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    SMART researchers develop method for early detection of bacterial infection in crops

    Researchers from the Disruptive and Sustainable Technologies for Agricultural Precision (DiSTAP) Interdisciplinary Research Group (IRG) ofSingapore-MIT Alliance for Research and Technology (SMART), MIT’s research enterprise in Singapore, and their local collaborators from Temasek Life Sciences Laboratory (TLL), have developed a rapid Raman spectroscopy-based method for detecting and quantifying early bacterial infection in crops. The Raman spectral biomarkers and diagnostic algorithm enable the noninvasive and early diagnosis of bacterial infections in crop plants, which can be critical for the progress of plant disease management and agricultural productivity.

    Due to the increasing demand for global food supply and security, there is a growing need to improve agricultural production systems and increase crop productivity. Globally, bacterial pathogen infection in crop plants is one of the major contributors to agricultural yield losses. Climate change also adds to the problem by accelerating the spread of plant diseases. Hence, developing methods for rapid and early detection of pathogen-infected crops is important to improve plant disease management and reduce crop loss.

    The breakthrough by SMART and TLL researchers offers a faster and more accurate method to detect bacterial infection in crop plants at an earlier stage, as compared to existing techniques. The new results appear in a paper titled “Rapid detection and quantification of plant innate immunity response using Raman spectroscopy” published in the journal Frontiers in Plant Science.

    “The early detection of pathogen-infected crop plants is a significant step to improve plant disease management,” says Chua Nam Hai, DiSTAP co-lead principal investigator, professor, TLL deputy chair, and co-corresponding author. “It will allow the fast and selective removal of pathogen load and curb the further spread of disease to other neighboring crops.”

    Traditionally, plant disease diagnosis involves a simple visual inspection of plants for disease symptoms and severity. “Visual inspection methods are often ineffective, as disease symptoms usually manifest only at relatively later stages of infection, when the pathogen load is already high and reparative measures are limited. Hence, new methods are required for rapid and early detection of bacterial infection. The idea would be akin to having medical tests to identify human diseases at an early stage, instead of waiting for visual symptoms to show, so that early intervention or treatment can be applied,” says MIT Professor Rajeev Ram, who is a DiSTAP principal investigator and co-corresponding author on the paper.

    While existing techniques, such as current molecular detection methods, can detect bacterial infection in plants, they are often limited in their use. Molecular detection methods largely depend on the availability of pathogen-specific gene sequences or antibodies to identify bacterial infection in crops; the implementation is also time-consuming and nonadaptable for on-site field application due to the high cost and bulky equipment required, making it impractical for use in agricultural farms.

    “At DiSTAP, we have developed a quantitative Raman spectroscopy-based algorithm that can help farmers to identify bacterial infection rapidly. The developed diagnostic algorithm makes use of Raman spectral biomarkers and can be easily implemented in cloud-based computing and prediction platforms. It is more effective than existing techniques as it enables accurate identification and early detection of bacterial infection, both of which are crucial to saving crop plants that would otherwise be destroyed,” explains Gajendra Pratap Singh, scientific director and principal investigator at DiSTAP and co-lead author.

    A portable Raman system can be used on farms and provides farmers with an accurate and simple yes-or-no response when used to test for the presence of bacterial infections in crops. The development of this rapid and noninvasive method could improve plant disease management and have a transformative impact on agricultural farms by efficiently reducing agricultural yield loss and increasing productivity.

    “Using the diagnostic algorithm method, we experimented on several edible plants such as choy sum,” says DiSTAP and TLL principal investigator and co-corresponding author Rajani Sarojam. “The results showed that the Raman spectroscopy-based method can swiftly detect and quantify innate immunity response in plants infected with bacterial pathogens. We believe that this technology will be beneficial for agricultural farms to increase their productivity by reducing their yield loss due to plant diseases.”

    The researchers are currently working on the development of high-throughput, custom-made portable or hand-held Raman spectrometers that will allow Raman spectral analysis to be quickly and easily performed on field-grown crops.

    SMART and TLL developed and discovered the diagnostic algorithm and Raman spectral biomarkers. TLL also confirmed and validated the detection method through mutant plants. The research is carried out by SMART and supported by the National Research Foundation of Singapore under its Campus for Research Excellence And Technological Enterprise (CREATE) program.

    SMART was established by MIT and the NRF in 2007. The first entity in CREATE developed by NRF, SMART serves as an intellectual and innovation hub for research interactions between MIT and Singapore, undertaking cutting-edge research projects in areas of interest to both Singapore and MIT. SMART currently comprises an Innovation Center and five IRGs: Antimicrobial Resistance, Critical Analytics for Manufacturing Personalized-Medicine, DiSTAP, Future Urban Mobility, and Low Energy Electronic Systems. SMART research is funded by the NRF under the CREATE program.

    Led by Professor Michael Strano of MIT and Professor Chua Nam Hai of Temasek Lifesciences Laboratory, the DiSTAP program addresses deep problems in food production in Singapore and the world by developing a suite of impactful and novel analytical, genetic, and biomaterial technologies. The goal is to fundamentally change how plant biosynthetic pathways are discovered, monitored, engineered, and ultimately translated to meet the global demand for food and nutrients. Scientists from MIT, TTL, Nanyang Technological University, and National University of Singapore are collaboratively developing new tools for the continuous measurement of important plant metabolites and hormones for novel discovery, deeper understanding and control of plant biosynthetic pathways in ways not yet possible, especially in the context of green leafy vegetables; leveraging these new techniques to engineer plants with highly desirable properties for global food security, including high-yield density production, and drought and pathogen resistance; and applying these technologies to improve urban farming. More

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    At UN climate change conference, trying to “keep 1.5 alive”

    After a one-year delay caused by the Covid-19 pandemic, negotiators from nearly 200 countries met this month in Glasgow, Scotland, at COP26, the United Nations climate change conference, to hammer out a new global agreement to reduce greenhouse gas emissions and prepare for climate impacts. A delegation of approximately 20 faculty, staff, and students from MIT was on hand to observe the negotiations, share and conduct research, and launch new initiatives.

