NTU scientists establish new records of Singapore's sea-level history

Nation's ability to predict sea-level rise boosted with record going back to 10,000 years ago

NANYANG TECHNOLOGICAL UNIVERSITY

Research News

 

IMAGE: THE NTU ASIAN SCHOOL OF THE ENVIRONMENT TEAM BEHIND THE STUDY OF SINGAPORE'S SEA-LEVEL INCLUDE (L-R): ASSOCIATE PROFESSOR ADAM SWITZER, RESEARCH FELLOW DR STEPHEN CHUA AND DIRECTOR OF THE EARTH... view more 

CREDIT: NTU SINGAPORE

Climate scientists at the Nanyang Technological University, Singapore (NTU, Singapore) have extended the known record of Singapore's sea-level to almost 10,000 years ago, providing a more robust dataset to aid future predictions of sea-level rise.

One of the main challenges in researching climate change is to reconstruct its history over thousands of years. To have a better sense of the potential causes and effects of future changes, scientists need to learn from and understand the past.

Extracting ancient sediments from a depth of up to 40 m underground at a site at Singapore's Marina South, an international team led by NTU researchers put the samples through rigorous laboratory methods (e.g., identifying microfossils such as foraminifera) and statistical analysis to obtain data to reconstruct Singapore's sea level history.

For climate scientists, the further the sea-level record goes back in time, the clearer the picture can be for future predictions. The transition at the beginning of the Holocene (10,000-7,000 years ago) represented the last major episode of natural global warming in Earth's history, when melting ice sheets and warming oceans led to a 20 m rise in sea level. For the last 3,000 years, the sea level in Singapore had been stable, before the recent acceleration in the 20th century due to climate change.

Lead author, Dr Stephen Chua, who completed the study as part of his doctoral work at the Earth Observatory of Singapore (EOS) and Asian School of the Environment (ASE) at NTU Singapore said, "By dating the Singapore sea-level record to 10,000 years ago, we retrieved crucial new information from the early Holocene period. This is a period that is characterised by rapid sea-level rise yet remains poorly understood - until now."

"This more refined sea-level record also has wider implications. For instance, it would lead to more robust and accurate local projection of sea-level rise, offering a strategic guide for Singapore as it moves to adapt to climate change."

Professor Maureen Raymo, Co-Founding Dean of the Columbia Climate School at Columbia University, who was not involved in the study, said: "This is the type of crucial information needed to effectively plan adaptation measures in the face of ongoing sea level rise due to global warming. Our past does inform our future."

Why Marina South site for investigations?

Developing an accurate ancient sea-level record required sediment extraction from an 'ideal' site where deposits such as marine mud and mangrove peats are present.

To pick the best possible coring site for accurate results, researchers looked through thousands of available borehole logs - records of holes that have been drilled into the ground for infrastructure projects.

Associate Professor Adam Switzer who leads the Coastal Lab at ASE and EOS and who was Dr Chua's supervisor, said, "Finding the right place to drill was a huge effort. Stephen spent well over a year going over old borehole information from a variety of construction efforts over the last 30 years just to find records that might be suitable. As a result, our understanding of the geology of the whole area has also dramatically improved."

Findings useful for Singapore's coastal defence plan against rising sea levels

The study, published in the peer-reviewed journal The Holocene on 4 June 2021, also found the first conclusive evidence that mangroves only existed in the Marina South area for around 300 years before succumbing to flooding associated with rising sea level at the time.

At a depth of 20 m below modern sea level, researchers found abundant mangrove pollen indicating that a mangrove shoreline existed in southern Singapore almost 10,000 years ago. The NTU findings reveal that sea-level rise during that time was as high as 10 - 15 mm per year which likely led to the mangrove's demise.

The findings provide Singapore with useful insights for current and future adaption methods as the island nation looks to go beyond engineering solutions and to incorporate natural methods to safeguard the country's coastlines.

Despite its adaptability and effectiveness as a coastal defence, the study highlights the limitations of mangroves in the event of rapid sea-level rise. This confirms an earlier study co-authored by NTU showing that mangroves will not survive if sea-level rise goes beyond 7 mm per year under a high carbon emissions scenario.

Co-author of the study, Professor Benjamin Horton, Director of EOS, said, "Sea-level rise is a potentially disastrous outcome of climate change, as rising temperatures melt ice sheets and warm ocean waters. Scenarios of future rise are dependent upon understanding the response of sea level to climate changes. Accurate estimates of past sea-level variability in Singapore provide a context for such projections".

Providing an independent comment on the research, Professor Philip Gibbard, a Quaternary geologist from the Scott Polar Research Institute at the University of Cambridge, underscored the importance of records from localities distant from the glaciated regions such as Singapore.

"They offer a model of the process of sea-level change uncomplicated by factors associated with deglaciation, meltwater discharge and more. This important systematic contribution from Singapore and the region provides a valuable record that spans the post-glacial Holocene period, thus allowing a general pattern of sea-level change in the region to be established. This record can then be further refined as more studies become available in the future."

