“In our analysis focusing on Los Angeles County, unexpected traffic delays beyond the usual congestion led to a 1% increase in fast food visits. That might not sound like a lot, but it’s equivalent to 1.2 million more fast food visits per year in LA County alone. We describe our results as being modest but meaningful in terms of potential for changing unhealthy food choices,” said study author Becca Taylor, assistant professor in the Department of Agricultural and Consumer Economics, part of the College of Agricultural, Consumer and Environmental Sciences at Illinois.

Taylor and her co-authors had access to daily highway traffic patterns over more than two years in Los Angeles, along with data showing how many cell phone users entered fast-food restaurants in the same time period. With these data, the team created a computational model showing a causal link between unexpected traffic slow-downs and fast food visits.

This pattern held at various time scales, including 24-hour cycles and by the hour throughout a given day. When analyzed by the day, traffic delays of just 30 seconds per mile were enough to spike fast-food visits by 1%.

“It might not be intuitive to imagine what a 30-second delay per mile feels like,” Taylor said. “I think of it as the difference between 10 a.m. traffic and 5 p.m. traffic.”

When the researchers broke the day into hour-long segments, they found a significantly greater number of fast food visits when traffic delays hit during the evening rush hour. At the same time, grocery store visits declined slightly.

“If there’s traffic between 5 and 7 p.m., which happens to be right around the evening meal time, we see an increase in fast food visits,” Taylor said. “Drivers have to make a decision about whether to go home and cook something, stop at the grocery store first, or just get fast food.”

Considering every major city has both traffic and fast food restaurants lining highway feeder roads, it’s not a stretch to extrapolate the pattern beyond Los Angeles. Taylor and her co-authors say the link between traffic and unhealthy food choices is just one more reason policymakers around the country and the globe should prioritize infrastructure reforms to ease congestion.

“Our results contribute to the literature suggesting time constraints are really important to the food choices people make. Any policies aimed at loosening time constraints — and traffic is essentially lost time — could help battle unhealthy eating,” Taylor said. “That could mean improvements in infrastructure to mitigate traffic congestion, expanding public transport availability, and potentially increasing work from home opportunities.”

The finding, reported in the science journal Geochimica et Cosmochimica Acta, is significant because the data reported by the study support the idea that water arrived towards the final stages of Earth’s development into a planet from dust and gas, what geologists refer to as late accretion.

Scientists seek to learn when the constituent materials necessary for life appeared so that they can understand how and when life began. According to present scientific understanding, at least three necessary ingredients are essential to kick-start life. These are water, energy and a soup of organic chemicals known as CHNOPS — scientific shorthand for carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur.

“When water was delivered to the planet is a major unanswered question in planetary science,” said Katherine Bermingham, an associate professor in the Department of Earth and Planetary Sciences in the Rutgers School of Arts and Sciences and lead author of the study. “If we know the answer, we can better constrain when and how life developed.”

Bermingham is a cosmogeochemist, a scientist who studies the chemical composition of matter in the solar system, particularly focusing on the origin and evolution of the solar system and its rocky planets by analyzing Earth rocks and extraterrestrial materials such as meteorites.

Using thermal ionization mass spectrometry and a new analytical method the team developed, Bermingham and colleagues studied isotopes of the element molybdenum. An isotope is a form of an element with the same number of protons but a different number of neutrons. This allows it to share the same chemical properties while having a different atomic mass.

“The molybdenum isotopic composition of Earth rocks provides us with a special window into events occurring around the time of Earth’s final core formation, when the last 10% to 20% of material was being assembled by the planet. This period is thought to coincide with the Moon’s formation,” Bermingham said.

They extracted molybdenum from meteorite samples obtained from the National Museum of Natural History of the Smithsonian Institution. The scientific community has divided meteorites into two general groups — the first, “CC,” with constituent elements suggesting the meteorites formed in the outer, presumably wetter, Solar System. The second group, “NC,” has characteristics indicating its meteorites formed in the inner, presumably drier, solar system. This study focused on samples that belong to the NC group.

They compared the molybdenum isotopic composition of these meteorites to Earth rocks from Greenland, South Africa, Canada, the United States and Japan collected by field geologists. The molybdenum in these rocks is generally considered to have been added to Earth during the time the Moon was formed, which is when final core formation occurred. This is precisely when the team wanted to search for the origins of water.

“Once we gathered the different samples and measured their isotopic compositions, we compared the meteorites signatures with the rock signatures to see if there was a similarity or a difference,” Bermingham said. “And from there, we drew inferences.”

