UC visiting assistant professor of biology Michael Booth studied the migration patterns of steelhead, a subpopulation of rainbow trout that migrates to the Pacific Ocean, where the growing fish hunt and feed until they return to their natal freshwater streams to spawn.

While working at the United Water Conservation District, Booth used 19 years of records from a designated fish trap on southern California’s Santa Clara River to identify potential environmental drivers that spur some fish to make the arduous trip to the Pacific Ocean. The trap is part of a diversion off the river where fish can be counted and, if necessary, relocated downstream past the river’s low or dry spots.

He found that steelhead migration was triggered by the lengthening daylight of spring rather than factors like recent rains, which had little correlation to migration.

The study was published in the North American Journal of Fisheries Management.

The Santa Clara River is one of the largest coastal watersheds in southern California. It’s an important source of water for Ventura County’s $2 billion agriculture industry, famed for its strawberries, lemons, peppers and avocados.

But sections of the river often go dry completely, isolating fish in upstream tributaries until the seasonal rains return.

“The Santa Clara River is a massive desert river,” Booth said. “The river channel is braided with sand and gravel. It’s about 1,000 feet wide in its lower sections and it’s always changing.”

The river is fed by cold-water mountain streams typically associated with rainbow trout. Some of the fish remain in these tributaries their entire lives, spawning and dying not far from where they hatched. Others undergo physiological changes that allow them to tolerate the saltwater of the Pacific Ocean. While rainbow trout are typically green and pink, steelhead can take on a silvery sheen, giving them their name.

Steelhead in southern California are federally protected as an endangered species. Anglers must release any they catch.

Booth said there are big genetic benefits to making the dangerous trip to the Pacific Ocean. Steelhead grow much faster in the food-rich ocean than trout that remain in the freshwater streams. Fish that migrate to the ocean have an advantage in passing on their genes to subsequent generations when they return to spawn, he said.

“A 3-year-old resident trout might be a foot long, but a steelhead might be 3 feet long,” he said. “Their fecundity is directly related to size. So the bigger the fish, the more eggs it can make. There’s a really strong genetic advantage to making more babies.”

The study recommended limiting the extraction of water from the Santa Clara River during the migration months of mid-March to May. Likewise, Booth said the water flow in the river should be maintained where possible to allow late migrating steelhead to return upstream.

The trout’s migration opportunities might shrink from climate change, the study warned.

“There are a lot of challenges in the Santa Clara River. The water levels go up and down,” he said. “This river has a massive sediment load. During a big storm, the river bed can erode 20 feet. The water looks like a smoothie coming downstream.”

Booth said steelheads likely wait for sediment-choked river water to settle before migrating.

Since the river in most years is only navigable after storms get water flowing again, Booth hypothesized that heavy rains triggered the steelhead’s movement to the ocean.

“We thought the fish would migrate when the river was flowing and wouldn’t migrate in years without storm events,” Booth said. “It turned out that wasn’t the case. They migrated regardless of whether the river was flowing to the ocean.”

Booth isn’t sure if the fish that reach dry spots head back upstream or simply perish in the main stem of the river.

The study is significant because it could help wildlife managers and government regulators make more informed decisions about water use. The Santa Clara River is a major source of water for agriculture and people who live in the watershed. Knowing what months are crucial for steelhead migration could help wildlife managers avoid conflicts.

“It’s really hard for a water manager to decide this is when we can and can’t divert water if you have no data on when the fish are migrating,” Booth said.

For fish that miss the narrow window to navigate the Santa Clara while it’s running, there are few practical solutions, Booth said.

“This is a very wicked problem. The water available is dependent on rain, snowfall and the recharge of the groundwater,” he said. “We can avoid taking water from the river or reducing extractions but there isn’t an extra water source to make the river flow during droughts.”

But Booth is optimistic the steelhead will persist in the Santa Clara River, at least for now.

