Wednesday, October 04, 2023

 

An ancient anti-cancer mechanism: DISE


Peer-Reviewed Publication

IMPACT JOURNALS LLC

Figure 1 

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FIGURE 1: SCHEMATIC OF THE POSTULATED DISE MECHANISM.

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CREDIT: 2023 PATEL AND PETER.




“DISE is effective against all cancers we tested.” 

A new editorial paper was published in Oncotarget's Volume 14 on September 25, 2023, entitled, “DISE, an ancient anti-cancer mechanism that senses mutational load in cancerous cells?

In their new editorial, researchers Monal Patel and Marcus E. Peter from Northwestern University discuss a recent breakthrough in cancer therapy. Despite the multiple advances in therapy, cancer remains one of the most common causes of death globally. It is a systemic disease affecting people of all ages and originates at the level of single cells which, upon acquisition of mutations, become neo-plastically transformed.

Cell division is the biggest risk factor for the accumulation of mutations, explaining why all multicellular organisms which evolved about 2 billion years ago, are prone to cancer. Given the recent achievements in cancer treatment with immune checkpoint blockade therapies, multicellular organisms may have developed the immune system as a mechanism to eradicate cancerous cells. 

“However, the immune system arose relatively recent, ~500 million years ago [3].” 

Moreover, studies have shown that cancer cells can become resistant to the anticancer activity of both the innate and the adaptive immune system. Therefore, while the immune system is important, it is likely not the most vital machinery that emerged in multicellular organisms to prevent cancer formation. The researchers believe that there are other more effective and archaic anti-cancer mechanisms that are conserved during evolution. 

Of note, RNA interference (RNAi) is a highly conserved biological mechanism for silencing gene expression. While RNAi likely emerged as a defense tool against viruses and other foreign nucleic acids, it has also evolved to have other activities in the cells. The team’s research has identified a new evolutionarily conserved RNAi-based form of cell death that targets essential survival genes: Death Induced by Survival gene Elimination (DISE).

“DISE was discovered through our work on CD95 and its ligand, CD95L, where we found that more than 80% of 26 different short interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs) derived from the two genes, killed multiple cancer cell lines via simultaneous activation of multiple cell death pathways; and we were unable to find a way to inhibit this form of cell death [9].”
 

Read the full paper: DOI: https://doi.org/10.18632/oncotarget.28466 

Correspondence to: Marcus E. Peter

Email: m-peter@northwestern.edu 

Keywords: cancer, cell death, evolution, RNAi, short RNAs
 

About OncotargetOncotarget (a primarily oncology-focused, peer-reviewed, open access journal) aims to maximize research impact through insightful peer-review; eliminate borders between specialties by linking different fields of oncology, cancer research and biomedical sciences; and foster application of basic and clinical science.

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Illinois-led project to sequence 400 soybean genomes, improve future crops


Grant and Award Announcement

UNIVERSITY OF ILLINOIS COLLEGE OF AGRICULTURAL, CONSUMER AND ENVIRONMENTAL SCIENCES

Matt Hudson 

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THE UNIVERSITY OF ILLINOIS-LED JOINT GENOME INSTITUTE PROJECT WILL SEQUENCE 400 SOYBEAN GENOMES TO GREATLY ENHANCE THE ABILITY OF CROP BREEDERS AND BIOTECHNOLOGY EXPERTS TO IDENTIFY IMPORTANT SOYBEAN GENES AND INCORPORATE THEM INTO BETTER CROPS. MATT HUDSON (PICTURED), PROFESSOR OF CROP SCIENCES AT ILLINOIS, WILL LEAD THE PROJECT.

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CREDIT: UNIVERSITY OF ILLINOIS




As a source of protein and biodiesel for cleaner renewable energy, soybean is an important crop worldwide. But is it performing to its full potential? An ambitious effort led by the University of Illinois Urbana-Champaign and the U.S. Department of Energy Joint Genome Institute (JGI) will sequence 400 soybean genomes to develop a “pangenome” — an attempt to characterize all the useful diversity in the genome to create an even more robust and resilient crop.

