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Unusual Labmates: Fruit flies
Greta Friar | Whitehead Institute
August 4, 2021

All the buzz in the lab

On a sunny summer morning in Cambridge, Massachusetts, Mariyah Saiduddin walked into a room and was met by the sight of thousands of fruit flies. For most people, this would be an emergency: time to call an exterminator, take out the trash, and scrub the room from top to bottom. However, this room full of flies is part of Whitehead Institute Director Ruth Lehmann’s lab, where fruit flies are seen not as pests but as valuable research tools—and are safely contained in vials. Saiduddin is a graduate student researcher in Lehmann’s lab who uses a fraction of the flies in the room in her research.

The flies found in Lehmann’s lab, and in the adjacent lab run by Whitehead Institute Member Yukiko Yamashita, are not exactly like their less-beloved wild counterparts. Fruit flies have been used in research for more than a century, and in that time, they have been engineered to become powerful, malleable models capable of answering questions in many areas of research. The most common species used in research is Drosophila melanogaster, often referred to simply as “Drosophila.” The researchers who use flies call themselves Drosophilists, and their community around the world works together to maintain a rich variety of flies and create new tools with which to manipulate those flies. In the past century, work in fruit flies has led to six Nobel Prizes in Physiology or Medicine, and has shed light on topics from the basics of genetics, to the principles of embryonic development, to circadian rhythms, to the immune system, to a plethora of diseases.

A very fly model organism

Fruit flies became a go-to research tool during the explosion of genetics research around the turn of the 20th century. What makes them such a good model organism? First of all, they are easy and relatively cheap to raise in large numbers. They have short lifespans and quick reproduction times, so researchers can rapidly breed and study multiple generations. Fruit flies are ready to reproduce—growing from embryo to larva to adult—in under two weeks and then can lay hundreds of eggs in a matter of days.

Fruit flies and humans have enough similarities in their genetics and development that research in fruit flies often reflects human biology. In particular, when it comes to genetics, fruit flies have more commonalities with humans than they have differences. Nearly three-quarters of the genes that cause diseases in humans have an equivalent gene—one derived from the same ancestral gene—in fruit flies.
Not only are fruit flies naturally suited for research, but over the years they have been engineered to become even better research subjects. One of the earliest improvements to fruit flies as a research model came from researchers discovering that they could create flies with genetic mutations that change things like a fly’s eye color, wing shape, body shape, or the bristles on its thorax. Researchers began selectively breeding different lines of fruit flies to have these distinctive physical traits or “markers,” which make them easy to tell apart.
Researchers can tie a visible genetic marker, such as curly wings, to a genetic mutation that they are studying that may not be visible, so that they can easily sort their flies. For example, Whitehead Institute researchers using flies to study mutations that affect the germ cells, the set of cells that make or become eggs and sperm, cannot tell just by looking at a fly whether it has a mutation that affects germ cells, but if they tie inheritance of the mutation to the curly wing marker, then the flies with the desired mutation become easy to identify.
Drosophila biologists have adapted tools from other model organisms to control and study essentially any gene in flies. The Gal4-UAS system, which was developed based on a gene and gene regulator found in yeast, is now commonly used in flies. The system lets researchers activate a gene only in certain tissues or sets of cells. For example, researchers may want to know what part of the brain a certain gene is active in, so they will use the Gal4-UAS system to express green fluorescent protein (GFP) only in cells that would also normally express the gene of interest, allowing researchers to map gene activity based on fluorescence. Or, Gal4-UAS can be used to turn off a gene involved in embryonic development, to see what changes when that gene is not active. This is a common approach that researchers use to figure out a gene’s function; it works in the same way that one could deduce the purpose of brakes on a car by taking the brakes off and observing the car being unable to stop when its driver steps on the brake pedal. Gal4 lines can be developed and tested quickly, in a couple of months, and because the Drosophilist community tends to share their resources, as soon as one lab has developed a Gal4 line for a gene, any fruit fly lab can use that tool to ask their own research questions. Thousands of Gal4 lines are maintained in centralized collections, making them very easy to access.

The embryonic days of fly research

The transformation of fruit flies from wild pests into top notch research tools began in the early 1900s. Charles W. Woodworth, at Harvard University at the turn of the 20th century, is credited with being the first researcher to breed Drosophila in large numbers and with suggesting that the species could be used to study genetics, then a new field of research.[2] Thomas Hunt Morgan, at Columbia University, was one of several researchers to follow Woodworth in using fruit flies for his research, and it was Morgan who really established fruit flies as a model organism, through both his own success and that of the students who came out of his lab and the soon-famous Columbia fly room.

For his research, Morgan bred fruit flies until one developed a mutation, white eyes (most fruit flies’ eyes are red), and then continued breeding the mutant and its descendants to track patterns in inheritance of the white-eyes trait. With these experiments, Morgan showed that genes, which had recently been established as the smallest units of inheritance, are organized on chromosomes, cellular structures each one of which contains a certain, consistent set of genes. One of Morgan’s students, Alfred Sturtevant, expanded on this work, showing that the genes on each chromosome can be mapped in a specific linear order. The proof of the chromosome theory of inheritance won Morgan the 1933 Nobel Prize in Physiology or Medicine and the mutation that Morgan identified, white, is still used as a marker in fruit flies today. Morgan and the scientists who came through his lab continued to do groundbreaking research, demonstrating the potency of fruit flies as a model, and soon flies became a popular research tool.

Research in fruit flies has led to five further Nobel Prizes since Morgan’s, including the 1995 prize awarded to Edward B. Lewis, Christiane Nüsslein-Volhard and Eric Wieschaus for their discoveries regarding “the genetic control of early embryonic development.” These three researchers identified and discovered the function of key genes involved in determining and carrying out the blueprint for a fly’s body during development. Nüsslein-Volhard and Wieschaus systematically mutated many flies in order to discover the genes involved in body patterning. After they introduced lots of mutations, they observed what happened to the flies, and then they determined which genes had been mutated to cause the effects to body patterning that they observed. Using this strategy, they identified and characterized many key genes involved in guiding the development of an embryo into a segmented body.