“Steelhead are very resilient. They’ve been holding on for a while,” he said

In a new study published recently in The Planetary Science Journal, a team of researchers from Arizona State University (ASU) and the University of Chicago have determined that some carbon-rich exoplanets, given the right circumstances, could be made of diamonds and silica.

“These exoplanets are unlike anything in our solar system,” says lead author Harrison Allen-Sutter of ASU’s School of Earth and Space Exploration.

Diamond exoplanet formation

When stars and planets are formed, they do so from the same cloud of gas, so their bulk compositions are similar. A star with a lower carbon to oxygen ratio will have planets like Earth, comprised of silicates and oxides with a very small diamond content (Earth’s diamond content is about 0.001%).

But exoplanets around stars with a higher carbon to oxygen ratio than our sun are more likely to be carbon-rich. Allen-Sutter and co-authors Emily Garhart, Kurt Leinenweber and Dan Shim of ASU, with Vitali Prakapenka and Eran Greenberg of the University of Chicago, hypothesized that these carbon-rich exoplanets could convert to diamond and silicate, if water (which is abundant in the universe) were present, creating a diamond-rich composition.

Diamond-anvils and X-rays

To test this hypothesis, the research team needed to mimic the interior of carbide exoplanets using high heat and high pressure. To do so, they used high pressure diamond-anvil cells at co-author Shim’s Lab for Earth and Planetary Materials.

First, they immersed silicon carbide in water and compressed the sample between diamonds to a very high pressure. Then, to monitor the reaction between silicon carbide and water, they conducted laser heating at the Argonne National Laboratory in Illinois, taking X-ray measurements while the laser heated the sample at high pressures.

As they predicted, with high heat and pressure, the silicon carbide reacted with water and turned into diamonds and silica.

Habitability and inhabitability

So far, we have not found life on other planets, but the search continues. Planetary scientists and astrobiologists are using sophisticated instruments in space and on Earth to find planets with the right properties and the right location around their stars where life could exist.

For carbon-rich planets that are the focus of this study, however, they likely do not have the properties needed for life.

While Earth is geologically active (an indicator habitability), the results of this study show that carbon-rich planets are too hard to be geologically active and this lack of geologic activity may make atmospheric composition uninhabitable. Atmospheres are critical for life as it provides us with air to breathe, protection from the harsh environment of space, and even pressure to allow for liquid water.

“Regardless of habitability, this is one additional step in helping us understand and characterize our ever- increasing and improving observations of exoplanets,” says Allen-Sutter. “The more we learn, the better we’ll be able to interpret new data from upcoming future missions like the James Webb Space Telescope and the Nancy Grace Roman Space Telescope to understand the worlds beyond on our own solar system.”

“We found that different aged individuals have different H3N2 flu virus antibody specificities,” Hensley said. “Our studies show that early childhood infections can leave lifelong immunological imprints that affect how individuals respond to antigenically distinct viral strains later in life.”

Most humans are infected with influenza viruses by three to four years of age, and these initial childhood infections can elicit strong, long lasting memory immune responses. H3N2 influenza viruses began circulating in humans in 1968 and have evolved substantially over the past 51 years. Therefore, an individual’s birth year largely predicts which specific type of H3N2 virus they first encountered in childhood.

Researchers completed a serological survey — a blood test that measures antibody levels — using serum samples collected in the summer months prior to the 2017-2018 season from 140 children (ages one to 17) and 212 adults (ages 18 to 90). They first measured the differences in antibody reactivity to various strains of H3N2, and then measured for neutralizing and non-neutralizing antibodies. Neutralizing antibodies can prevent viral infections, whereas non-neutralizing antibodies can only help after an infection takes place. Samples from children aged three to ten years old had the highest levels of neutralizing antibodies against contemporary H3N2 viruses, while most middle-aged samples had antibodies that could bind to these viruses but these antibodies could not prevent viral infections.