    On Saturday, Nov. 13, following two weeks of negotiations in the cavernous Scottish Events Campus, countries’ representatives agreed to the Glasgow Climate Pact. The pact reaffirms the goal of the 2015 Paris Agreement “to pursue efforts” to limit the global average temperature increase to 1.5 degrees Celsius above preindustrial levels, and recognizes that achieving this goal requires “reducing global carbon dioxide emissions by 45 percent by 2030 relative to the 2010 level and to net zero around mid-century.”

    “On issues like the need to reach net-zero emissions, reduce methane pollution, move beyond coal power, and tighten carbon accounting rules, the Glasgow pact represents some meaningful progress, but we still have so much work to do,” says Maria Zuber, MIT’s vice president for research, who led the Institute’s delegation to COP26. “Glasgow showed, once again, what a wicked complex problem climate change is, technically, economically, and politically. But it also underscored the determination of a global community of people committed to addressing it.”

    An “ambition gap”

    Both within the conference venue and at protests that spilled through the streets of Glasgow, one rallying cry was “keep 1.5 alive.” Alok Sharma, who was appointed by the UK government to preside over COP26, said in announcing the Glasgow pact: “We can now say with credibility that we have kept 1.5 degrees alive. But, its pulse is weak and it will only survive if we keep our promises and translate commitments into rapid action.”

    In remarks delivered during the first week of the conference, Sergey Paltsev, deputy director of MIT’s Joint Program on the Science and Policy of Global Change, presented findings from the latest MIT Global Change Outlook, which showed a wide gap between countries’ nationally determined contributions (NDCs) — the UN’s term for greenhouse gas emissions reduction pledges — and the reductions needed to put the world on track to meet the goals of the Paris Agreement and, now, the Glasgow pact.

    Pointing to this ambition gap, Paltsev called on all countries to do more, faster, to cut emissions. “We could dramatically reduce overall climate risk through more ambitious policy measures and investments,” says Paltsev. “We need to employ an integrated approach of moving to zero emissions in energy and industry, together with sustainable development and nature-based solutions, simultaneously improving human well-being and providing biodiversity benefits.”

    Finalizing the Paris rulebook

    A key outcome of COP26 (COP stands for “conference of the parties” to the UN Framework Convention on Climate Change, held for the 26th time) was the development of a set of rules to implement Article 6 of the Paris Agreement, which provides a mechanism for countries to receive credit for emissions reductions that they finance outside their borders, and to cooperate by buying and selling emissions reductions on international carbon markets.

    An agreement on this part of the Paris “rulebook” had eluded negotiators in the years since the Paris climate conference, in part because negotiators were concerned about how to prevent double-counting, wherein both buyers and sellers would claim credit for the emissions reductions.

    Michael Mehling, the deputy director of MIT’s Center for Energy and Environmental Policy Research (CEEPR) and an expert on international carbon markets, drew on a recent CEEPR working paper to describe critical negotiation issues under Article 6 during an event at the conference on Nov. 10 with climate negotiators and private sector representatives.

    He cited research that finds that Article 6, by leveraging the cost-efficiency of global carbon markets, could cut in half the cost that countries would incur to achieve their nationally determined contributions. “Which, seen from another angle, means you could double the ambition of these NDCs at no additional cost,” Mehling noted in his talk, adding that, given the persistent ambition gap, “any such opportunity is bitterly needed.”

    Andreas Haupt, a graduate student in the Institute for Data, Systems, and Society, joined MIT’s COP26 delegation to follow Article 6 negotiations. Haupt described the final days of negotiations over Article 6 as a “roller coaster.” Once negotiators reached an agreement, he says, “I felt relieved, but also unsure how strong of an effect the new rules, with all their weaknesses, will have. I am curious and hopeful regarding what will happen in the next year until the next large-scale negotiations in 2022.”

    Nature-based climate solutions

    World leaders also announced new agreements on the sidelines of the formal UN negotiations. One such agreement, a declaration on forests signed by more than 100 countries, commits to “working collectively to halt and reverse forest loss and land degradation by 2030.”

    A team from MIT’s Environmental Solutions Initiative (ESI), which has been working with policymakers and other stakeholders on strategies to protect tropical forests and advance other nature-based climate solutions in Latin America, was at COP26 to discuss their work and make plans for expanding it.

    Marcela Angel, a research associate at ESI, moderated a panel discussion featuring John Fernández, professor of architecture and ESI’s director, focused on protecting and enhancing natural carbon sinks, particularly tropical forests such as the Amazon that are at risk of deforestation, forest degradation, and biodiversity loss.

    “Deforestation and associated land use change remain one of the main sources of greenhouse gas emissions in most Amazonian countries, such as Brazil, Peru, and Colombia,” says Angel. “Our aim is to support these countries, whose nationally determined contributions depend on the effectiveness of policies to prevent deforestation and promote conservation, with an approach based on the integration of targeted technology breakthroughs, deep community engagement, and innovative bioeconomic opportunities for local communities that depend on forests for their livelihoods.”

    Energy access and renewable energy

    Worldwide, an estimated 800 million people lack access to electricity, and billions more have only limited or erratic electrical service. Providing universal access to energy is one of the UN’s sustainable development goals, creating a dual challenge: how to boost energy access without driving up greenhouse gas emissions.

