Despite their simplicity, 1-millimeter-long nematodes called Caenorhabditis elegans (C. elegans) share an important limitation with humans: They cannot make B12 and must get all they need from their diet. In a study published today in PLOS Genetics, researchers from the lab of Rice biochemist and cancer researcher Natasha Kirienko describe how a B12-deficient diet harms C. elegans‘ health at a cellular level, reducing the worms’ ability to metabolize branched-chain amino acids (BCAA). The research showed that the reduced ability to break down BCAAs led to a toxic buildup of partially metabolized BCAA byproducts that damaged mitochondrial health.

Researchers studied the health of two populations of worms, one with a diet sufficient in B12 and another that got too little B12 from its diet. Like the second population of worms, at least 10 percent of U.S. adults get too little B12 in their diet, a risk that increases with age.

“We used C. elegans to study the effect of diet on a host and found that one kind of food was able to dramatically increase resistance to multiple stressors — like heat and free radicals — as well as to pathogens,” said Kirienko, assistant professor of biosciences and a CPRIT Scholar in Cancer Research at Rice.

The lead scientist and co-author of the study, Kirienko said the B12 finding came as a surprise to her team, which first noticed the effect in experiments designed to investigate the mechanisms of pathogenesis of Pseudomonas aeruginosa (P. aeruginosa), a potentially deadly disease in both worms and humans that infects some 51,000 U.S. hospital patients each year, according to the Centers for Disease Control.

Her lab, like thousands of others worldwide, uses C. elegans as a model organism to study the effects of disease, drugs, toxins and other processes that affect humans and animals. In many C. elegans research labs worms are fed Escherichia coli (E. coli), a common human gut bacteria that is itself a model organism.

“We found that switching between E. coli strain OP50 and strain HT115 dramatically altered the worm’s stress tolerance,” Kirienko said. She said it took about two years of follow-up studies to isolate the biochemical mechanism of stress and pathogen resistance. Her research team included study lead co-author Alexey Revtovich and co-author Ryan Lee.

“The key difference between the two diets is the ability of HT115 and OP50 to acquire B12 from the environment,” said Revtovich, a research scientist. “We showed that HT115 is far more efficient at this, making about eight times as much of the protein that it needs to harvest B12 as compared to OP50.”

The researchers used numerous tests to confirm their results and rule out other possible mechanisms for the effect. They also found that C. elegans on an HT115 diet had the ability to resist infection by another deadly human pathogen, Enterococcus faecalis.

Lee, a Rice undergraduate student, said the study highlights the need for C. elegans labs worldwide to pay attention to the possible differential impacts of diet on experimental outcomes.

“Some labs use OP50 as their standard food, and others use HT115 or even another strain of E. coli,” Lee said. “Our results show there are significant metabolic differences between these diets, and it’s likely those differences could contribute to substantial uncertainty in research outcomes.”

Kirienko joined Rice’s faculty in 2015 thanks to a recruitment grant from the Cancer Prevention and Research Institute of Texas (CPRIT), a state ballot initiative approved in 2007 to provide $3 billion to support cancer research statewide. To date, CPRIT has awarded $2.2 billion in grants to Texas researchers, institutions and organizations through its academic research, prevention and product development research programs.

“This work is related in the sense that it focuses on mitochondrial health,” Kirienko said. “In this case, we are working to improve mitochondrial health to help fight infections. For CPRIT, we’re trying to do the opposite. We want to damage mitochondria in cancer cells to kill them. So, actually, now that we know this is important, it gives us another potential target in cancer cells.”

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Materials provided by Rice University. Original written by Jade Boyd. Note: Content may be edited for style and length.

Researchers at Stanford University have created such a map by analyzing the habitats occupied by more than 800 sharks and tunas and 900 industrial fishing vessels. Focusing on international waters in the northeast Pacific, they found that vessels from Taiwan, China, Japan, the United States and Mexico accounted for over 90 percent of fishing in key habitat areas for seven shark and tuna species.

“The high seas are the global commons of the oceans,” said Timothy White, a graduate student in biology at Stanford and lead author of the paper detailing this research, published March 13 in Science Advances. “Analyses like this open the door to conversations about whether we think that the current mode of operation in the high seas is most equitable, most effective and most desirable.”

The researchers hope their findings can help the United Nations member states currently formulating the world’s first legally binding treaty to protect international waters, known as the high seas.

“We may protect a species near the coastline of North America, but that same species may be exposed to a high level of international fishing in the open ocean. By increasing the transparency of where fish and ship fleets meet, we can identify hot spots where international protection may be required,” said Barbara Block, the Prothro Professor of Marine Sciences at Stanford University.

