Thawing permafrost releases greenhouse gas from depth

Which effects did the heat wave of summer 2020 have in Siberia? In a study led by the University of Bonn (Germany), geologists compared the spatial and temporal distribution of methane concentrations in the air of northern Siberia with geological maps. The result: the methane concentrations in the air after last year’s heat wave indicate that increased gas emissions came from limestone formations. The study is published in the journal Proceedings of the National Academy of Sciences (PNAS).

Permanently frozen permafrost soils cover large areas of the northern hemisphere, especially in northern Asia and North America. If they thaw in a warming world, this can pose dangers, because CO₂ and methane are released during thawing – and amplify the anthropogenic greenhouse gas effect. “Methane is particularly dangerous here because its warming potential is many times higher than that of CO₂,” explains Prof. Dr. Nikolaus Froitzheim from the Institute of Geosciences at the University of Bonn. Pessimists therefore already spoke of an imminent “methane bomb.” However, most previous projections showed that greenhouse gases from thawing permafrost will contribute “only” about 0.2 degrees Celsius to global warming by 2100. This assumption has now been challenged by a new study by Nikolaus Froitzheim and his colleagues Jaroslaw Majka (Krakow/Uppsala) and Dmitry Zastrozhnov (St. Petersburg).

Most previous studies only dealt with emissions from the decay of plant and animal remains in the permafrost soils themselves. In their current study, researchers led by Nikolaus Froitzheim made a comparison between methane concentrations in Siberian air, determined by satellite-based spectroscopy, and geological maps. They found significantly elevated concentrations in two areas of northern Siberia – the Taymyr Fold Belt and the rim of the Siberian Platform. What is striking about these two elongated areas is that the bedrock there is formed by limestone formations from the Paleozoic era (the period from about 541 million years ago to about 251.9 million years ago).

In both areas, the elevated concentrations appeared during the extreme heatwave in summer 2020 and persisted for months after. But how did the additional methane occur in the first place? “The soil formations in the observed areas are very thin to nonexistent, making methane emission from the decay of organic soil matter unlikely,” says Niko Froitzheim. He and his colleagues therefore suggest that fracture and cave systems in the limestone, which had been clogged by a mixture of ice and gas hydrate, became permeable upon warming. “As a result, natural gas being mainly methane from reservoirs within and below the permafrost can reach the Earth’s surface,” he says.

The scientists now plan to investigate this hypothesis by measurements and model calculations to find out how much and how fast natural gas may be released. “The estimated amounts of natural gas in the subsurface of North Siberia are huge. When parts of this will be added to the atmosphere upon thawing of the permafrost, this could have dramatic impacts on the already overheated global climate,” emphasizes Niko Froitzheim.

Participating institutions:

The universities of Bonn, Uppsala and AGH Krakow as well as the Karpinsky Russian Geological Research Institute in St. Petersburg were involved in the study.

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Making voting easier for previously incarcerated people

In March 2020, 83,000 New Jersey residents who had been ineligible to vote became eligible when a new law took effect restoring voting rights for people on parole or probation who had previously been convicted of felonies.

Ariel White, an associate professor in MIT’s Department of Political Science and an MIT Governance Lab faculty associate, is one of several researchers working with the New Jersey Institute for Social Justice (NJISJ) to inform these people of their eligibility.

NJISJ spearheaded the effort to get the law passed, and worked throughout 2020 to register people to vote before the presidential election. Now, White and her colleagues are gathering more information about the barriers making it more difficult for previously incarcerated people to vote, as well as what messaging might convince people to register.

People vote infrequently after being incarcerated, and the criminal legal system disproportionately incarcerates people of color. White has been studying this issue for several years, focusing in particular on situations where people legally can vote, but don’t manage to. Now, she’s trying to find ways to address this inequality. “I got sick of writing the ‘this is a problem’ papers,” she says. “I wanted to see what could be done about it.”

Increasing political participation among previously incarcerated people

In the first stage of their research in New Jersey, the researchers are interviewing previously incarcerated people. They’re talking with active voters to better understand what motivates them to participate in the political process. They’re also asking people who aren’t voting why they’re reluctant to do so, and seeing what arguments for voting might resonate with them.

