The scientists, who worked together as postdocs at MIT, are honored for their discovery of microRNA — a class of molecules that are critical for gene regulation.
Anne Trafton | MIT News
October 7, 2024
MIT alumnus Victor Ambros ’75, PhD ’79 and Gary Ruvkun, who did his postdoctoral training at MIT, will share the 2024 Nobel Prize in Physiology or Medicine, the Royal Swedish Academy of Sciences announced this morning in Stockholm.
Ambros, a professor at the University of Massachusetts Chan Medical School, and Ruvkun, a professor at Harvard Medical School and Massachusetts General Hospital, were honored for their discovery of microRNA, a class of tiny RNA molecules that play a critical role in gene control.
“Their groundbreaking discovery revealed a completely new principle of gene regulation that turned out to be essential for multicellular organisms, including humans. It is now known that the human genome codes for over one thousand microRNAs. Their surprising discovery revealed an entirely new dimension to gene regulation. MicroRNAs are proving to be fundamentally important for how organisms develop and function,” the Nobel committee said in its announcement today.
During the late 1980s, Ambros and Ruvkun both worked as postdocs in the laboratory of H. Robert Horvitz, a David H. Koch Professor at MIT, who was awarded the Nobel Prize in 2002.
While in Horvitz’s lab, the pair began studying gene control in the roundworm C. elegans — an effort that laid the groundwork for their Nobel discoveries. They studied two mutant forms of the worm, known as lin-4 and lin-14, that showed defects in the timing of the activation of genetic programs that control development.
In the early 1990s, while Ambros was a faculty member at Harvard University, he made a surprising discovery. The lin-4 gene, instead of encoding a protein, produced a very short RNA molecule that appeared in inhibit the expression of lin-14.
At the same time, Ruvkun was continuing to study these C. elegans genes in his lab at MGH and Harvard. He showed that lin-4 did not inhibit lin-14 by preventing the lin-14 gene from being transcribed into messenger RNA; instead, it appeared to turn off the gene’s expression later on, by preventing production of the protein encoded by lin-14.
The two compared results and realized that the sequence of lin-4 was complementary to some short sequences of lin-14. Lin-4, they showed, was binding to messenger RNA encoding lin-14 and blocking it from being translated into protein — a mechanism for gene control that had never been seen before. Those results were published in two articles in the journal Cell in 1993.
In an interview with the Journal of Cell Biology, Ambros credited the contributions of his collaborators, including his wife, Rosalind “Candy” Lee ’76, and postdoc Rhonda Feinbaum, who both worked in his lab, cloned and characterized the lin-4 microRNA, and were co-authors on one of the 1993 Cell papers.
In 2000, Ruvkun published the discovery of another microRNA molecule, encoded by a gene called let-7, which is found throughout the animal kingdom. Since then, more than 1,000 microRNA genes have been found in humans.
“Ambros and Ruvkun’s seminal discovery in the small worm C. elegans was unexpected, and revealed a new dimension to gene regulation, essential for all complex life forms,” the Nobel citation declared.
Ambros, who was born in New Hampshire and grew up in Vermont, earned his PhD at MIT under the supervision of David Baltimore, then an MIT professor of biology, who received a Nobel Prize in 1973. Ambros was a longtime faculty member at Dartmouth College before joining the faculty at the University of Massachusetts Chan Medical School in 2008.
Ruvkun is a graduate of the University of California at Berkeley and earned his PhD at Harvard University before joining Horvitz’s lab at MIT.
Understanding the Role of PARPs and UBF1 in Building Ribosomes
Noah Daly | Department of Biology
September 25, 2024
While pursuing her passion for research, BSG-MSRP-Bio student Adriana Camacho-Badillo made major contributions to research in the Calo Lab in the Department of Biology at MIT.
Growing up in Puerto Rico, Adriana Camacho-Badillo had no explanation for her recurrent multiple fracture injuries. In her teens, she was finally able to see a geneticist who diagnosed her with a genetic syndrome that affects connective tissue throughout the body.
This awakened an interest in genetics that led her to immerse herself in her genetic panel results, curious about the role of each gene that was tested.
“I realized I wanted to find out how mutations affect gene expression that could possibly lead to a distinct phenotype or even a genetic syndrome,” she says.
Within a few years of setting her sights on becoming a scientist, Camacho-Badillo began her first research experience working in the laboratory of Professors Hector Areizaga-Martínez and Elddie Román-Morales. Her work focused on experiments using enzymes to degrade Dichloro-diphenyl-trichloroethane, or DDT, a once-common pesticide known to be highly toxic to humans and other mammals that remains in the environment long after application to crops.
As she became familiar with the day-to-day routines of designing and executing research experiments, she realized she was drawn to biochemistry and molecular biology. Camacho-Badillo soon applied to the molecular neuroscience lab of Professor Miguel Méndez at the University of Puerto Rico at Aguadilla and joined their team working on the effects of high glucose in the central nervous system of mice.
Expanding Experiences While Narrowing Focus
When Camacho-Badillo was sixteen, alongside Méndez and other students, she participated in the Quantitative Methods Workshop at MIT. The workshop allows undergraduate students from universities around the United States and the Caribbean to come together for a few days in January to learn how to apply computational tools that can help biological research.
One of the sessions she attended was a talk about machine learning and studying the brain, presented by graduate student Taylor Baum.
“I loved Taylor’s workshop,” Camacho-Badillo said, “When Taylor asked if anyone would be interested in volunteering to teach Spanish-speaking students in grade school science, I said yes without hesitation.”
