Author: mantulin

Seven from MIT receive National Institutes of Health awards

Awards support high-risk, high-reward biomedical and behavioral research.

School of Science
October 8, 2021

On Oct. 5, the National Institutes of Health announced the names of 106 scientists who have been awarded grants through the High-Risk, High-Reward Research program to advance highly innovative biomedical and behavioral research. Seven of the recipients are MIT faculty members.

The High-Risk, High-Reward Research program catalyzes scientific discovery by supporting research proposals that, due to their inherent risk, may struggle in the traditional peer-review process despite their transformative potential. Program applicants are encouraged to pursue trailblazing ideas in any area of research relevant to the NIH’s mission to advance knowledge and enhance health.

“The science put forward by this cohort is exceptionally novel and creative and is sure to push at the boundaries of what is known,” says NIH Director Francis S. Collins. “These visionary investigators come from a wide breadth of career stages and show that groundbreaking science can happen at any career level given the right opportunity.”

New innovators

Four MIT researchers received New Innovator Awards, which recognize “unusually innovative research from early career investigators.” They are:

  • Pulin Li is a member at the Whitehead Institute for Biomedical Research and an assistant professor in the Department of Biology. Li combines approaches from synthetic biology, developmental biology, biophysics and systems biology to quantitatively understand the genetic circuits underlying cell-cell communication that creates multicellular behaviors.
  • Seychelle Vos, the Robert A. Swanson (1969) Career Development Professor of Life Sciences in the Department of Biology, studies the interplay of gene expression and genome organization. Her work focuses on understanding how large molecular machineries involved in genome organization and gene transcription regulate each others’ function to ultimately determine cell fate and identity.
  • Xiao Wang, the Thomas D. and Virginia Cabot Assistant Professor of Chemistry and a member of the Broad Institute of MIT and Harvard, aims to develop high-resolution and highly-multiplexed molecular imaging methods across multiple scales toward understanding the physical and chemical basis of brain wiring and function.
  • Alison Wendlandt is a Cecil and Ida Green Career Development Assistant Professor of Chemistry. Wendlandt focuses on the development of selective, catalytic reactions using the tools of organic and organometallic synthesis and physical organic chemistry. Mechanistic study plays a central role in the development of these new transformations.

Transformative researchers

Two MIT researchers have received Transformative Research Awards, which “promote cross-cutting, interdisciplinary approaches that could potentially create or challenge existing paradigms.” The recipients are:

  • Manolis Kellis is a professor of computer science at MIT in the area of computational biology, an associate member of the Broad Institute, and a principal investigator with MIT’s Computer Science and Artificial Intelligence Laboratory. He aims to further our understanding of the human genome by computational integration of large-scale functional and comparative genomics datasets.
  • Myriam Heiman is the Latham Family Career Development Associate Professor of Neuroscience in the Department of Brain and Cognitive Sciences and an investigator in the Picower Institute for Learning and Memory. Heiman studies the selective vulnerability and pathophysiology seen in two neurodegenerative diseases of the basal ganglia, Huntington’s disease, and Parkinson’s disease.

Together, Heiman, Kellis and colleagues will launch a five-year investigation to pinpoint what may be going wrong in specific brain cells and to help identify new treatment approaches for amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with motor neuron disease (FTLD/MND). The project will bring together four labs, including Heiman and Kellis’ labs at MIT, to apply innovative techniques ranging from computational, genomic, and epigenomic analyses of cells from a rich sample of central nervous system tissue, to precision genetic engineering of stem cells and animal models.

Pioneering researchers

  • Polina Anikeeva received a Pioneer Award, which “challenges investigators at all career levels to pursue new research directions and develop groundbreaking, high-impact approaches to a broad area of biomedical, behavioral, or social science.” Anikeeva is an MIT professor of materials science and engineering, a professor of brain and cognitive sciences, and a McGovern Institute for Brain Research associate investigator. She has established a research program that uniquely combines materials synthesis, device fabrication, neurophysiology, and animal models of behavior. Her group carries out projects that understand, invent, and design materials from the level of atoms to functional devices with applications in fundamental neuroscience.

The program is supported by the NIH Common Fund, which oversees programs that pursue major opportunities and gaps throughout the research enterprise that are of great importance to NIH and require collaboration across the agency to succeed. It issues four awards each year: the Pioneer Award, the New Innovator Award, the Transformative Research Award, and the Early Independence Award.

This year, NIH issued 10 Pioneer awards, 64 New Innovator awards, 19 Transformative Research awards (10 general, four ALS-related, and five Covid-19-related), and 13 Early Independence awards for 2021. Funding for the awards comes from the NIH Common Fund, the National Institute of General Medical Sciences, the National Institute of Mental Health, and the National Institute of Neurological Disorders and Stroke.

3 Questions: Sheena Vasquez and Christian Loyo on communicating science through poetry

PhD students discuss their participation in The Poetry of Science project and the importance of bringing the arts into science communication.

Grace van Deelen | Department of Biology
October 5, 2021

Christian Loyo of the Grossman lab and Sheena Vasquez of the Drennan lab, both graduate students in the Department of Biology, were recently selected to participate in The Poetry of Science. The project, founded by Joshua Sariñana PhD ’11, aims to advance racial justice at the intersection of science and art by bringing together Cambridge, Massachusetts-affiliated poets and scientists of color to create poems about scientific research. These poems will be on public display, along with the scientists’ portraits, at the Massachusetts General Hospital main lobby from Nov. 13 through Nov. 30 and the Rotch Library at MIT during Independent Activities Period (IAP) in January 2022.

For Loyo and Vasquez, The Poetry of Science was the ideal opportunity to create something of impact by combining their personal passions for poetry, science communication, and racial justice. They worked with two poets (Danielle Legros Georges and Luisa Fernanda Apolaya Torres, respectively) to create poems about their research. Loyo and Vasquez sat down to discuss the project.

Q: Both of you are accomplished scientists, but you also spend time working within your communities on various outreach programs. How have these experiences influenced the way you approach your scientific research or your roles as scientists?

Vasquez: I’ve conducted outreach from K-12 to the undergraduate level during my time here at MIT. My most recent outreach is targeted to local community colleges around MIT, including Bunker Hill Community College and Roxbury Community College. Outreach experiences really make me take a step back and think about how to make my science more accessible to the general public. Overall, experiences like these allow me to enhance my mentoring skills. Working with students from different backgrounds shows me how fortunate I am to conduct research at one of the top institutions in the world. If I can make it at an institute like MIT, I feel like anyone else can.

