Engineers at the University of California have developed a new data structure and compression technique that enables the field of pangenomics to handle unprecedented scales of genetic information. The team, led by UC San Diego electrical and computer engineering professor Yatish Turakhia, describe their compressive pangenomics approach in Nature Genetics.

Pangenomics, a subset of bioinformatics, is the study of many different genomes from one specific species. This can provide a more holistic picture of the natural variation and mutations that occur within a species than using one singular reference genome. This has many practical applications, such as studying how genomic mutations lead to increased transmissibility or drug resistance in pathogens.

Challenges in current pangenomic methods

Although advances in genome sequencing technologies have reduced the cost and increased the speed of sequencing, the data structures and analysis tools needed to study and graphically represent the relationships between millions of sequenced genomes remain a challenge.

While graph-based data formats for pangenomes have become popular and widely adopted, they only represent the genetic variation in a collection of genomes, not their shared evolutionary and mutational histories. They also have large storage requirements that do not scale well.

“The data structures used for pangenomics research are critical because they determine not only how efficiently genetic data is represented, but also what the data can represent,” said Sumit Walia, an electrical engineering Ph.D. candidate at the Jacobs School of Engineering and co-first author of the study.

The research team, which includes engineers from the Genomics Institute at UC Santa Cruz, pioneered a new data structure and file format, called Pangenome Mutation-Annotated Network (PanMAN).

How PanMAN works and its advantages

PanMAN not only provides unmatched compression for pangenomes but also significantly advances the representative power by encoding additional biologically relevant information, including phylogenies, mutations, and whole-genome alignments.Their compressive pangenomics approach can perform analysis on compressed pangenomic data, allowing researchers to handle vastly larger scales of genetic data than currently possible.

“Our compressive technique with PanMANs allows doing more with less, greatly improving the scale and scope of current pangenomic analysis,” said Turakhia, the study’s corresponding author.

PanMANs are composed of mutation-annotated trees, called PanMATs, which store a single ancestral genome sequence at the root and annotate mutations, such as substitutions, insertions, and deletions, on the different branches.

Multiple PanMATs are connected in the form of a network using edges to generate a PanMAN. These edges store complex mutations, such as recombination and horizontal gene transfer data, which result in sequences involving multiple parent sequences and violate the vertical inheritance assumption of single trees.

This representation is compact as it exploits the shared ancestry among genomes, representing each mutation only once on the branch where it arose instead of duplicating them across individual sequences.

In addition, PanMAN was crafted to represent a rich set of biologically meaningful information that current pangenome formats lack. Some information in PanMAN is explicitly stored, such as mutations, phylogeny, annotations, and root sequence, whereas other information can be derived, such as ancestral sequences, multiple whole-genome alignment, and genetic variation.

So far, the researchers have used PanMAN to study microbial genomes. They have found that this method is the most compressible format among variation-preserving pangenomic formats, providing up to hundreds or even thousands of times more compression. For example, the team built the largest pangenome for SARS-CoV-2, using more than 8 million separate genomes of the virus.

Using their PanMAN method, this vast amount of genetic data only required 366MB of file storage space, which is roughly 3,000 times less storage than its corresponding whole-genome alignment that PanMAN encodes.

Constructing an alignment for SARS-CoV-2 genomes at this scale was itself a formidable challenge, which was addressed by another computational tool developed at Turakhia’s lab, called TWILIGHT.

Future directions

Now, the researchers are expanding their use of TWILIGHT and PanMANs from microbes to human genomes. Turakhia and Melissa Gymrek, a professor of computer science and engineering at UC San Diego, received a Jacobs School Early Career Faculty Development Award to advance this effort.

“Extending compressive pangenomics to human genomes can fundamentally transform how we store, analyze, and share large-scale human genetic data,” said Turakhia.

“Besides enabling studies of human genetic diversity, disease, and evolution at unprecedented scale and speed, it can depict detailed evolutionary and mutational histories which shape diverse human populations, something that current representations do not capture.”

Much like humans, microbial organisms can be fickle in their productivity. One moment they’re cranking out useful chemicals in vast fermentation tanks, metabolizing feed to make products from pharmaceuticals and supplements to biodegradable plastics or fuels, and the next, they inexplicably go on strike.

Engineers at Washington University in St. Louis have found the source of the fluctuating metabolic activity in microorganisms and developed tools to keep every microbial cell at peak productivity during biomanufacturing.

The work, published in Nature Communications, tracks hundreds of E. coli cells as they produce a yellow food pigment—betaxanthin—while growing, dividing and carrying out normal metabolic activities.

Understanding metabolic noise in microbes

“Like the behavior of a person, sometimes microbes are motivated to work hard, but they ‘get tired’ much more quickly and easily,” said Fuzhong Zhang, the Francis F. Ahmann Professor in energy, environmental and chemical engineering (EECE) and co-director of the McKelvey School of Engineering’s Synthetic Biology Manufacturing of Advanced Materials Research Center. Zhang is the corresponding author of the research, along with Ph.D. students Xinyue Mu and Alexander Schmitz.

Bioengineers and biologists have long observed large cell-to-cell variations in microbial metabolism, often called metabolic noise, or more generally, cellular noise. However, it has remained unclear what caused these differences and how frequently highly productive cells switch to low-productivity states. This lack of understanding has limited engineers’ ability to develop effective strategies to enrich hardworking, high-producing cells for biomanufacturing.

Answers lie in single cells’ fluctuating behavior, which is extremely challenging to study. Researchers must be able to measure a low-abundant metabolite along with the enzyme that produces it inside a tiny single cell while that cell grows and divides. To address this challenge, the team built microfluidic devices and engineered E. coli to produce a unique, bright-yellow metabolite—betaxanthin—that can be easily distinguished from thousands of other cellular metabolites.

New tools and strategies for productivity

These new advances allowed them to discover that betaxanthin production fluctuates rapidly, with cells switching from high-production to low-production states within a few hours. Approximately 50% of this betaxanthin noise comes from fluctuations in the enzyme responsible for producing betaxanthin, which arise from natural randomness (stochasticity) in gene expression. Fluctuations in cell growth rate account for less than 10% of the betaxanthin variability.

Using experimental data, the team developed computational models to test four different control strategies to ramp up bioproduction. The models showed that enriching cells that stochastically overproduce the enzyme leads to substantial increases in betaxanthin production. The team later confirmed this prediction in fermentation experiments.

“We create a gene circuit that allows cells with higher stochastic enzyme expression to grow faster,” Zhang said. “These cells also become high betaxanthin producers, giving us more product overall.”

