Weather

Subterms

    Latest story

    113 Shares149 Views

    An AI dataset carves new paths to tornado detection

    by

    The return of spring in the Northern Hemisphere touches off tornado season. A tornado’s twisting funnel of dust and debris seems an unmistakable sight. But that sight can be obscured to radar, the tool of meteorologists. It’s hard to know exactly when a tornado has formed, or even why.

    A new dataset could hold answers. It contains radar returns from thousands of tornadoes that have hit the United States in the past 10 years. Storms that spawned tornadoes are flanked by other severe storms, some with nearly identical conditions, that never did. MIT Lincoln Laboratory researchers who curated the dataset, called TorNet, have now released it open source. They hope to enable breakthroughs in detecting one of nature’s most mysterious and violent phenomena.

    “A lot of progress is driven by easily available, benchmark datasets. We hope TorNet will lay a foundation for machine learning algorithms to both detect and predict tornadoes,” says Mark Veillette, the project’s co-principal investigator with James Kurdzo. Both researchers work in the Air Traffic Control Systems Group. 

    Along with the dataset, the team is releasing models trained on it. The models show promise for machine learning’s ability to spot a twister. Building on this work could open new frontiers for forecasters, helping them provide more accurate warnings that might save lives. 

    Swirling uncertainty

    About 1,200 tornadoes occur in the United States every year, causing millions to billions of dollars in economic damage and claiming 71 lives on average. Last year, one unusually long-lasting tornado killed 17 people and injured at least 165 others along a 59-mile path in Mississippi.  

    Yet tornadoes are notoriously difficult to forecast because scientists don’t have a clear picture of why they form. “We can see two storms that look identical, and one will produce a tornado and one won’t. We don’t fully understand it,” Kurdzo says.

    A tornado’s basic ingredients are thunderstorms with instability caused by rapidly rising warm air and wind shear that causes rotation. Weather radar is the primary tool used to monitor these conditions. But tornadoes lay too low to be detected, even when moderately close to the radar. As the radar beam with a given tilt angle travels further from the antenna, it gets higher above the ground, mostly seeing reflections from rain and hail carried in the “mesocyclone,” the storm’s broad, rotating updraft. A mesocyclone doesn’t always produce a tornado.

    With this limited view, forecasters must decide whether or not to issue a tornado warning. They often err on the side of caution. As a result, the rate of false alarms for tornado warnings is more than 70 percent. “That can lead to boy-who-cried-wolf syndrome,” Kurdzo says.  

    In recent years, researchers have turned to machine learning to better detect and predict tornadoes. However, raw datasets and models have not always been accessible to the broader community, stifling progress. TorNet is filling this gap.

    The dataset contains more than 200,000 radar images, 13,587 of which depict tornadoes. The rest of the images are non-tornadic, taken from storms in one of two categories: randomly selected severe storms or false-alarm storms (those that led a forecaster to issue a warning but that didn’t produce a tornado).

    Each sample of a storm or tornado comprises two sets of six radar images. The two sets correspond to different radar sweep angles. The six images portray different radar data products, such as reflectivity (showing precipitation intensity) or radial velocity (indicating if winds are moving toward or away from the radar).

    A challenge in curating the dataset was first finding tornadoes. Within the corpus of weather radar data, tornadoes are extremely rare events. The team then had to balance those tornado samples with difficult non-tornado samples. If the dataset were too easy, say by comparing tornadoes to snowstorms, an algorithm trained on the data would likely over-classify storms as tornadic.

    “What’s beautiful about a true benchmark dataset is that we’re all working with the same data, with the same level of difficulty, and can compare results,” Veillette says. “It also makes meteorology more accessible to data scientists, and vice versa. It becomes easier for these two parties to work on a common problem.”

    Both researchers represent the progress that can come from cross-collaboration. Veillette is a mathematician and algorithm developer who has long been fascinated by tornadoes. Kurdzo is a meteorologist by training and a signal processing expert. In grad school, he chased tornadoes with custom-built mobile radars, collecting data to analyze in new ways.

    “This dataset also means that a grad student doesn’t have to spend a year or two building a dataset. They can jump right into their research,” Kurdzo says.

    This project was funded by Lincoln Laboratory’s Climate Change Initiative, which aims to leverage the laboratory’s diverse technical strengths to help address climate problems threatening human health and global security.

