Study reveals how egg cells get so big

Oocyte growth relies on physical phenomena that drive smaller cells to dump their contents into a larger cell.

Anne Trafton | MIT News Office
March 10, 2021

Egg cells are by far the largest cells produced by most organisms. In humans, they are several times larger than a typical body cell and about 10,000 times larger than sperm cells.

There’s a reason why egg cells, or oocytes, are so big: They need to accumulate enough nutrients to support a growing embryo after fertilization, plus mitochondria to power all of that growth. However, biologists don’t yet understand the full picture of how egg cells become so large.

A new study in fruit flies, by a team of MIT biologists and mathematicians, reveals that the process through which the oocyte grows significantly and rapidly before fertilization relies on physical phenomena analogous to the exchange of gases between balloons of different sizes. Specifically, the researchers showed that “nurse cells” surrounding the much larger oocyte dump their contents into the larger cell, just as air flows from a smaller balloon into a larger one when they are connected by small tubes in an experimental setup.

“The study shows how physics and biology come together, and how nature can use physical processes to create this robust mechanism,” says Jörn Dunkel, an MIT associate professor of physical applied mathematics. “If you want to develop as an embryo, one of the goals is to make things very reproducible, and physics provides a very robust way of achieving certain transport processes.”

Dunkel and Adam Martin, an MIT associate professor of biology, are the senior authors of the paper, which appears this week in the Proceedings of the National Academy of Sciences. The study’s lead authors are postdoc Jasmin Imran Alsous and graduate student Nicolas Romeo. Jonathan Jackson, a Harvard University graduate student, and Frank Mason, a research assistant professor at Vanderbilt University School of Medicine, are also authors of the paper.

A physical process

In female fruit flies, eggs develop within cell clusters known as cysts. An immature oocyte undergoes four cycles of cell division to produce one egg cell and 15 nurse cells. However, the cell separation is incomplete, and each cell remains connected to the others by narrow channels that act as valves that allow material to pass between cells.

Members of Martin’s lab began studying this process because of their longstanding interest in myosin, a class of proteins that can act as motors and help muscle cells contract. Imran Alsous performed high-resolution, live imaging of egg formation in fruit flies and found that myosin does indeed play a role, but only in the second phase of the transport process. During the earliest phase, the researchers were puzzled to see that the cells did not appear to be increasing their contractility at all, suggesting that a mechanism other than “squeezing” was initiating the transport.

“The two phases are strikingly obvious,” Martin says. “After we saw this, we were mystified, because there’s really not a change in myosin associated with the onset of this process, which is what we were expecting to see.”

cluster of cells

Martin and his lab then joined forces with Dunkel, who studies the physics of soft surfaces and flowing matter. Dunkel and Romeo wondered if the cells might be behaving the same way that balloons of different sizes behave when they are connected. While one might expect that the larger balloon would leak air to the smaller until they are the same size, what actually happens is that air flows from the smaller to the larger.

This happens because the smaller balloon, which has greater curvature, experiences more surface tension, and therefore higher pressure, than the larger balloon. Air is therefore forced out of the smaller balloon and into the larger one. “It’s counterintuitive, but it’s a very robust process,” Dunkel says.

Adapting mathematical equations that had already been derived to explain this “two-balloon effect,” the researchers came up with a model that describes how cell contents are transferred from the 15 small nurse cells to the large oocyte, based on their sizes and their connections to each other. The nurse cells in the layer closest to the oocyte transfer their contents first, followed by the cells in more distant layers.

“After I spent some time building a more complicated model to explain the 16-cell problem, we realized that the simulation of the simpler 16-balloon system looked very much like the 16-cell network. It is surprising to see that such counterintuitive but mathematically simple ideas describe the process so well,” Romeo says.

The first phase of nurse cell dumping appears to coincide with when the channels connecting the cells become large enough for cytoplasm to move through them. Once the nurse cells shrink to about 25 percent of their original size, leaving them only slightly larger than their nuclei, the second phase of the process is triggered and myosin contractions force the remaining contents of the nurse cells into the egg cell.

