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ScienceDaily

Science News

Date:
January 12, 2017
Source:
University of California – San Diego
Summary:
Biologists have documented for the first time how very large viruses reprogram the cellular machinery of bacteria during infection to more closely resemble an animal or human cell — a process that allows these alien invaders to trick cells into producing hundreds of new viruses, which eventually explode from and kill the cells they infect.
FULL STORY

Cryo-electron tomography shows how the bacterial cell is reorganized to resemble a more complicated plant or animal cell with a red nucleus-like compartment and ribosomes, the smaller light blue structures. The reproducing viruses appear with dark blue heads and pink tails.
Credit: Image by Vorrapon Chaikeeratisak, Kanika Khanna, Axel Brilot, Katrina Nguyen

Biologists at UC San Diego have documented for the first time how very large viruses reprogram the cellular machinery of bacteria during infection to more closely resemble an animal or human cell — a process that allows these alien invaders to trick cells into producing hundreds of new viruses, which eventually explode from and kill the cells they infect.

In a paper published in the January 13 issue of Science, the researchers conducted a series of experiments that allowed them to view in detail what happens inside bacterial cells as the invading viruses replicate.

“Scientists have been studying viruses for a hundred years, but we’ve never seen anything like this before,” said Joe Pogliano, a professor of molecular biology who headed the research team. “Every experiment produced something new and exciting about this system.”

Viruses that infect bacteria, also known as bacteriophages, are some of the most numerous entities on earth.

“We chose to study a family of unusually large bacteriophage and to apply cutting edge methods to watch their replication in unprecedented detail,” said Kit Pogliano, a professor of molecular biology who participated in the study.

Joe Pogliano and his colleagues found that shortly after bacteriophages infect bacteria, they destroy much of the existing architecture of the bacterial cells, including bacterial DNA, then hijack the remaining cellular machinery. The viruses then reorganize the entire cell into an efficient, centralized factory to produce the next generation of viruses.

“This factory and the surrounding arrangement of the infected cell are remarkably similar to the organization seen in plant and animal cells,” said Pogliano.

Bacteria lack many of the specialized structures that compartmentalize cellular processes in plant or animal cells, which biologists call “eukaryotic” cells. Bacteria, for example, lack an enclosed nucleus, which contains genetic information and acts as the control center of the cell.

But Vorrapon Chaikeeratisak, a postdoctoral fellow, and Katrina Nguyen, a graduate student in Pogliano’s laboratory, found that invading viruses organize the structures within bacteria to mimic those found in eukaryotic cells.

Using fluorescent microscopy, the two biologists discovered that as viruses replicate within bacterial cells, they build compartments to separate the different processes going on during infection.

“These compartments enclose all the viral DNA, just as a nucleus does in a plant or mammalian cell,” said Chaikeeratisak, the first author of the paper. “DNA processes, like replication or transcription, occur inside the compartment while proteins are produced outside the compartment.”

Elizabeth Villa, a professor of chemistry and biochemistry at UC San Diego, and David Agard, a professor of biochemistry and biophysics at UC San Francisco, used a specialized technique, called “cryo-electron tomography,” to produce images of the processes that Chaikeeratisak and Nguyen initially discovered at extremely high magnification.

Those pictures showed viral offspring being assembled around the nucleus-like compartment in the bacterium. Eventually, these new viruses burst the cell open and spread out to infect neighboring cells.

“These observations of viral manipulation of a cell are completely unexpected, as no bacterial virus has been seen to reorganize a cell in so drastic a manner,” said Pogliano. “The restructuring of a simple cell to resemble an existing, more complicated system blurs the line between simple bacterial cells and those of ‘higher’ organisms, such as plants and animals.”

Could this be how multicellular organisms evolved? One existing theory, called “viral eukaryogenesis,” suggests that the first eukaryotic cell was created when a large virus took over a bacterium. Eventually, the bacterium and virus formed a compound cell, in which the virus evolved into the nucleus.

“It may be too early to know if this particular virus is an intermediate step in the transition from bacteria and viruses to multicellular eukaryotes, but this discovery could broaden knowledge about the origins of life as we know it,” said Pogliano.

The study was supported by grants from the National Institutes of Health (GM031627, GM104556, GM57045, 1DP2GM123494-01) and the Howard Hughes Medical Institute.