Some people are hesitant to vote because they’re simply not sure if they’re eligible, and don’t want to get in trouble. Others feel like their votes don’t make a difference, or that their voice isn’t valued. “This is something they have learned through personal experience with a system that doesn’t generally reward speaking up and making your opinion known,” says White. “The criminal legal system is both scary and disempowering to interact with.”

White and her colleagues have attended NJISJ organizing meetings to learn from a group that has a lot of experience mobilizing people to vote. “We’ve gotten to learn about what they’re already doing, what kinds of things are working for them, what kinds of messages they think are resonating,” she says.

This work is in line with MIT GOV/LAB’s engaged scholarship approach, which promotes collaborating with partners to gain valuable insights from people living these issues and to make research more valuable to decision-makers.

Adding to the voter mobilization literature 

Early interviews have suggested that particularly convincing messaging might focus on the importance of local politics, as well as how it might be meaningful to someone’s friends and family that they vote.

White says that while the existing literature has shown that these and other strategies are effective at increasing turnout among people who are already registered, “there is actually a lot less published work on how you register people who are not currently registered.” There is also little evidence specifically on increasing turnout among people who have had contact with the criminal legal system.

Once interviews are completed, the researchers will put their findings to the test by reaching out to people via mail before New Jersey’s state and municipal elections this November. They’ll try some different messages for convincing people that their votes matter and collect data on which are most effective at getting people registered and voting.

This project comes on the heels of similar research White and other researchers conducted in North Carolina and Texas leading up to the 2020 presidential election. In this instance, the research team wanted to see if mailing certain pieces of information to people with criminal records increased registration and turnout. “Does it matter whether you include, for example, the registration form itself, or is it more just the information about eligibility,” White explains. Results from this project are forthcoming.

People rarely vote after being incarcerated

Voting rates are low not only among people who have served longer sentences for felonies, but also among people who have served shorter sentences for misdemeanors. In a 2019 paper, White found that jail time for a first-time misdemeanor offense actually made it less likely that someone would vote after they were released.

White explains that fewer people vote after a misdemeanor conviction because even the shortest jail stint can turn someone’s life upside down. “Going to jail for a couple weeks could mean that you lose your job, it could mean that you lose your housing,” she says. People can also lose custody of their children. “You’re likely to have a lot of other stuff on your plate that could just make it really unlikely that you manage to vote,” says White.

While incarceration didn’t affect voting among white people in the study, voting dropped significantly among Black people, who were more than twice as likely to have voted before being incarcerated, a difference White suggests could be attributable to racial disparities in policing and the criminal legal system.

White says that a lot of research on incarceration and voting has focused on legal restrictions on voting, like felony disenfranchisement laws. “These [legal restrictions] are important for a whole range of reasons,” she says. “But there are millions of people who pass through the criminal legal system with their voting rights intact, but who do not manage to exercise those rights.”

She also points out that we should incarcerate fewer people to begin with. But there will need to continue to be efforts to increase voting among previously incarcerated people. “We have this system that incarcerates an enormous number of people who have this intense personal knowledge, this particularly intimate understanding of how that system works,” she says. “But they are rarely involved in electing the people who could potentially change the way the system works.”

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A comprehensive study of technological change

The societal impacts of technological change can be seen in many domains, from messenger RNA vaccines and automation to drones and climate change. The pace of that technological change can affect its impact, and how quickly a technology improves in performance can be an indicator of its future importance. For decision-makers like investors, entrepreneurs, and policymakers, predicting which technologies are fast improving (and which are overhyped) can mean the difference between success and failure.

New research from MIT aims to assist in the prediction of technology performance improvement using U.S. patents as a dataset. The study describes 97 percent of the U.S. patent system as a set of 1,757 discrete technology domains, and quantitatively assesses each domain for its improvement potential.

“The rate of improvement can only be empirically estimated when substantial performance measurements are made over long time periods,” says Anuraag Singh SM ’20, lead author of the paper. “In some large technological fields, including software and clinical medicine, such measures have rarely, if ever, been made.”