Hensley said his team’s findings are consistent with a concept known as “original antigenic sin” (OAS), originally proposed by Tom Francis, Jr. in 1960. “Most individuals born in the late 1960s and 1970s were immunologically imprinted with H3N2 viruses that are very different compared to contemporary H3N2 viruses. Upon infection with recent H3N2 viruses, these individuals tend to produce antibodies against regions that are conserved with older H3N2 strains and these types of antibodies typically do not prevent viral infections.”

According to the research team, it is possible that the presence of high levels of non-neutralizing antibodies in middle-aged adults has contributed to the continued persistence of H3N2 viruses in the human population. Their findings might also relate to the unusual age distribution of H3N2 infections during the 2017-2018 season, in which H3N2 activity in middle-aged and older adults peaked earlier compared to children and young adults.

The researchers say that it will be important to continually complete large serological surveys in different aged individuals, including donors from populations with different vaccination rates. A better understanding of immunity within the population and within individuals will likely lead to improved models that are better able to predict the evolutionary trajectories of different influenza virus strains.

“Large serological studies can shed light on why the effectiveness of flu vaccines varies in individuals with different immune histories, while also identifying barriers that need to be overcome in order to design better vaccines that are able to elicit protective responses in all age groups,” said Sigrid Gouma, PhD, a postdoctoral researcher of Microbiology and first author on the paper.

Other Penn authors include Madison Weirick and Megan E. Gumina. Additional authors include Angela Branche, David J. Topham, Emily T. Martin, Arnold S. Monto, and Sarah Cobey.

This work was supported by the National Institute of Allergy and Infectious Diseases (1R01AI113047, S.E.H.; 1R01AI108686, S.E.H.; 1R01AI097150, A.S.M.; CEIRS HHSN272201400005C, S.E.H., S.C., E.T.M., A.S.M. A.B., D.J.T.) and Center for Disease Control (U01IP000474, A.S.M.). Scott E. Hensley holds an Investigators in the Pathogenesis of Infectious Disease Awards from the Burroughs Wellcome Fund.

A research team led by University of California, Berkeley, archaeologists has discovered that unglazed ceramic cookware can retain the residue of not just the last supper cooked, but, potentially, earlier dishes cooked across a pot’s lifetime, opening a window onto the past.

The findings, reported in the journal Scientific Reports, suggest that gastronomic practices going back millennia — say, to cook Aztec turkey, hominy pozole or the bean stew likely served at the Last Supper — can be reconstructed by analyzing the chemical compounds adhering to and absorbed by the earthenware in which they were prepared.

“Our data can help us better reconstruct the meals and specific ingredients that people consumed in the past which, in turn, can shed light on social, political and environmental relationships within ancient communities,” said study co-lead author Melanie Miller, a researcher at Berkeley’s Archaeological Research Facility and a postdoctoral scholar at the University of Otago in New Zealand.

In a yearlong cooking experiment led by Miller and Berkeley archaeologist Christine Hastorf, seven chefs each prepared 50 meals made from combinations of venison, maize (corn) and wheat flour in newly purchased La Chamba ceramic pots. This robust, burnished black clay cookware dates back to pre-Columbian South America, and the handcrafted vessels remain popular for preparing and serving traditional foods today.

The group came up with the idea in Hastorf’s Archaeology of Food graduate seminar at Berkeley. By analyzing the chemical residues of the meals cooked in each pot, the researchers sought to learn whether the deposits found in ancient cooking vessels would reflect the remains of only the last dish cooked, or previous meals, as well.

In addition to receiving donated deer roadkill, they purchased large quantities of whole grains and a mill, which Hastorf set up in her garage, to grind them. The group then developed a repertoire of six recipes using deer meat and whole and milled grain.

They picked staple ingredients that could be found in many parts of the world. For example, two recipes focused on hominy, which is made from soaking maize in an alkaline solution, while two others used wheat flour.

“We chose the food based on how easy it would be to distinguish the chemicals in the food from one another and how the pots would react to the isotopic and chemical values of the food,” said Hastorf, a Berkeley professor of anthropology who studies food archaeology, among other things.