Story Source:

Materials provided by University of California – San Diego. Note: Content may be edited for style and length.


Journal Reference:

  1. Vorrapon Chaikeeratisak, Katrina Nguyen, Kanika Khanna, Axel F. Brilot, Marcella L. Erb, Joanna K. C. Coker, Anastasia Vavilina, Gerald L. Newton, Robert Buschauer, Kit Pogliano, Elizabeth Villa, David A. Agard, Joe Pogliano. Assembly of a nucleus-like structure during viral replication in bacteria. Science, 2017; 355 (6321): 194 DOI: 10.1126/science.aal2130

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Delta Farm Press Daily

peanut-dryland-field-june-2015-burrower-bug

Unravelling the mysteries of the peanut burrower bug

Peanut farmers who don’t know the peanut burrower bug are fortunate. Growers who’ve battled the yield- and quality-reducing pest know something needs to be done to control it, and those growers can help find answers.

Brad Haire 1 | Jan 06, 2017

Peanut farmers who personally don’t know the peanut burrower bug are fortunate. Growers who’ve battled the yield- and quality-reducing pest know something needs to be done to control it, and those growers can help find answers.

A Georgia-based research project will hit the high-gears in 2017 to develop an index growers can use to gauge their risk for the pest and implement better ways to defend against it.

When Mark Abney arrived in Georgia in 2013 as the new peanut entomologist, there was plenty of interest (and pressure) to find ways to stop the ground-dwelling, peanut-pod-feeding bug, which for several years prior suddenly started causing major problems in parts of the state’s peanut-growing region, especially troublesome to dryland peanuts.

“There wasn’t a whole lot known about it then. There was some work done in South Carolina in the ‘90s and a little bit of work in Texas in the ‘70s,” Abney said. “We’ve learned some things in the past few years, but the reality is there still isn’t a whole lot known about it from a standpoint of its biology or why it became a pest for peanut.”

The peanut burrower bug is not an invasive species, which it is mistakenly believed to be. It is a native species to Georgia and confirmed to be as far north as Connecticut. So, it must have a wide range of host plants it can survive on — not just peanuts, he said.

“We think of it as the peanut burrower bug, and that is its common name but it eats other things or it couldn’t survive the northeast,” he said.

In 2013, Abney received money from the National Peanut Board and the Georgia Peanut Commission to do research projects with University of Georgia Extension county agents, putting light traps in 15 counties to find out when the bug was most active and distributed across the state. Another project looked at how tillage influences the pest and on-farm insecticide trials.

After a couple of years of collecting that preliminary data, Abney and a team used that data to get a USDA Crop Protection and Pest Management grant.

The CPPM project has several objectives, but the main two are:

  1. To find out how peanut burrower bugs communicate with their own special pheromone. Similar to how boll weevil traps work by using an artificially-made boll weevil pheromone to attract and trap what once was a devastating cotton pest, the burrower bug project will develop pheromone-based traps, which are much cheaper and more practical than light-based traps. To pinpoint the peanut burrower bug pheromone, Abney is collaborating with a Maryland-based USDA scientist who discovered the brown marmorated stink bug pheromone, which can now be synthesized to monitor for that invasive stink bug.
  2. To develop a risk index, or risk assessment tool, in which a grower can enter production information — such as crop history, soil type, insecticides, peanut variety, tillage system and location – and from that know how at risk a particular field might be for the burrower bug and if a level of treatment is economically needed and what precise treatment is recommended to lower that risk.

“We want to develop a way they can manage their risk before they even put a peanut in the ground,” he said.

There are not many management tactics for the peanut burrower bug available to growers. But the use of granular chlorpyrifos (Lorsban), irrigation and bottom plowing can reduce risk of burrower bug damage. But there is no one Silver Bullet.

One of the sneakiest problems with the peanut burrower bug is it feeds underground and unseen on the peanut pod, which lowers yield potential and in doing so also opens the door for aflatoxin to enter the pod. Every load of peanuts grown in the U.S. is graded. Even if a slight percentage of burrower bug damage (2.5 percent or greater of internal damage) is detected in a farmer’s load of peanuts, the grade of that peanut load drops to Seg. 2 and that farmer’s potential revenue for the load gets slashed.

