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In the brain at rest, neurons rehearse future experience

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In the brain at rest, neurons rehearse future experience


Some dreams may, in fact, predict the future: New research has found that during sleep, some neurons not only replay the recent past but also anticipate future experience.

The discovery is one in a series of insights afforded by a study on sleep and learning published in Nature by a team of researchers from Rice University and the University of Michigan. The research offers an unprecedented view of how individual neurons in the hippocampus of rats stabilize and tune spatial representations during periods of rest following the animals’ first time running a maze.

“Certain neurons fire in response to specific stimuli,” said Kamran Diba, an associate professor of anesthesiology at Michigan and corresponding author on the study. “Neurons in the visual cortex fire when presented with the appropriate visual stimulus. The neurons we’re studying show place preferences.”

Together with collaborators in Michigan’s Neural Circuits and Memory Lab led by Diba, Rice neuroscientist Caleb Kemere has been studying the process by which these specialized neurons produce a representation of the world after a new experience. Specifically, the researchers tracked sharp wave ripples, a pattern of neuronal activation known to play a role in consolidating new memories and, more recently, also shown to tag which parts of a new experience are to be stored as memories.

“For the first time in this paper, we observed how these individual neurons stabilize spatial representations during rest periods,” said Kemere, associate professor of electrical and computer engineering and bioengineering at Rice.

Sleep is critical for memory and learning — science has quantified this age-old intuition by measuring performance on memory tests after a nap as opposed to after a period of waking or even sleep deprivation.

A couple of decades ago, scientists also discovered that neurons in the brains of sleeping animals that had been allowed to explore a new setting just before resting were firing in ways that replayed the animals’ trajectories during exploration. This finding aligned with the knowledge that sleep helps new experiences crystallize into stable memories, thus suggesting that the spatial representations of many of these specialized neurons in the hippocampus are stable during sleep. However, the researchers wanted to see if there was more to the story.

“We imagined that some neurons might change their representations — reflecting the experience we’ve all had of waking up with a new understanding of a problem,” Kemere said. “Showing this, however, required that we track how individual neurons achieve spatial tuning, i.e., the process by which the brain learns to navigate a new route or environment.”

The researchers trained rats to run back and forth on a raised track with liquid reward at either end and observed how individual neurons in the animals’ hippocampus would “spike” in the process. By calculating an average spiking rate over many laps back and forth, the researchers were able to estimate the neurons’ place field — or the area in the environment that a given neuron “cared” about most.

“The critical point here is that place fields are estimated using the behavior of the animal,” Kemere said, highlighting the challenge of assessing what happens to place fields during rest periods when the animal is not physically moving through the maze.

“I’ve been thinking for a long time about how we can evaluate the preferences of neurons outside of the maze, such as during sleep,” Diba said. “We addressed this challenge by relating the activity of each individual neuron to the activity of all the other neurons.”

This was the study’s key innovation: The researchers developed a statistical machine learning approach that used the other neurons surveyed to map out an estimate of where the animal was dreaming of being. They next used those dreamed positions to estimate the spatial tuning process for each neuron in their data sets.

“The ability to track the preferences of neurons even without a stimulus was an important breakthrough for us,” Diba said.

Both Diba and Kemere commended Kourosh Maboudi, a postdoctoral researcher at Michigan and the lead author on the study, for his role in the development of the learned tuning approach.

The method confirmed that the spatial representations that form during the experience of a new environment are, for most neurons, stable across several hours of postexperience sleep. But as the researchers had anticipated, there was more to the story.

“The thing that I loved the most about this research and the reason that I was so excited about it is finding that it’s not necessarily the case that during sleep the only thing these neurons do is to stabilize a memory of the experience,” Kemere said. “It turns out some neurons end up doing something else.

“We can see these other changes occurring during sleep, and when we put the animals back in the environment a second time, we can validate that these changes really do reflect something that was learned while the animals were asleep. It’s as if the second exposure to the space actually happens while the animal is sleeping.”

This is significant because it constitutes direct observation of neuroplasticity as it is happening during sleep. Kemere underscored that almost all plasticity research — which examines the mechanisms that allow neurons to rewire and form new representations — looks at what happens during waking periods as stimuli are being presented rather than during sleep when the relevant stimuli are absent.

