategy is to keep this disease out. This goal is supported by both federal and state quarantine regulations and the University of California’s Citrus Clonal Protection Program, which provides a mechanism for the safe introduction of citrus germplasm into California.

A July 7, 2020 news item on phys.org announces what researchers hope can be used commercially as a new treatment for citrus greening disease from researchers University of California at Riverside (UCR), Note: Links have been removed,

UC Riverside scientists have found the first substance capable of controlling Citrus Greening Disease, which has devastated citrus farms in Florida and also threatens California.

The new treatment effectively kills the bacterium causing the disease with a naturally occurring molecule found in wild citrus relatives. This molecule, an antimicrobial peptide, offers numerous advantages over the antibiotics currently used to treat the disease.

UCR geneticist Hailing Jin, who discovered the cure after a five-year search, explained that unlike antibiotic sprays, the peptide is stable even when used outdoors in high heat, easy to manufacture, and safe for humans.

A July 7, 2020 UCR news release (also on EurekAlert) by Jules Bernstein, which originated the news item, provides technical detail and information about plans to commercialize the product,

“This peptide is found in the fruit of Australian finger limes, which can naturally tolerate Citrus Greening bacteria and has been consumed for hundreds of years,” Jin said. “It is much safer to use this natural plant product on agricultural crops than other synthetic chemicals.”

Currently, some growers in Florida are spraying antibiotics and pesticides in an attempt to save trees from the CLas bacterium that causes citrus greening, also known as Huanglongbing or HLB.

“Most antibiotics are temperature sensitive, so their effects are largely reduced when applied in the hot weather,” Jin said. “By contrast, this peptide is stable even when used in 130-degree heat.”

Jin found the peptide by examining plants such as the Australian finger lime known to possess natural tolerance for the bacteria that causes Citrus Greening Disease, and she isolated the genes that contribute to this innate immunity. One of these genes produces the peptide, which she then tested over the course of two years. Improvement was soon visible.

“You can see the bacteria drastically reduced, and the leaves appear healthy again only a few months after treatment,” Jin said.

Because the peptide only needs to be reapplied a few times per year, it is highly cost effective for growers. This peptide can also be developed into a vaccine to protect young healthy plants from infection, as it is able to induce the plant’s innate immunity to the bacteria.

Jin’s peptide can be applied by injection or foliage spray, and it moves systemically through plants and remains stable, which makes the effect of the treatment stronger.

The treatment will be further enhanced with proprietary injection technology made by Invaio Sciences. UC Riverside has entered into an exclusive, worldwide license agreement with Invaio, ensuring this new treatment goes exactly where it’s needed in plants.

“Invaio is enthusiastic to partner with UC Riverside and advance this innovative technology for combating the disease known as Citrus Greening or Huanglongbing,” said Invaio Chief Science Officer Gerardo Ramos. “The prospect of addressing this previously incurable and devastating crop disease, helping agricultural communities and improving the environmental impact of production is exciting and rewarding,” he said. “This is crop protection in harmony with nature.”

The need for an HLB cure is a global problem, but hits especially close to home as California produces 80 percent of all the fresh citrus in the United States, said Brian Suh, director of technology commercialization in UCR’s Office of Technology Partnerships, which helps bring university technology to market for the benefit of society through licenses, partnerships, and startup companies.

“This license to Invaio opens up the opportunity for a product to get to market faster,” Suh said. “Cutting edge research from UCR, like the peptide identified by Dr. Jin, has a tremendous amount of commercial potential and can transform the trajectory of real-world problems with these innovative solutions.”

You can find out more about Invaio Sciences here.

Citrus greening has been featured here before in an April 7, 2015 posting titled, Citrus canker, Florida, and Zinkicide. There doesn’t seem to have been much progress made with this Florida solution for citrus greening. This 2018 document on nano.gov was the most recent I could find, ZinkicideTM- a systemic nano-ZnO based bactericide/fungicide for crop protection by Swadeshmukul Santra.

New US regulations exempt many gene-edited crops from government oversight

A June 1, 2020 essay by Maywa Montenegro (Postdoctoral Fellow, University of California at Davis) for The Conversation posits that new regulations (which in fact result in deregulation) are likely to create problems,

In May [2020], federal regulators finalized a new biotechnology policy that will bring sweeping changes to the U.S. food system. Dubbed “SECURE,” the rule revises U.S. Department of Agriculture regulations over genetically engineered plants, automatically exempting many gene-edited crops from government oversight. Companies and labs will be allowed to “self-determine” whether or not a crop should undergo regulatory review or environmental risk assessment.

Initial responses to this new policy have followed familiar fault lines in the food community. Seed industry trade groups and biotech firms hailed the rule as “important to support continuing innovation.” Environmental and small farmer NGOs called the USDA’s decision “shameful” and less attentive to public well-being than to agribusiness’s bottom line.

But the gene-editing tool CRISPR was supposed to break the impasse in old GM wars by making biotechnology more widely affordable, accessible and thus democratic.

In my research, I study how biotechnology affects transitions to sustainable food systems. It’s clear that since 2012 the swelling R&D pipeline of gene-edited grains, fruits and vegetables, fish and livestock has forced U.S. agencies to respond to the so-called CRISPR revolution.

Yet this rule change has a number of people in the food and scientific communities concerned. To me, it reflects the lack of accountability and trust between the public and government agencies setting policies.

Is there a better way?

… I have developed a set of principles and practices for governing CRISPR based on dialogue with front-line communities who are most affected by the technologies others usher in. Communities don’t just have to adopt or refuse technology – they can co-create [emphasis mine] it.

One way to move forward in the U.S. is to take advantage of common ground between sustainable agriculture movements and CRISPR scientists. The struggle over USDA rules suggests that few outside of industry believe self-regulation is fair, wise or scientific.

h/t: June 1, 2020 news item on phys.org

If you have the time and the inclination, do read the essay in its entirety.