Baum, a neuroscientist and computer scientist working in the Munther Dahleh Research Group at MIT, is also the founder of Sprouting, Inc. The organization equips high-school students and undergraduates in Puerto Rico with STEM skills to help them pursue careers in science and technology.
The BSG-MSRP-Bio program offers lab experience and extracurricular activities such as journal clubs and dinners with professors. At one of these events, she met Associate Professor of Biology Eliezer Calo.
Camacho-Badillo and her mentor Eliezer Calo, Associate Professor of Biology. Photo Credit: Mandana Sassanfar.
“I loved meeting another scientist from Puerto Rico working on molecular biology, so I decided to look further into his research,” Camacho-Badillo recalls.
In 2024, she was delighted to have the opportunity to return to the BSG-MSRP-Bio Program for a second time, and now to work in Calo’s Lab.
The Unsolved Mysteries of UBF1
Although BSG-MSRP-Bio students are often mentored by graduate students or postdocs, Calo spent the summer mentoring Camacho-Badillo directly. As an alumnus of the MSRP-Bio program himself, Calo understands firsthand how much of an impact meaningful research can have for an undergraduate student spending a few months experiencing life in the lab at MIT.
In the Calo Lab, Camacho-Badillo spent the early days of this summer poring over past research papers on genetic transcription, trying to answer a big question in molecular biology. Camacho-Badillo has been helping Calo understand how a particular protein affects the production of ribosomes in cells.
A ribosome is the molecular machinery that synthesizes proteins, and an average cell can produce around 10 million ribosomes to sustain its essential functions. Creating these protein engines requires the transcription of ribosomal DNA, or rDNA.
In order to synthesize RNA, specific proteins called polymerases must bind to the DNA. Camacho-Badillo’s work focuses on one of those binding proteins called upstream binding factor, or UBF1. UBF1 is essential for the synthesis of the ribosomal RNA. The UBF1 transcription factor is responsible for recruiting the polymerase, RNA polymerase I, to transcribe the rDNA into rRNA.
Despite knowing the importance of UBF1 in ribosomal production, it’s unclear what its full purpose is in this process. Calo and Camacho-Badillo think that clarifying the role of UBF1 in ribosomal biogenesis will help scientists understand how certain neurological diseases occur. UBF1 is known to be associated with diseases such as acute myeloid leukemia and childhood-onset neurodegeneration with brain atrophy, but the mechanism is not yet understood.
UBF1 is a peculiar transcription factor. Before it can transcribe a gene, UBF1 must first dimerize, forming a bond with another UBF1 protein. After binding to the rDNA, UBF1 can recruit the remaining RNA transcription machinery. The dimer is crucial for transcription to occur, yet this protein can make further connections with other UBF1 monomers, a process called oligomerization.
Nothing is concretely understood about how oligomers of UBF1 form: they could be critical for transcription, forming clusters that can no longer bind with rDNA or inhibit the recruitment of the remaining RNA transcription machinery. These clusters could also be directly contributing to a variety of neurological diseases.
“The genome contains multiple rDNA copies, but not all are utilized,” Calo explains. “UBF1 must precisely identify the correct copies to activate while avoiding the formation of aggregates that could impair its function.”
The regulation of these dimers is also a mystery. Early in the summer, Camacho-Badillo helped make an important connection: prior research from the Calo Lab showed that enzymes called poly ADP-ribose polymerases, or PARPs, play a role in maintaining chemical properties in the nucleolus, where ribosomes are produced and assembled. The main target of these proteins within the RNA transcriptional machinery before transcription is initiated is UBF1.
Based on this initial result, Camacho-Badillo’s entire summer project shifted to further characterize PARPs in ribosome biogenesis.
“This observation about the role PARPs plays is a big deal for us,” Calo says. “We do many experiments in my lab, but Adriana’s work this summer has opened a key gateway to understanding the mysteries behind UBF1 regulation, leading to proper ribosome production and allowing the Calo lab to pursue this goal. She’s going to be a superstar.”
Camacho-Badillo’s work hasn’t ended with the BSG-MSRP-Bio program, however. She’ll spend the fall semester at MIT, continuing to work on understanding how rDNA transcription is regulated as a visiting student in the Calo Lab. Although she still has a year and a half to go in her undergraduate degree, she’s already set her sights on graduate school.
“This program has meant so much to me and brought so much into my life,” she says. “All I want to do right now is keep this research going.”
All It takes to titer: discovering a love of troubleshooting at MIT
Noah Daly | Department of Biology
September 25, 2024
BSG-MSRP-Bio student Yeongseo Son breathed new life into her love of science over the summer in the Spranger Lab studying immune responses in the lung in the Department of Biology at MIT.
Back home at the University of Georgia, Son studies neutrophils, a kind of innate immune cell that serves as the body’s first line of defense against foreign pathogens. After taking a graduate-level course on immunology last semester, Son realized she needed to increase her basic understanding of the broad discipline.
“I knew that coming to work with Professor Spranger would give me a chance to work on cancer immunology and T cell biology, two really cool and important fields I haven’t been exposed to,” Son says.
It took several attempts from the Senior Lecturer and BSG-MSRP-Bio program coordinator Mandana Sassanfar to reach her before Son accepted.
“Before I arrived, I was worried it would be too intense or that I wouldn’t fit in,” Son says. “I couldn’t have been more wrong: yes, the work is challenging, but everyone is here because they truly love science.”
This quest involved multiple steps, such as culturing cells, infecting the cells with the virus, and measuring how lethal it is to host cells, working with a strain that her lab hadn’t used before.
To test the strength of the virus, the virus is mixed with host cells in order to infect them. Then the host cells are placed on a layer of agar, a gelatinous substance that provides nutrients for the host cells. When a virus-infected cell dies, it creates a hole in the layer of cells called a plaque. The number of plaques is recorded to determine the virus’s titer, or frequency.