“It seems like plasticity or rewiring in the brain requires really fast timescales,” Diba said, pointing to the fascinating relationship between the duration of actual experience, “which can take up the span of seconds, minutes but also hours or days,” and actual memories, “which are super compressed.”

“If you remember anything, the memory — it’s instant,” Diba said, referencing a famous literary passage by French modernist writer Marcel Proust in which a childhood memory unspools a whole lost world of past experience at barely a moment’s notice.

The study is an example of advancements in neuroscience enabled in the past few decades by technological progress in the design of stable, high-resolution neural probes as well as by machine learning-backed computation power.

In light of these advancements, Kemere said brain science stands poised to make significant progress in the future, while at the same time expressing concern for the impact of recent budget cuts on continued research.

“It’s quite possible that if we were starting this work today, we might not have been able to do these experiments and get these results,” Kemere said. “We’re definitely grateful that the opportunity was there.”



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Paleontology: New fossil fish genus discovered

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Paleontology: New fossil fish genus discovered


Gobies or Gobioidei are one of the most species-rich groups of marine and freshwater fish in Europe. Spending most of their lives on the bottom of shallow waterbodies, they make substantial contributions to the functioning of many ecosystems. With the identification of a new genus of a fossil freshwater goby, students of the international master program ‘Geobiology and Paleobiology’ at LMU and paleontologist Bettina Reichenbacher, professor at the Department of Earth and Environmental Sciences at LMU, have made a discovery that provides critical insights into the evolutionary history of these fish.

Measuring up to 34 mm, the small fish of the new genus †Simpsonigobius were discovered in 18-million-year-old rocks in Turkey and are marked by a distinct combination of morphological features, including otoliths (hearing stones) with a unique shape.

Modern research techniques elucidate position in family tree

To determine the relationships of †Simpsonigobius within the gobioid phylogenetic tree, the researchers utilized a “total-evidence” phylogenetic dataset, which they enhanced in order to combine a total of 48 morphological characters and genetic data from five genes for 48 living and 10 fossil species. In addition, the team employed “tip-dating” for fossil gobioid species for the first time. This is a phylogenetic method in which the age of the fossils (= tips) included in the phylogenetic tree is used to infer the timing of the evolutionary history of the entire group.

The results show that the new genus is the oldest skeleton-based member of the family Oxudercidae — which is classified among the “modern” gobies (families Gobiidae and Oxudercidae) — and the oldest freshwater goby within this modern group. The tip-dating analysis estimated the emergence of the Gobiidae at 34.1 million years ago and that of the Oxudercidae at 34.8 million years ago, which is consistent with previous dating studies using other methods. Moreover, stochastic habitat mapping, in which the researchers incorporated fossil gobies for the first time, revealed that the gobies probably possessed broad salinity tolerance at the beginning of their evolutionary history, which challenges previous assumptions.

“The discovery of †Simpsonigobius not only adds a new genus to the Gobioidei, but also provides vital clues about the evolutionary timeline and habitat adaptations of these diverse fishes. Our research highlights the importance of analyzing fossil records using modern methods to achieve a more accurate picture of evolutionary processes,” says Reichenbacher. First author Moritz Dirnberger, currently a doctoral candidate at the University of Montpellier, adds: “The findings are expected to pave the way for further studies on gobioid evolution and the role of environmental factors in shaping their diversity.”



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Ancient ocean slowdown warns of future climate chaos

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Ancient ocean slowdown warns of future climate chaos


When it comes to the ocean’s response to global warming, we’re not in entirely uncharted waters. A UC Riverside study shows that episodes of extreme heat in Earth’s past caused the exchange of waters from the surface to the deep ocean to decline.

This system has been described as the “global conveyer belt,” because it redistributes heat around the globe through the movement of the ocean waters, making large portions of the planet habitable.

Using tiny, fossilized shells recovered from ancient deep-sea sediments, the study in the Proceedings of the National Academy of Sciences demonstrates how the conveyor belt responded around 50 million years ago. At that time, Earth’s climate resembled conditions predicted by the end of this century, if significant action is not taken to reduce carbon emissions.