A big mystery about the peanut burrower bug is why its presence and damage is so sporadic. It can be a big problem in one field and then a mile down the road at another field never be a problem. Very smart people, Abney said, from those at buying points to county agents, have tried to figure out this anomaly, but the investigations have mostly been confined to just one county or small region.

One of the biggest aspects of this new burrower bug project will be to find out on a state level exactly where, when and hopefully how the pest is a problem. Peanut growers who’ve dealt with the pest can help, Abney said.

“We’re working with Federal State Inspection Service to get information on all the burrower bug damage in the state. With that information we can go back, with the cooperation of buying point operators, county agents and especially the growers, potentially all of the growers who had burrower bug problem even if it was just 1-percent damage, and talk to that grower,” he said.

With that sort of statewide data set, you can better tweeze out commonalities, “and hopefully figure out why we see burrower bugs in this field and not in that field,” he said. “The scientist in me has to believe this is not random and that there has to be a pattern there and it is up to us to figure it out.”

Abney said he is working to get final permission to receive the names of peanut growers whose peanuts show burrower bug damage. He said the names of those growers will be protected and confidential to the project, and he hopes the growers will help.

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veg-ipm-book-img_2871

The majority of the information in this book is drawn from technologies developed, tested, validated, and implemented by the Integrated Pest Management Innovation Lab (previously known as the  Integrated Pest Management Collaborative Research Support Program-IPM CRSP), supported by  USAID  Cooperative Agreements awarded to Virginia Tech.

Contents

Chap.1 – IPM for Food and Environmental Security in the Tropics

Chap. 2 – IPM Packages for Tropical Vegetable Crops

Chap. 3 – Virus Diseases of Tropical Vegetable Crops and Their Management

Chap. 4 – Exploring the Potential of Trichoderma for the Management of Seed and Soil-Borne Diseases of Crops

Chap. 5 – Physical, Mechanical and Cultural Control of Vegetable Insects

Chap. 6 – Integrated Pest Management of Cruciferous Vegetables

Chap. 7 – Integrated Pest Management of Okra in India

Chap. 8 – Integrated Pest Management of Onion in India

Chap. 9 – IPM Packages for Naranjilla: Sustainable Production in an Environmentally Fragile Region

Chap. 10 – IPM Technologies for Potato Producers in Highland Ecuador

Chap. 11 – Integrated Pest Management for Vegetable Crops in Bangladesh

Chap. 12 – Development and Dissemination of Vegetable IPM Practices in Nepal

Chap. 13 – IPM Vegetable Systems in Uganda

Chap. 14 – Impacts of IPM on Vegetable Production in the Tropics

 

ISBN 978-94-024-0922-2  ISBN 978-94-024-0924-6 (eBook)

Library of Congress Control Number: 2016957790

 

E.A. Heinrichs

IAPPS Secretary General

Asia Program Manager, IPM Innovation Lab

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Western Farm Press

 

Unlike the Beach Boys musical group of old, Rodrigo Krugner is picking up bad vibrations.

It’s the sounds that glassy-winged sharpshooters make as they seek to find and mate with each other. That’s the focus of research by Krugner, research entomologist with the U.S. Department of Agriculture’s Agricultural Research Service in Parlier, Calif.

Krugner discussed “Mating disruption of the Glassy-Winged Sharpshooter: How does that sound?” at this year’s Grape Day event at California State University, Fresno (Fresno State). The insect can spread the deadly Pierce’s disease in grapevines faster than its smaller sharpshooter cousins, and Pierce’s costs California more than $100 million per year.

Krugner explained how the insects communicate with each other through seismic vibrational signals produced by their abdominal muscles. He is studying the degree at which “courtship signals” sent in call-response fashion can be disrupted.

Right now, the means for combatting the pest include insecticide applications in citrus orchards where they congregate, and releasing egg parasitoids.

Doppler vibrometer

Krugner explained that a laser Doppler vibrometer, a technology used in the aerospace industry to listen for vibrations, figured into his research. Both white noise and female calls reduced mating under laboratory conditions, but did not affect insect aggregation.

The efficacy of these and other signals in disrupting GWSS communication is being evaluated under field conditions in collaboration with Fresno State.