Where fishing meets fish

The team’s work builds on a 2018 study led by Global Fishing Watch, the Block Lab and other researchers, published in Science. In that study, researchers took four years of data from the Automatic Identification System (AIS) — which tracks vessel movements via satellite — and developed a machine learning algorithm that mapped the footprint of 70,000 individual fishing vessels across the globe, down to details about the fishing methods of each vessel. In the current paper, the researchers narrowed their focus to the activities of over 900 vessels from 12 countries in the northeast Pacific Ocean to better understand the degree of overlap among fishing fleets, sharks and tunas in those waters.

Meaningful solutions to overfishing of some shark and tuna populations have been hindered by two significant mysteries: where fishing is happening and where the fish are. In order to help solve these mysteries, the researchers combined ship positions with the ocean habitat preferences obtained from the decade-long tracking program called Tagging of Pacific Predators (TOPP). This program included Pacific bluefin tuna, yellowfin tuna, albacore tuna, white shark, shortfin mako shark, salmon shark and blue shark. With the exception of the salmon shark, all of these species are currently listed as Threatened or Near-Threatened on the IUCN (International Union for Conservation of Nature) Red List of Threatened Species, though some populations are sustainably fished in the northeast Pacific region.

Over the 10 years of the TOPP program, 876 electronic tags were deployed on individual sharks and tunas. Hundreds of individual journeys — each spanning hundreds to thousands of kilometers — showed the researchers which areas of the ocean are preferred habitats for each species.

By integrating the animal, ship and environmental data, the researchers predicted what ocean regions and commercial fishing fleets have the highest overlap.

“The biggest challenge was in combining these very different datasets,” said White. “By adding the latest vessel tracking and machine learning techniques to the toolboxes of marine scientists, we were able to paint a clearer picture of how fish and fisheries interact, and this information can inform how our management strategies should reflect this.”

High seas protection

The United Nations’ high seas treaty discussions, which are ongoing through 2020, are very much on the minds of these researchers. As a window into human-animal interactions on the high seas, they believe their work could help guide which parts of the northeast Pacific Ocean deserve special consideration, what kinds of fishing activities should be addressed and what nations have a major role to play in protecting these waters.

“These analyses have given us the chance to look more deeply into the dynamics of this ocean and see where managers and stakeholders should focus their attention,” said Francesco Ferretti, a research associate at Stanford’s Hopkins Marine Station and co-author of the paper. “We need to push harder to preserve this corner of the planet because these are some of the best ocean environments in the world.”

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Materials provided by Stanford University. Original written by Taylor Kubota. Note: Content may be edited for style and length.

Published March 12 in Aquatic Mammals, the paper is a major revision of the first such assessment, published in 2007 in the same journal. Both efforts were led by Brandon Southall, a research associate at the Institute of Marine Sciences at UC Santa Cruz and senior scientist at Southall Environmental Associates.

“One of the things we did in 2007 was to identify major gaps in our knowledge, and we now have considerably more data. We thought there was enough new science to reconvene the panel and revisit these issues,” said Southall, who served as director of NOAA’s Ocean Acoustics Program from 2004 to 2009.

Concern about the potential for ocean noise to cause hearing damage or behavioral changes in marine mammals began to mount in the 1990s, focusing initially on activities related to the oil and gas industry. In the early 2000s, the association of sonar with mass strandings of deep-diving whales became another focus of concern. Shipping and construction activities are other important sources of ocean noise pollution.

Loud noises can cause temporary or permanent hearing loss, can mask other sounds, and can disturb animals in various ways. The new paper focuses on direct effects of noise pollution on hearing in marine mammals. Separate papers addressing behavioral effects and the acoustics of different sound sources will be published later this year.

“Noise-induced hearing loss occurs in animals the same way it does in humans. You can have a short-term change in response to exposure to loud noise, and you can also have long-term changes, usually as a result of repeated insults,” said coauthor Colleen Reichmuth, a research scientist who leads the Pinniped Cognition and Sensory Systems Laboratory at UC Santa Cruz.

Because animals vary in their sensitivities to different types and frequencies of sound, the panel categorized marine mammal species into groups based on what was known about their hearing. The new paper includes all living species of marine mammals.

“The diversity of species is such that a one-size-fits-all approach isn’t going to work,” said coauthor Darlene Ketten, a neuro-anatomist with joint appointments at Woods Hole Oceanographic Institute and Boston University’s Hearing Research Center. “We need to understand how to avoid harm, and the aim is to provide guidelines to say, if this or that species is in your area, here’s what you need to avoid.”

Over the past decade, the number of scientific studies on hearing in marine mammals has grown rapidly, enabling the panel to refine and improve its groupings and assessments. Accompanying the paper is a set of appendices compiling all the relevant information for 129 species of marine mammals.

“We did a comprehensive review, species by species, for all living marine mammals,” said Reichmuth, who led the work on the appendices. “We pulled together the available knowledge covering all aspects of hearing, sound sensitivity, anatomy, and sound production. That’s the scientific basis for the species groupings used in the noise exposure criteria.”