Lewis, meanwhile, identified and determined the function of what would come to be known as homeotic genes, the genes that determine which specific body parts grow in each body segment: these genes essentially determine the blueprint for the fly’s body, and—as Lewis showed—when mutated lead to some very unusual body plans. Collectively, these researchers’ discoveries illuminated both the genetics and the evolution of the body plan in flies—work that was quickly extrapolated to other species, including humans, whose development occurs in a similar fashion.

Lewis, Nüsslein-Volhard and Wieschaus’ work set the stage for future researchers such as Lehmann and Yamashita who study development in flies. In fact, Nüsslein-Volhard had a direct influence on Lehmann: Lehmann trained with her as a graduate student. Nüsslein-Volhard’s later work provided important insights into the morphogen gradients that help guide the developing embryo in assembling itself correctly, and included an in-depth gene screen of zebrafish using the same extensive process of mutation and observation that she and Wieschaus had used in Drosophila.

Researchers at Whitehead Institute are using fruit flies to answer a wide variety of questions. In previous years, former Whitehead Institute Member Terry Orr-Weaver used Drosophila to study the process of cell division during development. She looked at questions such as what determines cell size, what regulates the transition from egg to embryo, and how DNA is accurately replicated and sorted into dividing cells. Whitehead Institute Member David Bartel, also a professor of biology at the Massachusetts Institute of Technology (MIT) and an HHMI investigator, studies RNA and has done some of that research in flies. His work has improved our understanding of how tiny regulatory RNAs called microRNAs target and initiate the destruction of the RNAs that code for proteins in many species, including flies. He used these insights to create TargetScanFly, a database that provides researchers around the world with fly microRNAs’ predicted targets. Bartel’s lab also recently discovered how some microRNAs are rapidly degraded in Drosophila cells and how other types of small regulatory RNAs are protected from this degradation. In other studies of gene regulation in flies, performed in collaboration with Orr-Weaver, the Bartel lab identified the RNAs that are first produced by the developing embryo and determined why RNAs of some genes are much better than those of others at producing proteins in fly oocytes and early embryos.

Lehmann and Yamashita use fruit flies to study germ cells, the cells set aside to make or become eggs and sperm—as did Orr-Weaver. The germ line is set aside from the rest of the body’s cells early on, and has the rare property of being, essentially, immortal: all of the other cell lines in the body will eventually die with it, but germ cells survive to become offspring, which contain new germ cells, and so on through the generations.

Rewiring cell division to make eggs and sperm
Whitehead Institute
July 30, 2021

To create eggs and sperm, cells must rewire the process of cell division. Mitosis, the common type of cell division that our bodies use to grow everything from organs to fingernails and to replace aging cells, produces two daughter cells with the same number of chromosomes and approximately the same DNA sequence as the original cell. Meiosis, the specialized cell division that makes egg and sperm in two rounds of cell division, creates four granddaughter cells with new variations in their DNA sequence and half as many chromosomes in each cell. Meiosis uses most of the same cellular machinery as mitosis to achieve this very different outcome; only a few key molecular players prompt the rewiring from one type of division to another. One such key player is the protein Meikin, which is found exclusively in cells undergoing meiosis.

New research from Whitehead Institute Member Iain Cheeseman, graduate student Nolan Maier and collaborators Professor Michael Lampson and senior research scientist Jun Ma at the University of Pennsylvania demonstrates how Meikin is elegantly controlled, and sheds light on how the protein acts to serve multiple roles over different stages of meiosis. The findings, which appear in Developmental Cell on July 30, reveal that Meikin is precisely cut in half midway through meiosis. Instead of this destroying the protein, one half of the molecule, known as C-Meikin, goes on to play a critical role as a previously hidden protein actor in meiosis.

“Cells have this fundamental process, mitosis, during which they have to divide chromosomes evenly or it will cause serious problems like cancer, so the system has to be very robust,” Maier says. “What’s incredible is that you can add one or two unique meiotic proteins like Meikin and dramatically change the whole system very quickly.”

Helping chromosomes stick together

During both mitosis and meiosis, sister chromatids — copies of the same chromosome — pair up to form the familiar “X” shape that we recognize as a chromosome. In mitosis, each chromatid—each half of the X — is connected to a sort of cellular fishing line and these lines reel the chromatids to opposite ends of the cell, where the two new cells are formed around them. However, in the first round of division in meiosis, the sister chromatids stick together, and one whole “X” is reeled into each new cell. Meikin helps to achieve this different outcome by ensuring that, while the chromosomes are being unstuck from each other in preparation for being pulled apart, each pair of sister chromatids stays glued together in the right place. Meikin also helps ensure that certain cellular machinery on the sister chromatids is fused so that they will connect to the same line and be reeled together to the same side of the cell.

More specifically, when chromosomes are first paired up, they are glued together by adhesive molecules in three regions: the centromere, or center of the X, where Meikin localizes; the region around the center; and the arms of the X. In the first round of meiosis, Meikin helps to keep the glue in the region around the center intact, so the sister chromatids will stick together. Simultaneously, Meikin helps to prime the center region to be unglued, while a separate process unglues the arms. This ungluing allows the chromosomes to separate and be prepared for later stages of meiosis.

