Wednesday, July 09, 2025

 

Fecal samples from bowhead whales link ocean warming to rising algal toxins in Arctic waters




Filter-feeding whales sample the Arctic food web, tracking decades of change.




Woods Hole Oceanographic Institution

Bowhead whales 

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Aerial view of six bowhead whales traversing the Beaufort Sea. 

 

 

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Credit: Photo credit: Amelia Brower NOAA Fisheries/AFSC/MML, Seattle, WA, 98125 USA & North Slope Borough. National Marine Fisheries Service (NMFS) Permit No. 14245





Woods Hole, Mass. (July 9, 2025) -- Rising toxins found in bowhead whales, harvested for subsistence purposes by Alaska Native communities, reveal that ocean warming is causing higher concentrations of algal toxins in Arctic food webs, according to new research published today in the journal Nature.

Researchers from the Woods Hole Oceanographic Institution (WHOI), were a part of the multi-institutional, multi-year study that focused on this critical issue, which threatens food security for coastal communities that rely on marine life, including clams, fish, and whales, for food and other resources. Communities in Alaska are now asking researchers to help them understand and monitor the emergence of algal toxins in the Arctic ecosystems that they depend on.

“These are new risks that were previously unknown,” said Kathi Lefebvre, a research scientist at NOAA Fisheries’ Northwest Fisheries Science Center in Seattle and lead author of the new study. “The people in remote communities in northern and western Alaska rely on marine resources for nutritional and cultural well-being. Now we’re finding that these resources are at risk.”

“Native communities know intimately the ecosystems they rely on and were among the first to recognize the effects of warming,” said Raphaela Stimmelmayr, a wildlife veterinarian with the North Slope Borough in Barrow, Alaska, and a coauthor of the new research. She said the communities now need reliable tools such as field tests, so they can test for the presence of algal toxins in traditional foods in real-time. These tests, as well as information from monitoring programs and instruments, also help them make informed decisions on whether the marine mammals or other marine wildlife—such as clams, fish, and birds—are safe to eat.

“It is very difficult to walk away from resources that they need and have relied on since time immemorial,” she said.

WHOI senior scientists Don Anderson and Bob Pickart, as well as Anderson’s graduate student Evie Fachon, are part of this study, as well as other investigations focused on the oceanography and bloom dynamics of the algal species that produce these dangerous toxins.

In addition to running an active research program, Anderson leads the US National Office for Harmful Algal Blooms based at WHOI, whose mission is to facilitate coordination and communication of activities for the U.S HAB community at a national level.  One of those activities was assisting with the publication of a national science strategy for the research and response of HABs.

“I have shifted a significant portion of my lab’s research focus to the Alaskan Arctic in recent years,” said Anderson.  “It is a new frontier in HAB research given the rapid warming of waters in the region and the massive scale of the Alexandrium populations we have documented”.

That research has revealed that the world’s largest beds of Alexandrium cysts, which are dormant cells of the toxic algae, lie on the seafloor sediments of the Alaskan Arctic. These cysts accumulate over time as blooms that originate in the Bering Sea drift northward and deposit their cysts in cold waters like those of the Chukchi Sea, where frigid bottom temperatures have historically suppressed germination.

“For years, these cysts have remained inactive, essentially preserved by the cold,” explained  Anderson. “But as bottom water temperatures periodically warm, we see conditions that allow germination, and that changes the risk landscape dramatically.”

The local cyst germination represents a second source for blooms of this species that augment the episodic transported blooms from the south.  These two bloom mechanisms are consistent with studies conducted by Anderson, Pickart, and Fachon documenting massive cyst accumulations (cyst beds) in Alaskan Arctic waters, as well as equally massive blooms of the cells in surface waters.

Warming conditions could trigger local blooms from these long-dormant cysts, increasing the threat to Arctic ecosystems and coastal communities from the potent neurotoxins the algae produce.

In this new study, Pickart and his former postdoc Peigen Lin, now at Shanghai Jao Tong University, analyzed currents and water properties through time, demonstrating a critical linkage between warming temperatures and the bowhead toxicity.

“My Arctic research has become increasingly interdisciplinary over the years, including exploring the role of circulation patterns, atmospheric forcing, and water properties in HAB dynamics,” Pickart explained.