The soybean pangenome project will sequence and analyze at least 50 soybean genomes from cultivated lines and wild relatives at reference quality, the gold standard of modern sequencing. A further 350 genomes will be sequenced as high-quality drafts by the JGI. The plan is to include a diverse set of soybean lines, including perennial relatives and lines selected to yield in harsh conditions, preparing the industry to move toward a climate-resilient future.    

“There have been soybean pangenome efforts before, but this will be a big step forward. We want to identify all of the variation present within this diverse set of cultivated soybeans. Knowing details of all of the genetic variation should very much enhance and speed up the ability of crop breeders and biotechnology experts to identify important genes and incorporate them into better crops,” said project leader Matt Hudson, professor in the Department of Crop Sciences, part of the College of Agricultural, Consumer and Environmental Sciences (ACES) at U. of I. He is also co-director of the Center for Digital Agriculture, science integration chair for the Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), and faculty affiliate at the Carl R. Woese Institute for Genomic Biology.

 Hudson and his multi-institution collaborators will select and grow soybean lines, shipping extracted DNA to the JGI for long-read sequencing as part of the JGI’s Community Science Program. Hudson’s team, along with partners at U. of I.’s AIFARMS, will take the lead in analyzing the output. 

“AIFARMS was designed to deal with large datasets coming out of agriculture projects,” Hudson said. “Having this dataset is going to be a boost for our other digital ag activities.”

With its inclusion of wild relatives and the sheer number of reference and high-quality draft genomes set for sequencing, the project will drastically improve the current soybean reference genome. Hudson explains that genetic diversity is the raw material for crop improvement, but the crop’s diversity is not reflected in the reference genome. He likens it to the first human genome, which was pieced together only from Caucasian individuals. 

“There’s an increasing effort to have the reference human genome reflect all of the variation in people. We think there are equally big reasons to do the same thing in crops,” Hudson said. “But it’s hard to locate the missing diversity by any other means than sequencing more genomes.”

The team plans to consult the global soybean breeding community, including industry partners, in deciding priority lines to include. 

Ultimately, Hudson said, the project will “enable deep analysis of the evolution and domestication of modern soybean and empower soybean researchers and breeders to directly select for otherwise hidden genetic variation in genes that can be targeted for variety development. As soybean is becoming increasingly important as a worldwide crop, as well as being a key bioenergy crop, this project will have global impact and be particularly relevant to U.S. agriculture."

Read more about JGI's 2024 awardees

 

Interconnected factors increase household food insecurity in Brazil


Peer-Reviewed Publication

PLOS




Food insecurity is four times higher in Brazilian households headed by single women of colour than those headed by married white men, according to research published in the open access journal PLOS Global Public Health. Gender inequities, skin colour and children in the home increase the risk of food insecurity and the authors argue that policy makers need to consider intersectionality in programmes to reduce it.

In 2021 there were 2.37 billion people suffering from food insecurity, with prevalence higher among women than men. The gender gap has increased in recent years, especially in the economic crisis triggered by the COVID-19 pandemic. In Brazil, work to address food insecurity in the early 2000s led to improvements until 2013, but since 2016 the trend has reversed.

Lissandra Amorim Santos of the Federal University of Rio de Janeiro, Rafael Perez-Escamilla of Yale University School of Public Health, and colleagues, were interested in whether factors other than gender increase food insecurity. Using data from 2004-18 from three Brazilian national surveys that include population health information, they analysed the relationship between food insecurity and gender, race/skin colour, marital status of the head of the household, and the presence of children under five.

Households with children under five headed by single women of colour were three times more likely to report food insecurity compared with those headed by married white men in 2004 and 2013, but four times more likely in 2018. In 2018, compared to households headed by married white men, those headed by married white women had a 1.35 higher probability; by single white women a 1.85 higher probability; and by men of colour two times as likely to suffer food insecurity. Compared to those without children under five, households with young children had a higher probability of reporting food insecurity for most profiles.

The authors conclude that only policies centered on gender equality, antiracism and attention to families with young children can reduce poverty and improve the current picture. The National Food and Nutrition Security Council was reestablished in Brazil by the newly elected government in early 2023, and these findings call for reestablishment of other relevant ministries, including the ministries of Women and of Racial Equity, as well as increased funding to programs to fight hunger.

