Uncovering the secret masks behind algae growth in the south-to-north water diversion project using advanced AI

Peer-Reviewed Publication

KEAI COMMUNICATIONS CO., LTD.

 

IMAGE: FIGURE 1 SKETCH MAP OF SAMPLING STATIONS DISTRIBUTION IN THE MIDDLE SECTION OF THE SOUTH-NORTH WATER DIVERSION PROJECT AND DRIVING FACTORS OF ALGAL GROWTH BASED ON BLOOMFORMER-1 MODELLING view more 

CREDIT: JING QIAN, KARLSRUHE INSTITUTE OF TECHNOLOGY (KIT), GERMANY, AND INSTITUTE OF HYDROBIOLOGY (IHB), CHINA

Identifying the factors contributing to algal growth accurately and reliably is vital for sustainable use and scientific management of freshwater resources. As scientific research evolves from using small data sets to larger ones, the shortcomings of traditional machine learning become clearer, and deep learning which is adept at processing large amounts of data, is getting more attention. Although it has been used occasionally for forecasting chlorophyll-a (Chl-a) time series, deep learning has hardly been employed to identify important factors concerning algal growth.

To address this gap, a cross-national team of researchers from China, Germany and The Netherland developed a deep learning-based Transformer model, Bloomformer-1, designed for end-to-end identification of algal growth driving factors.

“Deep learning models have lower operational transparency compared to traditional machine learning, but they exhibit significant advantages in performance,” said Jing Qian, the first author of the paper. “The development of Bloomformer-1 aims to create a win-win situation in terms of interpretability and performance, enabling the driving factors of algal growth to be identified transparently and accurately.”

Qian, a doctoral student from the Karlsruhe Institute of Technology in Germany, conducted this research as a jointly-cultivated doctoral student at the Institute of Hydrobiology in China.

The Middle Route of the South-to-North Water Diversion Project (MRP), a national large-scale project in China, was selected as the study site to demonstrate the superior performance of Bloomformer-1. It was compared to four widely used traditional machine learning models—extra trees regression (ETR), gradient boosting regression tree (GBRT), support vector regression (SVR), and multiple linear regression (MLR)—with the highest R2 (0.80 to 0.94) and lowest RMSE (0.22 to 0.43 μg/L).

"Bloomformer-1 employs the multi-head-self-attention mechanism, which compares each token in the input sequence with other tokens to collect and learn dynamic contextual information, thus enabling a thorough understanding of all the field sampling data. This is one of the reasons for its superior performance," said co-author Stefan Norra from the University of Potsdam.

The results of study, published in the KeAi journal Water Biology & Security, revealed that total phosphorus (TP) was the most significant factor affecting the MRP, especially in the Henan section, while total nitrogen (TN) had the most substantial impact on algal growth in the Hebei section.

“Controlling and reducing phosphorus is an important strategy for controlling algal growth and maintaining stable MRP water quality, while nitrogen control in the Hebei region is also worth paying attention to," said Yonghong Bi from the Institute of Hydrobiology, Chinese Academy of Sciences, who is the corresponding author of the study. "Furthermore, the promotion and application of Bloomformer-1 in other water bodies will be an important task going forward.”

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Contact the author: Jing Qian, Karlsruhe Institute of Technology (KIT), Germany, and Institute of Hydrobiology (IHB), China, jing.qian@partner.kit.edu

The publisher KeAi was established by Elsevier and China Science Publishing & Media Ltd to unfold quality research globally. In 2013, our focus shifted to open access publishing. We now proudly publish more than 100 world-class, open access, English language journals, spanning all scientific disciplines. Many of these are titles we publish in partnership with prestigious societies and academic institutions, such as the National Natural Science Foundation of China (NSFC).

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JOURNAL

Water Biology and Security

DOI

10.1016/j.watbs.2023.100184 

METHOD OF RESEARCH

Computational simulation/modeling

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Identification of driving factors of algal growth in the South-to-North Water Diversion Project by Transformer-based deep learning.

Compound from magnolia tree bark impedes SARS-CoV-2 replication in certain cells

Peer-Reviewed Publication

AMERICAN SOCIETY FOR MICROBIOLOGY

Washington, DC – A compound called honokiol, which is found in the bark of multiple species of magnolia tree, inhibits replication of SARS-CoV-2 virus in several types of cells, according to a team of researchers in the Netherlands. The research is published in Microbiology Spectrum, a journal of the American Society for Microbiology. 

The researchers found that Honokiol inhibits replication of SARS-CoV-2 in several cell types, causing production of infectious SARS-CoV-2 particles in treated cells to fall to around 1,000th of the previous level. 