Son excitedly executed her plaque assay after breezing through the first two steps. The next day, to her surprise and disappointment, all her cells — including the negative control — had died.
“The first time it failed, I was crushed because I had written the protocol over and over,” Son says.
That initial disappointment, however, turned into excitement to solve the problem. She worked closely with her mentor, Postdoc Taylor Heim, who helped motivate her to keep trying to figure out what had gone wrong.
Son spent weeks designing a process to effectively titer the virus. She laid out a plan of action to assess what could be toxic to the cells and systematically tested each component of the protocol that could affect the growth of her strain of influenza.
It took Son four attempts before she had a eureka moment: the success of her cell cultures depended on the precise measurement of just one reagent.
Too much of the reagent meant the cells would all die on arrival, but just a little bit, and they would survive. It took Son three more attempts — seven experiments in total — to fully ensure the success of the assay.
Throughout this process, and despite her many failures, Son realized she finds troubleshooting very enjoyable. Each failure was unique and crucial for her eventual success.
“I’m making a difference — I’m figuring something out that can really help with future experiments,” Son says. “That moment of success is why I gained such confidence in being a scientist.”
Yeongseo Son and Professor Spranger in the lab at the Koch Institute. Photo credit: Mandana Sassanfar.
Lighting Up the Lungs
In the Spranger Lab, Son’s other summer project focused on the respiratory system. She was examining a type of specialized cell called resident memory CD8+ T cells in the lungs and lymph nodes of mice infected with influenza. These specialized T cells gain a kind of memory of how to fight off a virus and remain in the lungs and lung-draining lymph node tissues long after the tissues have overcome the immune challenge of something like influenza.
Son’s postdoctoral student mentor Taylor Heim is especially interested in the potential of these cells for cancer immunotherapy.
To better understand how the resident memory T cell populations change over time, Son and Heim conducted a time-point experiment in which mice were studied at different points after being infected with influenza. They do this by injecting antibodies into the mouse’s bloodstream after infection, which mark any immune cells circulating in the blood, allowing the researchers to gauge if the cells are recruited to help fight a virus.
Son’s work this summer goes deeper, examining proteins known as cytokines that enable the immune system to combat germs or other substances that can harm an organism.
Son used a genetically modified mouse to track the production of interferon-gamma, IFN‐γ. IFN‐γ is a cytokine that plays a key role in regulating immune responses, often helping fight off infection and cancer. Son found evidence that resident memory T cells produce this cytokine in both the lungs and lung-draining lymph nodes.
The goal of this research is to one day use the information collected on resident memory CD8+ T cell populations and cytokine expression to help systematically target cancerous cells that appear in the body.
“Yeongseo has helped us pioneer a system to track how these cells move within tissues of living mice,” Spranger explains. “By using this approach, we will be able to understand how they are affecting cancer development and how cancer is affecting them, and that’s pretty exciting.”
Learning Outside the Lab
The BSG-MSRP-Bio program also gave Son near-constant access to faculty from across the biology department, both through extracurricular offerings such as dinner seminars and journal clubs as well as departmental retreats.
She’s also sat down with professors individually and heard more about their stories and research as part of her podcast Let’s Talk Chemistry. Nobel Laureate Phil Sharp, whose office is on the same floor as the Spranger Lab, joined the show after Son dropped by his office to introduce herself. Son learned more about his discoveries in RNA splicing and the behind-the-scenes details of his Nobel Prize ceremonies.
At MIT, Son has found a welcoming community of enthusiastic scientists working towards common goals, especially in her lab. Every day, members of the Spranger Lab actively seek each other out to have lunch together, and she feels right at home with them.
“I realized that yes, the people in this community are intensely passionate about their work, but they’re also multi-dimensional with a ton of different interests,” Son says. “One of the graduate students in my lab even gave me tennis lessons, and I’m already a better player because of it.”
As she returns to her studies in Georgia and begins the process of applying to graduate schools, Son is excited about her future in science. Armed with new knowledge, confidence, and community, she’s ready for whatever curveball her career in science will throw her next.
A scientist’s toolkit: practice, patience, and plenty of questions
Noah Daly | Department of Biology
September 24, 2024
A childhood interest in the complex worlds within an organism that the naked eye cannot see ultimately led Praise Lasekan to the BSG-MSRP-Bio program at MIT working in the Vos Lab in the Department of Biology at MIT.
Praise Lasekan talks about the fast protein liquid chromatography machines he used in the Vos Lab as though they were colleagues.
“We have two of them,” he explains. “Sam and Frodo.”
FPLC machines separate and analyze proteins based on their properties, such as size, charge, and binding affinity. When Lasekan first saw the FPLC machines, the tubing and valves, hooked up to a computer, reminded him of a fancy piece of plumbing. Much like an expert plumber, proficiency with these machines required him to understand every valve and tube.
Although Lasekan is a Biology major with a Chemistry Minor at the University of Maryland, Baltimore County, Lasekan had the opportunity to spend his summer living in Boston and working on MIT’s campus as a Bernard S. and Sophie G. Gould MIT Summer Research Program in Biology student.
“I loved every part of this summer: Waking up in the morning, coming to the lab, setting up some stuff — whether it goes well or not,” Lasekan says. “Taking that experience and coming back the next day, you’re ready to keep going and improving.”
Lasekan spent his days in the lab of Seychelle Vos, Robert A. Swanson Career Development Professor of Life Sciences and HHMI Freeman Hrabowski Scholar. The Vos Lab examines how genetic information is stored so compactly yet is still accessible enough for genes to be expressed. All cells in an organism have the same DNA, but the organization of that DNA and how genes are expressed determine why one cell becomes part of the liver and another cell part of the brain.