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The research team examines a core sample, which was extracted from a depth of up to 40 m underground at a site at Singapore's Marina South.

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A close up of the core sample. The sample is put through rigorous laboratory methods and statistical analysis to obtain data to reconstruct Singapore's sea level history.

CREDIT

NTU Singapore

 

Underground storage of carbon captured directly from air -- green and economical

New study shows that geological storage of low-purity carbon dioxide mixed with oxygen and nitrogen from direct air capture is an environmentally friendly and economically viable approach to remove carbon from the atmosphere

KYUSHU UNIVERSITY, I2CNER

Research News

 

IMAGE: SCHEMATIC IMAGE OF LOW-PURITY CO2 STORAGE WITH THE MEMBRANE-BASED DIRECT AIR CAPTURE (DAC). view more 

CREDIT: TAKESHI TSUJI

Fukuoka, Japan - The global threat of ongoing climate change has one principal cause: carbon that was buried underground in the form of fossil fuels is being removed and released into the atmosphere in the form of carbon dioxide (CO2). One promising approach to addressing this problem is carbon capture and storage: using technology to take CO2 out of the atmosphere to return it underground.

In a new study published in Greenhouse Gases Science and Technology, researchers from Kyushu University and the National Institute of Advanced Industrial Science and Technology, Japan, investigated geological storage of low-purity CO2 mixed with nitrogen (N2) and oxygen (O2), produced by direct air capture (DAC) using membrane-based technology.

Many current carbon capture projects are carried out at localized sources using concentrated CO2 emissions, such as coal-fired power plants, and require intensive purification storage owing to the presence of hazardous compounds such as nitrogen oxide and sulfur oxide. They also have high transportation costs because viable geological storage sites are typically far from the sources of CO2. In contrast, direct air capture of CO2 can be performed anywhere, including at the storage site, and does not require intensive purification because the impurities, O2 and N2, are not hazardous. Therefore, low-purity CO2 can be captured and injected directly into geological formations, at least in theory. Understanding how the resulting mixture of CO2, O2, and N2 behaves when it is injected and stored in geological formations is necessary before underground storage of low-purity CO2 from direct air capture can be widely adopted. As the study's lead author, Professor Takeshi Tsuji, explains, "It is difficult to capture high-purity CO2 using DAC. We performed molecular dynamic simulations as a preliminary evaluation of the storage efficiency of CO2-N2-O2 mixtures at three different temperature and pressure conditions, corresponding to depths of 1,000 m, 1,500 m, and 2,500 m at the Tomakomai CO2 storage site in Japan."

Although further research is still needed, such as investigations of the chemical reactions of injected O2 and N2 at great depths, the results of these simulations suggest that geological storage of CO2-N2-O2 mixtures produced by direct air capture is both environmentally safe and economically viable.

According to Professor Tsuji, "Because of the ubiquity of ambient air, direct air capture has the potential to become a ubiquitous means of carbon capture and storage that can be implemented in many remote areas, such as deserts and offshore platforms. This is important both for reducing transportation costs and ensuring social acceptance."

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The article, "Geological storage of CO2-N2-O2 mixtures produced by membrane-based direct air capture (DAC)," is published in Greenhouse Gases Science and Technology at DOI: https://doi.org/10.1002/ghg.2099

Corals tell Arabian Sea story of global warming

HOKKAIDO UNIVERSITY

Research News

 

IMAGE: COLLECTING CORAL SAMPLES IN THE WATERS OFF OMAN (PHOTO: TSUYOSHI WATANABE). view more 

CREDIT: TSUYOSHI WATANABE

Coral insights into 1,000 years of seasonal changes in the Arabian Sea warn of significant impacts caused by global warming.

Every year, the southwesterly winds of the summer monsoon sweep down the Arabian Peninsula, pushing the surface waters of the Arabian Sea away from the coast and driving an upwelling of deep waters to the surface. This rising seawater is colder and less saline than the surface water and is rich in nutrients, providing energy for the various organisms living in the Arabian Sea and Indian Ocean.

Scientists from Japan, Taiwan and Germany, including coral reef scientist Dr. Tsuyoshi Watanabe of Hokkaido University, have uncovered evidence from corals off the coast of Oman suggesting that global warming is causing changes to the Arabian Sea that could impact the climate, ecosystems and socioeconomics of the densely populated areas surrounding the Indian Ocean. The findings were published in the journal Geophysical Research Letters.

Stronger summer monsoon winds lead to a stronger upwelling in the Arabian Sea. Stronger winds form when the air over the Indian subcontinent warms more rapidly than the air over the Indian Ocean. Recently, however, the opposite has been happening. Scientists wanted to know how this change affects the Arabian Sea upwelling, but the phenomenon has not been monitored continuously, so available measurements aren't enough to tell the whole story.