A previous MIT study provided empirical measures for 30 technological domains, but the patent sets identified for those technologies cover less than 15 percent of the patents in the U.S. patent system. The major purpose of this new study is to provide predictions of the performance improvement rates for the thousands of domains not accessed by empirical measurement. To accomplish this, the researchers developed a method using a new probability-based algorithm, machine learning, natural language processing, and patent network analytics.

Overlap and centrality

A technology domain, as the researchers define it, consists of sets of artifacts fulfilling a specific function using a specific branch of scientific knowledge. To find the patents that best represent a domain, the team built on previous research conducted by co-author Chris Magee, a professor of the practice of engineering systems within the Institute for Data, Systems, and Society (IDSS). Magee and his colleagues found that by looking for patent overlap between the U.S. and international patent-classification systems, they could quickly identify patents that best represent a technology. The researchers ultimately created a correspondence of all patents within the U.S. patent system to a set of 1,757 technology domains.

To estimate performance improvement, Singh employed a method refined by co-authors Magee and Giorgio Triulzi, a researcher with the Sociotechnical Systems Research Center (SSRC) within IDSS and an assistant professor at Universidad de los Andes in Colombia. Their method is based on the average “centrality” of patents in the patent citation network. Centrality refers to multiple criteria for determining the ranking or importance of nodes within a network.

“Our method provides predictions of performance improvement rates for nearly all definable technologies for the first time,” says Singh.

Those rates vary — from a low of 2 percent per year for the “Mechanical skin treatment — Hair removal and wrinkles” domain to a high of 216 percent per year for the “Dynamic information exchange and support systems integrating multiple channels” domain. The researchers found that most technologies improve slowly; more than 80 percent of technologies improve at less than 25 percent per year. Notably, the number of patents in a technological area was not a strong indicator of a higher improvement rate.

“Fast-improving domains are concentrated in a few technological areas,” says Magee. “The domains that show improvement rates greater than the predicted rate for integrated chips — 42 percent, from Moore’s law — are predominantly based upon software and algorithms.”

TechNext Inc.

The researchers built an online interactive system where domains corresponding to technology-related keywords can be found along with their improvement rates. Users can input a keyword describing a technology and the system returns a prediction of improvement for the technological domain, an automated measure of the quality of the match between the keyword and the domain, and patent sets so that the reader can judge the semantic quality of the match.

Moving forward, the researchers have founded a new MIT spinoff called TechNext Inc. to further refine this technology and use it to help leaders make better decisions, from budgets to investment priorities to technology policy. Like any inventors, Magee and his colleagues want to protect their intellectual property rights. To that end, they have applied for a patent for their novel system and its unique methodology.

“Technologies that improve faster win the market,” says Singh. “Our search system enables technology managers, investors, policymakers, and entrepreneurs to quickly look up predictions of improvement rates for specific technologies.”

Adds Magee: “Our goal is to bring greater accuracy, precision, and repeatability to the as-yet fuzzy art of technology forecasting.”

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Researchers make tiny, aged brains to study Alzheimer’s

Researchers led by City of Hope, a world-renowned research and treatment center for cancer, diabetes and other life-threatening diseases, have developed a powerful miniature brain platform to study the mechanistic causes of Alzheimer’s disease and to test dementia drugs in development, reports a new study published today in Advanced Science.

“Drug development for Alzheimer’s disease has run into challenges due to incomplete understanding of the disease’s pathological mechanisms,” said Yanhong Shi, Ph.D., the Herbert Horvitz Professor in Neuroscience and director of the Division of Stem Cell Biology Research within the Department of Developmental and Stem Cell Biology at Beckman Research Institute of City of Hope.

“Preclinical research in this arena predominantly uses animal models, but there is a huge difference between humans and animals such as rodents, especially when it comes to brain architecture. We, at City of Hope, have created a miniature brain model that uses human stem cell technology to study Alzheimer’s disease and, hopefully, to help find treatments for this devastating illness.”

