Within our collective of zebrafish labs at UCL, the sheer volume of single-use plastic Petri dishes we breeze through is staggering – a staggering 130 kg per year, to be exact. To put this into perspective, it’s a whopping 8.4% more plastic waste than the average person in the UK generates annually, and that’s solely from our Petri dish used for housing larvae. And petri dishes are not the only problem, we use thousands of plastic tips, tubes, PCR plates…and on and on. It’s a dilemma that resonates deeply with many of us in the scientific community. As sustainability takes centre stage across institutions, our host, UCL, has set commendable goals: aiming to eliminate non-essential single-use plastic on campus by 2024 and achieve net-zero carbon status by 2030. While sweeping institutional initiatives mark significant progress, the reality remains that not all these strides trickle down to our individual laboratories. In the scientific community, single-use plastic consumables are gold-standard, and ultracold storage is indispensable. Finding ourselves in this situation, all the fish groups sharing the communal labs got together and sat down to brainstorm ways to make our work more sustainable. We came up with ideas to reduce our environmental impact while continuing our research, in three main areas:
Plastics
Even though single-use plastic tips and Petri dishes aren’t yet on UCL’s sustainability radar for 2024, we’re already taking steps to reduce our use across the groups. Where possible, we are swapping plastic for glassware and when we can’t use glassware, we are finding ways to reuse plastic tips and petri dishes whenever we can. For instance, to reuse Petri-dishes for housing zebrafish embryos we remove labels with ethanol, soak them in hot water for at least 20’ and then dry, ready to be re-used! We’ve also tracked our plastic usage by weighing our Petri dish bins weekly. This not only gauges our sustainability efforts but also aids in estimating equipment stock levels.
One lab protocol that significantly contributes to plastic usage is genotyping, a routine procedure consuming lots of plastic tips and PCR plates. Not commonly known is the practice of reusing tips for gel loading, a neat plastic-saving tip resurrected by the more mature lab members involved in large genetic screens and manual mapping of mutants. These mapping projects required running copious amounts of PCRs on lots of embryos and we did it reusing the same tips again and again. Credit originally to William Talbot’s lab in Stanford University (the master mapper!) for this thrifty and sustainable tip!
Not quite sure how to re-use pipette tips? Check out our video at http://zebrafishucl.org/plastic for simple tips. Reusing tips can serve various purposes, from simple DNA digestion controls to PCR products and RNA checks – any application where gel band extraction or subsequent analysis isn’t necessary. To reduce plastic use further, we also keep partially-used PCR plates for future runs. Start now by collecting used tips in a dedicated box for hassle-free diagnostic gel loading today!
And it’s not only for loading gels, pipette tips can have multiple lives. From water and buffers to alcohol and various solutions that are often used, tips can be reused! Everyone has their unique and fun way to store pipette and Pastette tips – discover yours or explore some ideas here.
Now that we can re-use some tips, what about plastic tubes and falcons? We all use lots of Eppendorf tubes and there isn’t much we can do about this. At a recent sustainability event at the Royal Society, Eppendorf’s life cycle assessment delivered a sobering result – their biobased tubes only show an underwhelming reduction of 16% in CO2 compared to their standard fossil-based counterpart. While there’s a projected 27% decrease in this, the current findings are disappointing. Not to mention the biobased tips are unfortunately more expensive.
As we left the conference, we felt there was room for improvement. How often do we use a classic 1.5 mL Eppendorf for a miniscule 50 µL sample or for storing small aliquots of enzymes and antibodies? Turns out, the comfortably-stored volume for:
PCR tube – 0.220 mL
0.5 mL Eppendorf – 0.6 mL
1.5 mL Eppendorf – 1.6 mL
2 mL Eppendorf – 2.2 mL
Therefore, by just considering the right tube size for an experiment, instead of defaulting to the larger more commonly used 1.5 mL could drastically reduce our plastic usage and associated CO2 footprint. It seems we have the power to make a bigger impact than even Eppendorf can achieve currently, with minimum effort.