The work is part of ongoing efforts at the McKelvey EECE department to develop new biomanufacturing capabilities in support of a zero-waste circular economy. This includes the challenging task of keeping microbial “workers” focused on making renewable products.

A new technique which slashes the time taken to diagnose microbial infections from days to minutes could help save lives and open up a new front in the battle against antibiotic resistance, researchers say.

Engineers and clinicians from the UK and China are behind the breakthrough system, called AutoEnricher. It combines microfluidic technology with sophisticated analysis and machine learning to enable the diagnosis of pathogens in just 20 minutes.

The team’s paper, titled “Rapid culture-free diagnosis of clinical pathogens via integrated microfluidic-Raman micro-spectroscopy,” is published in Nature Communications.

How AutoEnricher works and its impact

The researchers show how they validated the effectiveness of their system on hundreds of real patient samples, delivering diagnoses with 95% accuracy even in samples with very low concentrations of pathogens. They also demonstrate how AutoEnricher can diagnose multiple simultaneous infections.

In the future, the system could be a valuable tool to tackle antimicrobial resistance, a rapidly-accelerating global threat to human health which caused five million deaths in 2019 and is projected to kill 10 million people a year by 2050.

Dr. Jiabao Xu of the University of Glasgow’s James Watt School of Engineering is one of the paper’s first authors. She said, “One of the major drivers of antibiotic resistance is the misuse or overuse of drugs to treat infections. Currently, it can take days or even weeks to culture microbes taken from patient samples in the lab to enable diagnosis.

“That means doctors often have to act urgently and use antibiotics to treat patients suffering from life-threatening conditions like sepsis or pneumonia without knowing for sure if they actually have a bacterial infection.”

The University of Glasgow’s Professor Jon Cooper, a corresponding author, said, “AutoEnricher advances personalized medicine by compressing diagnostic timelines and enhancing antimicrobial decision-making. This new instrument will help enable doctors to match the right antibiotic to an infection at the right time, improving patient outcomes while reducing the potential for the emergence of antimicrobial resistance.”

Technical details and validation of the system

The team’s system combines innovative hardware and software to enable a rapid two-stage diagnosis. In the first stage, the system uses a microfluidic device developed by the team to scrub human cells from samples of patients’ blood, urine or spinal fluid, leaving behind only pathogen cells.

In the second stage, the unique chemical fingerprint of the pathogen cells is identified using a technique called Raman spectroscopy. The fingerprint is then analyzed by a machine learning tool developed by the team. The tool, which was trained on a database of 342 clinical isolates from 36 species of bacteria and fungi, can provide a diagnosis by analyzing as few as 10 pathogen cells in less than 20 minutes.

The team validated AutoEnricher’s performance with the help of three hospitals in China, who provided samples from a total of 305 patients. The samples were also tested using conventional lab methods to culture the bacteria to enable diagnosis.

AutoEnricher’s diagnosis matched the conventional lab method’s outcomes 95% of the time, and also managed to pick out mixed infections which were missed by the lab culture tests.

Professor Wei Huang of the University of Oxford, a co-investigator on the project, said, “These are really encouraging results from the largest study of its kind conducted on real patient samples. We’ve shown that this single-cell approach to diagnosis can rapidly deliver remarkably accurate results, and even pick out multiple infections which are much harder to spot using conventional lab culture methods.”

Professor Huabing Yin of the University of Glasgow, the senior author of the paper, said, “The next step is to apply AutoEnricher to a much larger cohort of patient samples in a proper clinical study. We’re already working on the first steps towards making that happen, and we hope that AutoEnricher will make a real difference in addressing the spread of antimicrobial resistance in the years to come.”

There are hundreds of cell types in the human body, each with a specific role spelled out in their DNA. In theory, all it takes for cells to behave in desired ways—for example, getting them to produce a therapeutic molecule or assemble into a tissue graft—is the right DNA sequence. The problem is figuring out what DNA sequence codes for which behavior.

“There are many possible designs for any given function, and finding the right one can be like looking for a needle in a haystack,” said Rice University scientist Caleb Bashor, the senior author on a study published today in the journal Nature that reports a solution to this long-standing challenge in synthetic biology.

“We created a new technique that makes hundreds of thousands to millions of DNA designs all at once—more than ever before,” Bashor said.

How the CLASSIC technique works

The technique is called CLASSIC—an acronym for “combining long- and short-range sequencing to investigate genetic complexity.” It not only makes finding useful DNA designs (“genetic circuits”) much faster, but it also creates datasets of unprecedented scale and complexity—exactly what is needed for artificial intelligence and machine learning to be meaningfully deployed for genetic circuit analysis and design.

“Our work is the first demonstration you can use AI for designing these circuits,” said Bashor, who serves as deputy director for the Rice Synthetic Biology Institute.

CLASSIC could usher in a new generation of cell-based therapies, which entail the use of engineered cells as living drugs for treating cancer and other diseases. Demonstrating the approach in a human cell line also highlights its translational potential, since human cell-based therapies promise higher biological compatibility and the capacity to dynamically respond to changing disease states.

Kshitij Rai and Ronan O’Connell, co-first authors on the study, worked on the project during their time as doctoral students in the Bashor laboratory. Their work took four and a half years and involved “a lot of molecular cloning—cutting DNA into pieces and pasting it together in new ways.”

“We invented a way to do this in large batches, which allowed us to make really large sets—known as ‘libraries’—of circuits,” said Rai, now a recent doctoral alum about to embark on a postdoctoral fellowship at the University of Washington in Seattle.

The team also used two different types of next-generation sequencing (NGS) techniques known as long-read and short-read NGS. Long-read sequencing scans long stretches of DNA—thousands or even tens of thousands of bases—in one continuous pass. It is slow and noisy, but it captures the entire genetic circuit at once. Short-read sequencing reads only a few hundred bases at a time but does so with high accuracy and throughput.

“Most people do one or the other, but we found using both together unlocked our ability to build and test the libraries,” said O’Connell, who is now a postdoctoral researcher at Baylor College of Medicine.

Building and testing genetic circuits

The Rice team developed a library of proof-of-concept genetic circuits incorporating reporter genes designed to produce a glowing protein, then used long reads to record each circuit’s complete sequence. Each of these sequences was then tagged with a short, unique DNA barcode.

Next, the pooled library of gene circuits was inserted into human embryonic kidney cells, where they produced a measurable phenotype with some cells glowing brighter while others expressed a dimmer glow. The researchers then sorted the cells into several groups based on gene expression levels—essentially how bright (high expression) or dim (low expression) they were. Short-read sequencing was then used to scan the DNA barcodes in each group of cells, creating a master map linking every circuit’s complete genetic blueprint—its genotype—to its performance, or phenotype.