    Rob Stoner, deputy director for science and technology of the MIT Energy Initiative (MITEI), and Ignacio Pérez-Arriaga, a visiting professor at the Sloan School of Management, attended COP26 to share their work as members of the Global Commission to End Energy Poverty, a collaboration between MITEI and the Rockefeller Foundation. It brings together global energy leaders from industry, the development finance community, academia, and civil society to identify ways to overcome barriers to investment in the energy sectors of countries with low energy access.

    The commission’s work helped to motivate the formation, announced at COP26 on Nov. 2, of the Global Energy Alliance for People and Planet, a multibillion-dollar commitment by the Rockefeller and IKEA foundations and Bezos Earth Fund to support access to renewable energy around the world.

    Another MITEI member of the COP26 delegation, Martha Broad, the initiative’s executive director, spoke about MIT research to inform the U.S. goal of scaling offshore wind energy capacity from approximately 30 megawatts today to 30 gigawatts by 2030, including significant new capacity off the coast of New England.

    Broad described research, funded by MITEI member companies, on a coating that can be applied to the blades of wind turbines to prevent icing that would require the turbines’ shutdown; the use of machine learning to inform preventative turbine maintenance; and methodologies for incorporating the effects of climate change into projections of future wind conditions to guide wind farm siting decisions today. She also spoke broadly about the need for public and private support to scale promising innovations.

    “Clearly, both the public sector and the private sector have a role to play in getting these technologies to the point where we can use them in New England, and also where we can deploy them affordably for the developing world,” Broad said at an event sponsored by America Is All In, a coalition of nonprofit and business organizations.

    Food and climate alliance

    Food systems around the world are increasingly at risk from the impacts of climate change. At the same time, these systems, which include all activities from food production to consumption and food waste, are responsible for about one-third of the human-caused greenhouse gas emissions warming the planet.

    At COP26, MIT’s Abdul Latif Jameel Water and Food Systems Lab announced the launch of a new alliance to drive research-based innovation that will make food systems more resilient and sustainable, called the Food and Climate Systems Transformation (FACT) Alliance. With 16 member institutions, the FACT Alliance will better connect researchers to farmers, food businesses, policymakers, and other food systems stakeholders around the world.

    Looking ahead

    By the end of 2022, the Glasgow pact asks countries to revisit their nationally determined contributions and strengthen them to bring them in line with the temperature goals of the Paris Agreement. The pact also “notes with deep regret” the failure of wealthier countries to collectively provide poorer countries $100 billion per year in climate financing that they pledged in 2009 to begin in 2020.

    These and other issues will be on the agenda for COP27, to be held in Sharm El-Sheikh, Egypt, next year.

    “Limiting warming to 1.5 degrees is broadly accepted as a critical goal to avoiding worsening climate consequences, but it’s clear that current national commitments will not get us there,” says ESI’s Fernández. “We will need stronger emissions reductions pledges, especially from the largest greenhouse gas emitters. At the same time, expanding creativity, innovation, and determination from every sector of society, including research universities, to get on with real-world solutions is essential. At Glasgow, MIT was front and center in energy systems, cities, nature-based solutions, and more. The year 2030 is right around the corner so we can’t afford to let up for one minute.” More

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    J-WAFS launches Food and Climate Systems Transformation Alliance

    Food systems around the world are increasingly at risk from the impacts of climate change. At the same time, these systems, which include all activities from food production to consumption and food waste, are responsible for about one-third of the human-caused greenhouse gas emissions warming the planet. 

    To drive research-based innovation that will make food systems more resilient and sustainable, MIT’s Abdul Latif Jameel Water and Food Systems Lab (J-WAFS) announced the launch of a new initiative at an event during the UN Climate Change Conference in Glasgow, Scotland, last week. The initiative, called the Food and Climate Systems Transformation (FACT) Alliance, will better connect researchers to farmers, food businesses, policymakers, and other food systems stakeholders around the world. 

    “Time is not on our side,” says Greg Sixt, the director of the FACT Alliance and research manager for food and climate systems at J-WAFS. “To date, the research community hasn’t delivered actionable solutions quickly enough or in the policy-relevant form needed if time-critical changes are to be made to our food systems. The FACT Alliance aims to change this.”

    Why, in fact, do our food systems need transformation?

    At COP26 (which stands for “conference of the parties” to the UN Framework Convention on Climate Change, being held for the 26th time this year), a number of countries have pledged to end deforestation, reduce methane emissions, and cease public financing of coal power. In his keynote address at the FACT Alliance event, Professor Pete Smith of the University of Aberdeen, an alliance member institution, noted that food and agriculture also need to be addressed because “there’s an interaction between climate change and the food system.” 

    The UN Intergovernmental Panel on Climate Change warns that a two-degree Celsius increase in average global temperature over preindustrial levels could trigger a worldwide food crisis, and emissions from food systems alone could push us past the two-degree mark even if energy-related emissions could be zeroed out. 

    Smith said dramatic and rapid transformations are needed to deliver safe, nutritious food for all, with reduced environmental impact and increased resilience to climate change. With a global network of leading research institutions and collaborating stakeholder organizations, the FACT Alliance aims to facilitate new, solutions-oriented research for addressing the most challenging aspects of food systems in the era of climate change. 

    How the FACT Alliance works

    Central to the work of the FACT Alliance is the development of new methodologies for aligning data across scales and food systems components, improving data access, integrating research across the diverse disciplines that address aspects of food systems, making stakeholders partners in the research process, and assessing impact in the context of complex and interconnected food and climate systems. 

    The FACT Alliance will conduct what’s known as “convergence research,” which meets complex problems with approaches that embody deep integration across disciplines. This kind of research calls for close association with the stakeholders who both make decisions and are directly affected by how food systems work, be they farmers, extension services (i.e., agricultural advisories), policymakers, international aid organizations, consumers, or others. By inviting stakeholders and collaborators to be part of the research process, the FACT Alliance allows for engagement at the scale, geography, and scope that is most relevant to the needs of each, integrating global and local teams to achieve better outcomes. 