Anyone who has read my COVID-19 op-ed for the Canadian Science Policy may see some similarity between Montenegro’s “co-create” and this from my May 15, 2020 posting which included my reference materials or this version on the Canadian Science Policy Centre where you can find many other COVID-19 op-eds)

In addition to engaging experts as we navigate our way into the future, we can look to artists, writers, citizen scientists, elders, indigenous communities, rural and urban communities, politicians, philosophers, ethicists, religious leaders, and bureaucrats of all stripes for more insight into the potential for collateral and unintended consequences.

To be clear, I think times of crises are when a lot of people call for more co-creation and input. Here’s more about Montenegro’s work on her profile page (which includes her academic credentials, research interests and publications) on the University of California at Berkeley’s Department of Environmental Science, Policy, and Management webspace. She seems to have been making the call for years.

I am a US-Dutch-Peruvian citizen who grew up in Appalachia, studied molecular biology in the Northeast, worked as a journalist in New York City, and then migrated to the left coast to pursue a PhD. My indigenous ancestry, smallholder family history, and the colonizing/decolonizing experiences of both the Netherlands and Peru informs my personal and professional interests in seeds and agrobiodiversity. My background engenders a strong desire to explore synergies between western science and the indigenous/traditional knowledge systems that have historically been devalued and marginalized.

Trained in molecular biology, science writing, and now, a range of critical social and ecological theory, I incorporate these perspectives into research on seeds.

I am particularly interested in the relationship between formal seed systems – characterized by professional breeding, certification, intellectual property – and commercial sale and informal seed systems through which farmers traditionally save, exchange, and sell seeds. …

You can find more on her Twitter feed, which is where I discovered a call for papers for a “Special Feature: Gene Editing the Food System” in the journal, Elementa: Science of the Anthropocene. They have a rolling deadline, which started in February 2020. At this time, there is one paper in the series,

Democratizing CRISPR? Stories, practices, and politics of science and governance on the agricultural gene editing frontier by Maywa Montenegro de Wit. Elem Sci Anth, 8(1), p.9. DOI: http://doi.org/10.1525/elementa.405 Published February 25, 2020

The paper is open access. Interestingly, the guest editor is Elizabeth Fitting of Dalhousie University in Nova Scotia, Canada.

Plants as a source of usable electricity

A friend sent me a link to this interview with Iftach Yacoby of Tel Aviv University talking about some new research into plants and electricity. From a June 8, 2020 article by Omer Kabir for Calcalist (CTech) on the Algemeiner website,

For years, scientists have been trying to understand the evolutionary capabilities of plants to produce energy and have had only partial success. But a recent Tel Aviv University [TAU] study seems to make the impossible possible, proving that any plant can be transformed into an electrical source, producing a variety of materials that can revolutionize the global economy — from using hydrogen as fuel to clean ammonia to replace the pollutants in the agriculture industry.

“People are unaware that their plant pots have an electric current for everything,” Iftach Yacoby, head of the Laboratory of Renewable Energy Studies at Tel Aviv University’s Faculty of Life Sciences said in a recent interview with Calcalist.

“Our study opens the door to a new field of agriculture, equivalent to wheat or corn production for food security — generating energy,” he said. However, Yacoby makes it clear that it will take at least a decade before the research findings can be transferred to the commercial level.

At the heart of the research is the understanding that plants have particularly efficient capacities when it comes to electricity generation. “Anything green that is not dollars, but rather leaves, grass, and seaweed for example, contains solar panels that are completely identical to the panels the entire country is now building,” Yacoby explained. “They know how to take in solar radiation and make electrons flow out of it. That’s the essence of photosynthesis. Most people think of oxygen and food production, but the most basic phase of photosynthesis is the same as silicon panels in the Negev and on rooftops — taking in sunlight and generating electric current.”

… “At home, an electric current can be wired to many devices. Just plug the device into a power outlet. But when you want to do it in plants, it’s about the order of nanometers. We have no idea where to plug the plugs. That’s what we did in this study. In plant cells, we found they can be used as a socket for anything, at just a nanometer size. We have an enzyme, which is equivalent to a biological machine that can produce hydrogen. We took this enzyme, put it together so that it sits in the socket in the plant cell, which was previously only hypothetical. When he started to produce hydrogen, we proved that we had a socket for everything, though nanotermically-sized. Now we can take any plant or kelp and engineer it so that their electrical outlet can be used for production purposes,” Yacoby explained.

“If you attach an enzyme that produces hydrogen you get hydrogen, it’s the cleanest fuel that can be,” he said. “There are already electric cars and bicycles with a range of 150 km that travel on hydrogen. There are many types of enzymes in nature that produce valuable substances, such as ammonia needed for the fertilizer industry and today is still produced by a very toxic and harmful method that consumes a lot of energy. We can provide a plant-based alternative for the production of materials that are made in chemical manufacturing facilities. It’s an electric platform inside a living plant cell.”

You might find it helpful to read Kabir’s article in its entirety before moving on to the news release about the work. The work was conducted with researchers from Arizona State University (ASU;US) and a researcher from Yogi Vemana University (India), as well as, Yacoby. There’s a May 7, 2020 ASU news release (also on EurekAlert but published on May 6, 2020) detailing the work,

Hydrogen is an essential commodity with over 60 million tons produced globally every year. However over 95 percent of it is made by steam reformation of fossil fuels, a process that is energy intensive and produces carbon dioxide. If we could replace even a part of that with algal biohydrogen that is made via light and water, it would have a substantial impact.

This is essentially what has just been achieved in the lab of Kevin Redding, professor in the School of Molecular Sciences and director of the Center for Bioenergy and Photosynthesis. Their research, entitled Rewiring photosynthesis: a Photosystem I -hydrogenase chimera that makes hydrogen in vivo was published very recently in the high impact journal Energy and Environmental Science.

“What we have done is to show that it is possible to intercept the high energy electrons from photosynthesis and use them to drive alternate chemistry, in a living cell” explained Redding. “We have used hydrogen production here as an example.”

“Kevin Redding and his group have made a true breakthrough in re-engineering the Photosystem I complex,” explained Ian Gould, interim director of the School of Molecular Sciences, which is part of The College of Liberal Arts and Sciences. “They didn’t just find a way to redirect a complex protein structure that nature designed for one purpose to perform a different, but equally critical process, but they found the best way to do it at the molecular level.”