 

Whales collect samples

NOAA’s Lefebvre leads the Wildlife Algal-toxin Research and Response Network for the U.S. West Coast. This alliance of agencies and institutions collects wildlife tissue samples from as far North as the Beaufort Sea in Alaska to Southern California. Members then send the samples to her Seattle lab to test for the presence of algal toxins. The lab’s early work found that many species in Alaska had evidence of exposure, although not at levels high enough to be considered harmful to the animals sampled.

Over two decades, the lab regularly tested bowhead whales harvested during annual fall subsistence hunts in the Beaufort Sea off the North Slope of Alaska. The whales filter seawater for their food, consuming krill that contain algal toxins acquired from the food web. The research team realized that fecal samples from the whales could reveal toxins in the marine environment the whales depend on.

“Nobody had a data set like this,” Lefebvre said. “Instead of going out every year and collecting samples across the marine environment, the whales did it for us. Their samples give us a snapshot of what is in the food web every year, as sampled by the whales.”

After testing 205 bowhead whales over 19 years from 2004 to 2022, the team decided they had enough data to look for changes over time. In particular, they wanted to track the concentrations of domoic acid, produced by a marine algae called Pseudo-nitzschia, and saxitoxin, produced by Alexandrium.

They found saxitoxin in at least half to 100% of the bowhead whales sampled each year over 19 years. While domoic acid was less prevalent (in some years no DA was detected), this study shows for the first time that domoic acid exposures in Arctic waters are increasing due to warming and loss of sea ice.

 

Winds, Currents, and Ice Cover Affect Toxins

Scientists used data from a monitoring mooring in the Beaufort Sea, funded by the National Science foundation’s Arctic Observing Network, to compare toxins in the bowhead whales to environmental conditions. “It was fortuitous that we’ve maintained a long-term mooring near the whale feeding site, which provided the opportunity to investigate the role of the changing circulation and water properties over this two-decade period,” said Pickart. The researchers found that periods of increased toxicity in the whales were associated with enhanced northward heat flux, which in turn was driven by specific wind patterns.

These warmer conditions are more favorable for HAB growth and are correlated with higher toxin concentrations in the food web. Atmospheric conditions thus influence the oceanography which in turn influences the HAB dynamics.

They also used climate data to compare the bowhead samples to changes in sea ice. Sea ice historically covered large sections of the Arctic but has radically declined in recent decades. When there is less sea ice, sunlight warms the ocean more quickly and algae grow faster. Years with the largest reductions in sea ice cover in June led to warmer water in July. This boosted the odds of HABs and rising toxin levels in the whales. Warmer ocean conditions and loss of sea ice are all linked to higher toxin levels in the food web.

“As an early career researcher, I never got to see what a “normal” arctic should look like,” said WHOI”s Fachon.  “Learning about these blooms alongside scientists who have been working in the region for decades has really impressed upon me the novelty of HABs in this part of the world.”

This extensive research was accomplished through decades of collaboration among researchers from tribal, state, and federal governments, academic institutions, and private organizations. Arctic science is best when there is teamwork amongst Native and western science. The research team included specialists in Arctic traditional ecological knowledge, oceanography, climatology, HABs, food web ecology, and experts in bowhead whale health and ecology. These researchers were able to fill in a piece of the Arctic HAB risk puzzle. This study confirms the need for continued and increased monitoring of HAB risks to food security and food safety of marine subsistence resources used by rural Alaskan communities.

Image shows the harmful algal cells that produce potent neurotoxins described in study: Pseudo-nitzschia (cigar shaped diatoms that produce domoic acid) and Alexandrium (roundish shaped dinoflagellates that produce saxitoxin).

 

Credit

Photo credit: Brian Bill NOAA Fisheries/Northwest Fisheries Science Center, Seattle, WA, 98112 USA

This work was supported by the NSF Office of Polar Programs (OPP-1823002; OPP-2135537); NOAA's Arctic Research program (through the Cooperative Institute for the North Atlantic Region [NA14OAR4320158 and NA19OAR4320074]); NOAA Centers for Coastal and Ocean  Science (NCCOS) Competitive Research Program (NA20NOS4780195; the Woods Hole Center for Oceans and Human Health (National Science Foundation grant OCE-1840381 and National Institutes of Health grant NIEHS-1P01-ES028938-01).