The compound also inhibited replication of other highly pathogenic human coronaviruses, including MERS- and SARS-CoV. “This suggests that it has a broad spectrum of activity and would likely also inhibit novel coronaviruses that might emerge in the future,” said Martijn J. van Hemert, Ph.D., Associate Professor, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands. 

The motivation for the research was the lack of vaccines and treatments early in the pandemic, and the desire to be prepared for the next new coronavirus. To this end, van Hemert emphasized that his group, as well as others from around the world, responded to COVID-19 by testing many compounds for antiviral effects. 

“If honokiol can be developed into a drug, possibly in combination with other compounds, stockpiling it would help us to increase our preparedness for the emergence of the next coronavirus,” said van Hemert. “Broad-spectrum drugs could then be used to treat early patients and prevent spread, or they could be used prophylactically among healthcare workers, and in high-risk groups, such as among nursing home residents.”  

Honokiol also has anti-inflammatory properties, van Hemert noted. That, he said, could be helpful in cases where patients wait until a relatively late stage of the disease to obtain medical treatment—a frequent occurrence—by which time the body’s own inflammatory responses to the infection are causing symptoms. “At that point, inhibition of virus replication might no longer be helpful, but honokiol’s anti-inflammatory response might mitigate the illness,” van Hemert explained.

Honokiol inhibits a later step of the viral replication cycle—one that takes place after the virus has entered the cell. The investigators suspect that honokiol does so by triggering processes in the host cell that impede replication of the virus. It did so in the case of the original SARS-CoV-2 variants, and also in that of the more recent omicron variants. 

At this early stage in the research, “Our study merely provides the basis for further research into potential therapeutic applications,” said van Hemert. “It is important to mention that it is too early to claim that honokiol might be used in SARS-CoV-2 patients. This requires much more research and—if successful—properly conducted clinical trials.” 

Van Hemert learned about honokiol from Jack Arbiser, M.D., Ph.D., of Emory School of Medicine, during the early stages of the pandemic. Arbiser had been researching honokiol’s anticancer properties, and he told van Hemert he thought that the effects of the compound on the host cell might be beneficial for treatment of COVID-19 patients as well.

Clarisse Salgado-Benvindo, a Ph.D. student in van Hemert’s group, performed most of the experiments, using cultured cells that the researchers infected with SARS-CoV-2, or the highly pathogenic coronaviruses SARS-CoV and MERS-CoV. Experimenters worked inside a BSL-3 lab, which is a special high containment lab, while wearing protective suits with full-face masks to prevent infection.

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The American Society for Microbiology is one of the largest professional societies dedicated to the life sciences and is composed of 30,000 scientists and health practitioners. ASM's mission is to promote and advance the microbial sciences.

ASM advances the microbial sciences through conferences, publications, certifications, educational opportunities and advocacy efforts. It enhances laboratory capacity around the globe through training and resources. It provides a network for scientists in academia, industry and clinical settings. Additionally, ASM promotes a deeper understanding of the microbial sciences to diverse audiences.

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JOURNAL

Microbiology Spectrum

Effective capital markets are needed to protect the climate

Peer-Reviewed Publication

POTSDAM INSTITUTE FOR CLIMATE IMPACT RESEARCH (PIK)

A new study investigates the role of effective capital markets for climate protection and the energy transition. Banks collect savings and make them available as loans and the greater the difference between savings and loan interest rates, the more it costs to invest. This affects, for example, investments in fossil-free steel plants, power generation, or heating systems. The analysis by the Potsdam Institute for Climate Impact Research (PIK) and the Mercator Research Institute on Global Commons and Climate Change (MCC) has now been published in the renowned Journal of the Association of Environmental and Resource Economists (JAERE).

The study shows that the effect on climate protection is striking: the current difference between savings and lending rates, 5.1 percentage points on average globally, results in additional global heating of 0.2 degrees Celsius, when compared with a frictionless economy with zero interest spread. To calculate this in its model-based analysis, the research team assumes a climate policy according to the cost-benefit principle. This implies: the government would know the exact level of climate damage that increases over time, rendering CO2 emissions more expensive in accordance with the damage caused by them, and would thus achieve a cost-optimal time path for accelerated carbon pricing. Alternatively, if the policy is oriented on a fixed temperature target, the current interest spread means that a 27 percent higher carbon price would be needed than in a world without the credit cost premium.