    Chasing answers with deep learning

    Using the dataset, the researchers developed baseline artificial intelligence (AI) models. They were particularly eager to apply deep learning, a form of machine learning that excels at processing visual data. On its own, deep learning can extract features (key observations that an algorithm uses to make a decision) from images across a dataset. Other machine learning approaches require humans to first manually label features. 

    “We wanted to see if deep learning could rediscover what people normally look for in tornadoes and even identify new things that typically aren’t searched for by forecasters,” Veillette says.

    The results are promising. Their deep learning model performed similar to or better than all tornado-detecting algorithms known in literature. The trained algorithm correctly classified 50 percent of weaker EF-1 tornadoes and over 85 percent of tornadoes rated EF-2 or higher, which make up the most devastating and costly occurrences of these storms.

    They also evaluated two other types of machine-learning models, and one traditional model to compare against. The source code and parameters of all these models are freely available. The models and dataset are also described in a paper submitted to a journal of the American Meteorological Society (AMS). Veillette presented this work at the AMS Annual Meeting in January.

    “The biggest reason for putting our models out there is for the community to improve upon them and do other great things,” Kurdzo says. “The best solution could be a deep learning model, or someone might find that a non-deep learning model is actually better.”

    TorNet could be useful in the weather community for others uses too, such as for conducting large-scale case studies on storms. It could also be augmented with other data sources, like satellite imagery or lightning maps. Fusing multiple types of data could improve the accuracy of machine learning models.

    Taking steps toward operations

    On top of detecting tornadoes, Kurdzo hopes that models might help unravel the science of why they form.

    “As scientists, we see all these precursors to tornadoes — an increase in low-level rotation, a hook echo in reflectivity data, specific differential phase (KDP) foot and differential reflectivity (ZDR) arcs. But how do they all go together? And are there physical manifestations we don’t know about?” he asks.

    Teasing out those answers might be possible with explainable AI. Explainable AI refers to methods that allow a model to provide its reasoning, in a format understandable to humans, of why it came to a certain decision. In this case, these explanations might reveal physical processes that happen before tornadoes. This knowledge could help train forecasters, and models, to recognize the signs sooner. 

    “None of this technology is ever meant to replace a forecaster. But perhaps someday it could guide forecasters’ eyes in complex situations, and give a visual warning to an area predicted to have tornadic activity,” Kurdzo says.

    Such assistance could be especially useful as radar technology improves and future networks potentially grow denser. Data refresh rates in a next-generation radar network are expected to increase from every five minutes to approximately one minute, perhaps faster than forecasters can interpret the new information. Because deep learning can process huge amounts of data quickly, it could be well-suited for monitoring radar returns in real time, alongside humans. Tornadoes can form and disappear in minutes.

    But the path to an operational algorithm is a long road, especially in safety-critical situations, Veillette says. “I think the forecaster community is still, understandably, skeptical of machine learning. One way to establish trust and transparency is to have public benchmark datasets like this one. It’s a first step.”

    The next steps, the team hopes, will be taken by researchers across the world who are inspired by the dataset and energized to build their own algorithms. Those algorithms will in turn go into test beds, where they’ll eventually be shown to forecasters, to start a process of transitioning into operations.

    In the end, the path could circle back to trust.

    “We may never get more than a 10- to 15-minute tornado warning using these tools. But if we could lower the false-alarm rate, we could start to make headway with public perception,” Kurdzo says. “People are going to use those warnings to take the action they need to save their lives.” More

    More stories

    • 125 Shares119 Views

      in Data Management & Statistics

      Using deep learning to image the Earth’s planetary boundary layer

      by

      Although the troposphere is often thought of as the closest layer of the atmosphere to the Earth’s surface, the planetary boundary layer (PBL) — the lowest layer of the troposphere — is actually the part that most significantly influences weather near the surface. In the 2018 planetary science decadal survey, the PBL was raised as an important scientific issue that has the potential to enhance storm forecasting and improve climate projections.  

      “The PBL is where the surface interacts with the atmosphere, including exchanges of moisture and heat that help lead to severe weather and a changing climate,” says Adam Milstein, a technical staff member in Lincoln Laboratory’s Applied Space Systems Group. “The PBL is also where humans live, and the turbulent movement of aerosols throughout the PBL is important for air quality that influences human health.” 

      Although vital for studying weather and climate, important features of the PBL, such as its height, are difficult to resolve with current technology. In the past four years, Lincoln Laboratory staff have been studying the PBL, focusing on two different tasks: using machine learning to make 3D-scanned profiles of the atmosphere, and resolving the vertical structure of the atmosphere more clearly in order to better predict droughts.  

