Friday, September 20, 2024

 

Crop diseases, spoilage can hurt the food supply. Could plant prebiotics help?



Research points to a potential new ally in the fight against plant pathogens that cost hundreds of billions of dollars per year in lost food production.



Duke University





DURHAM, N.C. -- When we talk about the microbiome, most of us think of the trillions of microorganisms that live in our bodies, supporting everything from digestion to mental health.

But plants have a world of microbes living on and inside them too. And evidence is beginning to emerge that these hidden residents play a key role in promoting plant health, in part by helping their immune system identify which bacteria to attack and which ones to tolerate.

In a new study, researchers find that disruptions to the community of microbes that live inside the leaves of a spindly plant called Arabidopsis can compromise a plant’s ability to tell harmless invaders from harmful ones -- effectively turning the plant’s defensive arsenal against itself.

The findings could eventually lead to new ways to help safeguard our food supply, said Sheng Yang He, professor of biology at Duke University and senior author of the study.

Indeed, the Food and Agriculture Organization of the United Nations estimates that crop pathogens cost the global economy some $220 billion each year.

The research was published on Sept. 6 in the journal Nature Plants.

In the study, He and colleagues, including lead author Yu Ti Cheng, a postdoctoral researcher in the He lab, were looking for genes involved in keeping the plant microbiome in balance when they noticed something odd.

They found that plants with a mutation in a gene called TIP1 had an excess of otherwise harmless bacteria inside their leaves. But these plants also had other perplexing symptoms, Cheng said.

For one, they were small and stunted compared with their wild counterparts. And they had dead patches on their leaves that normally occur when plants are fighting infection, even though no “bad” bacteria were present.

Cheng recognized these symptoms as signs of an errant immune system, when a plant’s defenses kick into gear even thoughthere’s no real threat and attack healthy tissues instead of protecting them.

Plants carrying the tip1 mutation had multiple defense genes turned up in their cells even though they weren’t under attack, the researchers found -- a sign that their immune system is in overdrive.

“The plants still have the ability to defend themselves,” Cheng said. They’ve just lost the ability to distinguish between microbial friends and foes, she added.

When this process goes wrong, previously “good” bacteria can cause the immune system to overreact in a way that is counterproductive.

“The host mistakes itself as the enemy,” Cheng said.

At first the researchers weren’t sure what was causing the plants’ immune systems to malfunction. But they wondered if the out-of-balance leaf microbiome was part of the answer.

To test the idea, they grew Arabidopsis seedlings with and without microorganisms, using a germ-free growth system He’s lab developed.

Sure enough, when tip1 mutant plants were grown to be devoid of microorganisms, their mysterious autoimmune issues nearly vanished.

“That was our eureka moment,” the researchers said.

The health problems that arise when the body’s microbiome is out of balance are well-studied in humans. For example, changes in the community of microbes in our intestines have been linked to autoimmune disorders such as Crohn’s disease, type 1 diabetes and multiple sclerosis.

But the new findings, together with two previous studies from the He lab published in 2020 and 2023, represent the first time a link between unbalanced microbiomes and autoimmunity has been shown in plants, Cheng said.

The molecular mechanism behind the link remains unclear. The TIP1 gene encodes an enzyme called S-acyltransferase, whose genetic code has remained largely unchanged as new species have branched off from old ones in the tree of life -- which means it may play a role in keeping microbiomes in balance for other species as well.

As a next step, the researchers are trying to identify the molecule or substance that the S-acyltransferase enzyme binds to and how it functions.

The details could ultimately pave the way to prebiotics that support or reset the microbiome to “help plants maintain a better balance” and reduce losses in food crops caused by pathogens or spoilage, Cheng said.

“The more knowledge we have, the more tools we can use,” she said.

This work was supported by the Natural Sciences and Engineering Research Council of Canada, the Howard Hughes Medical Institute, and the U.S. National Institutes of Health (1R01AI155441).

CITATION: "Roles of Microbiota in Autoimmunity in Arabidopsis Leaves," Yu Ti Cheng, Caitlin A. Thireault, Li Zhang, Bradley C. Paasch, Reza Sohrabi & Sheng Yang He. Nature Plants, Sept. 6, 2024. DOI: 10.1038/s41477-024-01779-9.