The study's key message for policymakers is summarised by its PIK lead author, Kai Lessmann, as follows: “Governments need to take a close look at whether the higher interest rate for loans merely reflects the actual intermediation costs or whether it is also a result of too little banking competition, for which there is some evidence. If the market structure is indeed the reason for the spread, and cannot be modified in the medium term, then policymakers can effectively counteract it in the short term by subsidising investment.” In this context, the study shows that if the government decides to provide economy-wide investment support, this is better for the climate and the economy than if eco-projects alone are subsidised. “The structural change toward fossil-free technologies then occurs automatically,” Lessmann points out. “These are generally more capital-intensive and thus benefit to a greater extent from reduced credit costs. Also, the carbon price, which increases over time, exerts its steering effect."

For the study, the research team has developed a sophisticated computational model, and has fed it with empirical data. “We identify eight different channels through which the credit cost premium ultimately affects climate gas emissions,” explains Co-author Matthias Kalkuhl of MCC. “To be sure, there are also restraining effects – for example, high interest rates reduce the growth of economic output and thus also of energy consumption. But the climate-damaging impact predominates. For example, the credit cost premium increases the abatement costs per tonne of CO2, so that when oriented to the cost-benefit calculation, less climate protection is then practiced as a result.”

The adverse impact of high borrowing costs on climate protection, which is now illustrated more sharply than before, is a major issue primarily in the Global South. In many countries, it is not uncommon for the annual costs of capital as a percentage of the investment sum to be in double digits. While many solar or wind power parks would be more profitable than gas or coal-fired power plants in the long term, they are not being built there, because the initial capital required per megawatt of installed capacity is greater. Governments often lack the money to react, so they rely on help from the rich north.

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JOURNAL

Journal of the Association of Environmental and Resource Economists

DOI

10.1086/725920 

ARTICLE TITLE

Climate finance intermediation: interest spread effects in a climate policy model

 

Prevalence of mental health diagnoses in children and adolescents before, during pandemic

JAMA Network Open

Peer-Reviewed Publication

JAMA NETWORK

About The Study: The results of this cross-sectional study suggest that trends in mental health diagnoses among children and adolescents in the U.S. differed greatly by age and sex over the course of the COVID-19 pandemic. Female youth, especially female adolescents, represented the most vulnerable population with regard to marked increases in the prevalence of mental health diagnoses during the pandemic, the most pronounced being the prevalence of eating disorders. 

Authors: Loreen Straub, M.D., M.S., of Brigham and Women’s Hospital and Harvard Medical School in Boston, is the corresponding author. 

To access the embargoed study: Visit our For The Media website at this link https://media.jamanetwork.com/ 

(doi:10.1001/jamanetworkopen.2023.14415)

Editor’s Note: Please see the article for additional information, including other authors, author contributions and affiliations, conflict of interest and financial disclosures, and funding and support.

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About JAMA Network Open: JAMA Network Open is an online-only open access general medical journal from the JAMA Network. On weekdays, the journal publishes peer-reviewed clinical research and commentary in more than 40 medical and health subject areas. Every article is free online from the day of publication.

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JOURNAL

JAMA Network Open

'Lost' immune cells partly to blame for reduced vaccine response in older people

Consequences of cells not being in the right place at the right time lead to immune system defects.

Peer-Reviewed Publication

BABRAHAM INSTITUTE

 

IMAGE: MICROSCOPY IMAGE OF A GERMINAL CENTRE STRUCTURE WHICH IS ALTERED IN AGED MICE. view more 

CREDIT: BABRAHAM INSTITUTE

Understanding the ways our immune response changes as we age holds the key to designing better vaccines and boosting protection for people most at risk. Research published by Dr Michelle Linterman and her group today in Nature Immunology has explained that the organisation of the germinal centre, which is vital to the generation of longer-lived protection following vaccination, is altered in ageing. By demonstrating that these age-related changes can be reversed in mice, the research sets the foundation for interventions that bolster an effective vaccine response.

After a vaccination our immune system reacts by creating specialised structures called germinal centres that produce the immune cells (B cells) that provide long-term protection through the production of antibodies. Due to an age-dependent impairment in antibody production, older people have lower levels of protection from vaccination which also wanes more quickly compared to younger people. Protection by vaccination is essential to protect older people who become more susceptible to infections with age. Therefore, understanding how the age-related decline of the immune system can be reversed or mitigated is an important part of securing better health in later years.

The correct function of the germinal centre response requires the coordination of cellular interactions across time and space. Germinal centres are made up of two distinct regions – the light zone and dark zone, with some cells located in specific areas, and others which move between the zones. B cells are shaped by their interactions in first the dark zone and then in the light zone.

Through a combination of mouse research, computer modelling and analysis of human vaccination data, the Linterman lab research team were able to show that changes to key interactors of B cells in the light zone of the germinal centre, T follicular helper cells, and also to light-zone specific cells called follicular dendritic cells (FDCs), were at the heart of the diminished vaccination response.

