Category Archives: agriculture

Use AI to reduce worries about nanoparticles in food

A June 16, 2021 news item on ScienceDaily announces research into the impact that engineered metallic nanoparticles used in agricultural practices have on food,

While crop yield has achieved a substantial boost from nanotechnology in recent years, alarms over the health risks posed by nanoparticles within fresh produce and grains have also increased. In particular, nanoparticles entering the soil through irrigation, fertilizers and other sources have raised concerns about whether plants absorb these minute particles enough to cause toxicity.

In a new study published online in the journal Environmental Science and Technology, researchers at Texas A&M University have used machine learning [a form of artificial intelligence {AI}] to evaluate the salient properties of metallic nanoparticles that make them more susceptible for plant uptake. The researchers said their algorithm could indicate how much plants accumulate nanoparticles in their roots and shoots.

A June 16, 2021 Texas A&M University news release (also on EurekAlert), which originated the news item, describes the research, which employed two different machine learning algorithms, in more detail,

Nanoparticles are a burgeoning trend in several fields, including medicine, consumer products and agriculture. Depending on the type of nanoparticle, some have favorable surface properties, charge and magnetism, among other features. These qualities make them ideal for a number of applications. For example, in agriculture, nanoparticles may be used as antimicrobials to protect plants from pathogens. Alternatively, they can be used to bind to fertilizers or insecticides and then programmed for slow release to increase plant absorption.

These agricultural practices and others, like irrigation, can cause nanoparticles to accumulate in the soil. However, with the different types of nanoparticles that could exist in the ground and a staggeringly large number of terrestrial plant species, including food crops, it is not clearly known if certain properties of nanoparticles make them more likely to be absorbed by some plant species than others.

“As you can imagine, if we have to test the presence of each nanoparticle for every plant species, it is a huge number of experiments, which is very time-consuming and expensive,” said Xingmao “Samuel” Ma, associate professor in the Zachry Department of Civil and Environmental Engineering. “To give you an idea, silver nanoparticles alone can have hundreds of different sizes, shapes and surface coatings, and so, experimentally testing each one, even for a single plant species, is impractical.”

Instead, for their study, the researchers chose two different machine learning algorithms, an artificial neural network and gene-expression programming. They first trained these algorithms on a database created from past research on different metallic nanoparticles and the specific plants in which they accumulated. In particular, their database contained the size, shape and other characteristics of different nanoparticles, along with information on how much of these particles were absorbed from soil or nutrient-enriched water into the plant body.

Once trained, their machine learning algorithms could correctly predict the likelihood of a given metallic nanoparticle to accumulate in a plant species. Also, their algorithms revealed that when plants are in a nutrient-enriched or hydroponic solution, the chemical makeup of the metallic nanoparticle determines the propensity of accumulation in the roots and shoots. But if plants are grown in soil, the contents of organic matter and the clay in soil are key to nanoparticle uptake.

Ma said that while the machine learning algorithms could make predictions for most food crops and terrestrial plants, they might not yet be ready for aquatic plants. He also noted that the next step in his research would be to investigate if the machine learning algorithms could predict nanoparticle uptake from leaves rather than through the roots.

“It is quite understandable that people are concerned about the presence of nanoparticles in their fruits, vegetables and grains,” said Ma. “But instead of not using nanotechnology altogether, we would like farmers to reap the many benefits provided by this technology but avoid the potential food safety concerns.”

This image accompanies the paper’s research abstract,

[downloaded frm https://pubs.acs.org/doi/full/10.1021/acs.est.1c01603]

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

Prediction of Plant Uptake and Translocation of Engineered Metallic Nanoparticles by Machine Learning by Xiaoxuan Wang, Liwei Liu, Weilan Zhang, and Xingmao Ma. Environ. Sci. Technol. 2021, 55, 11, 7491–7500 DOI: https://doi.org/10.1021/acs.est.1c01603 Publication Date:May 17, 2021 Copyright © 2021 American Chemical Society

This paper is behind a paywall.

Nanotechnology in agriculture: an introduction and a 15th anniversary

It’s not often that I publish a posting meant for beginners since I tend to take an understanding of nanotechnology for granted. For anyone who has stumbled across this posting and needs an introduction to nanotechnology, M Cynthia Goh’s* (professor, Chemistry, University of Toronto) April 25, 2021 essay about nanotechnology and agriculture, on The Conversation website, provides a good entry point (Note 1: The excerpts are not in the order in which they appear in the essay Note 2: Links have been removed) ,

Nanotechnology is the science of objects that are a few nanometres — billionths of a metre — across. At this size, objects acquire unique properties. For example, the surface area of a swarm of nanoscale particles is enormous compared to the same mass collected into single large-scale clump.