The authors add: “The joint consideration of gender, race/skin color, marital status of the household head, as well as the presence of children in households follows a stepwise trend increasing FI risk.”

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In your coverage please use this URL to provide access to the freely available article in PLOS Global Public Healthhttps://journals.plos.org/globalpublichealth/article?id=10.1371/journal.pgph.0002324        

Citation: Santos LA, Pérez-Escamilla R, Cherol CCdS, Ferreira AA, Salles-Costa R (2023) Gender, skin color, and household composition explain inequities in household food insecurity in Brazil. PLOS Glob Public Health 3(10): e0002324. https://doi.org/10.1371/journal.pgph.0002324

Author Countries: Brazil, USA

Funding: This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brasil (CAPES) – Finance Code 001. LAS received financial support by Coordination for the Improvement of Higher Education Personnel (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES) (Grant: 88887.511179/2020-00). The research group (GISAN - UFRJ), coordinated by RS-C, is supported by The Brazilian National Council for Scientific and Technological Development (Conselho Nacional de Desenvolvimento Científico e Tecnológico - CNPq) (Edital Universal, Grant 423174/2018-5) and Foundation Carlos Chagas Filho Research Support of the State of Rio de Janeiro (Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro - FAPERJ) (Edital APQ1 2019, Grant E-26/10.001596/2019). CAPES, CNPq or FAPERJ had no role in the study design, analysis, decision to publish, or preparation of the manuscript.

 

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Rural counties showing steeper decline in health measures compared to urban counties in 2015 versus 2019—though all areas showed declines in health measures over time


Peer-Reviewed Publication

PLOS

Rural counties showing steeper decline in health measures compared to urban counties in 2015 versus 2019—though all areas showed declines in health measures over time 

IMAGE: A NATIONAL MAP VIEW OF THE HEALTH EQUITY DASHBOARD, SHOWING: THE 2019 DISTRIBUTION IN QUINTILES OF A NATIONAL INDEX FORMED FROM FIVE MEASURES (LIFE EXPECTANCY, PERCENTAGE OF THE ADULT POPULATION THAT IS OBESE, PERCENTAGE OF THE POPULATION THAT IS UNINSURED, INCOME INEQUALITY, AND AIR QUALITY) AND THE PERCENTAGE OF RURAL, SUBURBAN, AND URBAN COUNTIES WITH INDEX VALUES IN THE BEST TO WORST QUINTILES (TOP); THE COUNTY-LEVEL DISTRIBUTION OF THAT INDEX ACROSS URBAN, SUBURBAN, AND RURAL COUNTY DESIGNATIONS (MIDDLE); AND A COMPARISON OF THE 2015 AND 2019 VALUES OF ONE MEASURE (PERCENTAGE OF THE POPULATION IN FAIR OR POOR HEALTH) AT THE STATE LEVEL (BOTTOM). THE HEALTH EQUITY DASHBOARD TOOL IS PUBLICLY AVAILABLE AT: AKA.MS/HEALTHEQUITY. THE BASE LAYERS FOR THE MAPS ARE SHAPEFILES FROM THE US CENSUS TIGER FILE REPOSITORY. view more 

CREDIT: WEEKS ET AL., 2023, PLOS GLOBAL PUBLIC HEALTH, CC-BY 4.0 (HTTPS://CREATIVECOMMONS.ORG/LICENSES/BY/4.0/)




Residents of rural counties have overall worse health outcomes than their urban counterparts. A study published in PLOS Global Public Health  by William Weeks at Microsoft Corporation, Redmond, Washington, United States and colleagues introduces a Health Equity Dashboard for policy makers to visualize health disparities in specific locations, and to examine the relationship between health-related measures and socio-demographic characteristics.