Dr Michelle Linterman, a group leader in the Institute’s Immunology programme, explains “In this study we looked at what was happening to different cell types in the germinal centre, particularly the structure and organisation of the germinal centre across its two functionally distinct zones, to try and understand what causes the reduced germinal centre response with age.

"What we found is that the T follicular helper cells aren’t where they should be and as a result, antibody-producing cells lose essential selection cues. Surprisingly we also uncovered an unknown role for T follicular helper cells in supporting the expansion of follicular dendritic cells in the light zone after vaccination."

The team used 3D computer modelling to simulate the loss of Tfh cells from the light zone and a reduced FDC network, which recapitulate their findings and strengthened their hypothesis that these two factors were enough to be responsible for a suboptimal germinal centre response in aged mice.

Having identified the dependencies between the cell types, the researchers used genetically modified mice to control the location of Tfh cells in the germinal centre, demonstrating that the defective FDC response was caused by loss of Tfh from the light zone. Importantly, they were also able to correct the defective FDC response and boost the germinal centre response in aged mice by providing T cells that could correctly localise to the light zone.  

The team also utilised data from human vaccination studies and found similar age-dependent changes in mice and humans.

“These findings give us a more complete picture of what the effects of age are on the germinal centre and vital insight into how we might address these in terms of developing effective strategies for enhancing vaccine response in older people” concluded Dr Linterman.

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JOURNAL

Nature Immunology

DOI

10.1038/s41590-023-01519-9 

METHOD OF RESEARCH

Experimental study

ARTICLE TITLE

Spatial dysregulation of T follicular helper cells impairs vaccine responses in aging

ARTICLE PUBLICATION DATE

22-May-2023

Corals mark friendly algae for ingestion—revealing possible conservation target

Understanding how corals tell which algae to take up is an important step in gathering information that will help experts mitigate coral bleaching

Peer-Reviewed Publication

CARNEGIE INSTITUTION FOR SCIENCE

 

IMAGE: THE SOFT, PULSING XENIA CORAL GROWING IN CARNEGIE’S CORAL RESEARCH FACILITY IN BALTIMORE. view more 

CREDIT: PHOTOGRAPH BY ED HIRSCHMUGL AND NAVID MARVI, COURTESY OF THE CARNEGIE INSTITUTION FOR SCIENCE.

Baltimore, MD—New research led by Carnegie’s Yixian Zhen and Minjie Hu reveals how coral cells tag friendly algae before ingesting them, initiating a mutually beneficial relationship. This information could guide next-level coral conservation efforts.  

Their work is published in Nature Microbiology. 

Corals are marine invertebrates that build large exoskeletons from which reefs are constructed. But this architecture is only possible because of a mutually beneficial relationship between the coral and various species of single-celled algae called dinoflagellates that live inside individual coral cells. These algae convert the Sun’s energy into food using a process called photosynthesis and they share some of the nutrients they produce with their coral hosts.

Coral reefs have great ecological, economic, and aesthetic value. Many communities depend on them for food and tourism. Despite this, human activity is putting strain on these fragile communities. Warming oceans, pollution, and acidification all affect this symbiotic relationship.

“Many corals are particularly sensitive to elevated temperatures,” explained Hu. “As oceans heat up, they lose algae, starve due to the lack of nutrients, and die off, a phenomenon called bleaching, because it leaves the coral skeleton looking ghostly white."

For several years, teams of Carnegie researchers, including Zheng and Hu, have been elucidating the molecular and cellular mechanisms underpinning coral-algae symbiosis. Understanding these processes could inform strategies to prevent bleaching and promote coral resilience. 

In this new study, the researchers—including Carnegie’s Yun Bai and Xiaobin Zheng—deployed sophisticated bioinformatic and molecular biology tools to reveal the early steps of symbiosis, during which the algae are taken up into the coral. They found a molecule called LePin, which the coral secretes. It is concentrated in the mouth of corals, where it may bind to incoming algae, marking them for uptake into coral cells. 

“Understanding how corals tell which algae to take up is an important step in gathering information that will help us mitigate coral bleaching,” Zheng said. 

LePin is evolutionarily conserved among soft corals, stony corals, and anemones that perform symbiosis with algae, which means that it could be a good target for efforts to genetically engineer at-risk corals to increase their hardiness in the face of temperature increases. 

“Gaining a deeper understanding of LePin could enable us to differentiate how some species of coral are better able to identify and take up heat-resistant algae than others,” Zheng explained. “Once isolated, the LePin sequences that are capable of identifying hardier and more heat-resistant algae could be transplanted into vulnerable coral populations to reduce bleaching events.”