The analyses showed that the Earth rocks they studied were more similar to meteorites sourced from the inner solar system meteorites (NC) rather than meteorites sourced from the outer solar system (CC).

“We have to figure out from where in our solar system Earth’s building blocks — the dust and the gas — came and around when that happened,” Bermingham said. “That’s the information needed to understand when the stage was set for life to begin.”

Since the chemical composition of the Earth rocks they studied matches that of the presumed inner solar system (NC) meteorites, the scientists concluded that the Earth had not received as much water from the Moon-forming event as previously thought. The finding is significant, Bermingham said, because a popular theory of water delivery is that a significant amount of the Earth’s water was added when the Moon was formed.

This research, however, showed that a substantial amount of water likely did not come during this period of growth. Instead, the data support the interpretation that water was delivered to Earth in smaller portions after the Moon was formed, far later during Earth’s formation.

“Our results suggest that the Moon-forming event was not a major supplier of water, unlike what has been thought previously,” Bermingham said. “These findings, however, permit a small amount of water to be added after final core formation, during what is called late accretion.”

Other Rutgers authors of the study include Linda Godfrey, an assistant research professor, and laboratory researcher Hope Tornebene, both of the Department of Earth and Planetary Sciences.

Program for teens adapted to seniors

The O’stress program is based on DeStress for Success, an innovative program created by the Centre for Studies on Human Stress to help teens deal with the stress of transitioning to high school.

In a groundbreaking study led by Sonia Lupien, the Centre’s director, published in Neuroscience in 2013, DeStress for Success was shown to decrease cortisol levels and depressive symptoms in participating teens who were experiencing strong negative emotions at the start of the school year.

Since then, DeStress for Success has been adapted in partnership with Plusquellec’s team for several populations, including teens at high risk for behavioural problems (2016) and young people with autism spectrum disorder (2018).

Countering emotional contagion

In her doctoral research under the supervision of Université de Montréal professors Pierrich Plusquellec and Sébastien Grenier, Marie-Josée Richer adapted DeStress for Success to the specific needs of seniors.

“Aging, like adolescence but for different reasons, is a particularly sensitive period when individuals are more vulnerable to chronic stress and its consequences,” Plusquellec noted.

O’stress incorporates elements relevant to aging, social relationships and, in particular, emotional contagion, the tendency to get caught up in the emotions of others. According to a recent study by the same researchers, emotional contagion is a significant factor in psychological distress among seniors. An educational component on emotional contagion was therefore included in the O’stress program to help participants recognize and manage this dynamic on a daily basis.

O’stress uses a variety of approaches including small-group workshops to help seniors identify symptoms of stress and release that energy through activities such as bopping to The Beatles’ “Twist and Shout.” Participants also analyze their social network to identify sources of support, pressure and emotional contagion, and then problem-solve to find solutions.

The success of O’stress highlights the enormous potential of short, accessible interventions to counteract the harmful effects of chronic stress in the elderly.

“By demystifying stress and its effects, and then teaching effective techniques for coping with that stress, we equip participants to strengthen their resilience and overall well-being,” said Richer.

The research team now hopes to expand the O’stress program and evaluate its effectiveness in other contexts and populations. Their work could also inspire similar interventions in the areas of mental health and aging.

A new study of Colorado grasshoppers shows that, while the answers are complicated, biologists have much of the knowledge they need to make these predictions and prepare for the consequences.

The findings, published Jan. 30 in the journal PLOS Biology, come thanks to the serendipitous discovery of 13,000 grasshoppers all collected from the same Colorado mountain site between 1958 and 1960 by a biologist at the University of Colorado Boulder (CU Boulder). After that scientist’s untimely death in 1973, the collection was rescued by his son and donated to the CU Museum, where it languished until 2005, when César Nufio, then a postdoctoral fellow, rediscovered it. Nufio set about curating the collection and initiated a resurvey of the same sites to collect more grasshoppers.

The newly collected insects allowed Nufio and his colleagues — Caroline Williams of the University of California, Berkeley, Lauren Buckley of the University of Washington in Seattle and postdoctoral fellow Monica Sheffer, who has an appointment at both institutions — to assess the impact of climate change over the past 65 years on the sizes of six species of grasshopper. Because insects are cold-blooded and don’t generate their own heat, their body temperatures and rates of development and growth are more sensitive to warming in the environment.

