ECOCIDE

Maternal exposure to crude oil, flame retardants can affect later generations

Research on killifish sheds light on human and wildlife exposure risks

University of California - Davis

Facebook

XLinkedInWeChatBlueskyMessageWhatsAppEmail

 

image: 

UC Davis research on embryonic killifish reveals new insights into the multi-generational impacts of exposure to crude oil and flame retardants.

view more 

Credit: Bryan Clark, U.S. EPA

A tiny fish with transparent embryos is helping University of California, Davis, researchers shed light on how exposure to crude oil and flame retardants can affect behavior, skeletal growth, cardiac health and other internal functions in offspring and subsequent generations.

The research on multiple generations of Atlantic killifish (mummichogs) was published across three papers in the journal Environmental Science and Technology.

The work, some dating back to the 2010 Deepwater Horizon oil spill off the Gulf coast, offers insight into how toxic exposures – even short ones – can unfold over time in many species.

“We need to broaden our thinking of risk,” said Professor Andrew Whitehead, chair of the Department of Environmental Toxicology and senior author on the papers. “Toxic exposures can have effects that propagate well beyond the lifetime of directly exposed individuals.”

The researchers chose to focus on killifish because they are important ecologically and were the most abundant species in the marshy areas affected by the Deepwater Horizon oil spill. Their embryos are transparent, allowing developmental changes to be seen with a microscope. Their genetics, gene functions, cell biology and developmental biology are very similar to humans and other wildlife.

“The same genes and cell biology that regulates heart, brain and skeletal development in a fish are the same as those that regulate development in humans,” Whitehead said. 

Generational effects differ

Whitehead began his oil spill research in 2010 while at Louisiana State University when the Deepwater Horizon accident released more than 3 million gallons of crude oil into the Gulf of Mexico. Researchers exposed killifish to Deepwater Horizon oil and compared their offspring with those of unexposed adults.

They found that if parents had been exposed to oil, their first-generation offspring exhibited altered functioning of genes that affect nerve and brain processes. In the second generation after exposure, genes that affect heart function were different from those of killifish whose parent or grandparent weren’t exposed. Also, growth and skeleton shapes were affected by that initial exposure in both first- and second-generation offspring.

“Exposure affected body shape and the function of many hundreds of genes many years and at least two generations later,” Whitehead said. “That’s a pretty durable impact.” 

Exposures with lasting effects

The research into flame retardants centered on polybrominated diphenyl ether, or PBDE, which has largely been phased out due to its toxicity, but is still manufactured in Asia and is ubiquitous in air, soil, the environment, wildlife and humans. It can be passed through the placenta to breast milk and eggs.

“Every single one of us has detectable levels of flame retardants in our bodies,” Whitehead said. “They are everywhere in the environment and in everything.”

The researchers looked at the neurobehavioral and molecular effects of PBDE. In one group, they exposed adult fish to PBDE via diet, which passed the chemical on to offspring. The other group consisted of embryos exposed directly to contaminated water. In offspring of exposed fish, they measured various aspects of behavior that represents brain function, and molecular effects in the brain.

In both groups, researchers noticed that in the generation after exposure, behavior was altered. Exposed moms passed chemicals to their offspring so exposures started in the earliest stages of development. This had life-long impacts on behavior and on molecular function within the brain. Even if fish were exposed for just one week during development, then raised for the rest of their life in clean water, their offspring inherited altered behavior.

“That very narrow window of exposure during development has effects on your babies,” Whitehead said.

Nicole McNabb-Kelada, who earned her Ph.D. at UC Davis and is the first author on the PBDE papers, called the long-term effects surprising: "It was eye-opening to see that both maternal and environmental early-life exposures caused changes across the lifetime and into the next generation, each in its own way, showing multiple pathways for these chemicals to have lasting impacts," she said.

Looking back to determine risk

Oil spills, which contain chemicals similar to those in air pollution, and fire retardants are commonly encountered in the environment. This research provides insights into how humans, fish and other species are affected by contamination that can last generations.

“The legacy of toxic exposures can be long — much longer than people tend to think and much longer than our regulatory structures think about,” Whitehead said. “If we want to be smart about public health and wildlife health, we need to think about these longer-term outcomes and orient our science toward discovering them, both the causes and the consequences. The intervention that’s necessary is to prevent exposure in the first place.”