City of Hope researchers were able to model sporadic Alzheimer’s disease, the most common form of the condition, using “brain organoids” derived using human induced pluripotent stem cell (hiPSC) technology. Because Alzheimer’s is a disease of age, the scientists exposed the models to serum to mimic age-associated blood-brain barrier breakdown. Then they ran the organoids through different experiments to test known Alzheimer’s biomarkers, including elevated levels of amyloid plaques and tau tangles as well as synaptic breaks linked to cognitive decline, among other pathological phenotypes brought on by the condition.

More than 6 million people are living with Alzheimer’s disease, which kills more people than breast and prostate cancer combined, reports the Alzheimer’s Association. The heartbreaking degenerative disease affects not only the individual diagnosed with the condition, but also their primary caregiver, family and friends. No cure currently exists, and available treatments merely address symptoms rather than the root cause.

“Other studies using brain organoids to examine Alzheimer’s disease used miniature brain models that are phenotypically young, but to truly understand what happens when Alzheimer’s strikes, we need to use age-associated models, and that’s what we did in this research project when we exposed the miniature brains to serum,” said Xianwei Chen, Ph.D., first author of the study and postdoctoral fellow at City of Hope. “We believe the age-associated brain organoids we generated will provide a powerful platform for us to find effective treatments for disorders affecting the human body’s most complex organ.”

Preclinical research using brain organoids found that exposure to serum from blood could induce multiple Alzheimer’s symptoms, suggesting combination therapies targeting multiple pathological alterations likely would be more effective than single-target therapies currently in development. The researchers studied late-onset or sporadic Alzheimer’s disease, which accounts for most cases (95% sporadic vs. 5% inherited). They found that attempting a single therapy — for example inhibiting only amyloid or tau proteins — did not reduce the levels of tau or amyloid, respectively, suggesting that these two key biomarkers likely cause disease progression independently. Moreover, exposure to serum from blood — which mimics a leaky blood-brain barrier — could cause breaks in synaptic connections that help brains remember things and function properly.

Matt Huentelman, Ph.D., professor of neurogenomics at the Translational Genomics Research Institute (TGen), said the brain model developed by City of Hope provides a new avenue for examining emerging treatments for this memory-robbing disease. Huentelman is a leading expert in the genetic study of Alzheimer’s disease and was not part of this study.

“Using the model developed in this City of Hope-led study could help accelerate the evaluation of potential treatment options, giving a new sense of hope to Alzheimer’s patients and their families,” he said.

The study, “Modeling sporadic Alzheimer’s disease in human brain organoids under serum exposure,” was done in collaboration with University of California Irvine, Banner Sun Health Research Institute, Banner Alzheimer’s Institute and Washington University in St. Louis. It was supported by the Louise and Herbert Horvitz Charitable Foundation, the Sidell-Kagan Foundation, the Christopher Family Endowed Innovation Fund, the National Institute on Aging of the National Institutes of Health (R01 AG056305, RF1 AG061794, R56 AG061171, P30 AG019610, RF1 DA048813, R01 AG056303, P30 AG066519) and the National Cancer Institute of the National Institutes of Health (P30CA33572).

CONTACT
Zen Vuong
626-409-9367
zvuong@coh.org

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Scientists explore the latent regenerative potential of the inner ear

Scientists from the USC Stem Cell laboratory of Neil Segil have identified a natural barrier to the regeneration of the inner ear’s sensory cells, which are lost in hearing and balance disorders. Overcoming this barrier may be a first step in returning inner ear cells to a newborn-like state that’s primed for regeneration, as described in a new study published in Developmental Cell.

“Permanent hearing loss affects more than 60 percent of the population that reaches retirement age,” said Segil, who is a Professor in the Department of Stem Cell Biology and Regenerative Medicine, and the USC Tina and Rick Caruso Department of Otolaryngology – Head and Neck Surgery. “Our study suggests new gene engineering approaches that could be used to channel some of the same regenerative capability present in embryonic inner ear cells.”

In the inner ear, the hearing organ, which is the cochlea, contains two major types of sensory cells: “hair cells” that have hair-like cellular projections that receive sound vibrations; and so-called “supporting cells” that play important structural and functional roles.

