It’s possible that I shall make an ass of myself. But in that case one can always get out of it with a little dialectic. I have, of course, so worded my proposition as to be right either way (K.Marx, Letter to F.Engels on the Indian Mutiny)
Friday, October 04, 2024
BOTANICALS
New research uncovers how climate and soil shape tree and shrub wood density across ecosystems
Institute of Atmospheric Physics, Chinese Academy of Sciences
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Climate and soil factors have important effects on wood density of trees and shrubs.
A recent study published in Advances in Atmospheric Sciences has provided new insights into how wood density in trees and shrubs adapts to different climate and soil conditions. Led by Dr. SONG Xiang from the Institute of Atmospheric Physics at the Chinese Academy of Sciences, the research offers a more detailed understanding of vegetation responses to environmental factors, with implications for improving Earth system models and dynamic global vegetation models (DGVMs).
Wood density, a critical trait for both the quality and function of plant species, plays a significant role in predicting vegetation distributions and ecosystem dynamics. However, current global models typically treat wood density as a uniform constant across plant functional types, such as broadleaf trees, needle-leaf trees, and shrubs. This generalization can lead to inaccuracies when predicting how different plant types interact with their environments.
Climate and soil factors have important effects on wood density of trees and shrubs. (Image by SONG Xiang)
“Our research shows that this simplification in current models could introduce serious biases,” explained Dr. SONG. “By incorporating the variability in wood density across different plant functional types and environmental gradients, we can greatly enhance the accuracy of simulations, particularly for tree morphology and forest dynamics.”
The team conducted an extensive analysis of 138,604 wood density observations from around the globe, examining how climate and soil factors influence wood density across six different functional types. Their findings reveal that for tree species, climate factors play a more dominant role than soil characteristics in determining wood density. In contrast, both climate and soil exert nearly equal influence on shrub species.
The models developed by the researchers showed strong predictive power, with correlation coefficients between observed and predicted wood density values ranging from 0.49 to 0.93 across all functional types. Notably, the predictions aligned well with actual wood density measurements across different climate conditions, underscoring the robustness of the findings.
“Our results highlight the importance of considering spatial variability in wood density when modeling vegetation dynamics,” Dr. SONG continued. “In future studies, we plan to integrate this spatial heterogeneity into DGVMs, which we expect will improve the simulation of forest characteristics, such as tree height and forest coverage, especially in central forest areas and transition zones.”
The study represents a significant step forward in understanding how vegetation adapts to environmental changes. By refining wood density parameterizations, the research could lead to more accurate predictions of ecosystem responses to climate change, aiding efforts to manage forests and other ecosystems more effectively.
The morning glory transcription factor EPH1 binds in the vicinity of genes associated with programmed cell death after a certain time after flowering and activates the expression of these genes. The activation of genes associated with programmed cell death induces the degradation of proteins and nucleic acids in the flower cells, resulting in flower wilting. (Morning glory photo, courtesy of NARO).
The longevity of plant flowers is controlled by genetically programmed mechanisms. After a certain amount of time after flowering, the expression of genes associated with programmed cell death is induced and cellular components such as proteins and nucleic acids are degraded, causing the flower to wilt and die. In the horticultural field, flower longevity is an important trait that determines the commercial value of ornamental plants, and the development of technologies to prolong flower longevity is desired.
In our previous research, we identified a transcription factor EPHEMERAL1 as a regulator of flower longevity in the Japanese morning glory (Fig.1), and it was thought that if a chemical could be found that suppressed the function of EPHEMERAL1, it would be possible to extend flower longevity.
In this study, we succeeded in constructing an assay system that can detect the binding of EPH1 to DNA using a wheat cell-free protein synthesis system and an AlphaScreen system, a molecular interaction analysis technology that PROS has independently developed. Using the AlphaScreen system, we succeeded in isolating Everlastin1 and Everlastin2, compounds that inhibit the binding of EPH1 to DNA (Fig.2). The analysis using the AlphaScreen system revealed that EPH1 binds to DNA by dimerisation and that Everlastin1 and Everlastin2 inhibit this EPH1 dimerisation, thereby reducing the ability of EPH1 to bind to DNA. Floating cut morning glory flowers in water with dissolved Everlastin1 or Everlastin2 inhibited DNA and protein degradation and prolonged the longevity of the flowers by approximately twofold (Fig.3).