It is common knowledge that plants and algae, as well as cyanobacteria, use photosynthesis to produce oxygen and “fuels,” the latter being oxidizable substances like carbohydrates and hydrogen. There are two pigment-protein complexes that orchestrate the primary reactions of light in oxygenic photosynthesis: Photosystem I (PSI) and Photosystem II (PSII).

Algae (in this work the single-celled green alga Chlamydomonas reinhardtii, or ‘Chlamy’ for short) possess an enzyme called hydrogenase that uses electrons it gets from the protein ferredoxin, which is normally used to ferry electrons from PSI to various destinations. A problem is that the algal hydrogenase is rapidly and irreversibly inactivated by oxygen that is constantly produced by PSII.

In this study, doctoral student and first author Andrey Kanygin has created a genetic chimera of PSI and the hydrogenase such that they co-assemble and are active in vivo. This new assembly redirects electrons away from carbon dioxide fixation to the production of biohydrogen.

“We thought that some radically different approaches needed to be taken — thus, our crazy idea of hooking up the hydrogenase enzyme directly to Photosystem I in order to divert a large fraction of the electrons from water splitting (by Photosystem II) to make molecular hydrogen,” explained Redding.

Cells expressing the new photosystem (PSI-hydrogenase) make hydrogen at high rates in a light dependent fashion, for several days.

This important result will also be featured in an upcoming article in Chemistry World – a monthly chemistry news magazine published by the Royal Society of Chemistry. The magazine addresses current developments in the world of chemistry including research, international business news and government policy as it affects the chemical science community.

The NSF grant funding this research is part of the U.S.-Israel Binational Science Foundation (BSF). In this arrangement, a U.S. scientist and Israeli scientist join forces to form a joint project. The U.S. partner submits a grant on the joint project to the NSF, and the Israeli partner submits the same grant to the ISF (Israel Science Foundation). Both agencies must agree to fund the project in order to obtain the BSF funding. Professor Iftach Yacoby of Tel Aviv University, Redding’s partner on the BSF project, is a young scientist who first started at TAU about eight years ago and has focused on different ways to increase algal biohydrogen production.

In summary, re-engineering the fundamental processes of photosynthetic microorganisms offers a cheap and renewable platform for creating bio-factories capable of driving difficult electron reactions, powered only by the sun and using water as the electron source.

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

Rewiring photosynthesis: a photosystem I-hydrogenase chimera that makes H2in vivo by Andrey Kanygin, Yuval Milrad, Chandrasekhar Thummala, Kiera Reifschneider, Patricia Baker, Pini Marco, Iftach Yacoby and Kevin E. Redding. Energy Environ. Sci., 2020, Advance DOI: https://doi.org/10.1039/C9EE03859K First published: 17 Apr 2020

In order to gain access to the paper, you must have or sign up for a free account.

This image was used to illustrate the research,

A model of Photosystem 1 core subunits Courtesy: ASU

An artificial tongue, gold, and maple syrup

I have always imagined the love of maple syrup to be a universal love. A friend who moved to Canada from somewhere else in the world disillusioned me on that subject. She claims to be unable to grasp why anyone would love maple syrup. Should you recognize yourself in those words you may not find this post all that interesting.

However, maple syrup lovers may find this May 5, 2020 news item on Nanowerk a bit disconcerting,

It’s said that maple syrup is Quebec’s liquid gold. Now scientists at Université de Montréal have found a way to use real gold — in the form of nanoparticles — to quickly find out how the syrup tastes.

The new method — a kind of artificial tongue — is validated in a study published in Analytical Methods (“High-throughput plasmonic tongue using an aggregation assay and nonspecific interactions: classification of taste profiles in maple syrup”), the journal of the Royal Society of Chemistry, in the United Kingdom.

The “tongue” is a colorimetric test that detects changes in colour to show how a sample of maple syrup tastes. The result is visible to the naked eye in a matter of seconds and is useful to producers.

“The artificial tongue is simpler than a human tongue: it can’t distinguish the complex flavour profiles that we can detect,” said UdeM chemistry professor Jean-François Masson, who led the study. “Our device works specifically to detect flavour differences in maple syrup as it’s being produced.”

A chemistry professor at Université de Montréal has developed a new test using gold nanoparticles to establish the flavour profile of maple syrup and help producers evaluate its quality. Courtesy: Université de Montréal

There is more information but the central question as to why anyone would want an artificial tongue for tasting maple syrup is never answered (presumably they want to speed up production and ensure more consistent classification) nor is there much in the way of technical detail in a May 5, 2019 Université de Montréal news release (also on EurekAlert),

1,818 samples tested

The artificial tongue was validated by analyzing 1,818 samples of maple syrup from different regions of Quebec. The syrups that were analyzed represented the various known aromatic profiles and colours of syrup, from golden to dark brown.

“We designed the ‘tongue’ at the request of the Québec Maple Syrup Producers to detect the presence of different flavour profiles,” explained Simon Forest, the study’s first author. “The tool takes into account the product’s olfactory and taste properties.”

Maple syrup has a molecular complexity similar to that of wine. Its taste is delicate, without bitterness, and it has a subtle aroma. During the production process, specialized human tasters are employed to judge which profile each batch fits into.

“The development of the artificial tongue is intended to support the colossal work that is being done in the field to do the first sorting of syrups quickly and classify them according to their qualities,” said Masson.

Red for the best, blue for the rest

The researchers compare the artificial tongue to a pH test for a swimming pool. You simply pour a few drops of syrup into the gold nanoparticle reagent and wait about 10 seconds.

If the result stays in the red spectrum, it has the characteristics of a premium quality syrup, the kind best loved by consumers and sold in grocery stores or exported.

If, on the other hand, the test turns blue, the syrup may have a flavour “defect”, which may be treated as an industrial syrup for use in processing.