Despite much speculation that animals will decrease in size to lessen heat stress as the climate warms, the biologists found that some of the grasshopper species actually got larger over the decades, taking advantage of an earlier spring to fatten up on greenery. This worked only for species that overwinter as juveniles — a stage called nymphal diapause — and thus can get a head start on chowing down in the spring. Species that hatch in the spring from eggs laid in the fall — the egg diapausers — did not have this advantage and became smaller over the years, likely as a result of vegetation drying up earlier.

“This research emphasizes that there will certainly be species that are winners and losers, but subgroups within those species populations, depending on their ecological or environmental context, will have different responses,” Sheffer said.

The authors of the new study predicted much of this based on the life cycles of the grasshoppers and the environmental conditions at the site.

“We sat down and looked at all that was known about the system, such as elevational gradients and how that should modify responses and how different grasshoppers might respond, with all the wealth of information we knew about their natural history. And while not all our predictions were supported, many of them actually were,” said Williams, the John L. and Margaret B. Gompertz Chair in Integrative Biology at UC Berkeley.

“Understanding what species are likely to be winners and losers with climate change has been really challenging so far,” Buckley said. “Hopefully this work starts to demonstrate some principles by which we can improve predictions and figure out how to appropriately respond to ecosystem changes stemming from climate change.”

Rescued grasshoppers

The 65-year-old grasshopper collection was assembled by entomologist Gordon Alexander of CU Boulder over three summers. He not only collected and mounted the specimens from plots in the Rocky Mountains near Boulder but also documented the timing of six different life stages of the grasshoppers. His death in a plane crash in 1973 left the specimens, pinned in neat rows in 250 wooden boxes, in limbo until Nufio came across them in 2005 and recognized their value if they could be compared to grasshoppers today.

Museum collections have become invaluable for long-term studies of the effects of climate change, as exemplified by a survey of mammals, birds, reptiles and amphibians conducted between 1904 and 1940 by Joseph Grinnell of UC Berkeley’s Museum of Vertebrate Zoology. Recent resurveys of the same areas 100 years later that Grinnell visited helped biologists document the effects of climate change on California wildlife.

Nufio and many others eventually collected about 17,000 new grasshopper specimens from the same or similar sites around Boulder. While the new paper is the first to report the grasshopper size changes between 1960 and 2015, the authors leveraged previous studies in the lab and from experimental plots to understand why they found the patterns they did.

The insects were from a large group of non-descript grasshoppers in the Acrididae family that are so-called short-horned grasshoppers. Most were generalized grazers, though some specialized in grasses. Two species (Eritettix simplex and Xanthippus corallipes) were nymphal diapausers, achieving adulthood as early as May; two (Aeropedellus clavatus and Melanoplus boulderensis) were early season egg diapausers, maturing in mid-June; and two (Camnula pellucida and Melanoplus sanguinipes) were late season egg diapausers, maturing in late July.

The researchers found that the nymphal diapausers increased in size at lower elevations, around 6,000 feet, while the early and late emergers from overwintering eggs decreased in size over the decades at these elevations.

“For those that come out in late August, when it’s very crispy and dry and we get very hot temperatures, we saw the most negative impacts of climate change,” Williams said.

One thing that surprised the researchers, however, was that none of the species increased in size at higher elevations, up to about 13,000 feet, despite the fact that summer warming due to climate change is greater at higher elevations. This may be because, at higher elevations, snow inhibits early season greening up, reducing the food supply. The results confirm what the team found when it caged grasshoppers at various elevations to see how they adapted to elevational changes in heat and dryness.

“The data are consistent with grasshoppers either being able to take advantage of warming by getting bigger and coming out earlier, or for grasshoppers to experience stress and get smaller,” Buckley said.

Other experiments performed by Buckley on butterflies show some of the same trends.

“We find a pretty similar message with butterflies, which is hopeful to me, in that if we can consider some basic biological principles, we really increase our ability to predict climate change responses,” she said.

The team is continuing its collaboration to understand the metabolic, biochemical and genetic changes that underlie the size changes.

“Using those museum collections allowed us to go back in time to compare exactly the same sites — there hadn’t been any changes in the land use over this 60-year period of warming — using exactly the same methodology,” Williams said. “Having those unique historical specimens enabled us to look at the changes through time.”

Other co-authors of the study are Julia Smith of the University of Washington; Simran Bawa of UC Berkeley; and Ebony Taylor, Michael Troutman and Sean Schoville of the University of Wisconsin, Madison. The work was supported by the National Science Foundation (DEB-1951356, DEB-1951588, DEB-1951364).