The principles of “reduce and reuse” can also be applied to other areas of the lab such as reagents. For diagnostics requiring only a few lanes, consider using a smaller gel. Here, we laser-cut a miniature electrophoresis gel mould for running extra small gels by repurposing our old/broken electrophoresis chamber plastics lids that uses only a third of agarose compare to our smallest commercially bought mould. You can download the laser cutting template from our website here.
Energy
We reduce energy consumption by turning off equipment when not in use, utilizing energy-efficient appliances, and optimizing equipment settings. This can be as simple as switching freezers from -80°C to -70°C (and reduce 30-40% energy consumption!) or switching off PC monitors after work, to deleting any useless data accumulating in the cloud! We also find that installing plug timers set to working hours on appliances such as water baths and heat blocks works really well.
Certain labs are still hesitant to switch ultra-low temperature freezer to -70°C because of sample safety concerns. We store our plasmid and antibodies stocks as well as most of our RNA at -20°C while total RNA, tissues, and competent cells are stored at -70°C. And we’re not the only ones, check out this list of samples successfully stored at higher temperatures by universities in the US. Increasing number of labs have now made the switch. Start 2024 right by joining a sustainability framework like the Freezer Challenge.
It’s always useful to regularly rethink ingrained lab practice. Some procedures appear to be engrained without clear origins. Take, for instance, the ‘cold hold’ – the infinite hold step at the end of a PCR protocol at the 4˚ C. Considering that our PCR products are double-stranded DNA, a fairly stable molecule, the need for this step becomes questionable. Don’t believe us? Here’s the evidence. Now, we’ve opted to terminate the cycle after the final extension, not only conserving energy but also prolonging the machine’s lifespan!
Culture of change
To maintain a consistent and concerted effort toward sustainability, we initiated a floor-wide green committee comprising volunteers from each of our labs. This committee also serves as a bridge between labs and core facilities, such as the UCL Fish Facility. Expanding on this initiative, we’ve established similar committees at the Departmental level, ensuring sustainability remains a priority. As part of this commitment, every new member, including students, postdocs, and PIs, undergoes sustainability training, and we’ve mandated plastic-free events throughout the department (take your own glass to socials, for instance). Our efforts are bolstered by frameworks like the laboratory efficient assessment framework (LEAF) which standardises sustainable practices. We joined LEAF in 2018 and thanks to contributions from many participants, the framework has evolved over the years and will keep improving and expanding. Being part of a framework that is endorsed by leading scientists and that is recognised by funding bodies helps with the acquisition, reinforcement and spreading of good, ideally, GOLD practices. Our entire department has set its sights on having all laboratories taking part of the LEAF and achieving Gold awards by 2025, a testament to our commitment to sustainability.
Despite having come a long way, there is still lots to do including in the way we think about how we conduct and publish research. Open research practices and open access publishing is indeed helping scientists to have better access to data, methods and resources and to minimise unnecessary duplication (while acknowledging that validating results is of course critical!). Sharing protocols and reagents pre-publication as well as publishing negative results should become the norm and we would love to see sustainability approaches within the methods section of papers (including positive as well as the negative outcomes).
While lots of science will remain competitive and sometimes secretive, the balance is shifting to more cooperative, collaborative, sustainable research with funders recognising the importance of community projects and resources that bring widespread benefits to the global research endeavour.
