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    Angela Belcher delivers 2023 Dresselhaus Lecture on evolving organisms for new nanomaterials

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    “How do we get to making nanomaterials that haven’t been evolved before?” asked Angela Belcher at the 2023 Mildred S. Dresselhaus Lecture at MIT on Nov. 20. “We can use elements that biology has already given us.”

    The combined in-person and virtual audience of over 300 was treated to a light-up, 3D model of M13 bacteriophage, a virus that only infects bacteria, complete with a pull-out strand of DNA. Belcher used the feather-boa-like model to show how her research group modifies the M13’s genes to add new DNA and peptide sequences to template inorganic materials.

    “I love controlling materials at the nanoscale using biology,” said Belcher, the James Mason Crafts Professor of Biological Engineering, materials science professor, and of the Koch Institute of Integrative Cancer Research at MIT. “We all know if you control materials at the nanoscale and you can start to tune them, then you can have all kinds of different applications.” And the opportunities are indeed vast — from building batteries, fuel cells, and solar cells to carbon sequestration and storage, environmental remediation, catalysis, and medical diagnostics and imaging.

    Belcher sprinkled her talk with models and props, lined up on a table at the front of the 10-250 lecture hall, to demonstrate a wide variety of concepts and projects made possible by the intersection of biology and nanotechnology.

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    2023 Mildred S. Dresselhaus Lecture: Angela BelcherVideo: MIT.nano

    Energy storage and environment

    “How do you go from a DNA sequence to a functioning battery?” posed Belcher. Grabbing a model of a large carbon nanotube, she explained how her group engineered a phage to pick up carbon nanotubes that would wind all the way around the virus and then fill in with different cathode or anode materials to make nanowires for battery electrodes.

    How about using the M13 bacteriophage to improve the environment? Belcher referred to a project by former student Geran Zhang PhD ’19 that proved the virus can be modified for this context, too. He used the phage to template high-surface-area, carbon-based materials that can grab small molecules and break them down, Belcher said, opening a realm of possibilities from cleaning up rivers to developing chemical warfare agents to combating smog.

    Belcher’s lab worked with the U.S. Army to produce protective clothing and masks made of these carbon-based virus nanofibers. “We went from five liters in our lab to a thousand liters, then 10,000 liters in the army labs where we’re able to make kilograms of the material,” Belcher said, stressing the importance of being able to test and prototype at scale.

    Imaging tools and therapeutics in cancer

    In the area of biomedical imaging, Belcher explained, a lot less is known in near-infrared imaging — imaging in wavelengths above 1,000 nanometers — than other imaging techniques, yet with near-infrared scientists can see much deeper inside the body. Belcher’s lab built their own systems to image at these wavelengths. The third generation of this system provides real-time, sub-millimeter optical imaging for guided surgery.

    Working with Sangeeta Bhatia, the John J. and Dorothy Wilson Professor of Engineering, Belcher used carbon nanotubes to build imaging tools that find tiny tumors during surgery that doctors otherwise would not be able to see. The tool is actually a virus engineered to carry with it a fluorescent, single-walled carbon nanotube as it seeks out the tumors.

    Nearing the end of her talk, Belcher presented a goal: to develop an accessible detection and diagnostic technology for ovarian cancer in five to 10 years.

    “We think that we can do it,” Belcher said. She described her students’ work developing a way to scan an entire fallopian tube, as opposed to just one small portion, to find pre-cancer lesions, and talked about the team of MIT faculty, doctors, and researchers working collectively toward this goal.

    “Part of the secret of life and the meaning of life is helping other people enjoy the passage of time,” said Belcher in her closing remarks. “I think that we can all do that by working to solve some of the biggest issues on the planet, including helping to diagnose and treat ovarian cancer early so people have more time to spend with their family.”

    Honoring Mildred S. Dresselhaus

    Belcher was the fifth speaker to deliver the Dresselhaus Lecture, an annual event organized by MIT.nano to honor the late MIT physics and electrical engineering Institute Professor Mildred Dresselhaus. The lecture features a speaker from anywhere in the world whose leadership and impact echo Dresselhaus’s life, accomplishments, and values.

    “Millie was and is a huge hero of mine,” said Belcher. “Giving a lecture in Millie’s name is just the greatest honor.”

    Belcher dedicated the talk to Dresselhaus, whom she described with an array of accolades — a trailblazer, a genius, an amazing mentor, teacher, and inventor. “Just knowing her was such a privilege,” she said.

    Belcher also dedicated her talk to her own grandmother and mother, both of whom passed away from cancer, as well as late MIT professors Susan Lindquist and Angelika Amon, who both died of ovarian cancer.

    “I’ve been so fortunate to work with just the most talented and dedicated graduate students, undergraduate students, postdocs, and researchers,” concluded Belcher. “It has been a pure joy to be in partnership with all of you to solve these very daunting problems.” More

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      in Environment

      Putting public service into practice

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      Salomé Otero ’23 doesn’t mince words about the social impact internship she had in 2022. “It was transformational for me,” she says.

      Otero, who majored in management with a concentration in education, always felt that education would play some role in her career path after MIT, but she wasn’t sure how. That all changed her junior year, when she got an email from the Priscilla King Gray Public Service Center (PKG Center) about an internship at The Last Mile, a San Francisco-based nonprofit that provides education and technology training for justice-impacted individuals.

      Otero applied and was selected as a web curriculum and re-entry intern at The Last Mile the summer between her junior and senior year — an eye-opening experience that cemented her post-graduation plans. “You hear some amazing stories, like this person was incarcerated before the iPhone had come out. Now he’s a software developer,” she explains. “And for me, the idea of using computer science education for good appealed to me on many fronts. But even if I hadn’t gotten the opportunity to work at The Last Mile, the fact that I saw a job description for this role and learned that companies have the resources to make a difference … I didn’t know that there were people and organizations dedicating their time and energy into this.”

      She was so inspired that, when she returned for her senior year, Otero found work at two education labs at MIT, completed another social impact internship over Independent Activities Period (IAP) at G{Code}, an education nonprofit that provides computer science education to women and nonbinary people of color, and decided to apply to graduate school. “I can tell you with 100 percent certainty that I would not be pursuing a PhD in education policy right now if it weren’t for the PKG Center,” she says. She will begin her doctorate this fall.

      Otero’s experience doesn’t surprise Jill Bassett, associate dean and director of the PKG Center. “MIT students are deeply concerned about the world’s most challenging problems,” she says. “And social impact internships are an incredible way for them to leverage their unique talents and skills to help create meaningful change while broadening their perspectives and discovering potential career paths.”

      “There’s a lot more out there”

      Founded 35 years ago, the PKG Center offers a robust portfolio of experiential learning programs broadly focused on four themes: climate change, health equity, racial justice, and tech for social good. The Center’s Social Impact Internship Program provides funded internships to students interested in working with government agencies, nonprofits, and social ventures. Students reap rich rewards from these experiences, including learning ways to make social change, informing their academic journey and career path, and gaining valuable professional skills.

      “It was a really good learning opportunity,” says Juliet Liao ’23, a graduate of MIT’s Naval ROTC program who commissioned as a submarine officer in June. She completed a social impact internship with the World Wildlife Fund, where she researched greenhouse gas emissions related to the salmon industry. “I haven’t had much exposure to what work outside of the Navy looks like and what I’m interested in working on. And I really liked the science-based approach to mitigating greenhouse gas emissions.”

      Amina Abdalla, a rising junior in biological engineering, arrived at MIT with a strong interest in health care and determined to go to medical school. But her internship at MassHealth, the Medicaid and Children’s Health Insurance Program provider for the state of Massachusetts, broadened her understanding of the complexity of the health care system and introduced her to many career options that she didn’t know existed.

      “They did coffee chats between interns and various people who work in MassHealth, such as doctors, lawyers, policy advocates, and consultants. There’s a lot more out there that one can do with the degree that they get and the knowledge they gain. It just depends on your interests, and I came away from that really excited,” she says. The experience inspired her to take a class in health policy before she graduates. “I know I want to be a doctor and I have a lot of interest in science in general, but if I could do some kind of public sector impact with that knowledge, I would definitely be interested in doing that.”

      Social impact internships also provide an opportunity for students to hone their analytical, technical, and people skills. Selma Sharaf ’22 worked on developing a first-ever climate action plan for Bennett College in Greensboro, North Carolina, one of two all-women’s historically Black colleges and universities in the United States. She conducted research and stakeholder interviews with nonprofits; sustainability directors at similar colleges; local utility companies; and faculty, staff, and students at Bennett.

