Category Archives: agriculture

Getting the dirt on dirt: a podcast interview with soil biogeochemist Asmeret Asefaw Berhe

The podcast People I (Mostly) Admire isn’t technically speaking a science podcast but its host Steven Levitt, University of Chicago economist and co-author of the “Freakonomics” books, features quite a few scientists in his podcast series on the Freakonomics Radio Network.

One of Levitt’s latest episodes, No. 74 Getting our Hands Dirty on May 6, 2022 features,

Soil scientist Asmeret Asefaw Berhe could soon hold one of the most important jobs in science. She explains why the ground beneath our feet is one of our greatest resources — and, possibly, one of our deadliest threats.

Episode Transcript

My guest today Asmeret Asefaw Berhe is a leading soil scientist and President Biden’s nominee to be the director of the Department of Energy’s Office of Science. If confirmed, she will manage a $7 billion research budget.

ASEFAW BERHE: If you were to think about where the large global reservoirs of carbon are — beyond fossil fuel deposits, and the ocean — the next largest reservoir of carbon on the earth system is in soil.

Welcome to People I (Mostly) Admire, with Steve Levitt.

I got interested in soil science a few weeks back and I started doing a little bit of reading. And I stumbled onto Asmeret and her amazing story. Born and raised in civil-war ravaged Eritrea, she became a leading scientist and is poised to take over one of the most important jobs in science. I knew right away I needed to have her on this show.

LEVITT: Have you heard of a man named Sadhguru? He’s an Indian guru who’s currently riding a motorcycle across Europe and the Middle East to bring attention to soil degradation.

ASEFAW BERHE: I’ve seen some social media posts, and I also saw recently the interview he did with Trevor Noah.

LEVITT: Believe it or not, the idea for having you on this podcast came because his publicist somehow got in my inbox of my email. At first, I thought it was a joke, but then he was on Trevor Noah and I said, “Whoa, he must be doing something serious, but it’s not very scientific. I better learn something about the science.” And then I found you because you’re the first name that comes up if you look into soil science.

Here’s a selection of STEM (science, technology, engineering, and mathematics) episodes (from a May 9, 2022 announcement received via email about the People I [Mostly] Admire podcast series),

While People I (Mostly) Admire hosts guests from all walks of life, Levitt’s conversations with scientists have been some of the most illuminating episodes. If you’re not familiar with the show, here’s a short guide to some of the STEM episodes:

  • We Can Play God Now (Ep. 67, 3/18/22) Gene-editing pioneer Jennifer Doudna worries that humanity might not be ready for the technology she helped develop.
  • The Professor Who Said “No” to Tenure (Ep. 66, 3/11/22) Columbia astrophysicist David Helfand is an academic who does things his own way — from turning down job security to helping found a radically unconventional university.
  • A Rockstar Chemist and Her Cancer-Attacking “Lawn Mower” (Ep. 65, 3/4/22) Stanford professor Carolyn Bertozzi’s imaginative ideas for treating disease have led to ten start-ups. She talks with Steve about the new generation of immune therapy she’s created, and why she might rather be a musician.
  • Cassandra Quave Thinks the Way Antibiotics Are Developed Might Kill Us (Ep. 60, 1/28/22) By mid-century, 10 million people a year are projected to die from untreatable infections. Can Cassandra, an ethnobotanist at Emory University convince Steve that herbs and ancient healing are key to our medical future?
  • Why Aren’t All Drugs Legal? (Ep. 28, Replay 1/14/22) The Columbia neuroscientist and psychology professor Carl Hart believes that recreational drug use, even heroin, methamphetamines, and cocaine, is an inalienable right. Can he convince Steve?
  • Max Tegmark on Why Superhuman Artificial Intelligence Won’t be Our Slave (Part 2) (Ep. 52, 11/19/21) He’s an M.I.T. cosmologist, physicist, and machine-learning expert, and once upon a time, almost an economist. Max and Steve continue their conversation about the existential threats facing humanity, and what Max is doing to mitigate our risk. The co-founder of the Future of Life Institute thinks that artificial intelligence can be the greatest thing to ever happen to humanity — if we don’t screw it up.
  • Max Tegmark on Why Treating Humanity Like a Child Will Save Us All (Ep. 51, 11/5/21) How likely is it that this conversation is happening in more than one universe? Should we worry more about Covid or about nuclear war? Is economics a form of “intellectual prostitution?” Steve discusses these questions, and more, with Max, an M.I.T cosmologist, physicist, and machine-learning expert — who was once almost an economist. He also tells Steve why we should be optimistic about the future of humanity (assuming we move Earth to a larger orbit before the sun evaporates our oceans).
  • Mathematician Sarah Hart on Why Numbers are Music to Our Ears (Ep. 49, 10/29/21) Playing notes on her piano, she demonstrates for Steve why whole numbers sound pleasing, why octaves are mathematically imperfect, and how math underlies musical composition. Sarah, a professor at the University of London and Gresham College, also talks with Steve about the gender gap in mathematics and why being interested in everything can be a problem.