 

 

Heatwaves may increase likelihood of seizures in people with epilepsy




University College London



The research, published in Brain Communications, used intracranial electroencephalography (icEEG) tests – where small electrodes are inserted into the substance of the brain to measure electrical impulses – to track the brain activity of nine patients being evaluated for surgical treatment of medication-resistant epilepsy at the National Hospital for Neurology and Neurosurgery, in the summer months (May-August) of 2015 – 2022.

Genomic testing showed that none of the participants had known genetic epilepsies that are already associated with worsening of seizures during heatwaves.

In London, a heatwave is defined as three or more consecutive days with daily maximum temperatures of more than 28 degrees Celsius.

The nine patients involved in the study were, by chance, having icEEG recordings taken during spontaneous heatwaves in London, allowing the researchers to directly examine their brain activity during periods of unusually hot weather.

The researchers then compared this data to icEEG recordings taken from the patients during non-heatwave periods – while ensuring that all other conditions (apart from temperature) remained the same.

For each participant, the team logged any abnormal electrical activity across four 10-minute segments within and outside of heatwaves. They also tracked all seizures.

They found that, overall, more seizures were recorded by the icEEG during heatwaves compared with the non-heatwave period. Meanwhile, three patients also had more abnormal electrical brain activity aside from seizures during heatwaves.

Senior author, Professor Sanjay Sisodiya (UCL Queen Square Institute of Neurology), said: “Our research shows that for some people with epilepsy – in particular those with the most severe epilepsies – higher ambient temperatures increase the likelihood of having seizures.

“This is an important finding, providing some of the first evidence that for some people who already have epilepsy, higher temperatures seen during heatwaves can make their condition worse.

“Such information is important for the care of individual people with epilepsy, and also for broader efforts to ensure people with epilepsy can be kept safe as the climate changes.”

The current study sample size is relatively small as icEEG is not commonly undertaken and a heatwave had to have happened, by chance, during the recording.

However, the team now hope to have a bigger prospective study, and data are currently being collected.

Professor Sisodiya said: “Despite the study’s limited sample size, our findings remain valuable in the context of climate change. As global temperatures rise and extreme weather events become more frequent, understanding the effects of heatwaves on brain activity is crucial.”

Professor Sisodiya recently led a review of 332 papers published across the world, that explored that scale of potential effects of climate change on neurological diseases*.

The researchers found that the effect of climate change on weather patterns and adverse weather events is likely to negatively affect the health of people with brain conditions, including stroke, migraine, Alzheimer’s, meningitis, epilepsy and multiple sclerosis. The new research adds to this analysis.

The research was carried out in collaboration with researchers at UCLH and funded by the Epilepsy Society, The Amelia Roberts Fellowship, and a UCL Grand Challenges Climate Crisis Special Initiative award.

https://www.ucl.ac.uk/news/2024/may/climate-change-likely-aggravate-brain-conditions

 

Swallowing triggers a feeling of elation



A study carried out at the University of Bonn identifies a control circuit in flies essential for the consumption of food



University of Bonn

Larvae of the fruit fly Drosophila (foreground) 

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have a kind of stretch sensor in the esophagus (grey structure in the middle). It reports swallowing processes to the brain. If food is ingested, special neurons of the enteric nervous system (red) release serotonin. 

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Credit: Image: Dr. Anton Miroschnikow/University of Bonn




Researchers at the University of Bonn and the University of Cambridge have identified an important control circuit involved in the eating process. The study has revealed that fly larvae have special sensors, or receptors, in their esophagus that are triggered as soon as the animal swallows something. If the larva has swallowed food, they tell the brain to release serotonin. This messenger substance – which is often also referred to as the feel-good hormone – ensures that the larva continues to eat. The researchers assume that humans also have a very similar control circuit. The results were recently published in the journal “Current Biology.”

Imagine you are hungry and sitting in a restaurant. There is a pizza on the table in front of you that smells extremely inviting. You take a bite, chew and swallow it and feel elated at that precise moment: Oh boy that was tasty! You quickly cut the next piece of the pizza and cram it into your mouth.