“In the first part of the process, there’s very little squeezing going on, and the cells just shrink uniformly. Then this second process kicks in toward the end where you start to get more active squeezing, or peristalsis-like deformations of the cell, that complete the dumping process,” Martin says.

Cell cooperation

The findings demonstrate how cells can coordinate their behavior, using both biological and physical mechanisms, to bring about tissue-level behavior, Imran Alsous says.

“Here, you have several nurse cells whose job it is to nurse the future egg cell, and to do so, these cells appear to transport their contents in a coordinated and directional manner to the oocyte,” she says.

Oocyte and early embryonic development in fruit flies and other invertebrates bears some similarities to those of mammals, but it’s unknown if the same mechanism of egg cell growth might be seen in humans or other mammals, the researchers say.

“There’s evidence in mice that the oocyte develops as a cyst with other interconnected cells, and that there is some transport between them, but we don’t know if the mechanisms that we’re seeing here operate in mammals,” Martin says.

The researchers are now studying what triggers the second, myosin-powered phase of the dumping process to start. They are also investigating how changes to the original sizes of the nurse cells might affect egg formation.

The research was funded by the National Institute of General Medical Sciences, a Complex Systems Scholar Award from the James S. McDonnell Foundation, and the Robert E. Collins Distinguished Scholarship Fund.

Grace Johnson earns Harold M. Weintraub Graduate Student Award
March 3, 2021

Grace Johnson, a graduate student in Gene-Wei Li’s lab, has received a 2021 Harold M. Weintraub Graduate Student Award from the Fred Hutchinson Cancer Research Center. Johnson is one of 13 recipients who were honored for the quality, originality, and significance of their work in the biological sciences.

The Weintraub Graduate Student Award was established in 2000, and since then more than 300 graduate students have been recognized for their research contributions. The 2021 awardees study a spectrum of topics, including immunology, molecular biology, neurobiology, and cancer.

Johnson’s research focuses on bacterial gene expression. In bacteria such as Escherichia coli — a widely-studied model organism — the RNA polymerase, which transcribes DNA into RNA, is followed in close pursuit by the ribosome, which translates the RNA into proteins. However, Johnson recently helped to show that the Bacillus subtilis bacterium does not display this common “coupled” transcription-translation. She demonstrated that, rather than working in tandem with the ribosome, the polymerase in B. subtilis speeds ahead. This system of “runaway” transcription creates alternative mechanisms for RNA quality control, and provides insights into the range of molecular processes present in bacteria.

“To me, this work is really exciting because it provides a glimpse into how differences in basic biological properties can shape the evolution of diverse bacteria,” Johnson says. “I was extremely humbled when I heard I had received the Weintraub Award and recognized alongside 12 other graduate students. It is always great to learn that others find my work as exciting as I do.”

“Grace’s thesis work, in collaboration with physics graduate student Jean-Benoît Lalanne, provides an excellent example of how interdisciplinary approaches can generate new knowledge and challenge our understanding of biological mechanisms,” says Li, Johnson’s advisor. “What’s remarkable about Grace is not just her science, but also her deep devotion to make research institutions safer and more inclusive places.”

The Weintraub Award is supported by the Weintraub/Groudine Fellowship for Science and Human Disease, which was established to foster intellectual exchange by promoting programs for graduate students, fellows, and visiting scholars.

Cells are known by the company they keep
Eva Frederick
March 2, 2021

In the paper, published online March 1 in the journal Cell Metabolism, researchers at Whitehead Institute and the Morgridge Institute for Research performed CRISPR-based genetic screens of cells cultured in either traditional media or a new physiologic medium previously designed in the Sabatini Lab at Whitehead Institute designed to more closely reflect the nutrient composition of human blood. The screen revealed that different genes became essential for survival and reproduction in the various conditions.

“This work underscores the importance of using more human-like, physiologically relevant media for culturing human cancer cell lines,” said Whitehead Institute Member and co-senior author David Sabatini, who is also a professor of biology at the Massachusetts Institute of Technology and an investigator of the Howard Hughes Medical Institute. “The information we can learn from screens in human plasma-like media — or media designed to mimic other fluids throughout the body — may inform new therapeutic methods down the line.”