In 2020, Zheng was selected as one of 15 scientists awarded a highly competitive grant from the Gordon and Betty Moore Foundation to support research on symbiosis in aquatic systems. She has been building on Carnegie’s long-standing tradition of model organism development to understand the molecular mechanisms of endosymbiosis in coral. These efforts illustrate how modern biomedical techniques can be applied to solving urgent ecological challenges—a research priority for Carnegie.  

An illustration showing how LePin tags (shown in blue) are secreted from the coral cell and used to mark algae for uptake.

CREDIT

Artwork by Navid Marvi courtesy of the Carnegie Institution for Science.

__________________

This work was supported by the Gordon and Betty Moore Foundation.

The Carnegie Institution for Science (carnegiescience.edu) is a private, nonprofit organization headquartered in Washington, D.C., with three research divisions on both coasts. Since its founding in 1902, the Carnegie Institution has been a pioneering force in basic scientific research. Carnegie scientists are leaders in the life and environmental sciences, Earth and planetary science, and astronomy and astrophysics.

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JOURNAL

Nature Microbiology

DOI

10.1038/s41564-023-01397-9 

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

Animals

ARTICLE TITLE

'Coral–algal endosymbiosis characterized using RNAi and single-cell RNA-seq

ARTICLE PUBLICATION DATE

22-May-2023

WVU researchers see need to strengthen mental health programs for first responders

Peer-Reviewed Publication

WEST VIRGINIA UNIVERSITY

 

IMAGE: MENTAL HEALTH PROGRAMS TO COMBAT INCREASING STRESS AMONG FIRST RESPONDERS NEED STRENGTHENED, ACCORDING TO WEST VIRGINIA UNIVERSITY RESEARCH. view more 

CREDIT: WVU ILLUSTRATION/AIRA BURKHART

Controlling traumatic situations is synonymous with the daily duties of first responders, yet many mental health programs to combat the increasing stress they encounter are lacking. That’s why West Virginia University researchers are identifying steps policymakers and community members can take to aid front-line workers.

“With elevated risk for suicide and other mental health issues among first responders, we have a significant public health problem,” said Michael Fisher, assistant professor in the WVU School of Public Health Department of Health Policy Management and Leadership, who led a study analyzing mental health and first responders in one state.

“These issues rarely make front-page news and may not always garner widespread support and financial resources. This situation began to change amid the COVID-19 pandemic, but policymakers and the public need to be informed about these issues so that appropriate policies, programs and resources can ensue.”

Results of the study led researchers to offer five recommendations: link first responders with culturally competent clinicians; establish one or more centralized organizations to coordinate policy and programming activities; examine models of regional collaboration; expand mental health policy and program research and evaluation efforts; and pass legislation to advance mental health policy and program coordination and implementation.

Two federal proposals — the Fighting Post-Traumatic Stress Disorder Act and the Helping Emergency Responders Overcome Act — haven’t gained traction. However, measures on state and local levels are showing promise and those are the ones Fisher and his team want to hold up as examples.

“I wanted to investigate some of those activities,” Fisher said. “There is a dynamic landscape of emerging approaches to mental health prevention and treatment for first responders, but there is still so much to be learned, both about the effectiveness of specific approaches and about the landscape of programs available or, in some cases, not available.”

Fisher chose to focus on Ohio for the study because it is one of the few states where extensive support measures for first responders have been enacted. In 2021, legislation was passed to examine expanding eligibility for workers’ compensation benefits for first responders suffering from PTSD. The same year, Ohio implemented a state-level office focused on the well-being of first responders to coordinate specialized support and training.

The study, published in the Community Mental Health Journal, elicits perspectives on policy and programmatic activities for front-line personnel. Joining Fisher in the study was Catherine D. Lavender, Department of Occupational Therapy & Occupational Science, College of Health Professions, Towson University.

“We were not looking to quantify or evaluate aspects of policies or programs, but instead seeking to understand contextual factors influencing policy or program development and implementation,” Fisher said. “We had two research questions guiding our study. First, how are Ohio’s first responder communities advancing mental health policies and programs? Second, what are the opportunities and challenges faced by these individuals?”

Between March 2021 and June 2022, researchers interviewed firefighters, emergency medical service professionals and law enforcement officers employed in Ohio. Their insights revealed increases in job stress and first responder deaths by suicide as factors intensifying the need for mental health programs and policies. At the same time, they said a decrease in mental health stigma opens the door for more people to seek help. 