Jane Park in the Department of Environmental Toxicology and David Rocke from the Department of Biomedical Engineering at UC Davis contributed to the oil spill research, as did Chelsea Hess, Fernando Galvez and Charles Brown from Louisiana State University and Christoph Aeppli from the Bigelow Laboratory for Ocean Sciences. It was funded by the National Institute of Environmental Health Sciences and National Science Foundation.

Nicole McNabb-Kelada and Ashley De La Torre in the Department of Environmental Toxicology contributed to the flame retardant research, as did Tara Burke, Bryan Clark, Saro Jayaraman, Lesley Mills, Diane Nacci, Hannah Schrader and Madison Silvia with the U.S. Environmental Protection Agency’s Atlantic Coastal Environmental Sciences Division. The National Institute of Environmental Health Sciences, Fumio Matsumura Memorial Endowment, Jastro-Shields Research Awards, UC Davis Wildlife Health Center Fellowship, Emmy Werner and Stanley Jacobsen Fellowship, Lewin Family Fellowship and Schwall Dissertation Fellowship funded the research.

Scientists have found killifish like this one to be surprisingly adaptable to polluted environments. 

Credit

Andrew Whitehead, UC Davis

\

Embryonic killifish faces are visible through their transparent embryos. 

Credit

Bryan Clark, U.S. EPA

UC Davis environmental toxicology Professor Andrew Whitehead carries minnow traps while collecting Gulf killifish from the Mississippi coast following the Deepwater Horizon oil spill in 2010.

Credit

Patrick Sullivan

Journal

Environmental Science & Technology

DOI

10.1021/acs.est.5c05887 

Article Title

PBDE Flame Retardant Exposure Causes Neurobehavioral and Transcriptional Effects in First-Generation but Not Second-Generation Offspring Fish

Article Publication Date

26-Aug-2025

New research makes first broad-spectrum antiviral

Scientists at the Advanced Science Research Center at the CUNY Graduate Center target the viral envelop to fight multiple viruses

Advanced Science Research Center, GC/CUNY

Facebook

XLinkedInWeChatBlueskyMessageWhatsAppEmail

 

image: 

Synthetic carbohydrate receptors act as broad-spectrum antivirals by binding to conserved N-glycans and in doing so, blocking virus binding and virus fusion.

view more 

Credit: Khushabu Thakur

NEW YORK, August 27, 2025 — Researchers at the Nanoscience Initiative at the Advanced Science Research Center at the CUNY Graduate Center (CUNY ASRC) have made a breakthrough in the fight against viral diseases. Their study, published in the journal Science Advances, offers a promising path toward the development of the world’s first broad-spectrum antiviral (BSA), which could be deployed against a wide range of deadly viruses, including future pandemic threats.

Unlike bacterial infections, which doctors often begin immediately treating with broad-spectrum antibiotics while they work to determine the specific bacteria, viral infections are treated with antivirals, which are narrowly targeted and effective against only a small set of related viruses.

“This lack of treatments can leave populations vulnerable for years, while vaccines and therapeutics are being developed,” said Principal Investigator Adam Braunschweig, a Nanoscience Initiative professor at CUNY ASRC and a Chemistry and Biochemistry professor at Hunter College.

Braunschweig’s team set out to address this global health challenge by targeting a shared feature found on the surface of many viruses: viral envelope glycans—sugar molecules that are structurally conserved across unrelated viral families. These widely shared have until now remained an untapped target for antiviral drug development.

The researchers screened 57 synthetic carbohydrate receptors (SCRs), which are small molecules designed to bind to viral glycans. They identified four lead compounds that successfully blocked infection from seven different viruses across five unrelated families, including some of the world’s most dangerous pathogens: Ebola, Marburg, Nipah, Hendra, SARS-CoV-1, and SARS-CoV-2.

In a critical test, one of the lead SCR compounds was used to treat mice infected with SARS-CoV-2. Ninety percent of the mice receiving the SCR survived, compared to none in the control group. Further analysis confirmed that the compounds work by binding to viral envelope glycans—a novel mechanism of action with potential applications not only for infectious diseases but also for cancer and immune disorders.

“This is the kind of antiviral tool the world urgently needs,” said Braunschweig. “If a new virus emerges tomorrow, we currently have nothing to deploy. These compounds offer the potential to be that first line of defense.”

The next phase of the team’s research will focus on advancing the most promising compounds into clinical trials.

This work was supported by the Army Research Office, National Institutes of Health, New York State Biodefense Commercialization Fund, Air Force Office of Scientific Research, and the COVID-19 High Performance Computing Consortium.