Electrodynamic shakers were attached to plant stems to generate disruptive and-or masking signals. The idea is to learn if the playback of selected GWSS signals onto grapevines will determine whether mating behavior is affected by disruptive signals and whether GWSS individuals can be either attracted or repelled by signals.

Krugner said males sometimes naturally mimic females to lure rivals away, and noted the process of mates locating each other often takes up to three hours.

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Western Farm Press Daily
Maricopa, Ariz.

What is in this article?:

  • The largest agricultural robot on Earth working in an Arizona energy sorghum varietal trial.
  • The crop analytic robot is a Volkswagen-sized field scanner measuring crop growth with unprecedented resolution.
  • Plant data collected by the field scanner will be shared with crop breeders to speed up the breeding process in energy sorghum.

Pedro Andrade, left, University of Arizona, and Jeff White, USDA Agricultural Research Service, based in Maricopa, Ariz., stand in an energy sorghum variety trial where the world’s largest crop analytical robot records critical plant data.

 

Captain Kirk of Star Trek movie fame would feel right at home operating the controls of Planet Earth’s largest agricultural robot, currently operating in an energy sorghum varietal trial in Maricopa, Ariz.

The crop analytic robot, similar in appearance to a gantry crane, features a Volkswagen-sized field scanner loaded with the latest precision agriculture tools to precisely measure crop growth with unprecedented resolution.

The field scanner which moves east-to-west, north-to-south, and up-and-down above the field is located at the University of Arizona’s (UA) Maricopa Agricultural Center (MAC).

Over time, plant data collected by the field scanner will be shared with commercial and university crop breeders to help speed up the natural breeding process in energy sorghum varieties to boost yields and biomass content. The same tools could one day by use to collect plant data for breeding other types of crops.

Over the long term, improved energy sorghum varieties can help growers increase biofuel production, thus helping reduce this nation’s dependence on foreign oil.

Robot ribbon cutting

At a June ribbon-cutting ceremony for the robot field scanner system, DOE Advanced Research Projects Agency-Energy (ARPA-E) Director Joe Cornelius described the project as “agriculture’s version of the Hubble” (telescope), saying the project’s faster breeding results could place improved varieties in growers’ hands sooner.

The DOE’s Ellen Williams said the project would “revolutionize plant breeding.” She believes the sorghum project could accelerate the plant breeding process by two to three fold.

Shane Burgess, UA Dean of the College of Agriculture and Natural Resources, noted, “This is history in the making.”

Led by the Donald Danforth Plant Science Center in St. Louis, Mo., the field scanner robot project includes specialists from several universities, the federal government, and the private sector.

In the first year of the four-year project, the sorghum trial is largely funded by the U.S. Department of Energy (DOE). The project budget is about $8 million, not including the field scanner.

The UA receives about $1.6 million to cover the costs to construct the site and for its day-to-day operation.

 

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Public Release: 4-Feb-2016

John Innes Centre scientists disable infectious bacteria by removing key protein

John Innes Centre

IMAGE
IMAGE: This image shows an infection of horse blood cells with wild type Pseudomonas aeruginosa bacteria (left) and Pseudomonas aeruginosa bacteria with RimK protein deleted (right). view more

Credit: Dr Lucia Grenga, The John Innes Centre

<Scientists at the John Innes Centre and the University of East Anglia have made an exciting discovery that could provide a new way to prevent bacterial infections in both humans and plants without triggering multi-drug resistance in bacteria.

When bacteria infect either a plant or a human they first have to move across the surface to a likely site of infection. Without this migration, the bacteria find it difficult to get inside the host and are far less able to cause infection.

The research team, led by Dr Jacob Malone from the JIC and UEA’s School of Biological Sciences, was curious about why there were high levels of a particular protein in bacteria when they came into contact with plants. Upon investigating this protein further they discovered it is an important, high-level controller of bacterial movement during plant and human infection. This protein could become a new target against which to develop anti-infective drugs and because the bacteria aren’t killed outright, also reduces the likelihood of the bacteria evolving to develop resistance to the drugs.

Dr Malone and his team study a type of bacteria called Pseudomonas, of which there are dozens of different species, including the pathogen P. aeruginosa, which causes around 7% of hospital acquired infections in the UK and is a major cause of mortality in cystic fibrosis patients. Understanding these bacteria is medically very important.