The widespread use of a human plasma-like medium could open the door for many researchers to conduct experiments in the lab that could have more relevance to human disease, but without complicated methods or prohibitive costs.

“Medium composition is both relatively accessible and quite flexible,” said co-senior author Jason Cantor, an Investigator at the Morgridge Institute for Research and an assistant professor of biochemistry at the University of Wisconsin-Madison, and a former postdoc in Sabatini’s lab. “Not all researchers have access to specialized tissue culture incubators, nor can everyone easily pursue some of the more complex 3D and co-culture methods, but most can get their hands on a bottle of media.”

The big screen

The idea that different environmental conditions may lead to different genes being essential is not a new one. “People have done this in microorganisms, and shown that if you throw [bacteria] into different growth conditions — the contributions of different genes to cell fitness can change,” Cantor said.

With this reasoning in mind — that medium composition could affect which genes become necessary for human cells to grow — the researchers set up screens to identify essential genes in a single leukemia cell line in different kinds of culture media. One batch was grown in a traditional medium, and another cultured in the lab’s new medium called Human Plasma-Like Medium, or HPLM, which has a metabolic composition more reflective of that in human blood.

The approach they used — called a CRISPR screen —  takes advantage of CRISPR-Cas9 gene editing technology to systematically snip and knock out genes across the genome, with the goal of creating a population of cells in which every possible gene knockout is represented. The expression of some genes is essential to survival, and cells grow substantially slower or die when those genes are deleted. Other cells may have trouble functioning, and some may grow even faster. Once the pooled cells have had a chance to grow and proliferate, researchers sequence the genetic material of the entire population to determine which genes were critical for survival within the given screen.

Once they completed the initial screens, the researchers identified hundreds of genes that were conditionally essential — that is, necessary for cell growth in one medium versus another. Interestingly, these medium-dependent essential genes collectively had roles in a number of different biological processes.

To determine how much these genes were dependent on the type of cells studied, the researchers then ran similar screens across a panel of human blood cancer cell lines, and then pursued follow-up work to understand why certain genes were identified as conditionally essential.

Ultimately, they uncovered the underlying gene-nutrient interactions, and specifically for these hit genes, traced the effects to availability of certain metabolites — the nutrients and small molecules necessary for metabolism — that are uniquely defined in HPLM versus the traditional media.

The next steps

CRISPR screens can help scientists identify potential drug targets and map out important cellular interactions to inform cancer therapies. “There are so many ways that people use CRISPR screens right now,” said Cantor. “What this study is showing is that the availability metabolites can have a major impact on which genes are important for cell growth, and so I think there are a lot of implications here in terms of how these types of screens could be performed in the future in order to potentially increase the fidelity of what we see in the lab and what might happen in the body.”

The research also establishes more nuanced relationships between cells’ genes and their environment. “What this allows us to do down the line, theoretically, is to tune how important a gene is — how important the encoded protein is — by manipulating metabolite levels in the blood,” said Cantor. “That’s one of our bigger-picture ideas.”

In the future, these relationships could inform cancer treatments. For example, if scientists could “tune” the importance of a specific gene for cancer cell growth, then the protein encoded by that gene could become a more promising drug target — in effect, tricking cancer cells into revealing possible context-dependent vulnerabilities. “The idea of targeting metabolites to treat cancer isn’t itself new — in fact, it [underlies] a well-established anti-cancer therapeutic enzyme still in use today — but I think our work maybe enables us to look for ways to couple this type of approach with other targeted therapies.”

“At our core, we are a basic cell biology lab,” added Nicholas Rossiter, a technician in Cantor’s lab and the first author of the study. “But whenever you’re studying basic cell biology, there’s the potential to translate it into therapeutic strategy. Our plan is just to keep on chugging along in our lab and studying how exactly cell biology can be influenced by these environmental factors. We do the basics, and then there will hopefully be some auspicious findings that can be carried on into therapeutics.”

Seychelle Vos investigates how the genome is organized so it can fit inside the cell — and how that careful organization affects gene expression.

February 24, 2021
How this biology lab class went virtual during the pandemic

Instructor Mandana Sassafar found creative ways to teach first-years experimental techniques and laboratory protocols remotely.

