A new workflow to standardize fossil pollen datasets for ecological research

Peer-Reviewed Publication

THE UNIVERSITY OF BERGEN

 

IMAGE: THE FOSSILPOL WORKFLOW. view more 

CREDIT: UIB

A new study published in Global Ecology and Biogeography presents a step-by-step guide to compile numerous fossil pollen datasets into a user-specific, standardized and clean compilation – ready for further analysis.

Palaeoecology (‘the study of the past’) is important for understanding the history of biodiversity and the biosphere changes over time. By using palaeoecological data such as fossil pollen, scientists try to understand how ecosystems and vegetation changes through time, and how humans have affected the environment throughout history.

In the last ten years, there has been a substantial increase in fossil pollen data from all over the world in open-access databases, opening new avenues for research. But there are some challenges to putting this information together in a way that scientists can use it to study biodiversity changes. Researcher at The Department of Biological Sciences, UiB, and leading first author of the paper “A guide to the processing and standardization of global palaeoecological data for large-scale syntheses using fossil pollen”, Suzette Flantua, has been working on these datasets.

In the last ten years, there has been a substantial increase in fossil pollen data from all over the world in open-access databases. Opening new avenues for research. But, there are some challenges to putting this information together in a way that scientists can use it to study biodiversity changes. Researcher at The Department of Biological Sciences, UiB, and leading first author of the paper “A guide to the processing and standardization of global palaeoecological data for large-scale syntheses using fossil pollen”, Suzette Flantua, has been working on these datasets.

"For several years now we have been compiling thousands of fossil pollen datasets together, and we’ve realized along the way that many critical steps exist that any researcher using these data should be aware of, but there were no clear guidelines anywhere. It was also often unclear how other people processed their data", says Flantua.

To ensure a standardized use of fossil pollen data and minimize the risk of erroneous interpretations, Flantua and her colleagues have created a guide with tips and tricks for compiling fossil pollen data.

"These datasets come from many different environments around the world, they are cored and analyzed by many different researchers, and they represent highly diverse plant assemblages. Before any analysis can be done, such compilation needs to be carefully selected to guarantee good data quality. That is why we have developed a guide on how to standardize these data that are now accessible for many researchers in different fields", says Flantua.

Discipline-friendly guideline to process fossil pollen data

Ondřej Mottl, the leading developer of the software in the guide, and co-leading first author of the paper, says that the guide is designed to make data preparation easy and accessible for everyone, regardless of their coding skills.  

"We understand that handling all data preparation steps can be technically challenging, which is why we've structured our workflow step-by-step and provided clear signposts at each critical juncture. Our software interacts with users throughout the process, guiding them towards the desired dataset for analysis", says Mottl.

The fossil pollen dataset guide consists of a workflow called FOSSILPOL, an R-package (RFossilpol) and a website. The FOSSILPOL workflow handles most of the processing steps (related to depositional environments, chronologies, filtering and taxonomic harmonization, Figure 3), while requiring input from the user at certain steps. All criteria and configurations are defined in one main configuration file, and several R packages are used throughout the workflow. The final outputs of the workflow include a standardized compilation of taxonomically harmonized fossil pollen data, plots of modelled age-depth curves and a pollen diagram for each record, and several overview figures and maps.

Co-leading first authors Vivian Felde and Kuber Bhatta highlight the guide’s potential to increase reproducibility and transparency. 

"It can also be seen as a tool that allows full reproducibility of major data analyses as all decisions throughout the data processing steps are transparent, well documented, and easily reported in studies. In addition, the data compilation is dynamic and will change together with the open access databases as increasingly more data becomes available. This is all thanks to constant data sharing within and between research communities, which we are really excited about”, agree Felde and Bhatta. 

This paper is a contribution to the Humans on Planet Earth - Long-term impacts on biosphere dynamics (HOPE) project at The Department of Biological Sciences, University of Bergen. The HOPE project is funded by a European Research Council Advanced Grant and the project’s goal is to addresses a critical question in Earth system science - what was the impact of prehistoric people on the biosphere and its dynamics?