Cheeseman and Maier initially predicted that Meikin’s role ended after meiosis I, the first round of meiotic cell division. In meiosis II, the second round of cell division, the cells being created should end up with only one sister chromatid each, and so the chromatids must not be kept glued together. Maier found that near the end of meiosis I, Meikin is cleaved in two by an enzyme called Separase, the same molecule that cleaves the adhesive molecules gluing together the chromosomes. At first, this cleavage seemed like the end of Meikin and the end of this story.
A hidden role for a hidden proteinHowever, unexpectedly, the researchers found that cells lacking Meikin during the second half of meiosis do not divide properly, prompting them to take another look at what happens to Meikin after it gets cleaved. They found that Separase cleaves Meikin at a specific point — carving it with the precision of a surgeon’s scalpel — to create C-Meikin, a previously unknown protein that turns out to be necessary for meiosis II. C-Meikin has many of the same properties as the intact Meikin molecule, but it is just different enough to take on a different role: helping to make sure that the chromosomes align properly before their final division.

“There’s a lot of protein diversity in cells that you would never see if you don’t go looking for it, if you only look at the DNA or RNA. In this case, Separase is creating a completely different protein variant of Meikin than can function differently in meiosis II,” says Cheeseman, who is also a professor of biology at Massachusetts Institute of Technology. “I’m very excited to see what we might discover about other hidden protein forms in cell division.”

Recombining ideas

Answering the question of Meikin’s role and regulation throughout meiosis required a close collaboration and partnership between Maier and Lampson lab researcher Ma – the Lampson lab being experts on studying meiosis using mouse models. Working with mouse oocytes (immature egg cells), Ma was able to reveal the behaviors and critical contributions of Meikin cleavage in meiotic cells in mice. Both labs credit the close exchange with helping them to get a deeper understanding of how cells rewire for meiosis.

“It was a pleasure working together to understand how some of the specialized meiotic functions that are necessary for making healthy eggs and sperm are controlled,” Lampson says.

Finally, once cells have completed these specialized meiotic divisions, the researchers found that it was critical for oocytes to fully eliminate Meikin. The researchers determined that, after meiosis two, C-Meikin is degraded by another molecule (the anaphase-promoting complex or APC/C)—this time for good. With Meikin gone and the rewiring of cell division reversed, eggs and sperm are ready for mitosis; should they fuse and form an embryo, that is the next cell division they will undergo. The researchers note that the way Meikin is regulated by being broken down — first into C-Meikin and then completely — may help cells to organize their timing during meiosis. Breaking apart a protein is an irreversible step that creates a clear demarcation between before and after in a multi-step process.The researchers hope that by uncovering the intricacies of meiosis, they may shed light on what happens when the creation of eggs and sperm goes wrong, and so perhaps contribute to our understanding of infertility. Cheeseman also hopes that by studying how mitotic processes are rewired for meiosis, his lab can gain new insights into the original wiring of mitosis.

Probing pathogen spread during a global pandemic

Bailey Bowcutt investigated COVID-19 cases in rural Wyoming before coming to MIT for the summer and applying her knowledge to a new cellular invader.

Raleigh McElvery
July 23, 2021

The first time Bailey Bowcutt saw a lab it was nothing like she expected. Rather than a stark, sterile setting with sullen figures floating around like ghosts in white lab coats, the atmosphere was cordial and the dress casual. Some scientists even sported vibrant shirts with Marvel characters. A high school senior on a class field trip, Bowcutt couldn’t have predicted that the next time she’d set foot in the Wyoming Public Health Laboratory she’d no longer be a visitor, but a researcher performing diagnostic testing during a global pandemic. Now, as COVID-19 restrictions begin to lift, she’s taking the research tools she’s learned to Cambridge, Massachusetts to complete the Bernard S. and Sophie G. Gould MIT Summer Research Program in Biology (BSG-MSRP-Bio) and investigate how other types of pathogens spread.

Growing up in rural Wyoming, Bowcutt had little exposure to science because there were few research institutes close by. But watching family members suffer from gastrointestinal illness and other infections spurred her to pursue a degree in microbiology at Michigan State University (MSU). Shortly after she arrived on campus in the fall of 2019, she joined Shannon Manning’s lab studying antibiotic resistance in cattle.

Cows are prone to contracting a bacterial infection of the udder called mastitis. (In humans, a similar inflammation can occur in breast tissue.) Manning’s lab is looking at how antibiotic treatments affect the bovine gut microbiome and emergence of antibiotic resistance genes. Bowcutt’s role was to help identify these super bugs inside the cows’ gastrointestinal tracts.

“I got to go to the farm to take samples, which involved a glove that goes all the way up to the shoulder and some invasive maneuvers inside cows,” she explains. “Luckily, I was just the bag holder!”

Intimate sample collection aside, Bowcutt was excited about the work because it combined agriculture and human health research to solve issues plaguing rural communities. But her time on the farm was cut short when COVID-19 cases climbed in early 2020. She headed back to her home in Wyoming to begin remote MSU classes and, reminiscing about her field trip to the Wyoming Public Health Laboratory, reached out to the director to see if there were any internship opportunities.

“I’d barely learned how to do science at that point, but they needed people who could handle a pipette, so they took me,” she says. “I ended up being one of the first people there helping with COVID research, and I stayed for about a year-and-a-half while I took online classes.”

The lab would receive nasopharyngeal swabs from COVID-19 patients, and Bowcutt’s first task was to help extract RNA from the samples. Later, she transitioned to another project, which required performing PCR on untreated wastewater samples to glean a population-level understanding of where COVID-19 outbreaks were occurring.

She began toying with the idea of pursuing a PhD, but wasn’t sure what it would entail. So, in early 2021, she started Googling summer science programs and stumbled on BSG-MSRP-Bio. She was accepted, and paired with one of the very labs that had caught her eye online: assistant professor Becky Lamason’s group.

Microscopy image of parasites rocketing around inside cells
Listeria monocytogenes (yellow) rocket around their host cells (outlined in cyan) before ramming through the host’s membrane and that of its neighbor, forming a protrusion that is engulfed by the recipient cell. Image by Cassandra Vondrak.