      “Our external outreach efforts with certain organizations allowed me to practice having conversations about energy justice and climate issues with people who aren’t already in this space. I learned how useful it can be to not only discuss the overall issues of climate change and carbon emissions, but to also zoom in on more relatable personal-level impacts,” she says. Sharaf is currently working in clean energy consulting and plans to pursue a master’s degree at Stanford University’s Atmosphere/Energy Program this fall.

      Working with “all stars”

      Organizations that partner with the PKG Center are often constrained by limited technical and financial resources. Since the program is funded by the PKG Center, these internships help expand their organizational capacity and broaden their impact; MIT students can take on projects that might not otherwise get done, and they also bring fresh skills and ideas to the organization — and the zeal to pursue those ideas.

      Emily Moberg ’11, PhD ’16 got involved with the social impact internship programs in 2020. Moberg, who is the director of Scope 3 Carbon Measurement and Mitigation at the World Wildlife Fund, has worked with 20 MIT students since then, including Liao. The body of work that Liao and several other interns completed has been published in the form of 10 briefs onmitigating greenhouse gas emissions from key commodities, such as soy, beef, coffee, and palm oil.

      “Social impact interns bring technical skills, deep curiosity, and tenacity,” Moberg says. “I’ve worked with students across many majors, including computer and materials science; all of them bring a new, fresh perspective to our problems and often sophisticated quantitative ability. Their presence often helps us to investigate new ideas or expand a project. In some cases, interns have proposed new projects and ideas themselves. The support from the PKG Center for us to host these interns has been critical, especially for these new explorations.”

      Anne Carrington Hayes, associate professor and executive director of the Global Leadership and Interdisciplinary Studies program at Bennett College, calls the MIT interns she’s worked with since 2021 “all stars.” The work Sharaf and three other students performed has culminated in a draft climate action plan that will inform campus renovations and other measures that will be implemented at the college in the coming years.

      “They have been foundational in helping me to research, frame, collect data, and engage with our students and the community around issues of environmental justice and sustainability, particularly from the lens of what would be impactful and meaningful for women of color at Bennett College,” she says.

      Balancing supply and demand

      Bassett says that the social impact internship program has grown exponentially in the past few years. Before the pandemic, the program served five students from summer 2019 to spring 2020; it now serves about 125 students per year. Over that time, funding has become a significant limiting factor; demand for internships was three times the number of available internships in summer 2022, and five times the supply during IAP 2023.

      “MIT students have no shortage of opportunities available to them in the private sector, yet students are seeking social impact internships because they want to apply their skills to issues that they care about,” says Julie Uva, the PKG Center’s program administrator for social impact internships and employment. “We want to ensure every student who wants a social impact internship can access that experience.”

      MIT has taken note of this financial shortfall: the Task Force 2021 report recommended fundraising to alleviate the under-supply of social impact experiential learning opportunities (ELOs), and MIT’s Fast Forward Climate Action Plan called on the Institute to make a climate or clean-energy ELOs available to every undergraduate who wants one. As a result, the Office of Experiential Learning is working with Resource Development to raise new funding to support many more opportunities, which would be available to students not only through the PKG Center but also other offices and programs, such as MIT D-Lab, Undergraduate Research Opportunity Programs, MISTI, and the Environmental Solutions Initiative, among others.

      That’s welcome news to Salomé Otero. She’s familiar with the Institute’s fundraising efforts, having worked as one of the Alumni Association’s Tech Callers. Now, as an alumna herself and a former social impact intern, she has an appreciation for the power of philanthropy.

      “MIT is ahead of the game compared to so many universities, in so many ways,” she says. “But if they want to continue to do that in the most impactful way possible, I think investing in ideas and missions like the PKG Center is the way to go. So when that call comes, I’ll tell whoever is working that night shift, ‘Yeah, I’ll donate to the PKG Center.’” More

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      in Environment

      A clean alternative to one of the world’s most common ingredients

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      Never underestimate the power of a time crunch.

      In 2016, MIT classmates David Heller ’18, Shara Ticku, and Harry McNamara PhD ’19 were less than two weeks away from the deadline to present a final business plan as part of their class MAS.883 (Revolutionary Ventures: How to Invent and Deploy Transformative Technologies). The students had connected over a shared passion for using biology to solve climate challenges, but their first few ideas didn’t pan out, so they went back to the drawing board.

      In a brainstorming session, Ticku began to reminisce about a trip to Singapore she’d taken where the burning of forests had cast a dark haze over the city. The story sparked a memory from halfway across the world in Costa Rica, where McNamara had traveled and noticed endless rows of palm plantations, which are used to harvest palm oil.

      “Besides Shara’s experience in Singapore and Harry’s in Costa Rica, palm was a material none of us had seriously thought about,” Heller recalls. “That conversation made us realize it was a big, big industry, and there’s major issues to the way that palm is produced.”

      The classmates decided to try using synthetic biology to create a sustainable alternative to palm oil. The idea was the beginning of C16 Biosciences. Today C16 is fulfilling that mission at scale with a palm oil alternative it harvests from oil-producing yeast, which ferment sugars in a process similar to brewing beer.

      The company’s product, which it sells to personal care brands and directly to consumers, holds enormous potential to improve the sustainability of the personal care and food industries because, as it turns out, the classmates had stumbled onto a massive problem.

      Palm oil is the most popular vegetable oil in the world. It’s used in everything from soaps and cosmetics to sauces, rolls, and crackers. But palm oil can only be harvested from palm trees near the equator, so producers often burn down tropical rainforests and swamps in those regions to make way for plantations, decimating wildlife habitats and producing a staggering amount of greenhouse gas emissions. One recent study found palm expansion in Southeast Asia could account for 0.75 percent of the world’s total greenhouse gas emissions. That’s not even including the palm expansion happening across west Africa and South America. Among familiar creatures threatened by palm oil deforestation are orangutans, all three species of which are now listed as “critically endangered” — the most urgent status on the IUCN Red List of Threatened Species, a global endangered species list.

      “To respond to increasing demand over the last few decades, large palm producers usually inappropriately seize land,” Heller explains. “They’ll literally slash and burn tropical rainforests to the ground, drive out indigenous people, they’ll kill or drive out local wildlife, and they’ll replace everything with hectares and hectares of palm oil plantations. That land conversion process has been emitting something like a gigaton of CO2 per year, just for the expansion of palm oil.”

      From milliliters to metric tons

      Heller took Revolutionary Ventures his junior year as one of the few undergraduates in the Media Lab-based class, which is also open to students from nearby colleges. On one of the first days, students were asked to stand in front of the class and explain their passions, or “what makes them tick,” as Heller recalls. He focused on climate tech.

      McNamara, who was a PhD candidate in the Harvard-MIT Program in Health Sciences and Technology at the time, talked about his interest in applying new technology to global challenges in biotech and biophysics. Ticku, who was attending Harvard Business School, discussed her experience working in fertility health and her passion for global health initiatives. The three decided to team up.

      “The core group is very, very passionate about using biology to solve major climate problems,” says Heller, who majored in biological engineering while at MIT.

      After a successful final presentation in the class, the founders received a small amount of funding by participating in the MIT $100K Pitch Competition and from the MIT Sandbox Innovation Fund.

      “MIT Sandbox was one of our first bits of financial support,” Heller says. “We also received great mentorship. We learned from other startups at MIT and made connections with professors whom we learned a lot from.”

      By the time Heller graduated in 2018, the team had experimented with different yeast strains and produced a few milliliters of oil. The process has gradually been optimized and scaled up from there. Today C16 is producing metric tons of oil in 50,000-liter tanks and has launched a consumer cosmetic brand called Palmless.

      Heller says C16 started its own brand as a way to spread the word about the harms associated with palm oil and to show larger companies it was ready to be a partner.

      “The oil palm tree is amazing in terms of the yields it generates, but the location needed for the crop is in conflict with what’s essential in our ecosystem: tropical rainforests,” Heller says. “There’s a lot of excitement when it comes to microbial palm alternatives. A lot of brands have been under pressure from consumers and even governments who are feeling the urgency around climate and are feeling the urgency from consumers to make changes to get away from an oil ingredient that is incredibly destructive.”

      Scaling with biology

      C16’s first offering, which it calls Torula Oil, is a premium product compared to traditional palm oil, but Heller notes the cost of palm oil today is deflated because companies don’t factor in its costs to the planet and society. He also notes that C16 has a number of advantages in its quest to upend the $60 billion palm oil industry: It’s far easier to improve the productivity of C16’s precision fermentation process than it is to improve agricultural processes. C16 also expects its costs to plummet as it continues to grow.

      “What’s exciting for us is we have these economies of scale,” Heller says. “We have the opportunity to expand vertically, in large stainless steel tanks, as opposed to horizontally on land, so we can drive down our cost curve by increasing the size of the infrastructure and improving the optimization of our strain. The timelines for improvement in a precision fermentation process are a fraction of the time it takes in an agricultural context.”