    “Doing research in isolation of all the stakeholders and in isolation of the goals that we want to achieve will not deliver the transformation that we need,” said Smith. “The problem is too big for us to solve in isolation, and we need broad alliances to tackle the issue, and that’s why we developed the FACT Alliance.” 

    Members and collaborators

    Led by MIT’s J-WAFS, the FACT Alliance is currently made up of 16 core members and an associated network of collaborating stakeholder organizations. 

    “As the central convener of MIT research on food systems, J-WAFS catalyzes collaboration across disciplines,” says Maria Zuber, vice president for research at MIT. “Now, by bringing together a world-class group of research institutions and stakeholders from key sectors, the FACT Alliance aims to advance research that will help alleviate climate impacts on food systems and mitigate food system impacts on climate.”

    J-WAFS co-hosted the COP26 event “Bridging the Science-Policy Gap for Impactful, Demand-Driven Food Systems Innovation” with Columbia University, the American University of Beirut, and the CGIAR research program Climate Change, Agriculture and Food Security (CCAFS). The event featured a panel discussion with several FACT Alliance members and the UK Foreign, Commonwealth and Development Office (FCDO). More

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    Saving seaweed with machine learning

    Last year, Charlene Xia ’17, SM ’20 found herself at a crossroads. She was finishing up her master’s degree in media arts and sciences from the MIT Media Lab and had just submitted applications to doctoral degree programs. All Xia could do was sit and wait. In the meantime, she narrowed down her career options, regardless of whether she was accepted to any program.

    “I had two thoughts: I’m either going to get a PhD to work on a project that protects our planet, or I’m going to start a restaurant,” recalls Xia.

    Xia poured over her extensive cookbook collection, researching international cuisines as she anxiously awaited word about her graduate school applications. She even looked into the cost of a food truck permit in the Boston area. Just as she started hatching plans to open a plant-based skewer restaurant, Xia received word that she had been accepted into the mechanical engineering graduate program at MIT.

    Shortly after starting her doctoral studies, Xia’s advisor, Professor David Wallace, approached her with an interesting opportunity. MathWorks, a software company known for developing the MATLAB computing platform, had announced a new seed funding program in MIT’s Department of Mechanical Engineering. The program encouraged collaborative research projects focused on the health of the planet.

    “I saw this as a super-fun opportunity to combine my passion for food, my technical expertise in ocean engineering, and my interest in sustainably helping our planet,” says Xia.

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    From MIT Mechanical Engineering: “Saving Seaweed with Machine Learning”

    Wallace knew Xia would be up to the task of taking an interdisciplinary approach to solve an issue related to the health of the planet. “Charlene is a remarkable student with extraordinary talent and deep thoughtfulness. She is pretty much fearless, embracing challenges in almost any domain with the well-founded belief that, with effort, she will become a master,” says Wallace.

    Alongside Wallace and Associate Professor Stefanie Mueller, Xia proposed a project to predict and prevent the spread of diseases in aquaculture. The team focused on seaweed farms in particular.

    Already popular in East Asian cuisines, seaweed holds tremendous potential as a sustainable food source for the world’s ever-growing population. In addition to its nutritive value, seaweed combats various environmental threats. It helps fight climate change by absorbing excess carbon dioxide in the atmosphere, and can also absorb fertilizer run-off, keeping coasts cleaner.

    As with so much of marine life, seaweed is threatened by the very thing it helps mitigate against: climate change. Climate stressors like warm temperatures or minimal sunlight encourage the growth of harmful bacteria such as ice-ice disease. Within days, entire seaweed farms are decimated by unchecked bacterial growth.

    To solve this problem, Xia turned to the microbiota present in these seaweed farms as a predictive indicator of any threat to the seaweed or livestock. “Our project is to develop a low-cost device that can detect and prevent diseases before they affect seaweed or livestock by monitoring the microbiome of the environment,” says Xia.

    The team pairs old technology with the latest in computing. Using a submersible digital holographic microscope, they take a 2D image. They then use a machine learning system known as a neural network to convert the 2D image into a representation of the microbiome present in the 3D environment.

    “Using a machine learning network, you can take a 2D image and reconstruct it almost in real time to get an idea of what the microbiome looks like in a 3D space,” says Xia.

    The software can be run in a small Raspberry Pi that could be attached to the holographic microscope. To figure out how to communicate these data back to the research team, Xia drew upon her master’s degree research.

    In that work, under the guidance of Professor Allan Adams and Professor Joseph Paradiso in the Media Lab, Xia focused on developing small underwater communication devices that can relay data about the ocean back to researchers. Rather than the usual $4,000, these devices were designed to cost less than $100, helping lower the cost barrier for those interested in uncovering the many mysteries of our oceans. The communication devices can be used to relay data about the ocean environment from the machine learning algorithms.

    By combining these low-cost communication devices along with microscopic images and machine learning, Xia hopes to design a low-cost, real-time monitoring system that can be scaled to cover entire seaweed farms.

    “It’s almost like having the ‘internet of things’ underwater,” adds Xia. “I’m developing this whole underwater camera system alongside the wireless communication I developed that can give me the data while I’m sitting on dry land.”

    Armed with these data about the microbiome, Xia and her team can detect whether or not a disease is about to strike and jeopardize seaweed or livestock before it is too late.

    While Xia still daydreams about opening a restaurant, she hopes the seaweed project will prompt people to rethink how they consider food production in general.