Lasekan worked with a highly conserved protein that plays a role in gene transcription called CCCTCF-binding factor, or CTCF. He worked to understand how adding a phosphate group, a process called phosphorylation, affects CTCF’s binding to DNA. Binding to DNA is the first step in the process of transcription, which creates proteins within a cell.
The Vos lab uses various tools and techniques that Vos learned during her training, often using simple systems with limited components to study phenomena such as molecular structures, the dynamics of proteins and nucleic acids, and how structural alterations affect the function of these molecules. The lab has also recently been delving into more systemic work, such as removing genes from cells to observe how that affects gene expression.
“My lab is a little unconventional in some ways,” Vos says. “We use a lot of biochemistry and structural biology, but we want to use the tools of genetics and cell biology as well to understand how genome organization and genome expression are coupled.”
BSG-MSRP-Bio Student Praise with Graduate Student and mentor, Bonnie Su, of the Vos Lab.
CTCF can play many roles during transcription, able to act as an activator or as a roadblock for transcription. Lasekan’s mentor, graduate student Bonnie Su, has been trying to figure out how cells control CTCF behavior.
“What if the cell needed something done ASAP, and CTCF was blocking its route to its destination on a DNA sequence?” Vos asks. “How does the cell regulate it?”
Praise mutated different sites on CTCF that have been reported in previous research as possible points of phosphorylation of the CTCF protein. Several other amino acids can also be phosphorylated. Still, Su was particularly interested in the work other researchers have done on three specific sites along a segment called the zinc finger domain. A zinc finger domain is a zinc ion that helps proteins stabilize their shape and the domain has a function in various cellular processes such as genetic transcription. The ion is regulated by amino acids to give it a finger-like structure that helps in binding the protein to DNA during transcription.
“Before we went on a wild goose chase,” Lasekan explains, “we needed to identify a specific area of the protein to concentrate on and examine the behavior of CTCF locally there.”
Off of the Drawing Board and Into the Laboratory
Lasekan was introduced to the microscopic world of the body — cells, organelles, molecules, and even atoms — in the pages of his secondary school science textbooks in Ondo, Nigeria. There began his curiosity about atomic structures, cells, and the complex worlds within an organism that the naked eye cannot see. He would spend much of his class time flipping through the pages of diagrams and ultimately decided to pursue science as his core focus during senior secondary school.
“It was there that I could take my first classes in chemistry, biology, and physics,” he says. “I realized I love all of the sciences, so my focus in school was science and technology.”
Initially drawn to engineering, Lasekan ended up dropping out of a technical drawing course.
“I loved the course,” Lasekan smiles, “but the course didn’t like me one bit.”
Lasekan’s dreams shifted toward medicine and, with it, more science and math courses.
When he graduated valedictorian from Staff Secondary School at the Federal University of Technology in Akure, his parents — both pharmacists — encouraged him to apply to university to become a medical doctor. However, getting into a good university is challenging in Nigeria.
Praise opted instead to remain at home after graduating, building a successful business doing portrait photography. He also took chemistry, physics, and biology courses through Cambridge University International.
Despite making good money with photography, Praise was determined to go to university but wasn’t confident that he would get in. Nevertheless, an acquaintance encouraged him to apply to UMBC.
“It was the only school I applied to, and I couldn’t believe that I got in,” says Lasekan.
At UMBC, Lasekan discovered the pre-med track he’d signed up for was not a good fit for him either — many of the fundamental questions he was curious about were beyond the scope of his courses. A friend who was working in a research lab on campus suggested that Lasekan should try to find a lab to work in, too.
“They told me I might like what they’re doing there because of the level of questions that I ask,” Lasekan says. “Sometimes people didn’t have answers for me, and maybe I could find some of those answers through research.”
Dr. Green focuses on trying to understand how post-translational modifications of proteins regulate functions, such as the establishment of proper states of gene expression and the ability of cells to respond to stress.
“Dr. Green took a chance with me,” Lasekan says. “I am forever grateful to her for that.”
MIT: A Destination for Scientific Discovery
When considering summer research programs, Praise applied to MIT, one institution he’d always remembered from his childhood textbooks as the birthplace of many great inventions and scientific discoveries.It’s also one of the few programs in the U.S. that accepts international students.
“I’ve always had MIT at the back of my mind, but I didn’t think they’re looking for people like me,” Lasekan says. When he saw the notification for his acceptance to the program pop up on his smartwatch, he screamed, startling some students walking by him in the hallway.
“This is one of the best institutions in the world, and I just got an opportunity to go there for ten weeks, actually do a project of my own under the mentorship of my PI,” Lasekan recalls thinking. “This was a dream come true for me.”
In the Vos lab, Lasekan’s interest in the fundamental questions of biology was not only acceptable but encouraged, especially by his mentor, Su.
“Bonnie always had the patience to sit down with me, explain concepts to me, and write out the math with me if I need her to,” Lasekan says, “and sometimes I need it 25 times, but she’s there for me.”
Now that the BSG-MSRP-Bio program has wrapped up, Praise has the confidence to set his sights higher than ever before — on the “big guys,” the universities and institutions doing the sort of cutting-edge research that first caught his eye in the textbooks back home. Praise is eagerly preparing his graduate school applications for fall 2025, including MIT.
“After being here, surrounded by people from everywhere driven by the same purpose, I know there’s an exciting future in science for me.”