      Heller says C16 is currently focused on partnering with large personal care brands and expects to announce some important deals in coming months. Further down the line, C16 also hopes to use its product to replace the palm oil in food products, although additional regulations mean that dream is still a few years away.

      With all of its efforts, C16 tries to shine a light on the problems associated with the palm industry, which the company feels are underappreciated despite palm oil’s ubiquitous presence in our society.

      “We need to find a way to reduce our reliance on deforestation products,” Heller says. “We do a lot of work to help educate people on the palm oil industry. Just because something has palm oil in it doesn’t mean you should stop using it, but you should understand what that means for the world.” More

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      in Environment

      J-WAFS announces 2023 seed grant recipients

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      Today, the Abdul Latif Jameel Water and Food Systems Lab (J-WAFS) announced its ninth round of seed grants to support innovative research projects at MIT. The grants are designed to fund research efforts that tackle challenges related to water and food for human use, with the ultimate goal of creating meaningful impact as the world population continues to grow and the planet undergoes significant climate and environmental changes.Ten new projects led by 15 researchers from seven different departments will be supported this year. The projects address a range of challenges by employing advanced materials, technology innovations, and new approaches to resource management. The new projects aim to remove harmful chemicals from water sources, develop monitoring and other systems to help manage various aquaculture industries, optimize water purification materials, and more.“The seed grant program is J-WAFS’ flagship grant initiative,” says J-WAFS executive director Renee J. Robins. “The funding is intended to spur groundbreaking MIT research addressing complex issues that are challenging our water and food systems. The 10 projects selected this year show great promise, and we look forward to the progress and accomplishments these talented researchers will make,” she adds.The 2023 J-WAFS seed grant researchers and their projects are:Sara Beery, an assistant professor in the Department of Electrical Engineering and Computer Science (EECS), is building the first completely automated system to estimate the size of salmon populations in the Pacific Northwest (PNW).Salmon are a keystone species in the PNW, feeding human populations for the last 7,500 years at least. However, overfishing, habitat loss, and climate change threaten extinction of salmon populations across the region. Accurate salmon counts during their seasonal migration to their natal river to spawn are essential for fisheries’ regulation and management but are limited by human capacity. Fish population monitoring is a widespread challenge in the United States and worldwide. Beery and her team are working to build a system that will provide a detailed picture of the state of salmon populations in unprecedented, spatial, and temporal resolution by combining sonar sensors and computer vision and machine learning (CVML) techniques. The sonar will capture individual fish as they swim upstream and CVML will train accurate algorithms to interpret the sonar video for detecting, tracking, and counting fish automatically while adapting to changing river conditions and fish densities.Another aquaculture project is being led by Michael Triantafyllou, the Henry L. and Grace Doherty Professor in Ocean Science and Engineering in the Department of Mechanical Engineering, and Robert Vincent, the assistant director at MIT’s Sea Grant Program. They are working with Otto Cordero, an associate professor in the Department of Civil and Environmental Engineering, to control harmful bacteria blooms in aquaculture algae feed production.

      Aquaculture in the United States represents a $1.5 billion industry annually and helps support 1.7 million jobs, yet many American hatcheries are not able to keep up with demand. One barrier to aquaculture production is the high degree of variability in survival rates, most likely caused by a poorly controlled microbiome that leads to bacterial infections and sub-optimal feed efficiency. Triantafyllou, Vincent, and Cordero plan to monitor the microbiome composition of a shellfish hatchery in order to identify possible causing agents of mortality, as well as beneficial microbes. They hope to pair microbe data with detail phenotypic information about the animal population to generate rapid diagnostic tests and explore the potential for microbiome therapies to protect larvae and prevent future outbreaks. The researchers plan to transfer their findings and technology to the local and regional aquaculture community to ensure healthy aquaculture production that will support the expansion of the U.S. aquaculture industry.