The smell of the pizza and how it tastes on your tongue motivate you to start your meal. However, it’s the good feeling you have after swallowing that is largely responsible for you continuing to eat. “But how exactly does this process work? Which neural circuits are responsible? Our study has provided an answer to these questions,” says Prof. Dr. Michael Pankratz from the LIMES Institute (the acronym stands for “Life & Medical Sciences”) at the University of Bonn.

The researchers didn’t gain their insights from humans but instead by studying the larvae of the fruit fly Drosophila. These flies have around 10,000 to 15,000 nerve cells – which is a manageable number compared to the 100 billion in the human brain. However, these 15,000 nerve cells already form an extremely complex network: Every neuron has branching projections via which it contacts dozens or even hundreds of other nerve cells.

All nerve connections in fly larvae investigated for the first time

“We wanted to gain a detailed understanding of how the digestive system communicates with the brain when consuming food,” says Pankratz. “In order to do this, we had to understand which neurons are involved in this flow of information and how they are triggered.” Therefore, the researchers analyzed not only the paths of all of the nerve fibers in the larvae but also the connections between the different neurons. For this purpose, the researchers cut a larva into thousands of razor-thin slices and photographed them under an electron microscope.

“We used a high-performance computer to create three-dimensional images from these photographs,” explains the researcher, who is also a member of the transdisciplinary research area “Life and Health” and the “ImmunoSensation” Cluster of Excellence. The next step was a real herculean task: The project assistants Dr. Andreas Schoofs and Dr. Anton Miroschnikow investigated how all the nerve cells are “wired” to one another – neuron for neuron and synapse for synapse.

The stretch receptor is wired to serotonin neurons

This process enabled the researchers to identify a sort of “stretch receptor” in the esophagus. It is wired to a group of six neurons in the larva’s brain that are able to produce serotonin. This neuromodulator is also sometimes called the “feel-good hormone.” It ensures, for example, that we feel rewarded for certain actions and are encouraged to continue doing them.

The serotonin neurons receive additional information about what the animal has just swallowed. “They can detect whether it is food or not and also evaluate its quality,” explains the lead author of the study Dr. Andreas Schoofs. “They only produce serotonin if good quality food is detected, which in turn ensures that the larva continues to eat.”

This mechanism is of such fundamental importance that it probably also exists in humans. If it is defective, it could potentially cause eating disorders such as anorexia or binge eating. It may therefore be possible that the results of this basic research could also have implications for the treatment of such disorders. “But we don’t know enough at this stage about how the control circuit in humans actually works,” says Pankratz to dampen any overly high expectations. “There is still years of research required in this area.”

Participating institutes and funding:

The University of Bonn, University of Cambridge (UK), HHMI’s Janelia Research Campus (Ashburn, USA) and the Allen-Institute for Brain Sciences (Seattle, USA) participated in the study. The project was funded by the German Research Foundation (DFG).

Publication: Andreas Schoofs, Anton Miroschnikow, Philipp Schlegel, Ingo Zinke, Casey M. Schneider-Mizell, Albert Cardona and Michael J. Pankratz: Serotonergic modulation of swallowing in a complete fly vagus nerve connectome; https://doi.org/10.1016/j.cub.2024.08.025

 ICYMI

New method for fingerprint analysis holds great promise


Overlapping and weak fingerprints pose challenges in criminal cases. A new study offers a solution and brings hope for using chemical residues in fingerprints for personal profiling.



Aarhus University

The researcher 

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Postdoc Kim Frisch from the Department of Forensic Medicine at Aarhus University is the first to use chemical imaging to reveal fingerprints lifted from various surfaces using gelatin lifters. Photo: Line Rønn

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Credit: Line Rønn, Aarhus University




 

A groundbreaking study has made it possible to extract much more information from fingerprints as evidence than what is currently achievable.

A new study from the Department of Forensic Medicine at Aarhus University is the first in the world to analyze fingerprints on gelatin lifters using chemical imaging. This could be crucial in criminal cases where current methods fall short.