MIT Digital Learning Lab’s high school interns gain professional experience working on the backend of open online MITx courses. The program emerged after Mary Ellen Wiltrout, PhD '09, digital learning scientist at MIT Open Learning, connected with the executive director and founder of Empowr, a nonprofit that serves low-income communities by creating a school-to-career pipeline through software development skills.
Katherine Ouellette | MIT Open Learning
August 26, 2024
Switching programming languages is not as simple as switching word processors. Yet high schooler Thomas Esayas quickly adapted from Swift to Python during his 2023 internship with the MIT Digital Learning Lab, a joint program between MIT Open Learning and the Institute’s academic departments. One year later, Esayas returns to the Institute for a second internship and as a new undergraduate student.
“I felt thoroughly challenged and learned a lot of new skills,” says Esayas.
Through this remote opportunity, interns gain real-world coding experience and practice professional skills by collaborating on MIT’s open online courses. The four interns from Digital Learning Lab’s 2023 and 2024 cohorts also participate in Empowr, a four-year program for low-income high school students that teaches in-demand software development skills and helps them secure paid internships.
The Digital Learning Lab program emerged after Mary Ellen Wiltrout PhD ’09, digital learning scientist at MIT Open Learning, connected with Adrian Devezin, executive director and founder of Empowr, at a conference about making education more accessible and equitable.
“It was affirming to have someone else see what Empowr is trying to do,” says Devezin about the organization’s goal to strengthen the school-to-career pipeline. “Being able to collaborate was beautiful for me, and more importantly, to the students.”
Building technical skills and self-confidence
The Digital Learning Lab internship empowers students to build confidence in their technical abilities, career skills, and the college application process. Interns assist the lab’s digital learning scientists with their work developing and maintaining online MITx courses at Open Learning across multiple academic areas.
“I found myself always busy with something interesting to work on,” says Esayas.
The interactive open education resources that Esayas produced last summer are now being used in live courses. He also helped find and fix bugs on the platform that hosts the MITx courses.
The internship’s flexible design allows projects to be adapted based on the student’s personal progress and interests.
“The students became co-creators of their educational experiences,” says Wiltrout, noting this is beneficial from a pedagogical standpoint.
Devezin adds, “I definitely saw a big improvement in their problem-solving abilities. Having to switch their mindset to a new language, work in new frameworks, and work on teams solving real problems enhanced their ability to adapt to new situations.”
The students’ also strengthened their professional repertoire in areas such as collaboration, communication, and project management. The 2023 cohort, Devezin says, developed the initiative to help other students and take on leadership roles.
Now that Esayas has completed his 2024 internship, he says, “I’m glad that I got to collaborate with more people and work on more projects. Overall, I’m very happy I was able to return.”
Adrian Devezin, executive director and founder of Empowr (left), and Mary Ellen Wiltrout, digital learning scientist at MIT Open Learning (right), presented their takeaways from the first year of the MIT Digital Learning Lab internship at the 2024 Open edX conference. Photo courtesy of Empowr.
Learning from both sides
Learning occurred for both students and educators alike. Wiltrout says that the Digital Learning Lab values the opportunity to see the interns’ growth day-to-day and week-to-week, since digital learning scientists rarely follow the trajectory of individual learners who are using the course materials they create. Having instant feedback informs how they can adjust their teaching approaches for various problems.
The positive impact of the Digital Learning Lab internship’s hands-on learning experiences has made Devezin rethink the way he teaches class moving forward, and “the problems I want them to be solving,” he says.
Now, Devezin tries to emulate the real-world experience of working on a project for his Empowr students. Instead of assigning coding exercises where he provides the exact methods to solve the problems, he started asking students to determine the correct approach on their own.
The fact that Wiltrout and Devezin are open to adapting their teaching methods based on student feedback is indicative of a key factor to the internship’s success — active participation in students’ growth. It was mutually beneficial for the students and the educators to have determined stakeholders at both Digital Learning Lab and Empowr.
“A lot of dedicated educators understand that there’s a lot of inequities in education, and we need to come together to solve them,” Devezin says.
The Digital Learning Lab internship shows how open source learning materials can make educational and professional opportunities more accessible. The 2024 cohort has been able to increase their annual household income by an average of 75%, a recent Empowr report revealed. Wiltrout says that the two new Empowr students seem more confident with coding and showed enthusiasm and dedication to their tasks as they also consider colleges.
Wiltrout and Devezin presented their takeaways from the internship’s first year at the 2024 Open edX conference.
“I think it’s important to try making sure that more people are aware of tools and resources that are out there,” Wiltrout says. “Then giving people opportunities where they may not have otherwise had that chance.”
Now, Devezin is thinking about how Empowr students can come full circle with their relationship to open educational materials. He’s asking, “How can I help my students contribute to the open source world to give back to others?”
Nine shifts in pedagogical and learning approaches since the global pandemic.
Yvonne Ng | MIT Open Learning
August 7, 2024
The Covid-19 pandemic created radical shifts in approaches to teaching and learning. And while the social, emotional, and mental toll of the pandemic has diminished greatly over the last four years, residual challenges still remain for students and educators. Mary Ellen Wiltrout PhD ’09, director of online and blended learning initiatives, lecturer, and digital learning scientist in Biology at MIT, has identified these shifts in her article, “How to build the future of teaching and learning while growing from the changes and challenges of 2020–21.”
In her article, published in 2022 in Advances in Online Education: A Peer-Reviewed Journal, Wiltrout hypothesized on the lasting impacts of the 2020–2021 events on teaching and learning organized across seven themes: course logistics, tools, activities and assessment for learning, student services and programs, work culture, attitudes, and relationships. Now in 2024 at MIT, Wiltrout can see the positive changes continuing and progressing in these areas:
Flexibility: During the pandemic, instructors were more flexible about coursework requirements, scheduling, grading structure, and expanded the number and types of assignments beyond summative exams. Some enacted policies enabling partial flexibility such as dropping the lowest score on assignments or allowing for late submissions. Now, with student support services approval, instructors remain open to working with students in need of flexibility.