      David Des Marais is the Cecil and Ida Green Career Development Professor in the Department of Civil and Environmental Engineering. His 2023 J-WAFS project seeks to understand plant growth responses to elevated carbon dioxide (CO2) in the atmosphere, in the hopes of identifying breeding strategies that maximize crop yield under future CO2 scenarios.Today’s crop plants experience higher atmospheric CO2 than 20 or 30 years ago. Crops such as wheat, oat, barley, and rice typically increase their growth rate and biomass when grown at experimentally elevated atmospheric CO2. This is known as the so-called “CO2 fertilization effect.” However, not all plant species respond to rising atmospheric CO2 with increased growth, and for the ones that do, increased growth doesn’t necessarily correspond to increased crop yield. Using specially built plant growth chambers that can control the concentration of CO2, Des Marais will explore how CO2 availability impacts the development of tillers (branches) in the grass species Brachypodium. He will study how gene expression controls tiller development, and whether this is affected by the growing environment. The tillering response refers to how many branches a plant produces, which sets a limit on how much grain it can yield. Therefore, optimizing the tillering response to elevated CO2 could greatly increase yield. Des Marais will also look at the complete genome sequence of Brachypodium, wheat, oat, and barley to help identify genes relevant for branch growth.Darcy McRose, an assistant professor in the Department of Civil and Environmental Engineering, is researching whether a combination of plant metabolites and soil bacteria can be used to make mineral-associated phosphorus more bioavailable.The nutrient phosphorus is essential for agricultural plant growth, but when added as a fertilizer, phosphorus sticks to the surface of soil minerals, decreasing bioavailability, limiting plant growth, and accumulating residual phosphorus. Heavily fertilized agricultural soils often harbor large reservoirs of this type of mineral-associated “legacy” phosphorus. Redox transformations are one chemical process that can liberate mineral-associated phosphorus. However, this needs to be carefully controlled, as overly mobile phosphorus can lead to runoff and pollution of natural waters. Ideally, phosphorus would be made bioavailable when plants need it and immobile when they don’t. Many plants make small metabolites called coumarins that might be able to solubilize mineral-adsorbed phosphorus and be activated and inactivated under different conditions. McRose will use laboratory experiments to determine whether a combination of plant metabolites and soil bacteria can be used as a highly efficient and tunable system for phosphorus solubilization. She also aims to develop an imaging platform to investigate exchanges of phosphorus between plants and soil microbes.Many of the 2023 seed grants will support innovative technologies to monitor, quantify, and remediate various kinds of pollutants found in water. Two of the new projects address the problem of per- and polyfluoroalkyl substances (PFAS), human-made chemicals that have recently emerged as a global health threat. Known as “forever chemicals,” PFAS are used in many manufacturing processes. These chemicals are known to cause significant health issues including cancer, and they have become pervasive in soil, dust, air, groundwater, and drinking water. Unfortunately, the physical and chemical properties of PFAS render them difficult to detect and remove.Aristide Gumyusenge, the Merton C. Assistant Professor of Materials Science and Engineering, is using metal-organic frameworks for low-cost sensing and capture of PFAS. Most metal-organic frameworks (MOFs) are synthesized as particles, which complicates their high accuracy sensing performance due to defects such as intergranular boundaries. Thin, film-based electronic devices could enable the use of MOFs for many applications, especially chemical sensing. Gumyusenge’s project aims to design test kits based on two-dimensional conductive MOF films for detecting PFAS in drinking water. In early demonstrations, Gumyusenge and his team showed that these MOF films can sense PFAS at low concentrations. They will continue to iterate using a computation-guided approach to tune sensitivity and selectivity of the kits with the goal of deploying them in real-world scenarios.Carlos Portela, the Brit (1961) and Alex (1949) d’Arbeloff Career Development Professor in the Department of Mechanical Engineering, and Ariel Furst, the Cook Career Development Professor in the Department of Chemical Engineering, are building novel architected materials to act as filters for the removal of PFAS from water. Portela and Furst will design and fabricate nanoscale materials that use activated carbon and porous polymers to create a physical adsorption system. They will engineer the materials to have tunable porosities and morphologies that can maximize interactions between contaminated water and functionalized surfaces, while providing a mechanically robust system.Rohit Karnik is a Tata Professor and interim co-department head of the Department of Mechanical Engineering. He is working on another technology, his based on microbead sensors, to rapidly measure and monitor trace contaminants in water.Water pollution from both biological and chemical contaminants contributes to an estimated 1.36 million deaths annually. Chemical contaminants include pesticides and herbicides, heavy metals like lead, and compounds used in manufacturing. These emerging contaminants can be found throughout the environment, including in water supplies. The Environmental Protection Agency (EPA) in the United States sets recommended water quality standards, but states are responsible for developing their own monitoring criteria and systems, which must be approved by the EPA every three years. However, the availability of data on regulated chemicals and on candidate pollutants is limited by current testing methods that are either insensitive or expensive and laboratory-based, requiring trained scientists and technicians. Karnik’s project proposes a simple, self-contained, portable system for monitoring trace and emerging pollutants in water, making it suitable for field studies. The concept is based on multiplexed microbead-based sensors that use thermal or gravitational actuation to generate a signal. His proposed sandwich assay, a testing format that is appealing for environmental sensing, will enable both single-use and continuous monitoring. The hope is that the bead-based assays will increase the ease and reach of detecting and quantifying trace contaminants in water for both personal and industrial scale applications.Alexander Radosevich, a professor in the Department of Chemistry, and Timothy Swager, the John D. MacArthur Professor of Chemistry, are teaming up to create rapid, cost-effective, and reliable techniques for on-site arsenic detection in water.Arsenic contamination of groundwater is a problem that affects as many as 500 million people worldwide. Arsenic poisoning can lead to a range of severe health problems from cancer to cardiovascular and neurological impacts. Both the EPA and the World Health Organization have established that 10 parts per billion is a practical threshold for arsenic in drinking water, but measuring arsenic in water at such low levels is challenging, especially in resource-limited environments where access to sensitive laboratory equipment may not be readily accessible. Radosevich and Swager plan to develop reaction-based chemical sensors that bind and extract electrons from aqueous arsenic. In this way, they will exploit the inherent reactivity of aqueous arsenic to selectively detect and quantify it. This work will establish the chemical basis for a new method of detecting trace arsenic in drinking water.Rajeev Ram is a professor in the Department of Electrical Engineering and Computer Science. His J-WAFS research will advance a robust technology for monitoring nitrogen-containing pollutants, which threaten over 15,000 bodies of water in the United States alone.Nitrogen in the form of nitrate, nitrite, ammonia, and urea can run off from agricultural fertilizer and lead to harmful algal blooms that jeopardize human health. Unfortunately, monitoring these contaminants in the environment is challenging, as sensors are difficult to maintain and expensive to deploy. Ram and his students will work to establish limits of detection for nitrate, nitrite, ammonia, and urea in environmental, industrial, and agricultural samples using swept-source Raman spectroscopy. Swept-source Raman spectroscopy is a method of detecting the presence of a chemical by using a tunable, single mode laser that illuminates a sample. This method does not require costly, high-power lasers or a spectrometer. Ram will then develop and demonstrate a portable system that is capable of achieving chemical specificity in complex, natural environments. Data generated by such a system should help regulate polluters and guide remediation.Kripa Varanasi, a professor in the Department of Mechanical Engineering, and Angela Belcher, the James Mason Crafts Professor and head of the Department of Biological Engineering, will join forces to develop an affordable water disinfection technology that selectively identifies, adsorbs, and kills “superbugs” in domestic and industrial wastewater.Recent research predicts that antibiotic-resistance bacteria (superbugs) will result in $100 trillion in health care expenses and 10 million deaths annually by 2050. The prevalence of superbugs in our water systems has increased due to corroded pipes, contamination, and climate change. Current drinking water disinfection technologies are designed to kill all types of bacteria before human consumption. However, for certain domestic and industrial applications there is a need to protect the good bacteria required for ecological processes that contribute to soil and plant health. Varanasi and Belcher will combine material, biological, process, and system engineering principles to design a sponge-based water disinfection technology that can identify and destroy harmful bacteria while leaving the good bacteria unharmed. By modifying the sponge surface with specialized nanomaterials, their approach will be able to kill superbugs faster and more efficiently. The sponge filters can be deployed under very low pressure, making them an affordable technology, especially in resource-constrained communities.In addition to the 10 seed grant projects, J-WAFS will also fund a research initiative led by Greg Sixt. Sixt is the research manager for climate and food systems at J-WAFS, and the director of the J-WAFS-led Food and Climate Systems Transformation (FACT) Alliance. His project focuses on the Lake Victoria Basin (LVB) of East Africa. The second-largest freshwater lake in the world, Lake Victoria straddles three countries (Uganda, Tanzania, and Kenya) and has a catchment area that encompasses two more (Rwanda and Burundi). Sixt will collaborate with Michael Hauser of the University of Natural Resources and Life Sciences, Vienna, and Paul Kariuki, of the Lake Victoria Basin Commission.The group will study how to adapt food systems to climate change in the Lake Victoria Basin. The basin is facing a range of climate threats that could significantly impact livelihoods and food systems in the expansive region. For example, extreme weather events like droughts and floods are negatively affecting agricultural production and freshwater resources. Across the LVB, current approaches to land and water management are unsustainable and threaten future food and water security. The Lake Victoria Basin Commission (LVBC), a specialized institution of the East African Community, wants to play a more vital role in coordinating transboundary land and water management to support transitions toward more resilient, sustainable, and equitable food systems. The primary goal of this research will be to support the LVBC’s transboundary land and water management efforts, specifically as they relate to sustainability and climate change adaptation in food systems. The research team will work with key stakeholders in Kenya, Uganda, and Tanzania to identify specific capacity needs to facilitate land and water management transitions. The two-year project will produce actionable recommendations to the LVBC. More

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      in Environment

      Inaugural J-WAFS Grand Challenge aims to develop enhanced crop variants and move them from lab to land

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      According to MIT’s charter, established in 1861, part of the Institute’s mission is to advance the “development and practical application of science in connection with arts, agriculture, manufactures, and commerce.” Today, the Abdul Latif Jameel Water and Food Systems Lab (J-WAFS) is one of the driving forces behind water and food-related research on campus, much of which relates to agriculture. In 2022, J-WAFS established the Water and Food Grand Challenge Grant to inspire MIT researchers to work toward a water-secure and food-secure future for our changing planet. Not unlike MIT’s Climate Grand Challenges, the J-WAFS Grand Challenge seeks to leverage multiple areas of expertise, programs, and Institute resources. The initial call for statements of interests returned 23 letters from MIT researchers spanning 18 departments, labs, and centers. J-WAFS hosted workshops for the proposers to present and discuss their initial ideas. These were winnowed down to a smaller set of invited concept papers, followed by the final proposal stage. 

      Today, J-WAFS is delighted to report that the inaugural J-WAFS Grand Challenge Grant has been awarded to a team of researchers led by Professor Matt Shoulders and research scientist Robert Wilson of the Department of Chemistry. A panel of expert, external reviewers highly endorsed their proposal, which tackles a longstanding problem in crop biology — how to make photosynthesis more efficient. The team will receive $1.5 million over three years to facilitate a multistage research project that combines cutting-edge innovations in synthetic and computational biology. If successful, this project could create major benefits for agriculture and food systems worldwide.

      “Food systems are a major source of global greenhouse gas emissions, and they are also increasingly vulnerable to the impacts of climate change. That’s why when we talk about climate change, we have to talk about food systems, and vice versa,” says Maria T. Zuber, MIT’s vice president for research. “J-WAFS is central to MIT’s efforts to address the interlocking challenges of climate, water, and food. This new grant program aims to catalyze innovative projects that will have real and meaningful impacts on water and food. I congratulate Professor Shoulders and the rest of the research team on being the inaugural recipients of this grant.”

      Shoulders will work with Bryan Bryson, associate professor of biological engineering, as well as Bin Zhang, associate professor of chemistry, and Mary Gehring, a professor in the Department of Biology and the Whitehead Institute for Biomedical Research. Robert Wilson from the Shoulders lab will be coordinating the research effort. The team at MIT will work with outside collaborators Spencer Whitney, a professor from the Australian National University, and Ahmed Badran, an assistant professor at the Scripps Research Institute. A milestone-based collaboration will also take place with Stephen Long, a professor from the University of Illinois at Urbana-Champaign. The group consists of experts in continuous directed evolution, machine learning, molecular dynamics simulations, translational plant biochemistry, and field trials.

      “This project seeks to fundamentally improve the RuBisCO enzyme that plants use to convert carbon dioxide into the energy-rich molecules that constitute our food,” says J-WAFS Director John H. Lienhard V. “This difficult problem is a true grand challenge, calling for extensive resources. With J-WAFS’ support, this long-sought goal may finally be achieved through MIT’s leading-edge research,” he adds.

      RuBisCO: No, it’s not a new breakfast cereal; it just might be the key to an agricultural revolution

      A growing global population, the effects of climate change, and social and political conflicts like the war in Ukraine are all threatening food supplies, particularly grain crops. Current projections estimate that crop production must increase by at least 50 percent over the next 30 years to meet food demands. One key barrier to increased crop yields is a photosynthetic enzyme called Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (RuBisCO). During photosynthesis, crops use energy gathered from light to draw carbon dioxide (CO2) from the atmosphere and transform it into sugars and cellulose for growth, a process known as carbon fixation. RuBisCO is essential for capturing the CO2 from the air to initiate conversion of CO2 into energy-rich molecules like glucose. This reaction occurs during the second stage of photosynthesis, also known as the Calvin cycle. Without RuBisCO, the chemical reactions that account for virtually all carbon acquisition in life could not occur.