“It doesn’t mean the syrup is not good for consumption or that it has a different sugar level,” Masson said of the “blue” type syrup, which the food industry uses as a natural sweetener in other products. “It just may not have the usual desired characteristics, and so can’t be sold directly in bottles to consumers.”

60 categories of taste

Caramelized, woody, green, smoked, salty, burnt — the taste of maple syrup has as many as 60 categories to fit into. Maple syrup is essentially a concentrated sugar solution of 66 per cent sucrose and 33 per cent water; the remaining one per cent of other compounds determines the taste.

Like wine, the taste of maple syrup changes according to a variety of factors, including the harvest period, the region, production and storage methods and, of course, the weather. Too much variation in temperature over a weekend, for instance, can greatly affect the taste profile of the product.

The artificial tongue developed at UdeM could someday be adapted for tasting wine or fruit juice, Masson said, as well as be useful in a number of other agrifood contexts.

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

A high-throughput plasmonic tongue using an aggregation assay and nonspecific interactions: classification of taste profiles in maple syrup by Simon Forest, Trevor Théorêt, Julien Coutu, and Jean-Francois Masson. Anal. Methods, 2020, Advance Article DOI: https://doi.org/10.1039/C9AY01942A First published 05 May 2020

This paper is behind a paywall.

Increased food security with hexanal for younger looking, fresher tasting fruits and vegetables

Also known as an anti-aging agent for your fruit and vegetables, hexanal is an environmentally friendly chemical, which is found naturally. Research has led to a synthesized nanotechnology-enabled product now being commercialized. I’ve been following the story off and on since 2012 (see my ‘India, Sri Lanka, and Canada team up for nanotechnology-enabled food packaging‘ posting). I last wrote about the project in a December 29, 2015 posting.

For some reason, hexanal hit the news hard in 2019 having been preceded by some interest in 2018. What follows is an update and a timeline of sorts.

January 2019: More funding

A January 24,2019 essay (also published on the University of Guelph website on January 29, 2019) by Jayasankar Subramanian and Elizabeth Finnis, both are lead researchers on the the project and professors at the University of Guelph (Canada), provides an overview and an update of the hexanal project (Note: Links have been removed) ,

Fruits like mangoes, bananas, papayas and limes are shipped long distances before they get to your table. Many fruits are delicate, and there may be a long period of time that elapses between when the fruit is picked and its arrival in grocery stores and other markets. They’re often picked before they’re truly ripe in order to increase their shelf life.

Even so, globally, up to 40 per cent of all picked fruit can be lost and this represents billions of dollars. But what if we had the technology to delay fruit’s natural degradation process? This is where hexanal can make a difference.

Fruits like mangoes, bananas, papayas and limes are shipped long distances before they get to your table. Many fruits are delicate, and there may be a long period of time that elapses between when the fruit is picked and its arrival in grocery stores and other markets. They’re often picked before they’re truly ripe in order to increase their shelf life.

Even so, globally, up to 40 per cent of all picked fruit can be lost and this represents billions of dollars. But what if we had the technology to delay fruit’s natural degradation process? This is where hexanal can make a difference.

Hexanal is naturally produced by plants to ward off pests; our research at the University of Guelph has found that when it’s applied externally, hexanal can also slow down the aging process.

Like everything else, fruit ages with time. The shrivelling and rot is triggered by the enzyme phospholipase D (PLD), which causes the eventual collapse of the fruit’s membrane. Essentially, fruit membranes are snug, and function like a brick wall of phospholipid bilayers. Phospholipase D breaks the alignment of the bricks, causing the membrane to crumble. Hexanal acts by reducing and slowing the formation of PLD, which in turn slows the collapse of the fruit’s membrane.

In partnership with agricultural and social science researchers in Canada and five other countries, we have tested nine hexanal technologies. These include a spray formulation that gets applied to fruit when they’re still on trees, post-harvest dips, fruit wraps, stickers and sachets embedded with hexanal.

Our findings have implications for consumers, retailers and, more importantly, farmers. For example, when applied as a pre-harvest spray, hexanal can keep fruit on trees longer and keep it fresher after harvest — up to three weeks longer for mangoes.

Hexanal is naturally produced by all plants and is already found as an additive in some food products. Hexanal is also approved by Health Canada as a flavour formula. Our tests of synthesized hexanal sprays, dips and other technologies showed that there were no negative effects on plants, insects or other animals. In addition, hexanal evaporates within 24 hours, which means there’s no residue left on fruit.

Farmers who participated in hexanal testing in Canada and elsewhere were happy with the product both in terms of its effectiveness and bio-safety.

Currently, hexanal for agricultural use is in the two-year regulatory clearance process in Canada and the U.S. Once the process is complete, hexanal formulations are expected to be available for farmer use and can be accessed through companies with a license for production.

Hexanal slows down the ripening and aging process in fresh produce. Author provided

That’s a stunning difference, eh?

Funding

At about the same time as the Conversation essay by Subramanian and Finnis, the University of Guelph published (on the Council of Ontario Universities website) a January 27, 2019 news release announcing new funds for the project,

A University of Guelph research project that has already improved the livelihoods of small-scale Asian farmers will further expand worldwide, thanks to more than $4.2 million in federal support announced Friday afternoon.

The project involves innovative packaging developed in part by Guelph researchers using nanotechnology to improve the shelf life of mangoes, a major fruit crop in much of the world.

Already, the technology has helped to significantly reduce post-harvest losses in Sri Lanka and India. Poor storage meant that farmers routinely lost up to 40 per cent of their crops, worth upwards of $800 million a year. The new technology has also boosted per-acre revenue.

New funding support from the International Development Research Centre (IDRC) and Foreign Affairs, Trade and Development Canada will allow researchers to broaden this successful initiative to Kenya, Tanzania, and Trinidad and Tobago.

Researchers will also look at other fruit — bananas, grapes, papaya, nectarines and berries — and investigate ways to commercialize the technologies.

… it will also be a main pillar of the Guelph-East Africa Initiative, which U of G established to bring together stakeholders to support research and teaching in food, health, water, education, environment and community.