Department of Biology
February 23, 2021

Each January, MIT hosts a four-week term known as Independent Activities Period (IAP). This year, though, was different: All IAP activities were held online due to Covid-19 restrictions. Like many other IAP instructors, the Department of Biology’s director of outreach, Mandana Sassafar, was facing a dilemma. How could she transfer a fast-paced, hands-on lab class to the virtual realm?

Sassanfar has been teaching class 7.102 (Introduction to Molecular Biology Techniques) for over a decade. The class was originally designed to familiarize first-year undergraduates with lab equipment, troubleshooting, and basic methods in molecular biology in preparation for MIT’s Undergraduate Research Opportunities Program (UROP). She felt this goal was now more important than ever, given that too many students had already lost precious chances to work in labs due to the pandemic.

After weeks of consideration, she came up with a solution: create a remote version of the class called 7.S391 (Special Subject in Biology) using video clips. She filmed more than 15 graduate students and postdocs on her iPhone, maintaining at least 6 feet of distance as the trainees wore masks and demonstrated various lab techniques.

The 7.S391 students then watched the videos, described each experiment, compared techniques, and devised protocols based on their observations. Although they did not have lab equipment in their homes, observing researchers in action is the first step toward learning-by-doing, according to Sassanfar.

“Because so many first-years are eager to start UROPs, this seemed like the best way to prepare them,” Sassanfar said. “They were exposed to research and lab tools on a daily basis, and watching experiments helped them gain knowledge and confidence.”

The class was capped at 24 students, who met for two-and-a-half hours each day for 12 days. Thanks to Sassanfar’s videos, the students learned to grow bacteria; set up polymerase chain reaction (PCR) tests; design primers to construct recombinant plasmids; do tissue culture; and perform gel electrophoresis, western blots, and affinity chromatography. They also practiced interpreting the results.

During the final days of the class, MIT lab groups hoping to recruit UROPs gave short presentations about their research. In total, 10 labs from the departments of Biology, Brain and Cognitive Sciences, and Biological Engineering participated.

One graduate student presenter, Kristina Lopez ’18, had completed her undergraduate degree at MIT before beginning her PhD in the Knouse lab. She advised undergraduate students to find a lab they like and work there until they graduate. “I joined a lab my freshman year and stayed there all four years,” she said. “It allowed me to really delve into the project and make important contributions.”

First-year Alesandra (Alysse) Pusey says the class introduced her to an array of lab techniques for investigating biological questions. “I feel more prepared and eager to take on a UROP,” she adds. “Most virtual classes lack organic social interactions, but the implementation of breakout rooms and break time in this class allowed me to bond with my classmates, each of whom share an interest in biology with me.”

Her classmate Antonella Rebolledo-Ledesma also enjoyed the experience. “I was surprised by how much I could learn about lab work in a virtual setting,” she says. “I would highly recommend this course to anyone who is thinking about taking it next year — although hopefully it will be in-person!”

Eight from MIT named 2021 Sloan Research Fellows

Awards honor, support young professors in the Media Lab and departments of Biology, Brain and Cognitive Sciences, Chemical Engineering, EECS, and Mathematics.

MIT News Office
February 19, 2021

The Alfred P. Sloan Foundation announced Feb. 16 that it has awarded Sloan Research Fellowships to eight MIT professors in the MIT Media Lab and in the departments of Biology, Brain and Cognitive Sciences, Chemical Engineering, Electrical Engineering and Computer Science, and Mathematics. The fellowships, which honor pre-tenure faculty members, will support their research with two-year, $75,000 awards.

“The Sloan Research Fellowship Program recognizes and rewards outstanding early-career faculty who have the potential to revolutionize their fields of study,” according to the Sloan Foundation.

Fadel Adib, associate professor and Doherty Chair in Ocean Utilization, directs the Signal Kinetics group at the MIT Media Lab. His group invents, builds, and deploys wireless and sensor technologies to address complex problems in society, industry, and ecology. His team’s work focuses on bringing wireless capabilities to extreme domains like the ocean and the human body and to enable new applications that are infeasible using today’s technologies. His research extends beyond communication and networking to enabling novel micro-sensing, powering, and perception tasks. These capabilities aim at helping address major societal challenges in health care, climate change, and automation.