They have found that the ability of Pseudomonas to cause infection is compromised at an early stage when one key protein is removed from the bacterium.

The key protein is called RimK, and is present in hundreds of species of bacteria, including several important human pathogens, but its biological function has remained largely unknown.

Dr Malone’s team discovered a completely new function for RimK. When they removed it from bacteria, those bacteria weren’t able to move properly, which in turn affected their ability to initiate infections. When scientists examined the effect of RimK deletion on plants they found that spraying a plant with RimK deleted bacteria resulted in milder disease symptoms compared to when wild type bacteria were sprayed on the plant. However, if the early stages of infection were bypassed, for example, by injecting or forcing the bacteria into plant tissue, the RimK mutant bacteria were able to infect normally. This suggests that RimK is important during the early stages of (plant) infection only. Similar results were seen for both plant and human pathogenic Pseudomonas, suggesting a common mechanism for RimK activity in both types of bacteria.

In their paper published in PLoS Genetics, Dr Malone’s team showed that RimK works to control the way that many other proteins are made within bacteria. The research suggests that when a bacterium senses that it is in a new place to grow, such as on a plant leaf or on a human cell, it adapts to that environment by changing the production of hundreds of proteins. The RimK protein controls this change, making sure that the bacteria are able to move around and thrive in their new environment. When bacteria are modified in the laboratory so they don’t contain a RimK protein, this process doesn’t work properly and the bacteria are out of sync with their surroundings, meaning they don’t migrate when they should.

Dr Malone said:

“We have found a completely new way in which bacteria control their responses to the environment: by modifying their production of proteins. This affects how a bacteria that grows on humans and plants can infect its host – if you disrupt that process, they find it difficult to start an infection.”

Dr Malone’s team hope that their insight into how the RimK-regulatory process works will influence future medical and plant research, by targeting this protein to help prevent both human and plant diseases.

Dr Malone said: “This information will be extremely useful for researchers working on plant and human diseases. Many people will have heard about the emergence of multidrug resistant bacteria – if we can target a protein that specifically controls infection rather than killing the bacteria outright, the bacteria are less likely to evolve and become resistant. This finding could give scientists a new target against which to develop anti-infective drugs.”

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Nematode pheromone ascr#18 has been shown to alert plants to the presence of plant-parasitic nematodes and to activate their immune responses.

Nematodes, or roundworms, are the most numerous animals on earth, parasitizing most plants and animals. These infections are responsible for many of the most common neglected tropical diseases, causing significant morbidity and mortality. Soil-dwelling nematodes also put food security at risk by attacking agriculturally important plants. While the human response to dealing with parasite infection has been thoroughly researched; it has only recently been discovered that plant-parasitic nematodes not only activate defensive responses in plants, but also provide nematode-mediated immunity to subsequent attack by pathogens and viruses.

Numerous nematodes

Root-knot nematode galls on plant roots. Source: commons wikimedia
Root-knot nematode galls on plant roots. Source: commons wikimedia

Despite more than 4,100 species of plant-parasitic roundworms being identified, two major groups of nematodes are responsible for most agricultural plant damage. The root-knot nematodes, Meloidogyne spp. damage plants by producing galls on roots; whereas, the cyst nematodes, Heterodera and Globodera spp., by the formation of root cysts.

Soil-dwelling nematodes are ubiquitous and rich arable soil may contain up to 3 billion worms per acre. It therefore comes as no surprise that infected crops result in over $100 billion worth of agricultural damage globally per annum. For British crops alone, damage by cyst nematodes, Globodera rostochiensis and G. pallida, account for an estimated  £50 million damage each year.

Cyst nematodes damage to potato roots. Source: commons wikimedia

Cyst nematodes damage to potato roots. Source: commons wikimedia

Nematode control therefore is a serious business; however, following the current tightening of legislation, withdrawal from use of inorganic pesticides (the primary source of pest and disease management over the past decades) and a lack of resistant plant varieties, there is an urgent need to understand more about plant natural defenses to promote resistance to nematodes and other invaders.

Plant defenses against pathogens

Plant defenses can be broadly grouped into constitutive (continuous) defenses and inducible defenses. Toxic chemicals or defense-related proteins are typically only produced after pathogens are detected due to the high energy costs associated with their production and maintenance. To allow detection of, and rapid response to, potentially harmful pathogens plants have evolved several layers of highly developed surveillance mechanisms to try and circumvent serious damage.