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JOURNAL

Global Ecology and Biogeography

DOI

10.1111/geb.13693 

ARTICLE TITLE

A guide to the processing and standardization of global palaeoecological data for large-scale syntheses using fossil pollen

Understanding crop pest evolution may boost biocontrol

Peer-Reviewed Publication

INRAE - NATIONAL RESEARCH INSTITUTE FOR AGRICULTURE, FOOD AND ENVIRONMENT

 

IMAGE: EGYPTIAN COTTON LEAFWORM (SPODOPTERA LITTORALIS) view more 

CREDIT: INRAE - MICHEL RENOU

The Egyptian cotton leafworm (Spodoptera littoralis) is a pest species in France. It is found throughout the Mediterranean Basin as well as in Africa and the Middle East. Moth larvae are extremely polyphagous[1] and cause damage to diverse crop species (e.g., corn, legumes, cotton, tomatoes, peppers). As part of broader efforts to reduce pesticide levels, we must develop effective biocontrol methods. Such strategies often rely on disrupting reproduction and trapping moths using, most commonly, sex pheromones. However, pheromone synthesis is an expensive process, and it thus remains important to have other control strategies on hand. To this end, we need to improve our understanding of olfactory receptors in this moth.

In 2019, these research collaborators identified OR5, an olfactory receptor in the Egyptian cotton leafworm that recognises the main compound in the female sex pheromone blend. In this new study, the scientists explored the receptor’s evolutionary trajectory within Spodoptera to better characterise its functionality and specificity. They used a combined approach in which they resurrected ancestral receptors in the laboratory, with the help of computer analysis, and they modelled the 3D structure of the receptors. They were thus able to determine that OR5 appeared around 7 million years ago. The researchers also employed site-directed mutagenesis[2] to explore OR5’s genetic fine-tuning, which allowed them to identify the eight amino acids (AAs) behind the receptor’s high degree of specificity. This finding is particularly unexpected, given that past research on receptor evolution has suggested just one or two AA substitutions suffice to change the functionality of ecologically important receptors.

We must clarify how olfactory receptors emerge and acquire specificity over evolutionary time if we wish to anticipate the development of resistance to pheromone-based plant protection products. This research advances the above goal and, additionally, clarifies the function of OR5, a highly specific receptor that is essential in the reproduction of two Spodoptera species—the Egyptian cotton leafworm and the tobacco cutworm (S. litura). The latter occurs mostly in Asia and is also polyphagous. The discoveries detailed above will help spur the development of new biocontrol strategies that rely on (1) agonist molecules, which occupy receptors to the exclusion of the key pheromone compound, or (2) antagonist molecules, which block the receptor from being activated by the key pheromone compound.

 

This study arose from a collaboration between the Institute of Ecology and Environmental Sciences of Paris (iEES Paris; under the aegis of INRAE, Sorbonne University, CNRS, IRD, UPEC, and Paris Cité University) and the Chinese National Institute of Plant Protection. It was the fruit of the BiPi International Associated Laboratory.

 

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[1]Polyphagous organisms feed on many different species

[2]Site-directed mutagenesis is a technique that introduces one or more precise mutations into a gene to study the functional impacts on the encoded protein.

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JOURNAL

Proceedings of the National Academy of Sciences

DOI

10.1073/pnas.2221166120 

ARTICLE TITLE

A tale of two copies: Evolutionary trajectories of moth pheromone receptors

ARTICLE PUBLICATION DATE

12-May-2023

Disclaimer: AAAS and 

Population analysis reveals the roles of DNA methylation in tomato domestication and metabolic diversity

Peer-Reviewed Publication

SCIENCE CHINA PRESS

 

IMAGE: A: SUMMARY OF WHOLE GENOME BISULFITE SEUQNEICNG DATA. PIM: WILD CURRANT TOMATO (S.PIMPINELLIFOLIUM);CER: CHERRY TOMATO (S.LYCOPERSICUM VAR.CERASIFORME);BIG: CULTIVATED TOMATO (S.LYCOPERSICUM). B, DISTRIBUTION OF DMR ON TOMATO CHROMOSOMES DURING DOMESTICATION AND IMPROVEMENT. C, MULTI-OMICS NETWORK BASED ON ASSOCIATION ANALYSIS OF METABOLITES, SNPS AND DMRS. DOTS, TRIANGLES OF DIFFERENT COLORS REPRESENT DIFFERENT CLASSES OF METABOLITES AND DIFFERENT TYPES OF VARIANT MARKERS, AND LINES REPRESENT SIGNIFICANT ASSOCIATIONS BETWEEN THE TWO. D, IT SHOWS THE IDENTIFIED KNOWN GENES INVOLVED IN THE POLYPHENOL BIOSYNTHESIS PATHWAY AND THE CANDIDATE GENES VERIFIED IN THIS STUDY ARE SHOWN. THE DIFFERENT COLORS OF THE GENES REPRESENT THE GENES IDENTIFIED BY SNP, DMR, OR BOTH. view more 