About Woods Hole Oceanographic Institution

Woods Hole Oceanographic Institution (WHOI) is a private, non-profit organization on Cape Cod, Massachusetts, dedicated to marine research, engineering, and higher education. Established in 1930, its mission is to understand the ocean and its interactions with the Earth as a whole, and to communicate an understanding of the ocean’s role in the changing global environment. WHOI’s pioneering discoveries stem from an ideal combination of science and engineering—one that has made it one of the most trusted and technically advanced leaders in fundamental and applied ocean research and exploration anywhere. WHOI is known for its multidisciplinary approach, superior ship operations, and unparalleled deep-sea robotics capabilities. We play a leading role in ocean observation and operate the most extensive suite of ocean data-gathering platforms in the world. Top scientists, engineers, and students collaborate on more than 800 concurrent projects worldwide—both above and below the waves—pushing the boundaries of knowledge to inform people and policies for a healthier planet. Learn more at whoi.edu.

 

Branching out: Tomato genes point to new medicines



Cold Spring Harbor Laboratory
Tomato vine 

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Tomatoes grow on the vine at Uplands Farm, about a mile east of Cold Spring Harbor Laboratory’s main campus on Long Island. The agricultural research station offers a shared resource for CSHL scientists studying various topics, from plant genetics to quantitative biology and cancer.

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Credit: Lippman lab/CSHL





Picture juicy red tomatoes on the vine. What do you see? Some tomato varieties have straight vines. Others are branched. The question is why. New research from Cold Spring Harbor Laboratory (CSHL) provides the strongest evidence to date that the answer lies in what are called cryptic mutations. The findings have implications for agriculture and medicine, as they could help scientists fine-tune plant breeding techniques and clinical therapeutics.

Cryptic mutations are differences in DNA that don’t affect physical traits unless certain other genetic changes occur at the same time. CSHL Professor & HHMI Investigator Zachary Lippman has been researching cryptic mutations’ effects on plant traits alongside CSHL Associate Professor David McCandlish and Weizmann Institute Professor Yuval Eshed. Their latest study, published in Nature, reveals how interactions between cryptic mutations can increase or decrease the number of reproductive branches on tomato plants. Such changes result in more or fewer fruits, seeds, and flowers. The interactions in question involve genes known as paralogs.

“Paralogs emerge across evolution through gene duplication and are major features of genetic networks,” Lippman explains. “We know paralogs can buffer against each other to prevent gene mutations from affecting traits. Here, we found that collections of natural and engineered cryptic mutations in two pairs of paralogs can impact tomato branching in myriad ways.”

One crucial component of the project was the pan-genome Lippman and colleagues completed for Solanum plants around the globe, including cultivated and wild tomato species. Where genomes typically encompass one species, pan-genomes capture DNA sequences and traits across many species. The pan-genome pointed Lippman’s lab toward natural cryptic mutations in key genes controlling branching. Lippman lab postdoc Sophia Zebell then engineered other cryptic mutations using CRISPR. That enabled Lippman’s lab to count the branches on more than 35,000 flower clusters with 216 combinations of gene mutations. From there, McCandlish lab postdoc Carlos Martí-Gómez used computer models to predict how interactions between specific combinations of mutations in the plants would change the number of branches.

“We can now engineer cryptic mutations in tomatoes and other crops to modify important agricultural traits, like yield,” Lippman says.

Additionally, the kind of modeling done here could have many other applications. McCandlish explains: “When making mutations or using a drug that mimics the effects of a mutation, you often see side effects. By being able to map them out, you can choose the manner of controlling your trait of interest that has the least undesirable side effects.”

In other words, this research points not only to better crops but also better medicines. So, you see tomatoes? Science sees tomorrow.

Charité study analyzes 400 million years of enzyme evolution



AlphaFold AI proved the key to success




Charité - Universitätsmedizin Berlin

Three-dimensional shape of the yeast enzyme Erg11 © Charité | Markus Ralser 

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Three-dimensional shape of the yeast enzyme Erg11, generated by AlphaFold2. Erg11 is inhibited by azoles, a specific class of antifungal drugs. If Erg11 changes, the fungus can develop a tolerance to the drugs. © Charité | Markus Ralser

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Credit: © Charité | Markus Ralser





Enzymes catalyze chemical reactions in organisms - without which life would not be possible. Leveraging AlphaFold2 artificial intelligence, researchers at Charité – Universitätsmedizin Berlin have now succeeded in analyzing the laws of their evolution on a large scale. In the journal Nature*, they describe the parts of enzymes that change comparatively quickly and the parts that remain practically unchanged over time. These findings are relevant to the development of new antibiotics, for example.