“The appendices are a really important resource that does not exist anywhere else,” Southall said. “The 2007 paper was the most impactful single paper I’ve ever published — it’s been cited in the literature more times than all my other papers combined — and I expect this new paper will have a similar impact.”

The 2007 paper covered only those species under the jurisdiction of the National Marine Fisheries Service (NOAA Fisheries). NOAA Fisheries issued U.S. regulatory guidance in 2016 and 2018 based on the 2007 paper and a 2016 Navy technical report by James Finneran, a researcher at the U.S. Navy Marine Mammal Program in San Diego and a coauthor of both papers.

In addition to covering all marine mammals for the first time, the new paper also addresses the effects of both airborne and underwater noise on amphibious species in coastal environments, such as sea lions. According to Southall, publishing the new noise exposure criteria along with a comprehensive synthesis of current knowledge in a peer-reviewed journal is a major step forward.

“There are regulatory agencies around the world that are thirsting for this kind of guidance,” Southall said. “There are still holes where we need more data, but we’ve made some big strides.”

Research on seals, sea lions, and sea otters at the UCSC Pinniped Lab now run by Reichmuth has provided much of the new data on hearing in amphibious marine mammals. Working with trained animals at UCSC’s Long Marine Laboratory, Reichmuth’s team is able to conduct controlled experiments and perform hearing tests similar to those used to study human hearing.

Finneran’s program in San Diego and coauthor Paul Nachtigall’s program at the University of Hawaii have provided much of the data for dolphins and other cetaceans.

But some marine mammals, such as baleen whales and other large whales, simply can’t be held in a controlled environment where researchers could conduct hearing tests. That’s where Ketten’s research comes in. Ketten uses biomedical imaging techniques, including CT and MRI, to study the auditory systems of a wide range of species.

“Modeling an animal’s hearing based on the anatomy of its auditory system is a very well-established technique that can be applied to baleen whales,” Ketten explained. “We also do this modeling for the species that we can test in captivity, and that enables us to hone the models and make sure they’re accurate. There has been a lot of resistance to modeling, but it’s the only way to study hearing in some of the species with the greatest potential for harm from human sounds.”

Southall said he regularly hears from people around the world looking for guidance on regulating noise production by activities ranging from wind farm construction to seismic surveys. “This paper has significant international implications for regulation of noise in the ocean,” he said.

The study, “Wildfires and Climate Change Push Low-elevation Forests Across a Critical Climate Threshold for Tree Regeneration,” was published March 11 in the Proceedings of the National Academy of Sciences and is available online at http://bit.ly/2HeZc8t.

Kimberley Davis, a postdoctoral research associate in the W.A. Franke College of Forestry and Conservation at UM, and her co-authors examined the relationship between annual climate and post-fire regeneration of ponderosa pine and Douglas fir in low-elevation forests of western North America.

“Forests in the western U.S. are increasingly affected by both climate change and wildfires,” said Davis, the study’s lead author. “The ability of forests to recover following wildfire depends on annual climate conditions, because tree seedlings are particularly vulnerable to hot and dry weather. We wanted to identify the specific conditions necessary for post-fire tree regeneration to better understand how climate change has been affecting forests through time.”

The authors used tree rings to determine establishment dates of more than 2,800 trees that regenerated after fires in Arizona, California, Colorado, Idaho, Montana and New Mexico between 1988 and 2015. Annual tree regeneration rates were much lower when seasonal climate conditions, including temperature, humidity and soil moisture, crossed specific threshold values.

Over the past 20 years, climate conditions have crossed these thresholds at the majority of study sites, leading to abrupt declines in how often annual conditions are suitable for tree regeneration. The study results highlight how future fires in similar sites may catalyze transitions from forest to non-forest ecosystems.

“Adult trees can survive in warmer and drier conditions than seedlings, and our study found that some low-elevation areas that are currently forested no longer have climate conditions that are suitable for tree regeneration,” Davis said. “In these areas, high-severity fire may lead to ecosystem transitions from forests to grasslands or shrublands.

“It is important to understand how climate change and wildfires will affect tree regeneration because forests are important economically, ecologically and culturally,” she said. “Ponderosa pine and Douglas fir are two of the most dominant tree species in the western U.S., and they are critical for the regional forestry industry. Forests also contain high levels of biodiversity and provide a variety of ecosystem services, such as carbon sequestration and water regulation and supply. Additionally, people love to recreate in forests, which is an increasingly important part of the economy in western states.”

Other UM co-authors include Solomon Dobrowski, Philip Higuera, Anna Sala and Marco Maneta. Additional co-authors include researchers from the U.S. Forest Service; the University of Colorado, Boulder; and the Aldo Leopold Wilderness Research Institute.

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Materials provided by The University of Montana. Note: Content may be edited for style and length.