“We end up with measurements for a lot of the possible designs but not all of them, and that is where building the ML model comes in,” O’Connell said. “We use the data to train a model that can understand this landscape and predict things we were not able to generate data on, and then we kind of go back to the start: We have all of these predictions—let’s see if they’re correct.”

Rai said he and O’Connell first realized the platform worked when measurements derived via CLASSIC matched manual checks on a smaller, random set of variants in the design space.

“We started lining them up, and first one worked, then another, and then they just started hitting,” he said. “All 40 of them matched perfectly. That’s when we knew we had something.”

Implications for synthetic biology and AI

The long hours spent poring over bacterial plates, cell cultures and algorithms paid off.

“This was the first time AI/ML could be used to analyze circuits and make accurate predictions for untested ones, because up to this point, nobody could build libraries as large as ours,” Rai said.

By testing such vast numbers of complete circuits at once, CLASSIC gives scientists a clearer picture of the “rules” that determine how genetic parts behave in context. The data can train ML models to analyze, design and eventually predict new genetic programs for specific targeted functions.

The study shows that ML/AI models, if given the right amount of training data, are actually much more accurate at predicting the function of circuits than the physics-based models people have used up to this point. Moreover, the team also found that circuits do not have just one “right” solution, but many.

“This is akin to navigation apps: There are multiple routes to reach your destination, some highways, some backroads, but all get you to your destination,” O’Connell said.

Another takeaway was that medium-strength circuit components such as transcription factors, proteins that bind to specific DNA sequences and control gene expression, and promoters, short DNA segments upstream of a gene that act as its on/off switches, often outperformed strong or weak variants.

“Call it biology’s version of ‘Goldilocks zones’ where everything is just right,” Rai said.

The researchers say this combination of high-throughput circuit characterization and AI-driven understanding may be able to speed up synthetic biology and lead to faster development of biotechnology.

“We think AI/ML-driven design is the future of synthetic biology,” Bashor said. “As we collect more data using CLASSIC, we can train more complex models to make predictions for how to design even more sophisticated and useful cellular biotechnology.”

The collaborative effort and expert perspectives

Both Rai and O’Connell said the collaborative environment at Rice made the work really enjoyable despite setbacks. Also, working with teams from other universities was a key ingredient for success. This collaborative effort included Pankaj Mehta’s group in the Department of Physics at Boston University and Todd Treangen’s group in Rice’s computer science department.

“I think a big part of what we did in this project is to show that while the same individual parts might not have any spectacular function by themselves, if you put the right combination of things together, it gives you these dramatically better genetic circuits,” Rai said. “That holds true for science as well. And that was the best part of this project behind the scenes—all of us bringing our different skill sets together.”

To help put the achievement of this research project in context, James Collins, a biomedical engineer at the Massachusetts Institute of Technology who has helped establish synthetic biology as a field, pointed to early successes such as the genetic toggle switch—a synthetic circuit comprised of two genes designed to repress each other’s expression; and the repressilator—a circuit of at least three genes that form a negative feedback loop where each gene represses the next, as historic reference points for the discipline which has now, with the Rice scientists’ work, reached a new defining milestone.

“Twenty-five years ago, those early circuits showed that we could program living cells, but they were built one at a time, each requiring months of tuning,” said Collins, who was one of the inventors of the toggle switch. “Bashor and colleagues have now delivered a transformative leap: CLASSIC brings high-throughput engineering to gene circuit design, allowing exploration of combinatorial spaces that were previously out of reach. Their platform doesn’t just accelerate the design-build-test-learn cycle; it redefines its scale, marking a new era of data-driven synthetic biology.”

Michael Elowitz, whose foundational work in synthetic biology was recognized by a 2007 MacArthur Fellowship for his design of the repressilator, said that “synthetic biologists have dreamed of programming cells by snapping together biological circuits from interacting genes and proteins.

“However, there is a huge space of potential biological components and circuits, and this dream has remained out of reach in most cases. Bashor’s work demonstrates how we can systematically explore biological design space and make biological engineering more predictable. In the future, it will be exciting to generalize this approach to other interactions and components, bringing us closer to making cells fully programmable.”

A small revolution is happening in the fishing industry. Freshly frozen fish can now be thawed in a new way, and that means you will have access to super-fresh food from the sea—even if you live thousands of miles away.

As a child living in Northern Norway, I was often at the fish market. Grandpa would grunt and wrinkle his nose as he poked the fish and leaned forward to smell it. “When was this caught?” he’d ask the person who was standing at the ready with a sharp knife and an apron glistening with fish scales.

If the answer was more than two days ago, buying it was out of the question. Nothing is in more of a hurry than a dead fish.

“This is exactly what we have been working on!” says Anders Haugland, founder and CTO of Icefresh. He previously worked on concepts for defrosting fish as a researcher at SINTEF.

“People who are going to eat fish want it as fresh as possible, and we have to find ways to give it to them—even if they are a long way from the unloading dock. Often on the other side of the globe.”

The current method is to load the fish onto a plane, and hope for the best in getting it to the customer’s dinner table as quickly as possible. The countdown begins as soon as the fish are out of the water.

That scenario is how the process used to be—a race against the clock. But that’s not the only reason to make changes to the fish’s travel route to distant destinations. The researchers you will hear about have been working for a couple of decades to solve the crucial puzzle:

How can we ensure that the fish quality is super-fresh when it reaches the customer, and at the same time avoid a lot of food waste, climate emissions, and uncertainty around demand?

“Thawing fish might seem simple, but it actually involves advanced interactions between heat, air flow and raw material quality,” says Trond Andresen, a senior research scientist at SINTEF.

“This is precisely where SINTEF’s strength lies,” he says. “We can combine food technology with our in-depth expertise in heat transport and flow science. The adaptive process we are developing will allow the system to find the best way to thaw, regardless of the type of fish, the cut and packaging. I find it inspiring to see how theory and computer models can be turned into practical solutions that both improve quality and save energy and emissions.”

And although that might sound feasible, there was no shortcut as to how it could be done in practice, so frozen fish could “become fresh again.”

The race against the clock starts on the unloading dock

The first piece of the puzzle is Haugland, the researcher who went into depth on how we can thaw frozen fish in a way that actually makes it taste as fresh as when it came off the fishing boat.

“The overarching idea is that if we can have the fish as close as possible to the customer before the ‘freshness window’ expires, then it will be a win for everyone. To achieve that we have to stop time, in a way. And we do that with a freezer. But the challenge arises when you have to thaw the fish.

Freezing fish is good, old knowledge. But everyone knows that as soon as the fish has thawed on the kitchen counter, it is something completely different from a dock-fresh delicacy. So what the researchers did was look for a way to thaw the fish that allows it to retain all its fresh qualities.