      Unfortunately, RuBisCO has biochemical shortcomings. Notably, the enzyme acts slowly. Many other enzymes can process a thousand molecules per second, but RuBisCO in chloroplasts fixes less than six carbon dioxide molecules per second, often limiting the rate of plant photosynthesis. Another problem is that oxygen (O2) molecules and carbon dioxide molecules are relatively similar in shape and chemical properties, and RuBisCO is unable to fully discriminate between the two. The inadvertent fixation of oxygen by RuBisCO leads to energy and carbon loss. What’s more, at higher temperatures RuBisCO reacts even more frequently with oxygen, which will contribute to decreased photosynthetic efficiency in many staple crops as our climate warms.

      The scientific consensus is that genetic engineering and synthetic biology approaches could revolutionize photosynthesis and offer protection against crop losses. To date, crop RuBisCO engineering has been impaired by technological obstacles that have limited any success in significantly enhancing crop production. Excitingly, genetic engineering and synthetic biology tools are now at a point where they can be applied and tested with the aim of creating crops with new or improved biological pathways for producing more food for the growing population.

      An epic plan for fighting food insecurity

      The 2023 J-WAFS Grand Challenge project will use state-of-the-art, transformative protein engineering techniques drawn from biomedicine to improve the biochemistry of photosynthesis, specifically focusing on RuBisCO. Shoulders and his team are planning to build what they call the Enhanced Photosynthesis in Crops (EPiC) platform. The project will evolve and design better crop RuBisCO in the laboratory, followed by validation of the improved enzymes in plants, ultimately resulting in the deployment of enhanced RuBisCO in field trials to evaluate the impact on crop yield. 

      Several recent developments make high-throughput engineering of crop RuBisCO possible. RuBisCO requires a complex chaperone network for proper assembly and function in plants. Chaperones are like helpers that guide proteins during their maturation process, shielding them from aggregation while coordinating their correct assembly. Wilson and his collaborators previously unlocked the ability to recombinantly produce plant RuBisCO outside of plant chloroplasts by reconstructing this chaperone network in Escherichia coli (E. coli). Whitney has now established that the RuBisCO enzymes from a range of agriculturally relevant crops, including potato, carrot, strawberry, and tobacco, can also be expressed using this technology. Whitney and Wilson have further developed a range of RuBisCO-dependent E. coli screens that can identify improved RuBisCO from complex gene libraries. Moreover, Shoulders and his lab have developed sophisticated in vivo mutagenesis technologies that enable efficient continuous directed evolution campaigns. Continuous directed evolution refers to a protein engineering process that can accelerate the steps of natural evolution simultaneously in an uninterrupted cycle in the lab, allowing for rapid testing of protein sequences. While Shoulders and Badran both have prior experience with cutting-edge directed evolution platforms, this will be the first time directed evolution is applied to RuBisCO from plants.

      Artificial intelligence is changing the way enzyme engineering is undertaken by researchers. Principal investigators Zhang and Bryson will leverage modern computational methods to simulate the dynamics of RuBisCO structure and explore its evolutionary landscape. Specifically, Zhang will use molecular dynamics simulations to simulate and monitor the conformational dynamics of the atoms in a protein and its programmed environment over time. This approach will help the team evaluate the effect of mutations and new chemical functionalities on the properties of RuBisCO. Bryson will employ artificial intelligence and machine learning to search the RuBisCO activity landscape for optimal sequences. The computational and biological arms of the EPiC platform will work together to both validate and inform each other’s approaches to accelerate the overall engineering effort.

      Shoulders and the group will deploy their designed enzymes in tobacco plants to evaluate their effects on growth and yield relative to natural RuBisCO. Gehring, a plant biologist, will assist with screening improved RuBisCO variants using the tobacco variety Nicotiana benthamianaI, where transient expression can be deployed. Transient expression is a speedy approach to test whether novel engineered RuBisCO variants can be correctly synthesized in leaf chloroplasts. Variants that pass this quality-control checkpoint at MIT will be passed to the Whitney Lab at the Australian National University for stable transformation into Nicotiana tabacum (tobacco), enabling robust measurements of photosynthetic improvement. In a final step, Professor Long at the University of Illinois at Urbana-Champaign will perform field trials of the most promising variants.

      Even small improvements could have a big impact

      A common criticism of efforts to improve RuBisCO is that natural evolution has not already identified a better enzyme, possibly implying that none will be found. Traditional views have speculated a catalytic trade-off between RuBisCO’s specificity factor for CO2 / O2 versus its CO2 fixation efficiency, leading to the belief that specificity factor improvements might be offset by even slower carbon fixation or vice versa. This trade-off has been suggested to explain why natural evolution has been slow to achieve a better RuBisCO. But Shoulders and the team are convinced that the EPiC platform can unlock significant overall improvements to plant RuBisCO. This view is supported by the fact that Wilson and Whitney have previously used directed evolution to improve CO2 fixation efficiency by 50 percent in RuBisCO from cyanobacteria (the ancient progenitors of plant chloroplasts) while simultaneously increasing the specificity factor. 

      The EPiC researchers anticipate that their initial variants could yield 20 percent increases in RuBisCO’s specificity factor without impairing other aspects of catalysis. More sophisticated variants could lift RuBisCO out of its evolutionary trap and display attributes not currently observed in nature. “If we achieve anywhere close to such an improvement and it translates to crops, the results could help transform agriculture,” Shoulders says. “If our accomplishments are more modest, it will still recruit massive new investments to this essential field.”

      Successful engineering of RuBisCO would be a scientific feat of its own and ignite renewed enthusiasm for improving plant CO2 fixation. Combined with other advances in photosynthetic engineering, such as improved light usage, a new green revolution in agriculture could be achieved. Long-term impacts of the technology’s success will be measured in improvements to crop yield and grain availability, as well as resilience against yield losses under higher field temperatures. Moreover, improved land productivity together with policy initiatives would assist in reducing the environmental footprint of agriculture. With more “crop per drop,” reductions in water consumption from agriculture would be a major boost to sustainable farming practices.

      “Our collaborative team of biochemists and synthetic biologists, computational biologists, and chemists is deeply integrated with plant biologists and field trial experts, yielding a robust feedback loop for enzyme engineering,” Shoulders adds. “Together, this team will be able to make a concerted effort using the most modern, state-of-the-art techniques to engineer crop RuBisCO with an eye to helping make meaningful gains in securing a stable crop supply, hopefully with accompanying improvements in both food and water security.” More

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      in Environment

      Recycling plastics from research labs

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      In 2019, MIT’s Environment, Health, and Safety (EHS) Office collaborated with several research labs in the Department of Biology to determine the feasibility of recycling clean lab plastics. Based on early successes with waste isolation and plastics collection, EHS collaborated with GreenLabs Recycling, a local startup, to remove and recycle lab plastics from campus. It was a huge success.

      Today, EHS spearheads the campus Lab Plastics Recycling Program, and its EHS technicians regularly gather clean lab plastics from 212 MIT labs, transferring them to GreenLabs for recycling. Since its pilot stage, the number of labs participating in the program has grown, increasing the total amount of plastic gathered and recycled. In 2020, EHS collected 170 pounds of plastic waste per week from participating labs. That increased to 250 pounds per week in 2021. In 2022, EHS collected a total of 19,000 pounds, or 280 pounds of plastic per week.

      Joanna Buchthal, a research assistant with the MIT Media Lab, indicates that, prior to joining the EHS Lab Plastics Recycling Program, “our laboratory was continuously troubled by the substantial volume of plastic waste we produced and disheartened by our inability to recycle it. We frequently addressed this issue during our group meetings and explored various ways to repurpose our waste, yet we never arrived at a viable solution.”

      The EHS program now provides a solution to labs facing similar challenges with plastics use. After pickup and removal, the plastics are shredded and sold as free stock for injection mold product manufacturing. Buchthal says, “My entire lab is delighted to recycle our used tip boxes and transform them into useful items for other labs!”

      Recently, GreenLabs presented EHS with a three-gallon bucket that local manufacturers produced from 100 percent recycled plastic gathered from MIT labs. No fillers or additives were used in its production.

      Keeping it clean

      The now-growing EHS service and operation started as a pilot. In June 2019, MIT restricted which lab-generated items could be placed in single-stream recycling. MIT’s waste vendors were no longer accepting possibly contaminated waste, such as gloves, pipette tip boxes, bottles, and other plastic waste typically generated in biological research labs. The waste vendors would audit MIT’s single-stream recycling and reject items if they observed any contamination.