    “We should think about farming and food production in terms of the entire ecosystem,” she says. “My meta-goal for this project would be to get people to think about food production in a more holistic and natural way.” More

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    How diet affects tumors

    In recent years, there has been some evidence that dietary interventions can help to slow the growth of tumors. A new study from MIT, which analyzed two different diets in mice, reveals how those diets affect cancer cells, and offers an explanation for why restricting calories may slow tumor growth.

    The study examined the effects of a calorically restricted diet and a ketogenic diet in mice with pancreatic tumors. While both of these diets reduce the amount of sugar available to tumors, the researchers found that only the calorically restricted diet reduced the availability of fatty acids, and this was linked to a slowdown in tumor growth.

    The findings do not suggest that cancer patients should try to follow either of these diets, the researchers say. Instead, they believe the findings warrant further study to determine how dietary interventions might be combined with existing or emerging drugs to help patients with cancer.

    “There’s a lot of evidence that diet can affect how fast your cancer progresses, but this is not a cure,” says Matthew Vander Heiden, director of MIT’s Koch Institute for Integrative Cancer Research and the senior author of the study. “While the findings are provocative, further study is needed, and individual patients should talk to their doctor about the right dietary interventions for their cancer.”

    MIT postdoc Evan Lien is the lead author of the paper, which appears today in Nature.

    Metabolic mechanism

    Vander Heiden, who is also a medical oncologist at Dana-Farber Cancer Institute, says his patients often ask him about the potential benefits of various diets, but there is not enough scientific evidence available to offer any definitive advice. Many of the dietary questions that patients have focus on either a calorie-restricted diet, which reduces calorie consumption by 25 to 50 percent, or a ketogenic diet, which is low in carbohydrates and high in fat and protein.

    Previous studies have suggested that a calorically restricted diet might slow tumor growth in some contexts, and such a diet has been shown to extend lifespan in mice and many other animal species. A smaller number of studies exploring the effects of a ketogenic diet on cancer have produced inconclusive results.

    “A lot of the advice or cultural fads that are out there aren’t necessarily always based on very good science,” Lien says. “It seemed like there was an opportunity, especially with our understanding of cancer metabolism having evolved so much over the past 10 years or so, that we could take some of the biochemical principles that we’ve learned and apply those concepts to understanding this complex question.”

    Cancer cells consume a great deal of glucose, so some scientists had hypothesized that either the ketogenic diet or calorie restriction might slow tumor growth by reducing the amount of glucose available. However, the MIT team’s initial experiments in mice with pancreatic tumors showed that calorie restriction has a much greater effect on tumor growth than the ketogenic diet, so the researchers suspected that glucose levels were not playing a major role in the slowdown.

    To dig deeper into the mechanism, the researchers analyzed tumor growth and nutrient concentration in mice with pancreatic tumors, which were fed either a normal, ketogenic, or calorie-restricted diet. In both the ketogenic and calorie-restricted mice, glucose levels went down. In the calorie-restricted mice, lipid levels also went down, but in mice on the ketogenic diet, they went up.

    Lipid shortages impair tumor growth because cancer cells need lipids to construct their cell membranes. Normally, when lipids aren’t available in a tissue, cells can make their own. As part of this process, they need to maintain the right balance of saturated and unsaturated fatty acids, which requires an enzyme called stearoyl-CoA desaturase (SCD). This enzyme is responsible for converting saturated fatty acids into unsaturated fatty acids.

    Both calorie-restricted and ketogenic diets reduce SCD activity, but mice on the ketogenic diet had lipids available to them from their diet, so they didn’t need to use SCD. Mice on the calorie-restricted diet, however, couldn’t get fatty acids from their diet or produce their own. In these mice, tumor growth slowed significantly, compared to mice on the ketogenic diet.

    “Not only does caloric restriction starve tumors of lipids, it also impairs the process that allows them to adapt to it. That combination is really contributing to the inhibition of tumor growth,” Lien says.

    Dietary effects

    In addition to their mouse research, the researchers also looked at some human data. Working with Brian Wolpin, an oncologist at Dana-Farber Cancer Institute and an author of the paper, the team obtained data from a large cohort study that allowed them to analyze the relationship between dietary patterns and survival times in pancreatic cancer patients. From that study, the researchers found that the type of fat consumed appears to influence how patients on a low-sugar diet fare after a pancreatic cancer diagnosis, although the data are not complete enough to draw any conclusions about the effect of diet, the researchers say.

    Although this study showed that calorie restriction has beneficial effects in mice, the researchers say they do not recommend that cancer patients follow a calorie-restricted diet, which is difficult to maintain and can have harmful side effects. However, they believe that cancer cells’ dependence on the availability of unsaturated fatty acids could be exploited to develop drugs that might help slow tumor growth.

    One possible therapeutic strategy could be inhibition of the SCD enzyme, which would cut off tumor cells’ ability to produce unsaturated fatty acids.

    “The purpose of these studies isn’t necessarily to recommend a diet, but it’s to really understand the underlying biology,” Lien says. “They provide some sense of the mechanisms of how these diets work, and that can lead to rational ideas on how we might mimic those situations for cancer therapy.”

    The researchers now plan to study how diets with a variety of fat sources — including plant or animal-based fats with defined differences in saturated, monounsaturated, and polyunsaturated fatty acid content — alter tumor fatty acid metabolism and the ratio of unsaturated to saturated fatty acids.