Transcription factors are generally difficult to synthesize and purify and were considered very difficult proteins to develop as chemicals. In this study, by using the wheat germ cell-free protein synthesis system developed by PROS, which can synthesize any protein with high efficiency, and the AlphaScreen system, which can analyze the binding between DNA and unpurified proteins, we succeed in the synthesis of the transcription factor EPH1 and the binding analysis system of EPH1 and DNA. By using these technologies, it became possible to carry out compound screening targeting transcription factors and succeeded for the first time in the world to screen compounds that inhibit the function of transcription factors in plants. The methods used in this study are expected to stimulate the development of chemicals targeting transcription factors that were previously considered ‘Undruggable’. The analogous protein of the transcription factor EPH1 targeted in this study is also thought to be involved in the longevity of major cut flowers such as lilies, and it is hoped that an approach similar to the present study will lead to the development of chemicals that extend the longevity of the colorful flowers sold in flower shops.
Microscopic pores on the surface of leaves called stomata help plants “breathe” by controlling how much water they lose to evaporation. These stomatal pores also enable and control carbon dioxide intake for photosynthesis and growth.
As far back as the 19th century, scientists have known that plants increase their stomatal pore openings to transpire, or “sweat,” by sending water vapor through stomata to cool off. Today, with global temperatures and heat waves on the rise, widening stomatal pores are considered a key mechanism that can minimize heat damage to plants.
But for more than a century, plant biologists have lacked a full accounting of the genetic and molecular mechanisms behind increased stomatal “breathing” and transpiration processes in response to elevated temperatures.
University of California San Diego School of Biological Sciences PhD student Nattiwong Pankasem and Professor Julian Schroeder have constructed a detailed picture of these mechanisms. Their findings, published in the journal New Phytologist, identify two paths that plants use to handle rising temperatures.
“With increasing global temperatures, there’s obviously a threat to agriculture with the impact of heat waves,” said Schroeder. “This research describes the discovery that rising temperatures cause stomatal opening by one genetic pathway (mechanism), but if the heat steps up even further, then there’s another mechanism that kicks in to increase stomatal opening.”
For decades, scientists struggled to find a clear method to decipher the mechanisms underlying rising temperature-mediated stomatal openings due to the intricate measurement processes required. The difficulty is rooted in the complex mechanics involved in setting air humidity (also known as the vapor pressure difference, or VPD) to constant values while the temperature increases, and the trickiness of picking apart temperature and humidity responses.
Pankasem helped solve this problem by developing a novel approach for clamping the VPD of leaves to fixed values under increasing temperatures. He then teased out the genetic mechanisms of a range of stomatal temperature responses, including factors such as blue-light sensors, drought hormones, carbon dioxide sensors and temperature-sensitive proteins.
Important for this research was a new generation gas exchange analyzer that allows improved control of the VPD (clamping the VPD to fixed values). Researchers can now conduct experiments that elucidate the temperature effects on stomatal opening without the need to remove leaves from whole living plants.
The results revealed that the stomatal warming response is dictated by a mechanism found across plant lineages. In this study, Pankasem investigated the genetic mechanisms of two plant species, Arabidopsis thaliana, a well-studied weed species and Brachypodium distachyon, a flowering plant that is related to major grain crops such as wheat, maize and rice, representing an opportune model for these crops.
The researchers found that carbon dioxide sensors are a central player in the stomatal warming-cooling responses. Carbon dioxide sensors detect when leaves undergo rapid warming. This starts an increase in photosynthesis in the warming leaves, which results in a reduction in carbon dioxide. This then initiates the stomatal pores to open, allowing plants to benefit from the increase in carbon dioxide intake.
Interestingly, the study also found a second heat response pathway. Under extreme heat, photosynthesis in plants is stressed and declines and the stomatal heat response was found to bypass the carbon dioxide sensor system and disconnect from normal photosynthesis-driven responses. Instead, the stomata employ a second heat response pathway, not unlike gaining entry through a backdoor to a house, to “sweat” as a cooling mechanism.
“The impact of the second mechanism, in which plants open their stomata without gaining benefits from photosynthesis would result in a reduction in water use efficiency of crop plants,” said Pankasem. “Based on our study, plants are likely to demand more water per unit of CO2 taken in. This may have direct implications on irrigation planning for crop production and large-scale effects of increased transpiration of plants in ecosystems on the hydrological cycle in response to global warming.”
“This work shows the importance of curiosity-driven, fundamental research in helping to address societal challenges, build resiliency in key areas like agriculture, and, potentially, advance the bioeconomy,” said Richard Cyr, a program director in the U.S. National Science Foundation Directorate for Biological Sciences, which partially funded the research. “Further understanding of the molecular complexities that control the basis of stomatal function at higher temperatures could lead to strategies to limit the amount of water needed for farming in the face of global increases in temperature.”