When the delicate hair cells incur damage from loud noises, certain prescription drugs, or other harmful agents, the resulting hearing loss is permanent in older mammals. However, for the first few days of life, lab mice retain an ability for supporting cells to transform into hair cells through a process known as “transdifferentiation”, allowing recovery from hearing loss. By one week of age, mice lose this regenerative capacity—also lost in humans, probably before birth.

Based on these observations, postdoctoral scholar Litao Tao, PhD, graduate student Haoze (Vincent) Yu, and their colleagues took a closer look at neonatal changes that cause supporting cells to lose their potential for transdifferentiation.

In supporting cells, the hundreds of genes that instruct transdifferentiation into hair cells are normally turned off. To turn genes on and off, the body relies on activating and repressive molecules that decorate the proteins known as histones.  In response to these decorations known as “epigenetic modifications,” the histone proteins wrap the DNA into each cell nucleus, controlling which genes are turned “on” by being loosely wrapped and accessible, and which are turned “off” by being tightly wrapped and inaccessible. In this way, epigenetic modifications regulate gene activity and control the emergent properties of the genome.

In the supporting cells of the newborn mouse cochlea, the scientists found that hair cell genes were suppressed by both the lack of an activating molecule, H3K27ac, and the presence of the repressive molecule, H3K27me3.  However, at the same time, in the newborn mouse supporting cells, the hair cell genes were kept “primed” to activate by the presence of yet a different histone decoration, H3K4me1.  During transdifferentiation of a supporting cell to a hair cell, the presence of H3K4me1 is crucial to activate the correct genes for hair cell development.

Unfortunately with age, the supporting cells of the cochlea gradually lost H3K4me1, causing them to exit the primed state. However, if the scientists added a drug to prevent the loss of H3K4me1, the supporting cells remained temporarily primed for transdifferentiation. Likewise, supporting cells from the vestibular system, which naturally maintained H3K4me1, were still primed for transdifferentiation into adulthood.

“Our study raises the possibility of using therapeutic drugs, gene editing, or other strategies to make epigenetic modifications that tap into the latent regenerative capacity of inner ear cells as a way to restore hearing,” said Segil. “Similar epigenetic modifications may also prove useful in other non-regenerating tissues, such as the retina, kidney, lung, and heart.”

Additional co-authors of the study include Juan Llamas, Talon Trecek, Xizi Wang, and Zlatka Stojanova in the Segil Lab at USC, and Andrew K. Groves at Baylor College of Medicine.

Sixty percent of this project was supported by federal funding from the National Institute on Deafness and Other Communication Disorders (R01DC015829, R01DC014832, T32DC009975, F31DC017376). Additional funding came from the Hearing Restoration Project at Hearing Health Foundation.

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Stinkweed could make a cleaner bio-jet fuel

A common farm weed could make a “greener” jet fuel with fewer production-related environmental impacts than other biofuels, a new study indicates.

Growing the weed, pennycress – often called stinkweed – as a crop requires less fertilizer and fewer pesticides than other plants that can be used to make renewable jet fuel, according to the study. Pennycress also requires fewer farm operations, such as soil tilling, than other potential biofuel crops, reducing the associated environmental costs. Those costs include carbon dioxide emissions that cause the climate to change, as well as other emissions that pollute the air.

Environmental impacts could be further mitigated through farm management techniques that keep fertilizer on fields, rather than allowing it to run off into nearby watersheds, the study suggests. Such techniques can add to the financial cost of growing crops, but reduce their environmental footprints.

“Reducing greenhouse gas emissions from air travel will mean not just incremental changes, but a fundamental change in how we have been producing fuel and where that fuel comes from,” said Ajay Shah, senior author of the study and associate professor of food, agricultural and biological engineering at The Ohio State University in Wooster. “And what we found is that pennycress might make a very good alternative fuel, especially when you consider the environmental costs of producing it.”

The study was published recently online in the journal Applied Energy.