      This PBL-focused research effort builds on more than a decade of related work on fast, operational neural network algorithms developed by Lincoln Laboratory for NASA missions. These missions include the Time-Resolved Observations of Precipitation structure and storm Intensity with a Constellation of Smallsats (TROPICS) mission as well as Aqua, a satellite that collects data about Earth’s water cycle and observes variables such as ocean temperature, precipitation, and water vapor in the atmosphere. These algorithms retrieve temperature and humidity from the satellite instrument data and have been shown to significantly improve the accuracy and usable global coverage of the observations over previous approaches. For TROPICS, the algorithms help retrieve data that are used to characterize a storm’s rapidly evolving structures in near-real time, and for Aqua, it has helped increase forecasting models, drought monitoring, and fire prediction. 

      These operational algorithms for TROPICS and Aqua are based on classic “shallow” neural networks to maximize speed and simplicity, creating a one-dimensional vertical profile for each spectral measurement collected by the instrument over each location. While this approach has improved observations of the atmosphere down to the surface overall, including the PBL, laboratory staff determined that newer “deep” learning techniques that treat the atmosphere over a region of interest as a three-dimensional image are needed to improve PBL details further.

      “We hypothesized that deep learning and artificial intelligence (AI) techniques could improve on current approaches by incorporating a better statistical representation of 3D temperature and humidity imagery of the atmosphere into the solutions,” Milstein says. “But it took a while to figure out how to create the best dataset — a mix of real and simulated data; we needed to prepare to train these techniques.”

      The team collaborated with Joseph Santanello of the NASA Goddard Space Flight Center and William Blackwell, also of the Applied Space Systems Group, in a recent NASA-funded effort showing that these retrieval algorithms can improve PBL detail, including more accurate determination of the PBL height than the previous state of the art. 

      While improved knowledge of the PBL is broadly useful for increasing understanding of climate and weather, one key application is prediction of droughts. According to a Global Drought Snapshot report released last year, droughts are a pressing planetary issue that the global community needs to address. Lack of humidity near the surface, specifically at the level of the PBL, is the leading indicator of drought. While previous studies using remote-sensing techniques have examined the humidity of soil to determine drought risk, studying the atmosphere can help predict when droughts will happen.  

      In an effort funded by Lincoln Laboratory’s Climate Change Initiative, Milstein, along with laboratory staff member Michael Pieper, are working with scientists at NASA’s Jet Propulsion Laboratory (JPL) to use neural network techniques to improve drought prediction over the continental United States. While the work builds off of existing operational work JPL has done incorporating (in part) the laboratory’s operational “shallow” neural network approach for Aqua, the team believes that this work and the PBL-focused deep learning research work can be combined to further improve the accuracy of drought prediction. 

      “Lincoln Laboratory has been working with NASA for more than a decade on neural network algorithms for estimating temperature and humidity in the atmosphere from space-borne infrared and microwave instruments, including those on the Aqua spacecraft,” Milstein says. “Over that time, we have learned a lot about this problem by working with the science community, including learning about what scientific challenges remain. Our long experience working on this type of remote sensing with NASA scientists, as well as our experience with using neural network techniques, gave us a unique perspective.”

      According to Milstein, the next step for this project is to compare the deep learning results to datasets from the National Oceanic and Atmospheric Administration, NASA, and the Department of Energy collected directly in the PBL using radiosondes, a type of instrument flown on a weather balloon. “These direct measurements can be considered a kind of ‘ground truth’ to quantify the accuracy of the techniques we have developed,” Milstein says.

      This improved neural network approach holds promise to demonstrate drought prediction that can exceed the capabilities of existing indicators, Milstein says, and to be a tool that scientists can rely on for decades to come. More

    • 88 Shares149 Views

      in Data Management & Statistics

      Q&A: Are far-reaching fires the new normal?

      by

      Where there’s smoke, there is fire. But with climate change, larger and longer-burning wildfires are sending smoke farther from their source, often to places that are unaccustomed to the exposure. That’s been the case this week, as smoke continues to drift south from massive wildfires in Canada, prompting warnings of hazardous air quality, and poor visibility in states across New England, the mid-Atlantic, and the Midwest.

      As wildfire season is just getting going, many may be wondering: Are the air-polluting effects of wildfires a new normal?