    The research was funded by the Damon Runyon Cancer Research Foundation, the National Institutes of Health, the Lustgarten Foundation, the Dana-Farber Cancer Institute Hale Family Center for Pancreatic Cancer Research, Stand Up to Cancer, the Pancreatic Cancer Action Network, the Noble Effort Fund, the Wexler Family Fund, Promises for Purple, the Bob Parsons Fund, the Emerald Foundation, the Howard Hughes Medical Institute, the MIT Center for Precision Cancer Medicine, and the Ludwig Center at MIT. More

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    New “risk triage” platform pinpoints compounding threats to US infrastructure

    Over a 36-hour period in August, Hurricane Henri delivered record rainfall in New York City, where an aging storm-sewer system was not built to handle the deluge, resulting in street flooding. Meanwhile, an ongoing drought in California continued to overburden aquifers and extend statewide water restrictions. As climate change amplifies the frequency and intensity of extreme events in the United States and around the world, and the populations and economies they threaten grow and change, there is a critical need to make infrastructure more resilient. But how can this be done in a timely, cost-effective way?

    An emerging discipline called multi-sector dynamics (MSD) offers a promising solution. MSD homes in on compounding risks and potential tipping points across interconnected natural and human systems. Tipping points occur when these systems can no longer sustain multiple, co-evolving stresses, such as extreme events, population growth, land degradation, drinkable water shortages, air pollution, aging infrastructure, and increased human demands. MSD researchers use observations and computer models to identify key precursory indicators of such tipping points, providing decision-makers with critical information that can be applied to mitigate risks and boost resilience in infrastructure and managed resources.

    At MIT, the Joint Program on the Science and Policy of Global Change has since 2018 been developing MSD expertise and modeling tools and using them to explore compounding risks and potential tipping points in selected regions of the United States. In a two-hour webinar on Sept. 15, MIT Joint Program researchers presented an overview of the program’s MSD research tool set and its applications.  

    MSD and the risk triage platform

    “Multi-sector dynamics explores interactions and interdependencies among human and natural systems, and how these systems may adapt, interact, and co-evolve in response to short-term shocks and long-term influences and stresses,” says MIT Joint Program Deputy Director C. Adam Schlosser, noting that such analysis can reveal and quantify potential risks that would likely evade detection in siloed investigations. “These systems can experience cascading effects or failures after crossing tipping points. The real question is not just where these tipping points are in each system, but how they manifest and interact across all systems.”

    To address that question, the program’s MSD researchers have developed the MIT Socio-Environmental Triage (MST) platform, now publicly available for the first time. Focused on the continental United States, the first version of the platform analyzes present-day risks related to water, land, climate, the economy, energy, demographics, health, and infrastructure, and where these compound to create risk hot spots. It’s essentially a screening-level visualization tool that allows users to examine risks, identify hot spots when combining risks, and make decisions about how to deploy more in-depth analysis to solve complex problems at regional and local levels. For example, MST can identify hot spots for combined flood and poverty risks in the lower Mississippi River basin, and thereby alert decision-makers as to where more concentrated flood-control resources are needed.

    Successive versions of the platform will incorporate projections based on the MIT Joint Program’s Integrated Global System Modeling (IGSM) framework of how different systems and stressors may co-evolve into the future and thereby change the risk landscape. This enhanced capability could help uncover cost-effective pathways for mitigating and adapting to a wide range of environmental and economic risks.  

    MSD applications

    Five webinar presentations explored how MIT Joint Program researchers are applying the program’s risk triage platform and other MSD modeling tools to identify potential tipping points and risks in five key domains: water quality, land use, economics and energy, health, and infrastructure. 

    Joint Program Principal Research Scientist Xiang Gao described her efforts to apply a high-resolution U.S. water-quality model to calculate a location-specific, water-quality index over more than 2,000 river basins in the country. By accounting for interactions among climate, agriculture, and socioeconomic systems, various water-quality measures can be obtained ranging from nitrate and phosphate levels to phytoplankton concentrations. This modeling approach advances a unique capability to identify potential water-quality risk hot spots for freshwater resources.

    Joint Program Research Scientist Angelo Gurgel discussed his MSD-based analysis of how climate change, population growth, changing diets, crop-yield improvements and other forces that drive land-use change at the global level may ultimately impact how land is used in the United States. Drawing upon national observational data and the IGSM framework, the analysis shows that while current U.S. land-use trends are projected to persist or intensify between now and 2050, there is no evidence of any concerning tipping points arising throughout this period.  

    MIT Joint Program Research Scientist Jennifer Morris presented several examples of how the risk triage platform can be used to combine existing U.S. datasets and the IGSM framework to assess energy and economic risks at the regional level. For example, by aggregating separate data streams on fossil-fuel employment and poverty, one can target selected counties for clean energy job training programs as the nation moves toward a low-carbon future. 

    “Our modeling and risk triage frameworks can provide pictures of current and projected future economic and energy landscapes,” says Morris. “They can also highlight interactions among different human, built, and natural systems, including compounding risks that occur in the same location.”  

    MIT Joint Program research affiliate Sebastian Eastham, a research scientist at the MIT Laboratory for Aviation and the Environment, described an MSD approach to the study of air pollution and public health. Linking the IGSM with an atmospheric chemistry model, Eastham ultimately aims to better understand where the greatest health risks are in the United States and how they may compound throughout this century under different policy scenarios. Using the risk triage tool to combine current risk metrics for air quality and poverty in a selected county based on current population and air-quality data, he showed how one can rapidly identify cardiovascular and other air-pollution-induced disease risk hot spots.

    Finally, MIT Joint Program research affiliate Alyssa McCluskey, a lecturer at the University of Colorado at Boulder, showed how the risk triage tool can be used to pinpoint potential risks to roadways, waterways, and power distribution lines from flooding, extreme temperatures, population growth, and other stressors. In addition, McCluskey described how transportation and energy infrastructure development and expansion can threaten critical wildlife habitats.

    Enabling comprehensive, location-specific analyses of risks and hot spots within and among multiple domains, the Joint Program’s MSD modeling tools can be used to inform policymaking and investment from the municipal to the global level.