Varying the size and other properties of nanoscale objects gives us an unprecedented ability to create precision surfaces with highly customized properties.

Agriculture is one of the oldest human inventions, but nanotech provides modern innovations that could dramatically improve the efficiency of our food supply and reduce the environmental impact of its production.

Agriculture comes with costs that farmers are only too familiar with: Crops require substantial amounts of water, land and fuel to produce. Fertilizers and pesticides are needed to achieve the necessary high crop yields, but their use comes with environmental side effects, even as many farmers explore how new technologies can reduce their impact.

Custom-made nanoscale systems can use precision chemistry to achieve high-efficiency delivery of fertilizers or pesticides. These active ingredients can be encapsulated in a fashion similar to what happens in targeted drug delivery. The encapsulation technique can also be used to increase the amount dissolved in water, reducing the need for large amounts.

Current applications

Starpharma, a pharmaceutical company, got into this game a few years ago, when it set up a division to apply its nanotechnological innovations to the agriculture sector. The company has since sold its agrochemical business.

Psigryph is another innovative nanotech company in agriculture. Its technology uses biodegradable nanostructures derived from Montmonercy sour cherries extract to deliver bioactive molecules across cell membranes in plants, animals and humans.

My lab has spent years working in nanoscience, and I am proud to see our fundamental understanding of manipulating polymer encapsulation at the nanoscale make its way to applications in agriculture. A former student, Darren Anderson, is the CEO of Vive Crop Protection [emphasis mine], named one of Canada’s top growing firms: they take chemical and biological pesticides and suspend them in “nanopackets” — which act as incredibly small polymer shuttles — to make them easily reach their target. The ingredients can be controlled and precisely directed when applied on crops.

*M Cynthia Goh was a co-founder of Vive Crop Protection but is not actively involved in the company. She receives funding from NSERC (Natural Sciences and Engineering Research Council) Canada and the Ontario Centre of Innovation.

Vive Crop Protection’s 15th anniversary

March 30, 2021 marked 15 years for Vive Crop Protection (formerly Vive Nano) according to the company’s March 30, 2021 news release. It’s been a number of years since I’ve written about the company and I’m glad to see they seem to be thriving. Chief Executive Officer (CEO), Darren Anderson (he was formerly the company’s Chief Technical Officer) was interviewed on camera by Kim Bolton for BNN Bloomberg; a link to the video is available from this April 29, 2021 Vive Crop news webpage.

(BTW, BNN Bloomberg is “(formerly Business News Network and Report on Business Television) is a Canadian English language specialty channel owned by Bell Media. It broadcasts programming related to business and financial news and analysis. Since April 30, 2018, the network has operated as a partner of the U.S. business channel Bloomberg Television, …” See more about BNN Bloomberg in its Wikipedia entry.)

For anyone interested in Vive Crop’s technology, see my December 31, 2013, posting.

Five country survey of reactions to food genome editing

Weirdly and even though most of this paper’s authors are from the University of British Columbia (UBC; Canada), only one press release was issued and that was by the lead author’s (Gesa Busch) home institution, the University of Göttingen (Germany).

I’m glad Busch, the other authors, and the work are getting some attention (if not as much as I think they should).

From a July 9, 2021 University of Göttingen press release (also on EurekAlert but published on July 12, 2021),

A research team from the University of Göttingen and the University of British Columbia (Canada) has investigated how people in five different countries react to various usages of genome editing in agriculture. The researchers looked at which uses are accepted and how the risks and benefits of the new breeding technologies are rated by people. The results show only minor differences between the countries studied – Germany, Italy, Canada, Austria and the USA. In all countries, making changes to the genome is more likely to be deemed acceptable when used in crops rather than in livestock. The study was published in Agriculture and Human Values.

Relatively new breeding technologies, such as CRISPR [clustered regularly interspaced short palindromic repeats) gene editing, have enabled a range of new opportunities for plant and animal breeding. In the EU, the technology falls under genetic engineering legislation and is therefore subject to rigorous restrictions. However, the use of gene technologies remains controversial. Between June and November 2019, the research team collected views on this topic via online surveys from around 3,700 people from five countries. Five different applications of gene editing were evaluated: three relate to disease resistance in people, plants, or animals; and two relate to achieving either better quality of produce or a larger quantity of product from cattle.