With the new details in hand, Pankasem and Schroeder are now working to understand the molecular and genetic mechanisms behind the secondary heat response system.
The coauthors of the study are: Nattiwong Pankasem, Po-Kai Hsu, Bryn Lopez, Peter Franks and Julian Schroeder. The research was funded by the Human Frontier Science Program (RGP0016/2020) and the National Science Foundation (MCB 2401310).
Warming triggers stomatal opening by enhancement of photosynthesis and ensuing guard cell CO2 sensing, whereas higher temperatures induce a photosynthesis-uncoupled response
Article Publication Date
2-Oct-2024
Plant compound used in traditional medicine may help fight tuberculosis
Penn State
UNIVERSITY PARK, Pa. — A compound found in African wormwood — a plant used medicinally for thousands of years to treat many types of illness — could be effective against tuberculosis, according to a new study that is available online and will be published in the October edition of the Journal of Ethnopharmacology.
The team, co-led by Penn State researchers, found that the chemical compound, an O-methylflavone, can kill the mycobacteria that causes tuberculosis in both its active state and its slower, hypoxic state, which the mycobacteria enters when it is stressed.
Bacteria in this state are much harder to destroy and make infections more difficult to clear, according to co-corresponding author Joshua Kellogg, assistant professor of veterinary and biomedical sciences in the College of Agricultural Sciences.
While the findings are preliminary, Kellogg said the work is a promising first step in finding new therapies against tuberculosis.
“Now that we’ve isolated this compound, we can move forward with examining and experimenting with its structure to see if we can improve its activity and make it even more effective against tuberculosis,” he said. “We’re also still studying the plant itself to see if we can identify additional molecules that might be able to kill this mycobacterium.”
Tuberculosis — caused by the bacteria Mycobacterium tuberculosis, or Mtb — is one of the world's leading killers among infectious diseases, according to the Centers for Disease Control and Prevention. There are about 10 million cases a year globally, with approximately 1.5 million of those being fatal.
While effective therapies exist for TB, the researchers said there are several factors that make the disease difficult to treat. A standard course of antibiotics lasts six months, and if a patient contracts a drug-resistant strain of the bacteria, it stretches to two years, making treatment costly and time consuming.
Additionally, the bacteria can take two forms in the body, including one that is significantly harder to kill.
“There’s a ‘normal’ microbial bacterial form, in which it’s replicating and growing, but when it gets stressed — when drugs or the immune system is attacking it — it goes into a pseudo-hibernation state, where it shuts down a lot of its cellular processes until it perceives that the threat has passed,” Kellogg said. “This makes it really hard to kill those hibernating cells, so we were really keen to look at potential new chemicals or molecules that are capable of attacking this hibernation state.”
Multiple species of the Artemisia plant have been used in traditional medicine for centuries, the researchers said, including African wormwood, which has been used to treat cough and fever. Recent studies in Africa have suggested that the plant also has clinical benefits in treating TB.
“When we look at the raw plant extract that has hundreds of molecules in it, it’s pretty good at killing TB,” Kellogg said. “Our question was: There seems to be something in the plant that's really effective — what is it?”
For their study, the researchers took raw extract of the African wormwood plant and separated it into “fractions” — versions of the extract that have been separated into simpler chemical profiles. They then tested each of the fractions against Mtb, noting whether they were effective or ineffective against the bacteria. At the same time, they created a chemical profile of all of the tested fractions.
“We also used machine learning to model how the changes in chemistry correlated with the changes in activity that we saw,” Kellogg said. “This allowed us to narrow our focus to two fractions that were really active.”
From these, the researchers identified and tested a compound that effectively killed the bacteria in the pathogen’s active and inactive states, which the researchers said is significant and rare to see in TB treatments. Further testing in a human cell model showed that it had minimal toxicity.
Kellogg said the findings have the potential to open new avenues for developing new, improved therapeutics.
“While the potency of this compound is too low to use directly as an anti-Mtb treatment, it may still be able to serve as the foundation for designing more potent drugs,” he said. “Furthermore, there appear to be other, similar chemicals in African wormwood that may also have the same type of properties.”
The researchers said that in the future, more studies are needed to continue exploring the potential for using African wormwood for treating TB.
Co-authors from Penn State are R. Teal Jordan, research technologist and lab manager in veterinary and biomedical sciences, and Xiaoling Chen, graduate student in pathobiology. Also co-authors on the paper were Scarlet Shell, Maria Natalia Alonso, Junpei Xiao, Juan Hilario Cafiero, Trevor Bush, Melissa Towler and Pamela Weathers, all at Worcester Polytechnic Institute.