“It’s possible to freeze something and then thaw it to optimal quality quite a while afterwards,” says Haugland. “This is done every day by people who work with in vitro fertilization.”

Our challenge was to be able to create a system that can accomplish the same thing with fish filets.

Many years and a lot of research later, the solution has arrived. The fish thaws on trays, in cabinets, with carefully calibrated air flow and temperatures. It may look a bit like an industrial bread oven, but it works the opposite way.

“We figured out the actual process of thawing fish in a good way a while ago. But it’s not enough to thaw it well, we also have to put this into use and reach the customer. A good product is useless without a place in the value chain for the raw material,” says Haugland.

He laughs a little because it took a few attempts to figure out how the thawing cabinets could be useful.

The trip to China—thawing trouble on two wheels

“Around 2010, the big idea was: We have the technology, we’ve managed to create a functioning thawing device in Norway—we can solve this! But Norway and the local market were too small—or maybe just too complicated? The solution was to turn the tables: Buy the very best, super-quality salmon, freeze it, and send it straight to China.”

Haugland says that the plan was to set up “thawing hubs” in China, and the salmon was launched as Icefresh via the online store Alibaba. The concept was as fresh as it was optimistic: Customers ordered online, and the freshly thawed fish would be delivered to their door by bike couriers on scooters, equipped with electric cooler bags. Brilliant, right? A kind of Foodora for fish. It might have worked out well.

But then, in the middle of this salmon dream, geopolitics threw a spoke in the wheel of the project. Liu Xiaobo received the Nobel Peace Prize, and suddenly Norway and Norwegians were about as popular in China as a smelly old salmon.

“As if that weren’t enough, it turned out that the high-tech bike operators were small, family-run companies with less than optimal coolers, to put it nicely.

So the online competition to sell fresh fish became a “race to the bottom” on price—regardless of quality. The thawing team had to find new markets. And more partners. The options looked pretty slim for a while, but on Christmas Eve 2021, Roger Hofseth signed a napkin agreement with the company—one that could perhaps be described as a small Christmas miracle for all of them.

Good enough for the fresh product counter

Who is the new partner in this project? The seafood group Hofseth may not be as well-known as Salmar and Lerøy to most of us, but they sell salmon and trout worth several million euros annually to their main market in the U.S.. Roger Hofseth says that IceFresh is a crucial addition to optimizing the value chain.

“Up until now, we have focused on frozen products, and had therefore already cut out air freight,” he says. “IceFresh gives us a fantastic opportunity, because we can now sell the “refreshed” products in the fresh produce counter with the good fresh quality that we created in Sunnmøre. The technology offers so many advantages that we’re convinced that the entire industry will follow suit,” he says.

The American dream: Everything is bigger over there

“We built some cabinets at Rustfrie Bergh in Dokka municipality and took one across the pond to show that it worked,” says Haugland.

First, the team went to a trade fair in Boston, where they experienced more learning than success. The next stop was Florida, where the team had made contact with one of the larger food chains.

“We were prepared for the introduction of new technology and routines in the value chains for fish at the grocery chains to be challenging. And even though we could show major improvements, the interest in demonstrating solutions that would change established working methods on a commercial scale was limited,” Haugland said.

But a few months later, another exciting supplier came on the scene. They wanted a comprehensive full-scale test, which was carried out in late summer 2024.

We sent out 230,000 portions of thawed salmon, and the same amount of fresh. Then the end users—the chefs and customers—were asked about the quality. The result was a resounding success, which confirmed the logistical gain: by buying, freezing and transporting the salmon by boat, high-quality fish could be thawed at the earliest two days before it is available for the customer.

This timing ensures a freshness that even a picky grandfather from Northern Norway would accept, and it prevents food waste.

Go big or go home

The large customer found the existing cabinets too cumbersome, so they issued an ultimatum. They wanted a thawing plant ready to go in Chicago before Christmas 2024.

Since neither the technology nor the financing for the future thawing tunnels were in place, the plant had to start with the classic, smaller thawing cabinets. Six of these cabinets were immediately shipped by container, and the hunt for an operational partner began.

After rebuilding and approving the premises, and recruiting people to run the thawing operations, they managed to make the very first delivery of freshly thawed salmon on 23 December 2024. Another little Christmas miracle for the thawing team.

Now things were moving fast. During this process, it had become clear that extensive research and development would be required to set up tunnel-based thawing plants.

SINTEF became more closely linked to the project at that point, establishing an IPN (Innovation Project for the Industrial Sector). The thawing team had now become a powerful consortium consisting of IceFresh, MMC First Process, Hofseth International and SINTEF.

The players joined forces to develop thawing tunnels, and through the project, which was named REFRESHING, it secured support from the Research Council of Norway. Now they could combine their expertise in seafood processing, food science, thermodynamics, fluid flow and system optimization.

In other words, everything you need to obtain the taste of fresh salmon from frozen filets.

“The goal is to develop groundbreaking technology for the large-scale thawing of fish, which safeguards all aspects of the fish’s quality combined with maximum energy efficiency and productivity in the thawing process,” says Andresen.

From small cabinets to large tunnels

“It’s one thing to create several large thawing cabinets, but quite another to create large systems that can thaw 250 000 portions a day and that will provide the same quality. At the same time, having such a large system to work with gives us more data and a better opportunity to create even more benefits.

A thawing plant will open in Miami in 2026, and the one already established in Los Angeles will be upgraded to the tunnel solution as the first full-scale pilot system, financed by Innovation Norway and equity.

Time to get salmon out to sea again?

Despite the progress, achieving coherence in the value chain is still a challenge. One of the great paradoxes of Norwegian exports is that salmon is flown to its destinations. Every single day, planes loaded with hundreds of tons of fish take off from Gardermoen and other airports. To the U.S.. To Asia. And to markets that are so far away from the fish’s origin that it is almost absurd to think about.

If all this fish were instead frozen, transported by freighter and then thawed, we would save six million tonnes of CO₂ emissions a year. That is three times the annual emissions from Mongstad, Norway’s largest oil refinery.

“The benefits of shipping fish this way are so great that this change is bound to happen no matter what,” says Hofseth. “When we stop flying fish, the footprint of the seafood industry will be dramatically reduced.”

He says the project now has to build capacity quickly, so that large volumes can be realized in the markets. “A lot is happening in a short amount of time, and the expertise and the thawing capacity have to be shared with the entire industry,” he says.

“Seafood currently accounts for only 2% of the world’s protein intake. When more of the leading players start using thawing hubs, the quality will increase—and along with it people’s seafood consumption. Cheaper products, less waste, a smaller footprint and better quality are win-wins for everyone.