Each of the seven chefs cooked an experimental meal weekly in a La Chamba pot using the group’s designated ingredients. “The mushy meals were bland, and we didn’t eat them,” Miller noted.

Every eighth meal was charred to replicate the kinds of carbonized residues that archaeologists often encounter in ancient pots and to mimic what would normally happen in a pot’s lifetime. Between each meal, the pots were cleaned with water and a branch from an apple tree. Surprisingly, none of them broke during the course of the study.

At Berkeley’s Center for Stable Isotope Biogeochemisty, the team conducted an analysis of the charred remains and the carbonized patinas that developed on the pots. Stable isotopes are atoms whose composition does not decay over time, which is useful for archaeological studies. An analysis of the fatty lipids absorbed into the clay cookware was performed at the University of Bristol in England.

Overall, chemical analyses of the food residues showed that different meal time scales were represented in different residues. For example, the charred bits at the bottom of a pot contained evidence of the latest meal cooked, while the remnants of prior meals could be found in the patina that built up elsewhere on the pot’s interior and in the lipid residue that was absorbed into the pottery itself.

These results give scientists a new tool to study long-ago diets and also provide clues to food production, supply and distribution chains of past eras.

“We’ve flung open the door for others to take this experiment to the next level and record even longer timelines in which food residues can be identified,” Miller said.

In addition to Miller and Hastorf, co-authors of the study are Alexandra McCleary and Geoffrey Taylor at UC Berkeley; Helen Whelton, Simon Hammann, Lucy Cramp and Richard Evershed at the University of Bristol; Jillian Swift at the Bernice Pauahi Bishop Museum in Hawai’i; Sophia Maline at the University of Southern California; Kirsten Vacca at the University of Hawai’i-West O’ahu and independent scholar Fanya Becks.

A new study led by the University of Colorado Boulder suggests that such volcanic ash may also have a larger influence on the planet’s climate than scientists previously suspected.

The new research, published in the journal Nature Communications, examines the eruption of Mount Kelut (or Kelud) on the Indonesian island of Java in 2014. Drawing on real-world observations of this event and advanced computer simulations, the team discovered that volcanic ash seems to be prone to loitering — remaining in the air for months or even longer after a major eruption.

“What we found for this eruption is that the volcanic ash can persist for a long time,” said Yunqian Zhu, lead author of the new study and a research scientist at the Laboratory for Atmospheric and Space Physics (LASP) at CU Boulder.

Lingering ash

The discovery began with a chance observation: Members of the research team had been flying an unmanned aircraft near the site of the Mount Kelut eruption — an event that covered large portions of Java in ash and drove people from their homes. In the process, the aircraft spotted something that shouldn’t have been there.

“They saw some large particles floating around in the atmosphere a month after the eruption,” Zhu said. “It looked like ash.”

She explained that scientists have long known that volcanic eruptions can take a toll on the planet’s climate. These events blast huge amounts of sulfur-rich particles high into Earth’s atmosphere where they can block sunlight from reaching the ground.

Researchers haven’t thought, however, that ash could play much of a role in that cooling effect. These chunks of rocky debris, scientists reasoned, are so heavy that most of them likely fall out of volcanic clouds not long after an eruption.

Zhu’s team wanted to find out why that wasn’t the case with Kelut. Drawing on aircraft and satellite observations of the unfolding disaster, the group discovered that the volcano’s plume seemed to be rife with small and lightweight particles of ash — tiny particles that were likely capable of floating in the air for long periods of time, much like dandelion fluff.

“Researchers have assumed that ash is similar to volcanic glass,” Zhu said. “But what we’ve found is that these floating ones have a density that’s more like pumice.”

Disappearing molecules

Study coauthor Brian Toon added that these pumice-like particles also seem to shift the chemistry of the entire volcanic plume.

Toon, a professor in LASP and the Department of Atmospheric and Oceanic Sciences at CU Boulder, explained that erupting volcanos spew out a large amount of sulfur dioxide. Many researchers previously assumed that those molecules interact with others in the air and convert into sulfuric acid — a series of chemical reactions that, theoretically, could take weeks to complete. Observations of real-life eruptions, however, suggest that it happens a lot faster than that.