While I’m at it, here’s a couple of my postings on soil,

There’s a lot more should you choose to search ‘soil’.

Getting back to Freakonomics, it’s been quite a while since I’ve come across that term. You can find out more about the community from the freakonomics.com About page,

Freakonomics began as a book, which led to a blog, a documentary film, more books, a pair of pants, and in 2010, a podcast called Freakonomics Radio. Hosted by Stephen J. Dubner,it became and remains one of the most popular podcasts in the world, with a reputation for storytelling that is both rigorous and entertaining. Its archive of more than 400 episodes is available, for free, on any podcast app, and the show airs weekly on NPR stations. Freakonomics Radio is now the flagship show of the Freakonomics Radio Network, which includes the podcasts No Stupid Questions (est. 2020), People I (Mostly) Admire (2020), Freakonomics, M.D. (2021), and a variety of special series. To keep up with everything, you can get our newsletter, read the FAQs, or send inquiries to radio@freakonomics.com.

Oddly, I too have heard from Sadhguru (mentioned early in the interview with Asmeret Asefaw Berhe).

Internet of living things (IoLT)?

It’s not here yet but there are scientists working on an internet of living things (IoLT). There are some details (see the fourth paragraph from the bottom of the news release excerpt) about how an IoLT would be achieved but it seems these are early days. From a September 9, 2021 University of Illinois news release (also on EurekAlert), Note: Links have been removed,

The National Science Foundation (NSF) announced today an investment of $25 million to launch the Center for Research on Programmable Plant Systems (CROPPS). The center, a partnership among the University of Illinois at Urbana-Champaign, Cornell University, the Boyce Thompson Institute, and the University of Arizona, aims to develop tools to listen and talk to plants and their associated organisms.

“CROPPS will create systems where plants communicate their hidden biology to sensors, optimizing plant growth to the local environment. This Internet of Living Things (IoLT) will enable breakthrough discoveries, offer new educational opportunities, and open transformative opportunities for productive, sustainable, and profitable management of crops,” says Steve Moose (BSD/CABBI/GEGC), the grant’s principal investigator at Illinois. Moose is a genomics professor in the Department of Crop Sciences, part of the College of Agricultural, Consumer and Environmental Sciences (ACES). 

As an example of what’s possible, CROPPS scientists could deploy armies of autonomous rovers to monitor and modify crop growth in real time. The researchers created leaf sensors to report on belowground processes in roots. This combination of machine and living sensors will enable completely new ways of decoding the language of plants, allowing researchers to teach plants how to better handle environmental challenges. 

“Right now, we’re working to program a circuit that responds to low-nitrogen stress, where the plant growth rate is ‘slowed down’ to give farmers more time to apply fertilizer during the window that is the most efficient at increasing yield,” Moose explains.

With 150+ years of global leadership in crop sciences and agricultural engineering, along with newer transdisciplinary research units such as the National Center for Supercomputing Applications (NCSA) and the Center for Digital Agriculture (CDA), Illinois is uniquely positioned to take on the technical challenges associated with CROPPS.

But U of I scientists aren’t working alone. For years, they’ve collaborated with partner institutions to conceptualize the future of digital agriculture and bring it into reality. For example, researchers at Illinois’ CDA and Cornell’s Initiative for Digital Agriculture jointly proposed the first IoLT for agriculture, laying the foundation for CROPPS.

“CROPPS represents a significant win from having worked closely with our partners at Cornell and other institutions. We’re thrilled to move forward with our colleagues to shift paradigms in agriculture,” says Vikram Adve, Donald B. Gillies Professor in computer science at Illinois and co-director of the CDA.

CROPPS research may sound futuristic, and that’s the point.

The researchers say new tools are needed to make crops productive, flexible, and sustainable enough to feed our growing global population under a changing climate. Many of the tools under development – biotransducers small enough to fit between soil particles, dexterous and highly autonomous field robots, field-applied gene editing nanoparticles, IoLT clouds, and more – have been studied in the proof-of-concept phase, and are ready to be scaled up.

“One of the most exciting goals of CROPPS is to apply recent advances in sensing and data analytics to understand the rules of life, where plants have much to teach us. What we learn will bring a stronger biological dimension to the next phase of digital agriculture,” Moose says. 