Watanabe and his colleagues analysed fossil and modern corals off an Omani island in the Arabian Sea. They identified the ages of the corals they collected and established a correlation between coral data and seawater temperature changes over a very fine timescale, and used that information to extrapolate salinity changes. The four fossil corals they used dated to approximately 1167 CE, 1624 CE, 1703 CE and 1968 CE, respectively. They took samples from the corals at different depths towards their cores, and then analysed the ratio of strontium to calcium in the samples, as well as the amounts of oxygen and carbon isotopes. The growth rate of the corals is steady over centuries, and the skeletons contain a record of the changes in elements. Generally, as water temperatures rise, the strontium-to-calcium ratio and isotope oxygen-18 in coral decrease.

The results showed that the summer Arabian Sea upwelling was relatively stable through the warmer period of the medieval climate anomaly in the 12th century; the cooler little ice age, which extended between the 14th and 19th centuries AD; and up until the mid-20th century. After this period, however, the scientists observed a clear weakening of the Arabian Sea upwelling. They reason this can most likely be explained by faster warming of the northern Indian Ocean, caused by greenhouse gases, and slowed warming of the Indian subcontinent, caused by the absorption of sunrays by aerosol emissions over South Asia. This then weakens the summer monsoon winds, impacting the strength of the Arabian Sea upwelling.

"The seasonal upwelling is vital for commercial fishing and has significant impacts on the regional climate, ecosystems and socioeconomics," says Tsuyoshi Watanabe. "Our findings imply that weakening of the Arabian Sea upwelling is likely to continue along with global warming, impacting monsoon rainfalls, sea levels, fisheries and even agricultural production."

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CAPTION

Warming trends of the northern Indian Ocean and the Indian subcontinent. The Arabian Sea has warmed to a much larger extent than the Indian subcontinent. The star indicates the sample site of modern and fossil Arabian Sea corals used in this study (Takaaki K. Watanabe, et al. Geophysical Research Letters. May 24, 2021).

CREDIT

Takaaki K. Watanabe, et al. Geophysical Research Letters. May 24, 2021

CAPTION

Tsuyoshi Watanbe, corresponding author of the current study, in Oman (Photo: Tsuyoshi Watanabe).

CREDIT

Tsuyoshi Watanbe

 

Fungus creates a fast track for carbon

Stanford scientists find epidemics of fungal infections in algae alter carbon cycling

STANFORD'S SCHOOL OF EARTH, ENERGY & ENVIRONMENTAL SCIENCES

Research News

 

IMAGE: FUNGUS CREATES AN UNDERAPPRECIATED EXPRESS LANE FOR CARBON, "SHUNTING " AS MUCH AS 20 PERCENT OF THE CARBON FIXED BY DIATOMS OUT OF THE MICROBIAL LOOP AND INTO THE FUNGAL PARASITE. view more 

CREDIT: KLAWONN ET AL. 2021, PNAS

Tiny algae in Earth's oceans and lakes take in sunlight and carbon dioxide and turn them into sugars that sustain the rest of the aquatic food web, gobbling up about as much carbon as all the world's trees and plants combined.

New research shows a crucial piece has been missing from the conventional explanation for what happens between this first "fixing" of CO2 into phytoplankton and its eventual release to the atmosphere or descent to depths where it no longer contributes to global warming. The missing piece? Fungus.

"Basically, carbon moves up the food chain in aquatic environments differently than we commonly think it does," said Anne Dekas, an assistant professor of Earth system science at Stanford University. Dekas is the senior author of a paper published June 1 in Proceedings of the National Academy of Sciences that quantifies how much carbon goes into parasitic fungi that attack microalgae.

Underwater merry-go-round

Researchers until now have predicted that most carbon fixed into colonies of hard-shelled, single-celled algae known as diatoms then funnels directly into bacteria - or dissolves like tea in the surrounding water, where it's largely taken up by other bacteria. Conventional thinking assumes carbon escapes from this microbial loop mainly through larger organisms that graze on the bacteria or diatoms, or through the CO2 that returns to the atmosphere as the microbes breathe.

This journey is important in the context of climate change. "For carbon sequestration to occur, carbon from CO2 needs to go up the food chain into big enough pieces of biomass that it can sink down into the bottom of the ocean," Dekas said. "That's how it's really removed from the atmosphere. If it just cycles for long periods in the surface of the ocean, it can be released back to the air as CO2."

It turns out fungus creates an underappreciated express lane for carbon, "shunting" as much as 20 percent of the carbon fixed by diatoms out of the microbial loop and into the fungal parasite. "Instead of going through this merry-go-round, where the carbon could eventually go back to the atmosphere, you have a more direct route to the higher levels in the food web," Dekas said.

The findings also have implications for industrial and recreational settings that deal with harmful algal blooms. "In aquaculture, in order to keep the primary crop, like fish, healthy, fungicides might be added to the water," Dekas said. That will prevent fungal infection of the fish, but it may also eliminate a natural check on algal blooms that cost the industry some $8 billion per year. "Until we understand the dynamics between these organisms, we need to be pretty careful about the management policies we're using."