Loyo: For me, it was not easy to get into science. It took a lot of people who became my mentors to teach me what I now know about being a scientist and navigating academia. As an undergrad, I was looking for a research lab and I emailed probably 50 professors; none of them had room. I was about to give up when I finally found one professor who wanted to meet and take a chance on me. This meant a lot to me and is actually in Luisa’s poem. I ended up having a great experience and exploring research questions at a pretty high level for an undergraduate. This opportunity made me realize it’s really important to pay it forward. There are a lot of people who are having a tougher time than I ever did getting into science. Helping them ensures that the future of science is more inclusive.

Q: Science and art are often seen as two distinct disciplines, but The Poetry of Science project is all about bridging that gap. How do you think combining science and the arts can further the goal of advancing racial justice?

Loyo: I think science is about understanding the universe that we live in, and art is about understanding what it means to be human. Because we are human, we all have biases. One of those biases can be racial bias. If you look at who has historically been doing science, it’s mostly white men. That’s not because those people were the best at science; that’s because everyone else was not traditionally allowed to do science. Art gives us an opportunity to share our experiences as people from these historically excluded groups, and to highlight how we became scientists — even if, growing up, we didn’t often see scientists who looked like us.

Vasquez: The Poetry of Science exhibition also offers a chance to create new and positive representations of people of color. More examples of people of color in science helps us break down stereotypes and learn more about the individuals themselves. It allows for more stories to be told in different ways, which creates room for different perspectives. For example — and Danielle included this in her poem — something I really wish people would know is that I’m human, and, just like all scientists, I make mistakes. I am still learning and growing.

Q: What was it like to communicate your research through poetry, and how do you think the arts contribute to scientific literacy?

Vasquez: It was interesting to see what Danielle latched onto when I was explaining my research to her. For example, there’s part of the poem where she writes about how the proteins spiral, and she compares them to a girl’s curly hair. That was the alpha helix I was showing her, and it does spiral like a girl’s hair — like both of our hair. It was neat to see how she made connections between my science and general life.

The arts bring science to life, which helps improve scientific literacy. That’s important because it puts us all on the same page about what’s true and what’s not true. If we didn’t have certain scientific understandings about viruses, for example, we would not have made it this far in combating the pandemic.

Loyo: When you write a poem about science, it becomes much less about the nitty-gritty details, and instead captures the love behind the research. There’s this wonder and awe that we have for the natural world, and when we can discover something about the natural world that we didn’t know before, that feels so good. People really connect to your work when they can feel that same sort of excitement and emotion.

People also take pride in art. For example, I’m of Mexican descent, and I am a big fan of Frida Kahlo and Diego Rivera, who are Mexican painters. Using art can connect people to science even if they don’t really know what the science is about. If they can see that the person doing the experiments, for example, also grew up where they grew up, that can really be beneficial.

David Julius ’77 shares the Nobel Prize in physiology or medicine

MIT alumnus and one other honored for their discoveries in how the nervous system senses temperature and touch.

Anne Trafton | MIT News Office
October 4, 2021

David Julius, a 1977 graduate of MIT, will share the 2021 Nobel Prize in physiology or medicine, the Royal Swedish Academy of Sciences announced this morning in Stockholm.

Julius, a professor at the University of California at San Francisco, shares the prize with Ardem Patapoutian, a professor at the Scripps Research Institute, for their discoveries in how the body senses touch and temperature.

Both scientists helped to answer a fundamental question regarding how the nervous system interprets our environment: How are temperature and mechanical stimuli converted into electrical impulses in the nervous system?

Using capsaicin, a compound that gives chili peppers their distinctive burning sensation, Julius was able to identify a receptor in the nerve endings of skin that responds to heat. His experiments revealed that this receptor, which he called TRPV1, is an ion channel that is activated by painful heat.

“David Julius’ discovery of TRPV1 was the breakthrough that allowed us to understand how differences in temperature can induce electrical signals in the nervous system,” according to today’s announcement by the Nobel committee.

Later, Julius and Patapoutian independently discovered a receptor called TRPM8, which responds to cold. Patapoutian was also honored for his discovery of receptors that respond to mechanical force in the skin and other organs. Their work on how the body senses temperature and mechanical stimuli is now being harnessed to develop treatments for a variety of diseases, including chronic pain.

Julius, who was born in New York, earned his bachelor’s degree in biology from MIT in 1977. He received a PhD in 1984 from University of California at Berkeley and was a postdoc at Columbia University before joining the faculty of the University of California at San Francisco in 1989.

He is the 39th MIT graduate to win a Nobel Prize.

Lindsey Backman: Biochemist, mentor, and advocate

The PhD candidate studies the human microbiome and its proteins, while also championing the Latinx community on MIT’s campus.

Hannah Meiseles | MIT News Office
September 28, 2021

Raised in Tampa, Florida, Lindsey Backman takes pride in her family’s history and its role in the vibrant Cuban American community there. She remembers the weekends she would spend as a kid, getting café con leche with her grandparents and dancing in the studio with her friends. The cultural experiences she shared with friends, family, and  neighbors growing up helped her feel comfortable being herself while growing up, and showed her from an early age how valuable a welcoming community could be to a person’s success.

Backman went on to pursue her BS in chemistry at the University of Florida. Surrounded by a diverse community, she felt supported as she leaned deeper into her interest in science. She was soon nominated to a program that matched students from underrepresented backgrounds in STEM with a university professor to pursue a summer research project. Although Backman was still uncertain about going to another university to do lab research, with encouragement from her department she gave the program a chance.

Backman matched with Professor Catherine Drennan at MIT to work on visualizing structural biology and took part in the MIT Summer Research Program in Biology (MSRP-Bio). The research clicked with her immediately and became a turning point; Backman returned to participate in the lab the following summer and then applied to graduate school.

“Getting nominated to the program changed my life. I certainly wouldn’t have applied to MIT otherwise,” says Backman. “At first, I was convinced I wouldn’t fit in, but soon found myself surrounded by people as passionate about science as I was. I knew I was in the right place.”