For this study, the researchers estimated the environmental impacts of growing pennycress, transporting it to a biorefinery and converting it to a usable jet fuel. They also accounted for the environmental costs of burning leftover byproducts of refining the pennycress seed into fuel.

Those environmental costs include fertilizer and pesticide use, water consumption and the energy required to harvest and transport pennycress seeds from a farm to a biorefinery and process them into usable fuel.

The researchers built computer models to determine how much total energy it would take to produce jet fuel from pennycress seeds and compared those estimates with the energy needed for producing biofuels from other crops. The data for the models came from existing studies about biofuel production.

Their models showed that it took about half as much energy to produce jet fuel from pennycress as it did to produce jet fuel from canola or sunflowers, two other potential bio-jet fuel crops. Pennycress oil production used about a third as much energy as soybean oil production, the researchers found, and the energy needed for turning pennycress into jet fuel was about the same as that used to produce fuel from the flowering plant camelina, another biofuel crop.

Renewable jetfuels are not yet financially competitive with fossil fuel-based fuels, Shah said. But calculating the environmental impacts of alternative bio-based fuels should help both farmers and policymakers as they try to limit carbon dioxide in the Earth’s atmosphere and, hopefully, to slow or stop climate change.

“Pennycress also makes an appealing alternative jet fuel because of its growing season,” Shah said. “It is a winter cover crop that can be grown between corn season and soybean season, giving the same body of farmland an extra production cycle each year.

“Pennycress can be planted when corn is still standing in the field, before the corn harvest,” he said. “And it can be harvested before the soybean crops are planted. The bottom line is it can be used as a cover crop, it doesn’t divert any agricultural production land, and it has suitable properties for renewable jet fuel production.”

Greenhouse gas emissions from air travel contribute to climate change, accounting for about 2% of all human-induced carbon-dioxide emissions, according to various groups that study the effects of transportation on climate change.

“Reducing those emissions will almost certainly mean finding cleaner alternatives to jet fuels made from fossil fuels,” Shah said. “Studies like this one can help determine the best alternative.

“When it comes to pennycress, production and logistics are the big contributors to both the environmental impacts and the costs, and those are the challenge areas ­– they have to be streamlined and solved to make it more efficient,” he said. “If we could improve those areas, we could make production more energy-efficient and substantially lower the costs and environmental impacts.”

This work was supported by funding from the U.S. Department of Energy.

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Artificial Intelligence May Find Signs Of Alzheimer’s In Neuroimaging Data

Shuiwang Ji, associate professor in the Department of Computer Science and Engineering at Texas A&M University, is one of the principal investigators on a $6 million grant from the National Institutes of Health to develop artificial intelligence-driven methods to automate the process of finding subtle telltale signs of Alzheimer’s disease in neuroimaging data. Ji’s team shares $1.2 million of the grant.

Ji will lead the research team tasked with developing advanced deep-learning methods for finding relevant neural signatures lurking within neuroimages taken using different techniques, such as PET scans and MRIs.

“I feel very excited with this collaborative opportunity to make scientific discoveries in medical domains using deep learning and artificial intelligence,” said Ji, who has extensive expertise in machine learning, deep learning and medical image analysis.

Alzheimer’s disease affects 5.6 million Americans over the age of 65, and its symptoms are most noticeably the progressive impairment of cognitive and memory functions. It is also currently the most common form of dementia in the elderly. Despite copious amounts of studies on Alzheimer’s over the years, researchers’ understanding of the biology and progression of the disease remains limited, so there are limited advances in therapeutics and preventive strategies.

Ji said the research team expects to discover new genetic biomarkers relevant to Alzheimer’s, which may lead to understanding the molecular basis of the disease, and in turn, uncover a potential new treatment.

Researchers will leverage existing neuroimaging and genetic data resources from the UK Biobank, the Alzheimer’s Disease Sequencing Project, the Alzheimer’s Disease Neuroimaging Initiative, and the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium.

Other collaborators on this research areDegui Zhi, associate professor with the UTHealth School of Biomedical Informatics, and Myriam Fornage, professor at the Center for Human Genetics at UTHealth.

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