“We are excited about continuing to push our technologies deeper into the oceans and the human body,” says Adib, whose team invented the world’s first net-zero power underwater communication technology and wireless systems that power and communicate with batteryless micro-implants inside the human body. He aims to use this funding to further his team’s efforts in underwater GPS, in-body sensing, and robotic automation. “This Sloan fellowship will allow my team to continue taking risks in pursuing high-impact projects to understand and address global challenges ranging from climate change to health care and automation.”

Joseph “Joey” Davis, the Whitehead Career Development Assistant Professor in Biology, investigates the massive molecular “machines” that carry out important cellular processes, such as protein synthesis and degradation. He uses cryo-electron microscopy (cryoEM) to visualize these molecules at near-atomic resolution as they are being assembled and changing shape while they work. In collaboration with Simons Professor of Mathematics Bonnie Berger, his team has developed a new computational tool. Called cryoDRGN, it leverages neural networks to extract molecular motions from cryoEM data and create 3D movies. The Sloan Foundation award will help Davis combine cryoDRGN with a related imaging technique — electron cryotomography — to observe molecular structures directly inside living cells. Using this powerful combination, he hopes to uncover how machines like the ribosome, which synthesizes proteins, assemble in their native cellular environment. Ultimately, he aims to identify new antibiotic targets in this assembly pathway.

“We hope that the combination of cryoDRGN and electron cryotomography will enable us to directly visualize how key molecular machines are assembled within the cell,” Davis says. “This information will be critical in truly understanding how nature builds these machines so rapidly and efficiently, and will help us understand what aspects of the assembly process fail when cells are mutated and as they age. I am incredibly grateful to the Sloan Foundation for their support of our work.”

Steven Flavell, the Lister Brothers Career Development Assistant Professor in Brain and Cognitive Sciences and The Picower Institute for Learning and Memory, said the Sloan Foundation’s award will help him conduct experiments to uncover how animal nervous systems generate internal states that represent needs and desires, such as hunger, and then produce behaviors, such as roaming around in search of food. His lab plans to use a multidisciplinary experimental approach in their studies, which employ the simple model of the C. elegans worm whose nervous system contains only 302 neurons. Though simple, the model has proven to produce important insights across many areas of biology.

“Over the course of each day, an animal’s nervous system may transition between a wide range of internal states that influence how sensory information is processed and how behaviors are generated,” Flavell says. “These states of arousal, motivation, and mood can persist for hours, play a central role in organizing human behavior, and are commonly disrupted in psychiatric disease. However, the fundamental neural mechanisms that generate these states remain poorly understood. We envision that these studies will ultimately reveal fundamental principles of neural circuit function that may generalize across animals.”

Heather Kulik, associate professor in chemical engineering, advances first-principles and machine learning computational chemistry to accelerate materials and catalyst discovery. Her group has developed the first machine learning models capable of predicting normally time-consuming quantum mechanical properties of transition metal complexes, rapidly uncovering design principles in weeks instead of lifetimes. Her group develops large-scale quantum mechanical modeling methods and applies them to reveal how enzymes work and how to take inspiration from nature to design next-generation catalysts.

“The award from the Sloan Foundation will enable my group to continue advancing computational materials and bio-inspired catalyst discovery,” Kulik says. “The flexible nature of the support ensures we can continue to push forward these interdisciplinary efforts at the boundaries between fields.”

Luquiao Liu, associate professor in the Department of Electrical Engineering and Computer Science, focuses on understanding and exploiting spin-related physics in solid-state material and devices. Most recently, Luqiao has been doing research on developing material and carrying out electrical measurement on charge-spin interactions to achieve electrically induced magnetic switching, and exploring new methods to realize quantum control over the transport of magnons and other quasiparticles, which could be useful in future hybrid quantum systems for information processing.

“This fellowship will strengthen our capabilities in identifying new material and physics mechanisms that can be used to achieve functions that are unique to spintronic systems, with the long-term goal of realizing efficient computing in the classical and quantum domains,” he says.