Most participants said they saw a heightened workload, often because of staffing constraints. On top of that, situations such as violent crime and drug overdoses added to their stress. Although they were able to complete their duties, they recognized it came with an emotional, physical and mental cost. For example, these pressures can result in compassion fatigue — physical and mental exhaustion and emotional withdrawal experienced by those who care for sick or traumatized people over an extended time.

While nearly all interviewees cited mental illness stigma as a concern for first responder professions, they noted a decline in those levels as colleagues — particularly the younger ones — are more open to peer discussion. However, they said a divide still exists with some first responders thinking they will appear weak or face job-related repercussions if they admit to mental health struggles.

The size of departments or jurisdictions played a role in the types of mental health support available, participants said. Access to programs ranged from extensive peer support to health-focused apps that connect them to resources. While small or rural departments sometimes face barriers to robust programming, others benefit from collaborations and less formal resources they term as “mutual aid agreements for mental health.” Insurance coverage for obtaining mental health treatment also reportedly varied, depending on the size and resources of the jurisdiction.

Fisher plans to use the study as preliminary data for future research which could focus on several themes raised by participants that he believes warrant further investigation.

“I hope this study, in conjunction with other research on first responder mental health and wellbeing, can raise awareness and inform policy and program development,” Fisher said.

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JOURNAL

Community Mental Health Journal

DOI

10.1007/s10597.023.01121.1 

ARTICLE TITLE

Ensuring Optimal Mental Health Programs and Policies for First Responders: Opportunities and Challenges in One U.S. State

ARTICLE PUBLICATION DATE

22-Mar-2023

Identifying the bee’s knees of bumble bee diets

Study details flower preferences for Midwest species

Peer-Reviewed Publication

OHIO STATE UNIVERSITY

COLUMBUS, Ohio – A new study has identified the bee’s knees of bumble bee dietary options in Ohio and the Upper Midwest.

By viewing almost 23,000 bumble bee-flower interactions over two years, researchers found that these bees don’t always settle for the most abundant flowers in their foraging area – suggesting they have more discerning dietary preferences than one might expect.

Being large, strong and social bees that can fly for long distances, bumble bees are major contributors to pollination, particularly for agriculture – but like other pollinators threatened by habitat loss, climate change and disease, the numbers of some species are dwindling.

This new data can help guide planting decisions for professional and amateur conservationists alike, researchers say.

“Getting over 20,000 observations of individual identified bumble bees visiting particular flower species is pretty incredible for a dataset,” said Karen Goodell, senior author of the study and a professor of evolution, ecology and organismal biology at The Ohio State University’s Newark campus. “One of the keys for this project was having flower associations, as well as estimates of flower abundance, so we counted the flowers, too.”

In no particular order, the top flower species preferred by an aggregate of bumble bee species in Ohio are milkweed, native thistles, morning glory, purple cone flower, bee balm, beardtongue, red clover, vetch and rosinweed, or cup plant. Two other “bee magnet” plants in low abundance that were crawling with the fuzzy buzzers are Culver’s root and wild indigo.

The study was published recently in the journal Ecosphere.

Of the 16 bumble bee species historically found in Ohio, researchers observed only 10 species, eight of which were abundant enough to include in the analysis – including the American Bumble Bee (Bombus pensylvanicus), which is under consideration for addition to the Federal Endangered Species List. As expected, the most frequently observed species – 11,555 visits in all – was the Common Eastern Bumble Bee (Bombus impatiens), compared to only 31 observations of the American Bumble Bee.

In fact, despite the extensive sampling, the authors are confident in the range of preferred flowers for only the three most common species. For the five less common species, researchers didn’t witness enough bee-flower interactions to fully account for what they eat. That sparseness of data on the rarer species speaks to the need for this comprehensive analysis, researchers said.

“It’s really important to know what species we do have and what they like to eat, because any of them could become rare,” Goodell said. “It’s not like we’re doing a fantastic job of taking care of our natural areas. The more information we have about their preferences, the better we can manage their habitat.”

Research team members visited 228 locations in Ohio during the summer months of 2017 and 2018, for a total of 477 hours, and observed bumble bees interacting with 96 different species of wildflowers. The sites included unmanaged fields, restored roadsides and meadows, and planted urban patches and hayfields.

The data analysis showed strong nonrandom patterns of bumble bee visits to flowers, meaning the bees selected specific plants in greater proportion than their availability would suggest. Researchers used a selection index to gauge bees’ flower preferences that compared the frequency of bumble bee species visits to the flowers’ overall percent abundance.