 

About the Graduate Center of The City University of New York
The CUNY Graduate Center is a leader in public graduate education devoted to enhancing the public good through pioneering research, serious learning, and reasoned debate. The Graduate Center offers ambitious students nearly 50 doctoral and master’s programs of the highest caliber, taught by top faculty from throughout CUNY — the nation’s largest urban public university. Through its nearly 40 centers, institutes, initiatives, and the Advanced Science Research Center, the Graduate Center influences public policy and discourse and shapes innovation. The Graduate Center’s extensive public programs make it a home for culture and conversation.

About the Advanced Science Research Center at the CUNY Graduate Center
The Advanced Science Research Center at the CUNY Graduate Center (CUNY ASRC) is a world-leading center of scientific excellence that elevates STEM inquiry and education at CUNY and beyond. The CUNY ASRC’s research initiatives span five distinctive, but broadly interconnected disciplines: nanoscience, photonics, neuroscience, structural biology, and environmental sciences. The center promotes a collaborative, interdisciplinary research culture where renowned and emerging scientists advance their discoveries using state-of-the-art equipment and cutting-edge core facilities.

 

---

Journal

Science Advances

DOI

10.1126/sciadv.ady3554 

Method of Research

Experimental study

Subject of Research

Not applicable

Article Title

Broad-spectrum Synthetic Carbohydrate Receptors (SCRs) Inhibit Viral Entry Across Multiple Virus Families

Article Publication Date

27-Aug-2025

 

Origin of life breakthrough: Chemists show how RNA might have started to make proteins on early Earth

University College London

LinkedInWeChatBlueskyMessageWhatsAppEmail

 

image: 

Grand Prismatic Spring, the largest hot spring at Yellowstone National Park in the US.

view more 

Credit: Frank Kovalchek

Chemists at UCL have shown how two of biology’s most fundamental ingredients, RNA (ribonucleic acid) and amino acids, could have spontaneously joined together at the origin of life four billion years ago.

Amino acids are the building blocks of proteins, the “workhorses” of life essential to nearly every living process. But proteins cannot replicate or produce themselves – they require instructions. These instructions are provided by RNA, a close chemical cousin of DNA (deoxyribonucleic acid).

In a new study, published in Nature, researchers chemically linked life’s amino acids to RNA in conditions that could have occurred on the early Earth – an achievement that has eluded scientists since the early 1970s.

Senior author Professor Matthew Powner, based at UCL’s Department of Chemistry, said: “Life relies on the ability to synthesise proteins – they are life’s key functional molecules. Understanding the origin of protein synthesis is fundamental to understanding where life came from.

“Our study is a big step towards this goal, showing how RNA might have first come to control protein synthesis.

“Life today uses an immensely complex molecular machine, the ribosome, to synthesise proteins. This machine requires chemical instructions written in messenger RNA, which carries a gene’s sequence from a cell’s DNA to the ribosome. The ribosome then, like a factory assembly line, reads this RNA and links together amino acids, one by one, to create a protein.

“We have achieved the first part of that complex process, using very simple chemistry in water at neutral pH to link amino acids to RNA. The chemistry is spontaneous, selective and could have occurred on the early Earth.”

Previous attempts to attach amino acids to RNA used highly reactive molecules, but these broke down in water and caused the amino acids to react with each other, rather than become linked to RNA.

For the new study, the researchers took inspiration from biology, using a gentler method to convert life’s amino acids into a reactive form. This activation involved a thioester, a high-energy chemical compound important in many of life’s biochemical processes and that has already been theorised to play a role at the start of life*.

Professor Powner said: “Our study unites two prominent origin of life theories – the ‘RNA world’, where self-replicating RNA is proposed to be fundamental, and the ‘thioester world’, in which thioesters are seen as the energy source for the earliest forms of life.”

In order to form these thioesters, the amino acids react with a sulphur-bearing compound called pantetheine. Last year, the same team published a paper demonstrating pantetheine can be synthesised under early Earth-like conditions, suggesting it was likely to play a role in starting life.

The next step, the researchers said, was to establish how RNA sequences could bind preferentially to specific amino acids, so that RNA could begin to code instructions for protein synthesis – the origin of the genetic code.

“There are numerous problems to overcome before we can fully elucidate the origin of life, but the most challenging and exciting remains the origins of protein synthesis,” said Professor Powner.