Oceans play a crucial role in regulating Earth’s climate. They move warm water from the equator toward the north and south poles, balancing the planet’s temperatures. Without this circulation system, the tropics would be much hotter and the poles much colder. Changes in this system are linked to significant and abrupt climate change.

Furthermore, the oceans serve a critical role in removing anthropogenic carbon dioxide from the atmosphere. “The oceans are by far the largest standing pool of carbon on Earth’s surface today,” said Sandra Kirtland Turner, vice-chair of UCR’s Department of Earth and Planetary Sciences and first author of the study.

“Today, the oceans contain nearly 40,000 billion tons of carbon — more than 40 times the amount of carbon in the atmosphere. Oceans also take up about a quarter of anthropogenic CO2 emissions,” Kirtland Turner said. “If ocean circulation slows, absorption of carbon into the ocean may also slow, amplifying the amount of CO2 that stays in the atmosphere.”

Previous studies have measured changes in ocean circulation in Earth’s more recent geologic past, such as coming out of the last ice age; however, those do not approximate the levels of atmospheric CO2 or warming happening to the planet today. Other studies provide the first evidence that deep ocean circulation, particularly in the North Atlantic, is already starting to slow.

To better predict how ocean circulation responds to greenhouse gas-driven global warming, the research team looked to the early Eocene epoch, between roughly 49 and 53 million years ago. Earth then was much warmer than today, and that high-heat baseline was punctuated by spikes in CO2 and temperature called hyperthermals.

During that period, the deep ocean was up to 12 degrees Celsius warmer than it is today. During the hyperthermals, the oceans warmed an additional 3 degrees Celsius.

“Though the exact cause of the hyperthermal events is debated, and they occurred long before the existence of humans, these hyperthermals are the best analogs we have for future climate change,” Kirtland Turner said.

By analyzing tiny fossil shells from different sea floor locations around the globe, the researchers reconstructed patterns of deep ocean circulation during these hyperthermal events. The shells are from microorganisms called foraminifera, which can be found living throughout the world’s oceans, both on the surface and on the sea floor. They are about the size of a period at the end of a sentence.

“As the creatures are building their shells, they incorporate elements from the oceans, and we can measure the differences in the chemistry of these shells to broadly reconstruct information about ancient ocean temperatures and circulation patterns,” Kirtland Turner said.

The shells themselves are made of calcium carbonate. Oxygen isotopes in the calcium carbonate are indicators of temperatures in the water the organisms grew in, and the amount of ice on the planet at the time.

The researchers also examined carbon isotopes in the shells, which reflect the age of the water where the shells were collected, or how long water has been isolated from the ocean surface. In this way, they can reconstruct patterns of deep ocean water movement.

Foraminifera can’t photosynthesize, but their shells indicate the impact of photosynthesis of other organisms nearby, like phytoplankton. “Photosynthesis occurs in the surface ocean only, so water that has recently been at the surface has a carbon-13 rich signal that is reflected in the shells when that water sinks to the deep ocean,” Kirtland Turner said.

“Conversely, water that has been isolated from the surface for a long time has built up relatively more carbon-12 as the remains of photosynthetic organisms sink and decay. So, older water has relatively more carbon-12 compared to ‘young’ water.”

Scientists often make predictions about ocean circulation today using computer climate models. They use these models to answer the question: ‘how is the ocean going to change as the planet keeps warming?’ This team similarly used models to simulate the ancient ocean’s response to warming. They then used the foraminifera shell analysis to help test results from their climate models.

During the Eocene, there were about 1,000 parts per million (ppm) of carbon dioxide in the atmosphere, which contributed to that era’s high temperatures. Today, the atmosphere holds about 425 ppm.

However, humans emit nearly 37 billion tons of CO2 into the atmosphere each year; if these emission levels continue, similar conditions to the Early Eocene could occur by the end of this century.

Therefore, Kirtland Turner argues it is imperative to make every effort to reduce emissions.

“It’s not an all-or-nothing situation,” she said. “Every incremental bit of change is important when it comes to carbon emissions. Even small reductions of CO2 correlate to less impacts, less loss of life, and less change to the natural world.”