“This confirms our commitment to improve agriculture in East Africa and around the world.” [said John Livernois, interim vice-president {research} ]

The project involves the use of hexanal, a natural plant product that delays fruit ripening and aging. Guelph plant agriculture professor Gopi Paliyath holds an American patent on the discovery of hexanal as a post-harvest agent. It’s also an FDA-approved food additive.

The project also involves Guelph plant agriculture professors Paliyath and Al Sullivan; Loong-tak Lim from Food Science; and Elizabeth Finnis, Sociology and Anthropology. Foreign research partners are based at Tamil Nadu Agricultural University, India; Industrial Technical Institute, Sri Lanka; University of Nairobi, Kenya; Sokoine University of Agriculture, Tanzania; and the University of [the] West Indies, Trinidad and Tobago.

Prior to more funding: a memorandum of understanding

I’m having to guess as the document about the memorandum of understanding (MOU) to commercialize hexanal is not dated but it seems to have been produced in March 2018. (Canada’s International Development Research Centre ([IDRC] has a webpage about the memorandum but no memorandum that I could find.) I stumbled across this account of the event where the MOU was signed,

Ms. Jennifer Daubeny, Consulate General of Canada, delivered the special address narrating the significance of Canadian fundingin developing nanotechnologies to reduce post-harvest losses that enables food security in Asian Countries. Dr. K. Ramasamy, Vice Chancellor, Tamil Nadu Agricultural University [TNAU], Coimbatore presided over the function and highlighted the role of TNAU in knitting nanotechnology research framework and serving as a torch bearer in the country. He emphasized that the GAC-IDRC Project helped more than 60 students and researchers, developed two technologies, filed patents for two inventions, extensive infrastructure development besides helping more than 12,000 fruit growers in the State of Tamil Nadu. Dr. Jayasankar Subramanian, Professor, University of Guelph, Canada, explained the evolution of the project till reached the stage of technology delivery to benefit farmers. Dr. K.S. Subramanian, NABARD Chair Professor, TNAU, Coimbatore, lead Principal Investigator of the Project for India presented nanotechnologies developed to assist in the entire value chain from the farm to fork. Mr. Arun Nagarajan, President, Tamil Nadu Fruit Growers’ Association, explained that the fruit growers are eager to use the technology to improve their farm income. Mr. Terence Park, Managing Director, Smart Harvest Agri, Canada, [emphasis mine] bestowed interest to take forward the technologies to the farm gate and signed MOU with TNAU for the Commercialization of the Hexanal Formulation. Dr. G.J. Janavi,Professor & Head, Department of Nano Science & Technology, TNAU, Coimbatore welcomed the gathering and Dr. C. Sekar, Dean, Imayam Agricultural College,Turaiyur, and Co-PI of the Project proposed a formal vote of thanks.

The Canadian Consul General Ms. Jennifer Daubeny visited all the exhibits and interacted with students, scholars and researchers besides the NGO partner Myrada. She was very impressed with the technologies developed by TNAU in collaboration with University of Guelph, Canada, and looking forward to support research programs in the near future. More than 200 Scientists and Diplomats from Canada, students, scholars, university officials participated in the event.

Products launch by ITI, Colombo

Two of the project’s technology outputs -hexanal incorporated ITI Bio-wax and the Tree Fresh Formulation spray [emphasis mine] were transferred to Hayleys Agriculture Pvt. Ltd., a reputed Agro Service provider in Sri Lanka. The products were launched on 22ndMarch 2018 at the Taj Samudra Hotel, Colombo. The chief guest at the event was the Hon. Susil Premajayantha, Minister of Science Technology and Research (Min. ST&R). The guest of honour was H.E. David McKinnon, High Commissioner for Canada in Sri Lanka. Others present included the Secretary to the Min. ST&R, The Chairman and Director General, ITI, Mr Rizvi Zaheed, Hayleys Agriculture and his team, the Chairman, National Science Foundation, Sri Lanka, representative of the Chairman Sri Lanka Export Development Board, representatives from the Dialog mobile service provider, the Registrar of Pesticides, representing the Dir. Gen., of Agriculture, President of the Lanka Fruit and Vegetable Producers, Processors and Exporters Association, leading large scale mango, papaya and pineapple growers, several export and fruit processing company representatives, senior officials from the ITI, the multi-disciplinary ITI research team and our partner from CEPA. The press was also well represented and a total of 100 persons were present on this occasion. The Managing Director Hayles, the two PIs’ of the project, the High Commissioner for Canada, The Minister and for ST&R and the Secretary to the Ministry addressed the gathering and the new video clip on the project was viewed. The new products were jointly uncovered for display by the Hon. Minister and H.E., the High Commissioner. Samples of the products were distributed to the President of the Lanka Fruit and Vegetable Producers Processors and Exporters Association and to two leading mango growers. The Project team also took this opportunity to run a presentation on the various stages of the project and related activities, display posters on their research findings and to print and distribute the pamphlets on the same as well as on hexanal, the latter as prepared by our partners from the University of Guelph. The launch ended with a time of fellowship providing a useful opportunity for networking.

A YouTube video about the product launch of hexanal-based Bio-wax and the Tree Fresh Formulation spray (I don’t know if those were the permanent names or if they are specific to Sri Lanka and other countries will adopt other names) helped to establish the date for the MOU. You can find the video here.

Judging from the media stories, the team in India has provided most of the leadership for commercializing hexanal.

Commercialization 2019 and beyond

To sum up, after a memorandum of understanding is signed and some prototype products have been unveiled in India in 2018 then, in early 2019, there’s more funding announced by IDRC to expand the number of countries involved and to continue research into efforts to save other types of produce.

Moving things along is an August 15, 2019 news item on Agropages.com,

Two nano formulations would be commercialized by the Directorate of Agri business development of Tamil Nadu Agricultural University (TNAU) soon.  

Fruity fresh is a liquid nano formulation containing hexanal that keeps fruits and vegetables fresh for more days. The pre-harvest spray of Fruity Fresh extends the shelf life of mango for two weeks on trees and another two weeks under storage conditions by employing post-harvest dip methodology, Dr. A. Lakshmanan, Professor and Head, Department of Nano Science and Technology told a meet on “Linking Nano Stakeholders” held at the University.  