Despite overall decreasing mortality rates prior to 2020, health disparities between rural and urban areas in the United States have increased. To better understand inequities in health-related measures between rural and non-rural populations, researchers collected publicly available health data from 3,131 U.S. counties. They classified counties as rural, suburban, or urban using the Centers for Disease Control and Prevention’s 2013 Urban-Rural Classification Scheme for Counties, and analyzed how 33 county level attributes relating to health outcomes, clinical care, health behaviors, physical environment, or social and economic factors changed in 2015 compared to 2019. Using this data, researchers developed a publicly available Health Equity Dashboard (aka.ms/healthequity) that could be used by policymakers and researchers to examine disparities within domains, to develop their own indices of up to five measures across a single or multiple domains, and to examine the relationship between health measures and socio-demographic characteristics.  

The Health Equity Dashboard showed that, although health measures in general declined across all counties in 2019 as compared to 2015, the decline tended to be steeper in rural counties, resulting in an increased rural-urban disparity. Specifically, there was a statistically significant and progressive worsening of 22 of the 33 health measures (such as life expectancy, reported mental or physical health, food insecurity, obesity, smoking, etc) when moving from urban to suburban to rural counties. (For the three measures of diabetes prevalence, preventable hospitalization, and deaths due to injury, values improved with increasing rurality.)

It's important to note the dashboard highlights relationships between geographic location and health-related variables which are correlated, but cannot be shown to be causative. Regardless, the dashboard underscores the need to prioritize rural settings for health and policy interventions in the United States.

According to the authors, “Our findings highlight the need for policymakers to prioritize rural settings for interventions designed to improve health outcomes. Timely, accurate, and high-quality data are a critical component of public health decision making. Data visualization tools can help the effective delivery and translation of data, thereby engaging key stakeholders and prompting action”.           

The authors add: “Using publicly available data, we developed a free, interactive health equity dashboard that can be used to examine county-level health inequities (available at aka.ms/healthequity).  In their quest for health equity, communities and their leaders can use the tool to explore relationships between health and its social determinants and identify areas that are ripe for intervention.”               

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In your coverage please use this URL to provide access to the freely available article in PLOS Global Public Healthhttps://journals.plos.org/globalpublichealth/article?id=10.1371/journal.pgph.0002420          

Citation: Weeks WB, Chang JE, Pagán JA, Lumpkin J, Michael D, Salcido S, et al. (2023) Rural-urban disparities in health outcomes, clinical care, health behaviors, and social determinants of health and an action-oriented, dynamic tool for visualizing them. PLOS Glob Public Health 3(10): e0002420. https://doi.org/10.1371/journal.pgph.0002420

Author Countries: USA, Switzerland

Funding: The authors received no specific funding for this work.

 

 

Despite increasing rates of tuberculosis in prisons across the globe, current WHO TB prevention guidelines fail to reach incarcerated populations


Programs should instead prioritize them, argue a group of researchers from Stanford, Harvard, UCL and a range of other global institutions.


Peer-Reviewed Publication

PLOS

Despite increasing rates of tuberculosis in prisons across the globe, current WHO TB prevention guidelines fail to reach incarcerated populations 

IMAGE: OPEN CELLS INSIDE A PRISON IN PARAGUAY. view more 

CREDIT: JASON ANDREWS (CC-BY 4.0, HTTPS://CREATIVECOMMONS.ORG/LICENSES/BY/4.0/)



Despite increasing rates of tuberculosis in prisons across the globe, current WHO TB prevention guidelines fail to reach incarcerated populations. Programs should instead prioritize them, argue a group of researchers from Stanford, Harvard, UCL and a range of other global institutions.

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In your coverage, please use this URL to provide access to the freely available paper in PLOS Medicinehttp://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1004288

Article Title: Prioritizing persons deprived of liberty in global guidelines for tuberculosis preventive treatment

Author Countries: United States

Funding: The authors received no specific funding for this work.