He paints a picture of thawing hubs around the world, which he believes will make airfreighting fish something we’ll come to read about in history books, and fresh fish something that everyone has access to. From then on, it will only be your own cooking skills that will determine whether the salmon turns into a delicious gourmet meal or not.

Infection with the pathogenic yeast fungus Candida auris (C. auris) can wreak havoc on the health of hospital patients and residents of nursing homes, especially those who are already weakened by other illnesses. The pathogen easily spreads and colonizes surfaces and objects where it can survive for weeks to months, and is often resistant to standard disinfectants.

C. auris infections are especially problematic for patients who receive organ transplants or chemotherapy, and whose immune systems are compromised, such as by HIV. Infections also are a threat to patients who are at high risk of infection, such as those requiring invasive devices, like breathing or feeding tubes, or different types of catheters.

Once C. auris infections reach the bloodstream or vital organs, they become life-threatening with symptoms and immune reactions similar to those caused by bacterial and viral pathogens.

Although C. auris infections, in principle, can be treated with several antifungal medications, strains of the pathogen that have developed antimicrobial resistance (AMR) against those drugs have emerged fast and become a difficult challenge for hospital physicians. This means that some infections have to be treated with a different drug than the initially chosen antifungal agent or, in the worst-case scenario, are impossible-to-treat with any of the available drugs, which, if still administered, pose an unnecessary additional burden on patients’ bodies.

“Clinicians need a much more effective diagnostic approach to accurately quantify the abundance of the pathogen in patients and assess its antifungal resistance in order to better respond to C. auris infections in their patients and help prevent future hospital-associated outbreaks,” said Justin Rolando, Ph.D., a first author on a new study that addresses this challenge head-on.

“Current diagnostic methods for detecting C. auris are too costly, slow, and dependent on complex equipment and trained personnel in order to effect real change.”

The new study offers a solution to this problem with a new precision diagnostic approach that, for the first time, enables fast and accurate quantification of C. auris strains from easily obtained swab samples, as well as the quantification of AMR-causing mutations in fungal populations with mixed antifungal susceptibility.

The findings are published in Nature Biomedical Engineering.

The next-generation test builds on previous diagnostic accomplishments of the groups of Wyss Institute Core Faculty members David Walt, Ph.D. and James Collins, Ph.D., who led the effort, and was greatly facilitated by the team’s collaboration with the Wadsworth Center Mycology Lab at New York State Department of Health, which provided a first cohort of patient samples (surveillance swabs) for the team’s initial technology validation.

The research team integrated SHERLOCK technology, a CRISPR-based diagnostic method pioneered by Collins’ group that allows the detection of pathogen-derived (or other) nucleic acid sequences with single nucleotide precision with ultra-sensitive single-molecule microarray technology advanced in Walt’s group.

By monitoring the development of finely tuned fluorescent signals produced by thousands of parallel single-molecule assays in real-time, and analyzing the signals using a machine learning-based artificial intelligence method, the team created a fast and quantitative approach, named dSHERLOCK (short for digital SHERLOCK), that measures the degree of fungal colonization of C. auris in patient samples and pinpoints the presence of mutations that cause specific antimicrobial resistances (AMRs).

A new case for SHERLOCK

In 2019, after having experienced several outbreaks of C. auris infection caused by strains that had become treatment-resistant, the NY State Department of Health released an urgent call to accelerate diagnostic developments that could help control future outbreaks.

Collins, along with co-authors Helena de Puig, Ph.D. and Xiao Tan, M.D., Ph.D., submitted a proposal to leverage the group’s SHERLOCK system for the cause.

Co-first author Nicole Weckman, Ph.D., who joined the team as a postdoctoral fellow in 2020, then took a deeper dive into CRISPR technology to design C. auris-detecting assays and started to collaborate with Rolando and other members of Collins’ and Walt’s groups with the common aim to turn the detection system into a quantitative and clinically useful diagnostic tool.

Using dSHERLOCK, the researchers were able to reliably detect C. auris in swab samples which they obtained from their collaborators at the Wadsworth Center. The assay is completed within 20 minutes and can accurately quantify how much of the pathogen the samples contained within 40 minutes.

Current clinical practice requires that samples obtained from patients in hospitals are sent to one of seven central laboratories, like the Wadsworth Center Mycology Lab, whose process to determine the presence of the pathogen and AMR can take up to a week, while infected patients need to be treated immediately.

Importantly, by tweaking the CRISPR-mediated detection mechanism, the researchers managed to amplify C. auris targets that contained mutations associated with AMR and showed these two common antifungal drugs displayed different “kinetics.”

According to Weckman, who is now an Assistant Professor and Paul Cadario Chair in Global Engineering at University of Toronto, dSHERLOCK’S single-molecule detection assays are designed such that positive fluorescent signals produced from distinct targets are generated at different rates.

This allowed the team to identify sequence-specific fluorescence signatures that corresponded to defined AMRs against the often-used azole and echinocandin antifungal drugs. They were able to trace several of these signatures in an individual sample, which is key to optimizing treatments since existing diagnostics only pick up one strain of C. auris in an all-or-nothing fashion, preventing them from giving true guidance.

Devising digital diagnostics

Rolando, Weckman and the team further streamlined the assay’s reaction conditions to greatly simplify its multistep process, basically converting it into a “one-pot-reaction” that proceeds autonomously from start to finish. But to realize dSHERLOCK’s full potential, they needed to enhance its usefulness with a computational analytical pipeline that was spearheaded by co-first author Anton Thieme, who had joined Walt’s group as a master’s student at the time of the study.

“One of our microarrays contains about 18,000 individual compartments, many of which contain a single C.auris target molecule—essentially the 1s in ‘digital’ SHERLOCK. Performing dSHERLOCK assays across all compartments provides us with an extraordinarily large amount of fluorescent data that represent the pathogen’s presence, extent of fungal infection, as well as the pathogen’s genetic variability,” said Rolando.

Thieme added that “translating these complex data into clinically actionable results is crucial. We developed a tailored computational solution that creates output that can be easily interpreted by trained hospital staff,” said Thieme.

“The machine learning algorithm that we devised decodes the developing fluorescence signatures in dSHERLOCK assays and determines the presence and quantity of both the pathogen and specific AMR strains.”

“The capabilities that we are introducing with dSHERLOCK satisfy the major clinical requirements for a next-generation assay to rapidly identify and quantify the C. auris burden in easily obtained patient samples and produce a quantitative snapshot of the AMR landscape in individual samples,” said Wyss Founding Core Faculty member and co-senior author Collins.