“If you’ve ever seen microscopy pictures from the Lamason lab, they’re just so beautiful,” Bowcutt explains. Beautiful, yes — but she would soon learn these snapshots capture a chilling cellular invasion and molecular heist.

The Lamason lab watches malicious bacteria as they hijack molecules in human host cells to build long tails, rocket around, and punch through the cell membrane to spread. Bowcutt’s mentor, graduate student Yamilex Acevedo-Sánchez, focuses on the food-borne bacterium Listeria monocytogenes, which targets the gastrointestinal tract. Acevedo-Sánchez’s research aims to understand the host cell pathways that Listeria commandeers to move from one cell to the next in a process called cell-to-cell spread.

Together, Acevedo-Sánchez and Bowcutt are investigating several proteins in the human host cell involved in cellular transport and membrane remodeling (Caveolin-1, Pacsin2, and Fes), which could regulate Listeria’s spread. Over the summer, the duo has been adjusting the levels of these proteins and observing what happens to Listeria’s ability to move from cell-to-cell.

Bowcutt spends most of her days doing Western blots; growing Listeria and mammalian cells; and combining immunofluorescence assays with fixed and live cell microscopy to take her own striking microscopy images and movies of the parasites.

“I expected the work environment at MIT to be very intense, but everyone has been really friendly and willing to answer questions,” she says. “Some of my favorite experiences have just been in the lab while everyone is bustling around. It’s a welcome change after so much COVID-19 isolation.”

Now that the COVID-era occupancy restrictions have lifted, Bowcutt’s lab bench neighbor is Lamason herself. “She’s next to me doing experiments all the time,” Bowcutt explains, “which is cool because she’s really engaging with the research in the same way we are.”

Bowcutt says her summer experience has given her some much-needed practice designing research questions and devising the experiments to answer them. She’s also acquired a new skill she didn’t anticipate: interpreting ambiguous results and developing follow-up experiments to clarify them.

These days, the prospect of a PhD seems much less intimidating. In fact, the Lamason lab has done more than simply pique Bowcutt’s interested in fundamental biology research. She’s now considering ways to combine her microbiology skills with her interest in rural health care.

“I didn’t expect to see this much growth in myself,” she says, “and I know it’s making me a better scientist. I’m excited to return to MSU in the fall because I feel like I can do so much more now — and I would totally do it again.”

Lodish receives lifetime achievement award
Merrill Meadow | Whitehead Institute
July 13, 2021

The American Society of Hematology (ASH), will honor Whitehead Institute Founding Member Harvey Lodish with its Wallace H. Coulter Award for Lifetime Achievement in Hematology.

The Coulter Award—ASH’s highest honor—recognizes an individual who has demonstrated a lasting commitment to the field of hematology through outstanding contributions to education, research, and practice.

Lodish is being honored for his six decades of key contributions to hematology, including his studies of the structure and biogenesis of red blood cells and his use of those cells as vehicles for delivering therapeutics. His research has provided important insights into several red cell diseases, including beta thalassemia and polycythemia vera; and he identified a new family of growth factor receptors, now known as the cytokine receptor superfamily. Lodish is also being recognized for his mentorship of more than 200 students and fellows, including two Nobel Prize recipients.

He will formally receive the Award at the 2021 ASH Annual Meeting in December.

A “tail” of two RNA regulatory systems
Greta Friar | Whitehead Institute
July 12, 2021

In new research, published in eLife on July 2, Bartel, who is also a professor of biology at Massachusetts Institute of Technology and an investigator with the Howard Hughes Medical Institute, and Bartel lab member Kehui Xiang, a CRI Irvington Postoctoral Fellow, have now discovered how cells establish this early gene regulatory regime and what conditions prompt a switch as the embryos mature. The researchers have observed the same regulatory switch in fish, frogs, and flies, and because the switch occurs across the animal kingdom, they would expect to see that the mechanism applies in other species including mammals.

“When I joined the lab, they had discovered that egg cells and early embryos had this different regulatory regime, and I wanted to know why,” Xiang says. “There must be fundamental changes to the cell, or to the molecules in the cell, that define this.”

The difference in how mRNAs are regulated during and after early development has to do with the length of their tails. mRNAs have tails made up of strings of adenines, one of the building blocks of RNA. Tail length varies between mRNAs from different genes and even between mRNAs from the same gene. Usually, the length of this “poly(A)-tail” corresponds to how long an mRNA lasts before getting degraded. An mRNA with a long tail is more stable, and will generally last longer. However, researchers had also observed that in some cases mRNA tail length corresponds to how readily an mRNA is used to make protein. Bartel’s earlier research had helped define when each of these connections occurs: mRNA tail length affects translational efficiency only in immature eggs and early embryos, and in other stages, it affects mRNA stability or lifespan.

In their new research, Xiang and Bartel uncovered three conditions that are required for the mRNA regulatory regime that exists in early development.

A competitive environment

The first condition is that there has to be a limited availability of a protein that binds to mRNA tails called cytoplasmic poly(A)-binding protein (PABPC). PABPC is known to help activate the translation of mRNA into protein. It binds to the mRNA tail and—in embryos—helps to increase translational efficiency; the researchers propose that it may do this by promoting a more favorable structure for translation. When PABPC is in limited supply, as it is in early embryos, then short-tailed mRNAs are less likely to bind any of the protein, as they will be outcompeted by long-tailed mRNAs, explaining the correlation between tail length and translational efficiency. Later in development, PABPC is in such ready supply that all of the mRNAs are able to bind at least one, decreasing the competitive edge of long-tailed mRNAs.