Microbial interactions

The authors based their estimates on experiments with populations of chytrid fungi called Rhizophydiales and their host, a type of freshwater algae or diatom named Asterionella formosa. Coauthors in Germany worked to isolate these microbes, as well as bacteria found in and around their cells, from water collected from Lake Stechlin, about 60 miles north of Berlin.

"Isolating one microorganism from nature and growing it in the laboratory is difficult, but isolating and maintaining two microorganisms as a pathosystem, in which one kills the other, is a true challenge," said lead author Isabell Klawonn, who worked on the research as a postdoctoral scholar in Dekas' lab at Stanford. "Only a few model systems are therefore available to research such parasitic interactions."

Scientists surmised as early as the 1940s that parasites played an important role in controlling the abundance of phytoplankton, and they observed epidemics of chytrid fungus infecting Asterionella blooms in lake water. Technological advances have made it possible to pick apart these invisible worlds in fine and measurable detail - and begin to see their influence in a much bigger picture.

"We're realizing as a community that it's not just the capabilities of an individual microorganism that's important for understanding what happens in the environment. It's how these microorganisms interact," Dekas said.

The authors measured and analyzed interactions within the Lake Stechlin pathosystem using genomic sequencing; a fluorescence microscopy technique that involves attaching fluorescent dye to RNA within microbial cells; and a highly specialized instrument at Stanford - one of only a few dozen in the world - called NanoSIMS, which creates nanoscale maps of the isotopes of elements that are present in materials in vanishingly small amounts. Dekas said, "To get these single-cell measurements to show how photosynthetic carbon is flowing between specific cells, from the diatom to the fungus to the associated bacteria, it's the only way to do it."

The exact amount of carbon diverted to fungus from the microbial merry-go-round may differ in other environments. But the discovery that it can be as high as 20 percent in even one setting is significant, Dekas said. "If you're changing this system by more than a few percent in any direction, it can have dramatic implications for biogeochemical cycling. It makes a big difference for our climate."

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Stanford coauthors include Alma E. Parada and Nestor Arandia-Gorostidi, postdoctoral research fellows in the Department of Earth System Science at the School of Earth, Energy & Environmental Sciences (Stanford Earth). Additional coauthors are affiliated with Leibniz-Institute of Freshwater Ecology and Inland Fisheries, the Swedish Museum of Natural History and Potsdam University. Klawonn is now affiliated with Leibniz Institute for Baltic Sea Research.

The research was supported by the German Academic Exchange Service, the Simons Foundation and the German Research Foundation.

 

Why scientists want to solve an underground mystery about where microbes live

BU researchers develop first-of-its-kind model to predict which species of soil organisms live in different environments, with huge implications for agriculture, climate change, and public health

BOSTON UNIVERSITY

Research News

 

IMAGE: BOSTON UNIVERSITY RESEARCHERS DEVELOP FIRST-OF-ITS-KIND MODEL TO PREDICT WHICH SPECIES OF SOIL ORGANISMS LIVE IN DIFFERENT ENVIRONMENTS, WITH HUGE IMPLICATIONS FOR AGRICULTURE, CLIMATE CHANGE, AND PUBLIC HEALTH view more 

CREDIT: IMAGE COURTESY OF FLORIAN VAN DUYN ON UNSPLASH

Though it might seem inanimate, the soil under our feet is very much alive. It's filled with countless microorganisms actively breaking down organic matter, like fallen leaves and plants, and performing a host of other functions that maintain the natural balance of carbon and nutrients stored in the ground beneath us.

"Soil is mostly microorganisms, both alive and dead," says Jennifer Bhatnagar, soil microbiologist and Boston University College of Arts & Sciences assistant professor of biology. It's typical to see several hundred different types of fungi and bacteria in a single pinch of soil off the ground, she says, making it one of the most diverse ecosystems that exist.

Because there's still so much unknown about soil organisms, until now scientists have not attempted to predict where certain species or groups of soil microbes live around the world. But having that knowledge about these organisms-- too small to see with the naked eye--is key to better understanding the soil microbiome, which is made up of the communities of different microbes that live together.

A team of BU biologists, including Bhatnagar, took on that challenge--and their research reveals, for the first time, that it is possible to accurately predict the abundance of different species of soil microbes in different parts of the world. The team recently published their findings in a new paper in Nature Ecology & Evolution.

"If we know where organisms are on earth, and we know how they change through space and time due to different environmental forces, and something about what different species are doing, then we can much better predict how the function of these communities will change in terms of carbon and nutrient cycling," Bhatnagar says. That kind of knowledge would have huge implications for agriculture, climate change, and public health.

"The health of the soils is so tied to the soil microbes," says Michael Dietze, senior author on the study and a BU College of Arts & Sciences professor of earth and environment. Dietze, Bhatnagar, and researchers from their labs joined forces to work on this project, which involved analyzing hundreds of soil samples collected by National Ecological Observatory Network (NEON) research sites. Bhatnagar and her lab members brought to the team their soil expertise, while Dietze and his lab offered their unique ability to develop precise ecological forecasts and near-term environmental predictions.