Danish police frequently collect fingerprints at crime scenes using so-called gelatin lifters. Unlike tape, these lifters are easy to use and are suitable for lifting fingerprints from delicate surfaces, such as peeling wall paint, and irregular objects like door handles.

Once collected, the fingerprints are photographed digitally so they can be processed through fingerprint databases. However, traditional photography cannot separate overlapping fingerprints, which are often found at crime scenes. Very faint prints are also problematic. As a result, many fingerprints that could otherwise contribute to investigations unfortunately have to be discarded.

A fine spray of solvent

A solution is presented in the new study from the Department of Forensic Medicine at Aarhus University, recently published in the scientific journal Analytical Chemistry.

"We are presenting a method that has the potential to be integrated into the police's traditional workflow. If this happens, more fingerprints from crime scenes could be used and evaluated both visually and chemically," says postdoc Kim Frisch, who is behind the study.

The method is based on a technique called Desorption Electrospray Ionization Mass Spectrometry (DESI-MS), which works by measuring the chemical compounds in fingerprints based on their mass.

"We send a very fine spray of solvent, consisting of electrically charged droplets of methanol. This releases and ionizes substances on the surface of the fingerprint on the gelatin lifter. The substances are then drawn into the instrument, where their masses are measured individually," explains Kim Frisch.

DESI-MS was invented about 20 years ago and was developed for general surface analysis. In 2008, it was shown that the technique could be used for chemical imaging of fingerprints on glass surfaces and tape.

"But now we show that the technique can also be used to analyze fingerprints collected on gelatin lifter, which are used by police in many countries, including Denmark. This is analytical chemistry used in a forensic context, and it has great potential," says the researcher.

Revealing fingerprints where traditional optical imaging fails

Overlapping fingerprints pose a significant challenge for investigators because they are difficult to separate. The study shows that the new method can be used to separate overlapping fingerprints (Figure 2) and to enhance faint fingerprints in situations where optical imaging fails.

So far, the method has been tested on fingerprints lifted in the laboratory, but the researchers are now testing the method on fingerprints from crime scenes. For this purpose, they have received fingerprints collected by the National Special Crime Unit of the Danish Police , and there are high hopes for the results at the Department of Forensic Medicine.

Can we analyze gender, age, and dietary habits?

The method is still under development, and the researchers are now focusing more on analyzing the chemical composition of fingerprints.

A fingerprint is much more than a unique pattern—it also contains a variety of chemical compounds from the person who left the print. These compounds include natural lipids, amino acids, and peptides secreted from the skin. However, the fingerprint can also contain nicotine, caffeine, drugs, cosmetic ingredients, and potentially incriminating substances such as lubricant from condoms and explosives that have been secreted through the skin or contaminated the skin upon contact.

Chemical imaging could potentially be used for profiling the person who left the fingerprint.

Many researchers around the world are working to develop methods for this purpose—not only using the technique employed at the Department of Forensic Medicine in Aarhus. There are examples in the literature that fingerprints can reveal whether people have ingested or touched substances of abuse such as cocaine, cannabis, and ayahuasca.

Studies have also been conducted with the aim of determining individuals' gender, age, and lifestyle factors such as diet, medication, and smoking from their fingerprints. The Department of Forensic Medicine continues to work on the study, supported by the Danish Victims Fundand ongoing for two and a half years, in an effort to maximize the information that can be obtained from fingerprints.

Research focused on practical application

The research is conducted in close collaboration with the National Special Crime Unit  of the Danish Police because it is important that the work is aimed at practical application.

So far, the results suggest that the method could be used in practice.

"When the police collect fingerprints at a crime scene, the gelatin lifters can, in principle, be sent to the Department of Forensic Medicine, where we scan the samples. However, the scanning process is time consuming, which means that we would not be able to analyze samples in the hundreds, as we do with, for example, blood samples. We expect that the method will be used in the future as a special analysis in more serious cases such as murder and rape," says Kim Frisch.

Behind the Research Results

 MUTUAL AID

Bacteria work together to thrive in difficult conditions


Study shows soil pH sets stage for microbial interactions, composition



Ohio State University




COLUMBUS, Ohio – Though a founding concept of ecology suggests that the physical environment determines where organisms can survive, modern scientists have suspected there is more to the story of how microbial communities form in the soil.