CREDIT: ©SCIENCE CHINA PRESS

This study is led by Dr. Shouchuang Wang (Sanya Nanfan Research Institute of Hainan University), revealing the role of epigenetic variation in tomato domestication and metabolic diversity from the perspective of population DNA methylation.

The breeding history of tomato which is a world recognized model plant with high nutritional value can be divided into two main stages: domestication and improvement, while metabolites show a rich diversity in the population due to the 'hitchhiking effect'. Previous studies on metabolic diversity in plant populations have been based on single nucleotide polymorphisms (SNPs) as genetic markers, but DNA methylation, as an important epigenetic modification, in relation to domestication and metabolic diversity, is not yet known. By whole genome bisulfite sequencing of nearly 100 tomato core germplasm varieties from around the world, about 10 billion pairs-ended sequencing data were obtained (Figure 1A), and a total of 8,375 differentially methylated regions (DMR) were identified during domestication and improvement (Figure 1B), founding that DNA methylation variation was gradually reduced in multiple dimensions during tomato breeding. By integrating multi-omics data such as vairome, transcriptome and metabolome and association analyzing, a multi-omics association network of metabolite-single nucleotide polymorphism-differential methylation regions was constructed (Figure 1C). Based on this network, 13 candidate genes required for polyphenol production were identified and verified (Figure 1D). Several candidate genes could be identified by two variants simultaneously, but part of candidate genes, such as UGT71AV3, could only be identified by DMR.

This study revealed the role of population DNA methylation variation on tomato domestication and metabolic diversity, and showed that DMR can not only affect the biosynthesis of tomato metabolites together with SNP, but also can identified candidate genes that cannot be captured by SNPs, enriching insights into metabolic diversity.

###

See the article:

Population analysis reveals the roles of DNA methylation in tomato domestication and metabolic diversity

https://link.springer.com/article/10.1007/s11427-022-2299-5

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DOI

10.1007/s11427-022-2299-5 

CRISPR CRITTER

Scientists create first humanised mouse model for rare genetic disease

Reports and Proceedings

EUROPEAN SOCIETY OF ENDOCRINOLOGY

Mice with a defected human gene responsible for a rare genetic disease, called congenital adrenal hyperplasia, have been developed for the first time. The achievement, presented at the 25th European Congress of Endocrinology, may help to develop new therapies for people with the most common type of congenital adrenal hyperplasia.

Congenital adrenal hyperplasia (CAH) is a group of inherited conditions, which affects about 1 in 15,000 births. In the most common form, called 21-hydroxylase deficiency, mutations in the CYP21A2 gene cause the adrenal glands – a pair of small organs located above the kidneys – to produce low levels of cortisol and excess amounts of androgen hormones, such as testosterone. This leads to early puberty, girls having male features, and various health issues. Currently steroid hormone replacement therapy is used for treatment, but this may often have harmful side effects.

In this study, researchers from the University Hospital Carl Gustav Carus in Dresden, Germany, replaced the gene Cyp21a1 in mice with the human gene CYP21A2 carrying a mutation. They found that the genetically modified mice at 20 weeks had enlarged adrenal glands while expressing the human mutated gene. In addition, similarly to the human disease, the mutation caused both male and female mice to have low levels of corticosterone – the main stress hormone in mice that is the equivalent to cortisol in humans – and other hormonal imbalances.

Although animal models for congenital adrenal hyperplasia exist, this is the first to reproduce the human condition in mice and able to survive without any treatments. “Our mice accurately mimic the symptoms seen in human patients,” said lead author Shamini Ramkumar Thirumalasetty. “For example, the female mutant mice also have issues with fertility, which we believe is most probably due to the hormonal imbalances triggered by congenital adrenal hyperplasia.”