The National Institutes of Health's National Institute for Allergies and Infectious Disease and the U.S. Department of Agriculture's National Institute of Food and Agriculture helped support this work.
An O-methylflavone from Artemisia afra kills non-replicating hypoxic Mycobacterium tuberculosis
Article Publication Date
1-Oct-2024
Plants have a backup plan
Cold Spring Harbor Laboratory
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Plants like Arabidopsis, seen here, have two options to ensure accurate chromosome division—a molecule called DDM1 and a process known as RNAi. If Arabidopsis loses one of these, it’s fine. But if it loses both, it’s in trouble.
Credit: Martienssen lab/Cold Spring Harbor Laboratory
Tending a garden is hard work. Imagine it from the plants’ perspective. Each relies on fine-tuned genetic processes to pass down accurate copies of chromosomes to future generations. These processes sometimes involve billions of moving parts. Even the tiniest disruption can have a cascading effect. So, for plants like Arabidopsis thaliana, it’s good to have a backup plan.
“Chromosomes have to be accurately partitioned every time a cell divides,” explains Cold Spring Harbor Laboratory (CSHL) Professor and HHMI Investigator Rob Martienssen. “For that to happen, each chromosome has a centromere. In plants, centromeres control chromosome partitioning with the help of a molecule called DDM1.”
Martienssen discovered DDM1 in 1993 with a team that included Tetsuji Kakutani, then a postdoc with CSHL Fellow Eric Richards. Kakutani and Martienssen recently reunited to investigate a question 30 years in the making. When humans lose their version of DDM1, centromeres can’t divide evenly. This causes a severe genetic condition called ICF syndrome. But if the molecule is so important, why isn’t Arabidopsis affected when DDM1 is lost?
“We wondered why it would be so different. About 10 years later, we found that in yeast, centromere function is controlled by small RNAs. That process is called RNAi. Plants actually have both DDM1 and RNAi. So, we thought, ‘Let’s isolate these two in Arabidopsis to see what happens.’ We did that, and sure enough, the plants looked really horrible," explains Martienssen.
When the team looked closer, they found that a single transposon inside chromosome 5 was responsible for the defects. Transposons move around the genome, switching genes on and off. In Arabidopsis, they trigger DDM1 or RNAi to help centromeres divide. But when DDM1 and RNAi are missing, the process is disrupted.
“We found very few copies of this transposon anywhere else in the genome,” Martienssen says. “But the centromere of chromosome 5 was infested with these things. We thought, ‘Wow, OK, this really might be it.’ Then we started working on how to restore healthy function.”
Martienssen and the study’s lead author, Atsushi Shimada, developed molecules called short hairpin RNAs that target the transposons.
“Those small RNAs make up for the loss of DDM1. They recognized every copy of the transposon in the centromere and, amazingly, restored centromere function. So now the plants were fertile again. They make seeds. They look much better, " explains Martienssen.
Of course, it’s not all about plants. In humans, uneven centromere division has been linked to conditions like ICF and early cancer progression. Martienssen hopes his team’s work may one day point to better treatments for these and other diseases.
A team of researchers in Italy have shown that use of microbial biofertilisers and algae-based biostimulants can significantly enhance both the yield and quality of organic tomatoes. Published in the Journal of the Science of Food and Agriculture, the study underscores the potential of plant growth-promoting microorganisms (PGPMs) in sustainable agriculture, offering a promising alternative to traditional chemical fertilisers.
A growing demand for eco-friendly and cost-effective crop production, coupled with declining soil health has led to a growing interest in the use of PGPMs, which can form mutually beneficial interactions with plants, enhancing crop performance and tolerance against stresses such as drought. While the benefits of using PGPMs have been well-studied, their application in agricultural management remains limited.
Explaining the motivation behind the study, Emanuele Radicetti, an associate professor at the University of Ferrara and corresponding author on the research, highlighted the pressing need for innovative, sustainable farming solutions. ‘There is an urgent need to develop sustainable agroecosystems that can ensure sufficient crop yield over a long-term period,’ he said. ‘Biofertilisers are gradually emerging as a promising, nature-based alternative that reduces agroecosystem inputs by enhancing organism interactions.’
In addition to PGPMs, the team applied natural algae-derived treatments to the tomato crops, which act as biostimulants to further promote plant health. These treatments improve processes like nutrient absorption and stress tolerance, supporting overall crop performance. ‘Algae extracts are considered a rich source of plant biostimulants and provide a renewable option for improving crop quality and yield,’ explained Radicetti. ‘Even at low doses they have the capacity to support plant development, especially under stressed conditions, which are becoming more frequent with climate change.’