Uncovering secrets about the human microbiome

Today, Backman is a graduate student in the Drennan lab and researches the chemistry of the human microbiome, a collection of gut microbes essential to sustaining the body. Backman is interested in how certain bacteria can outcompete other strains by producing unique proteins that process abundant nutrients or repair broken enzymes. Her use of X-ray crystallography has helped her produce atomic models that shed light on the structure of these proteins.

One type of protein Backman and her team have characterized is called a spare part protein. When produced, this protein can help restore a broken enzyme’s ability to catalyze essential reactions. “When fixing a car with a flat tire, you would replace the tire and not the whole car. A similar strategy is being used here. These spare-part proteins act to bind and restore the activity of the enzyme completely,” she says.

Over the years, Backman has seen the depth of questions surrounding the microbiome grow. Scientists have begun to recognize how important the microbiome is to human health. “Ever since my first summer research experience at MIT, I’ve been dedicated to studying this one unique repair mechanism,” says Backman. “We’ve gone from solving the structure of the proteins to now understanding how the mechanism works. But there’s still so much more to learn — we have started to suspect these repair mechanisms speak to a broader motif in other enzymes as well.”

Backman and her team have also been leaders in characterizing how an important enzyme, called hydroxy-L-proline dehydratase (HypD), performs its unusual chemistry. This abundant enzyme takes hydroxyproline, a common nutrient in the gut, and can obtain a competitive advantage by using it as a nutrient and source of energy.

“Only a unique subset of bacteria can process hydroxyproline. On the clinical side, we have seen during infection that virulent bacteria with this ability, such as C. difficile, will start rapidly consuming hydroxyproline to proliferate,” says Backman. “Conversely, we could one day create antibiotics that specifically inhibit HypD without killing our beneficial bacteria.”

Encouraging the future of science

Outside of her research, Backman cares deeply about serving and being a part of the Latinx community on campus. She helped co-found the MIT Latinx Graduate Student Association and has served for four years as a graduate resident assistant for La Casa, the Latinx undergraduate living community at New House. “La Casa is a really tight-knit and familial community,” says Backman. “Some of our original freshmen are now seniors, so it’s been really rewarding to see their whole transition throughout college. I love getting to watch students explore and come to realize what they’re passionate about.”

Backman has also been instrumental in spurring equity initiatives on campus. She is currently a student representative for the MIT Department of Chemistry Diversity, Equity, and Inclusion Committee and has worked to implement programs that support the success of underrepresented groups on campus. Her five years of service as an MIT Chemistry Access Program mentor have encouraged many underrepresented undergraduate students to pursue chemistry graduate programs. For all her hard work at improving MIT’s campus, Backman recently received the Hugh Hampton Young Fellowship.

In the future, Backman aspires to continue researching the microbiome and mentoring students by becoming a professor. She hopes to continue the cycle and inspire more young scientists to recognize their inner potential. “I was never one of those kids that knew I wanted to be a scientist someday. My PI completely changed my life, and I would not be at MIT today without her,” she says. “Having mentors that believe in you at critical points in your life can make all the difference.”

“I think there’s this wrong assumption that diversity initiative work takes away from time that could be spent doing science. In my mind, we need to recognize how these things go hand in hand,” says Backman.

“The only way we’re going to get the best scientists is by creating a healthier, more diverse environment where people of all backgrounds feel welcomed. It’s only when people feel comfortable that they can make their greatest contributions to the field.”

Biologists identify new targets for cancer vaccines

Vaccinating against certain proteins found on cancer cells could help to enhance the T cell response to tumors.

Anne Trafton | MIT News Office
September 16, 2021

Over the past decade, scientists have been exploring vaccination as a way to help fight cancer. These experimental cancer vaccines are designed to stimulate the body’s own immune system to destroy a tumor, by injecting fragments of cancer proteins found on the tumor.

So far, none of these vaccines have been approved by the FDA, but some have shown promise in clinical trials to treat melanoma and some types of lung cancer. In a new finding that may help researchers decide what proteins to include in cancer vaccines, MIT researchers have found that vaccinating against certain cancer proteins can boost the overall T cell response and help to shrink tumors in mice.

The research team found that vaccinating against the types of proteins they identified can help to reawaken dormant T cell populations that target those proteins, strengthening the overall immune response.

“This study highlights the importance of exploring the details of immune responses against cancer deeply. We can now see that not all anticancer immune responses are created equal, and that vaccination can unleash a potent response against a target that was otherwise effectively ignored,” says Tyler Jacks, the David H. Koch Professor of Biology, a member of the Koch Institute for Integrative Cancer Research, and the senior author of the study.

MIT postdoc Megan Burger is the lead author of the new study, which appears today in Cell.

T cell competition

When cells begin to turn cancerous, they start producing mutated proteins not seen in healthy cells. These cancerous proteins, also called neoantigens, can alert the body’s immune system that something has gone wrong, and T cells that recognize those neoantigens start destroying the cancerous cells.

Eventually, these T cells experience a phenomenon known as “T cell exhaustion,” which occurs when the tumor creates an immunosuppressive environment that disables the T cells, allowing the tumor to grow unchecked.

Scientists hope that cancer vaccines could help to rejuvenate those T cells and help them to attack tumors. In recent years, they have worked to develop methods for identifying neoantigens in patient tumors to incorporate into personalized cancer vaccines. Some of these vaccines have shown promise in clinical trials to treat melanoma and non-small cell lung cancer.

“These therapies work amazingly in a subset of patients, but the vast majority still don’t respond very well,” Burger says. “A lot of the research in our lab is aimed at trying to understand why that is and what we can do therapeutically to get more of those patients responding.”

Previous studies have shown that of the hundreds of neoantigens found in most tumors, only a small number generate a T cell response.

The new MIT study helps to shed light on why that is. In studies of mice with lung tumors, the researchers found that as tumor-targeting T cells arise, subsets of T cells that target different cancerous proteins compete with each other, eventually leading to the emergence of one dominant population of T cells. After these T cells become exhausted, they still remain in the environment and suppress any competing T cell populations that target different proteins found on the tumor.

However, Burger found that if she vaccinated these mice with one of the neoantigens targeted by the suppressed T cells, she could rejuvenate those T cell populations.

“If you vaccinate against antigens that have suppressed responses, you can unleash those T cell responses,” she says. “Trying to identify these suppressed responses and specifically targeting them might improve patient responses to vaccine therapies.”