“What we were trying to get at was if all else is equal, what do they actually prefer?” said first author Jessie Lanterman Novotny, who led much of the project as an Ohio State PhD student and postdoctoral researcher in Goodell’s lab. “There were flowers that were less abundant that bees actively sought out – they didn’t necessarily eat what was most abundant. There were also plants they avoided: No matter how many of certain flowers there were, they said, ‘No thanks.’”

The researchers identified a few plants that are highly abundant and commonly used in pollinator conservation plantings and seed mixes that bumble bees consistently ignored, including alsike clover, black-eyed Susan and prairie cone flower. Five of the eight bumble bee species also were strongly drawn to non-native plants, which poses a dilemma for conservation planters focused on preserving native plant species.

And it turns out the three most common species don’t all feast at the same flower “table.”

“We compared the flowers each bumble bee species used the most, and species only overlapped by one-third or less,” said Lanterman Novotny, now a visiting assistant professor of biology at Hiram College. “Low overlap could relieve competition, so all these species can coexist together.”

This work was supported by the Ohio Department of Transportation.

Additional co-authors included former Ohio State PhD student Andrew Lybbert, now at Methodist University, and Paige Reeher and Randall Mitchell of the University of Akron.  

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Contacts:
Karen Goodell, Goodell.18@osu.edu
Jessie Lanterman Novotny, JessieLantermanNovotny@gmail.com

Written by Emily Caldwell, Caldwell.151@osu.edu

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JOURNAL

Ecosphere

DOI

10.1002/ecs2.4425 

METHOD OF RESEARCH

Observational study

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Bumble bee banquet: Genus- and species-level floral selection by Midwestern Bombus

What constitutes a paradigm shift? An olive shrub’s mating system as a case study of Kuhn’s theory

Peer-Reviewed Publication

UNIVERSITY OF CHICAGO PRESS JOURNALS

Philosopher Thomas Kuhn’s influential theory of how scientific knowledge is built introduced the term “paradigm shift” to explain a transformation of a field’s ideas and methods. “A Paradigm Shift, or a Paradigm Adjustment? The Evolution of the Oleaceae Mating System as a Small-Scale Kuhnian Case Study,” a new paper published in The Quarterly Review of Biology, seeks to apply this analytical framework to a small controversy in population biology: the mating system of the shrub Phillyrea angustifolia.

Traditional theory states that the sex ratio of a population should be 1:1 male to female (or highly skewed towards hermaphrodites in male-hermaphrodite populations). But natural populations of P. angustifolia, a shrub in the olive family native to the Mediterranean, have unexpected high frequencies of males, note authors Alexandre Francq, Pierre Saumitou-Laprade, Philippe Vernet, and Sylvain Billiard.

Several possible solutions were floated to resolve this paradigm crisis. One postulated that hermaphroditic individuals were functionally female. Another suggested that a mechanism known as self-incompatibility made it so pollen emitted by males was more successful at fertilization than pollen emitted by hermaphrodites (and also eliminated the advantage of self-fertilization in hermaphrodites). 

The issue was ultimately resolved with the discovery of the link between a distortion segregation biased towards males and a diallelic self-incompatibility system, which advantaged male reproductive fitness. “Hermaphrodites can reproduce through their ovules and pollen, while males can only reproduce through their pollen, but hermaphrodites can only sire approximately one-half of the hermaphrodites … while males can sire all hermaphrodites,” the authors explain. 

Francq, Saumitou-Laprade, Vernet, and Billiard use several criteria to analyze if this discovery and change comports to Kuhn’s theory and represents a true paradigm shift, or only a paradigm adjustment. While the question of P. angustifolia’s sex ratio is a small one, the authors conclude it is indeed an example of an anomaly and associated crisis, central concepts in Kuhn’s theory. And while the discovery “did not change anything to the way most biologists of evolution practice science, it drastically changed the way groups dedicated to plant mating systems pursued their research.”

The question also embodies several examples of what Kuhn called the incommensurability of paradigms. These include the possibility that the same hermaphroditic P. angustifolia plant could be considered functionally as a female, in one paradigm or true hermaphrodites, in another, and the fact that different specialty fields studying the problem were too distinct from each other and unable to operate on common ground, the authors say. Resistances to the shift also arose after the discovery of the mating system, an inherent component to Kuhn’s theory, and the authors also discuss possible future challenges to the new paradigm. 

Ultimately, the authors conclude that the discovery of the diallelic self-incompatibility system in P. angustifolia does indeed fulfill the conditions necessary to constitute a paradigm shift. “Overall, a Kuhnian analysis of this small-scale case study offers a unique opportunity to analyze how science works in action, study some phenomena that are rarely observed for high-level paradigms (e.g., scientists’ conversion from the old to the new paradigm), and thoroughly analyze the roles played by the confrontation between models and data in a paradigm shift,” the authors write.

