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Breaking the surface: Lessons on resilience and rebuilding from planarians

CSM Lab

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Divya Shiroor is a vet grad student at Cornell University. She is a foodie, dancer, bookworm, blogger, dog mom, and twin! Her recent first-author publication titled “Injury Delays Stem Cell Apoptosis after Radiation in Planarians” was published by Current Biology on May 7, 2020. Her narrative below explores the unwritten stories behind the publication. You can follow Divya on Twitter @DivyaShiroor

Are you familiar with the iceberg illusion? that visible part of the iceberg peeking magnificently above the ocean? That’s success. Silently lurking beneath is a giant hunk of ice – a combined mass of failure, disappointment, exhaustion and pain, invisible to all but the iceberg. With my first-author research publication hot off the press, my tiny wedge of ice is now entering the sunlight. This narrative however is about that unseen, unspoken mass underneath, that each of us believes we singularly carry around.

I have the privilege of studying incredible flatworms called planarians. I’m enchanted by these worms for the same reason every other person that knows about their superpower is-their crazy ability to regenerate. My first encounter with planarians was in the early days of graduate school, when my advisor, a newly minted PI, showed us how these worms use special cells called stem cells to recover and regenerate from virtually any injury. When the first image of this squint worm flashed across the screen, I was in love. My stars must have aligned just right, and after a two-month rotation, I started out as the first official graduate student of our lab. 

When I look at my publication today, I can’t help but be struck by how 5 years of blood, sweat and tears coalesce so tidily into 5 pages of a journal. I wonder how differently things might have turned out, had I not had two amazing lab mentors pushing me along.

I kicked off my research like most others, by reading pertinent literature to come up to speed on planarian biology. It was while I was on this quest that I came across a curious result, tucked away in the supplementary data of a seminal paper. I have just waxed eloquent about how these worms regenerate because their stem cells respond rapidly to injury. This piece of data showed however that in a particular scenario, these incredible stem cells completely failed to react like they should. I didn’t know it then, but latching on to this curious observation would result in the birth of a project that gave me my first paper, and will one day give me a Ph.D.

I realize I make it sound like I had an instant eureka moment, but the actuality of it was far less dramatic. While I couldn’t get that result out of my head, I couldn’t really define why it stuck with me either. I had an extensive list of reasons explaining why it might not be worth the attention I was giving it. I didn’t know the literature well enough; I was too green behind the ears; it was supplemental data so it probably wasn’t important anyway; if there was something to it, someone else would have spotted it by now; A lot has been said about feeling like an imposter in science and I don’t have much to add, except to say that it almost kept me from pursuing my dream project. That voice telling me it was impossible that I spotted something interesting was loud, and I would have yielded had it not been for my advisor. We discussed the result and she told me to explore it, a brave move for a 2-month-old PI with an already well-developed project ready to go.

Once I began to accrue data, I realized that we had stumbled upon an exciting stem cell response in planarians – their ability to withhold from certain death.

Adding to my confused feelings of inadequacy was my inexperience at the bench – something I carried with me heavily. I didn’t fully understand the science behind the techniques I needed for my experiments. My minimal molecular/genetic training before starting graduate school meant that I wasn’t always equipped with the language needed to make sense of the science. When my advisor cottoned on to just how much I was struggling, she jumped on board to help out. We came up with a system where I would select one technique that we used in the lab and spend hours on google teaching myself everything about it. I would then relay to my advisor all that I had learned, and we’d discuss things that still didn’t make sense to me. While I felt incredibly incompetent at the time, learning how to figure things out turned out to be a great anti-dote that fueled early progress with my project.

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Once I began to accrue data, I realized that we had stumbled upon an exciting stem cell response in planarians – their ability to withhold from certain death. In order to definitively examine this however, we needed to quantify dying stem cells in these animals; this required us to either develop a new technique, or hone an existing one. This was my first real tryst with how slow, frustrating and defeatist science can be. I knew I’d never be able to publish my story without figuring this out, and there were long stretches where I was convinced we’d never get there. I finally managed to get one protocol to work, only to realize that it wasn’t sensitive enough to detect what we needed to determine. It took over two years of failing to finally nail down a technique that allowed us to efficiently quantify stem cell death in planarians – a crucial step for our publication.  If I didn’t have an amazing advisor and a brilliant post-doc cheering me on, I’m not sure I’d have crawled through those years. Science is ALWAYS a team effort, and I will never take for granted how much of its outcome depends on the people around you.