Hexanal has also been successfully encapsulated in polymer matrix either as an electro spun fibre matrix (Nano sticker) or nano-pellets that extends shelf life of fruits by 1-2 weeks during storage and transportation, he said.  

This sticker and pellets technology is highly user friendly and can be placed inside the cartons containing fruits during transport for enhancing the freshness.

According to a November 5, 2019 article by Pearly Neo for foodnavigator-asia.com, there is pricing for four products. Nano Sticker and Nano Pellet each will cost $US 0.028 and the spray, Fruity Fresh, will cost $US 4.23 to $US 5.65 for a one liter bottle diluted in 50 liters of water (for use on approximately five trees) and the Fruity Fresh dipping solution at $US 0.0071per kg.

As far as I’m aware none of these products are available in Canada but there is a website for Smart Harvest Agri, Canada although the name used is a little different. First, there’s the Federal Corporation Information listing for Smart Harvest Agritech Limited. You’ll notice there are two directors,

Amanjit Singh Bains
7685 150B Street
Surrey BC V3S 5P1
Canada

Terence Park
Yongsan CJ Nine Park
Seoul
Korea, Republic of

The company’s Smart Harvest website doesn’t list any products but it does discuss something they call “FRESHXtend technology” for fruits and vegetables.

Final comment

I sometimes hear complaints about government funding and what seems to be a lack of follow through with exciting research work being done in Canada. I hope that in the months to come that this story of an international collaboration, which started with three countries and has now expanded to at least six countries and has led to increased food security with an environmentally friendly material and commercialization of research, gets some attention.

From the few sources I’ve been able to find, it seems India and Sri Lanka are leading the commercialization charge while Canada has contributed to an Asian-led project which has now expanded to include Kenya, Tanzania, and Trinidad and Tobago. Bravo t them all!

Nano 2020: a US education initiative

The US Department of Agriculture has a very interesting funding opportunity, Higher Education Challenge (HEC) Grants Program, as evidenced by the Nano 2020 virtual reality (VR) classroom initiative. Before launching into the specifics of the Nano 2020 project, here’s a description of the funding program,

Projects supported by the Higher Education Challenge Grants Program will: (1) address a state, regional, national, or international educational need; (2) involve a creative or non-traditional approach toward addressing that need that can serve as a model to others; (3) encourage and facilitate better working relationships in the university science and education community, as well as between universities and the private sector, to enhance program quality and supplement available resources; and (4) result in benefits that will likely transcend the project duration and USDA support.

A February 3, 2020 University of Arizona news release by Stacy Pigott (also on EurekAlert but published February 7, 2020) announced a VR classroom where students will be able to interact with nanoscale data gained from agricultural sciences and the life sciences,

Sometimes the smallest of things lead to the biggest ideas. Case in point: Nano 2020, a University of Arizona-led initiative to develop curriculum and technology focused on educating students in the rapidly expanding field of nanotechnology.

The five-year, multi-university project recently met its goal of creating globally relevant and implementable curricula and instructional technologies, to include a virtual reality classroom, that enhance the capacity of educators to teach students about innovative nanotechnology applications in agriculture and the life sciences.

Here’s a video from the University of Arizona’s project proponents which illustrates their classroom,

For those who prefer text or like to have it as a backup, here’s the rest of the news release explaining the project,

Visualizing What is Too Small to be Seen

Nanotechnology involves particles and devices developed and used at the scale of 100 nanometers or less – to put that in perspective, the average diameter of a human hair is 80,000 nanometers. The extremely small scale can make comprehension challenging when it comes to learning about things that cannot be seen with the naked eye.

That’s where the Nano 2020 virtual reality classroom comes in. In a custom-developed VR classroom complete with a laboratory, nanoscale objects come to life for students thanks to the power of science data visualization.

Within the VR environment, students can interact with objects of nanoscale proportions – pick them up, turn them around and examine every nuance of things that would otherwise be too small to see. Students can also interact with their instructor or their peers. The Nano 2020 classroom allows for multi-player functionality, giving educators and students the opportunity to connect in a VR laboratory in real time, no matter where they are in the world.

“The virtual reality technology brings to life this complex content in a way that is oddly simple,” said Matt Mars, associate professor of agricultural leadership and innovation education in the College of Agriculture and Life Sciences and co-director of the Nano 2020 grant. “Imagine if you can take a student and they see a nanometer from a distance, and then they’re able to approach it and see how small it is by actually being in it. It’s mind-blowing, but in a way that students will be like, ‘Oh wow, that is really cool!'”

The technology was developed by Tech Core, a group of student programmers and developers led by director Ash Black in the Eller College of Management.

“The thing that I was the most fascinated with from the beginning was playing with a sense of scale,” said Black, a lifelong technologist and mentor-in-residence at the McGuire Center for Entrepreneurship. “What really intrigued me about virtual reality is that it is a tool where scale is elastic – you can dial it up and dial it down. Obviously, with nanotechnology, you’re dealing with very, very small things that nobody has seen yet, so it seemed like a perfect use of virtual reality.”

Black and Tech Core students including Robert Johnson, Hazza Alkaabi, Matthew Romero, Devon Oberdan, Brandon Erickson and Tim Lukau turned science data into an object, the object into an image, and the image into a 3D rendering that is functional in the VR environment they built.

“I think that being able to interact with objects of nanoscale data in this environment will result in a lot of light bulbs going off in the students’ minds. I think they’ll get it,” Black said. “To be able to experience something that is abstract – like, what does a carbon atom look like – well, if you can actually look at it, that’s suddenly a whole lot of context.”

The VR classroom complements the Nano 2020 curriculum, which globally expands the opportunities for nanotechnology education within the fields of agriculture and the life sciences.