“We were able to observe that the purpose of the gene modification plays a major role in how it is rated,” says first author Dr Gesa Busch from the University of Göttingen. “If the technology is used to make animals resistant to disease, approval is greater than if the technology is used to increase the output from animals.” Overall, however, the respondents reacted very differently to the uses of the new breeding methods. Four different groups can be identified: strong supporters, supporters, neutrals, and opponents of the technology. The opponents (24 per cent) identify high risks and calls for a ban of the technology, regardless of possible benefits. The strong supporters (21 per cent) see few risks and many advantages. The supporters (26 per cent) see many advantages but also risks. Whereas those who were neutral (29 per cent) show no strong opinion on the subject.

This study was made possible through funding from the Free University of Bozen-Bolzano and Genome BC.

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

Citizen views on genome editing: effects of species and purpose by Gesa Busch, Erin Ryan, Marina A. G. von Keyserlingk & Daniel M. Weary. Agriculture and Human Values (2021) Published: DOI: https://doi.org/10.1007/s10460-021-10235-9

This paper is open access.

Methodology

I have one quick comment about the methodology. It can be difficult to get a sample that breaks down along demographic lines that is close to or identical to national statistics. That said, it was striking to me that every country was under represented in the ’60 years+ ‘ category. In Canada, it was by 10 percentage points (roughly). For other countries the point spread was significantly wider. In Italy, it was a 30 percentage point spread (roughly).

I found the data in the Supplementary Materials yesterday (July 13, 2021). When I looked this morning, that information was no longer there but you will find what appears to be the questionnaire. I wonder if this removal is temporary or permanent and, if permanent, I wonder why it was removed.

Participants for the Canadian portion of the survey were supplied by Dynata, a US-based market research company. Here’s the company’s Wikipedia entry and its website.

Information about how participants were recruited was also missing this morning (July 14, 2021).

Genome British Columbia (Genome BC)

I was a little surprised when I couldn’t find any information about the program or the project on the Genome BC website as the organization is listed as a funder.

There is a ‘Genomics and Society’ tab (seems promising, eh?) on the homepage where you can find the answer to this question: What is GE³LS Research?,

GE3LS research is interdisciplinary, conducted by researchers across many disciplines within social science and humanities, including economics, environment, law, business, communications, and public policy.

There’s also a GE3LS Research in BC page titled Project Search; I had no luck there either.

It all seems a bit mysterious to me and, just in case anything else disappears off the web, here’s a July 13, 2021 news item about the research on phys.org as backup to what I have here.

A better quality of cultivated meat from McMaster University?

This could be a bit stomach-churning for some folks.

Researchers at Canada’s McMaster University have developed and are commercializing a technique for cultivated meat (the first experiment involved mouse meat). (You could call it vat-grown meat.) A January 19, 2021 news item on phys.org makes the announcement (Note: Links have been removed),

McMaster researchers have developed a new form of cultivated meat using a method that promises more natural flavor and texture than other alternatives to traditional meat from animals.

Researchers Ravi Selvaganapathy and Alireza Shahin-Shamsabadi, both of the university’s School of Biomedical Engineering, have devised a way to make meat by stacking thin sheets of cultivated muscle and fat cells grown together in a lab setting. The technique is adapted from a method used to grow tissue for human transplants.

A January 19, 2021 McMaster University news release (also on EurekAlert) by Wade Hemsworth, which originated the news item, offers more details,

The sheets of living cells, each about the thickness of a sheet of printer paper, are first grown in culture and then concentrated on growth plates before being peeled off and stacked or folded together. The sheets naturally bond to one another before the cells die.

The layers can be stacked into a solid piece of any thickness, Selvaganapathy says, and “tuned” to replicate the fat content and marbling of any cut of meat – an advantage over other alternatives.

“We are creating slabs of meat,” he says. “Consumers will be able to buy meat with whatever percentage of fat they like – just like they do with milk.”

As they describe in the journal Cells Tissues Organs, the researchers proved the concept by making meat from available lines of mouse cells. Though they did not eat the mouse meat described in the research paper, they later made and cooked a sample of meat they created from rabbit cells.