This mouse model will now allow the team to study the mechanisms of the disease and to find the most effective treatments. “Although novel treatments are being developed to minimise the side effects of steroid hormones, these drugs lack effective in vivo models for pre-clinical testing,” said Ms Thirumalasetty. “Our mouse can serve as an excellent model to test novel drugs and treatment options for patients with congenital adrenal hyperplasia, such as stem cell therapies, and will facilitate the transition from basic research to the clinic.”

--------ENDS-------

Notes for Editors:

The study “CYP21A2-R484Q mice, a humanized mutant animal model for Congenital Adrenal Hyperplasia” will be presented on Monday 15 May 2023 at the European Congress of Endocrinology at the Halic Congress Center in Istanbul, Turkey. See the full scientific programme here.

The European Society of Endocrinology (ESE) provides a platform to develop and share leading research and best knowledge in endocrine science and medicine. By uniting and representing every part of the endocrine community, we are best placed to improve the lives of patients. With over 5,000 individual members and through the 51 National Societies involved with the ESE Council of Affiliated Societies (ECAS), ESE represents a community of over 20,000 European endocrinologists. We inform policy makers on health decisions at the highest level through advocacy efforts across Europe.

H G WELLS THE ISLAND OF DR. MOREAU 1977

 

THE ISLAND OF LOST SOULS B/W 1932

Butterfly tree of life reveals an origin in North America

Peer-Reviewed Publication

FLORIDA MUSEUM OF NATURAL HISTORY

 

IMAGE: USING THE LARGEST BUTTERFLY TREE OF LIFE EVER CREATED, SCIENTISTS HAVE DETERMINED WHERE THE FIRST BUTTERFLIES ORIGINATED AND WHICH PLANTS THEY RELIED ON FOR FOOD. view more 

CREDIT: FLORIDA MUSEUM PHOTO BY KRISTEN GRACE AND PHYLOGENY BY HILLIS, ZWICKL, AND GUTELL

About 100 million years ago, a group of trendsetting moths started flying during the day rather than at night, taking advantage of nectar-rich flowers that had co-evolved with bees. This single event led to the evolution of all butterflies.

Scientists have known the precise timing of this event since 2019, when a large-scale analysis of DNA discounted an earlier hypothesis that pressure from bats prompted the evolution of butterflies after the extinction of dinosaurs.

Now, scientists have discovered where the first butterflies originated and which plants they relied on for food.

Before reaching these conclusions, researchers from dozens of countries had to create the world’s largest butterfly tree of life, assembled with DNA from more than 2,000 species representing all butterfly families and 92% of genera. Using this framework as a guide, they traced the movements and feeding habits of butterflies through time in a four-dimensional puzzle that led back to North and Central America. According to their results, published this Monday in the journal Nature Ecology and Evolution, this is where the first butterflies took flight.

For lead author Akito Kawahara, curator of lepidoptera at the Florida Museum of Natural History, the project was a long time coming.

“This was a childhood dream of mine,” he said. “It’s something I’ve wanted to do since visiting the American Museum of Natural History when I was a kid and seeing a picture of a butterfly phylogeny taped to a curator’s door. It’s also the most difficult study I’ve ever been a part of, and it took a massive effort from people all over the world to complete.”

There are some 19,000 butterfly species, and piecing together the 100 million-year history of the group required information about their modern distributions and host plants. Prior to this study, there was no single place that researchers could go to access that type of data.

“In many cases, the information we needed existed in field guides that hadn’t been digitized and were written in various languages,” Kawahara said.

Undeterred, the authors decided to make their own, publicly available database, painstakingly translating and transferring the contents of books, museum collections and isolated web pages into a single digital repository.

Underlying all these data were 11 rare butterfly fossils, without which the analysis would not have been possible. With paper-thin wings and threadlike, gossamer hairs, butterflies are rarely preserved in the fossil record. The few that are can be used as calibration points on genetic trees, allowing researchers to record timing of key evolutionary events.