Early durability

However, the researchers observed that reducing the amount of PABPC in adult cells so that it becomes limiting in these cells did not cause mRNAs with longer tails to be translated more efficiently, which showed that other conditions must also contribute to early embryos’ unique regulation. The second condition that Xiang identified is that mRNAs must be relatively stable in spite of their inability to compete for PABPC. In adult cells, RNAs without PABPC bound to their tails are very unstable, and so are likely to degrade. If the same were true in early embryos, then the short-tailed mRNAs would degrade quickly because they are outcompeted for binding PABPC, and so one would again see a link between tail length and stability, rather than between tail length and translational efficiency—short-tailed mRNAs would be eliminated rather than poorly translated. However, the processes that would normally degrade mRNAs without PABPC have not yet started occurring in early embryos, allowing the short-tailed mRNAs to survive.

Big fish in a small pond

Finally, Xiang discovered that in order for tail length and translational efficiency to be linked, PABPC has to be able to affect translational efficiency. He found that in adult cells PABPC does not appear to boost translational efficiency the way it does in embryos. The researchers hypothesize that this is because the process of translating mRNAs in adult cells is already so efficient that the small boost from binding PABPC does not make a significant difference. However, in early embryos PABPC is more of a big fish in a small pond. The cells do not have all of the machinery to maximize translational efficiency, so every bit of improvement, such as the benefit of binding PABPC, makes a noticeable difference.

Together, these three conditions enable early eggs and embryos to regulate their mRNA in a unique fashion that can control how much protein is made from each gene without destroying the limited pool of mRNA available. In the future, the researchers hope to recreate the three conditions in non-embryonic cells to confirm that the conditions Xiang identified are not only necessary but also sufficient to cause the switch in regulatory regimes.

“Knowing which function the poly(A)-tail is performing in a specific cell or scenario—providing mRNA stability or translational efficiency—is really critical for understanding how genes are regulated in the different cells,” Bartel says. “And understanding that is important for answering all kinds of questions about cells, from their functions to what can go wrong with them in diseases.”

Pursuing Discovery and Diversity at the National Institutes of Health
Ken Shulman
July 9, 2021

There were only 625 undergraduate women on campus—and far fewer Latina women—when Arlyn García-Pérez ’79 arrived at MIT in 1975. But her experience wasn’t unlike that of many other first-year students: used to being at the top of her class, she found herself failing some of her first MIT courses. “It was a terrible shock,” says García-Pérez, who was born in Cuba and grew up in Peru and Puerto Rico. “But it turned out to be an invaluable lesson. I learned that failure is inevitable, and that the important thing is knowing how to lift yourself up and get on with your work.”

García-Pérez, who is now director of policy and analysis at the National Institutes of Health (NIH) Office of Intramural Research, lifted herself up deftly after her first-semester stumble. She’d come to MIT thinking she’d go to medical school. Instead, she fell in love with research after her first biology lab. “I knew right then I wanted to be involved in discovery,” she says. “To make the sort of inquiries my professors were making.”

She graduated with a biology degree and enrolled in a biochemistry PhD program at Michigan State University, where she studied the human kidney. With a PhD and a fellowship in hand, she began a postdoc at the Laboratory of Kidney and Electrolyte Metabolism at NIH in Bethesda, Maryland. There she studied how organic osmolytes protect the kidney medulla—the inner part of the kidney—from the high levels of salt there that would otherwise destroy DNA and proteins in its cells. Organisms all along the evolutionary spectrum use the same compounds to protect themselves in high-salt environments.

In 1992, García-Pérez was awarded tenure at NIH as an independent senior investigator. And in 1999, she accepted an invitation to join the administration at the Office of Intramural Research—the office that oversees all research conducted in-house at NIH. Since then, she has focused on creating programs and policies that facilitate other scientists’ discoveries. For example, she established a 12-year pilot for the since-expanded NIH Academy, a post-baccalaureate research program supporting work that contributes to eliminating domestic health disparities.

García-Pérez has also made it a priority to advocate for inclusivity in recruitment and advancement at NIH, eager to pay forward the mentorship and support she received there throughout her career. “We have to make a conscious effort to think of people who may not be like us,” she says.

This article also appears in the July/August 2021 issue of MIT News magazine, published by MIT Technology Review.

Ruth Lehmann named Great Immigrant by Carnegie Corporation
Carnegie Corporation
July 1, 2021

The daughter of a teacher and an engineer, Lehmann won a Fulbright Fellowship in ecology in 1977 that brought her to Seattle, where she discovered her passion for developmental genetics. She has since been using flies to study germ cells, precursors of eggs and sperm, which play an essential role in our survival.

Lehmann, who calls herself a dog and data lover, is professor of biology and the director of the Whitehead Institute at MIT. Her research on the origins of germ cells — the only cells in the human body that have immortality — is shedding light on how they lead to reproduction, on the role of RNA regulation in germ cells, and on how harmful mutations are eliminated during oogenesis. She believes it is critical for scientists to push the envelope, following their instincts to pursue research on topics about which not much is known.

Lehmann’s long list of achievements includes membership in the National Academy of Sciences and the American Academy of Arts and Sciences, and in 2021 she was awarded the Vilcek Prize in Biomedical Science.

“It means so much to me to be recognized as an immigrant and a researcher,” Lehmann said upon receiving the Vilcek Prize. “In these days, immigrants don’t feel as welcomed as I did when I came to this country. For me, coming to the U.S. meant to be given a chance to live the dream of being a scientist.”

The power of two

Graduate student Ellen Zhong helped biologists and mathematicians reach across departmental lines to address a longstanding problem in electron microscopy.

Saima Sidik | Department of Biology
July 1, 2021

MIT’s Hockfield Court is bordered on the west by the ultramodern Stata Center, with its reflective, silver alcoves that jut off at odd angles, and on the east by Building 68, which is a simple, window-lined, cement rectangle. At first glance, Bonnie Berger’s mathematics lab in the Stata Center and Joey Davis’s biology lab in Building 68 are as different as the buildings that house them. And yet, a recent collaboration between these two labs shows how their disciplines complement each other. The partnership started when Ellen Zhong, a graduate student from the Computational and Systems Biology (CSB) Program, decided to use a computational pattern-recognition tool called a neural network to study the shapes of molecular machines. Three years later, Zhong’s project is letting scientists see patterns that run beneath the surface of their data, and deepening their understanding of the molecules that shape life.

