In June, 100 fruit fly scientists gathered on the Greek island of Crete for the biennial meeting. Among them was Canadian geneticist Cassandra Extavour of Harvard University. His lab works with fruit flies to study evolution and development – “evo devo”. Most often, such scientists choose as their “model organism” the species Drosophila melanogaster – a winged workhorse that has served as an insect collaborator for at least several Nobel Prizes in physiology and medicine.
But Dr. Extavouri is also known for cultivating alternative species as model organisms. He is particularly interested in crickets, especially Gryllus bimaculatus, the two-spotted field cricket, although he does not yet enjoy anything close to a fly-follower. (Approximately 250 principal investigators applied to attend the meeting in Crete.)
“It’s crazy,” he said during a video interview from his hotel room as he swatted the Beetle. “If we tried to meet with the heads of laboratories working on this cricket species, there might be five or 10 of us.”
Crickets have already been enrolled in research on circadian clocks, limb regeneration, learning, memory; They served as disease models and pharmaceutical factories. Real polymaths, cricketers! They are also becoming increasingly popular as edibles, chocolate covered or not. From an evolutionary perspective, crickets offer more opportunities to learn about the last common insect ancestor; They have more in common with other insects than with flies. (It should be noted that insects make up more than 85 percent of animal species).
Dr. Extavour’s research targets the basics: How do embryos work? And what can it reveal about how the first animal came to be? All animal embryos follow a similar journey: one cell becomes many, then they arrange themselves in layers on the surface of the egg, providing an early blueprint for all parts of the adult body. But how do embryonic cells—cells that have the same genome but don’t all do the same with that information—know where to go and what to do?
“It’s a mystery to me,” said Dr. Extavour. “I always want to go here.”
Seth Don, a biologist and data scientist at the University of Chicago and a graduate student in Dr. Extavour’s lab, described embryology as the study of how a developing animal makes “the right parts in the right place at the right time.” In some new research—shown in a striking video of a cricket embryo showing certain “right parts” (cell nuclei) moving in three dimensions—Dr. Extavoor, Dr. Dono and their colleagues found that old-fashioned geometry plays a key role.
Humans, frogs, and many other widely studied animals begin as a single cell that immediately divides into individual cells. In crickets and most other insects, initially only the nucleus of the cell divides, forming many nuclei that move through the common cytoplasm and only later form their own cell membranes.
In 2019, Stefano Di Talia, a quantitative developmental biologist at Duke University, studied the movement of nuclei in flies and showed that they are moved through the cytoplasm by pulsating currents—a bit like leaves moving in slow eddies. – Moving stream.
But another mechanism was at work in the cricket embryo. For hours, the researchers watched and analyzed the microscopic dance of the nuclei: bright knots that split and moved in a confusing pattern, neither ordered nor random, in different directions and speeds, with neighboring nuclei more synchronized than those farther away. The play rejected choreography beyond mere physics or chemistry.
“The geometries that nuclei adopt are a result of their ability to sense and respond to the density of other nuclei near them,” Dr. Extavoor said. Dr. Di Talia was not involved in the new study, but found it moving. “It’s a wonderful study of a beautiful system of great biological importance,” he said.
The journey of nuclei
At first, cricket researchers took a classic approach: observe and pay attention. “We just looked at it,” Dr. Extavour said.
They took videos using a laser light sheet microscope: footage was taken of the dancing nuclei every 90 seconds during the first eight hours of embryo development, when about 500 nuclei accumulated in the cytoplasm. (Crickets hatch after about two weeks.)
Biological material is usually transparent and difficult to see even with the most sophisticated microscope. But Taro Nakamura, then a postdoctoral fellow in Dr. Extavouri’s lab, now a developmental biologist at the National Institute of Basic Biology in Okazaki, Japan, created a special strain of crickets with nuclei that glowed fluorescent green. As Dr. Nakamura said when he recorded the embryo’s development, the results were “staggering.”
It was a “jumping off point” for the search process, Dr. Donough said. He paraphrased a remark sometimes attributed to science fiction author and biochemistry professor Isaac Asimov: “Most of the time, you don’t say ‘eureka!’ When you discover something, you say, ‘Huh. That’s weird.'”
At first, biologists watched videos on a conference room screen—the cricket equivalent of IMAX, given that embryos are about one-third the size of a grain of (long-grain) rice. They tried to discover patterns, but the data set was overwhelming. They needed more quantitative knowledge.
Dr. Don contacted Christopher Rycroft, an applied mathematician now at the University of Wisconsin-Madison, and showed him the dancing nuclei. ‘Wow!’ said Dr. Rycroft. He had never seen anything like it, but he recognized the potential of database collaboration; He and Jordan Hoffman, then a postdoctoral fellow in Dr. Rycroft’s lab, joined the study.