The results tell a dynamic story — one rife with rapid diversifications, faltering advances and improbable dispersals. Some groups traveled over impossibly vast distances while others seem to have stayed in one place, remaining stationary while continents, mountains and rivers moved around them.

Butterflies first appeared somewhere in Central and western North America. At the time, North America was bisected by an expansive seaway that split the continent in two, while present-day Mexico was joined in a long arc with the United States, Canada and Russia. North and South America hadn’t yet joined via the Isthmus of Panama, but butterflies had little difficulty crossing the strait between them.

Despite the relatively close proximity of South America to Africa, butterflies took the long way around, moving into Asia across the Bering Land Bridge. From there, they quickly covered ground, radiating into Southeast Asia, the Middle East and the Horn of Africa. They even made it to India, which was then an isolated island, separated by miles of open sea on all sides.

Even more astonishing was their arrival in Australia, which remained sutured to Antarctica, the last combined remnant of the supercontinent Pangaea. It’s possible butterflies once lived in Antarctica when global temperatures were warmer, making their way across the continent’s northern edge into Australia before the two landmasses separated.

Farther north, butterflies lingered on the edge of western Asia for potentially up to 45 million years before finally migrating into Europe. The reason for this extended pause is unclear, but its effects are still apparent today, Kawahara explained.

“Europe doesn’t have many butterfly species compared to other parts of the world, and the ones it does have can often be found elsewhere. Many butterflies in Europe are also found in Siberia and Asia, for example.”

Once butterflies had become established, they quickly diversified alongside their plant hosts. By the time dinosaurs were snuffed out 66 million years ago, nearly all modern butterfly families had arrived on the scene, and each one seems to have had a special affinity for a specific group of plants.

“We looked at this association over an evolutionary timescale, and in pretty much every family of butterflies, bean plants came out to be the ancestral hosts,” Kawahara said. “This was true in the ancestor of all butterflies as well.”

Bean plants have since increased their roster of pollinators to include various bees, flies, hummingbirds and mammals, while butterflies have similarly expanded their palate. According to study co-author Pamela Soltis, a Florida Museum curator and distinguished professor, the botanical partnerships that butterflies forged helped transform them from minor offshoot of moths to what is today one of the world’s largest groups of insects.

“The evolution of butterflies and flowering plants has been inexorably intertwined since the origin of the former, and the close relationship between them has resulted in remarkable diversification events in both lineages,” she said.

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JOURNAL

Nature Ecology & Evolution

DOI

10.1038/s41559-023-02041-9 

ARTICLE TITLE

A global phylogeny of butterflies reveals their evolutionary history, ancestral hosts and biogeographic origins

ARTICLE PUBLICATION DATE

15-May-2023

Coastal lights trick coral reefs into spawning earlier than they should

Peer-Reviewed Publication

UNIVERSITY OF PLYMOUTH

 

IMAGE: CORAL REEFS IN THE RED SEA - SUCH AS THIS ONE IN THE GULF OF EILAT/AQABA - AND PERSIAN GULF ARE PARTICULARLY AFFECTED BY LIGHT POLLUTION view more 

CREDIT: SAHCHAF BEN EZRA

The light pollution caused by coastal cities can trick coral reefs into spawning outside of the optimum times when they would normally reproduce, a new study has found.

Coral broadcast spawning events – in which lunar cycles trigger the release of eggs on certain nights of the year – are critical to the maintenance and recovery of reefs following mass bleaching and other similar events.

However, using a combination of light pollution data and spawning observations, researchers were able to show for the first time that corals exposed to artificial light at night (ALAN) are spawning one to three days closer to the full moon compared to those on unlit reefs.

Spawning on different nights could reduce the likelihood of coral eggs being fertilised and surviving to produce new adult corals that help reefs to recover after bleaching events and other disturbances.

The research, published in Nature Communications, is the latest to be carried out as part of the Artificial Light Impacts on Coastal Ecosystems (ALICE) project, which is funded by the Natural Environment Research Council.

It builds on research published in December 2021 which mapped out the areas of the ocean most affected by light pollution.

That study found that at a depth of one metre, 1.9 million sq km of coastal ocean are exposed to biologically important ALAN (around 3.1% of the global Exclusive Economic Zones).