      Facing these challenges, the EHS coordinator for biology, John Fucillo, and several EHS representatives from the department met with EHS staff to brainstorm potential recycling solutions. Ensuring the decontamination of the plastic and coordinating its removal in an efficient way were the primary challenges for the labs, says Fucillo, who shared his and lab members’ concerns about the amount of plastic being thrown away with Mitch Galanek, EHS associate director for the Radiation Protection Program. Galanek says, “I immediately recognized the frustration expressed by John and other lab contacts as an opportunity to collaborate.”

      In July 2019, Galanek and a team of EHS technicians began segregating and collecting clean plastic waste from several labs within the biology department. EHS provided the labs with collection containers, and its technicians managed the waste removal over a four-month period, which produced a snapshot of the volume and type of waste generated. An audit of the waste determined that approximately 80 percent of the clean plastic waste generated was empty pipette tip boxes and conical tube racks.

      Based on these data, EHS launched a lab plastics recycling pilot program in November 2019. Labs from the Department of Biology and the Koch Institute for Integrative Cancer Research were invited to participate by recycling their clean, uncontaminated pipette tip boxes and conical tube racks. In addition to providing these labs with collection boxes and plastic liners, EHS also developed an online waste collection request tool to submit plastic pickup requests. EHS also collected the waste containers once they were full.

      Assistant professor of biology Seychelle Vos joined the pilot program as soon as she started her lab in fall 2019. Vos shares that “we already use pipette tips boxes that produce minimal waste, and this program allows us to basically recycle any part of the box except for tips. Pipette boxes are a significant source of plastic waste. This program helps us to be more environmentally and climate friendly.” 

      Given the increased participation in the program, EHS technician Dave Pavone says that plastic pickup is now a “regular component of our work schedules.”

      Together, the EHS technicians, commonly known as “techs,” manage the pickup of nearly 300 plastic collection containers across campus. Normand Desrochers, one of the EHS techs, shares that each morning he plans his pickup route “to get the job done efficiently.” While weekly pickups are a growing part of their schedules, Desrochers notes that everyone has been “super appreciative in what we do for their labs. And what we do makes their job that much easier, being able to focus on their research.”

      Barbara Karampalas, a lab operations manager within the Department of Biological Engineering, is one of many to express appreciation for the program: “We have a fairly large lab with 35 researchers, so we generate a lot of plastic waste … [and] knowing how many tip boxes we were using concerned me. I really appreciate the effort EHS has made to implement this program to help us reduce our impact on the environment.” The program also “makes people in the lab more aware of the issue of plastic waste and MIT’s commitment to reduce its impact on the environment,” says Karampalas.

      Looking ahead

      MIT labs continue to enthusiastically embrace the EHS Lab Plastics Recycling Program: 112 faculty across 212 labs are currently participating in the program. While only empty pipette tip boxes and conical tube racks are currently collected, EHS is exploring which lab plastics could be manufactured into products for use in the labs and repeatedly recycled. Specifically, the EHS Office is considering whether recycled plastic could be used to produce secondary containers for collecting hazardous waste and benchtop transfer containers used for collecting medical waste. As Seychelle notes, “Most plastics cannot be recycled in the current schemes due to their use in laboratory science.”

      Says Fucillo, “Our hope is that this program can be expanded to include other products which could be recycled from the wet labs.” John MacFarlane, research engineer and EHS coordinator for civil and environmental engineering, echoes this sentiment: “With plastic recycling facing economic constraints, this effort by the Institute deserves to be promoted and, hopefully, expanded.”

      “Having more opportunities to recycle ’biologically clean’ plastics would help us have a smaller carbon footprint,” agrees Vos. “We love this program and hope it expands further!”

      MIT labs interested in participating in the EHS Lab Plastics Recycling Program can contact pipetip@mit.edu to learn more. More

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      in Environment

      Nanotube sensors are capable of detecting and distinguishing gibberellin plant hormones

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      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 collaborators from Temasek Life Sciences Laboratory have developed the first-ever nanosensor that can detect and distinguish gibberellins (GAs), a class of hormones in plants that are important for growth. The novel nanosensors are nondestructive, unlike conventional collection methods, and have been successfully tested in living plants. Applied in the field for early-stage plant stress monitoring, the sensors could prove transformative for agriculture and plant biotechnology, giving farmers interested in high-tech precision agriculture and crop management a valuable tool to optimize yield.

      The researchers designed near-infrared fluorescent carbon nanotube sensors that are capable of detecting and distinguishing two plant hormones, GA3 and GA4. Belonging to a class of plant hormones known as gibberellins, GA3 and GA4 are diterpenoid phytohormones produced by plants that play an important role in modulating diverse processes involved in plant growth and development. GAs are thought to have played a role in the driving forces behind the “green revolution” of the 1960s, which was in turn credited with averting famine and saving the lives of many worldwide. The continued study of gibberellins could lead to further breakthroughs in agricultural science and have implications for food security.

      Climate change, global warming, and rising sea levels cause farming soil to get contaminated by saltwater, raising soil salinity. In turn, high soil salinity is known to negatively regulate GA biosynthesis and promote GA metabolism, resulting in the reduction of GA content in plants. The new nanosensors developed by the SMART researchers allow for the study of GA dynamics in living plants under salinity stress at a very early stage, potentially enabling farmers to make early interventions when eventually applied in the field. This forms the basis of early-stage stress detection.

      Currently, methods to detect GA3 and GA4 typically require mass spectroscopy-based analysis, a time-consuming and destructive process. In contrast, the new sensors developed by the researchers are highly selective for the respective GAs and offer real-time, in vivo monitoring of changes in GA levels across a broad range of plant species.

      Described in a paper titled “Near-Infrared Fluorescent Carbon Nanotube Sensors for the Plant Hormone Family Gibberellins” published in the journal Nano Letters, the research represents a breakthrough for early-stage plant stress detection and holds tremendous potential to advance plant biotechnology and agriculture. This paper builds on previous research by the team at SMART DiSTAP on single-walled carbon nanotube-based nanosensors using the corona phase molecular recognition (CoPhMoRe) platform.

      Based on the CoPhMoRe concept introduced by the lab of MIT Professor Professor Michael Strano, the novel sensors are able to detect GA kinetics in the roots of a variety of model and non-model plant species, including Arabidopsis, lettuce, and basil, as well as GA accumulation during lateral root emergence, highlighting the importance of GA in root system architecture. This was made possible by the researchers’ related development of a new coupled Raman/near infrared fluorimeter that enables self-referencing of nanosensor near infrared fluorescence with its Raman G-band, a new hardware innovation that removes the need for a separate reference nanosensor and greatly simplifies the instrumentation requirements by using a single optical channel to measure hormone concentration.

      Using the reversible GA nanosensors, the researchers detected increased endogenous GA levels in mutant plants producing greater amounts of GA20ox1, a key enzyme in GA biosynthesis, as well as decreased GA levels in plants under salinity stress. When exposed to salinity stress, researchers also found that lettuce growth was severely stunted — an indication that only became apparent after 10 days. In contrast, the GA nanosensors reported decreased GA levels after just six hours, demonstrating their efficacy as a much earlier indicator of salinity stress.

      “Our CoPhMoRe technique allows us to create nanoparticles that act like natural antibodies in that they can recognize and lock onto specific molecules. But they tend to be far more stable than alternatives. We have used this method to successfully create nanosensors for plant signals such as hydrogen peroxide and heavy-metal pollutants like arsenic in plants and soil,” says Strano, the Carbon P. Dubbs Professor of Chemical Engineering at MIT who is co-corresponding author and DiSTAP co-lead principal investigator. “The method works to create sensors for organic molecules like synthetic auxin — an important plant hormone — as we have shown. This latest breakthrough now extends this success to a plant hormone family called gibberellins — an exceedingly difficult one to recognize.”

      Strano adds: “The resulting technology offers a rapid, real-time, and in vivo method to monitor changes in GA levels in virtually any plant, and can replace current sensing methods which are laborious, destructive, species-specific, and much less efficient.”

      Mervin Chun-Yi Ang, associate scientific director at DiSTAP and co-first author of the paper, says, “More than simply a breakthrough in plant stress detection, we have also demonstrated a hardware innovation in the form of a new coupled Raman/NIR fluorimeter that enabled self-referencing of SWNT sensor fluorescence with its Raman G-band, representing a major advance in the translation of our nanosensing tool sets to the field. In the near future, our sensors can be combined with low-cost electronics, portable optodes, or microneedle interfaces for industrial use, transforming how the industry screens for and mitigates plant stress in food crops and potentially improving growth and yield.”