Shrinking tumors

In this study, the researchers found that they had the most success when vaccinating with neoantigens that bind weakly to immune cells that are responsible for presenting the antigen to T cells. When they used one of those neoantigens to vaccinate mice with lung tumors, they found the tumors shrank by an average of 27 percent.

“The T cells proliferate more, they target the tumors better, and we see an overall decrease in lung tumor burden in our mouse model as a result of the therapy,” Burger says.

After vaccination, the T cell population included a type of cells that have the potential to continuously refuel the response, which could allow for long-term control of a tumor.

In future work, the researchers hope to test therapeutic approaches that would combine this vaccination strategy with cancer drugs called checkpoint inhibitors, which can take the brakes off exhausted T cells, stimulating them to attack tumors. Supporting that approach, the results published today also indicate that vaccination boosts the number of a specific type of T cells that have been shown to respond well to checkpoint therapies.

The research was funded by the Howard Hughes Medical Institute, the Ludwig Center at Harvard University, the National Institutes of Health, the Koch Institute Support (core) Grant from the National Cancer Institute, the Bridge Project of the Koch Institute and Dana-Farber/Harvard Cancer Center, and fellowship awards from the Jane Coffin Childs Memorial Fund for Medical Research and the Ludwig Center for Molecular Oncology at MIT.

Professor Emeritus Paul Schimmel donates $50 million to support MIT life sciences enterprise

Schimmel Family Program for Life Sciences will benefit graduate students and research.

School of Science
August 30, 2021

Professor Emeritus Paul Schimmel PhD ’66 and his family recently committed $50 million to support the life sciences at MIT. They provided an initial gift of $25 million to establish the Schimmel Family Program for Life Sciences. This gift matches $25 million secured from other sources in support of the Department of Biology. The remaining $25 million from the Schimmel family will go to support the Schimmel Family Program in the form of matching funds as other gifts are secured over the next five years. Schimmel, who is the John D. and Catherine T. MacArthur Professor of Biochemistry and Biophysics Emeritus, is a lifelong supporter of the Institute in teaching, research, and philanthropy.

“I am tremendously grateful to Paul and his family for their generosity and support, and for their advocacy for our department and the life sciences,” says department head Alan D. Grossman, the Praecis Professor of Biology.

This most recent gift is one among many that Schimmel and his family have provided to MIT during their more than 50-year affiliation with the Institute, which includes Paul’s doctorate and his 30 years of teaching and research in the department. While at MIT, Paul and Cleo, Paul’s wife and philanthropic partner, provided an anonymous donation for the construction of Building 68, the most recent home for the Department of Biology.

“We cannot overstate our gratitude for our MIT experience. It was MIT that provided a ‘frontier of knowledge, which has no bounds’ and introduced us to some of the finest minds and people in the world,” Schimmel says.  

“They educated and uplifted us, and convinced us of MIT’s singular role in making this a better world for all peoples,” says Cleo Schimmel, who was a past chair of the MIT Women’s League and, in her own right, contributed to the endowment of the league and other efforts to support women at MIT.

Currently, Paul Schimmel is the Ernst and Jean Hahn Professor at the Skaggs Institute for Chemical Biology at the Scripps Research Institute. Schimmel formally left MIT in 1997 to join Scripps Research, but he has remained actively involved in supporting the Institute’s research enterprise, specifically MIT graduate students.

Graduate funding for the future

Shortly after Paul left MIT, the Schimmels endowed four graduate fellowships for outstanding women in life sciences. “Since 2000, the Cleo and Paul Schimmel Scholars fellowships have helped the biology department recruit and retain the best talent,” says Grossman. Kristin Knouse PhD ’17 is a former Schimmel Scholar who rejoined the department this past July as an assistant professor.

“The MIT Department of Biology encompasses a remarkable breath of biology within a very close-knit community that places a strong emphasis on graduate training,” says Knouse. “Once in the lab, the resources and collaborations available through MIT provide unparalleled opportunities to accelerate and advance your research.”

Schimmel, who sits on the department’s Visiting Committee, continued to champion graduate student support by helping to endow the Teresa Keng Graduate Teaching Prize to support excellence in graduate student teaching in the department. In 2013, the Schimmel family donated the proceeds from the sale of their La Jolla, California, home for the purpose of training the next generation of MIT graduates in the life sciences. What formally became the department’s Graduate Training Initiative (GTI) was supported by others, including biology alumni Eric Schmidt PhD ’96 and Tracy Smith PhD ’96.

The GTI supports departmental efforts to enhance the graduate student experience in the form of both direct student support, including tuition and stipend, and indirect support, including programmatic activities such as seed funds for student-directed projects, shared computing facilities, and forums related to post-graduation employment.

This new gift to establish the Schimmel Family Program for Life Sciences will support not only the GTI in the Department of Biology, but also graduate students across MIT.

“The life sciences educational enterprise spreads across a dozen departments at MIT,” says Schimmel. “What makes the biology department and the life sciences at MIT so extraordinary is the singular ability to transfer knowledge and inventions to society for its benefit. That is much of why Kendall Square and Boston are what they are.”

To that end, Schimmel has also been an active player in shaping the MIT-Kendall Square innovation ecosystem, including the founding of companies such as Alnylam Pharmaceuticals in 2002. Alnylam — founded by Schimmel along with Institute Professor Phillip Sharp, MIT Professor David Bartel, MIT postdocs Thomas Tuschl and Phillip Zamore, and investors — has been a major player in the biopharma scene. Most recently, Alnylam partnered with Vir Biotechnology to develop therapeutics for coronavirus infections, including Covid-19.

Having a longstanding interest in the applications of basic biomedical research to human health, Schimmel holds numerous patents and is a co-founder or founding director of several biotechnology companies in addition to Alnylam, including aTyr Pharma, Alkermes, Cubist Pharmaceuticals, Metabolon, Repligen, and Sirtris Pharmaceuticals.

“I’ve been talking to the people that I’ve started companies with, reminding them that none of the extensive commercial and residential real estate development, restaurants, hotels, and the founding and locating of major biopharmaceutical enterprises would have happened without the MIT life sciences enterprise,” says Schimmel. “MIT’s Kendall Square is to biopharma what Silicon Valley is to technology. None of the robust economic impact would have occurred if it hadn’t been for MIT’s life sciences.”