For the new study, researchers paired that data with a global dataset of 2,135 coral spawning observations from the 21st century.

This enabled them to demonstrate that ALAN is possibly advancing the triggers for spawning by creating a perceived period of minimum illuminance between sunset and moonrise on nights following the full moon.

Dr Thomas Davies, Lecturer in Marine Conservation at the University of Plymouth, is the study’s lead author and also principal investigator of the ALICE project. He said: “Corals are critical for the health of the global ocean, but are being increasingly damaged by human activity. This study shows it is not just changes in the ocean that are impacting them, but the continued development of coastal cities as we try and accommodate the growing global population. If we want to mitigate against the harm this is causing, we could perhaps look to delay the switching on of night-time lighting in coastal regions to ensure the natural dark period between sunset and moonrise that triggers spawning remains in tact. That would potentially raise a number of economic and safety issues, but is something we potentially need to consider to ensure our coral reefs are given the best chance of survival.”

Dr Tim Smyth, Head of Science for Marine Biogeochemistry and Observations at Plymouth Marine Laboratory and the study’s senior author, added: “This study further emphasises the importance of artificial light pollution as a stressor of coastal and marine ecosystems, with the impacts on various aspects of biodiversity only now being discovered and quantified. A critical first step along that path was enabled with our global in-water light pollution atlas which highlighted for the first time the true extent of the problem, which hitherto had gone unrecognised.”

The study looked at coastal regions all over the world, but coral reefs in the Red Sea and Persian Gulf are particularly affected by light pollution.

They are areas where coastlines have been heavily developed in recent years and where coral reefs are both close to the shore and at particular risk.

Co-author Professor Oren Levy, who heads the Laboratory for Molecular Marine Ecology at Bar-Ilan University in Israel, added: “The Red Sea and the Gulf of Eilat/Aqaba are heavily impacted by Artificial Light at Night (ALAN) due to urbanization and the proximity of the reefs to the coastline. Despite the challenges posed by ALAN, corals in the Gulf of Eilat/Aqaba are known for their thermal tolerance and ability to withstand high temperatures. However, a disturbance in the timing of coral spawning with the moon phases can result in a decline in new coral recruits and a reduction in the coral population. It is crucial that we take immediate action to reduce the impact of ALAN on these fragile marine ecosystems. By implementing measures to limit light pollution, we can protect these vital habitats and safeguard the future of the world's oceans. It's our responsibility to ensure that we preserve the biodiversity of our planet and maintain a healthy and sustainable environment for generations to come.”

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JOURNAL

Nature Communications

DOI

10.1038/s41467-023-38070-y 

METHOD OF RESEARCH

Literature review

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Global disruption of coral broadcast spawning associated with artificial light at night

ARTICLE PUBLICATION DATE

15-May-2023

Numerical experiments reveal initial wind field structure as crucial factor in determining tropical cyclone size and intensity

Peer-Reviewed Publication

INSTITUTE OF ATMOSPHERIC PHYSICS, CHINESE ACADEMY OF SCIENCES

 

IMAGE: TROPICAL CYCLONES OLAF (TOP) AND NANCY (BOTTOM) ON FEBRUARY 16, 2005 OVER SOUTH PACIFIC. view more 

CREDIT: IMAGE COURTESY THE MODIS RAPID RESPONSE TEAM, NASA-GSFC

Tropical cyclones (TCs) are responsible for significant damage to property and human life. The size and intensity of these storms are critical factors in determining the level of destruction they can cause. However, the relationship between a TC's size and intensity during its development phase has been difficult to understand.

Now, a team of researchers led by Professor CHEN Guanghua at the Key Laboratory of Cloud-Precipitation Physics and Severe Storms of the Institute of Atmospheric Physics at the Chinese Academy of Sciences has shed light on this relationship by examining the wind field structure of TCs during their formation.

In a paper published in Advances in Atmospheric Science, the researchers analyzed the relative impacts of two critical parameters - the radius of maximum wind (RMW) and the radial decay of winds outside the RMW - on the degree of size expansion under the same level of intensity increment. 

They found that vortexes with larger RMW and broader wind fields tend to expand more under the same level of intensity increment, highlighting the importance of paying attention to incipient storms with large RMW.