Lead author Dr Jyoti Singh, from UCL Chemistry, said: “Imagine the day that chemists might take simple, small molecules, consisting of carbon, nitrogen, hydrogen, oxygen, and sulphur atoms, and from these LEGO pieces form molecules capable of self-replication. This would be a monumental step towards solving the question of life's origin.

“Our study brings us closer to that goal by demonstrating how two primordial chemical LEGO pieces (activated amino acids and RNA) could have built peptides**, short chains of amino acids that are essential to life.

“What is particularly groundbreaking is that the activated amino acid used in this study is a thioester, a type of molecule made from Coenzyme A, a chemical found in all living cells. This discovery could potentially link metabolism, the genetic code and protein building.”

While the paper focuses solely on the chemistry, the research team said that the reactions they demonstrated could plausibly have taken place in pools or lakes of water on the early Earth (but not likely in the oceans as the concentrations of the chemicals would likely be too diluted).

The reactions are too small to see with a visible-light microscope and were tracked using a range of techniques that are used to probe the structure of molecules, including several types of magnetic resonance imaging (which shows how the atoms are arranged) and mass spectrometry (which shows the size of molecules).

The work was funded by the Engineering and Physical Sciences Research Council (EPSRC), the Simons Foundation and the Royal Society.

*The Nobel laureate Christian de Duve proposed that life began with a “thioester world” – a metabolism-first theory that envisages life was started by chemical reactions powered by the energy in thioesters.

** Peptides typically consist of two to 50 amino acids, while proteins are larger, often containing hundreds or even thousands of amino acids, and are folded into a 3D shape. As part of their study, the research team showed how, once the amino acids were loaded on to the RNA, they could synthesise with other amino acids to form peptides.

---

Journal

Nature

DOI

10.1038/s41586-025-09388-y 

A stunning first look at the viruses inside us

LJI scientists uncover a new avenue for stopping cancers, autoimmune diseases, and more

La Jolla Institute for Immunology

Facebook

XLinkedInWeChatBlueskyMessageWhatsAppEmail

 

image: 

The new study, led by LJI scientists, shows the HERV-K Env structure from every angle. These renderings offer a top view and side view of the protein and reveal how the three parts of its trimer structure come together. (Image courtesy LJI/Saphire Lab)

view more 

Credit: LJI/Saphire Lab

LA JOLLA, CA—You are mostly but not entirely human. If we crunch the numbers, 8 percent of your genome actually comes from viruses that got stranded there. This viral detritus is a souvenir from our evolutionary past, a reminder that viruses have been with us from the very beginning. 

Usually, this 8 percent of your DNA—the viral bits—are kept silent. Scientists call it part of the “dark matter” in your genome.

Now scientists at La Jolla Institute for Immunology (LJI) have published a first look at a key viral protein. In a study published in Science Advances, LJI researchers revealed the first three-dimensional structure of a protein from one of these ancient “human endogenous retroviruses (HERVs).”

The team mapped the surface envelope glycoprotein (Env), the antibody target of the most active HERV, marking a milestone in structural biology. “This is the first human HERV protein structure ever solved—and only the third retroviral envelope structure solved overall, after human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV),” says Erica Ollmann Saphire, Ph.D., MBA, LJI President, CEO, and Professor.

This discovery opens the door to new strategies for diagnosing and treating disease. Back in the evolutionary past, HERV-K Env proteins studded the outside of the HERV-K retroviruses. But in modern humans, HERV-K Env proteins show up on the surface of certain tumor cells and in patients with autoimmune and neurodegenerative diseases, making them a valuable target for developing novel diagnostics and therapies.

"In many disease states, like autoimmune diseases and cancer, these genes re-awaken and start making pieces of these viruses," says Saphire. "Understanding the HERV-K Env structure, and the antibodies we now have, opens up diagnostic and treatment opportunities."

An unexpected "twist"

Until now, HERV proteins had been invisible. They've proven too mobile—and too twitchy—to be seen with even the most sophisticated imaging techniques. Solving the structure of HERV-K Env was especially challenging because the LJI team needed to capture the protein's delicate "pre-fusion" state.

Envelope proteins are full of potential energy—they're essentially spring-loaded to merge with a host cell to start the infection process. This means pre-fusion proteins are prone to spontaneous switching to their later, post-fusion state. "You can look at them funny, and they'll unfold," says LJI Postdoctoral Fellow Jeremy Shek, who spearheaded the study as co-first author with LJI Postdoctoral Fellow Chen Sun, Ph.D.