Teaching the Workforce of the Future

“There have been great advances to the use of nanotechnology in the health sciences, but many more opportunities for innovation in this area still exist in the agriculture fields. The idea is to be able to advance these opportunities for innovation by providing some educational tools,” said Randy Burd, who was a nutritional sciences professor at the University of Arizona when he started the Nano 2020 project with funding from a National Institute of Food and Agriculture Higher Education Challenge grant through the United States Department of Agriculture. “It not only will give students the basics of the understanding of the applications, but will give them the innovative thought processes to think of new creations. That’s the real key.”

Unknown Object

The goal of the Nano 2020 team, which includes faculty from the University of Arizona, Northern Arizona University and Johns Hopkins University, was to create an online suite of undergraduate courses that was not university-specific, but could be accessed and added to by educators to reach students around the world.

To that end, the team built modular courses in nanotechnology subjects such as glycobiology, optical microscopy and histology, nanomicroscopy techniques, nutritional genomics, applications of magnetic nanotechnology, and design, innovation, and entrepreneurship, to name a few. An online library will be created to facilitate the ongoing expansion of the open-source curricula, which will be disseminated through novel technologies such as the virtual reality classroom.

“It isn’t practical to think that other universities and colleges are just going to be able to launch new courses, because they still need people to teach those courses,” Mars said. “So we created a robust and flexible set of module-based course packages that include exercises, lectures, videos, power points, tools. Instructors will be able to pull out components and integrate them into what already exists to continue to move toward a more comprehensive offering in nanotechnology education.”

According to Mars, the highly adaptable nature of the curriculum and the ability to deliver it in various ways were key components of the Nano 2020 project.

“We approach the project with a strong entrepreneurial mindset and heavy emphasis on innovation. We wanted it to be broadly defined and flexible in structure, so that other institutions access and model the curricula, see its foundation, and adapt that to what their needs were to begin to disseminate the notion of nanotechnology as an underdeveloped but really important field within the larger landscape of agriculture and life sciences,” Mars said. “We wanted to also provide an overlay to the scientific and technological components that would be about adoption in human application, and we approached that through an innovation and entrepreneurial leadership lens.”

Portions of the Nano 2020 curriculum are currently being offered as electives in a certificate program through the Department of Agriculture Education, Technology and Innovation at the University of Arizona. As it becomes more widely disseminated through the higher education community at large, researchers expect the curriculum and VR classroom technology to transcend the boundaries of discipline, institution and geography.

“An online open platform will exist where people can download components and courses, and all of it is framed by the technology, so that these experiences and research can be shared over this virtual reality component,” Burd said. “It’s technologically distinct from what exists now.”

“The idea is that it’s not just curriculum, but it’s the delivery of that curriculum, and the delivery of that curriculum in various ways,” Mars said. “There’s a relatability that comes with the virtual reality that I think is really cool. It allows students to relate to something as abstract as a nanometer, and that is what is really exciting.”

As best I can determine, this VR Nano 2020 classroom is not yet ready for a wide release and, for now, is being offered exclusively at the University of Arizona.

The CRISPR yogurt story and a hornless cattle update

Clustered regularly interspaced short palindromic repeats (CRISPR) does not and never has made much sense to me. I understand each word individually it’s just that I’ve never thought they made much sense strung together that way. It’s taken years but I’ve finally found out what the words (when strung together that way) mean and the origins for the phrase. Hint: it’s all about the phages.

Apparently, it all started with yogurt as Cynthia Graber and Nicola Twilley of Gastropod discuss on their podcast, “4 CRISPR experts on how gene editing is changing the future of food.” During the course of the podcast they explain the ‘phraseology’ issue, mention hornless cattle (I have an update to the information in the podcast later in this posting), and so much more.

CRISPR started with yogurt

You’ll find the podcast (almost 50 minutes long) here on an Oct. 11, 2019 posting on the Genetic Literacy Project. If you need a little more encouragement, here’s how the podcast is described,

To understand how CRISPR will transform our food, we begin our episode at Dupont’s yoghurt culture facility in Madison, Wisconsin. Senior scientist Dennis Romero tells us the story of CRISPR’s accidental discovery—and its undercover but ubiquitous presence in the dairy aisles today.

Jennifer Kuzma and Yiping Qi help us understand the technology’s potential, both good and bad, as well as how it might be regulated and labeled. And Joyce Van Eck, a plant geneticist at the Boyce Thompson Institute in Ithaca, New York, tells us the story of how she is using CRISPR, combined with her understanding of tomato genetics, to fast-track the domestication of one of the Americas’ most delicious orphan crops [groundcherries].

I featured Van Eck’s work with groundcherries last year in a November 28, 2018 posting and I don’t think she’s published any new work about the fruit since. As for Kuzma’s point that there should be more transparency where genetically modified food is concerned, Canadian consumers were surprised (shocked) in 2017 to find out that genetically modified Atlantic salmon had been introduced into the food market without any notification (my September 13, 2017 posting; scroll down to the Fish subheading; Note: The WordPress ‘updated version from Hell’ has affected some of the formatting on the page).

The earliest article on CRISPR and yogurt that I’ve found is a January 1, 2015 article by Kerry Grens for The Scientist,

Two years ago, a genome-editing tool referred to as CRISPR (clustered regularly interspaced short palindromic repeats) burst onto the scene and swept through laboratories faster than you can say “adaptive immunity.” Bacteria and archaea evolved CRISPR eons before clever researchers harnessed the system to make very precise changes to pretty much any sequence in just about any genome.

But life scientists weren’t the first to get hip to CRISPR’s potential. For nearly a decade, cheese and yogurt makers have been relying on CRISPR to produce starter cultures that are better able to fend off bacteriophage attacks. “It’s a very efficient way to get rid of viruses for bacteria,” says Martin Kullen, the global R&D technology leader of Health and Protection at DuPont Nutrition & Health. “CRISPR’s been an important part of our solution to avoid food waste.”