Enzymes resemble nature's tiny little chemists: the nanometer-sized protein molecules ensure that chemical reactions can take place in every single cell of every organism. Unnoticed by most people, enzymes permeate our lives: they enable the digestion of food - both for us and for microorganisms. Without enzymes, there would be no bread, no beer and no cheese. They are also at work in industry, as evidenced in the production of medicines and detergents. And likewise, enzymes play a pivotal role in the effectiveness and mechanism of action of many medicines.

"We wanted to understand the rules according to which enzymes change their spatial shape over time," as study leader Prof. Markus Ralser, Director of the Institute of Biochemistry at Charité explains. "Because if we know these rules, we can predict, for example, where and how a bacterium will become resistant to an antibiotic." Many antibiotics and antifungal drugs are directed against specific enzymes of the pathogens they target. If these enzymes change their shape precisely where the respective active ingredient docks on, the drug will lose its effect. The same principle applies to numerous other drugs. Many cancer drugs target enzymes in the tumor that can change their shape during the course of treatment, rendering the drug ineffective as a result.

An AI system was the only way to solve the research questions

Determining the principles of enzyme evolution, however, is easier said than done. What is needed is a comparison of the three-dimensional shape of innumerable enzymes. This information, however, was not known for many enzymes, as determining the 3D structure of just a single enzyme by experimental means is time-consuming and can take up to several months. "Instead, by leveraging AlphaFold2, we calculated the shape of almost 10,000 enzymes in a matter of just a few months," says Markus Ralser.

AlphaFold2 is an AI model that deduces what an enzyme's 3D structure should look like based solely on its amino acid sequence, i.e. its chemical composition - and has proven to deliver exceptionally high accuracy. In 2020, AlphaFold2 was celebrated worldwide as a breakthrough and only four years later, last year, the developers of the AI model were awarded the Nobel Prize in Chemistry.

Supercomputing tracking the course of evolution

Unleashing AlphaFold2 calls for hefty computing power - and masses of it. "We harnessed the Berzelius supercomputer in Sweden for our calculations," as Dr. Oliver Lemke, a scientist in Markus Ralser's laboratory and one of the two lead authors of the paper related. The 300-petaflops computer is operated by the National Supercomputer Centre at Linköping University and is available to international research teams on request.

At Charité, the researchers finally analyzed the similarities and differences of a total of almost 11,300 enzymes and examined them in the context of the metabolic reactions for which they are responsible. In addition to the approximately 10,000 3D structures that they had calculated themselves, they took around 1,300 3D structures into account that had previously been predicted using AlphaFold2 and made publicly available.

The team’s work focused on enzymes from yeasts, i.e. unicellular fungi, which include baker's yeast, for example. As Dr. Benjamin Heineike, the second lead author of the study from the Ralser laboratory, explains: "Yeast fungi are among the best-studied organisms. Whether in terms of enzyme genes or metabolism, we had the most comprehensive data on them." The enzymes studied came from 27 different yeast species that have developed over an evolutionary period totaling 400 million years.

Chemistry determines enzyme change

The research team discovered several laws that govern the way in which enzymes evolve. For example, they change faster on their surface than underneath. By contrast, their so-called active center - the site where the chemical reaction takes place - barely changes over a long period of time. If the enzyme has to bind other molecules on its surface in order to fulfil its role, those areas are also frozen in terms of their shape. "To summarize, we can say that enzymes primarily undergo further development in areas that have no effect on the chemical reactions," Markus Ralser explains. "The metabolism itself therefore plays a key role in the evolution of the enzyme structure."

The results of the study are relevant to the optimization of biotechnological processes, for example, but also the development of new active ingredients. To return to the example of antibiotics: "Sometimes, when a new antibiotic comes onto the market, it does not take long before the first resist strains appear," Markus Ralser adds. "The reason for this is that the bacterial enzymes targeted by the active agents evolve at a rapid pace. Our data can be used to identify the parts of the enzymes unlikely to change much. New antibiotics that target precisely these areas could potentially retain their effect over a longer period of time."
 