During the many screenings, the math-bio team addressed many questions: How many nuclei were there? When did they start dividing? In which direction were they going? Where did they end up? Why did some swing around and others crawl?
Dr. Rycroft often works at the intersection of the life and physical sciences. (Last year he published on the physics of paper stretching.) “Mathematics and physics have been very successful in generating general rules that are widely applicable, and this approach may also help biology,” he said; Dr. Extavoor said the same thing.
The team spent a lot of time bouncing ideas around on the white board, often with drawings. The problem reminded Dr. Rycroft of the Voronoi diagram, a geometric construct that divides space into non-overlapping subregions—polygons or Voronoi cells—each originating from a seed point. It’s a versatile concept that applies to things as diverse as galaxy clusters, wireless networks, and the growth pattern of forest canopies. (Tree branches are seed points, and crowns are Voronoi cells that feed tightly but do not disturb each other, a phenomenon known as crown shyness.)
In the context of the cricket, the researchers calculated the Voronoi cell surrounding each nucleus and found that the shape of the cell helped predict the direction of the nucleus’ subsequent movement. Basically, Dr. Donough said, “there was a tendency in the nuclei to move into nearby open space.”
Geometry, he noted, offers an abstract way of understanding cellular mechanics. “For most of the history of cell biology, we couldn’t directly measure or observe mechanical forces,” he said, even though it was clear that “motors, shocks and pushes” were at play. But the researchers were able to observe higher-order geometric patterns resulting from these cellular dynamics. “So thinking about the spacing of cells, the sizes of cells, the shapes of cells — we know that they arise from mechanical constraints at very fine scales,” Dr. Doniu said.
To extract this kind of geometric information from cricket videos, Dr. Don and Dr. Hoffman tracked the nuclei step by step, measuring location, speed, and direction.
“It’s not a trivial process and it ends up involving many forms of computer vision and machine learning,” said Dr Hoffman, an applied mathematician now at DeepMind in London.
They also manually cross-checked the software’s results, clicking 100,000 positions to line up the cores in space and time. Dr. Hoffman found it exhausting; Dr. Donohue saw it as a video game, “zooming at high speed into a small world inside a single embryo and stitching together the threads of each nucleus’s journey.”
They then developed a computational model that tested and compared hypotheses that could explain the movement and location of the nuclei. On the whole, they ruled out the cytoplasmic streams that Dr. Di Talia saw visible in the fly. They rejected random motion and the idea that nuclei physically move away from each other.
Instead, they arrived at a plausible explanation based on another known mechanism in fruit fly and roundworm embryos: miniature molecular motors in the cytoplasm that extend bundles of microtubules from each nucleus, unlike the forest canopy.
The team proposed that a similar type of molecular force would pull cricket nuclei into unoccupied space. “The molecules may be microtubules, but we don’t know for sure,” Dr. Extavoor said in an email. “We will have to do more experiments in the future to find out.”
Geometry of manifolds
This cricket odyssey would not be complete without mentioning the “embryo compression device” commissioned by Dr. Donne to test various hypotheses. He replicated old-school techniques, but was motivated by previous work with Dr. Extavour and others on the evolution of egg size and shape.
This contraction enabled Dr. Donohue to perform the difficult task of wrapping a human hair around a cricket egg, thus forming two regions, one containing the original nucleus and the other a partially severed appendage.
The researchers then watched the nuclear choreography again. In the initial region, the nuclei slowed down once they reached the crowded density. But when a few cores crept into the constriction of the tunnel, they sped up again and ran like horses into the open pasture.
This was the strongest evidence yet that nuclear movement is governed by geometry, Dr. Donough said, and “is not controlled by global chemical signals, fluxes, or almost anything else hypothesized to plausibly coordinate the behavior of the whole embryo.”
By the end of the study, the team had collected more than 40 terabytes of data on 10 hard drives and refined a computational, geometric model that added to Cricket’s toolkit.
“We want to make cricket embryos more versatile to work with in the lab,” said Dr. Extavoor, that is, more useful for studying even more aspects of biology.
The model can simulate any egg size and shape, making it useful as “a testing ground for other insect embryos,” Dr. Extavoor said. He noted that this would make it possible to compare diverse species and delve deeper into evolutionary history.
But the greatest reward of research, all researchers agreed, was the spirit of collaboration.
“There is a place and a time for specialized knowledge,” Dr. Extavoor said. “Also often in scientific discovery, we have to expose ourselves to people who are not as invested as we are in any particular outcome.”
The questions asked by the mathematicians were “free of any bias”, Dr Extavoor said. “These are the most interesting questions.”