The team learned that microbe predictability increases as spatial area increases, so the bigger the piece of land their model makes forecasts about, the more likely the predictions about what types of microbes live there will be accurate.

Dietze says the ability to accurately predict which microbes would likely be found in a given soil sample also increased as the researchers looked at organism groupings higher up on the phylogenetic scale, a system that classifies organisms based on evolutionary relatedness. On the smallest end of the scale, a "species" represents the finest level of classification; on the other end, a "phylum" makes up the largest and most diverse groupings of organisms. They were surprised to find that they were better able to predict the presence of a whole phylum, as opposed to individual species.

After receiving the genomic data of the soil samples from NEON, the research team's forecasting models take into account environmental factors specific to the place where the soil came from--what plants live there, the soil acidity (pH), temperature, climate, and many others. They found their model was best able to predict the presence of microorganisms based on their symbiotic relationship with local plant species. Mycorrhizal fungi, for example, is a very common soil microbe that about 90 percent of plant families associate with, including pines and oak trees in New England.

In contrast, the team found it was more difficult to predict large groups of organisms based on their relationship with soil acidity. Despite knowing soil acidity levels, and what types of bacteria would typically like to live in that environment, their model couldn't accurately predict the amount of bacteria that were actually present in the soil sample, Bhatnagar says. "That means there is something else beyond the relationship with [acidity], beyond the relationship with any other environmental factor that we typically measure in our ecosystems," she says.

Now, Dietze and Bhatnagar's team are expanding their forecasts beyond predicting microbes based on only their location, to also include specific times of the year.

"Building a framework for forecasting the soil microbiome at sites across the US will improve our understanding of seasonal and interannual change," says Zoey Werbin, a PhD student working in Bhatnagar's lab and an author on the paper. "This could help us anticipate how climate change could affect microbial processes like decomposition or nitrogen cycling."

With her dissertation project, Werbin hopes to answer fundamental questions about how and why the soil microbiome varies over time and space.

"The more we learn, the more we realize how important soil microbes are for agriculture, public health, and climate change. It's really exciting to investigate how microscopic organisms can have such large-scale effects," Werbin says. "We know certain factors, like temperature and moisture, affect microbial communities. But we don't know how important those factors are compared to natural variability, or interactions between microbes. My PhD project will help identify the driving forces of the soil microbiome, as well as the biggest sources of uncertainty."

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SLAS Discovery's June issue on synthetic biology available now

SLAS (SOCIETY FOR LABORATORY AUTOMATION AND SCREENING)

Research News 

Oak Brook, IL - The June edition of SLAS Discovery features the cover article, "A Perspective on Synthetic Biology in Drug Discovery and Development--Current Impact and Future Opportunities" by Florian David, Ph.D. (Chalmers University of Technology, Gothenburg, Sweden), Andrew M. Davis, Ph.D. (AstraZeneca, Cambridge, England, UK). Michael Gossing, Ph.D., Martin A. Hayes, Ph.D., and Elvira Romero, Ph.D., and Louis H. Scott, Ph.D. (AstraZeneca, Gothenburg, Sweden), and Mark J. Wigglesworth, Ph.D. (AstraZeneca, London, England, UK).

In January 2021, a survey of immunologists, infectious-disease researchers and virologists found that 90% of respondents believe SARS-CoV-2 will become endemic, continuing to circulate in pockets of the global population for years to come. Even as vaccines are becoming more widely available, there are people who either do not respond to the treatment or are not suitable for vaccination. There is a critical need to develop small molecule inhibitors for this pathogen. The cover article highlights the work of the Drug Discovery Unit at the University of Dundee (Dundee, Scotland, UK) reporting on the development of a high-throughput biochemical assay to assess the impact of small molecules on the methyltransferase activity of SARS-CoV-2 nonstructural protein 14 (nsp14). This enzyme is responsible for the N7-methylation of the cap at the 5' end of viral RNA and is critical in helping coronaviruses evade host defenses. The label-free MS-based assay developed was used to screen a library of 1771 FDA-approved drugs. The chemical hits that were identified may serve as starting points for drug discovery programs aimed at delivering therapeutics for the SARS-CoV-2 virus.

The June issue of SLAS Discovery includes nine articles of original research.