Online learning: Residential colleges relying on completely in-person education now incorporate more blended learning and online courses for students interested in that option. Hybrid instruction and online assignments continue to be part of the curriculum.
Technology: The most valuable functions of the learning management system are the organization of course events and materials and the integration of the multitude of learning tools in one place with one login (for example, web conferencing, discussion forum, grading, video, and calendar). As a result of reducing barriers, more tools like online conferencing, polling, and tablet drawing software to teach, are being used by a larger percentage of teaching staff and students.
Reducing unconscious bias: Grading exams and assignments through an online tool increased the efficiency and consistency of grading with rubrics for every question. And the ability to anonymize submissions in the grading process helps reduce unconscious biases, while students also gain transparency from the rubrics to learn from mistakes and trust the process.
Rethinking in-person sessions: More conversations emerged on how to take advantage of in-person interactions to prioritize activities of value in that mode for learning and work. Instructors and students intentionally kept online approaches that enriched the experience as students returned to campuses. Some digital components enhance student learning, mental well-being, equity, or inclusion and could be as easy as providing a course chat channel for peer-to-peer and peer-to-staff conversations during synchronous sessions. Some instructors maintained more creative, open-ended assignments and online exam policies that seemed experimental during 2020.
Demand for student support services: The effects of the pandemic combined with normalizing taking care of mental health resulted in the sustained high demand for student support services. Institutions continue to invest more in the staffing of these services and programs, such as peer mentoring programs that result in positive academic and attitudinal gains for students. Instructors are generally more aware of how to positively influence students to seek help with simple actions, like speaking in a warm tone and intentionally including a statement about student services.
Belonging and inclusion: Racial and social injustices are being addressed more openly than ever before. Many institutions are recognizing the value and importance of diversity, equity, and inclusion in their students and staff and have invested in funding and training for their community to shift their culture in a positive way. At the course level, instructors have the training and resources available to learn how to become more inclusive teachers (through free resources such as massive open online courses or internal efforts) and have the student and institution pressure to do so.
Mentoring: With the help of online tools and technology, students, educators, and staff are able to foster and create meaningful internship programs. Mentoring in these online programs with students in disparate locations around the world continues to take place and have a positive impact for students and any research that may be part of a program.
Collaborations: Although possible before, more researchers see collaborations across states or countries as less of a hurdle, especially with the everyday use of tools like Zoom. Instructors enhance authentic experiences for students by bringing outside experts into the classroom virtually for discussion — a method that was not used often before the pandemic.
Wiltrout concludes that many opportunities for widespread maintenance of practices that worked well and benefited students during the pandemic can and should continue to persist and grow into the future. Instructors also expanded and improved their curricula and pedagogical approaches to nurture a more inclusive and engaging course for their students and themselves.
“The lasting impacts of the pandemic include profound lessons on what best served both learners and educators,” Wiltrout says. “It’s heartening to see changes and adjustments to pedagogy, student services and programs, attitudes, and relationships that continue to benefit everyone. If these new effective ways endure and grow, then a better future of education for students, staff, and instructors is possible.”
At the cutting edge of pedagogy, Mary Ellen Wiltrout has shaped blended and online learning at MIT and beyond.
Samantha Edelen | Department of Biology
September 18, 2024
When she was a child, Mary Ellen Wiltrout PhD ’09 didn’t want to follow in her mother’s footsteps as a K-12 teacher. Growing up in southwestern Pennsylvania, Wiltrout was studious with an early interest in science — and ended up pursuing biology as a career.
But following her doctorate at MIT, she pivoted toward education after all. Now, as the director of blended and online initiatives and a lecturer with the Department of Biology, she’s shaping biology pedagogy at MIT and beyond.
Establishing MOOCs at MIT
To this day, E.C. Whitehead Professor of Biology and Howard Hughes Medical Institute (HHMI) investigator emeritus Tania Baker considers creating a permanent role for Wiltrout one of the most consequential decisions she made as department head.
Since launching the very first MITxBio massive online open course 7.00x (Introduction to Biology – the Secret of Life) with professor of biology Eric Lander in 2013, Wiltrout’s team has worked with MIT Open Learning and biology faculty to build an award-winning repertoire of MITxBio courses.
MITxBio is part of the online learning platform edX, established by MIT and Harvard University in 2012, which today connects 86 million people worldwide to online learning opportunities. Within MITxBio, Wiltrout leads a team of instructional staff and students to develop online learning experiences for MIT students and the public while researching effective methods for learner engagement and course design.
“Mary Ellen’s approach has an element of experimentation that embodies a very MIT ethos: applying rigorous science to creatively address challenges with far-reaching impact,” says Darcy Gordon, instructor of blended and online initiatives.
Mentee to motivator
Wiltrout was inspired to pursue both teaching and research by the late geneticist Elizabeth “Beth” Jones at Carnegie Mellon University, where Wiltrout earned a degree in biological sciences and served as a teaching assistant in lab courses.
“I thought it was a lot of fun to work with students, especially at the higher level of education, and especially with a focus on biology,” Wiltrout recalls, noting she developed her love of teaching in those early experiences.
Though her research advisor at the time discouraged her from teaching, Jones assured Wiltrout that it was possible to pursue both.