“It felt and tasted just like meat,” says Selvaganapathy.

There is no reason to think the same technology would not work for growing beef, pork or chicken, and the model would lend itself well to large-scale production, Selvaganapathy says.

The researchers were inspired by the meat-supply crisis in which worldwide demand is growing while current meat consumption is straining land and water resources and generating troubling levels of greenhouse gases.

“Meat production right now is not sustainable,” Selvaganapathy says. “There has to be an alternative way of creating meat.”

Producing viable meat without raising and harvesting animals would be far more sustainable, more sanitary and far less wasteful, the researchers point out. While other forms of cultured meat have previously been developed, the McMaster researchers believe theirs has the best potential for creating products consumers will accept, enjoy and afford.

The researchers have formed a start-up company to begin commercializing the technology.

The researchers have included a picture of the ‘meat’,

Caption: A sample of meat cultivated by researchers at Canada’s McMaster University, using cells from mice. Credit: McMaster University

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

Engineering Murine Adipocytes and Skeletal Muscle Cells in Meat-like Constructs Using Self-Assembled Layer-by-Layer Biofabrication: A Platform for Development of Cultivated Meat by Alireza Shahin-Shamsabadi and P. R. (Ravi) Selvaganapathy. Cells Tissues Organs (2021). DOI: 10.1159/000511764

This paper is behind a paywall.

Living plants detect arsenic by way of embedded nanosensors

There’s a lot of arsenic in the world and it’s often a factor in making water undrinkable. When that water is used in farming It also pollutes soil and enters food-producing plants. A December 11, 2020 news item on Nanowerk announces research into arsenic detectors in plants,

Researchers have developed a living plant-based sensor that can in real-time detect and monitor levels of arsenic, a highly toxic heavy metal, in the soil. Arsenic pollution is a major threat to humans and ecosystems in many Asia Pacific countries.

Caption: Non-destructive plant nanobionic sensor embedded within leaves to report arsenic levels within plants to portable electronics, enabling real-time monitoring of arsenic uptake in living plants. Credit: Dr. Tedrick Thomas Salim Lew

I was not able to find the source for the news item but I did locate something close. From a December 13, 2020 Singapore-Massachusetts Institute of Technology (MIT) Alliance for Research and Technology (SMART), also on EurekAlert,

Scientists from the Disruptive and Sustainable Technologies for Agricultural Precision (DiSTAP) research group at the Singapore-MIT Alliance for Research and Technology (SMART), MIT’s research enterprise in Singapore, have engineered a novel type of plant nanobionic optical sensor that can detect and monitor, in real time, levels of the highly toxic heavy metal arsenic in the underground environment. This development provides significant advantages over conventional methods used to measure arsenic in the environment and will be important for both environmental monitoring and agricultural applications to safeguard food safety, as arsenic is a contaminant in many common agricultural products such as rice, vegetables, and tea leaves.

Arsenic and its compounds are a serious threat to humans and ecosystems. Long-term exposure to arsenic in humans can cause a wide range of detrimental health effects, including cardiovascular disease such as heart attack, diabetes, birth defects, severe skin lesions, and numerous cancers including those of the skin, bladder, and lung. Elevated levels of soil arsenic as a result of anthropogenic activities such as mining and smelting are also harmful to plants, inhibiting growth and resulting in substantial crop losses.

Food crops can absorb arsenic from the soil, leading to contamination of food and produce consumed by humans. Arsenic in underground environments can also contaminate groundwater and other underground water sources, the long-term consumption of which can cause severe health issues. As such, developing accurate, effective, and easy-to-deploy arsenic sensors is important to protect both the agriculture industry and wider environmental safety.

The novel optical nanosensors exhibit changes in their fluorescence intensity upon detecting arsenic. Embedded in plant tissues, with no detrimental effects on the plant, these sensors provide a nondestructive way to monitor the internal dynamics of arsenic taken up by plants from the soil. This integration of optical nanosensors within living plants enables the conversion of plants into self-powered detectors of arsenic from their natural environment, marking a significant upgrade from the time- and equipment-intensive arsenic sampling methods of current conventional methods.

“Our plant-based nanosensor is notable not only for being the first of its kind, but also for the significant advantages it confers over conventional methods of measuring arsenic levels in the below-ground environment, requiring less time, equipment, and manpower,” says Lew. “We envision that this innovation will eventually see wide use in the agriculture industry and beyond. I am grateful to SMART DiSTAP and the Temasek Life Sciences Laboratory (TLL), both of which were instrumental in idea generation and scientific discussion as well as research funding for this work.”