Zhong’s work builds on a technique from the 1970s called cryo-electron microscopy (cryo-EM), which lets researchers take high-resolution images of frozen protein complexes. Over the past decade, better microscopes and cameras have led to a “resolution revolution” in cryo-EM that’s allowed scientists to see individual atoms within proteins. But, as good as these images are, they’re still only static snapshots. In reality, many of these molecular machines are constantly changing shape and composition as cells carry out their normal functions and adjust to new situations.

Along with former Berger lab member Tristan Belper, Zhong devised software called cryoDRGN. The tool uses neural nets to combine hundreds of thousands of cryo-EM images, and shows scientists the full range of three-dimensional conformations that protein complexes can take, letting them reconstruct the proteins’ motion as they carry out cellular functions. Understanding the range of shapes that protein complexes can take helps scientists develop drugs that block viruses from entering cells, study how pests kill crops, and even design custom proteins that can cure disease. Covid-19 vaccines, for example, work partly because they include a mutated version of the virus’s spike protein that’s stuck in its active conformation, so vaccinated people produce antibodies that block the virus from entering human cells. Scientists needed to understand the variety of shapes that spike proteins can take in order to figure out how to force spike into its active conformation.

Getting off the computer and into the lab

Zhong’s interest in computational biology goes back to 2011 when, as a chemical engineering undergrad at the University of Virginia, she worked with Professor Michael Shirts to simulate how proteins fold and unfold. After college, Zhong took her skills to a company called D. E. Shaw Research, where, as a scientific programmer, she took a computational approach to studying how proteins interact with small-molecule drugs.

“The research was very exciting,” Zhong says, “but all based on computer simulations. To really understand biological systems, you need to do experiments.”

This goal of combining computation with experimentation motivated Zhong to join MIT’s CSB PhD program, where students often work with multiple supervisors to blend computational work with bench work. Zhong “rotated” in both the Davis and Berger labs, then decided to combine the Davis lab’s goal of understanding how protein complexes form with the Berger lab’s expertise in machine learning and algorithms. Davis was interested in building up the computational side of his lab, so he welcomed the opportunity to co-supervise a student with Berger, who has a long history of collaborating with biologists.

Davis himself holds a dual bachelor’s degree in computer science and biological engineering, so he’s long believed in the power of combining complementary disciplines. “There are a lot of things you can learn about biology by looking in a microscope,” he says. “But as we start to ask more complicated questions about entire systems, we’re going to require computation to manage the high-dimensional data that come back.”

Before rotating in the Davis lab, Zhong had never performed bench work before — or even touched a pipette. She was fascinated to find how streamlined some very powerful molecular biology techniques can be. Still, Zhong realized that physical limitations mean that biology is much slower when it’s done at the bench instead of on a computer. “With computational research, you can automate experiments and run them super quickly, whereas in the wet lab, you only have two hands, so you can only do one experiment at a time,” she says.

Zhong says that synergizing the two different cultures of the Davis and Berger labs is helping her become a well-rounded, adaptable scientist. Working around experimentalists in the Davis lab has shown her how much labor goes into experimental results, and also helped her to understand the hurdles that scientists face at the bench. In the Berger lab, she enjoys having coworkers who understand the challenges of computer programming.

“The key challenge in collaborating across disciplines is understanding each other’s ‘languages,’” Berger says. “Students like Ellen are fortunate to be learning both biology and computing dialects simultaneously.”

Bringing in the community

Last spring revealed another reason for biologists to learn computational skills: these tools can be used anywhere there’s a computer and an internet connection. When the Covid-19 pandemic hit, Zhong’s colleagues in the Davis lab had to wind down their bench work for a few months, and many of them filled their time at home by using cryo-EM data that’s freely available online to help Zhong test her cryoDRGN software. The difficulty of understanding another discipline’s language quickly became apparent, and Zhong spent a lot of time teaching her colleagues to be programmers. Seeing the problems that nonprogrammers ran into when they used cryoDRGN was very informative, Zhong says, and helped her create a more user-friendly interface.

Although the paper announcing cryoDRGN was just published in February, the tool created a stir as soon as Zhong posted her code online, many months prior. The cryoDRGN team thinks this is because leveraging knowledge from two disciplines let them visualize the full range of structures that protein complexes can have, and that’s something researchers have wanted to do for a long time. For example, the cryoDRGN team recently collaborated with researchers from Harvard and Washington universities to study locomotion of the single-celled organism Chlamydomonas reinhardtii. The mechanisms they uncovered could shed light on human health conditions, like male infertility, that arise when cells lose the ability to move. The team is also using cryoDRGN to study the structure of the SARS-CoV-2 spike protein, which could help scientists design treatments and vaccines to fight coronaviruses.

Zhong, Berger, and Davis say they’re excited to continue using neural nets to improve cryo-EM analysis, and to extend their computational work to other aspects of biology. Davis cited mass spectrometry as “a ripe area to apply computation.” This technique can complement cryo-EM by showing researchers the identities of proteins, how many of them are bound together, and how cells have modified them.

“Collaborations between disciplines are the future,” Berger says. “Researchers focused on a single discipline can take it only so far with existing techniques. Shining a different lens on the problem is how advances can be made.”

Zhong says it’s not a bad way to spend a PhD, either. Asked what she’d say to incoming graduate students considering interdisciplinary projects, she says: “Definitely do it.”