Jones, who received her postdoctoral training with late Professor Emeritus Boris Magasanik at MIT, encouraged Wiltrout to apply to the Institute and join American Cancer Society and HHMI Professor Graham Walker’s lab. In 2009, Wiltrout earned a PhD in biology for thesis work in the Walker lab, where she continued to learn from enthusiastic mentors.
“When I joined Graham’s lab, everyone was eager to teach and support a new student,” she reflects. After watching Walker aid a struggling student, Wiltrout was further affirmed in her choice. “I knew I could go to Graham if I ever needed to.”
After graduation, Wiltrout taught molecular biology at Harvard for a few years until Baker facilitated her move back to MIT. Now, she’s a resource for faculty, postdocs, and students.
“She is an incredibly rich source of knowledge for everything from how to implement the increasingly complex tools for running a class to the best practices for ensuring a rigorous and inclusive curriculum,” says Iain Cheeseman, the Herman and Margaret Sokol Professor of Biology and associate head of the biology department.
Stephen Bell, the Uncas and Helen Whitaker Professor of Biology and instructor of the Molecular Biology series of MITxBio courses, notes Wiltrout is known for staying on the “cutting edge of pedagogy.”
“She has a comprehensive knowledge of new online educational tools and is always ready to help any professor to implement them in any way they wish,” he says.
Gordon finds Wiltrout’s experiences as a biologist and learning engineer instrumental to her own professional development and a model for their colleagues in science education.
“Mary Ellen has been an incredibly supportive supervisor. She facilitates a team environment that centers on frequent feedback and iteration,” says Tyler Smith, instructor for pedagogy training and biology.
Prepared for the pandemic, and beyond
Wiltrout believes blended learning, combining in-person and online components, is the best path forward for education at MIT. Building personal relationships in the classroom is critical, but online material and supplemental instruction are also key to providing immediate feedback, formative assessments, and other evidence-based learning practices.
“A lot of people have realized that they can’t ignore online learning anymore,” Wiltrout noted during an interview on The Champions Coffee Podcast in 2023. That couldn’t have been truer than in 2020, when academic institutions were forced to suddenly shift to virtual learning.
“When Covid hit, we already had all the infrastructure in place,” Baker says. “Mary Ellen helped not just our department, but also contributed to MIT education’s survival through the pandemic.”
For Wiltrout’s efforts, she received a COVID-19 Hero Award, a recognition from the School of Science for staff members who went above and beyond during that extraordinarily difficult time.
“Mary Ellen thinks deeply about how to create the best learning opportunities possible,” says Cheeseman, one of almost a dozen faculty members who nominated her for the award.
Recently, Wiltrout expanded beyond higher education and into high schools, taking on several interns in collaboration with Empowr, a nonprofit organization that teaches software development skills to Black students to create a school-to-career pipeline. Wiltrout is proud to report that one of these interns is now a student at MIT in the class of 2028.
Looking forward, Wiltrout aims to stay ahead of the curve with the latest educational technology and is excited to see how modern tools can be incorporated into education.
“Everyone is pretty certain that generative AI is going to change education,” she says. “We need to be experimenting with how to take advantage of technology to improve learning.”
Ultimately, she is grateful to continue developing her career at MIT biology.
“It’s exciting to come back to the department after being a student and to work with people as colleagues to produce something that has an impact on what they’re teaching current MIT students and sharing with the world for further reach,” she says.
As for Wiltrout’s own daughter, she’s declared she would like to follow in her mother’s footsteps — a fitting symbol of Wiltrout’s impact on the future of education.
When Reynold I. Lopez-Soler, SB ’94, saw his first kidney transplant, during his medical residency, he found his life’s work.
Kathryn M. O'Neill | MIT Technology Review
September 6, 2024
When Reynold I. Lopez-Soler ’94 saw his first kidney transplant, during his medical residency, he found his life’s work.
“It’s such a magical and incredible thing that you can do this,” says Lopez-Soler, director of the renal transplant program at the Edward Hines Jr. Veterans Affairs Hospital outside Chicago. “You’re watching this organ that was taken out [of the donor], practically lifeless and inert, and through the expertise of surgery it comes to life and becomes pink; it starts to make urine.”
About 100,000 people in the United States are currently waiting for a kidney transplant; on average, they will wait five to seven years. Lopez-Soler is expanding access to this care for veterans.
Kidney transplants are life-changing, he says, not only because kidney disease can make people very sick, but because the main treatment—dialysis, which does some of the kidney’s job outside the body—is so demanding that many patients can’t work or even travel. “Getting a kidney transplant not only fixes the problem, but fixes their lives going forward,” he says. “There is this substantial transformation.”
Growing up in Puerto Rico, Lopez-Soler always expected to become a surgeon (his father is a surgical oncologist). During high school, he discovered the MIT Introduction to Technology, Engineering, and Science (MITES) program, spent a summer on campus, and fell in love with the Institute. “MIT was an incredibly inclusive place,” he says. “Whatever you did, you were welcome. I’ve brought that acceptance with me in my ethos in how I deal with people.”
After majoring in biology at MIT (with a minor in Spanish literature), Lopez-Soler earned his MD and PhD from Northwestern University and completed his surgical residency at Yale New Haven Hospital. Then he practiced in Virginia and New York, where he was director of research at Albany Medical Center.
In 2019, Lopez-Soler was tapped to establish the VA transplant program at Hines, and in its first year, it completed 36 kidney transplants. Last year, the center did 105. He now chairs the Department of Veterans Affairs Transplant Surgery Surgical Advisory Board, which helps develop transplant policies and procedures for the whole VA system.
The grandson of a brigadier general, Lopez-Soler is proud to serve veterans. “I was lucky enough to fall in love with the job because of the people we treat,” he says. “It exposed me to these amazing veterans who have done so much for this country.”