Besides detecting arsenic in rice and spinach, the team also used a species of fern, Pteris cretica, which can hyperaccumulate arsenic. This fern species can absorb and tolerate high levels of arsenic with no detrimental effect — engineering an ultrasensitive plant-based arsenic detector, capable of detecting very low concentrations of arsenic, as low as 0.2 parts per billion. In contrast, the regulatory limit for arsenic detectors is 10 parts per billion. Notably, the novel nanosensors can also be integrated into other species of plants. The researchers say this is the first successful demonstration of living plant-based sensors for arsenic and represents a groundbreaking advancement that could prove highly useful in both agricultural research (e.g., to monitor arsenic taken up by edible crops for food safety) and general environmental monitoring.

Previously, conventional methods of measuring arsenic levels included regular field sampling, plant tissue digestion, extraction, and analysis using mass spectrometry. These methods are time-consuming, require extensive sample treatment, and often involve the use of bulky and expensive instrumentation. The new approach couples nanoparticle sensors with plants’ natural ability to efficiently extract analytes via the roots and transport them. This allows for the detection of arsenic uptake in living plants in real time, with portable, inexpensive electronics such as a portable Raspberry Pi platform equipped with a charge-coupled device camera akin to a smartphone camera.

Co-author, DiSTAP co-lead principal investigator, and MIT Professor Michael Strano adds, “This is a hugely exciting development, as, for the first time, we have developed a nanobionic sensor that can detect arsenic — a serious environmental contaminant and potential public health threat. With its myriad advantages over older methods of arsenic detection, this novel sensor could be a game-changer, as it is not only more time-efficient, but also more accurate and easier to deploy than older methods. It will also help plant scientists in organizations such as TLL to further produce crops that resist uptake of toxic elements. Inspired by TLL’s recent efforts to create rice crops which take up less arsenic, this work is a parallel effort to further support SMART DiSTAP’s efforts in food security research, constantly innovating and developing new technological capabilities to improve Singapore’s food quality and safety.”

The research is carried out by SMART and supported by the National Research Foundation (NRF) Singapore under its Campus for Research Excellence And Technological Enterprise (CREATE) program.

Led by MIT’s Strano and Singapore co-lead principal investigator Professor Chua Nam Hai, DiSTAP is one of the five Interdisciplinary Research Groups (IRGs) in SMART. The DiSTAP program addresses deep problems in food production in Singapore and the world by developing a suite of impactful and novel analytical genetic and biosynthetic technologies. The goal is to fundamentally change how plant biosynthetic pathways are discovered, monitored, engineered, and ultimately translated to meet the global demand for food and nutrients. Scientists from MIT, TTL, Nanyang Technological University, and National University of Singapore are collaboratively developing new tools for the continuous measurement of important plant metabolites and hormones for novel discovery, deeper understanding and control of plant biosynthetic pathways in ways not yet possible, especially in the context of green leafy vegetables; leveraging these new techniques to engineer plants with highly desirable properties for global food security, including high yield density production, drought and pathogen resistance and biosynthesis of high-value commercial products; developing tools for producing hydrophobic food components in industry-relevant microbes; developing novel microbial and enzymatic technologies to produce volatile organic compounds that can protect and/or promote growth of leafy vegetables; and applying these technologies to improve urban farming.

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

Plant Nanobionic Sensors for Arsenic Detection by Tedrick Thomas Salim Lew, Minkyung Park, Jianqiao Cui, Michael S. Strano. Advanced Materials DOI: https://doi.org/10.1002/adma.202005683 First published: 26 November 2020

This paper is behind a paywall.

“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?

Sakatoon synchrotron gets dirty

“Some synchrotrons don’t want to have any dirt in their beamlines, so it makes it more difficult to analyze soil samples …”

Also known as the Canadian Light Source (CLS), the synchrotron in Saskatoon was used to analyze soil from Hawaii according to a Nov. 5, 2020 CLS news release (also received via email) by Erin Matthews,

With its warm weather and sandy beaches, Hawaii is a magnet for tourists every year. This unique ecosystem also attracts soil scientists interested in what surprises may lie beneath their feet.