In a new study, researchers have determined through both statistical analysis and in experiments that soil pH is a driver of microbial community composition – but that the need to address toxicity released during nitrogen cycling ultimately shapes the final microbial community.

“The physical environment is affecting the nature of microbial interactions, and that affects the assembly of the community,” said co-lead author Karna Gowda, assistant professor of microbiology at The Ohio State University. “People in the field understood these two things must be important at some level, but there wasn’t a lot of evidence for it. We’re adding some specificity and mechanisms to this idea.”

The work helps clarify the microbial underpinnings of global nitrogen cycling and may provide a new way to think about emissions of nitrous oxide, a potent greenhouse gas, Gowda said.

The research was published recently in Nature Microbiology.

Microbes keep soil healthy and productive by recycling nutrients, and are particularly important for converting nitrogen into forms that plants can use. Underground organisms living in the same environment are also highly interconnected, preying on each other, participating in chemical exchanges and providing community benefits.

For this work, Gowda and colleagues used a dataset from a worldwide collection of topsoil samples, sequencing the genomes of microbes present in the samples and analyzing important characteristics of the soil – such as nitrogen and carbon content and pH, a measure of soil’s acidity.

“We wanted to look at trends that were widespread and that would manifest around the planet across very different environments,” Gowda said.

With billions of bacteria present in a sample of soil, the researchers relied on the genetic makeup of microbial communities to determine their functional roles.

The team zeroed in on genes that identified which bacteria were involved in denitrification – converting nitrogen compounds from bioavailable forms into nitrous oxide and dinitrogen gas that’s released in the atmosphere. A bioinformatics analysis showed that soil pH was the most important environmental factor associated with the abundance of these organisms.

To test the statistical finding, the researchers conducted lab enrichment experiments, running a natural microbial community through different conditions of growth.

During denitrification, specific enzymes have roles in the conversion of nitrate into various nitrogen-containing compounds. One of these forms, nitrite, is more toxic in acidic soil (low pH) than it is under neutral conditions with higher pH.

The experiments showed that strains with enzymes called Nar, linked to creating toxic nitrite, and strains with enzymes called Nap, linked to consuming nitrite, fluctuated based on the acidity of the soil.

“We found more of Nar at low pH and less of Nap, and vice versa as the soil pH moved toward neutral,” Gowda said. “So we see two different types of organisms prevalent at acidic versus neutral pH, but we also find that that’s actually not explaining what’s going on. It’s not just the environment that’s determining who’s there – it’s actually the environment plus interactions between more organisms in the community.

“This means that pH is affecting the interaction between organisms in the community in a more or less consistent way – it’s always about the toxicity of nitrite. And this highlights how different bacteria work together to thrive in varying soil pH levels.”

That finding was novel and important, Gowda said. Bacteria and other microorganisms are known to be driven by a will to survive, but they also rely on each other to stay safe – and that cooperation has implications for environmental health, the research suggests.

“While individual fitness effects clearly play a role in defining patterns in many contexts, interactions are likely essential to explaining patterns in a variety of other contexts,” the authors wrote.

Understanding how interactions and the environment affect nitrous oxide emissions could provide new insights into reducing this potent greenhouse gas, Gowda said: Denitrifying bacteria are key sources and sinks of nitrous oxide in agricultural soils. While past studies have focused on the behavior of these nitrous oxide-emitting organisms in different pH conditions, considering their ecological interactions may offer new strategies to lower emissions.

This work was supported by the National Science Foundation, the University of Chicago, the National Institute of General Medical Sciences, a James S. McDonnell Foundation Postdoctoral Fellowship Award, and a Fannie and John Hertz Fellowship Award.

Co-authors include Seppe Kuehn, Kyle Crocker, Kiseok Keith Lee, Milena Chakraverti-Wuerthwein and Zeqian Li of the University of Chicago; Mikhail Tikhonov of Washington University in St. Louis; and Madhav Mani of Northwestern University.