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Pacific coast gray whales have gotten 13% shorter in the past 20-30 years, Oregon State study finds

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Pacific coast gray whales have gotten 13% shorter in the past 20-30 years, Oregon State study finds


Gray whales that spend their summers feeding in the shallow waters off the Pacific Northwest coast have undergone a significant decline in body length since around the year 2000, a new Oregon State University study found.

The smaller size could have major consequences for the health and reproductive success of the affected whales, and also raises alarm bells about the state of the food web in which they coexist, researchers say.

“This could be an early warning sign that the abundance of this population is starting to decline, or is not healthy,” said K.C. Bierlich, co-author on the study and an assistant professor at OSU’s Marine Mammal Institute in Newport. “And whales are considered ecosystem sentinels, so if the whale population isn’t doing well, that might say a lot about the environment itself.”

The study, published in Global Change Biology, looked at the Pacific Coast Feeding Group (PCFG), a small subset of about 200 gray whales within the larger Eastern North Pacific (ENP) population of around 14,500. This subgroup stays closer to shore along the Oregon coast, feeding in shallower, warmer waters than the Arctic seas where the bulk of the gray whale population spends most of the year.

Recent studies from OSU have shown that whales in this subgroup are smaller and in overall worse body condition than their ENP counterparts. The current study reveals that they’ve been getting smaller in recent decades.

The Marine Mammal Institute’s Geospatial Ecology of Marine Megafauna (GEMM) Lab has been studying this subgroup of gray whales since 2016, including flying drones over the whales to measure their size. Using images from 2016-2022 of 130 individual whales with known or estimated age, researchers determined that a full-grown gray whale born in 2020 is expected to reach an adult body length that is 1.65 meters (about 5 feet, 5 inches) shorter than a gray whale born prior to 2000. For PCFG gray whales that grow to be 38-41 feet long at full maturity, that accounts for a loss of more than 13% of their total length.

If the same trend were to happen in humans, that would be like the height of the average American woman shrinking from 5 feet, 4 inches to 4 feet, 8 inches tall over the course of 20 years.

“In general, size is critical for animals,” said Enrico Pirotta, lead author on the study and a researcher at the University of St. Andrews in Scotland. “It affects their behavior, their physiology, their life history, and it has cascading effects for the animals and for the community they’re a part of.”

Whale calves that are smaller at weaning age may be unable to cope with the uncertainty that comes with being newly independent, which can affect survival rates, Pirotta said.

For adult gray whales, one of the biggest concerns is reproductive success.

“With them being smaller, there are questions of how effectively these PCFG gray whales can store and allocate energy toward growing and maintaining their health. Importantly, are they able to put enough energy toward reproduction and keep the population growing?” Bierlich said.

Scarring on PCFG whales from boat strikes and fishing gear entanglement also makes the team concerned that smaller body size with lower energy reserves may make the whales less resilient to injuries.

The study also examined the patterns of the ocean environment that likely regulate food availability for these gray whales off the Pacific coast by tracking cycles of “upwelling” and “relaxation” in the ocean. Upwelling sweeps nutrients from deeper to shallower regions, while relaxation periods then allow those nutrients to remain in shallower areas where light allows for growth of plankton and other tiny organisms, including the prey of gray whales.

“Without a balance between upwelling and relaxation, the ecosystem may not be able to produce enough prey to support the large size of these gray whales,” said co-author Leigh Torres, associate professor and director of the GEMM Lab at OSU.

The data show that whale size declined concurrently with changes in the balance between upwelling and relaxation, Pirotta said.

“We haven’t looked specifically at how climate change is affecting these patterns, but in general we know that climate change is affecting the oceanography of the Northeast Pacific through changes in wind patterns and water temperature,” he said. “And these factors and others affect the dynamics of upwelling and relaxation in the area.”

Now that they know the PCFG gray whales’ body size is declining, researchers say they have a lot of new questions about downstream consequences of that decline and the factors that could be contributing to it.

“We’re heading into our ninth field season studying this PCFG subgroup,” Bierlich said. “This is a powerful dataset that allows us to detect changes in body condition each year, so now we’re examining the environmental drivers of those changes.”

The other co-authors on the paper were Lisa Hildebrand, Clara Bird and Alejandro Ajó at OSU and Leslie New at Ursinus College in Pennsylvania.



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