      MIT News spoke with Professor Colette Heald of the Department of Civil and Environmental Engineering and the Department of Earth, Atmospheric and Planetary Sciences, and Professor Noelle Selin of the Institute for Data, Systems and Society and the Department of Earth, Atmospheric and Planetary Sciences. Heald specializes in atmospheric chemistry and has studied the climate and health effects associated with recent wildfires, while Selin works with atmospheric models to track air pollutants around the world, which she uses to inform policy decisions on mitigating  pollution and climate change. The researchers shared some of their insights on the immediate impacts of Canada’s current wildfires and what downwind regions may expect in the coming months, as the wildfire season stretches into summer.  

      Q: What role has climate change and human activity played in the wildfires we’ve seen so far this year?

      Heald: Unusually warm and dry conditions have dramatically increased fire susceptibility in Canada this year. Human-induced climate change makes such dry and warm conditions more likely. Smoke from fires in Alberta and Nova Scotia in May, and Quebec in early June, has led to some of the worst air quality conditions measured locally in Canada. This same smoke has been transported into the United States and degraded air quality here as well. Local officials have determined that ignitions have been associated with lightning strikes, but human activity has also played a role igniting some of the fires in Alberta.

      Q: What can we expect for the coming months in terms of the pattern of wildfires and their associated air pollution across the United States?

      Heald: The Government of Canada is projecting higher-than-normal fire activity throughout the 2023 fire season. Fire susceptibility will continue to respond to changing weather conditions, and whether the U.S. is impacted will depend on the winds and how air is transported across those regions. So far, the fire season in the United States has been below average, but fire risk is expected to increase modestly through the summer, so we may see local smoke influences as well.

      Q: How has air pollution from wildfires affected human health in the U.S. this year so far?

      Selin: The pollutant of most concern in wildfire smoke is fine particulate matter (PM2.5) – fine particles in the atmosphere that can be inhaled deep into the lungs, causing health damages. Exposure to PM2.5 causes respiratory and cardiovascular damage, including heart attacks and premature deaths. It can also cause symptoms like coughing and difficulty breathing. In New England this week, people have been breathing much higher concentrations of PM2.5 than usual. People who are particularly vulnerable to the effects are likely experiencing more severe impacts, such as older people and people with underlying conditions. But PM2.5 affects everyone. While the number and impact of wildfires varies from year to year, the associated air pollution from them generally lead to tens of thousands of premature deaths in the U.S. overall annually. There is also some evidence that PM2.5 from fires could be particularly damaging to health.

      While we in New England usually have relatively lower levels of pollution, it’s important also to note that some cities around the globe experience very high PM2.5 on a regular basis, not only from wildfires, but other sources such as power plants and industry. So, while we’re feeling the effects over the past few days, we should remember the broader importance of reducing PM2.5 levels overall for human health everywhere.

      Q: While firefighters battle fires directly this wildfire season, what can we do to reduce the effects of associated air pollution? And what can we do in the long-term, to prevent or reduce wildfire impacts?

      Selin: In the short term, protecting yourself from the impacts of PM2.5 is important. Limiting time outdoors, avoiding outdoor exercise, and wearing a high-quality mask are some strategies that can minimize exposure. Air filters can help reduce the concentrations of particles in indoor air. Taking measures to avoid exposure is particularly important for vulnerable groups. It’s also important to note that these strategies aren’t equally possible for everyone (for example, people who work outside) — stressing the importance of developing new strategies to address the underlying causes of increasing wildfires.

      Over the long term, mitigating climate change is important — because warm and dry conditions lead to wildfires, warming increases fire risk. Preventing the fires that are ignited by people or human activities can help.  Another way that damages can be mitigated in the longer term is by exploring land management strategies that could help manage fire intensity. More

    • 125 Shares189 Views

      in Data Management & Statistics

      Hurricane-resistant construction may be undervalued by billions of dollars annually

      by

      In Florida, June typically marks the beginning of hurricane season. Preparation for a storm may appear as otherworldly as it is routine: businesses and homes board up windows and doors, bottled water is quick to sell out, and public buildings cease operations to serve as emergency shelters.

      What happens next may be unpredictable. If things take a turn for the worse, myriad homes may be leveled. A 2019 Congressional Budget Office report estimated that hurricane-related wind damage causes $14 billion in losses to the residential sector annually. 

      However, new research led by Ipek Bensu Manav, an MIT graduate student in civil and environmental engineering and research assistant at MIT’s Concrete Sustainability Hub, suggests that the value of mitigating this wind damage through stronger construction methods may be significantly underestimated. 

      In fact, the failure of wind loss models to account for neighborhood texture — the density and configuration of surrounding buildings with respect to a building of interest — may result in an over 80 percent undervaluation of these methods in Florida.