The $50 million commitment was a capstone gift to MIT’s Campaign for a Better World, supporting important campaign priorities of human health and discovery science. In addition, Schimmel has future plans to continue supporting the life sciences at MIT through his estate plan with the Institute.

“We are extraordinarily grateful to Paul, Cleo, and the entire family,” says Nergis Mavalvala PhD ’97, the Curtis and Kathleen Marble Professor of Astrophysics and the dean of the MIT School of Science. “Not only do the Schimmels understand, from a firsthand perspective, the need to support graduate students, but they also understand that these young researchers are the future of our life sciences endeavors outside of MIT, in fundamental research, biopharma industries, and beyond.”

Schimmel graduated from Ohio Wesleyan University, earned a doctorate from MIT, and completed postdoc research at Stanford University. His many accomplishments include the publication of more than 500 scientific papers, numerous awards and honorary degrees, and elected membership to the American Academy of Arts and Sciences, the National Academy of Sciences, the American Philosophical Society, the Institute of Medicine (National Academy of Medicine), and National Academy of Inventors.

A pivot from accounting to neuroscience

Through a summer research program at MIT, Patricia Pujols explored the neuromuscular junction, and a future in science.

Alison Gold | School of Science
August 26, 2021

Patricia Pujols grew up in the city of Ponce, Puerto Rico, fascinated by documentaries she had seen about human behavior and psychology. She wanted to learn the molecular roots of things like memory, love, hate, happiness, and anger. Despite her early curiosity, becoming a scientist and studying these phenomena didn’t seem like a possibility.

“Where I grew up, people didn’t really encourage me to study science,” she says. Instead, she initially pursued a career in accounting. “Later on, after the death of my father, I realized life is short. I prefer to do the thing that I love and am passionate about. And for me, that is teaching and learning science.”

With a strong network of mentors to inspire and push her, Pujols is now well on her way to becoming a scientist. She has a semester left in her undergraduate degree at Universidad Central de Bayamón in Puerto Rico, where she is pursuing a major in neuroscience and a minor in psychology. After she graduates, she plans to earn a PhD. This summer, she was part of the MIT Summer Research Program in Biology (MSRP-Bio), which invites non-MIT undergraduate science majors to the Institute for 10 weeks of summer research.

“MSRP-Bio is designed for students like Patricia, who are driven and passionate about science, with limited access to research at their own institution and ready for a challenging and rigorous research experience at MIT that will prepare them for graduate school and open a lot of doors,” says Mandana Sassanfar, the Department of Biology’s director of outreach. “In addition, the program greatly facilitates access to MIT faculty and graduate students and provides a strong community-building component to give students a sense of belonging.”

Pujols arrived at MIT through the guidance of one of her undergraduate professors, molecular neuroscientist Ramon Jorquera. Jorquera worked with Pujols back in Puerto Rico, and is now at the Universidad Andrés Bello in Santiago, Chile.

“He was the first person to invite me to a research lab,” Pujols says. “He has helped me a lot with everything, with gaining confidence, with my English language skills, and with seeing that I can really do this.”

Years ago, Jorquera worked as a fellow in the lab of Troy Littleton, the Menicon Professor of Biology at MIT and the Picower Institute for Learning and Memory. It was Jorquera who encouraged Pujols to apply to a research program at the University of North Carolina at Charlotte several summers ago, and then to apply to MSRP-Bio. Now, just like her mentor, Pujols is working in the Littleton lab to answer crucial questions about human behavior.

Every summer, the Littleton lab welcomes MSRP students.

“This year, while pairing candidates, Patricia was sort of an obvious match for us in terms of her prior research and interests,” Littleton says. “The major interest of my lab is to really understand how neurons talk to each other within the nervous system. The ability of neurons to rapidly communicate drives our behavior, ability to learn, and to remember. That biology all occurs at specific sites known as synapses, where neurons connect with each other.”

Problems in synapse formation or function contribute to the progression of brain disorders and diseases including Alzheimer’s, Parkinson’s, schizophrenia, and many others.

At each of the billions of synapses in the human nervous system, one neuron sends a chemical message and the next receives it –– just like two friends texting. The sender is known as the presynaptic neuron, and the receiver is called the postsynaptic neuron. To allow for seamless, rapid transit of information, the sites where the chemicals are released from on the presynaptic neuron must perfectly align with the receptors on the postsynaptic neuron.

“All of our work is built around genetics,” Littleton says. “We do manipulations where you take out a gene or alter its coding a bit and see how things change. This allows us to piece together how the individual proteins at synapses work to allow neurons to effectively talk to each other.”

To conduct their work, the Littleton lab uses Drosophila melanogaster, the common fruit fly whose genome is well-characterized and is widely used as a genetic model system. After removing a piece of genetic code, they can image the fly’s synapses to see if there was a change in the alignment of the synaptic chemical receptors. They also test if the synapses’ ability to actually transmit and receive chemical messages has changed.

This summer, Pujols is studying the neuromuscular junction, a particular type of synapse where a motor neuron communicates with a muscle cell. This communication enables movement.

In mammals, the motor neuron (the sender, in this case), secretes a protein called agrin that helps to align the key components of the synapse. Agrin is important for organizing acetylcholine receptors in the synapse. Acetylcholine is a neurotransmitter released from motor neurons that is essential for movement. Mutations in agrin in humans can therefore cause muscular dystrophies and various autoimmune disorders.

In Drosophila, it is a neurotransmitter called glutamate, not acetylcholine, that operates at the neuromuscular junction. Researchers want to know if the way that agrin organizes acetylcholine receptors in the mammalian neuromuscular junction is similar to the way that a protein called perlecan organizes the neuromuscular junctions in Drosophila.

To address this question, Pujols has spent her summer removing perlecan from either the sending motor neuron or the receiving muscle cell in Drosophila, and examining how synapse formation and clustering of glutamate receptors is altered. Pujols is working closely with PhD candidate Ellen Guss in a partnership she calls “the best experience ever.”

Both Littleton and Pujols stress the importance of mentorship in the journey to becoming a scientist. When he was an undergraduate at Louisiana State University, Littleton spent a summer at the University of Florida, working with a scientist whose guidance shaped him. That summer was one of his most influential experiences as a scientist, he says.