CROPPS will also foster innovations in STEM [science, technology[ engineering, and mathematics] education through programs that involve students at all levels, and each partner institution will share courses in digital agriculture topics. CROPPS also aims to engage professionals in digital agriculture at any career stage, and learn how the public views innovations in this emerging technology area.

“Along with cutting-edge research, CROPPS coordinated educational programs will address the future of work in plant sciences and agriculture,” says Germán Bollero, associate dean for research in the College of ACES.

I look forward to hearing more about IoLT.

Cellulose nanofiber (CNF) coating protects plants against rust disease

A September 8, 2021news item on ScienceDaily describes some new research into rust disease,

A water-absorbent coat to keep rust away? It may seem counterintuitive but when it comes to soybean plants and rust disease, researchers from Japan have discovered that applying a coating that makes leaf surfaces water absorbent helps to protect against infection.

Caption: Researchers from the University of Tsukuba have found that coating soybean plant leaves with cellulose nanofiber (CNF) gives protection against an aggressive fungal disease. The CNF coating changed leaf surfaces from water repellent to water absorbent, and suppressed pathogen gene expression associated with infection mechanisms, offering resistance to the destructive Asian rust disease. This is the first study to examine CNF application for controlling plant diseases, and it offers a sustainable alternative to managing plant disease.. Credit: University of Tsukuba

A September 7, 2021 University of Tsukuba press release (also on EurekAlert but published September 8, 2021), which originated the news item, describes the disease and proposed solution in more detail,

In a study published this month in Frontiers in Plant Science, researchers from the University of Tsukuba have revealed that coating soybean plant leaves with cellulose nanofiber changes the leaf surface from water repellent to water absorbent and offers resistance against Asian soybean rust.

Rusts are plant diseases that get their name from the powdery rust- or brown-colored fungal spores on the surfaces of infected plants. Asian soybean rust (ASR) is an aggressive disease of soybean plants, causing estimated crop yield losses of up to 90%. ASR is caused by Phakopsora pachyrhizi, a fungal pathogen that requires a living plant host to survive. The timely application of fungicide is currently the only way of controlling ASR in the field. But the use of fungicides can be problematic, resulting in negative environmental effects, increased production costs, and fungicide-resistant pathogens.

“We investigated cellulose nanofiber (CNF) as an alternative method of controlling ASR,” says senior author of the study, Professor Yasuhiro Ishiga. “Specifically, we wanted to know whether coating soybean plant leaves with CNF protected plants against P. pachyrhizi.

Of the available methods for isolating CNF, aqueous counter collision (ACC) has been shown to alter the hydrophilic (water absorbent) and hydrophobic (water repellent) properties of surfaces, switching one to the other. Previous research has indicated that CNF obtained via ACC has higher wettability than CNF isolated by other methods.

“We showed that CNF can change the soybean leaf surface from hydrophobic to hydrophilic,” explains senior author, Professor Yuji Yamashita. “This offers resistance against P. pachyrhizi.”

The team found fewer lesions and significantly reduced formation of P. pachyrhizi appressoria, which are specialized pre-infection structures used to break through the outer surface of the host plant, on CNF-treated leaves compared with control (untreated) leaves. The results also revealed suppressed gene expression linked to the formation of pre-infection structures in P. pachyrhizi on treated versus control leaves.

“In particular, chitin synthase gene expression was suppressed, and P. pachyrhizi needs chitin synthases to form pre-infection structures,” says Professor Ishiga.

This study is the first to investigate the application of CNF for controlling plant diseases in the field, and this technique offers new possibilities for sustainable and eco-friendly management of plant diseases.

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

Covering Soybean Leaves With Cellulose Nanofiber Changes Leaf Surface Hydrophobicity and Confers Resistance Against Phakopsora pachyrhizi by
Haruka Saito, Yuji Yamashita, Nanami Sakata, Takako Ishiga, Nanami Shiraishi, Giyu Usuki, Viet Tru Nguyen, Eiji Yamamura and Yasuhiro Ishiga. Front. Plant Sci., 03 September 2021 DOI: https://doi.org/10.3389/fpls.2021.726565

This paper appears to be open access.

Phytoremediation with lupin and arsenic

Is anyone else reminded of Arsène Lupin? (More about Lupin later in this posing)

An August 24, 2021 news item on ScienceDaily describes research on soils and phytoremediation (decontamination by plants),

Pollution of soils with highly toxic arsenic is a worldwide problem generating substantial risks to human health and the environment.