The researchers also discovered that the RMW plays a major role in the size-intensity relationship. Increasing the initial RMW significantly slows down the organization and development of the eyewall convection, leading to slow intensifying. On the other hand, initially broader winds allow for active outer convection and are favorable for size expansion, which can lower wind transports to the inner region and impede intensification when the RMW is large.

"This study is a preliminary attempt to comprehend the physical mechanisms responsible for the variation of size-intensity relationship," said Prof. Chen. "Further research is ongoing to incorporate more complex internal and external forces."

Understanding the size and intensity relationship of TCs is crucial for estimating their potential destruction to humanity. The findings of this study can help improve our ability to predict and prepare for these devastating natural disasters.

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JOURNAL

Advances in Atmospheric Sciences

DOI

10.1007/s00376-023-2233-4 

ARTICLE TITLE

Modulation of the wind field structure of initial vortex on the relationship between tropical cyclone size and intensity

ARTICLE PUBLICATION DATE

12-May-2023

Monkeypox viruses relatively stable on surfaces

Virology

Peer-Reviewed Publication

RUHR-UNIVERSITY BOCHUM

 

IMAGE: CLEANING SURFACES WITH ALCOHOL-BASED DISINFECTANT IS GOOD PROTECTION AGAINST INFECTION. view more 

CREDIT: © RUB, MARQUARD

Weeks of monitoring

Since 2022, the monkeypox virus has been transmitted more and more frequently from one human host to another. Although infections primarily result from direct physical contact, it’s also possible to contract the virus through contaminated surfaces, for example in the household or in hospital rooms. “Smallpox viruses are notorious for their ability to remain infectious in the environment for a very long time,” explains Dr. Toni Meister from the Department for Molecular and Medical Virology at Ruhr University Bochum. “For monkeypox, however, we didn’t know the exact time frames until now.”

The researchers therefore studied them by applying the virus to sanitised stainless steel plates and storing them at different temperatures: at four degrees, at 22 degrees, which roughly corresponds to room temperature, and at 37 degrees. They determined the amount of infectious virus after different periods of time, ranging from 15 minutes to several days to weeks.

Viruses remain infectious for a long time

Regardless of the temperature, there was little change in the amount of infectious virus during the first few days. At 22 and 37 degrees, the virus concentration dropped significantly only after five days. At 37 degrees, no virus capable of reproducing was detected after six to seven days, at 22 degrees it took ten to eleven days until infection was no longer possible. At four degrees, the amount of virus only dropped sharply after 20 days, and after 30 days there was no longer any danger of infection. “This is consistent with our experience that people can still contract monkeypox from surfaces in the household after almost two weeks,” points out Professor Eike Steinmann, Head of the Department for Molecular and Medical Virology.

In order to reduce the risk of infection in the event of an outbreak, it is therefore extremely important to disinfect surfaces. This is why the researchers tested the effectiveness of five common disinfectants. They found that alcohol-based or aldehyde-based disinfectants reliably reduced the risk of infection. A hydrogen peroxide-based disinfectant, however, didn’t inactivate the virus effectively enough in the study. “Our results support the WHO’s recommendation to use alcohol-based surface disinfectants,” concludes Toni Meister.

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JOURNAL

The Journal of Infectious Diseases

DOI

10.1093/infdis/jiad127 

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Stability and inactivation of monkeypox virus on inanimate surfaces

Comprehensive analysis of single plant cells provides new insights into natural product biosynthesis

Single-cell multi-omics reveals that cell types are differentially involved in the production and accumulation of medically relevant plant compounds

MAX PLANCK INSTITUTE FOR CHEMICAL ECOLOGY

 

IMAGE: THE MADAGASCAR PERIWINKLE (CATHARANTHUS ROSEUS) OF THE DOGBANE FAMILY PRODUCES A NUMBER OF ALKALOIDS OF MEDICINAL INTEREST. ANALYSES AT THE LEVEL OF DIFFERENT CELL TYPES ENABLED THE DISCOVERY OF STILL MISSING GENES FOR THE BIOSYNTHESIS OF THE TWO MOST IMPORTANT NATURAL PRODUCTS FROM THE PLANT, VINCRISTINE AND VINBLASTINE (SKELETAL FORMULA), WHICH ARE USED AS CHEMOTHERAPEUTIC AGENTS IN THE TREATMENT AGAINST CANCER. view more 

CREDIT: ANGELA OVERMEYER, MAX PLANCK INSTITUTE FOR CHEMICAL ECOLOGY

Plants are impressive in their diversity, but especially in the variety of metabolites they produce. Many plant natural products are highly complex molecules, such as the alkaloids vincristine and vinblastine, which are produced by the Madagascar periwinkle Catharanthus roseus. These two substances are already indispensable in cancer therapy.