 

Female animals may learn mate preferences based on what sets other females’ choices apart from the crowd


Mathematical model suggests females learn to prefer rare traits that distinguish successful males


Peer-Reviewed Publication

PLOS

Female animals may learn mate preferences based on what sets other females’ choices apart from the crowd 

IMAGE: BY FOCUSING ON THE CONTEXT OF FEMALE MATE CHOICES, THE INFERRED ATTRACTIVENESS HYPOTHESIS PROVIDES A NEW PERSPECTIVE ON HOW SEXUAL SELECTION MAY FUNCTION. ARTIST’S RENDERING OF MATE CHOICE BY A PEAHEN. view more 

CREDIT: COMPOSITE IMAGE BY EMILY DUVAL AND ELLIOT SCHUNKE, ORIGINAL IMAGES BY JEAN VAN DER MEULEN AND SALLY WYNN (PLATINUMPORTFOLIO) (CC-BY 4.0, HTTPS://CREATIVECOMMONS.ORG/LICENSES/BY/4.0/)




Females may infer what makes a male attractive by observing the choices of more experienced females, and the context of those choices matters, according to a mathematical model publishing October 3rd in the open access journal PLOS Biology. Rather than simply copying their peers, females might learn to prefer rare traits that set successful males apart from others, Emily DuVal at Florida State University, US, and colleagues report.

Sexual selection — where traits become more common because of their attractiveness to the opposite sex — can produce strange and elaborate characteristics, such as huge antlers, bright plumage, and flamboyant courtship dances. However, exactly why females prefer certain traits over others is poorly understood. Female preferences in a given population often change across generations, and sometimes preferences differ among individuals within one population. Existing theories suggest that females prefer traits indicating genetic quality; that male traits and female preferences are linked in a positive feedback loop; or that females’ senses bias them towards certain traits. But no theory fully explains the variety of traits and preferences seen in nature.

To address this, researchers developed a mathematical model in which females learn which traits are attractive by watching others. In the model, young females observe the mate choices of adult females and learn to prefer traits that distinguish the chosen male from other males. In other words, females learned to prefer the rarest trait of a successful male, but this trait was not necessarily what the observed female was really choosing. Over several generations, female preferences caused rare male traits to become more common, which then made them less attractive. This helped to maintain variation in male traits, rather than a single attractive trait outcompeting the others.

The results of this mathematical model are consistent with several features of sexual selection in nature, such as rapid evolutionary changes, and the persistence of variation in male traits and female preferences. Animals use social information to make decisions in many contexts. Inferring the attractiveness of potential mates may be an extension of this general tendency, the authors say.

DuVal and her co-authors add, “While scientists have known for a long time that females can copy each other’s choice of mates, no one has previously considered that these copying females aren’t mind-readers.  When we considered that females can make mistakes in identifying what traits others find attractive, we found this produces patterns that have long puzzled biologists, for example maintaining variety in male traits and female preferences over time.”

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In your coverage, please use this URL to provide access to the freely available paper in PLOS Biologyhttp://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002269  

Citation: DuVal EH, Fitzpatrick CL, Hobson EA, Servedio MR (2023) Inferred Attractiveness: A generalized mechanism for sexual selection that can maintain variation in traits and preferences over time. PLoS Biol 21(10): e3002269. https://doi.org/10.1371/journal.pbio.3002269

Author Countries: United States

Funding: Financial support during preparation of this work was provided by National Science Foundation Integrative Organismal Systems award 1453408, Division of Biological Infrastructure award 1457541, and Division of Environmental Biology 2243423 (to EHD), National Institutes of Health T32 HD049336 (to CLF), National Science Foundation Integrative Organismal Systems award 2015932 and The Santa Fe Institute (to EAH), and National Science Foundation Division of Environmental Biology award 1939290 (to MRS). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

 

Carbon capture method plucks CO2 straight from the air


Using humidity-powered technology, researchers found several new ions that facilitate low-energy carbon sequestration


Peer-Reviewed Publication

NORTHWESTERN UNIVERSITY

Carbon capture with new ions 

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NEW IONS FACILITATED CARBON CAPTURE.

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CREDIT: DRAVID LAB / NORTHWESTERN UNIVERSITY




Even as the world slowly begins to decarbonize industrial processes, achieving lower concentrations of atmospheric carbon requires technologies that remove existing carbon dioxide from the atmosphere — rather than just prevent the creation of it.