In Canada, over 7000 sites contaminated with metals such as arsenic are considered ‘highly concerning’ by the government, with some past and recent mining operations and wood preservative facilities having left their mark on the environment by increasing soil arsenic levels by up to 1000 times the maximum regulatory health limits.

One way in which arsenic contaminated soils could be rejuvenated is to exploit natural mechanisms which have evolved in certain plants for contamination tolerance.

“The legume crop white lupin (L. albus) is one such arsenic tolerant plant species being studied as for sustainable remediation,” explains Adrien Frémont, lead author of the study and a doctoral student in biological sciences at the Université de Montréal. “The mechanism behind arsenic tolerance in white lupin is thought to be the release of plant chemicals directly into soil by roots, but the nature of these compounds is unknown and hard to study due to the complexity of these belowground interactions.”

Caption: The legume crop white lupin (L. albus) is one such arsenic tolerant plant species being studied as for sustainable remediation. Credit: UMONTREAL

An August 24, 2021 University of Montreal (Université de Montréal) news release (also on EurekAlert), which originated the news item, describes the work in more detail,

Root chemicals an undiscovered country

To study this, the team developed nylon pouches which could be placed close to roots in soil to capture exuded molecules without damaging the root system. The complex mix of molecules collected from these pouches were analysed using advanced (metabolomic) chemical profiling to identify the compounds capable of binding metals produced by the Lupin plants in response to high concentrations of arsenic. Some of these metal-binding molecules, phytochelatins, are known to be used internally by plants to deal with metal stress but have never before been captured as exuded into polluted soils.

“We’re really excited to see how matching new root-soil sampling approaches with advanced metabolomic profiling can yield such unexpected discoveries”, notes Frémont. “We know that plants can drastically change soil properties and can transform or immobilise soil pollution, but the chemistry underlying how they achieve this, and in particular the makeup and function of root-exuded compounds, is still very much an undiscovered country.”
 

Plant roots directly altering polluted soils

The next steps of the research are to branch out into more detailed analysis of the precise chemical reactions taking place at the root-soil interface, including exploration of different plant species, interactions with microorganisms and the challenge of diverse soil pollution.

As Dr. Nicholas Brereton, University of Montreal and the study’s senior author, mentions: “It can be a real challenge to research the complex interactions going on belowground between plants and soil, but these findings are rewarding in telling us that natural mechanisms have evolved in plants to deal with this type of pollution. Although we’re still only just beginning to scratch below the surface of how these plant root strategies work, as we learn more, we can potentially utilise these natural processes to improve soil health and help to alleviate some of the most persistent anthropogenic damage to our environment.”

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

Phytochelatin and coumarin enrichment in root exudates of arsenic-treated white lupin by Adrien Frémont, Eszter Sas, Mathieu Sarrazin, Emmanuel Gonzalez, Jacques Brisson, Frédéric Emmanuel Pitre, Nicholas James Beresford Brereton. Plant Cell & Environment DOI: https://doi.org/10.1111/pce.14163 First published: 15 August 2021

This paper is behind a paywall.

For anyone interested in phytoremediation, I have a March 30, 2012 posting about it and there’s this Wikipedia entry. Depending on the circumstances, you might also consider phytoremediation as a form of phyto-mining, i.e., using plants to recover metals from mine tailings (see my March 5, 2013 posting).

Arsène Lupin

There are two of them (the first and the latest ones) being mentioned here; but there are many versions of Arsène Lupin in manga, anime, movies, etc.

The first fictional Arsène Lupin was created in 1905 by Maurice Leblanc. Here’s a description (on the Normandie tourisme website) of the first Lupin in an article about the latest Lupin, a series streamed on Netflix.

Maurice Leblanc was born in Rouen in 1864. Fascinated by legends of witches, Celts, Romans and the Vikings growing up, Leblanc would go on to develop a deep knowledge of and love for the region around Rouen, known as the Pays de Caux. After working in a factory in Rouen by day, writing only in his spare time, Leblanc eventually left his home town to study in Paris, where he then started working as a journalist for several publications including Le Figaro. Fate then struck, as publisher Pierre Lafitte launched the magazine Je sais tout and commissioned Leblanc to write a series of new crime stories where the hero would be a sort of French anti-Sherlock Holmes.

Who was the original Lupin? Not unlike Lupin in the TV series, the Arsène Lupin of the books was a thief, a master of disguise, a rascal but never a killer, a hit with the ladies and a righter of wrongs who takes from the rich, a French Robin Hood if you like. He takes on a multitude of personas in the books, constantly changing his looks and his name – examples include Prince Paul Sernine, Raoul d’Andrésy, Horace Velmont and Don Luis Perenna. In the [Lupin] series [2021], this is echoed by Assane’s alter-egos Paul Sernine, Luis Perenna and Salvatore813, as well as his choice of name for his son, Raoul. Yet superman Lupin, both in the books and on screen, always manages to triumph somehow over his enemies, even when all seems lost, through bending the rules, outsmarting the police and sheer self-belief.