Once we had identified a technique to measure stem cell death, we found that in certain scenarios – like when faced with an injury – planarian stem cells destined to die will pause this process, and choose to persist instead. We were excited about our discovery and our next hurdle was putting this story out into the world. So much of the fate of a lab hinges on its publications, and as a new lab we were still waiting on ours. This gave the final task of putting a paper together a constant, exhausting sense of urgency. After an unhealthy number of caffeine fueled sleepless nights, we finally submitted our work, incredibly proud of all we had pulled off. When our first round of reviews came in however, I was absolutely gutted by the amount of additional work we would have to do to see this publication through.

Around this time, I was also hit by tremendous personal loss, and grief felt like it would be the final straw that would break this camel’s back. We like to believe that we science in vacuum, but the reality is that we science despite the happenings of life, and we need to build a more sustainable culture that accommodates for it. While my instinct was to go full steam ahead with addressing reviewer comments, I had to take a step back and readjust my pace. I found a wonderful therapist, and eventually took some time away from work. While stepping on the brakes seemed counterintuitive at the time, it gave me the clarity and energy I needed to push through the review process. It also readjusted the insurmountable hopelessness I had felt with that first editorial decision. I am now utterly grateful for how much the reviewer’s suggestions helped improve the paper we finally ended up publishing.

When I look at my publication today, I can’t help but be struck by how 5 years of blood, sweat and tears coalesce so tidily into 5 pages of a journal. I wonder how differently things might have turned out, had I not had two amazing lab mentors pushing me along. I hope you are as fortunate as I am, and I hope, like me, you have supportive people around you. If you find yourself without an encouraging voice however, I hope you hear me when I tell you that your place in science is not accidental, and that your iceberg is much closer to the surface that you realize.

ABOUT: Stories in Science is a special series on the Civic Science Times. The main aim is to document the first-hand accounts of the human stories behind the science being published by scientists around the world. Such stories are an important element behind the civic nature of science.

SUBMISSION: Click here to access the story guidelines and submission portal. Please note that not all stories are accepted for publication. After submission, we will let you know whether we have selected the story for the review process.

CivicSciTimes - Stories in Science

Unexpected Stories and Spindle Mistakes: Discovering that Wild-type Cells are Full of Surprises

CSM Lab

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Natalie Nannas

Natalie Nannas is an Associate Professor of Biology at Hamilton College in Clinton, NY. She teaches courses in genetics, molecular biology, and bioethics. Dr. Nannas graduated from Grinnell College with bachelor’s degrees in biological chemistry and French. She received her Master’s and PhD from Harvard University in molecular biology and genetics. Dr. Nannas conducted her postdoctoral research at the University of Georgia where she won a National Science Foundation Plant Genome Postdoctoral Fellowship. At Hamilton College, Dr. Nannas enjoys teaching and sharing her passion for microscopy with her undergraduate research students. When not glued to a microscope, she loves spending time with her husband and two daughters. The narrative below by Natalie Nannas captures the human stories behind the science from a 2022 paper titled “Frequent spindle errors require structural rearrangement to complete meiosis in Zea mays” which was published by her group in 2022 in the International Journal of Molecular Sciences.

Science never works out the way we plan. As scientists, we ask questions, hypothesize and outline our goals … then reality of science occurs. The reality of science is often full of failed controls, endless troubleshooting, and sometimes strange findings that lead us in new and unpredictable directions. Our publications give the impression that we planned these scientific journeys from the beginning and do not tell the human side of the process with all of its twists and turns, dead-ends and U-turns. I want to tell you the real story behind my first publication as a faculty member with my own lab. It did not go as planned due to the COVID-19 pandemic. My lab was shut down in the middle of our investigation, and my students and I were unable to generate new data. In the beginning, it seemed like we were stranded with only control data and no story to tell, but the time away from the lab allowed us to spend more time looking carefully at wild-type cells. What seemed like a dead-end suddenly became its own story when we found something unexpected hiding within microscopy movies. Our wild-type cells were making mistakes, attempting fixes and changing directions, just like we do as scientists.

My scientific journey began with flickering green lights and a microscope (you can read more about it here). As an undergraduate, I was mesmerized by the beauty of watching living cells shuffle fluorescently labeled proteins throughout their cytoplasm. I followed this passion for microscopy into my doctoral dissertation research at Harvard University where I investigated how yeast cells build the machinery needed to pull their chromosomes apart. This machinery is a dynamic collection of long protein tubes called microtubules and other organizing proteins that help move and shuffle microtubules. I loved watching the delicate dance of chromosomes interacting with microtubules of the spindle, and I wanted to continue studying this process in my postdoctoral studies.