Phage infection of starter cultures is a widespread and significant problem in the dairy-product business, one that’s been around as long as people have been making cheese. Patrick Derkx, senior director of innovation at Denmark-based Chr. Hansen, one of the world’s largest culture suppliers, estimates that the quality of about two percent of cheese production worldwide suffers from phage attacks. Infection can also slow the acidification of milk starter cultures, thereby reducing creameries’ capacity by up to about 10 percent, Derkx estimates.
In the early 2000s, Philippe Horvath and Rodolphe Barrangou of Danisco (later acquired by DuPont) and their colleagues were first introduced to CRISPR while sequencing Streptococcus thermophilus, a workhorse of yogurt and cheese production. Initially, says Barrangou, they had no idea of the purpose of the CRISPR sequences. But as his group sequenced different strains of the bacteria, they began to realize that CRISPR might be related to phage infection and subsequent immune defense. “That was an eye-opening moment when we first thought of the link between CRISPR sequencing content and phage resistance,” says Barrangou, who joined the faculty of North Carolina State University in 2013.

One last bit before getting to the hornless cattle, scientist Yi Li has a November 15, 2018 posting on the GLP website about his work with gene editing and food crops,

I’m a plant geneticist and one of my top priorities is developing tools to engineer woody plants such as citrus trees that can resist the greening disease, Huanglongbing (HLB), which has devastated these trees around the world. First detected in Florida in 2005, the disease has decimated the state’s US$9 billion citrus crop, leading to a 75 percent decline in its orange production in 2017. Because citrus trees take five to 10 years before they produce fruits, our new technique – which has been nominated by many editors-in-chief as one of the groundbreaking approaches of 2017 that has the potential to change the world – may accelerate the development of non-GMO citrus trees that are HLB-resistant.

Genetically modified vs. gene edited

You may wonder why the plants we create with our new DNA editing technique are not considered GMO? It’s a good question.

Genetically modified refers to plants and animals that have been altered in a way that wouldn’t have arisen naturally through evolution. A very obvious example of this involves transferring a gene from one species to another to endow the organism with a new trait – like pest resistance or drought tolerance.

But in our work, we are not cutting and pasting genes from animals or bacteria into plants. We are using genome editing technologies to introduce new plant traits by directly rewriting the plants’ genetic code.

This is faster and more precise than conventional breeding, is less controversial than GMO techniques, and can shave years or even decades off the time it takes to develop new crop varieties for farmers.

There is also another incentive to opt for using gene editing to create designer crops. On March 28, 2018, U.S. Secretary of Agriculture Sonny Perdue announced that the USDA wouldn’t regulate new plant varieties developed with new technologies like genome editing that would yield plants indistinguishable from those developed through traditional breeding methods. By contrast, a plant that includes a gene or genes from another organism, such as bacteria, is considered a GMO. This is another reason why many researchers and companies prefer using CRISPR in agriculture whenever it is possible.

As the Gatropod’casters note, there’s more than one side to the gene editing story and not everyone is comfortable with the notion of cavalierly changing genetic codes when so much is still unknown.

Hornless cattle update

First mentioned here in a November 28, 2018 posting, hornless cattle have been in the news again. From an October 7, 2019 news item on ScienceDaily,

For the past two years, researchers at the University of California, Davis, have been studying six offspring of a dairy bull, genome-edited to prevent it from growing horns. This technology has been proposed as an alternative to dehorning, a common management practice performed to protect other cattle and human handlers from injuries.

UC Davis scientists have just published their findings in the journal Nature Biotechnology. They report that none of the bull’s offspring developed horns, as expected, and blood work and physical exams of the calves found they were all healthy. The researchers also sequenced the genomes of the calves and their parents and analyzed these genomic sequences, looking for any unexpected changes.

An October 7, 2019 UC Davis news release (also on EurekAlert), which originated the news item, provides more detail about the research (I have checked the UC Davis website here and the October 2019 update appears to be the latest available publicly as of February 5, 2020),

All data were shared with the U.S. Food and Drug Administration. Analysis by FDA scientists revealed a fragment of bacterial DNA, used to deliver the hornless trait to the bull, had integrated alongside one of the two hornless genetic variants, or alleles, that were generated by genome-editing in the bull. UC Davis researchers further validated this finding.

“Our study found that two calves inherited the naturally-occurring hornless allele and four calves additionally inherited a fragment of bacterial DNA, known as a plasmid,” said corresponding author Alison Van Eenennaam, with the UC Davis Department of Animal Science.

Plasmid integration can be addressed by screening and selection, in this case, selecting the two offspring of the genome-edited hornless bull that inherited only the naturally occurring allele.

“This type of screening is routinely done in plant breeding where genome editing frequently involves a step that includes a plasmid integration,” said Van Eenennaam.

Van Eenennaam said the plasmid does not harm the animals, but the integration technically made the genome-edited bull a GMO, because it contained foreign DNA from another species, in this case a bacterial plasmid.

“We’ve demonstrated that healthy hornless calves with only the intended edit can be produced, and we provided data to help inform the process for evaluating genome-edited animals,” said Van Eenennaam. “Our data indicates the need to screen for plasmid integration when they’re used in the editing process.”

Since the original work in 2013, initiated by the Minnesota-based company Recombinetics, new methods have been developed that no longer use donor template plasmid or other extraneous DNA sequence to bring about introgression of the hornless allele.

Scientists did not observe any other unintended genomic alterations in the calves, and all animals remained healthy during the study period. Neither the bull, nor the calves, entered the food supply as per FDA guidance for genome-edited livestock.

WHY THE NEED FOR HORNLESS COWS?

Many dairy breeds naturally grow horns. But on dairy farms, the horns are typically removed, or the calves “disbudded” at a young age. Animals that don’t have horns are less likely to harm animals or dairy workers and have fewer aggressive behaviors. The dehorning process is unpleasant and has implications for animal welfare. Van Eenennaam said genome-editing offers a pain-free genetic alternative to removing horns by introducing a naturally occurring genetic variant, or allele, that is present in some breeds of beef cattle such as Angus.

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

Genomic and phenotypic analyses of six offspring of a genome-edited hornless bull by Amy E. Young, Tamer A. Mansour, Bret R. McNabb, Joseph R. Owen, Josephine F. Trott, C. Titus Brown & Alison L. Van Eenennaam. Nature Biotechnology (2019) DOI: https://doi.org/10.1038/s41587-019-0266-0 Published 07 October 2019

This paper is open access.