      The new sensors could yet have a variety of industrial applications and use cases. Daisuke Urano, a Temasek Life Sciences Laboratory principal investigator, National University of Singapore (NUS) adjunct assistant professor, and co-corresponding author of the paper, explains, “GAs are known to regulate a wide range of plant development processes, from shoot, root, and flower development, to seed germination and plant stress responses. With the commercialization of GAs, these plant hormones are also sold to growers and farmers as plant growth regulators to promote plant growth and seed germination. Our novel GA nanosensors could be applied in the field for early-stage plant stress monitoring, and also be used by growers and farmers to track the uptake or metabolism of GA in their crops.”

      The design and development of the nanosensors, creation and validation of the coupled Raman/near infrared fluorimeter and related image/data processing algorithms, as well as statistical analysis of readouts from plant sensors for this study were performed by SMART and MIT. The Temasek Life Sciences Laboratory was responsible for the design, execution, and analysis of plant-related studies, including validation of nanosensors in living plants.

      This research was carried out by SMART and supported by the National Research Foundation of Singapore under its Campus for Research Excellence And Technological Enterprise (CREATE) program. The DiSTAP program, led by Strano and Singapore co-lead principal investigator Professor Chua Nam Hai, 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, Temasek Life Sciences Laboratory, Nanyang Technological University (NTU) and 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, and drought and pathogen resistance, and applying these technologies to improve urban farming.

      SMART was established by MIT and the National Research Foundation of Singapore in 2007. 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 interdisciplinary research groups: Antimicrobial Resistance, Critical Analytics for Manufacturing Personalized-Medicine, DiSTAP, Future Urban Mobility, and Low Energy Electronic Systems. More

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      in Energy

      Processing waste biomass to reduce airborne emissions

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      To prepare fields for planting, farmers the world over often burn corn stalks, rice husks, hay, straw, and other waste left behind from the previous harvest. In many places, the practice creates huge seasonal clouds of smog, contributing to air pollution that kills 7 million people globally a year, according to the World Health Organization.

      Annually, $120 billion worth of crop and forest residues are burned in the open worldwide — a major waste of resources in an energy-starved world, says Kevin Kung SM ’13, PhD ’17. Kung is working to transform this waste biomass into marketable products — and capitalize on a billion-dollar global market — through his MIT spinoff company, Takachar.

      Founded in 2015, Takachar develops small-scale, low-cost, portable equipment to convert waste biomass into solid fuel using a variety of thermochemical treatments, including one known as oxygen-lean torrefaction. The technology emerged from Kung’s PhD project in the lab of Ahmed Ghoniem, the Ronald C. Crane (1972) Professor of Mechanical Engineering at MIT.

      Biomass fuels, including wood, peat, and animal dung, are a major source of carbon emissions — but billions of people rely on such fuels for cooking, heating, and other household needs. “Currently, burning biomass generates 10 percent of the primary energy used worldwide, and the process is used largely in rural, energy-poor communities. We’re not going to change that overnight. There are places with no other sources of energy,” Ghoniem says.

      What Takachar’s technology provides is a way to use biomass more cleanly and efficiently by concentrating the fuel and eliminating contaminants such as moisture and dirt, thus creating a “clean-burning” fuel — one that generates less smoke. “In rural communities where biomass is used extensively as a primary energy source, torrefaction will address air pollution head-on,” Ghoniem says.

      Thermochemical treatment densifies biomass at elevated temperatures, converting plant materials that are typically loose, wet, and bulky into compact charcoal. Centralized processing plants exist, but collection and transportation present major barriers to utilization, Kung says. Takachar’s solution moves processing into the field: To date, Takachar has worked with about 5,500 farmers to process 9,000 metric tons of crops.

      Takachar estimates its technology has the potential to reduce carbon dioxide equivalent emissions by gigatons per year at scale. (“Carbon dioxide equivalent” is a measure used to gauge global warming potential.) In recognition, in 2021 Takachar won the first-ever Earthshot Prize in the clean air category, a £1 million prize funded by Prince William and Princess Kate’s Royal Foundation.

      Roots in Kenya

      As Kung tells the story, Takachar emerged from a class project that took him to Kenya — which explains the company’s name, a combination of takataka, which mean “trash” in Swahili, and char, for the charcoal end product.

      It was 2011, and Kung was at MIT as a biological engineering grad student focused on cancer research. But “MIT gives students big latitude for exploration, and I took courses outside my department,” he says. In spring 2011, he signed up for a class known as 15.966 (Global Health Delivery Lab) in the MIT Sloan School of Management. The class brought Kung to Kenya to work with a nongovernmental organization in Nairobi’s Kibera, the largest urban slum in Africa.

      “We interviewed slum households for their views on health, and that’s when I noticed the charcoal problem,” Kung says. The problem, as Kung describes it, was that charcoal was everywhere in Kibera — piled up outside, traded by the road, and used as the primary fuel, even indoors. Its creation contributed to deforestation, and its smoke presented a serious health hazard.

      Eager to address this challenge, Kung secured fellowship support from the MIT International Development Initiative and the Priscilla King Gray Public Service Center to conduct more research in Kenya. In 2012, he formed Takachar as a team and received seed money from the MIT IDEAS Global Challenge, MIT Legatum Center for Development and Entrepreneurship, and D-Lab to produce charcoal from household organic waste. (This work also led to a fertilizer company, Safi Organics, that Kung founded in 2016 with the help of MIT IDEAS. But that is another story.)

      Meanwhile, Kung had another top priority: finding a topic for his PhD dissertation. Back at MIT, he met Alexander Slocum, the Walter M. May and A. Hazel May Professor of Mechanical Engineering, who on a long walk-and-talk along the Charles River suggested he turn his Kenya work into a thesis. Slocum connected him with Robert Stoner, deputy director for science and technology at the MIT Energy Initiative (MITEI) and founding director of MITEI’s Tata Center for Technology and Design. Stoner in turn introduced Kung to Ghoniem, who became his PhD advisor, while Slocum and Stoner joined his doctoral committee.

      Roots in MIT lab

      Ghoniem’s telling of the Takachar story begins, not surprisingly, in the lab. Back in 2010, he had a master’s student interested in renewable energy, and he suggested the student investigate biomass. That student, Richard Bates ’10, SM ’12, PhD ’16, began exploring the science of converting biomass to more clean-burning charcoal through torrefaction.

      Most torrefaction (also known as low-temperature pyrolysis) systems use external heating sources, but the lab’s goal, Ghoniem explains, was to develop an efficient, self-sustained reactor that would generate fewer emissions. “We needed to understand the chemistry and physics of the process, and develop fundamental scaling models, before going to the lab to build the device,” he says.

      By the time Kung joined the lab in 2013, Ghoniem was working with the Tata Center to identify technology suitable for developing countries and largely based on renewable energy. Kung was able to secure a Tata Fellowship and — building on Bates’ research — develop the small-scale, practical device for biomass thermochemical conversion in the field that launched Takachar.

      This device, which was patented by MIT with inventors Kung, Ghoniem, Stoner, MIT research scientist Santosh Shanbhogue, and Slocum, is self-contained and scalable. It burns a little of the biomass to generate heat; this heat bakes the rest of the biomass, releasing gases; the system then introduces air to enable these gases to combust, which burns off the volatiles and generates more heat, keeping the thermochemical reaction going.

      “The trick is how to introduce the right amount of air at the right location to sustain the process,” Ghoniem explains. “If you put in more air, that will burn the biomass. If you put in less, there won’t be enough heat to produce the charcoal. That will stop the reaction.”

      About 10 percent of the biomass is used as fuel to support the reaction, Kung says, adding that “90 percent is densified into a form that’s easier to handle and utilize.” He notes that the research received financial support from the Abdul Latif Jameel Water and Food Systems Lab and the Deshpande Center for Technological Innovation, both at MIT. Sonal Thengane, another postdoc in Ghoniem’s lab, participated in the effort to scale up the technology at the MIT Bates Lab (no relation to Richard Bates).

      The charcoal produced is more valuable per ton and easier to transport and sell than biomass, reducing transportation costs by two-thirds and giving farmers an additional income opportunity — and an incentive not to burn agricultural waste, Kung says. “There’s more income for farmers, and you get better air quality.”

      Roots in India

      When Kung became a Tata Fellow, he joined a program founded to take on the biggest challenges of the developing world, with a focus on India. According to Stoner, Tata Fellows, including Kung, typically visit India twice a year and spend six to eight weeks meeting stakeholders in industry, the government, and in communities to gain perspective on their areas of study.