At MIT, Pujols says, “I stepped out of my comfort zone and strengthened my skills. MSRP gave me all the tools I needed to have an enriching experience in science, as well as the opportunity to meet colleagues that I will remember for the rest of my life.”

To other students thinking of pursuing a career as a scientist, Pujols says, “don’t be afraid.”

“You will get a lot of opinions about what to do, that it’s too difficult, or you don’t have the potential, or some other negative thing,” Pujols says. “I think the most important thing is that you do what you love, even though maybe you are going against the current. You don’t want to have regrets.”

School of Science welcomes new faculty

Seven professors begin in the departments of Biology; Chemistry; Earth, Atmospheric and Planetary Sciences; and Physics.

School of Science
August 25, 2021

This fall, MIT welcomes new faculty members — five assistant professors and two tenured professors — to the departments of Biology; Chemistry; Earth, Atmospheric and Planetary Sciences; and Physics.

A physicist, Soonwon Choi is interested in dynamical phenomena that occur in strongly interacting quantum many-body systems far from equilibrium and designing their applications for quantum information science. He takes a variety of interdisciplinary approaches from analytic theory and numerical computations to collaborations on experiments with controlled quantum degrees of freedom. Recently, Choi’s research has encompassed studying the phenomenon of a phase transition in the dynamics of quantum entanglement and information, drawing on machine learning to introduce a quantum convolutional neural network that can recognize quantum states associated with a one-dimensional symmetry-protected topological phase, and exploring a range of quantum applications of the nitrogen-vacancy color center of diamond.

After completing his undergraduate study in physics at Caltech in 2012, Choi received his PhD degree in physics from Harvard University in 2018. He then worked as a Miller Postdoctoral Fellow at the University of California at Berkeley before joining the Department of Physics and the Center for Theoretical Physics as an assistant professor in July 2021.

Olivia Corradin investigates how genetic variants contribute to disease. She focuses on non-coding DNA variants — changes in DNA sequence that can alter the regulation of gene expression — to gain insight into pathogenesis. With her novel outside-variant approach, Corradin’s lab singled out a type of brain cell involved in multiple sclerosis, increasing total heritability identified by three- to five-fold. A recipient of the Avenir Award through the NIH Director’s Pioneer Award Program, Corradin also scrutinizes how genetic and epigenetic variation influence susceptibility to substance abuse disorders. These critical insights into multiple sclerosis, opioid use disorder, and other diseases have the potential to improve risk assessment, diagnosis, treatment, and preventative care for patients.

Corradin completed a bachelor’s degree in biochemistry from Marquette University in 2010 and a PhD in genetics from Case Western Reserve University in 2016. A Whitehead Institute Fellow since 2016, she also became an institute member in July 2021. The Department of Biology welcomes Corradin as an assistant professor.

Arlene Fiore seeks to understand processes that control two-way interactions between air pollutants and the climate system, as well as the sensitivity of atmospheric chemistry to different chemical, physical, and biological sources and sinks at scales ranging from urban to global and daily to decadal. Combining chemistry-climate models and observations from ground, airborne, and satellite platforms, Fiore has identified global dimensions to ground-level ozone smog and particulate haze that arise from linkages with the climate system, global atmospheric composition, and the terrestrial biosphere. She also investigates regional meteorology and climate feedbacks due to aerosols versus greenhouse gases, future air pollution responses to climate change, and drivers of atmospheric oxidizing capacity. A new research direction involves using chemistry-climate model ensemble simulations to identify imprints of climate variability on observational records of trace gases in the troposphere.

After earning a bachelor’s degree and PhD from Harvard University, Fiore held a research scientist position at the Geophysical Fluid Dynamics Laboratory and was appointed as an associate professor with tenure at Columbia University in 2011. Over the last decade, she has worked with air and health management partners to develop applications of satellite and other Earth science datasets to address their emerging needs. Fiore’s honors include the American Geophysical Union (AGU) James R. Holton Junior Scientist Award, Presidential Early Career Award for Scientists and Engineers (the highest honor bestowed by the United States government on outstanding scientists and engineers in the early stages of their independent research careers), and AGU’s James B. Macelwane Medal. The Department of Earth, Atmospheric and Planetary Sciences welcomes Fiore as the first Peter H. Stone and Paola Malanotte Stone Professor.

With a background in magnetism, Danna Freedman leverages inorganic chemistry to solve problems in physics. Within this paradigm, she is creating the next generation of materials for quantum information by designing spin-based quantum bits, or qubits, based in molecules. These molecular qubits can be precisely controlled, opening the door for advances in quantum computation, sensing, and more. She also harnesses high pressure to synthesize new emergent materials, exploring the possibilities of intermetallic compounds and solid-state bonding. Among other innovations, Freedman has realized millisecond coherence times in molecular qubits, created a molecular analogue of an NV center featuring optical read-out of spin, and discovered the first iron-bismuth binary compound.

Freedman received her bachelor’s degree from Harvard University and her PhD from the University of California at Berkeley, then conducted postdoctoral research at MIT before joining the faculty at Northwestern University as an assistant professor in 2012, earning an NSF CAREER Award, the Presidential Early Career Award for Scientists and Engineers, the ACS Award in Pure Chemistry, and more. She was promoted to associate professor in 2018 and full professor with tenure in 2020. Freedman returns to MIT as the Frederick George Keyes Professor of Chemistry.

Kristin Knouse PhD ’17 aims to understand how tissues sense and respond to damage, with the goal of developing new approaches for regenerative medicine. She focuses on the mammalian liver — which has the unique ability to completely regenerate itself — to ask how organisms react to organ injury, how certain cells retain the ability to grow and divide while others do not, and what genes regulate this process. Knouse creates innovative tools, such as a genome-wide CRISPR screening within a living mouse, to examine liver regeneration from the level of a single-cell to the whole organism.

Knouse received a bachelor’s degree in biology from Duke University in 2010 and then enrolled in the Harvard and MIT MD-PhD Program, where she earned a PhD through the MIT Department of Biology in 2016 and an MD through the Harvard-MIT Program in Health Sciences and Technology in 2018. In 2018, she established her independent laboratory at the Whitehead Institute for Biomedical Research and was honored with the NIH Director’s Early Independence Award. Knouse joins the Department of Biology and the Koch Institute for Integrative Cancer Research as an assistant professor.