To study the three-dimensional structure of HERV-K Env, the researchers introduced small substitutions to lock the protein’s structure in place, while preserving its natural shape. Saphire and her team have used this approach before to reveal the structures of key proteins on Ebola virus, Lassa virus, and more. The researchers also discovered and characterized specific antibodies that helped anchor different versions of the viral proteins.

After stabilizing their HERV-K Env structures, the LJI team used a high-resolution imaging technique called cryo-electron microscopy to capture 3D images of HERV-K Env at three key moments: cell surface, in the act of driving infection, and when it locks together with antibodies.

Many viral envelope glycoproteins have a trimer structure, but HERV-K Env is different from anything scientists had seen before, including trimers from other retroviruses. Unlike the shorter, squatter trimers made by HIV and SIV, the HERV-K Env is tall and lean. Further, the protein's fold—the weaving together of strands and coils that build the working machine—is unlike any other retrovirus.

A new path for clinical research

The new LJI study opens the door to using HERV-K Env to our advantage. Understanding the HERV-K Env structure, and how antibodies target it, may prove useful for developing diagnostic tools or new therapeutics.

For example, many types of cancer cells—from breast cancers to ovarian cancers— but not healthy cells, are dotted with HERV-K Env proteins. This means antibodies against HERV could distinguish cancer cells from healthy cells. As Sun explains, scientists could develop cancer immunotherapies that zero in on HERV-K Env to track down tumor cells. "We can use it as a strategy to specifically target cancer cells," says Sun.

People with autoimmune diseases such as lupus or rheumatoid arthritis also express HERV-K Env on their cells. Some scientists suspect that patients’ immune cells see these strange proteins and think the body is under attack. Just like during a normal viral infection, their B cells start making antibodies against HERV-K Env proteins. 

"Understanding how antibodies recognize these proteins was challenging because there was no structure and precious few good antibodies yet available," says Saphire. 

So the LJI team made their own panel of antibodies to reveal how the immune system can target the different subunits of the molecule in all its different shapes. Once scientists understand how these antibody attacks work, they can try to intervene and stop harmful inflammation.

The scientists also tested the idea that their antibodies may also be useful tools for diagnosing many autoimmune diseases. They used the antibodies to try and hunt down immune cells in samples from patients with rheumatoid arthritis and lupus. When Saphire and her colleagues tagged these antibodies with a molecular flag, they were able to quickly detect HERV-K Env on neutrophils, a type of immune cell that can cause inflammation.

"These antibodies marked aberrant HERV display on neutrophils from rheumatoid arthritis and lupus patients, but not healthy controls," says Saphire.

The interest in HERVs is quickly growing, and scientists are finding more and more diseases where HERV-K Env crops up. "We can really pick whatever disease we're interested in and go down that route," says Shek.

These projects may someday advance clinical care—and our fundamental understanding of human biology. After all, we're all part virus. It's time to get to know that part of ourselves.

Additional authors of the study, "Human endogenous retrovirus K (HERV-K) envelope  structures in pre- and postfusion by cryo-EM," were Elise M. Wilson, Fatemeh Moadab, Kathryn M. Hastie,  Roshan R. Rajamanickam, Patrick J. Penalosa, Stephanie S. Harkins, Diptiben Parekh,  Chitra Hariharan, Dawid S. Zyla, Cassandra Yu, Kelly C.L. Shaffer, Victoria I. Lewis,  Ruben Diaz Avalos, and Tomas Mustelin,

This study was supported by a Curebound Discovery Grant (13502-01-000-408) and by LJI & Kyowa Kirin, Inc. (KKNA-Kyowa Kirin North America; and a Kirin North America Accelerator Grant [18030-01-000-408]).

DOI: 10.1126/sciadv.ady8168 

---

Journal

Science Advances

DOI

10.1126/sciadv.ady8168 

Method of Research

Experimental study

Subject of Research

Cells

Article Title

Human endogenous retrovirus K (HERV-K) envelope structures in pre- and post-fusion by cryo-EM

Article Publication Date

27-Aug-2025

COI Statement

The La Jolla Institute for Immunology has pending provisional patent coverage on the mAbs and proteins described herein. The applications, entitled “HERV-K Envelope Protein Binders and Compositions and Methods of Use Thereof” and “Stabilized Pre-Fusion HERV-K Envelope Ectodomain Trimer” lists inventors E.O.S., K.M.H., S.H., E.M.W., and J.S., respectively, and were assigned US Provisional Patent nos. 63/638,067 and 63/783,708. The authors declare that they have no other competing interests.