MIT chemists have now come up with a new way to determine those 3D genome structures, using generative artificial intelligence. Their technique can predict thousands of structures in just minutes, making it much speedier than existing experimental methods for analyzing the structures.

Using this technique, researchers could more easily study how the 3D organization of the genome affects individual cells’ gene expression patterns and functions.

“Our goal was to try to predict the three-dimensional genome structure from the underlying DNA sequence,” says Bin Zhang, an associate professor of chemistry and the senior author of the study. “Now that we can do that, which puts this technique on par with the cutting-edge experimental techniques, it can really open up a lot of interesting opportunities.”

MIT graduate students Greg Schuette and Zhuohan Lao are the lead authors of the paper, which appears today in Science Advances.

From sequence to structure

Inside the cell nucleus, DNA and proteins form a complex called chromatin, which has several levels of organization, allowing cells to cram 2 meters of DNA into a nucleus that is only one-hundredth of a millimeter in diameter. Long strands of DNA wind around proteins called histones, giving rise to a structure somewhat like beads on a string.

Chemical tags known as epigenetic modifications can be attached to DNA at specific locations, and these tags, which vary by cell type, affect the folding of the chromatin and the accessibility of nearby genes. These differences in chromatin conformation help determine which genes are expressed in different cell types, or at different times within a given cell.

Over the past 20 years, scientists have developed experimental techniques for determining chromatin structures. One widely used technique, known as Hi-C, works by linking together neighboring DNA strands in the cell’s nucleus. Researchers can then determine which segments are located near each other by shredding the DNA into many tiny pieces and sequencing it.

This method can be used on large populations of cells to calculate an average structure for a section of chromatin, or on single cells to determine structures within that specific cell. However, Hi-C and similar techniques are labor-intensive, and it can take about a week to generate data from one cell.

To overcome those limitations, Zhang and his students developed a model that takes advantage of recent advances in generative AI to create a fast, accurate way to predict chromatin structures in single cells. The AI model that they designed can quickly analyze DNA sequences and predict the chromatin structures that those sequences might produce in a cell.

“Deep learning is really good at pattern recognition,” Zhang says. “It allows us to analyze very long DNA segments, thousands of base pairs, and figure out what is the important information encoded in those DNA base pairs.”

ChromoGen, the model that the researchers created, has two components. The first component, a deep learning model taught to “read” the genome, analyzes the information encoded in the underlying DNA sequence and chromatin accessibility data, the latter of which is widely available and cell type-specific.

The second component is a generative AI model that predicts physically accurate chromatin conformations, having been trained on more than 11 million chromatin conformations. These data were generated from experiments using Dip-C (a variant of Hi-C) on 16 cells from a line of human B lymphocytes.

When integrated, the first component informs the generative model how the cell type-specific environment influences the formation of different chromatin structures, and this scheme effectively captures sequence-structure relationships. For each sequence, the researchers use their model to generate many possible structures. That’s because DNA is a very disordered molecule, so a single DNA sequence can give rise to many different possible conformations.

“A major complicating factor of predicting the structure of the genome is that there isn’t a single solution that we’re aiming for. There’s a distribution of structures, no matter what portion of the genome you’re looking at. Predicting that very complicated, high-dimensional statistical distribution is something that is incredibly challenging to do,” Schuette says.

Rapid analysis

Once trained, the model can generate predictions on a much faster timescale than Hi-C or other experimental techniques.

“Whereas you might spend six months running experiments to get a few dozen structures in a given cell type, you can generate a thousand structures in a particular region with our model in 20 minutes on just one GPU,” Schuette says.

After training their model, the researchers used it to generate structure predictions for more than 2,000 DNA sequences, then compared them to the experimentally determined structures for those sequences. They found that the structures generated by the model were the same or very similar to those seen in the experimental data.

“We typically look at hundreds or thousands of conformations for each sequence, and that gives you a reasonable representation of the diversity of the structures that a particular region can have,” Zhang says. “If you repeat your experiment multiple times, in different cells, you will very likely end up with a very different conformation. That’s what our model is trying to predict.”

The researchers also found that the model could make accurate predictions for data from cell types other than the one it was trained on. This suggests that the model could be useful for analyzing how chromatin structures differ between cell types, and how those differences affect their function. The model could also be used to explore different chromatin states that can exist within a single cell, and how those changes affect gene expression.

Another possible application would be to explore how mutations in a particular DNA sequence change the chromatin conformation, which could shed light on how such mutations may cause disease.

“There are a lot of interesting questions that I think we can address with this type of model,” Zhang says.