      Methodology

      Hazus, a loss estimation tool developed and currently used by the Federal Emergency Management Agency (FEMA), estimates physical and economic damage to buildings due to wind and windborne debris. However, the tool assumes that all buildings in a neighborhood experience the same wind loading.

      Manav notes that this assumption disregards the complexity of neighborhood texture. Buildings of different shapes and sizes can be arranged in innumerable ways. This arrangement can amplify or reduce the wind load on buildings within the neighborhood. 

      Wind load amplifications and reductions result from effects referred to as tunneling and shielding. Densely built-up areas with grid-like layouts are particularly susceptible to wind tunneling effects. You might have experienced these effects yourself walking down a windy street, such as Main Street in Cambridge, Massachusetts, near the MIT campus, only to turn the corner and feel calmer air.

      To address this, Manav and her team sought to create a hurricane loss model that accounts for neighborhood texture. By combining GIS files, census tract data, and models of wind recurrence and structural performance, the researchers constructed a high-resolution estimate of expected wind-related structural losses, as well as the benefits of mitigation to reduce those losses. 

      The model builds on prior research led by Jacob Roxon, a recent CSHub postdoc and co-author of this paper, who developed an empirical relationship that estimates building-specific wind gusts with information about building layout in a given neighborhood. 

      A challenge the researchers had to overcome was the fact that the building footprints that were available for this estimation have little-to-no information on occupancy and building type.

      Manav addressed this by developing a novel statistical model that assigns occupancy and building types to structures based on characteristics of the census tract in which they are located.

      Analysis and cost perspective

      The researchers then estimated the value of stronger construction in a case study of residential buildings in Florida. This involved modeling the impact of several mitigation measures applied to over 9.3 million housing units spread across 6.9 million buildings.

      A map of effective wind speed ratio in Florida. Orange coloration indicates census tracts where, on average, structures experience amplifications in wind loads beyond what current tools estimate. Blue coloration indicates census tracts where, on average, structures experience reductions in wind loads.

      Image courtesy of the MIT Concrete Sustainability Hub.

      Previous item
      Next item

      Texture-related loss implications were found to be higher in census tracts along the coast. This occurs because these areas tend to be more dense and ordered, leading to higher wind load amplifications. Also, these loss implications are particularly high for single-family homes, which are more susceptible to damage and have a higher replacement cost per housing unit.

      “Our results sound the alarm that wind loads are more severe than we think,” says Manav. “That is not even accounting for climate change, which might make hurricanes more frequent and their wind speeds more intense over time.”

      The researchers computed expected losses and benefits statewide for hurricane wind damage and its mitigation. They found that $8.1 billion could be saved per year in a scenario where all homes were mitigated with simple measures such as stronger connections between roofs and walls or tighter nail spacing.

      Conventional loss estimation models value these same measures as saving only $4.4 billion per year. This means that conventional models are underestimating the value of stronger construction by over 80 percent.

      “It is important that the benefits of resilient design be quantified so that financial incentives — whether lending, insurance, or otherwise — can be brought to bear to increase mitigation. Manav’s research will move the industry forward toward justifying these benefits,” says structural engineer Evan Reis, who is the executive director of the U.S. Resiliency Council.

      Further implications

      The paper recommends that coastal states enhance their building codes, especially in densely built-up areas, to save dollars and save lives. Manav notes that current building codes do not sufficiently account for texture-induced load amplifications. 

      “Even a building built to code may not be able to protect you and your family,” says Manav. “We need to properly quantify the benefits of mitigating in areas that are exposed to high winds so we promote the right standards of construction where losses can be catastrophic.”

      A goal of Manav’s work is to provide citizens with the information they need before disaster strikes. She has created an online dashboard where you can preview the potential benefits of applying mitigation measures in different communities — perhaps even your own.

      “During my research, I kept hitting a wall. I found that it was difficult to use publicly available information to piece together the bigger picture,” she comments. “We started developing the dashboard to equip homeowners and stakeholders with accessible and actionable information.”

      As a next step, Manav is investigating socioeconomic consequences of hurricane wind damage. 

      “High-resolution analysis, like our case study, allows us to simulate individual household impacts within a geographical context,” adds Manav. “With this, we can capture how differing availability of financial resources may influence how communities cope with the aftermath of natural hazards.” More

    • 88 Shares179 Views

      in Data Management & Statistics

      Research collaboration puts climate-resilient crops in sight

      by

      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