The first line of defense consists of inducible defenses, which are mounted when plant cells recognize microbe-associated molecular patterns (MAMPs), such as lipopolysaccharides, flagellin, peptidoglycan and other compounds commonly found in microbes. Plant cells then become fortified against attack, conferring protection from the invading pathogen. Although MAMP’s have been well characterized, up until recently, it remained unclear as to whether plants could detect conserved molecular patterns derived from plant-parasitic animals, such as soil-dwelling nematodes.

‘Nematode-associated molecular patterns’

A number of studies have previously shown that, in response to plant-parasitic nematode infection, plants quickly activate defense pathways similar to those induced by other pathogens. Although these findings were very promising, what the nematode-derived signals actually were remained a mystery.

Following the discovery that non-parasitic soil nematodes can also induce plant defenses, a conserved nematode signature molecule appeared to be a likely trigger for activating the plant defense response. Ascarosides are pheromones exclusive to nematodes that are used to regulate development and social behaviours. Ascarosides represent an evolutionarily conserved family of signalling molecules, of which more than 200 different ascaroside structures from over 20 different species have been identified. Due to the highly conserved nature of these molecules, it seemed plausible that plant hosts and nematode-associated microorganisms may have evolved the means to detect and respond to this ancient nematode molecule. A recent study published in Nature Communications investigated whether ascarosides can be detected by plants, and whether detection of the molecules induced the plant-defence response.

(a) Examples of ascarosides previously identified. (b) HPLC-MS analysis of nematode exo-metabolome samples, showing seven detected ascarosides. (c) Chemical structures of identified ascarosides and relative quantitative distribution. Source: http://www.nature.com/ncomms/2015/150723/ncomms8795/fig_tab/ncomms8795_F1.html
(a) Examples of ascarosides previously identified. (b) HPLC-MS analysis of nematode exo-metabolome samples, showing seven detected ascarosides. (c) Chemical structures of identified ascarosides and relative quantitative distribution. Source: http://www.nature.com/ncomms/2015/150723/ncomms8795/fig_tab/ncomms8795_F1.html

Profiles of ascarosides from adult and juvenile stages of a number of agriculturally relevant species of plant-parasitic nematodes were characterised using mass spectrometry (MS) to analyse the metabolome excreted into media supernatant. MS analysis of exo-metabolome samples revealed excretion of similar sets of ascarosides in all analysed species; however, ascr#18 was identified in all plant-parasitic nematodes as the most abundant molecule.

In order to determine whether ascr#18 could be perceived by plants and influence plant-defensive responses to different pathogens, the ascaroside was applied in various concentrations to Arabidopsis roots 24 h prior to leaf innoculation with pathogens. By monitoring expression of MAMP-triggered immunity (MTI) markers and defense-related genes in leaves at different time points after root treatment with ascr#18, characteristic defense responses such as MAMP-triggered immunity were shown to be induced. Interestingly, local and systemic defenses were also shown to be activated by ascr#18 application to leaves.

Detection of ascr#18 by plants increased resistance to viral, bacterial, oomycete, fungal and nematode infections in Arabidopsis, as well as tomato, potato and barley. Additionally, three other ascarosides applied to different plants showed defense responses were induced by structurally diverse ascarosides, but that this varied in a structure- and species-dependent manner.

Conclusions

A comparison of experimental wheat lines showing different levels of resistance to the disease spot blotch. Source: https://www.flickr.com/photos/cimmyt/6508078617
A comparison of experimental wheat lines showing different levels of resistance to the disease spot blotch.                                                                                                                                                                                                                                                                            Source: https://www.flickr.com/photos/cimmyt/6508078617

Plant crops suffer  considerable damage every year from parasites and pathogens, putting food security at great risk. The ability to activate plant immune responses as and when required by using signalling molecules, such as ascarosides, is an exciting discovery that could contribute to improving the economic and environmental sustainability of agriculture. One potential application could be spraying of ascr#18 on crop leaves; as although plants primarily encounter ascarosides via their roots, leaf exposure to low ascr#18 concentrations was also effective at inducing the defense responses to confer fortification against attack.

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