These include:

• Development and Validation of High-Content Analysis for Screening HDAC6-Selective Inhibitors
• In Vitro Pharmacokinetic/Pharmacodynamic Modeling of HIV Latency Reversal by Novel HDAC Inhibitors Using an Automated Platform
• Identification and Kinetic Characterization of Serum- and Glucocorticoid-Regulated Kinase Inhibitors Using a Fluorescence Polarization-Based Assay
• Reducing False Positives through the Application of Fluorescence Lifetime Technology: A Comparative Study Using TYK2 Kinase as a Model System
• Biochemical and Cellular Profile of NIK Inhibitors with Long Residence Times
• A Novel High-Throughput FLIPR Tetra-Based Method for Capturing Highly Confluent Kinetic Data for Structure-Kinetic Relationship Guided Early Drug Discovery
• A Multipronged Screening Approach Targeting Inhibition of ETV6 PNT Domain Polymerization
• Unbiased High-Throughput Drug Combination Pilot Screening Identifies Synergistic Drug Combinations Effective against Patient-Derived and Drug-Resistant Melanoma Cell Lines
• Regenerable Biosensors for Small-Molecule Kinetic Characterization Using SPR

Other articles include:

• A Perspective on Synthetic Biology in Drug Discovery and Development--Current Impact and Future Opportunities
• Public-Private Partnerships: Compound and Data Sharing in Drug Discovery and Development
• A High-Throughput RNA Displacement Assay for Screening SARS-CoV-2 nsp10-nsp16 Complex Toward Developing Therapeutics for COVID-19
• Development of a High-Throughput Assay to Identify Inhibitors of ENPP1

Access to June's SLAS Discovery issue is available at https://journals.sagepub.com/toc/jbxb/current. For more information about SLAS and its journals, visit https://www.slas.org/publications/slas-discovery/ Access a "behind the scenes" look at the latest issue with SLAS Discovery Author Insights podcast. Tune in by visiting https://www.buzzsprout.com/1099559.

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SLAS (Society for Laboratory Automation and Screening) is an international professional society of academic, industry and government life sciences researchers and the developers and providers of laboratory automation technology. The SLAS mission is to bring together researchers in academia, industry and government to advance life sciences discovery and technology via education, knowledge exchange and global community building.

SLAS Discovery: Advancing the Science of Drug Discovery, 2019 Impact Factor 2.195. Editor-in-Chief Robert M. Campbell, Ph.D., Twentyeight-Seven Therapeutics, Boston, MA (USA).

SLAS Technology: Translating Life Sciences Innovation, 2019 Impact Factor 2.174. Editor-in-Chief Edward Kai-Hua Chow, Ph.D., National University of Singapore (Singapore)

Beyond synthetic biology, synthetic ecology boosts health by engineering the environment

BU scientists are investigating how environmental molecules can be used to engineer 'designer' microbiomes for combating disease, pollution, and more

BOSTON UNIVERSITY

Research News

 

IMAGE: IN A NEW NATURE COMMUNICATIONS STUDY, RESEARCHERS FROM BU'S MICROBIOME INITIATIVE DISCOVERED THAT PROVIDING MICROBIAL COMMUNITIES WITH A BROADER VARIETY OF FOOD SOURCES DIDN'T INCREASE THE VARIETY OF MICROBIAL SPECIES... view more 

CREDIT: IMAGE COURTESY OF ALAN PACHECO AND DANIEL SEGRÈ.

There's a lot of interest right now in how different microbiomes--like the one made up of all the bacteria in our guts--could be harnessed to boost human health and cure disease. But Daniel Segrè has set his sights on a much more ambitious vision for how the microbiome could be manipulated for good: "To help sustain our planet, not just our own health."

Segrè, director of the Boston University Microbiome Initiative, says he and other scientists in his field of synthetic and systems biology are studying microbiomes--microscopic communities of bacteria, fungi, or a combination of those that exert influence over each other and the surrounding environment. They want to know how microbiomes might be directed to carry out important tasks like absorbing more atmospheric carbon, protecting coral reefs from ocean acidification, improving the fertility and yield of agricultural lands, and supporting the growth of forests and other plants despite changing environmental conditions.

"Microbes affect us as humans through their own metabolic processes, they affect our planet through what they consume and secrete, they help create the oxygen we breathe," says Segrè, a BU College of Arts & Sciences professor of biology and bioinformatics, and a College of Engineering professor of biomedical engineering. "A long time ago microbes are what made multicellular life possible."

But, unlike many other synthetic biologists who are working to enhance or genetically engineer microbes directly, Segrè is more interested in how to direct the behavior of a microbiome by tweaking the environmental conditions it lives within--an approach he says could be better described as "synthetic ecology."

"The more traditional synthetic biology approach would be to manipulate the genomes of the microbes," Segrè says. "But we're trying to manipulate microbial ecosystems using environmental molecules."

"We know that microbial interactions with the environment are important," says Alan Pacheco, who earned his PhD in bioinformatics working in Segrè's lab. Some of those interactions benefit several microbial species, some only benefit one species in a community, and some can be harmful to certain species, he says. "But there's still so much we don't know about why these interactions happen the way that they do."

In a new study recently published in Nature Communications, Segrè, Pacheco, and their collaborator Melisa Osborne, a research scientist in Segrè's lab, explored how the presence of 32 different environmental molecules or nutrients, alone or in combination with others, would influence the growth rate of microbial communities and the mix of diverse species making up a given microbiome.

"In the back of our minds we had this idea of diet, framed by studies that have looked at differences in the gut microbiome based on Western vs hunter-gatherer diets," says Pacheco, who is now a postdoctoral fellow at ETH Zürich. Hunter-gatherer diets, opportunistic and comprising a wide range of plant-based food sources, are considered much more diverse than the Western diet, which is why the hunter-gatherer diet is thought to cultivate a healthier gut.