Lina Necib PhD ’17 is an astroparticle physicist exploring the origin of dark matter through a combination of simulations and observational data that correlate the dynamics of dark matter with that of the stars in the Milky Way. She has investigated the local dynamic structures in the solar neighborhood using the Gaia satellite, contributed to building a catalog of local accreted stars using machine learning techniques, and discovered a new stream called Nyx, after the Greek goddess of the night. Necib is interested in employing Gaia in conjunction with other spectroscopic surveys to understand the dark matter profile in the local solar neighborhood, the center of the galaxy, and in dwarf galaxies.

After obtaining a bachelor’s degree in mathematics and physics from Boston University in 2012 and a PhD in theoretical physics from MIT in 2017, Necib was a Sherman Fairchild Fellow at Caltech, a Presidential Fellow at the University of California at Irvine, and a fellow in theoretical astrophysics at Carnegie Observatories. She returns to MIT as an assistant professor in the Department of Physics and a member of the MIT Kavli Institute for Astrophysics and Space Research.

Andrew Vanderburg studies exoplanets, or planets that orbit stars other than the sun. Conducting astronomical observations from Earth as well as space, he develops cutting-edge methods to learn about planets outside of our solar system. Recently, he has leveraged machine learning to optimize searches and identify planets that were missed by previous techniques. With collaborators, he discovered the eighth planet in the Kepler-90 solar system, a Jupiter-like planet with unexpectedly close orbiting planets, and rocky bodies disintegrating near a white dwarf, providing confirmation of a theory that such stars may accumulate debris from their planetary systems.

Vanderburg received a bachelor’s degree in physics and astrophysics from the University of California at Berkeley in 2013 and a PhD in Astronomy from Harvard University in 2017. Afterward, Vanderburg moved to the University of Texas at Austin as a NASA Sagan Postdoctoral Fellow, then to the University of Wisconsin at Madison as a faculty member. He joins MIT as an assistant professor in the Department of Physics and a member of the Kavli Institute for Astrophysics and Space Research.

Company founded by MIT alumnus lets anyone run DNA experiments

MiniPCR bio has sold thousands of its inexpensive polymerase chain reaction machines to researchers and schools around the world.

Zach Winn | MIT News Office
August 20, 2021

If you gave students around the world the power to study and manipulate genes in a test tube, what would they do with it?

MiniPCR bio first began selling its portable, inexpensive polymerase chain reaction (PCR) machines in 2013. The machines allow users to multiply specific strands of DNA in minutes, following along with experiments through a phone app.

Since then, the founders have been amazed at the amount of learning and research that has come from the devices.

Researchers have taken the machines into the Amazon rainforest, the deep oceans, and onto remote islands to do things like classify the DNA of the Ebola virus, sequence genes in endangered animals, and monitor for disease. Hundreds of thousands of students have used the machines for hands-on classroom experiments. The machines have even gone to the International Space Station as part of miniPCR bio’s Genes in Space initiative.

The space experiments are designed by middle and high school students as one of miniPCR bio’s projects in education, its main focus. To date, miniPCR bio has sold more than 20,000 of its machines to schools in 80 countries across the globe.

“I still find it shocking,” miniPCR bio’s co-founder Ezequiel Alvarez Saavedra PhD ’08 says of the company’s impact. “We get emails from teachers every week thanking us and telling us how much learning improved in the classroom because of our machine. I never would have thought this would happen.”

Making PCR mainstream

Alvarez Saavedra conducted thousands of experiments with PCR machines, which help researchers replicate specific pieces of DNA and RNA, as part of his PhD work at MIT studying the C. elegans worm. After completing his PhD in 2008, he wasn’t sure how to continue his research career, but he’d worked at MIT’s Hobby Shop in his free time and knew he liked building things, so he began working with a small engineering firm to design a simpler machine.

“I wasn’t thinking of starting a company at all,” Alvarez Saavedra says. “I just liked engineering and I was hoping to learn more about it.”

PCR machines work through a series of temperature changes. First, DNA is heated up inside the machine’s sample tubes. The heat breaks the DNA’s two strands apart. Then, during a cool down phase, molecules specifying the start and end point of the DNA that scientists want to replicate latch onto their targets. As the PCR machine heats the sample back up, an enzyme fills in the target section of DNA, matching the A nucleotides with Ts and the C nucleotides with Gs. The heat-cool-heat cycle is repeated over and over until millions of copies of the target section have been generated.

“PCR is really the workhorse of molecular biology,” Alvarez Saavedra says. “PCR lets you zoom into your region of interest — the starting material could be an entire genome or a small piece of DNA — and then do something with it. You can sequence it, for example, or you could remove a piece of it.”

Traditional PCR machines cost thousands of dollars and typically use thermoelectric cooling to change temperatures. MiniPCR’s machines, the most popular of which costs $650, use a fan and a thin-film heater, simplifying their design and making their operation far less energy-intensive.

Those changes make the machines cheap. They’re also far easier to use than their lab-based counterparts. A simple app lets users select what kind of experiment they want to run, and a temperature graph with animated depictions lets students and researchers follow along at every stage.

In 2013, Alvarez Saavedra partnered with Sebastian Kraves, a fellow Argentinian who’d earned his PhD at Harvard Medical School, to consider the best use case for the new invention. The co-founders decided to try expanding access to PCR machines for middle and high school students around the globe.

To show educators the machines for the first time, the founders attended a professional development training session for teachers at MIT.

“We showed it for 10 minutes and a teacher at the back of the room immediately said, ‘I want 10 of those,’” Alvarez Saavedra remembers. “We though okay, there’s something here.”

The founders ended up building the first 20 machines themselves, storing growing numbers of them in Ezequiel’s living room and basement until his wife suggested they find an office.

Fortunately, miniPCR bio was quickly gaining traction in the education space. Many schools buy batches of miniPCR machines for groups of students to work with directly.

“U.S. schools have been teaching PCR for years, but pretty much no one at the time had PCR machines,” Alvarez Saavedra says. “If a school did have a PCR machine, it would sit at the back of the classroom. When you’re teaching you want small groups of students doing experiments that allows each one to be more hands-on.”

As miniPCR bio’s impact on education scaled, it also gained a loyal following among researchers who appreciate the device’s low price point, efficiency, and suitability to travel to remote regions.