The researchers have made all of their data and the model available to others who wish to use it.

The research was funded by the National Institutes of Health.

Lithium-ion battery recyclers source materials from two main streams: defective scrap material from battery manufacturers, and so-called “dead” batteries, mostly collected from workplaces. The recycling process extracts lithium, nickel, cobalt, copper, manganese, and aluminum from these sources.

The study quantified the environmental footprint of this recycling process, and found it emits less than half the greenhouse gases (GHGs) of conventional mining and refinement of these metals and uses about one-fourth of the water and energy of mining new metals. The environmental benefits are even greater for the scrap stream, which comprised about 90% of the recycled supply studied, coming in at: 19% of the GHG emissions of mining and processing, 12% of the water use, and 11% of the energy use. While it was not specifically measured, reduced energy use also correlates with less air pollutants like soot and sulfur.

“This study tells us that we can design the future of battery recycling to optimize the environmental benefits. We can write the script,” said William Tarpeh (BS ’12), assistant professor of chemical engineering in the School of Engineering and the study’s senior author.

Location, location

Battery recycling’s environmental impacts depend heavily on the processing facility’s location and electricity source.

“A battery recycling plant in regions that rely heavily on electricity generated by burning coal would see a diminished climate advantage,” said Samantha Bunke, a PhD student at Stanford and one of the study’s three lead investigators.

“On the other hand, fresh-water shortages in regions with cleaner electricity are a great concern,” added Bunke.

Most of the study’s data for battery recycling came from Redwood Materials in Nevada — North America’s largest industrial-scale lithium-ion battery recycling facility — which benefits from the western U.S.’s cleaner energy mix, which includes hydropower, geothermal, and solar.

Transportation is also a crucial factor. In the mining and processing of cobalt, for example, 80% of the global supply is mined in the Democratic Republic of the Congo. Then, 75% of the cobalt supply for batteries travels by road, rail, and sea to China for refining. Meanwhile, most of the global supply of lithium is mined in Australia and Chile. Most of that supply also makes its way to China. The equivalent process for battery recycling is collecting used batteries and scrap, which must then be transported to the recycler.

“We determined that the total transport distance for conventional mining and refining of just the active metals in a battery averages about 35,000 miles (57,000 kilometers). That’s like going around the world one and a half times,” said Michael Machala, PhD ’17, also a lead author of the study.

“Our estimated total transport of used batteries from your cell phone or an EV to a hypothetical refinement facility in California was around 140 miles (225 kilometers),” added Machala, who was a postdoctoral scholar at Stanford’s Precourt Institute for Energy at the time of research and is now a staff scientist for the Toyota Research Institute. This distance was based on presumed optimal locations for future refining facilities amid ample U.S. recyclable batteries.

Patent advantage

Redwood’s environmental outcomes do not represent the nascent battery recycling industry’s overall environmental performance for recycling used batteries. Conventional pyrometallurgy, a key refining step, is very energy intensive, usually requiring temperatures of more than 2,550 degrees Fahrenheit (1,400 degrees Celsius).

Redwood, however, has patented a process called “reductive calcination,” which requires considerably lower temperatures, does not use fossil fuels, and yields more lithium than conventional methods.

“Other pyrometallurgical processes similar to Redwood’s are emerging in labs that also operate at moderate temperatures and don’t burn fossil fuels,” said the third lead author, Xi Chen, a postdoctoral scholar at Stanford during the time of research and now an assistant professor at City University of Hong Kong.

“Every time we spoke about our research, companies would ask us questions and incorporate what we were finding into more efficient practices,” added Chen. “This study can inform the scale-up of battery recycling companies, like the importance of picking good locations for new facilities. California doesn’t have a monopoly on aging lithium-ion batteries from cell phones and EVs.”

Looking ahead

Industrial-scale battery recycling is growing, but not quickly enough, according to senior author Tarpeh.

“We’re forecast to run out of new cobalt, nickel, and lithium in the next decade. We’ll probably just mine lower-grade minerals for a while, but 2050 and the goals we have for that year are not far away,” he said.

While the U.S. now recycles about 50% of available lithium-ion batteries, it has successfully recycled 99% of lead acid batteries for decades. Given that used lithium-ion batteries contain materials with up to 10 times higher economic value, the opportunity is significant, Tarpeh said.

“For a future with a greatly increased supply of used batteries, we need to design and prepare a recycling system today from collection to processing back into new batteries with minimal environmental impact,” he added. “Hopefully, battery manufacturers will consider recyclability more in their future designs, too.”