    “MSD takes on the challenge of linking human, natural, and infrastructure systems in order to inform risk analysis and decision-making,” says Schlosser. “Through our risk triage platform and other MSD models, we plan to assess important interactions and tipping points, and to provide foresight that supports action toward a sustainable, resilient, and prosperous world.”

    This research is funded by the U.S. Department of Energy’s Office of Science as an ongoing project. More

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    Research collaboration puts climate-resilient crops in sight

    Any houseplant owner knows that changes in the amount of water or sunlight a plant receives can put it under immense stress. A dying plant brings certain disappointment to anyone with a green thumb. 

    But for farmers who make their living by successfully growing plants, and whose crops may nourish hundreds or thousands of people, the devastation of failing flora is that much greater. As climate change is poised to cause increasingly unpredictable weather patterns globally, crops may be subject to more extreme environmental conditions like droughts, fluctuating temperatures, floods, and wildfire. 

    Climate scientists and food systems researchers worry about the stress climate change may put on crops, and on global food security. In an ambitious interdisciplinary project funded by the Abdul Latif Jameel Water and Food Systems Lab (J-WAFS), David Des Marais, the Gale Assistant Professor in the Department of Civil and Environmental Engineering at MIT, and Caroline Uhler, an associate professor in the MIT Department of Electrical Engineering and Computer Science and the Institute for Data, Systems, and Society, are investigating how plant genes communicate with one another under stress. Their research results can be used to breed plants more resilient to climate change.

    Crops in trouble

    Governing plants’ responses to environmental stress are gene regulatory networks, or GRNs, which guide the development and behaviors of living things. A GRN may be comprised of thousands of genes and proteins that all communicate with one another. GRNs help a particular cell, tissue, or organism respond to environmental changes by signaling certain genes to turn their expression on or off.

    Even seemingly minor or short-term changes in weather patterns can have large effects on crop yield and food security. An environmental trigger, like a lack of water during a crucial phase of plant development, can turn a gene on or off, and is likely to affect many others in the GRN. For example, without water, a gene enabling photosynthesis may switch off. This can create a domino effect, where the genes that rely on those regulating photosynthesis are silenced, and the cycle continues. As a result, when photosynthesis is halted, the plant may experience other detrimental side effects, like no longer being able to reproduce or defend against pathogens. The chain reaction could even kill a plant before it has the chance to be revived by a big rain.

    Des Marais says he wishes there was a way to stop those genes from completely shutting off in such a situation. To do that, scientists would need to better understand how exactly gene networks respond to different environmental triggers. Bringing light to this molecular process is exactly what he aims to do in this collaborative research effort.

    Solving complex problems across disciplines

    Despite their crucial importance, GRNs are difficult to study because of how complex and interconnected they are. Usually, to understand how a particular gene is affecting others, biologists must silence one gene and see how the others in the network respond. 

    For years, scientists have aspired to an algorithm that could synthesize the massive amount of information contained in GRNs to “identify correct regulatory relationships among genes,” according to a 2019 article in the Encyclopedia of Bioinformatics and Computational Biology. 

    “A GRN can be seen as a large causal network, and understanding the effects that silencing one gene has on all other genes requires understanding the causal relationships among the genes,” says Uhler. “These are exactly the kinds of algorithms my group develops.”

    Des Marais and Uhler’s project aims to unravel these complex communication networks and discover how to breed crops that are more resilient to the increased droughts, flooding, and erratic weather patterns that climate change is already causing globally.

    In addition to climate change, by 2050, the world will demand 70 percent more food to feed a booming population. “Food systems challenges cannot be addressed individually in disciplinary or topic area silos,” says Greg Sixt, J-WAFS’ research manager for climate and food systems. “They must be addressed in a systems context that reflects the interconnected nature of the food system.”

    Des Marais’ background is in biology, and Uhler’s in statistics. “Dave’s project with Caroline was essentially experimental,” says Renee J. Robins, J-WAFS’ executive director. “This kind of exploratory research is exactly what the J-WAFS seed grant program is for.”

    Getting inside gene regulatory networks

    Des Marais and Uhler’s work begins in a windowless basement on MIT’s campus, where 300 genetically identical Brachypodium distachyon plants grow in large, temperature-controlled chambers. The plant, which contains more than 30,000 genes, is a good model for studying important cereal crops like wheat, barley, maize, and millet. For three weeks, all plants receive the same temperature, humidity, light, and water. Then, half are slowly tapered off water, simulating drought-like conditions.

    Six days into the forced drought, the plants are clearly suffering. Des Marais’ PhD student Jie Yun takes tissues from 50 hydrated and 50 dry plants, freezes them in liquid nitrogen to immediately halt metabolic activity, grinds them up into a fine powder, and chemically separates the genetic material. The genes from all 100 samples are then sequenced at a lab across the street.

    The team is left with a spreadsheet listing the 30,000 genes found in each of the 100 plants at the moment they were frozen, and how many copies there were. Uhler’s PhD student Anastasiya Belyaeva inputs the massive spreadsheet into the computer program she developed and runs her novel algorithm. Within a few hours, the group can see which genes were most active in one condition over another, how the genes were communicating, and which were causing changes in others. 

    The methodology captures important subtleties that could allow researchers to eventually alter gene pathways and breed more resilient crops. “When you expose a plant to drought stress, it’s not like there’s some canonical response,” Des Marais says. “There’s lots of things going on. It’s turning this physiologic process up, this one down, this one didn’t exist before, and now suddenly is turned on.” 

    In addition to Des Marais and Uhler’s research, J-WAFS has funded projects in food and water from researchers in 29 departments across all five MIT schools as well as the MIT Schwarzman College of Computing. J-WAFS seed grants typically fund seven to eight new projects every year.