“This has not been possible using previous diagnostic methods and is a technological feat that, in addition to CRISPR engineering, required us to deeply integrate the SHERLOCK technology with the Walt group’s cutting-edge single molecule detection technology and a tailored machine learning approach.” Collins is also the Termeer Professor of Medical Engineering & Science at MIT.

The other senior author, Walt, who leads the Wyss Institute’s Diagnostics for Human and Planetary Health platform, highlighted, “Through this convergence of breakthrough technologies initiated by the pull of an acute clinical need, we engineered a compelling solution.

“But the dSHERLOCK platform has a much broader utility beyond the C. auris threat: by allowing us to refit the specifics of the CRISPR-based detection machinery, it can be relatively easily adopted to detect, quantify, and characterize multiple other pathogens that pose serious health problems. This is exactly what we are striving to do at the Wyss’ Diagnostics platform.”

Walt is also the Hansjörg Wyss Professor of Biologically Inspired Engineering at Harvard Medical School and Professor of Pathology at Brigham and Women’s Hospital in Boston.

“This study beautifully shows the power of collaboration at the Wyss Institute and how disparate cutting-edge technologies can converge to solve pressing unmet medical needs that could have a huge impact on patients and our health care system. The potential ripple effects of dSHERLOCK technology can’t be overestimated,” said Wyss Founding Director Donald Ingber, M.D., Ph.D.

Ingber is also the Judah Folkman Professor of Vascular Biology at Harvard Medical School and Boston Children’s Hospital, and the Hansjörg Wyss Professor of Biologically Inspired Engineering at Harvard John A. Paulson School of Engineering and Applied Sciences.

Genetic disorders occur due to alterations in the primary genetic material—deoxyribonucleic acid (DNA)—of an organism.

Transthyretin amyloidosis (ATTR) is a progressive disorder involving amyloid deposits of misfolded transthyretin (TTR) proteins. The deposits, mainly affecting the heart and the nerves, can lead to symptoms like heart failure and neuropathy. While one of its two major forms is associated with age, the other one is hereditary, resulting from destabilizing mutations in the TTR gene.

The therapeutic efficacy of suppressing TTR production has been clearly demonstrated. Although ribonucleic acid (RNA) interference-based drugs can reduce TTR production, they require long-term administration and do not provide a curative treatment.

Advances in gene-editing approaches

Currently, several gene-editing strategies are being utilized to precisely alter the DNA, correcting the mutations or deleting the harmful genetic sequences. These approaches offer enhanced precision and can completely cure genetic disorders. Clustered regularly interspaced short palindromic repeats (CRISPR) refer to the small fragments of viral DNA that are stored by the bacteria as a part of their defense mechanism.

CRISPR–Cas9 is a revolutionary gene-editing tool, adapted from this bacterial immune system, which has been widely explored for its clinical applications in recent times. While the CRISPR–Cas9 shows promising results in developing revolutionary therapies, it has certain limitations, including unintended DNA cuts.

Exploring the CRISPR–Cas3 system

Recently, a group of scientists from Japan, led by Professor Tomoji Mashimo and Dr. Saeko Ishida from the Institute of Medical Science, The University of Tokyo, Japan, evaluated the efficacy of the CRISPR–Cas3 system in safely achieving a permanent reduction of TTR production through genome editing of the TTR gene.

“Genome editing holds the unique potential to correct inherited disease-associated genetic abnormalities. We wanted to see if the CRISPR–Cas3 system could be developed as an efficient therapeutic genome-editing tool,” says Prof. Mashimo, discussing his motivation for the study.

The work is published in the journal Nature Biotechnology.

How CRISPR–Cas3 differs from Cas9

The CRISPR–Cas3 system has fundamental structural and functional differences when compared to the CRISPR–Cas9 system. In CRISPR–Cas9, a small fragment of RNA, another genetic material, is used as a guide. This guide RNA (gRNA) binds to the target DNA sequence, and the Cas9 protein bound to the gRNA, acts like a molecular scissor and cuts the DNA.

However, a multiprotein cascade complex is involved in the CRISPR–Cas3 system, which acts like a guide for the associated Cas3 helicase–nuclease enzyme, which shreds large DNA regions unidirectionally. This long-range degradation strategy is different from the precise double-strand break technology seen in the CRISPR–Cas9 system.

As TTR is mainly expressed in the liver, the study aimed to understand the efficacy of CRISPR–Cas3 in controlling hepatic TTR expression. A mouse model of ATTR and a lipid nanoparticle (LNP)-based delivery system were used for the research. Results showed that the CRISPR–Cas3 system can induce reliable, extensive deletions of the TTR gene.

“Through CRISPR RNA optimization, we achieved around 59% editing at the TTR locus in our in vitro experiments. In a mice model, a single LNP-based treatment helped us to achieve more than 48% hepatic editing and reduced serum TTR levels by 80%,” explains Prof. Mashimo.

This system did not induce indels at the off-target sites, which is considered a major limitation for the CRISPR–Cas9 system.

Potential impact on genetic therapies

The findings of this study can influence societal perspectives on genetic therapies by highlighting a safer alternative to CRISPR–Cas9, as it avoids the risk of generating unintended, potentially harmful mutant proteins. With further optimization and safety evaluation, this CRISPR–Cas3 can be established as a new and safer platform for genome-editing-based therapies, providing patients with durable, possibly one-time treatments that directly address the root genetic causes of their conditions. This can ultimately improve both life expectancy and quality of life for many individuals.

“In the coming years, this technology could lead to clinical applications not only for ATTR, but also for other currently incurable inherited diseases,” explains Prof. Mashimo.

Cilia are micrometer-sized biological structures that occur frequently in nature. Their characteristic high-frequency, three-dimensional beating motions (5–40 Hz) play indispensable roles inside the body.

In the human brain, ciliary motion is crucial for neuronal maturation; in the lungs, it is essential for clearing the respiratory tract; and in the reproductive system, cilia transport gametes. Conversely, impaired or damaged cilia can lead to neurodevelopmental disorders, respiratory dysfunction, infertility, or malformations of the embryo.

Scientists from the Physical Intelligence Department at the Max Planck Institute for Intelligent Systems (MPI-IS) in Stuttgart, from Hong Kong University of Science and Technology and Koç University in Istanbul created artificial cilia from hydrogel, which they can move individually or in groups applying an electric field.

Their work, published in Nature, is titled “3D-printed low-voltage-driven ciliary hydrogel microactuators.”

Each microactuator or microrobot is only 18 micrometers in length with a diameter of around 2 micrometers, nearly as small as real cilia. The scientists placed hundreds of their cilia on a flexible foil-like substrate that contains built-in electrodes.