The study found that PGPMs significantly improved root development, shoot biomass, and overall health of tomato plant seedlings. ‘We observed well-developed root systems in tomato crops just 30 days after transplanting, demonstrating the function of PGPMs in mitigating transplanting stress,’ Radicetti explained.
The highest crop yield, 67.2 tons per hectare, was achieved with a combined application of a PGPM product called MYCOUP and a 1.0% algae-based biostimulant. ‘The results were evident,’ Radicetti noted, ‘and we were fascinated by the idea that an environmentally-friendly approach like this could produce such strong results.’
Looking ahead, the researchers believe that the use of PGPMs and algae-based biostimulants can be easily adopted. However, Radicetti stresses the need for further studies: ‘More research is needed to evaluate their full potential, especially under stressed conditions like drought, which will be a major concern in the coming years.’
The findings contribute to a growing body of work which can influence future innovations in organic and sustainable farming. ‘Organic farming requires a dynamic and creative approach to crop management,’ Radicetti said. ‘Each study that improves the knowledge on crop growth and production are a step toward the goals of sustainability, in terms of environmental, social and economic factors.’
The team plans to continue evaluating the benefits of these treatments under drought conditions, a critical factor for the future of agriculture. They are also exploring the integration of other environmentally friendly tools, such as biochar, cover crops, and no-till farming, in combination with microbial biofertilisers and algae-based biostimulants.
Microbial biofertilizers and algae-based biostimulant affect fruit yield characteristics of organic processing tomato
Turning plants into workout supplement bio-factories
American Chemical Society
It’s important to eat your veggies, but some essential vitamins and nutrients can only be found in animals, including certain amino acids and peptides. But, in a proof-of-concept study published in ACS’ Journal of Agricultural and Food Chemistry, researchers developed a method to produce creatine, carnosine and taurine — all animal-based nutrients and common workout supplements — right inside a plant. The system allows for different synthetic modules to be easily stacked together to boost production.
Plants can be surprisingly receptive when asked to produce compounds they’re not used to making. Using a specialized bacterium, scientists have transferred DNA instructions for all manner of amino acids, peptides, proteins or other molecules into different plants’ cells. This technology helped create lettuce with peptide components that reduced bone loss, for example. But when it comes to more complex compounds, the transferred DNA instructions could alter the host’s natural metabolism enough to eventually reduce the output of the desired product. Pengxiang Fan and colleagues wanted to address this issue by introducing instructions in the form of synthetic modules that not only encoded their intended product, but also the molecules used to build it. They hoped to increase the yield of three desired nutrients: creatine, carnosine and taurine.
The team put the swappable synthetic modules to the test in Nicotiana benthamiana, a tobacco-like plant used as a model organism in synthetic biology applications:
The creatine module containing the two genes for creatine synthesis resulted in 2.3 micrograms of the peptide per gram of plant material.
The carnosine peptide was produced using a module for carnosine and another module for one of the two amino acids used to build the peptide, β-alanine. Though β-alanine is naturally found in N. benthamiana, it’s in small amounts, so stacking the modules together increased carnosine production by 3.8-fold.
Surprisingly, for taurine, a double-module approach was unsuccessful for creating the amino acid. Instead, a larger disruption to the metabolism occurred, and little taurine was produced as the plant tried to get things back on track.
Overall, this work demonstrates an effective framework for producing some of the complex nutrients typically found in animals in a living plant system. The researchers say that future work could apply this method to edible plants — including fruits or vegetables, rather than just leaves — or other plants that could act as bio-factories to sustainably produce these nutrients.
The authors acknowledge funding from the National Natural Science Foundation of Zhejiang Province and the Starry Night Science Fund of Zhejiang University Shanghai Institute for Advanced Study.
The American Chemical Society (ACS) is a nonprofit organization chartered by the U.S. Congress. ACS’ mission is to advance the broader chemistry enterprise and its practitioners for the benefit of Earth and all its people. The Society is a global leader in promoting excellence in science education and providing access to chemistry-related information and research through its multiple research solutions, peer-reviewed journals, scientific conferences, e-books and weekly news periodical Chemical & Engineering News. ACS journals are among the most cited, most trusted and most read within the scientific literature; however, ACS itself does not conduct chemical research. As a leader in scientific information solutions, its CAS division partners with global innovators to accelerate breakthroughs by curating, connecting and analyzing the world’s scientific knowledge. ACS’ main offices are in Washington, D.C., and Columbus, Ohio.
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