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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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    Cleaning up industrial filtration

    If you wanted to get pasta out of a pot of water, would you boil off the water, or use a strainer? While home cooks would choose the strainer, many industries continue to use energy-intensive thermal methods of separating out liquids. In some cases, that’s because it’s difficult to make a filtration system for chemical separation, which requires pores small enough to separate atoms.

    In other cases, membranes exist to separate liquids, but they are made of fragile polymers, which can break down or gum up in industrial use.

    Via Separations, a startup that emerged from MIT in 2017, has set out to address these challenges with a membrane that is cost-effective and robust. Made of graphene oxide (a “cousin” of pencil lead), the membrane can reduce the amount of energy used in industrial separations by 90 percent, according to Shreya Dave PhD ’16, company co-founder and CEO.

    This is valuable because separation processes account for about 22 percent of all in-plant energy use in the United States, according to Oak Ridge National Laboratory. By making such processes significantly more efficient, Via Separations plans to both save energy and address the significant emissions produced by thermal processes. “Our goal is eliminating 500 megatons of carbon dioxide emissions by 2050,” Dave says.

    Play video

    What do our passions for pasta and decarbonizing the Earth have in common? MIT alumna Shreya Dave PhD ’16 explains how she and her team at Via Separations are building the equivalent of a pasta strainer to separate chemical compounds for industry.

    Via Separations began piloting its technology this year at a U.S. paper company and expects to deploy a full commercial system there in the spring of 2022. “Our vision is to help manufacturers slow carbon dioxide emissions next year,” Dave says.

    MITEI Seed Grant

    The story of Via Separations begins in 2012, when the MIT Energy Initiative (MITEI) awarded a Seed Fund grant to Professor Jeffrey Grossman, who is now the Morton and Claire Goulder and Family Professor in Environmental Systems and head of MIT’s Department of Materials Science and Engineering. Grossman was pursuing research into nanoporous membranes for water desalination. “We thought we could bring down the cost of desalination and improve access to clean water,” says Dave, who worked on the project as a graduate student in Grossman’s lab.

    There, she teamed up with Brent Keller PhD ’16, another Grossman graduate student and a 2016-17 ExxonMobil-MIT Energy Fellow, who was developing lab experiments to fabricate and test new materials. “We were early comrades in figuring out how to debug experiments or fix equipment,” says Keller, Via Separations’ co-founder and chief technology officer. “We were fast friends who spent a lot of time talking about science over burritos.”

    Dave went on to write her doctoral thesis on using graphene oxide for water desalination, but that turned out to be the wrong application of the technology from a business perspective, she says. “The cost of desalination doesn’t lie in the membrane materials,” she explains.

    So, after Dave and Keller graduated from MIT in 2016, they spent a lot of time talking to customers to learn more about the needs and opportunities for their new separation technology. This research led them to target the paper industry, because the environmental benefits of improving paper processing are enormous, Dave says. “The paper industry is particularly exciting because separation processes just in that industry account for more than 2 percent of U.S. energy consumption,” she says. “It’s a very concentrated, high-energy-use industry.”

    Most paper today is made by breaking down the chemical bonds in wood to create wood pulp, the primary ingredient of paper. This process generates a byproduct called black liquor, a toxic solution that was once simply dumped into waterways. To clean up this process, paper mills turned to boiling off the water from black liquor and recovering both water and chemicals for reuse in the pulping process. (Today, the most valuable way to use the liquor is as biomass feedstock to generate energy.) Via Separations plans to accomplish this same separation work by filtering black liquor through its graphene oxide membrane.

    “The advantage of graphene oxide is that it’s very robust,” Dave says. “It’s got carbon double bonds that hold together in a lot of environments, including at different pH levels and temperatures that are typically unfriendly to materials.”

    Such properties should also make the company’s membranes attractive to other industries that use membrane separation, Keller says, because today’s polymer membranes have drawbacks. “For most of the things we make — from plastics to paper and gasoline — those polymers will swell or react or degrade,” he says.

    Graphene oxide is significantly more durable, and Via Separations can customize the pores in the material to suit each industry’s application. “That’s our secret sauce,” Dave says, “modulating pore size while retaining robustness to operate in challenging environments.”

    “We’re building a catalog of products to serve different applications,” Keller says, noting that the next target market could be the food and beverage industry. “In that industry, instead of separating different corrosive paper chemicals from water, we’re trying to separate particular sugars and food ingredients from other things.”

    Future target customers include pharmaceutical companies, oil refineries, and semiconductor manufacturers, or even carbon capture businesses.

    Scaling up

    Dave, Keller, and Grossman launched Via Separations in 2017 — with a lot of help from MIT. After the seed grant, in 2015, the founders received a year of funding and support from the J-WAFS Solutions program to explore markets and to develop their business plans. The company’s first capital investment came from The Engine, a venture firm founded by MIT to support “tough tech” companies (tech businesses with transformative potential but long and challenging paths to success). They also received advice and support from MIT’s Deshpande Center for Technological Innovation, Venture Mentoring Service, and Technology Licensing Office. In addition, Grossman continues to serve the company as chief scientist.

    “We were incredibly fortunate to be starting a company in the MIT entrepreneurial ecosystem,” Keller says, noting that The Engine support alone “probably shaved years off our progress.”

    Already, Via Separations has grown to employ 17 people, while significantly scaling up its product. “Our customers are producing thousands of gallons per minute,” Keller explains. “To process that much liquid, we need huge areas of membrane.”

    Via Separations’ manufacturing process, which is now capable of making more than 10,000 square feet of membrane in one production run, is a key competitive advantage, Dave says. The company rolls 300-400 square feet of membrane into a module, and modules can be combined as needed to increase filtration capacity.

    The goal, Dave says, is to contribute to a more sustainable world by making an environmentally beneficial product that makes good business sense. “What we do is make manufacturing things more energy-efficient,” she says. “We allow a paper mill or chemical facility to make more product using less energy and with lower costs. So, there is a bottom-line benefit that’s significant on an industrial scale.”

    Keller says he shares Dave’s goal of building a more sustainable future. “Climate change and energy are central challenges of our time,” he says. “Working on something that has a chance to make a meaningful impact on something so important to everyone is really fulfilling.”

    This article appears in the Spring 2021 issue of Energy Futures, the magazine of the MIT Energy Initiative.  More