You can find out more about the latest Lupin in its IMDb entry,

Inspired by the adventures of Arsène Lupin, gentleman thief Assane Diop sets out to avenge his father for an injustice inflicted by a wealthy family.

The television series starring Omar Sy was a huge hit in France and has been seen worldwide.

‘Playing telephone’ with multivalent gold nanoparticles

A July 7, 2021 news item on phys.org describes what ‘playing telephone’ has to do with gold nanoparticles,

Cells play a precise game of telephone, sending messages to each other that trigger actions further on. With clear signaling, the cells achieve their goals. In disease, however, the signals break up and result in confused messaging and unintended consequences. To help parse out these signals and how they function in health—and go awry in disease—scientists tag proteins with labels they can follow as the proteins interact with the molecular world around them.

The challenge is figuring out which proteins to label in the first place. Now, a team led by researchers from Tokyo University of Agriculture and Technology (TUAT) has developed a new approach to identifying and tagging the specific proteins. They published their results on June 1 [2021] in Angewandte Chemie.

A July 8, 2021 TUAT press release on EurekAlert, which originated the news item, delves further into the research (I appreciate how clearly the work is explained),

“We are interested in exploring protein receptors of certain carbohydrate molecules that are involved in mediating cell signaling, particularly in cancer cells,” said paper author Kaori Sakurai, associate professor in the Department of Biotechnology and Life Science at TUAT.

The carbohydrate molecules, called ligands, are typically expressed on the surface of cells and are known to dynamically form complexes with protein receptors to coordinate complicated cellular functions. However, Sakurai said, the proteins responsible for binding the carbohydrates have been difficult to identify because they bond so weakly with the molecules.

The researchers designed a new type of carbohydrate probe that would not only link to the molecules, but tightly bind to them.

“We used gold nanoparticles as a scaffold to attach both carbohydrate ligands and electrophiles — a chemical that loves to react with other molecules — in a multivalent fashion,” Sakurai said. “This way, we were able to greatly increase binding affinity and reaction efficiency toward carbohydrate-binding proteins.”

The researchers applied the designed probes to cell lysate, a fluid containing the innards of broken-apart cells.

“The probes quickly found the target carbohydrate-binding proteins, triggering the electrophilic groups to react with electron-donating amino acid residues on nearby proteins,” Sakurai said. “This resulted in proteins firmly cross-linked to the gold nanoparticles’ surface, making it easy to subsequently analyze their identities.”

The team evaluated several electrophilic groups to identify the most efficient type for labeling their target proteins.

“We found that a particular electrophilic group called aryl sulfonyl fluoride is best suited for affinity labeling of carbohydrate-binding proteins,” said co-author Nanako Suto, a graduate student in the Department of Biotechnology and Life Science of TUAT. “However, they have rarely been used to identify target proteins, presumably because they would non-selectively react with various other, undesired proteins.”

However, the scale of aryl sulfonyl fluoride use appears to mitigate the issue.

“The non-selectivity isn’t a problem if aryl sulfonyl fluoride is used at very low concentrations, at the range of the nanoscale,” said co-author Shione Kamoshita, also a graduate student in the Department of Biotechnology and Life Science, TUAT.

The gold nanoparticle scaffolding displays many copies of the electrophilic group, which keeps aryl sulfonyl fluoride’s local concentration high on the nanoparticle surface but restrains them from the general cell system and reacting to undesired proteins. With the high concentration at the nano-level, some copies of electrophilic groups can efficiently react with target proteins.

“Through this process, we were able to achieve highly efficient and selective affinity labeling of carbohydrate-binding proteins in cell lysate,” Sakurai said. “We will apply the new method in target identification of several cancer-related carbohydrate ligands and investigate their function in cancer development. In parallel, we aim to explore the general utility of this new probe design for various other bioactive small molecules, so that we can accelerate the elucidation of their mechanisms.”

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

Exploration of the Reactivity of Multivalent Electrophiles for Affinity Labeling: Sulfonyl Fluoride as a Highly Efficient and Selective Label by Nanako Suto, Shione Kamoshita, Dr. Shoichi Hosoya, Prof. Kaori Sakurai. Angewandte Chemie Volume 60, Issue 31 July 26, 2021 Pages 17080-17087 DOI: https://doi.org/10.1002/anie.202104347 First published: 01 June 2021

This paper is behind a paywall.

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.