Around each cilium, they placed four small electrodes. When the electrodes are switched on, they create an electric field that causes ions inside the hydrogel to move. This controlled ion migration is what sets the cilia into motion.

Depending on how the scientists power the electrodes, the hydrogel cilia can bend or spin. Turning on the electrodes on one side pushes the ions in that direction, causing the cilium to bend toward that side. To make the cilium rotate, the four electrodes are turned on in sequence, which makes the ions move in a circular path. The cilium then follows this motion and rotates smoothly in 3D.

“At small scales, using electrical signals to drive ion movement for actuation has proven to be a highly effective and efficient method. For example, the human body relies on electrical muscle signals to control the distribution of ions in muscle tissue, which then generates motion,” says Zemin Liu, who is the first author of the study.

“Inspired by this principle, we developed micrometer-scale ion-driven hydrogels. Just like human muscle, these hydrogels move when electrical signals stimulate the ions inside them. In our work, we use only 1.5 volts, which is below the electrolysis threshold in aqueous environments and is completely safe, for instance, inside the human body.”

To build the tiny arrays, the scientists use a method called Two-Photon Polymerization, also known as 2PP. The team printed the hydrogel cilia nanometer small layer by layer to optimize the hydrogel network structure and actuation performance.

“The fluid inside our hydrogel moves fast because we created tiny, nanometer-scale pores throughout the material. These pores act like miniature highways that let the fluid flow more quickly and in greater volume, which produces stronger and more effective motions,” says Wenqi Hu, who led the Bioinspired Autonomous Miniature Robot Group at MPI-IS and who is now an Assistant Professor at The Hong Kong University of Science and Technology.

“With our fabrication technique, even a very low voltage is enough to create a strong electric field, which pushes the ions to move rapidly. Thanks to both the pore structure and the strong electric field, our artificial cilia can react extremely fast.”

The team tested their microrobotic cilia more than 330,000 times. The tiny structures showed almost no signs of wear. This number of cycles corresponds to about a full day of continuous beating at 5 Hz—roughly the natural working lifespan of real biological cilia. The researchers also demonstrated that their artificial cilia could operate in different types of fluids, including biologically relevant liquids, such as human serum and mouse plasma.

“In the past, researchers could only observe how natural cilia behave. Now we finally have a robotic platform that lets us study cilia in action: how they move, how they work together as a collective group, and what kinds of fluids they can transport or mix,” says Metin Sitti, who led the Physical Intelligence Department at MPI-IS and who is now President of Koç University in Istanbul.

“These hydrogel cilia could one day be used in biomedical settings to help restore or replace damaged cilia. As an important step forward in microactuation technology, they also open up fresh opportunities for designing miniature robotic systems, such as the flapping micromachine we demonstrated in this work.”

What could this cilia-technology enable in the real world? The research paves the way for several promising future applications:

• A new platform for studying how biological cilia work: Researchers can now use these artificial cilia arrays to carefully test how natural cilia move, how they collectively work together, and how they help with important tasks, such as development, sensing the environment, and moving fluids.
• Potential medical applications: The soft, controllable hydrogel cilia may inspire future therapeutic devices designed to help replace or support damaged cilia in the human body, especially with diseases where natural cilia no longer function properly in our respiratory and reproductive systems and brain ventricles.
• A foundation for next-generation microrobots and microdevices: The fast, low-voltage actuation showcased in this work could be used to design new types of tiny robots, microfluidic tools, and advanced engineering systems at the small scale.

An innovative product with the potential to replace polymers used in soil fertilizers is being developed in São Carlos in the state of São Paulo, Brazil.

The innovation consists of starch sachets reinforced with nanoparticles that contain powdered or granulated fertilizers. Starch is a biodegradable polymer, and in sachet form, it can be filled with a mixture of various nutrients that are essential for crops.

This work is enabled by a collaboration between the National Nanotechnology Laboratory for Agriculture (LNNA) of EMBRAPA Instrumentation, one of the decentralized units of EMBRAPA (the Brazilian Agricultural Research Corporation), and the Federal University of São Carlos (UFSCar).

“There are essential and irreplaceable nutrients for plants, such as the trio of nitrogen, phosphorus, and potassium [NPK]—usually applied to the soil in the form of highly soluble potassium chloride salt. Farmers generally apply a large amount to the field to ensure absorption. However, the cultivated plant cannot immediately absorb all of this fertilizer,” explains chemist João Otávio Donizette Malafatti.

“This excess becomes an economic loss and can contaminate the surrounding environment. The sachets aim to control the release so that the plant feeds gradually. In this sense, we modulate different types of sachets depending on the nutrients we’re going to add inside them.”

Malafatti is the first author of the resulting article published in the Journal of Inorganic and Organometallic Polymers and Materials. She was supervised by EMBRAPA Instrumentation researcher Elaine Cristina Paris. Paris is a researcher in the Graduate Program in Chemistry (PPGQ) at UFSCar.

Malafatti developed starch sachets that were processed with urea and citric acid and reinforced with zeolite that was rich in copper ions. Zeolite is a porous mineral with a high adsorption capacity for ions, such as copper.

“Starch is a material that’s susceptible to degradation,” she says. “Therefore, a formulation is needed so that the sachets preserve their characteristics until they reach their destination in the soil. In this process, the copper ions present in zeolite have a dual function: They have great antimicrobial properties, both for fungi and bacteria, controlling the growth of microorganisms, and, in addition, they’re sources of mineral micronutrients, which are subsequently absorbed by the roots.”

In the study, the presence of copper controlled the growth of the fungus Alternaria alternata, Malafatti explains: “The goal is to strike a balance between preserving the sachets in the final application in the soil and subsequently making their contents available to the external environment.”

Resistance and stability

According to Malafatti, biodegradable polymers and starch matrices still must overcome certain challenges compared to similar petroleum-derived products, especially regarding mechanical resistance and stability over time. Therefore, the research seeks to develop formulations capable of improving these properties.

In the study, the group evaluated various zeolite concentrations and found that a maximum value of 3% relative to starch significantly increased mechanical resistance. Above that limit, however, the particles tend to agglomerate, which weakens the film. In addition to releasing nutrients, zeolite fulfills another function during periods of drought.

“It can store water because it’s very porous and hydrophilic, meaning it has a high affinity for water molecules,” Paris explains. The researcher compares the sachet to a tea bag to which granular fertilizer is added.

Versatile sachets

According to the scientists, the sachets are versatile because they increase the solubility of stored fertilizers and control the release of highly soluble sources. This reduces fertilizer loss through aerial dispersion and leaching from rainfall.