In a recent paper published in Geoderma, European researchers outline how they used the rich soils of Hawaii to study the critical movement of phosphorous through the environment. By better understanding the amount and type of phosphorus in the soil, they can help crops become more successful and maintain the health of our ecosystems for years to come.

The project was led by Agroscope scientist Dr. Julian Helfenstein, Prof. Emmanuel Frossard with the Institute of Agricultural Sciences, ETH Zurich; and Dr. Christian Vogel, a researcher at the Federal Institute for Materials Research and Testing in Berlin.

The team used the Canadian Light Source (CLS) at the University of Saskatchewan to help analyze the different types of phosphorus in their samples and track their origins.

“Some synchrotrons don’t want to have any dirt in their beamlines, so it makes it more difficult to analyze soil samples,” Vogel said. That is why the team went to the CLS, a facility that prioritizes agricultural research and welcomes soil science projects. [emphasis mine] Vogel analyzed the samples using different spectroscopy techniques on the VLS-PGM beamline at CLS, which uses extremely bright light.

Phosphorus generally comes from apatite found in the bedrock, Helfenstein explained. So, the group was surprised to discover that some of the phosphorus in their weathered Hawaiian  Hawaiian topsoil samples had originated from dust that was deposited by air currents. This dust, and the phosphorus contained within, traveled thousands of kilometers before settling on the island.

Researchers would expect to find apatite in soils in dry areas where it would not get washed away by rainfall. So, finding evidence of apatite in wet soils amazed the scientists.

“On the wet end of the gradient, these soils are extremely weathered so primary apatite was gone, but we still found these small grains of apatite in the soil co-located with quartz, suggesting that it’s coming from somewhere else. It’s not coming from the bottom, it’s coming from the air,” Helfenstein said.

The team collaborated with atmospheric physicists who used modeling to trace the backward trajectory of the dust, pinpointing the air currents that the dust had traveled in and the origin of the apatite.

Frossard explained that extended rainfall can lead to very old and weathered ecosystems that researchers would expect to collapse from limited phosphorus. However, if apatite comes from somewhere else, like dust carried on air currents, then you will see healthy, productive ecosystems. This helps to explain plant growth on highly weathered soils in Hawaii.

Frossard has worked on climate sequences for decades, including studying the climate gradient in the Canadian prairies, and has been following news from the CLS since its construction in 1999.

“What I see here is a very powerful instrument ­–– the fact they allow us to study soil is really something superb. It allows us to improve our knowledge in biology and in [the] chemistry of soil.” The team looks forward to unearthing more environmental secrets in the future.

Before getting to the citation and giving a second link to the paper, here’s a little more about Saskatchewan (Wikipedia entry), which explains why a synchrotron in that province might develop expertise in agricultural research and soil science projects (Note: Links have been removed),

Historically, Saskatchewan’s economy was primarily associated with agriculture, with wheat being the precious symbol on the province’s flag [emphasis mine]. Increasing diversification has resulted in agriculture, forestry, fishing, and hunting only making up 8.9% of the province’s GDP in 2018. Saskatchewan grows a large portion of Canada’s grain.[49] In 2017, the production of canola surpassed the production of wheat, which is Saskatchewan’s most familiar crop and the one most often associated with the province. Total net income from farming was $3.3 billion in 2017, which was $0.9 billion less than the income in 2016.[47] Other grains such as flax, rye, oats, peas, lentils, canary seed, and barley are also produced in the province. Saskatchewan is the world’s largest exporter of mustard seed.[50]Beef cattle production by a Canadian province is only exceeded by Alberta. In the northern part of the province, forestry is also a significant industry.[48]

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

Microspectroscopy reveals dust-derived apatite grains in acidic, highly-weathered Hawaiian soils by Christian Vogel, Julian Helfenstein, Michael S.Massey, Ryo Sekine, Ruben Kretzschmar, Luo Beiping, Thomas Peter, Oliver A.Chadwick, Federica Tamburini, Camille Rivard, Hannes Herzel, Christian Adam, Ana E.Pradas del Real, Hiram Castillo-Michel, Lucia Zuin, Dongniu Wang, Roberto Félix, Benedikt Lassalle-Kaiser, Emmanuel Frossard. Geoderma Volume 381, 1 January 2021, 114681 DOI: https://doi.org/10.1016/j.geoderma.2020.114681 Published first online: online 30 August 2020.

This paper is open access.

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.