Typical carbon capture catches CO2 directly from the source of a carbon-intensive process. Ambient carbon capture, or “direct air capture” (DAC) on the other hand, can take carbon out of typical environmental conditions and serves as one weapon in the battle against climate change, particularly as reliance on fossil fuels begins to decrease and with it, the need for point-of-source carbon capture.

New research from Northwestern University shows a novel approach to capture carbon from ambient environmental conditions that looks at the relationship between water and carbon dioxide in systems to inform the “moisture-swing” technique, which captures CO2 at low humidities and releases it at high humidities. The approach incorporates innovative kinetic methodologies and a diversity of ions, enabling carbon removal from virtually anywhere.

The study was published today (Oct. 3) in the journal Environmental Science and Technology.

“We are not only expanding and optimizing the choice of ions for carbon capture, but also helping unravel the fundamental underpinnings of complex fluid-surface interactions,” said Northwestern’s Vinayak P. Dravid, a senior author on the study. “This work advances our collective understanding of DAC, and our data and analyses provide a strong impetus to the community, for theorists and experimentalists alike, to further improve carbon capture under practical conditions.”

Dravid is the Abraham Harris Professor of Materials Science and Engineering at Northwestern’s McCormick School of Engineering and director of global initiatives at the International Institute for Nanotechnology. Ph.D. students, John Hegarty and Benjamin Shindel, were the paper’s co-first authors.

Shindel said the idea behind the paper came from a desire to use ambient environmental conditions to facilitate the reaction.

“We liked moisture-swing carbon capture because it doesn't have a defined energy cost,” Shindel said. “Even though there’s some amount of energy required to humidify a volume of air, ideally you could get humidity ‘for free,’ energetically, by relying on an environment that has natural dry and wet reservoirs of air close together.”

The group also expanded the number of ions used to make the reaction possible.

“Not only have we doubled the number of ions that exhibit the desired humidity-dependent carbon capture, we have also discovered the highest-performing systems yet,” John Hegarty said.

In recent years, moisture-swing capture has taken off. Traditional carbon capture methods use sorbents to capture CO2 at point-of-source locations, and then use heat or generated vacuums to release CO2 from the sorbent. It comes with a high-energy cost.

“Traditional carbon capture holds onto CO2 tightly, which means it takes significant energy to release it and reuse it,” Hegarty said.

It also doesn’t work everywhere, Shindel said. Agriculture, concrete and steel manufacturers, for example, are major contributors to emissions but take up large footprints that make it impossible to capture carbon at a single source.

Shindel added that wealthier countries should be attempting to get below zero emissions as developing countries, which rely more on the carbon economy, ramp down CO2 production.

Another senior author, chemistry professor Omar Farha, has experience exploring the role of metal-oxide framework (MOF) structures for diverse applications, including CO2 capture and sequestration.

“DAC is a complex and multifaceted problem that requires an interdisciplinary approach,” Farha said. “What I appreciate about this work is the detailed and careful measurements of complex parameters. Any proposed mechanism must explain these intricate observations."

Researchers in the past have zeroed in on carbonate and phosphate ions to facilitate moisture-swing capture and have specific hypotheses relating to why these specific ions are effective. But Dravid’s team wanted to test a wider breadth of ions to see which were the most effective. Overall, they found ions with the highest valency — mostly phosphates — were most effective and they began going down a list of polyvalent ions, ruling out some, as well as finding new ions that worked for this application, including silicate and borate.

The team believes that future experiments, coupled with computational modeling, will help better explain why certain ions are more effective than others.

There are already companies working to commercialize direct air carbon capture, using carbon credits to incentivize companies to offset their emissions. Many are capturing carbon that would already have been captured through activities such as modified agricultural practices, whereas this approach unambiguously sequesters CO2 directly from the atmosphere, where it could then be concentrated and ultimately stored or reused.

Dravid’s team plans to integrate such CO2 capturing materials with their earlier porous sponge platform, which has been developed to remove environmental toxins including oil, phosphates and microplastics.

The research on direct air capture of carbon dioxide was supported by the Department of Energy (DOE-BES DE-SC0022332), and made use of the SHyNE Resource facilities, supported by NSF-NNCI Program (NSF ECCS-2025633).