In previous work supervised by Paris, UFSCar doctoral student Camila Rodrigues Sciena had investigated a fertilizer candidate: hydroxyapatite, a phosphorus source. The goal was to increase its solubility. The scientists discovered that acidifying the medium using pectin in the starch sachet composition increased solubility when combined with nanoparticulated hydroxyapatite.

“With water, the starch becomes gelatinous and holds the fertilizer in the soil available for the plant, so that future losses due to rain or wind can be minimized. The goal is to reduce percolation [the passage of water through porous material, causing the extraction of compounds] and the dragging of particulate fertilizer inside the sachet,” says Sciena.

In the case of Malafatti’s work, the group is working with a highly soluble fertilizer that quickly dissolves when it comes into contact with water.

“In this case, the intention is for the fertilizer to be released gradually, avoiding losses due to leaching or air dispersion. It’s a sustained release, which will depend on the formulation of the sachets,” says Paris.

To test the nutrient release capacity, the sachets were kept in an aqueous medium for 30 days. The experiment demonstrated the partial release of copper ions (7 mg L^-1) and urea (300 mg L^-1). The hydrophilic properties of the sachets favored contact with the external environment, helping water permeation and potassium chloride release.

“The sachets obtained could minimize losses in fertilizer application, in addition to controlling the amount of nutrient that would be in contact with the soil,” say the authors.

Solubility and cytotoxicity tests were also performed on copper zeolite to determine its properties and potential interaction with the environment after release from the sachets. Cytotoxicity tests performed on cress root growth suggest 92% germination viability after one hour of exposure to zeolite, indicating its potential use in agriculture.

To verify copper availability, solubility tests were performed in water (neutral pH) and citric acid. Desorption efficiency, or the process by which a substance is released from the mass or surface of another substance, increased the availability of copper in an acidic environment, rising from 5% to 45% of the expected total.

Costs and customization

According to Paris, ongoing research is seeking alternatives to reduce the cost of processes and materials for the prolonged release of fertilizers.

“Starch is a promising raw material, although the addition of extra components can influence the final cost of the material. In Malafatti’s work, we didn’t use starch from other sources, such as waste, for example. It’s commercial starch,” says the researcher. “But for soil fertilization, it isn’t necessary to use high-purity starch, such as that used in the food industry. So, the goal is to try to make it as cheap as possible so that agribusiness can incorporate it. Thus, the sachets have greater potential to be effectively marketed, contributing to technological advancements in agriculture.”

Another advantage is that the added fertilizer does not affect the formulation or format of the sachet during processing.

“Any granular or particulate fertilizer can be inserted into the sachet, which is another positive point for its incorporation by the industry,” Malafatti points out. Additionally, the sachet eliminates the need for agricultural workers to handle fertilizers in particle form directly.

According to Paris, the technology is still in the laboratory phase. Initial applications would be in landscaping, gardening, hydroponics, and greenhouses. For large-scale agricultural production, however, optimizations in scaling and economic viability are necessary, which are the next steps planned by the group.

Sciena points out that the sachet can be used for different crops.

“Grapes have different needs than tomatoes, for example. It’s a form of customized fertilization where you can adapt the mixture of nutrients and the type of sachet. One can be more acidic to enhance the solubilization of poorly soluble fertilizer, while another can be less acidic to slowly solubilize soluble fertilizer,” she summarizes.

The agricultural industry may be producing more food than ever before, but it is also damaging the climate, harming the soil and eroding biodiversity.

A team of researchers from the PhenoRob Cluster of Excellence at the University of Bonn has published a paper in the journal Agricultural Systems that explains the key role technological innovations will need to play to make agriculture sustainable in the future and why these will have to be accompanied by shrewd policies and new business models.

What the research is about

Humanity is now producing more food than at any time in its history. The agriculture sector urgently needs to be made more sustainable, however, because the solutions that have increased its productivity throughout the past few centuries are also causing environmental problems in the form of climate change, biodiversity loss, soil degradation and water pollution.

One of the main reasons for this is that people are seeking individual solutions for each problem rather than actually planning the innovation process. The result is that these isolated solutions never produce any new systems in the agriculture sector except under the guiding hand of policymakers.

YA vision for a more sustainable agricultural system

Instead of numerous individual innovations, we need a unified system of innovation that’s geared toward a vision shared by the whole of society. The first thing to do is decide what sustainable agriculture needs to look like, which will determine suitable technologies, business models and policymaking rules.

It’s important to get all the stakeholders on board and consider both opportunities and risks at an early stage in order to foster areas of potential and avoid negative side effects.

In a paper published in the journal Agricultural Systems, researchers indicate how such a rot-and-branch transformation of Europe’s agriculture industry can succeed.

The biggest challenges facing agrotechnology

By far the biggest challenge is to make sustainable agricultural technologies attractive enough for farmers to invest in them. There’s a lot that can be done from a purely technical perspective, but there’ll never be widespread take-up of new technologies if they’re less profitable than existing ones while also being risky to boot.

In other words, policymakers need to create the right environment: strengthening environmental regulations that make environmentally harmful technologies less profitable, increasing the agri-environmental payments that create a financial incentive for green entrepreneurship and forming broad coalitions—especially partnerships with industry—to create new markets and leverage synergy effects.

How policy guidelines need to change

Policy should be made more ambitious but also more straightforward. There’s great discontent among farmers, because there’s too much micromanagement and red tape. Society wants more sustainability, but not at the expense of affordable food. European countries are currently having to invest large sums in a great many areas, such as defense and the energy transition.

So we need policies that are extremely effective while also delivering value for money. And the timing is propitious, because there’s now some high-quality underlying data available—from satellite measurements, drones and sensors on board agricultural machinery—coupled with advances in machine learning and causal inference. It’s never been easier to get a faster and more comprehensive idea of what works, what doesn’t and why.

Five risks of smart farming explained

The first risk is the widespread belief that digital, automated agriculture is automatically more environmentally friendly. Although smart farming offers a lot of opportunities, the innovations it brings can also harm the environment depending on how they’re used. The second risk is that power and profits get concentrated in the hands of a few large corporations.

New technologies could leave small businesses facing a tougher time and accelerate structural change in the agriculture sector. Third, there’s the danger of poor or misguided policymaking. If they’re guided mainly by what’s easy to measure rather than what’s really important, then policy steps might miss the mark.

The fourth risk is that new technologies don’t work as intended. Innovation needs experience and learning, and mistakes will sometimes happen. Plus, technical systems—such as AI-powered robots—can also make the wrong decisions. The fifth risk, and one that’s particularly important, is that technical solutions squeeze out other necessary changes.

New technologies aren’t sufficient on their own to solve the major environmental problems facing agriculture. Less attention risks being paid to mindful consumption or other changes to people’s behavior, for example, if too much hope is being invested in technology.