Researchers have run the machines off batteries charged with solar panels and done experiments without leaving the field. When one researcher was trying to sequence the Ebola virus in a makeshift lab in Sierra Leone, the miniPCR machines he’d brought to train lab technicians proved more effective than the traditional — far more expensive — PCR machines he’d brought for his work.

“It’s very nice to get reminded what you’re doing has an impact,” Alvarez Saavedra says.

PCR and beyond

Early on, the founders had the idea for students to design experiments for astronauts to run in space. The idea grew into a national competition held in partnership with Boeing that invites middle and high school students to propose pioneering DNA experiments that address challenges in space exploration. Finalist teams receive miniPCR machines for their schools, and winners get to see their experiments carried out in the International Space Station.

“Kids find space and molecular biology very exciting,” Alvarez Saavedra says.

MiniPCR has done eight missions so far. The program is just one example of the miniPCR team’s ability to keep innovating. The company also offers inexpensive systems for visualizing DNA and enzymes. It’s also developed projects for running classroom experiments using gene editing and synthetic biology. The latter project, called Biobits, was codeveloped in the lab of Jim Collins, the Termeer Professor of Medical Engineering and Science at MIT.

Biobits gives students a hands-on introduction to synthetic biology by letting them create molecular factories that churn out brightly colored proteins, functional enzymes, and more. Ally Huang, a grad student in Collins’ lab who helped develop Biobits, joined the miniPCR team to help launch the first Biobits labs and has helped scale the program to classrooms across the country.

“We try to go where the exciting science is,” Alvarez Saavedra says. “With all these programs, it’s been crazy. You put it out and you start hearing from people in all these crazy places. In the beginning, this wasn’t even supposed to be a company. But it’s incredibly simple. I guess that’s the beauty of it.”

Jacqueline Lees and Rebecca Saxe named associate deans of science

Professors will help guide school-level initiatives and strategy.

Julia C. Keller | School of Science
August 16, 2021

Jaqueline Lees and Rebecca Saxe have been named associate deans serving in the MIT School of Science. Lees is the Virginia and D.K. Ludwig Professor for Cancer Research and is currently the associate director of the Koch Institute for Integrative Cancer Research, as well as an associate department head and professor in the Department of Biology at MIT. Saxe is the John W. Jarve (1978) Professor in Brain and Cognitive Sciences and the associate head of the Department of Brain and Cognitive Sciences (BCS); she is also an associate investigator in the McGovern Institute for Brain Research.

Lees and Saxe will both contribute to the school’s diversity, equity, inclusion, and justice (DEIJ) activities, as well as develop and implement mentoring and other career-development programs to support the community. From their home departments, Saxe and Lees bring years of DEIJ and mentorship experience to bear on the expansion of school-level initiatives.

Lees currently serves on the dean’s science council in her capacity as associate director of the Koch Institute. In this new role as associate dean for the School of Science, she will bring her broad administrative and programmatic experiences to bear on the next phase for DEIJ and mentoring activities.

Lees joined MIT in 1994 as a faculty member in MIT’s Koch Institute (then the Center for Cancer Research) and Department of Biology. Her research focuses on regulators that control cellular proliferation, terminal differentiation, and stemness — functions that are frequently deregulated in tumor cells. She dissects the role of these proteins in normal cell biology and development, and establish how their deregulation contributes to tumor development and metastasis.

Since 2000, she has served on the Department of Biology’s graduate program committee, and played a major role in expanding the diversity of the graduate student population. Lees also serves on DEIJ committees in her home department, as well as at the Koch Institute.

With co-chair with Boleslaw Wyslouch, director of the Laboratory for Nuclear Science, Lees led the ReseArch Scientist CAreer LadderS (RASCALS) committee tasked to evaluate career trajectories for research staff in the School of Science and make recommendations to recruit and retain talented staff, rewarding them for their contributions to the school’s research enterprise.

“Jackie is a powerhouse in translational research, demonstrating how fundamental work at the lab bench is critical for making progress at the patient bedside,” says Nergis Mavalvala, dean of the School of Science. “With Jackie’s dedicated and thoughtful partnership, we can continue to lead in basic research and develop the recruitment, retention, and mentoring and necessary to support our community.”

Saxe will join Lees in supporting and developing programming across the school that could also provide direction more broadly at the Institute.

“Rebecca is an outstanding researcher in social cognition and a dedicated educator — someone who wants our students not only to learn, but to thrive,” says Mavalvala. “I am grateful that Rebecca will join the dean’s leadership team and bring her mentorship and leadership skills to enhance the school.”

For example, in collaboration with former department head James DiCarlo, the BCS department has focused on faculty mentorship of graduate students; and, in collaboration with Professor Mark Bear, the department developed postdoc salary and benefit standards. Both initiatives have become models at MIT.

With colleague Laura Schulz, Saxe also served as co-chair of the Committee on Medical Leave and Hospitalizations (CMLH), which outlined ways to enhance MIT’s current leave and hospitalization procedures and policies for undergraduate and graduate students. Saxe was also awarded MIT’s Committed to Caring award for excellence in graduate student mentorship, as well as the School of Science’s award for excellence in undergraduate teaching.

In her research, Saxe studies human social cognition, using a combination of behavioral testing and brain imaging technologies. She is best known for her work on brain regions specialized for abstract concepts, such as “theory of mind” tasks that involve understanding the mental states of other people. Her TED Talk, “How we read each other’s minds” has been viewed more than 3 million times. She also studies the development of the human brain during early infancy.

She obtained her PhD from MIT and was a Harvard University junior fellow before joining the MIT faculty in 2006. In 2014, the National Academy of Sciences named her one of two recipients of the Troland Award for investigators age 40 or younger “to recognize unusual achievement and further empirical research in psychology regarding the relationships of consciousness and the physical world.” In 2020, Saxe was named a John Simon Guggenheim Foundation Fellow.

Saxe and Lees will also work closely with Kuheli Dutt, newly hired assistant dean for diversity, equity, and inclusion, and other members of the dean’s science council on school-level initiatives and strategy.

“I’m so grateful that Rebecca and Jackie have agreed to take on these new roles,” Mavalvala says. “And I’m super excited to work with these outstanding thought partners as we tackle the many puzzles that I come across as dean.”