Researchers give yeast a boost to make biofuels from discarded plant matter
Eva Frederick | Whitehead Institute
June 27, 2021

“Stover is produced in huge amounts, on the scale of petroleum,” said Whitehead Institute Member and Massachusetts Institute of Technology (MIT) biology professor Gerald Fink. “But there are enormous technical challenges to using it cheaply to create biofuels and other important chemicals.”

And so, year after year, most of the woody corn material is left in the fields to rot.

Now, a new study from Fink and MIT chemical engineering professor Gregory Stephanopolous led by MIT postdoctoral researcher Felix Lam offers a way to more efficiently harness this underutilized fuel source. By changing the growth medium conditions surrounding the common yeast model, baker’s yeast Saccharomyces cerevisiae, and adding a gene for a toxin-busting enzyme, they were able to use the yeast to create ethanol and plastics from the woody corn material at near the same efficiency as typical ethanol sources such as corn kernels.

Sugarcoating the issue

For years, the biofuels industry has relied on microorganisms such as yeast to convert the sugars glucose, fructose and sucrose in corn kernels to ethanol, which is then mixed in with traditional gasoline to fuel our cars.

Corn stover and other similar materials are full of sugars as well, in the form of a molecule called cellulose. While these sugars can be converted to biofuels too, it’s more difficult since the plants hold onto them tightly, binding the cellulose molecules together in chains and wrapping them in fibrous molecules called lignins. Breaking down these tough casings and disassembling the sugar chains results in a chemical mixture that is challenging for traditional fermentation microorganisms to digest.

To help the organisms along, workers in ethanol production plants pretreat high-cellulose material with an acidic solution to break down these complex molecules so yeast can ferment them. A side effect of this treatment, however, is the production of molecules called aldehydes, which are toxic to yeast. Researchers have explored different ways to reduce the toxicity of the aldehydes in the past, but solutions were limited considering that the whole process needs to cost close to nothing. “This is to make ethanol, which is literally something that we burn,” Lam said. “It has to be dirt cheap.”

Faced with this economic and scientific problem, industries have cut back on creating ethanol from cellulose-rich materials. “These toxins are one of the biggest limitations to producing biofuels at a low cost.” said Gregory Stephanopoulos, who is the Willard Henry Dow Professor of Chemical Engineering at MIT.

Lending yeast a helping hand

To tackle the toxin problem, the researchers decided to focus on the aldehydes produced when acid is added to break down tough molecules. “We don’t know the exact mechanism by which aldehydes attack microbes, so then the question was, if we don’t really know what it attacks, how do we solve the problem?” Lam said. “So we decided to chemically convert these aldehydes into alcohol forms.”

The team began looking for genes that specialized in converting aldehydes to alcohols, and landed on a gene called GRE2. They optimized the gene to make it more efficient through a process called directed evolution, and then introduced it into the yeast typically used for ethanol fermentation, Saccharomyces cerevisiae. When the yeast cells with the evolved GRE2 gene encountered aldehydes, they were able to convert them into alcohols by tacking on extra hydrogen atoms.

The resultant high levels of ethanol and other alcohols produced from the cellulose might have posed a problem in the past, but at this point Lam’s past research came into play. In a 2015 paper from Lam, Stephanopoulos and Fink, the researchers developed a system to make yeast more tolerant to a wide range of alcohols, in order to produce greater volumes of the fuel from less yeast. That system involved measuring and adjusting the pH and potassium levels in the yeast’s growth media, which chemically stabilized the cell membrane.

By combining this method with their newly modified yeast, “we essentially channeled the aldehyde problem into the alcohol problem, which we had worked on before,” Lam said. “We changed and detoxified the aldehydes into a form that we knew how to handle.”

When they tested the system, the researchers were able to efficiently make ethanol and even plastic precursors from corn stover, miscanthus and other types of plant matter. “We were able to produce a high volume of ethanol per unit of material using our system,” Fink said. “That shows that there’s great potential for this to be a cost-effective solution to the chemical and economic issues that arise when creating fuel from cellulose-rich plant materials.”

Scaling up

Alternative fuel sources often face challenges when it comes to implementing them on a nationwide scale; electric cars, for example, require a nationwide charging infrastructure in order to be a feasible alternative to gas vehicles.

An essential feature of the researchers’ new system is the fact that the infrastructure is already in place; ethanol and other liquid biofuels are compatible with existing gasoline vehicles so require little to no change in the automotive fleet or consumer fueling habits. “Right now [the US produces around] 15 billion gallons of ethanol per year, so it’s on a massive scale,” he said. “That means there are billions of dollars and many decades worth of infrastructure. If you can plug into that, you can get to market much faster.”

And corn stover is just one of many sources of high-cellulose material. Other plants, such as wheat straw and miscanthus, also known as silvergrass, can be grown extremely cheaply. “Right now the main source of cellulose in this country is corn stover,” Lam said. “But if there’s demand for cellulose because you can now make all these petroleum-based chemicals in a sustainable fashion, then hopefully farmers will start planting miscanthus, and all these super dense straws.”

In the future, the researchers hope to investigate the potential of modifying yeasts with these anti-toxin genes to create diverse types of biofuels such as diesel that can be used in typical fuel-combusting engines. “If we can [use this system for other fuel types], I think that would go a huge way toward addressing sectors such as ships and heavy machinery that continue to pollute because they have no other electric or non-emitting solution,” Lam said.

Scaling up

Alternative fuel sources often face challenges when it comes to implementing them on a nationwide scale; electric cars, for example, require a nationwide charging infrastructure in order to be a feasible alternative to gas vehicles.

An essential feature of the researchers’ new system is the fact that the infrastructure is already in place; ethanol and other liquid biofuels are compatible with existing gasoline vehicles so require little to no change in the automotive fleet or consumer fueling habits. “Right now [the US produces around] 15 billion gallons of ethanol per year, so it’s on a massive scale,” he said. “That means there are billions of dollars and many decades worth of infrastructure. If you can plug into that, you can get to market much faster.”