But the experimental results surprised the team. They expected they would see growth and diversity of microbiomes increase as the "bugs" had more access to a variety of foods--a range of carbons, including sugars, amino acids, and complex polymers--but that's not what their carefully controlled experiments revealed. Instead, they observed that competition for food between different species of microbes hampered diversification within the microbial community.

"Our results demonstrate that environmental complexity alone is not sufficient for maintaining community diversity, and provide practical guidance for designing and controlling microbial ecosystems," the authors write.

So, what are the mechanisms that control a microbiome's diversity? "It's going to take some time to figure out the cause of all these interactions," Segrè says.

Although increasing the variety of food sources didn't increase the variety of microbial species within their experiments, more food did fuel more microbial growth. "We found yield depends on the total number of carbon sources, but not on the variety of those sources," Segrè says. "It's like people at a picnic--if enough people come to a picnic, no matter what the spread of different foods, eventually everything will be eaten up. In many of our experiments, the microbial communities used up every last bit of carbon source to the fullest extent."

Pacheco adds that if somebody can consume something, somebody else can outcompete them for it. "Our experiments showed that the crucial modulator in microbial diversity is how much these different organisms compete with one another for resources," he says. "The more organisms compete, the less diverse that community is going to be."

The team plans to do more research into additional environmental factors, investigating how nutrient access and variety changes microbial communities over time, and how the medium that the microbial community lives in affects their consumption and secretion of molecules. They are also exploring how metabolic processes amongst different microbial species could interact and interplay with each other, and how the ability of some organisms to sequentially or simultaneously consume multiple resources affects the microbiome overall.

Further unlocking and eventually harnessing all these environmental "dials and knobs" could open doors to using microbiomes to influence human metabolisms and health or disease states in people and in natural ecosystems.

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Funders: Howard Hughes Medical Institute, National Academies of Sciences, Engineering, and Medicine, Ford Foundation, US Department of Energy, National Institutes of Health, National Science Foundation, Human Frontiers Science Program, Boston University Interdisciplinary Biomedical Research Office

Genomics-informed decisions can help save species from extinction

LUND UNIVERSITY

Research News

Researchers in Lund, Copenhagen and Norwich have shown that harmful mutations present in the DNA play an important - yet neglected - role in the conservation and translocation programs of threatened species.

"Many species are threatened by extinction, both locally and globally. For example, we have lost about ten vertebrate species in Sweden in the last century. However, all these species occur elsewhere in Europe, which means that they could be reintroduced into Sweden. Our computer simulations show how we could theoretically maximize the success of such reestablishments", says Bengt Hansson, biologist at Lund University.

In a new study published in Science, the researchers investigated which individuals might be most suited for translocation to new populations. To date, conservation geneticists have opted to select the most genetically variable individuals. However, the authors argue that is important to consider what type of genetic variation is being move around. Using computer simulations, they showed that harmful mutations present in the genome of translocated individuals can cause problems in future generations. This so called "mutation load" could jeopardize the viability of the new population in the long run and eventually led to extinction.

According to Hansson and van Oosterhout, geneticist at University of East Anglia, Norwich, who led the study, the best choice is to exclude individuals with many harmful mutations, whilst at the same time, selecting individuals from multiple different source populations.

"Active translocation of animals between localities is sometimes the last option available to conservation biologists. By carefully selecting individuals based on their low mutation load, we can minimize the loss of fitness that is normally associated with inbreeding in small populations", says Bengt Hansson.

Huge advances have been made in DNA sequencing technologies, and the whole genomes of individuals can now be sequenced for relatively little costs. This opens up new possibilities to improve the conservation management of threatened species.

"For many species of mammals and birds, we now know which mutations are harmful. Similar mutations are also found in humans, so we understand what they do, and hence, we know what to look out for when analyzing the sequence data of those species. The advantage of using DNA sequencing is that we can see these mutations in the genome, even if an individual carries just a single copy of the mutant gene. This means we can select against those bad mutations even before they cause a problem. Our computer model shows that at least theoretically, this ensures the best probability for population survival. This could help conservation managers in picking the optimal individuals of a threatened species for translocation into a new habitat", says van Oosterhout.

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A shark mystery millions of years in the making

YALE UNIVERSITY

Research News

 

The biggest shark attack in history did not involve humans.

A new study by Earth scientists from Yale and the College of the Atlantic has turned up a massive die-off of sharks roughly 19 million years ago. It came at a period in history when there were more than 10 times more sharks patrolling the world's oceans than there are today.

For now, researchers don't know the cause of the shark die-off.

"We happened upon this extinction almost by accident," said Elizabeth Sibert, a Hutchinson postdoctoral associate in Yale's Department of Earth and Planetary Sciences and the Yale Institute for Biospheric Studies. She is lead author of the new study, which appears in the journal Science.