    “The grants are really aimed at catalyzing new ideas, providing the sort of support [for MIT researchers] to be pushing boundaries, and also bringing in faculty who may have some interesting ideas that they haven’t yet applied to water or food concerns,” Robins says. “It’s an avenue for researchers all over the Institute to apply their ideas to water and food.”

    Alison Gold is a student in MIT’s Graduate Program in Science Writing. More

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    Researchers design sensors to rapidly detect plant hormones

    Researchers from the Disruptive and Sustainable Technologies for Agricultural Precision (DiSTAP) interdisciplinary research group of the Singapore-MIT Alliance for Research and Technology (SMART), MIT’s research enterprise in Singapore, and their local collaborators from Temasek Life Sciences Laboratory (TLL) and Nanyang Technological University (NTU), have developed the first-ever nanosensor to enable rapid testing of synthetic auxin plant hormones. The novel nanosensors are safer and less tedious than existing techniques for testing plants’ response to compounds such as herbicide, and can be transformative in improving agricultural production and our understanding of plant growth.

    The scientists designed sensors for two plant hormones — 1-naphthalene acetic acid (NAA) and 2,4-dichlorophenoxyacetic acid (2,4-D) — which are used extensively in the farming industry for regulating plant growth and as herbicides, respectively. Current methods to detect NAA and 2,4-D cause damage to plants, and are unable to provide real-time in vivo monitoring and information.

    Based on the concept of corona phase molecular recognition (​​CoPhMoRe) pioneered by the Strano Lab at SMART DiSTAP and MIT, the new sensors are able to detect the presence of NAA and 2,4-D in living plants at a swift pace, providing plant information in real-time, without causing any harm. The team has successfully tested both sensors on a number of everyday crops including pak choi, spinach, and rice across various planting mediums such as soil, hydroponic, and plant tissue culture.

    Explained in a paper titled “Nanosensor Detection of Synthetic Auxins In Planta using Corona Phase Molecular Recognition” published in the journal ACS Sensors, the research can facilitate more efficient use of synthetic auxins in agriculture and hold tremendous potential to advance plant biology study.

    “Our CoPhMoRe technique has previously been used to detect compounds such as hydrogen peroxide and heavy-metal pollutants like arsenic — but this is the first successful case of CoPhMoRe sensors developed for detecting plant phytohormones that regulate plant growth and physiology, such as sprays to prevent premature flowering and dropping of fruits,” says DiSTAP co-lead principal investigator Michael Strano, the Carbon P. Dubbs Professor of Chemical Engineering at MIT. “This technology can replace current state-of-the-art sensing methods which are laborious, destructive, and unsafe.”

    Of the two sensors developed by the research team, the 2,4-D nanosensor also showed the ability to detect herbicide susceptibility, enabling farmers and agricultural scientists to quickly find out how vulnerable or resistant different plants are to herbicides without the need to monitor crop or weed growth over days. “This could be incredibly beneficial in revealing the mechanism behind how 2,4-D works within plants and why crops develop herbicide resistance,” says DiSTAP and TLL Principal Investigator Rajani Sarojam.

    “Our research can help the industry gain a better understanding of plant growth dynamics and has the potential to completely change how the industry screens for herbicide resistance, eliminating the need to monitor crop or weed growth over days,” says Mervin Chun-Yi Ang, a research scientist at DiSTAP. “It can be applied across a variety of plant species and planting mediums, and could easily be used in commercial setups for rapid herbicide susceptibility testing, such as urban farms.”

    NTU Professor Mary Chan-Park Bee Eng says, “Using nanosensors for in planta detection eliminates the need for extensive extraction and purification processes, which saves time and money. They also use very low-cost electronics, which makes them easily adaptable for commercial setups.”

    The team says their research can lead to future development of real-time nanosensors for other dynamic plant hormones and metabolites in living plants as well.

    The development of the nanosensor, optical detection system, and image processing algorithms for this study was done by SMART, NTU, and MIT, while TLL validated the nanosensors and provided knowledge of plant biology and plant signaling mechanisms. The research is carried out by SMART and supported by NRF under its Campus for Research Excellence And Technological Enterprise (CREATE) program.

    DiSTAP is one of the five interdisciplinary research roups in SMART. The DiSTAP program addresses deep problems in food production in Singapore and the world by developing a suite of impactful and novel analytical, genetic, and biosynthetic technologies. The goal is to fundamentally change how plant biosynthetic pathways are discovered, monitored, engineered, and ultimately translated to meet the global demand for food and nutrients.

    Scientists from MIT, TTL, NTU, and National University of Singapore (NUS) are collaboratively developing new tools for the continuous measurement of important plant metabolites and hormones for novel discovery, deeper understanding and control of plant biosynthetic pathways in ways not yet possible, especially in the context of green leafy vegetables; leveraging these new techniques to engineer plants with highly desirable properties for global food security, including high yield density production, drought, and pathogen resistance and biosynthesis of high-value commercial products; developing tools for producing hydrophobic food components in industry-relevant microbes; developing novel microbial and enzymatic technologies to produce volatile organic compounds that can protect and/or promote growth of leafy vegetables; and applying these technologies to improve urban farming.

    DiSTAP is led by Michael Strano and Singapore co-lead principal investigator Professor Chua Nam Hai.

    SMART was established by MIT, in partnership with the NRF, in 2007. SMART, the first entity in CREATE, serves as an intellectual and innovation hub for research interactions between MIT and Singapore, undertaking cutting-edge research projects in areas of interest to both. SMART currently comprises an Innovation Center and five interdisciplinary research groups: Antimicrobial Resistance (AMR), Critical Analytics for Manufacturing Personalized-Medicine (CAMP), DiSTAP, Future Urban Mobility (FM), and Low Energy Electronic Systems (LEES). SMART is funded by the NRF. More