      “A unique part of Tata is that you’re considering the ecosystem as a whole,” says Kung, who interviewed hundreds of smallholder farmers, met with truck drivers, and visited existing biomass processing plants during his Tata trips to India. (Along the way, he also connected with Indian engineer Vidyut Mohan, who became Takachar’s co-founder.)

      “It was very important for Kevin to be there walking about, experimenting, and interviewing farmers,” Stoner says. “He learned about the lives of farmers.”

      These experiences helped instill in Kung an appreciation for small farmers that still drives him today as Takachar rolls out its first pilot programs, tinkers with the technology, grows its team (now up to 10), and endeavors to build a revenue stream. So, while Takachar has gotten a lot of attention and accolades — from the IDEAS award to the Earthshot Prize — Kung says what motivates him is the prospect of improving people’s lives.

      The dream, he says, is to empower communities to help both the planet and themselves. “We’re excited about the environmental justice perspective,” he says. “Our work brings production and carbon removal or avoidance to rural communities — providing them with a way to convert waste, make money, and reduce air pollution.”

      This article appears in the Spring 2022 issue of Energy Futures, the magazine of the MIT Energy Initiative. More

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      in Security

      Assay determines the percentage of Omicron, other variants in Covid wastewater

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      Wastewater monitoring emerged amid the Covid-19 pandemic as an effective and noninvasive way to track a viral outbreak, and advances in the technology have enabled researchers to not only identify but also quantify the presence of particular variants of concern (VOCs) in wastewater samples.

      Last year, researchers with the Singapore-MIT Alliance for Research and Technology (SMART) made the news for developing a quantitative assay for the Alpha variant of SARS-CoV-2 in wastewater, while also working on a similar assay for the Delta variant. Previously, conventional wastewater detection methods could only detect the presence of SARS-CoV-2 viral material in a sample, without identifying the variant of the virus.

      Now, a team at SMART has developed a quantitative RT-qPCR assay that can detect the Omicron variant of SARS-CoV-2. This type of assay enables wastewater surveillance to accurately trace variant dynamics in any given community or population, and support and inform the implementation of appropriate public health measures tailored according to the specific traits of a particular viral pathogen.

      The capacity to count and assess particular VOCs is unique to SMART’s open-source assay, and allows researchers to accurately determine displacement trends in a community. Hence, the new assay can reveal what proportion of SARS-CoV-2 virus circulating in a community belongs to a particular variant. This is particularly significant, as different SARS-CoV-2 VOCs — Alpha, Delta, Omicron, and their offshoots — have emerged at various points throughout the pandemic, each causing a new wave of infections to which the population was more susceptible.

      The team’s new allele-specific RT-qPCR assay is described in a paper, “Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater,” published this month in Water Research. Senior author on the work is Eric Alm, professor of biological engineering at MIT and a principal investigator in the Antimicrobial Resistance (AMR) interdisciplinary research group within SMART, MIT’s research enterprise in Singapore. Co-authors include researchers from Nanyang Technological University (NTU), Singapore National University (NUS), MIT, Singapore Centre for Environmental Life Sciences Engineering (SCELSE), and Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER) in Italy.

      Omicron overtakes delta within three weeks in Italy study

      In their study, SMART researchers found that the increase in booster vaccine population coverage in Italy concurred with the complete displacement of the Delta variant by the Omicron variant in wastewater samples obtained from the Torbole Casaglia wastewater treatment plant, with a catchment size of 62,722 people. Taking less than three weeks, the rapid pace of this displacement can be attributed to Omicron’s infection advantage over the previously dominant Delta in vaccinated individuals, which may stem from Omicron’s more efficient evasion of vaccination-induced immunity.

      “In a world where Covid-19 is endemic, the monitoring of VOCs through wastewater surveillance will be an effective tool for the tracking of variants circulating in the community and will play an increasingly important role in guiding public health response,” says paper co-author Federica Armas, a senior postdoc at SMART AMR. “This work has demonstrated that wastewater surveillance can be used to quickly and quantitatively trace VOCs present in a community.”

      Wastewater surveillance vital for future pandemic responses

      As the global population becomes increasingly vaccinated and exposed to prior infections, nations have begun transitioning toward the classification of SARS-CoV-2 as an endemic disease, rolling back active clinical surveillance toward decentralized antigen rapid tests, and consequently reducing sequencing of patient samples. However, SARS-CoV-2 has been shown to produce novel VOCs that can swiftly emerge and spread rapidly across populations, displacing previously dominant variants of the virus. This was observed when Delta displaced Alpha across the globe after the former’s emergence in India in December 2020, and again when Omicron displaced Delta at an even faster rate following its discovery in South Africa in November 2021. The continuing emergence of novel VOCs therefore necessitates continued vigilance on the monitoring of circulating SARS-CoV-2 variants in communities.

      In a separate review paper on wastewater surveillance titled “Making Waves: Wastewater Surveillance of SARS-CoV-2 in an Endemic Future,” published in the journal Water Research, SMART researchers and collaborators found that the utility of wastewater surveillance in the near future could include 1) monitoring the trend of viral loads in wastewater for quantified viral estimates circulating in a community; 2) sampling of wastewater at the source — e.g., taking samples from particular neighborhoods or buildings — for pinpointing infections in neighborhoods and at the building level; 3) integrating wastewater and clinical surveillance for cost-efficient population surveillance; and 4) genome sequencing wastewater samples to track circulating and emerging variants in the population.

      “Our experience with SARS-CoV-2 has shown that clinical testing can often only paint a limited picture of the true extent of an outbreak or pandemic. With Covid-19 becoming prevalent and with the anticipated emergence of further variants of concern, qualitative and quantitative data from wastewater surveillance will be an integral component of a cost- and resource-efficient public health surveillance program, empowering authorities to make more informed policy decisions,” adds corresponding author Janelle Thompson, associate professor at SCELSE and NTU. “Our review provides a roadmap for the wider deployment of wastewater surveillance, with opportunities and challenges that, if addressed, will enable us to not only better manage Covid-19, but also future-proof societies for other viral pathogens and future pandemics.”

      In addition, the review suggests that future wastewater research should comply with a set of standardized wastewater processing methods to reduce inconsistencies in wastewater data toward improving epidemiological inference. Methods developed in the context of SARS-CoV-2 and its analyses could be of invaluable benefit for future wastewater monitoring work on discovering emerging zoonotic pathogens — pathogens that can be transmitted from animals to humans — and for early detection of future pandemics.

      Furthermore, far from being confined to SARS-CoV-2, wastewater surveillance has already been adapted for use in combating other viral pathogens. Another paper from September 2021 described an advance in the development of effective wastewater surveillance for dengue, Zika, and yellow fever viruses, with SMART researchers successfully measuring decay rates of these medically significant arboviruses in wastewater. This was followed by another review paper by SMART published in July 2022 that explored current progress and future challenges and opportunities in wastewater surveillance for arboviruses. These developments represent an important first step toward establishing arbovirus wastewater surveillance, which would help policymakers in Singapore and beyond make better informed and more targeted public health measures in controlling arbovirus outbreaks such as dengue, which is a significant public health concern in Singapore.

      “Our learnings from using wastewater surveillance as a key tool over the course of Covid-19 will be crucial in helping researchers develop similar methods to monitor and tackle other viral pathogens and future pandemics,” says Lee Wei Lin, first author of the latest SMART paper and research scientist at SMART AMR. “Wastewater surveillance has already shown promising utility in helping to fight other viral pathogens, including some of the world’s most prevalent mosquito-borne diseases, and there is significant potential for the technology to be adapted for use against other infectious viral diseases.”

      The research is carried out by SMART and its collaborators at SCELSE, NTU, and NUS, co-led by Professor Eric Alm (SMART and MIT) and Associate Professor Janelle Thompson (SCELSE and NTU), and is supported by Singapore’sNational Research Foundation (NRF) under its Campus for Research Excellence And Technological Enterprise (CREATE) program. The research is part of an initiative funded by the NRF to develop sewage-based surveillance for rapid outbreak detection and intervention in Singapore.

      SMART was established by MIT in partnership with the NRF in 2007. SMART is the first entity in CREATE developed by NRF and 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 Centre and five interdisciplinary research groups: AMR, Critical Analytics for Manufacturing Personalized-Medicine, Disruptive & Sustainable Technologies for Agricultural Precision, Future Urban Mobility, and Low Energy Electronic Systems.

      The AMR IRG is a translational research and entrepreneurship program that tackles the growing threat of antimicrobial resistance. By leveraging talent and convergent technologies across Singapore and MIT, they tackle AMR head-on by developing multiple innovative and disruptive approaches to identify, respond to, and treat drug-resistant microbial infections. Through strong scientific and clinical collaborations, our goal is to provide transformative, holistic solutions for Singapore and the world. More