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JOURNAL

The Quarterly Review of Biology

DOI

10.1086/725275 

ARTICLE TITLE

A Paradigm Shift, or a Paradigm Adjustment? The Evolution of the Oleaceae Mating System as a Small-Scale Kuhnian Case Study

New book eyes Earth's excavators, from microbes to elephants and dinosaurs

Paleontologist explores a billion years of animals breaking up rocks, bones, shells and wood

Book Announcement

EMORY UNIVERSITY

22-MAY-2023

 

IMAGE: EMORY UNIVERSITY PALEONTOLOGIST ANTHONY MARTIN'S LATEST BOOK IS AIMED AT GENERAL AUDIENCES. view more 

CREDIT: ANTHONY MARTIN

The ordinary person looks at Georgia’s Stone Mountain and sees a solid, unmovable monolith. Emory University paleontologist Anthony Martin, who thinks in geologic time, sees something more akin to a giant sugar cube.

Ever since the crystalized mass of igneous-born minerals rose from deep underground, pushed by the upwelling of magma that formed the Blue Ridge Mountains around 350 million years ago, the giant rock’s flanks have faced continuous assault — and not just from weather and water.

Stone Mountain “is fighting a battle against life, and life is winning,” Martin writes in the preface of his new book, “Life Sculpted: Tales of the Animals, Plants and Fungi That Drill, Break and Scrape to Shape the Earth.”

The University of Chicago Press is publishing “Life Sculpted” June 9, marking the fifth book during the past 10 years by Martin, professor of practice in Emory’s Department of Environmental Sciences.

Martin is a geologist and paleontologist focused primarily on ichnology — the study of traces of life such as tracks, burrows, nests and tooth marks. Among his discoveries are the only known burrowing dinosaur and the oldest bird tracks in Australia. His other passion is great science communication, which his books exemplify.

“Life Sculpted” is a follow-up to Martin’s 2017 book “The Evolution Underground: Burrows, Bunkers and the Marvelous Subterranean World Beneath Our Feet.” The current volume, also aimed at anyone interested in Earth sciences, goes beyond burrowing to cover how myriad forms of life have broken down the hard substrates of rock, shells, bones and wood during the past billion years.

“Yes, life can be hard,” Martin quips, “but life also makes everything less hard every day. Bioerosion shapes the world, literally. It’s changed entire ecosystems.”

It has also changed human history. Martin cites the wood-boring clams that perforated the hulls of the Spanish Armada, helping tip the odds toward the English Navy in 1588, when it won a decades-long fight for maritime dominance.

Bioeroders come in all sizes, he writes, from microbes that transport calcium away from rock and shells to elephants that dig caves with their tusks to obtain salt.

Bioeroders can change the soundscape as well as the landscape. In a chapter entitled “Your Beach Is Made of Parrotfish Poop,” Martin describes hearing “a crunching and popping reminiscent of sugary breakfast cereals meeting milk” while snorkeling over a Bahamian reef. The crunching, he explains, is actually the sound of parrotfishes biting out chunks of the reef with jaws and teeth capable of breaking apart rock. Reefs and the surrounding shallow-marine environments have been shaped by millions of years of such fishes gnawing on coral and defecating sediments.

Martin doesn’t just want readers to visualize and hear bioerosion. He also wants them to smell it.

He describes how dinosaurs chewed up rotten wood to get at insects and how insects, in turn, bored into the limb bones of large Jurassic dinosaurs that apparently became trapped in a stinking mud pit of decomposing flesh in Colorado.

The book gives many more familiar, modern-day examples of bioeroders. Georgia “hosts small, furry, bone-destroying beings that descend from the trees and eat skulls,” Martin writes. He knows this from personal observation of gray squirrels that relentlessly gnawed to bits a cow skull he and his wife had hanging in their courtyard.

“It’s their calcium supplement,” he explains.

And then there are all the bioeroders who have been busily at work on Stone Mountain.

Lichens colonized the enormous rock’s surface as soon as it emerged into the air, starting the process of soil formation that then allowed plants to take root. Animals began scurrying across and digging into its crumbling surface. Those animals eventually included humans, among the leading biological excavators of hard materials on the planet.

Humans have chiseled massive chunks from Stone Mountain’s side and removed tons of granite from its core. And any time you hike up Stone Mountain, Martin wants you to consider that you are taking a bit of its powdery dust with you on your footwear when you leave.

“The book is filled with ‘aha’ moments for the reader,” Martin says. “I want to encourage people to look for the evidence and to expand their awareness of how life is shaping the Earth.”