*Lemke O, Heineike BM et al. The role of metabolism in shaping enzyme structures over 400 million years. Nature 2025 Jul 09. doi: 10.1038/s41586-025-09205-6
 

About the study
The study was led by Prof. Markus Ralser, Einstein Professor of Biochemistry. He heads a research group at the Nuffield Department of Medicine at the University of Oxford in addition to the Institute of Biochemistry at Charité. Markus Ralser is also a fellow at the Max Planck Institute for Molecular Genetics (MPIMG) and the Berlin Institute of Health at Charité (BIH).

 

Ancient Rhino tooth helps push the boundaries of evolutionary research



University of York
Rhino tooth 

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Ancient rhino tooth

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Credit: University of York




Scientists have shed new light on the rhino family tree after recovering a protein sequence from a fossilised tooth from more than 20 million years ago.

The recovered protein sequences allowed researchers to determine that this ancient rhino diverged from other rhinocerotids during the Middle Eocene-Oligocene epoch, around 41-25 million years ago. 

The data also shed new light on the divergence between the two main subfamilies of rhinos, Elasmotheriinae and Rhinocerotinae, suggesting a more recent split in the Oligocene, around 34-22 million years ago, than shown previously through bone analysis.

The successful extraction and sequencing of ancient enamel proteins from a fossilized rhino tooth extends the timescale for recoverable, evolutionary-informative protein sequences by ten-fold compared to the oldest known ancient DNA.

The team at York were involved in confirming that the proteins and amino acids were genuinely ancient. They analysed the rhino tooth, which was unearthed in Canada's High Arctic, using a technique known as chiral amino acid analysis to gain a clearer understanding of how the proteins within it had been preserved. 

By measuring the extent of protein degradation and comparing it to previously analysed rhino material, they were able to confirm that the amino acids were original to the tooth and not the result of later contamination. 

Dr Marc Dickinson, co-author and postdoctoral researcher at the University of York’s Department of Chemistry, said: “It is phenomenal that these tools are enabling us to explore further and further back in time. Building on our knowledge of ancient proteins, we can now start asking fascinating new questions about the evolution of ancient life on our planet.”

The rhino is of particular interest as it is now classified as an endangered species, and so understanding its deep-time evolutionary history, allows us to gain vital insights into how past environmental changes and extinctions shaped the diversity we see today. 

To date, scientists have relied on the shape and structure of fossils or, more recently, ancient DNA (aDNA) to piece together the evolutionary history of long-extinct species. However, aDNA rarely survives beyond 1 million years, limiting its utility for understanding deep evolutionary past. 

While ancient proteins have been found in fossils from the Middle-Late Miocene, - roughly the last 10 million years - obtaining sequences detailed enough for robust reconstructions of evolutionary relationships was previously limited to samples no older than four million years. 

The new study, published in the journal Nature, significantly expands that window, demonstrating the potential of proteins to persist over vast geological timescales under the right conditions.

Fazeelah Munir, who analysed the tooth as part of her doctoral research at the University of York’s Department of Chemistry, said: “Successful analysis of ancient proteins from such an old sample gives a fresh perspective to scientists around the globe who already have incredible fossils in their collections. This important fossil helps us to understand our ancient past.”

The fossil was in a region of Canada currently characterized by permafrost, and researchers say that dental enamel and the relatively cold environment the fossil was found in, played an important part in the long preservation of the proteins. 

Dental enamel provides a stable ‘scaffold’ that can protect ancient proteins from degradation over geological time. The hardness of enamel, which results from a complex structure of minerals, acts as a protective barrier, slowing down the breakdown of proteins that occurs after death.

Professor Enrico Cappellini, from Globe Institute, University of Copenhagen, said: "The Haughton Crater may be a truly special place for palaeontology: a biomolecular vault protecting proteins from decay over vast geological timescales. 

“Its unique environmental history has created a site with exceptional preservation of ancient biomolecules, akin to how certain sites preserve soft tissues. This finding should encourage more paleontological fieldwork in regions around the world." 

Ryan Sinclair Paterson, postdoctoral researcher at the Globe Institute, University of Copenhagen, added: “This discovery is a game-changer for how we can study ancient life.”