"I study microfossil fish teeth and shark scales in deep-sea sediments, and we decided to generate an 85-million-year-long record of fish and shark abundance, just to get a sense of what the normal variability of that population looked like in the long term," Sibert said. "What we found, though, was this sudden drop-off in shark abundance around 19 million years ago, and we knew we had to investigate further."

How big was the drop-off? Sibert said more than 70% of the world's sharks died off -- with an even higher death toll for sharks in the open ocean, rather than coastal waters. It was twice the level of extinction that sharks experienced during the Cretaceous-Paleogene mass extinction event 66 million years ago that wiped out three-quarters of the plant and animal species on Earth.

Adding to the mystery is the fact that there is no known climate calamity or ecosystem disruption that occurred at the time of the steep drop in shark populations. "This interval isn't known for any major changes in Earth's history," said Sibert, "yet it completely transformed the nature of what it means to be a predator living in the open ocean."

Co-author Leah Rubin, an incoming doctoral student at the State University of New York College of Environmental Science and Forestry, was a student at the College of the Atlantic at the time of the research.

"The current state of declining shark populations is certainly cause for concern and this paper helps put these declines in the context of shark populations through the last 40 million years," Rubin said. "This context is a vital first step in understanding what repercussions may follow dramatic declines in these top marine predators in modern times."

The researchers noted that past discoveries of extinction events have led to waves of new research to learn the origins of the die-off and whether it signaled a larger, previously unknown, perturbance in global ecosystems.

For example, further research might confirm whether the shark-off caused remaining shark populations to change their habitat preferences to avoid the open ocean, Sibert and Rubin said. Additional research might also help to explain why shark populations did not rebound after the die-off 19 million years ago.

"This work could tip-off a race to understand this time period and its implications for not only the rise of modern ecosystems, but the causes of major collapses in shark diversity," said Pincelli Hull, an assistant professor of Earth and planetary science at Yale, who was not part of the study. "It represents a major change in ocean ecosystems at a time that was previously thought to be unremarkable."

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Stone Age raves to the beat of elk tooth rattles?

UNIVERSITY OF HELSINKI

 VIDEO: HYPOTHETICAL RECONSTRUCTION OF TOOTH ORNAMENTS FOUND IN THE LATE MESOLITHIC GRAVES OF YUZHNIY OLENIY OSTROV: 94 EURASIAN ELK TEETH SEWN ON AN APRON HIT AND BOUNCE OFF THE SUBSTRATUM AND... view more 

CREDIT: JULIA SHPINITSKAYA

"Ornaments composed of elk teeth suspended from or sown on to clothing emit a loud rattling noise when moving," says auditory archaeologist and Academy of Finland Research Fellow Riitta Rainio from the University of Helsinki. "Wearing such rattlers while dancing makes it easier to immerse yourself in the soundscape, eventually letting the sound and rhythm take control of your movements. It is as if the dancer is led in the dance by someone."

Rainio is well versed in the topic, as she danced, for research purposes, for six consecutive hours, wearing elk tooth ornaments produced according to the Stone Age model. Rainio and artist Juha Valkeapää held a performance to find out what kind of wear marks are formed in the teeth when they bang against each other and move in all directions. The sound of a tooth rattler can be clear and bright or loud and pounding, depending on the number and quality of the teeth, as well as the intensity of movement.

Microanalysis demonstrates that tooth wear marks are the result of dancing

The teeth worn out by dancing were analysed for any microscopic marks before and after the dancing. These marks were then compared to the findings made in the Yuzhniy Oleniy Ostrov graves by Evgeny Girya, an archaeologist specialised in micro-marks at the Russian Academy of Sciences. Girya documented and analysed the wear marks in the elk teeth found in four graves chosen for the experiment. Comparing the chips, hollows, cuts and smoothened surfaces of the teeth, he observed a clear resemblance between teeth worn out by dancing and the Stone Age teeth. However, the marks in the Stone Age teeth were deeper and more extensive. According to Girya, the results show that the marks are the result of similar activity.

"As the Stone Age teeth were worn for years or even decades, it's no surprise that their marks are so distinctive," Girya says.

Associate Professor of Archaeology Kristiina Mannermaa from the University of Helsinki is excited by the research findings.

"Elk tooth rattlers are fascinating, since they transport modern people to a soundscape that is thousands of years old and to its emotional rhythms that guide the body. You can close your eyes, listen to the sound of the rattlers and drift on the soundwaves to a lakeside campfire in the world of Stone Age hunter-gatherers."

A total of 177 graves of women, men and children have been found in the Yuzhniy Oleniy Ostrov burial site, of which more than half contain several elk tooth ornaments, some of them composed of as many as over 300 individual teeth.

CAPTION

Adult male from grave 76a in Yuzhniy Oleniy Ostrov drawn as if he were alive during a dance session: 140 elk teeth on the chest, waist, pelvis, and thighs rattle rhythmically and loudly.

CREDIT

Artist Tom Bjorklund