This story also appears in the September/October issue of MIT Alumni News magazine, published by MIT Technology Review.
Photo illustration by Mary Zyskowski; image of Reynold I. Lopez-Soler courtesy of Lopez-Soler.
From the intricacies of plant reproduction to genome-wide analyses, Gehring’s lab delves deep into the epigenetic mechanisms shaping plant biology.
Jayashabari Shankar and Alex Tang | The Tech
September 5, 2024
Dr. Mary Gehring is a professor of biology at MIT and a core member of the Whitehead Institute for Biomedical Research. Her research focuses on how epigenetic mechanisms like DNA methylation influence gene regulation during plant reproduction and seed development in the model organism Arabidopsis thaliana. In the classroom, she teaches genetics (7.03), a required course for biology and biological engineering majors.
With her recent appointment as an Howard Hughes Medical Institute (HHMI) investigator, Gehring joins an elite legion of HHMI investigators at the Institute. New cohorts of investigators are only announced once every three years, and they receive $11 million in funding over a seven year term (which can be renewed). Three other MIT faculty received HHMI appointments this year: Gene-Wei Li, associate professor of biology, and brain and cognitive sciences professors Mehrdad Jazayeri and Steven Flavell.
Here, she shares her lab’s research, journey into plant biology, and what she values in undergraduate researchers.
TT: What does your lab conduct research in, and how has being named an HHMI investigator changed your plans, if at all?
My lab focuses on plant biology, particularly on how epigenetic mechanisms like DNA methylation affect gene regulation in plants, especially during reproduction and seed development. We mostly work with Arabidopsis thaliana, a model plant, but we’re also exploring other plant systems.
A typical day in the lab can vary, but it often starts with checking on our plants in the greenhouse. Depending on the day, we might pollinate plants for genetic crosses or genotyping them by isolating DNA and performing PCR. We’re particularly focused on understanding gene expression within seeds: we isolate different seed tissues, sort nuclei based on their properties, and then perform RNA sequencing. We also do a lot of chromatin profiling, histone modifications and DNA methylation analyses across the genome. Since much of our work is genome-wide, bioinformatics plays a big role in our research, with a significant amount of time spent on analyzing data.
It’s still sinking in, but being named an HHMI investigator certainly provides a new level of freedom. It allows us to pursue ideas without the constraints of specific grant funding, which is incredibly liberating. We’re considering expanding our research into new areas beyond epigenetics, like genome structure and chromosome dosage changes, while sticking with plant biology. This recognition has encouraged us to think bigger and explore new directions in our work.
TT: How far back do these interests extend for you?
My interest in plant biology started during my undergraduate years. I majored in biology and was eager to get involved in research. My real fascination with plants began when a new professor, with a background in plant biology, came to my school. I took her course on plant growth and development, which I found incredibly exciting. I was drawn to how plants communicate within their tissues and with each other. This led me to work on a research project for two years, culminating in a senior thesis on root development. After college, I took a year off to work in environmental consulting before heading to graduate school in Plant Biology at UC Berkeley.
TT: What perspectives and characteristics do you appreciate in undergraduate researchers?
Whether it’s undergraduates or postdocs, I value curiosity and dedication. For undergraduates, especially those in UROPs, it’s crucial that they are genuinely interested in the research and willing to ask questions when they don’t understand something. Balancing research with coursework and extracurriculars at MIT is challenging, so I also look for students who can manage their time well. It’s about being curious, dedicated, and communicative.
I hope there are students at MIT who are excited about plant research. It’s a vital area of biology, especially with the growing focus on climate change. While there isn’t a large presence of plant biology at MIT yet, I’m hopeful that it will expand in the coming years, and I’d love to see more students getting involved in this important field.
The Koch Institute at MIT is pleased to announce the winners of the 2024 Angelika Amon Young Scientist Award, Anna Uzonyi and Lukas Teoman Henneberg.
Koch Institute
September 3, 2024
The Koch Institute at MIT is pleased to announce the winners of the 2024 Angelika Amon Young Scientist Award, Anna Uzonyi and Lukas Teoman Henneberg.
The prize was established in 2021 to recognize graduate students in the life sciences or biomedical research from institutions outside the United States who embody Dr. Amon’s infectious enthusiasm for discovery science.
Both of this year’s winners work to unravel the fundamental biology of chromatin, the densely structured complex of DNA, RNA, and proteins that makes up a cell’s genetic material.
Uzonyi is pursuing her PhD at the Weizmann Institute of Science in Israel under the supervision of Schraga Schwartz and Yonatan Stelzer. In her thesis, Uzonyi focuses on deciphering the principles of RNA editing code via large-scale systematic probing.
Henneberg is a doctoral candidatein the Department of Molecular Machines and Signaling, at the Max Planck Institute of Biochemistry in Germany, works under the supervision of Professor Brenda Schulman and Professor Matthias Mann. For his research project, he probes active ubiquitin E3 ligase networks within cells. He works on the development of probes targeting active ubiquitin E3 ligases within cells and utilizing them in mass spectrometry-based workflows to explore the response of these ligase networks to cellular signaling pathways and therapeutics.
This fall, Anna Uzonyi and Lukas Teoman Henneberg, will visit the Koch Institute. The MIT community and Amon Lab alumni are invited to attend their scientific presentations on Thursday, November 14 at 2:00 p.m. in the Luria Auditorium, followed by a 3:30 p.m. reception in the KI Galleries.
Uzonyi will present on “Inosine and m6A: Deciphering the deposition and function of adenosine modifications” and Henneberg will present on “Capturing active cellular destroyers: Probing dynamic ubiquitin E3 ligase networks.“