#

Contact: Karna Gowda, Gowda.51@osu.edu

Written by Emily Caldwell, Caldwell.151@osu.edu; 614-292-8152

 

 

An ‘invasive’ marine organism has become an economic resource in the eastern Mediterranean



Skeletons and shells from an invasive species of foraminifera are helping build beaches in the eastern Mediterranean Sea



University of South Florida

beach sand in Greece foraminifera - image 5.jpg 

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Sand sample from Elafonisos, Greece, with abundant A. lobifera shells, as well as shells and shell fragments from snails and other organisms.

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Credit: Olga Koukousioura




KEY TAKEAWAYS:

  • A species of single-celled organisms called foraminifera (forams) is increasing in warm, alkaline waters of the eastern Mediterranean, building beaches with their calcium carbonate skeletons.
  • In regions like Turke, forams are creating sandy shorelines where there used to be rocky terrain, benefiting tourism.
  • Forams thrive in warm waters with high CO2, suggesting they might continue growing as climate change accelerates.
  • This species of foram, once native to the Mediterranean, is returning as human activities make their preferred environment suitable again.

TAMPA, Fla. (Sept. 13, 2024) – Pamela Hallock, a biogeological oceanographer and distinguished university professor at the University of South Florida College of Marine Science, typically finds little comfort in climate change.

Hallock has spent her career studying the ocean. She leads USF’s Reef Indicators Lab and is no stranger to the impacts of human activities on marine environments.

Still, she couldn’t help but notice a bright spot in the results of her recent paper on a species of single-celled organisms called foraminifera (forams), published in the Journal of Foraminiferal Research.

“These forams have been increasing in numbers in suitable environments,” Hallock said. “Now they’re so prolific that they’re becoming an economic resource in regions with warm waters and high alkalinity because they’re building beaches.”

The foram species in question, Amphistegina lobifera, found favorable conditions in the warm, nutrient-poor waters of the Mediterranean Sea after traveling north through the Suez Canal 60-80 years ago. A. lobifera populations have since proliferated in the eastern Mediterranean and spread westward, raising concerns about its invasive potential in the region.

Despite these concerns, A. lobifera may be boon for tourism in countries like Turkey, Hallock said. Their calcium carbonate skeletons make excellent beach sand. Shorelines once covered in jagged volcanic and limestone rock have accumulated a half meter or more of sand comprised of dead foram skeletons and other shells.

“The rate at which these forams are building beaches in the region is comparable to the rate of sea level rise,” Hallock said.

There’s reason to believe A. lobifera may continue to flourish in a warming world replete with atmospheric CO2. The genus Amphistegina emerged on Earth during a period of higher atmospheric CO2 concentrations, Hallock noted in her paper, and warm waters with elevated alkalinity increase their rates of metabolism and shell formation.

While A. lobifera may currently be considered invasive in the Mediterranean Sea, its presence in the region is really a return to ancestral waters.

“These are a kind of critter that previously inhabited the region,” she said. “Now, through our influence on the environment, we’re making the habitat once again suitable for them.”

The recent study offers a unique perspective about the impacts of humans on marine environments, and vice versa.

As Hallock and her co-authors state in the study, “Might this return of prolific shallow-water carbonate production ultimately prove at least locally beneficial as climate change progresses?”

The coastal areas of the Mediterranean Sea shown in yellow indicating regions where A. lobifera can live abundantly if water quality is suitable.

Credit

Olga Koukousioura


 

About the University of South Florida

The University of South Florida, a high-impact research university dedicated to student success and committed to community engagement, generates an annual economic impact of more than $6 billion. With campuses in Tampa, St. Petersburg and Sarasota-Manatee, USF serves approximately 50,000 students who represent nearly 150 different countries. U.S. News & World Report has ranked USF as one of the nation’s top 50 public universities for five consecutive years, and this year USF earned its highest ranking ever among all universities public or private. In 2023, USF became the first public university in Florida in nearly 40 years to be invited to join the Association of American Universities, a prestigious group of the leading universities in the United States and Canada. Through hundreds of millions of dollars in research activity each year and as one of the top universities in the world for securing new patents, USF is a leader in solving global problems and improving lives. USF is a member of the American Athletic Conference. Learn more at www.usf.edu.