Karthish Manthiram, the Theodore T. Miller Career Development Chair and assistant professor in chemical engineering, studies the carbon footprint behind most chemicals and materials that we encounter every day — there is a carbon footprint associated even with the fabric of the clothes we wear, the food we eat, and the disinfectants we spray, he says. To find ways to synthesize these chemicals and materials in a sustainable manner that eliminates the carbon footprint, the Manthiram lab is pioneering the development of a paradigm in which carbon dioxide, dinitrogen, and water can be converted into a wide range of chemicals and materials using renewable electricity. In essence, this would mean that a device that breathes air, drinks water, and takes in solar photons could in principle someday make many of the chemicals that society relies on. The lab specifically looks for ways to facilitate the molecular-level dance through which chemical bonds are broken and formed, so that desired molecules can be made more selectively, efficiently, and at faster rates.

“The support of the Sloan Research Fellowship will allow my group to advance the decarbonization of the material world, through electrically driven synthesis of critical chemicals beginning with just carbon dioxide, dinitrogen, and water,” Manthiram says. “We will pursue new frontiers in synthesizing even more complex molecules starting with these ubiquitous feedstocks.”

Dor Minzer, assistant professor of mathematics, works in the fields of mathematics and theoretical computer science. His interests revolve around computational complexity theory, or — more explicitly — probabilistically checkable proofs, Boolean function analysis, and combinatorics. Minzer’s more recent research has utilized and extended some of the insights gained from the work on probabilistically checkable proofs in order to make progress on several open problems in the field of analysis of Boolean functions, such as the Fourier Entropy conjecture and the stability problem for the edge isoperimetric inequality, as well as to other problems in theoretical computer science.

“The Sloan fellowship will allow us to continue pursuing difficult and important challenges in theoretical computer science, whose solution is likely to have wide impact on the field,” Minzer says.

Lisa Piccirillo, assistant professor mathematics, specializes in the study of three- and four-dimensional spaces. She is broadly interested in low-dimensional topology and knot theory, and employs constructive techniques in four-manifolds. Her work in four-manifold topology has surprising applications to the study of mathematical knots. She received an inaugural 2021 Maryam Mirzakhani New Frontiers Prize, created in 2019 by the Breakthrough Foundation to recognize outstanding early-career women in mathematics, for “resolving the classic problem that the Conway knot is not smoothly sliced.” For all other small knots, “sliceness” is readily determined, but this particular knot had remained a mystery since John Conway presented it in the mid-1900s. After hearing about the problem at a conference, Piccirillo took only a week to formulate a proof.

In all, the Sloan Foundation awarded fellowships to 128 tenure-track, but not-yet-tenured, scholars in the United States and Canada this year.

Vander Heiden and Lourido receive promotions
February 18, 2021

Effective July 1, Matthew Vander Heiden and Sebastian Lourido will be promoted to Full Professor and Associate Professor (Without Tenure), respectively.

Vander Heiden is Associate Director of the Koch Institute for Integrative Cancer Research, a member of the MIT Center for Precision Cancer Medicine, a member of the Ludwig Center for Molecular Oncology, and a member of the Broad Institute. He joined the department in 2010 and earned tenure in 2017. His work focuses on the biochemical pathways cells use and how they are regulated to meet the metabolic requirements of cells in different physiological situations. His lab investigates the role of metabolism in cancer, particularly how metabolic pathways support cell proliferation. They aim to translate their understanding of cancer cell metabolism into novel cancer therapies. His promotion to full professor reflects his international standing in his field, his excellent and dedicated teaching, and his service to the department and the broader scientific community.

Lourido is a member of the Whitehead Institute and Latham Family Career Development Professor. He joined the department and Whitehead Institute in 2017. His lab is interested in the molecular events that enable apicomplexan parasites to remain widespread and deadly, infectious agents. They study many important human pathogens, including Toxoplasma gondii, to model features conserved throughout the phylum. They seek to expand our understanding of eukaryotic diversity and identify specific features that can be targeted to treat parasite infections.

Posted: 2.18.21