And corn stover is just one of many sources of high-cellulose material. Other plants, such as wheat straw and Miscanthus, also known as silvergrass, can be grown extremely cheaply. “Right now the main source of cellulose in this country is corn stover,” Lam said. “But if there’s demand for cellulose because you can now make all these petroleum-based chemicals in a sustainable fashion, then hopefully farmers will start planting Miscanthus, and all these super dense straws.”

In the future, the researchers hope to investigate the potential of modifying yeasts with these anti-toxin genes to create diverse types of biofuels such as diesel that can be used in typical fuel-combusting engines. “If we can [use this system for other fuel types], I think that would go a huge way toward addressing sectors such as ships and heavy machinery that continue to pollute because they have no other electric or non-emitting solution,” Lam said.

Engineered yeast could expand biofuels’ reach

By making the microbes more tolerant to toxic byproducts, researchers show they can use a wider range of feedstocks, beyond corn.

Anne Trafton | MIT News Office
June 28, 2021

Boosting production of biofuels such as ethanol could be an important step toward reducing global consumption of fossil fuels. However, ethanol production is limited in large part by its reliance on corn, which isn’t grown in large enough quantities to make up a significant portion of U.S. fuel needs.

To try to expand biofuels’ potential impact, a team of MIT engineers has now found a way to expand the use of a wider range of nonfood feedstocks to produce such fuels. At the moment, feedstocks such as straw and woody plants are difficult to use for biofuel production  because they first need to be broken down to fermentable sugars, a process that releases numerous byproducts that are toxic to yeast, the microbes most commonly used to produce biofuels.

The MIT researchers developed a way to circumvent that toxicity, making it feasible to use those sources, which are much more plentiful, to produce biofuels. They also showed that this tolerance can be engineered into strains of yeast used to manufacture other chemicals, potentially making it possible to use “cellulosic” woody plant material as a source to make biodiesel or bioplastics.

“What we really want to do is open cellulose feedstocks to almost any product and take advantage of the sheer abundance that cellulose offers,” says Felix Lam, an MIT research associate and the lead author of the new study.

Gregory Stephanopoulos, the Willard Henry Dow Professor in Chemical Engineering, and Gerald Fink, the Margaret and Herman Sokol Professor at the Whitehead Institute of Biomedical Research and the American Cancer Society Professor of Genetics in MIT’s Department of Biology, are the senior authors of the paper, which appears today in Science Advances.

Boosting tolerance

Currently, around 40 percent of the U.S. corn harvest goes into ethanol. Corn is primarily a food crop that requires a great deal of water and fertilizer, so plant material known as cellulosic biomass is considered an attractive, noncompeting source for renewable fuels and chemicals. This biomass, which includes many types of straw, and parts of the corn plant that typically go unused, could amount to more than 1 billion tons of material per year, according to a U.S. Department of Energy study — enough to substitute for 30 to 50 percent of the petroleum used for transportation.

However, two major obstacles to using cellulosic biomass are that cellulose first needs to be liberated from the woody lignin, and the cellulose then needs to be further broken down into simple sugars that yeast can use. The particularly aggressive preprocessing needed generates compounds called aldehydes, which are very reactive and can kill yeast cells.

To overcome this, the MIT team built on a technique they had developed several years ago to improve yeast cells’ tolerance to a wide range of alcohols, which are also toxic to yeast in large quantities. In that study, they showed that spiking the bioreactor with specific compounds that strengthen the membrane of the yeast helped yeast to survive much longer in high concentrations of ethanol. Using this approach, they were able to improve the traditional fuel ethanol yield of a high-performing strain of yeast by about 80 percent.

In their new study, the researchers engineered yeast so that they could convert the cellulosic byproduct aldehydes into alcohols, allowing them to take advantage of the alcohol tolerance strategy they had already developed. They tested several naturally occurring enzymes that perform this reaction, from several species of yeast, and identified one that worked the best. Then, they used directed evolution to further improve it.

“This enzyme converts aldehydes into alcohols, and we have shown that yeast can be made a lot more tolerant of alcohols as a class than it is of aldehydes, using the other methods we have developed,” Stephanopoulos says.

Yeast are generally not very efficient at producing ethanol from toxic cellulosic feedstocks; however, when the researchers expressed this top-performing enzyme and spiked the reactor with the membrane-strengthening additives, the strain more than tripled its cellulosic ethanol production, to levels matching traditional corn ethanol.

Abundant feedstocks

The researchers demonstrated that they could achieve high yields of ethanol with five different types of cellulosic feedstocks, including switchgrass, wheat straw, and corn stover (the leaves, stalks, and husks left behind after the corn is harvested).

“With our engineered strain, you can essentially get maximum cellulosic fermentation from all these feedstocks that are usually very toxic,” Lam says. “The great thing about this is it doesn’t matter if maybe one season your corn residues aren’t that great. You can switch to energy straws, or if you don’t have high availability of straws, you can switch to some sort of pulpy, woody residue.”
The researchers also engineered their aldehyde-to-ethanol enzyme into a strain of yeast that has been engineered to produce lactic acid, a precursor to bioplastics. As it did with ethanol, this strain was able to produce the same yield of lactic acid from cellulosic materials as it does from corn.

This demonstration suggests that it could be feasible to engineer aldehyde tolerance into strains of yeast that generate other products such as diesel. Biodiesels could potentially have a big impact on industries such as heavy trucking, shipping, or aviation, which lack an emission-free alternative like electrification and require huge amounts of fossil fuel.

“Now we have a tolerance module that you can bolt on to almost any sort of production pathway,” Stephanopoulos says. “Our goal is to extend this technology to other organisms that are better suited for the production of these heavy fuels, like oils, diesel, and jet fuel.”

The research was funded by the U.S. Department of Energy and the National Institutes of Health.