Carly Martin looks into a microscope

Carly Martin


Madeleine Turner/Whitehead Institute

A day in the life of graduate student and plant scientist Carly Martin

Carly Martin is developing a detailed map showcasing which genes are turned on or off across cell types during seed development. Step into her world as a graduate student in the Gehring Lab at Whitehead Institute and see — through a combination of video and text — what a typical day is like for her, as she explores innovative ways to enhance agricultural sustainability.


As Whitehead Institute Member Mary Gehring’s lab buzzes with a flurry of activity, graduate student Carly Martin approaches her workstation with a sense of purpose. With one hand deftly maneuvering a culture plate containing plant seeds, and the other poised over a pipette, she begins a ritual that has become second nature to her.

Martin carefully measures and dispenses water into each seed sample before setting the plate onto a gentle rocker. During these pivotal moments in the lab, she is not just a graduate student, but an emerging researcher who’s on a path to pioneer new frontiers in plant biology.

Martin's journey to this point has been far from straightforward — she made a bold leap from neuroscience to plant biology a few years ago. But now, under the mentorship of Gehring, who is also a professor of biology at the Massachusetts Institute of Technology, she has found a scientific question that ignites her curiosity: investigating gene expression changes across various cell types at different stages of seed development of a small flowering plant in the mustard family, Arabidopsis thaliana. She hopes that one day this work can lead to the development of crops that are capable of thriving in fluctuating environmental conditions, solving the global food insecurity crisis.

Join Martin as she walks us through a day in her life in the lab and beyond, offering a firsthand glimpse of the challenges and triumphs of being a graduate student and an early-career plant researcher.

The outlier

With the seed samples primed, Martin’s next move is already mapped out: in situ hybridization. Preparing for this reaction typically takes up most of her afternoon. The technique is used by researchers to label genetic material within cells and tissues, pinpointing the location where specific genes are expressed, or read into RNA.

For Martin, the experiment is crucial. It helps her understand how genes function within different cells of Arabidopsis, where and when they're active, and the roles they play in the seed development process. Special probes, which act like tiny, colorful tags, are used in the experiment to latch onto targets within a cell. Once the probes have attached, Martin can examine the sample under a microscope and precisely track the location and temporal expression patterns of the genes she’s interested in investigating.

Martin came to the Whitehead Institute in 2019, bringing along extensive experience in single nuclei RNA sequencing — a method for scrutinizing how and which genes are expressed in individual nuclei within cells. She had developed these skills as a research associate in the Macosko Lab at Broad Institute of MIT and Harvard, where she used the technique to study different cell types in the mammalian brain.

While the work was intriguing, for graduate school, she sought a different kind of challenge — she wanted to harness her skills to address a personal question that had little to do with neuroscience, but had been on her mind for years: protecting plant biodiversity in the face of climate change. The Gehring lab seemed like the perfect fit for this pursuit.

“Although my neuroscience background was very different from other people in the lab, Mary embraced it with a type of openness you rarely see,” Martin reflects.

Since then, she has utilized her training in single nuclei RNA sequencing to develop a detailed map of gene expression, also known as a transcription atlas, in Arabidopsis cells.

Within each cell, there's a unique set of genes, some of which are active and others that are inactive. Active genes produce messenger RNA (mRNA) that guides the production of proteins necessary for various cellular processes.
The atlas reveals which genes are active within a cell at any given time during seed development and how they influence the cell’s behavior. Martin then uses the in-situ hybridization reaction to confirm these findings.

“With the depth and resolution of these methods, we’ve been able to identify new cell types that haven't been characterized before,” she says.

But that’s not all.

While analyzing the data in the atlas, she stumbled upon numerous new peptide sequences. These short proteins can act as signaling molecules, playing a crucial role in coordinating cellular activities by transmitting signals between different cells and tissues in a developing seed.

Identifying if and how these peptides influence seed tissue coordination in Arabidopsis would bring Martin closer to uncovering the answers she’s been seeking.

Science as a practice of introspection

Once the prep work for the in-situ hybridization experiment is complete, Martin devotes the rest of her afternoon to performing bioinformatics analysis that will help her determine where, in a developing Arabidopsis seed, specific peptide families are more common.

Among the new peptide sequences she’s discovered in the atlas data, some seem to belong to a family known as RALF or Rapid Alkalinization Factor peptides. These plant hormones regulate pollen tube growth — the process by which a pollen grain extends a long tube to transport male genetic material to the female part of the flower — and the subsequent release of sperm cells during fertilization.

“But the RALFs we’ve identified are not the same ones that are involved in fertilization, so we want to see if they’re playing different functions in seed development,” Martin says.

She hypothesizes that these peptides may be helping direct resources from the maternal plant to its offspring. If confirmed, this discovery would offer valuable insights into seed development, with potential applications in improving agricultural practices and increasing crop yield.

Testing this hypothesis entails probing for interactions between the RALF peptides and specific receptors within Arabidopsis cells. But Martin has encountered her fair share of challenges in conducting these experiments.

“Early on, I thought that I should express and purify all the peptides and receptors. But then I realized that there were way too many peptide-receptor pairs I wanted to test, and expressing and purifying all of them was not very practical,” she explains.

Since then, she’s transitioned to using a different system known as the yeast 2-hybrid assay. Though less precise, this method is faster and it allows her to investigate multiple peptide-receptor interactions simultaneously. Five years into her graduate work, changing tactics has become a standard aspect of scientific inquiry.

“I think that PhD programs are designed in a way that you spend a couple of months in your first year thinking about a problem, then you develop hypotheses, and then you spend years testing out those ideas. But I don't think there's enough emphasis placed on introspection, or the willingness to take assumptions that are inaccurate and then build onto them to match what's really going on in the natural world,” she adds.

Despite facing roadblocks along the way, as long as Martin can continue to explore the mysteries of seed development and inspire budding scientists to pursue questions that ignite their curiosity — much like Gehring’s mentorship has done for her — she will consider herself a successful plant scientist.



Communications and Public Affairs
Phone: 617-452-4630

Mary Gehring stands smiling in front of a window.

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