“There has been a puzzle of why these reactions occur so fast,” Toon said.

He and his colleagues think they’ve discovered the answer: Those molecules of sulfur dioxide seem to stick to the particles of ash floating in the air. In the process, they may undergo chemical reactions on the surface of the ash itself — potentially pulling around 43% more sulfur dioxide out of the air.

Ash, in other words, may hasten the transformation of volcanic gases in the atmosphere.

Just what the impact of those clouds of ash are on the climate isn’t clear. Long-lasting particles in the atmosphere could, potentially, darken and even help to cool the planet after an eruption. Floating ash might also blow all the way from sites like Kelut to the planet’s poles. There, it could kickstart chemical reactions that would damage Earth’s all-important ozone layer.

But the researchers say that one thing is clear: When a volcano blows, it may be time to pay a lot more attention to all that ash and its true impact on Earth’s climate.

“I think we’ve discovered something important here,” Toon said. “It’s subtle, but it could make a big difference.”

The rush to publish results has resulted in missteps, say Ganesh Mani, an investor, technology entrepreneur and adjunct faculty member in Carnegie Mellon University’s Institute for Software Research, and Tom Hope, a post-doctoral researcher at the Allen Institute for AI. In an opinion article in today’s issue of the journal Patterns, they argue that new policies and technologies are needed to ensure relevant, reliable information is properly recognized.

Those potential solutions include ways to combine human expertise with AI as one way to keep pace with a knowledge base that is expanding geometrically. AI might be used to summarize and collect research on a topic, while humans serve to curate the findings, for instance.

“Given the ever-increasing research volume, it will be hard for humans alone to keep pace,” they write.

In the case of COVID-19 and other new diseases, “you have a tendency to rush things because the clinicians are asking for guidance in treating their patients,” Mani said. Scientists certainly have responded — by mid-August, more than 8,000 preprints of scientific papers related to the novel coronavirus had been posted in online medical, biology and chemistry archives. Even more papers had been posted on such topics as quarantine-induced depression and the impact on climate change from decreased transportation emissions.

At the same time, the average time to perform peer review and publish new articles has shrunk; in the case of virology, the average dropped from 117 to 60 days.

This surge of information is what the World Health Organization calls an “infodemic” — an overabundance of information, ranging from accurate to demonstrably false. Not surprisingly, problems such as the hydroxycholoroquine controversy have erupted as research has been rushed to publication and subsequently withdrawn.

“We’re going to have that same conversation with vaccines,” Mani predicted. “We’re going to have a lot of debates.”

Problems in scientific publication are nothing new, he said. As a grad student 30 years ago, he proposed an electronic archive for scientific literature that would better organize research and make it easier to find relevant information. Many ideas continue to circulate about how to improve scientific review and publication, but COVID-19 has exacerbated the situation.

Some of the speed bumps and guard rails that Mani and Hope propose are new policies. For instance, scientists usually emphasize experiments and therapies that work; highlighting negative results, on the other hand, is important for clinicians and discourages other scientists from going down the same blind alleys. Identifying the best reviewers, sharing review comments and linking papers to related papers, retraction sites or legal rulings are among other ideas they explore.

Greater use of AI to digest and consolidate research is a major focus. Previous attempts to use AI to do so have failed in part because of the often figurative and sometimes ambiguous language used by humans, Mani noted. It may be necessary to write two versions of research papers — one written in a way that draws the attention of people and another written in a boring, uniform style that is more understandable to machines.

Mani said he and Hope have no illusions that their paper will settle the debate about improving scientific literature, but hope that it will spur changes in time for the next global crisis.

“Putting such infrastructure in place will help society with the next strategic surprise or grand challenge, which is likely to be equally, if not more, knowledge intensive,” they concluded.

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Materials provided by Carnegie Mellon University. Original written by Byron Spice. Note: Content may be edited for style and length.