Researchers are very interested in finding out which individual biosynthetic steps are required to form the complex molecules. "Currently, these compounds are still obtained in very small quantities from the plant's leaf extract. We can learn from the plant how this compound is produced and use this knowledge to develop production systems that are more cost-effective, scalable and sustainable," said first author Chenxin Li of the University of Georgia's Center for Applied Genetic Technologies, describing the research goal.

 

Assigning genetic and metabolic information to individual cells of plant organs

The scientists know that gene activity is not the same in all cells of a plant and that the chemistry can differ drastically from cell to cell. Therefore, the goal of the current study was to use a new set of methods collectively termed single-cell omics to investigate specialized and rare cell types that play a central role in the biosynthesis of plant natural products, and whose signals are often obscured by more abundant cell types in plant organs.  "With single-cell omics, we have a method that allows researchers to assign genetic and metabolic information to individual cells. The term omics refers to the fact that an entire collection of genes or metabolites is quantified and analyzed," says Lorenzo Caputi, head of the Alkaloid Biosynthesis Project Group in the Department of Natural Product Biosynthesis in Jena and one of the lead authors, explaining the methodological approach.

 

Biosynthetic pathway of vinblastine - organized in three distinct cell types

As the analyses showed, the entire biosynthetic pathway for the alkaloid vinblastine is organized in three stages and three discrete cell types. "The first stage is expressed exclusively in specialized cells associated with vascular bundles in the leaf, called IPAP.  The second stage of the biosynthetic pathway is expressed only in cells of the epidermis, the layer of cells that cover the leaves, and the last known steps of the biosynthetic pathway are expressed exclusively in idioblasts, a rare cell type of the leaf," Chenxin Li summarizes the results.

The researchers measured the concentrations of several intermediates in the metabolic pathway for vinblastine in single cells and were surprised: "Two important precursors of vinblastine, catharanthine and vindoline, occur in the idioblast cells at millimolar concentrations, about three orders of magnitude higher than vinblastine itself. The concentration of the two precursors in these cells was much higher than we expected and even exceeded their concentrations in whole organ extracts. However, this observation makes sense in that catharanthine and vindoline were found only in the rare idioblast cells. The abundant other cells in the leaf dilute the high concentration when whole leaves are crushed," says Sarah O’Connor, head of the Department of Natural Product Biosynthesis.

The research team is confident that the organization of biosynthetic pathways for medicinally relevant alkaloids in Catharanthus roseus is not an isolated phenomenon. "We are just beginning to understand how and why such a cell type-specific organization exists. In addition, analysis of genes expressed simultaneously in a particular cell type has helped us identify new players in this metabolic pathway. The same technique can be used to study the biosynthesis of many other natural products. Finally, the exact sites of accumulation of plant compounds, such as the epidermis, the vascular system, or latex duct, can help us hypothesize the ecological roles of natural products. For example, depending on the pattern of accumulation, the compounds may be more effective against biting insects than they are against sap-sucking insects," says Robin Buell, Professor at Georgia University.

A better understanding of the biosynthetic pathways of the anti-cancer drugs vincristine and vinblastine may also help to produce or harvest these compounds more effectively in the long term. The use of methods described is also promising for the study of many other interesting and medically important natural products from the plant kingdom. The approach described here will help to narrow down these rare and specialized cells and uncover the gene activities and chemistry that are exclusive to them.

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JOURNAL

Nature Chemical Biology

DOI

10.1038/s41589-023-01327-0 

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

Cells

ARTICLE TITLE

Single-cell multi-omics in the medicinal plant Catharanthus roseus

ARTICLE PUBLICATION DATE

15-May-2023