During postdoctoral studies at the University of Georgia, I won a fellowship from the National Science Foundation to develop a new technique in microscopy. No one had ever watched plants building their spindles in meiosis, the specialized cell division that produces egg and sperm. Other scientists had performed beautiful microscopy studies observing how mitotic spindles function inside of plant cells, but due to the technical challenges, no one had ever observed live plant cells building spindles in meiosis. I was thrilled to take on this challenge by using version of maize that had fluorescently labeled tubulin, the protein that makes up microtubules of the spindle. With this line of maize, spindles would glow fluorescent green, allowing me to image if only I could extract the meiotic cells.

Dr. Natalie Nannas

We were so busy collecting data and prepping for our mutant studies that we never really took time to analyze the wild-type cells.

After almost a year spent dissecting maize plants, I finally managed to develop a method to isolate these tiny cells and keep them alive in a growth media long enough to image them. This new method of live imaging was going to serve as the foundation of my new lab at Hamilton College, a primarily undergraduate institution. With my students, I planned to investigate the pathways governed spindle assembly. Most animal mitotic cells have a structure called a centrosome that dictates how spindles are formed; however, female animal meiotic cells lack these structures and must use other pathways to direct spindle assembly. Plants also lack centrosomes, and I wanted to inhibit these known animal pathways in our plant live imaging system.

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As I set up my lab, my students and I collected live movies of wild-type maize cells building their spindles. I told my students and myself that these movies were not the main event, they were just the control cells so we would have a baseline comparison for our experimental conditions. We were so busy collecting data and prepping for our mutant studies that we never really took the time to analyze the wild-type cells. At the surface level, they built spindles and segregated chromosomes in a generally expected amount of time, so we focused on preparing for our upcoming experiments…. then March 2020 occurred.

The pandemic forced us to slow down and look more carefully at our wild-type data, and I am grateful for the detour.

My students headed home for spring break with a warning that there may be a delay in coming back to campus due to the spread of COVID-19. None of us were prepared for the shutdown that followed. Like many colleges and universities, our campus was closed for the remainder of the spring 2020 semester and the summer of 2020. My students and I began meeting on Zoom, trying to make a new plan for our research. The only data we had to work with were the microscopy of wild-type maize cells, so we decided to spend time digging more deeply into these movies. Originally, we had only measured the total time it took to build a spindle as it would be a baseline for comparison to our mutants. We had not looked carefully at any of the intermediate time points in the assembly process. When my students looked more closely at our movies, they discovered that wild-type cells built an incorrectly shaped spindle over 60% of the time!

We found that maize meiotic cells often built spindles with three poles instead of two, and they had to actively rearrange their spindle structure to correct this mistake. We also found that in these cells, there was a delay in meiosis as cells refused to progress until this correction had been made. This is an exciting discovery as it showed that plants are error-prone in their spindle assembly, much like human female meiotic cells. Our findings also suggested that meiotic cells were monitoring their spindle shape when determining if they should move forward in meiosis. Previous work has shown that cells monitor the attachment of chromosomes to the spindle to make this decision, but our work adds a new dimension, showing that they also monitor spindle shape. As we continued to analyze our videos, we also learned that cells corrected their spindle morphology in a predictable way. They always collapsed the two poles that were closest together, creating a single pole and resulting in a correct bipolar spindle.

The image shows the first page of the paper which can be accessed here.

My students and I had begun our scientific journey planning to breeze over wild-type cells, moving on to what we envisioned would be a more exciting story of spindle mutants. The pandemic forced us to slow down and look more carefully at our wild-type data, and I am grateful for the detour. I rediscovered my love of closely watching flickering green fluorescent lights, the dance of microtubules sliding into place or making missteps and shuffling into new arrangements. Watching life attempt a complicated process, make mistakes, and try again, is a lesson that never grows old. It reminds me that our scientific journeys are just the same, they start in one direction but are fluid and constantly changing, and hopefully, they end with a functional spindle!

Read the Published Paper

Weiss, J.D., McVey, S.L., Stinebaugh, S.E., Sullivan, C.F., Dawe, R.K., and N.J. Nannas. 2022. Frequent spindle errors require structural rearrangement to complete meiosis in Zea maysInternational Journal of Molecular Sciences, 23 (8):4293–4312.

ABOUT: Stories in Science is a special series on the Civic Science Times. The main aim is to document the first-hand accounts of the human stories behind the science being published by scientists around the world. Such stories are an important element behind the civic nature of science.

SUBMISSION: Click here to access the story guidelines and submission portal. Please note that not all stories are accepted for publication. After submission, we will let you know whether we have selected the story for the review process.

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