Alexandros Sountoulidis, Alexandra Firsova, Andreas Liontos, Jonas Theelke, Janine Koepke, Pamela Millar-Büchner, Louise Mannerås-Holm, Åsa Björklund, Athanasios Fysikopoulos, Konstantin Gaengel, Fredrik Bäckhed, Christer Betsholtz, Werner Seeger, Saverio Bellusci, Christos Samakovlis
Kieran M. Short, Giovane G. Tortelote, Lynelle K. Jones, Fabiola Diniz, Francesca Edgington-Giordano, Luise A. Cullen-McEwen, Jan Schröder, Ashley Spencer, Andrew Keniry, Jose M. Polo, John F. Bertram, Marnie E. Blewitt, Ian M. Smyth, Samir S. El-Dahr
Pedro Vallecillo-García, Mira Nicola Kühnlein, Mickael Orgeur, Nils Rouven Hansmeier, Georgios Kotsaris, Bernd Timmermann, Claudia Giesecke-Thiel, René Hägerling, Sigmar Stricker
Silvia Carvalho, Luna Zea-Redondo, Tsz Ching Chloe Tang, Philipp Stachel-Braum, Duncan Miller, Paulo Caldas, Alexander Kukalev, Sebastian Diecke, Stefanie Grosswendt, Ana Rita Grosso, Ana Pombo
Anish Dattani, Elena Corujo-Simon, Arthur Radley, Tiam Heydari, Yasaman Taheriabkenar, Francesca Carlisle, Simeng Lin, Jonathan Mill, Peter Zandstra, Jennifer Nichols, Ge Guo
Valerio E.C. Piscopo, Alexandra Chapleau, Gabriela J. Blaszczyk, Julien Sirois, Zhipeng You, Vincent Soubannier, Geneviève Bernard, Jack P. Antel, Thomas M. Durcan
Stephanie Farhat, Bahaeddine Tilouche, Spencer Short, Medjie Piron, T. Mark Campbell, Alex Fernandes, Mariya Somyk, Hina Bandukwala, Eric Arezza, Quentin Sastourne-Arrey, Katherine Reilly, Maria Abou Chakra, Gary Bader, Leo Kunz, Timm Schroeder, Sasha Carsen, Pierre Mattar, Jeffrey Dilworth, Daniel L. Coutu
Karina O. Brandão, Viviana Meraviglia, Daniela Salvatori, Xu Cao, Luca Sala, Loukia Yiangou, Mervyn P.H. Mol, Milena Bellin, Christine L. Mummery, Richard P. Davis
Kuan-Hung Lin, Jamie E Hibbert, Jake L Lemens, Melissa M. Torbey, Nathaniel D. Steinert, Philip M. Flejsierowicz, Kiley M. Melka, Marcos Lares, Vijayasaradhi Setaluri, Troy A. Hornberger
Ioannis Oikonomakos, Melina Tedesco, Fariba Jian Motamedi, Mirko Peitzsch, Serge Nef, Stefan Bornstein, Andreas Schedl, Charlotte Steenblock, Yasmine Neirijnck
Anthony E. Postiglione, Allison M. Delange, Mohammad Foteh Ali, Maarten Houben, Eric Y. Wang, Stacy L. Hahn, Colleen M. Roark, Molly Davis, Robert W. Reid, James B. Pease, Ann E. Loraine, Gloria K. Muday
Nataliya E. Yelina, Eftychios Frangedakis, Zhemin Wang, Tina B. Schreier, Jenna Rever, Marta Tomaselli, Edith Forestier, Kumari Billakurthi, Sibo Ren, Yahui Bai, Julia Stewart-Wood, Jim Haseloff, Silin Zhong, Julian M. Hibberd
Yuan Zhang, Deepak Sharma, Yan Liang, Nick Downs, Fleur Dolman, Kristen Thorne, Ian Black, Jose Henrique Pereira, Paul D. Adams, Henrik Scheller, Malcolm O’Neill, Breeannna R Urbanowicz, Jenny C Mortimer
Anastasia I. Kurtova, Alexander D. Finoshin, Margarita S. Aparina, Guzel R. Gazizova, Olga S. Kozlova, Svetlana N. Voronova, Elena I. Shagimardanova, Evgeny G. Ivashkin, Elena E. Voronezhskaya
Luis Baudouin Gonzalez, Anna Schönauer, Amber Harper, Saad Arif, Daniel J. Leite, Philip O. M. Steinhoff, Matthias Pechmann, Valeriia Telizhenko, Atal Pande, Carolin Kosiol, Alistair P. McGregor, Lauren Sumner-Rooney
Matthew T Biegler, Kirubel Belay, Wei Wang, Christina Szi, Paul G Collier, Ji-Dung Luo, Bettina Haase, Gregory L. Gedman, Asha V. Sidhu, Elijah Harter, Carlos Rivera-Lopez, Kwame Amoako-Boadu, Olivier Fedrigo, Hagen U. Tilgner, Thomas T Carroll, Erich D. Jarvis, Anna L. Keyte
Sona Relovska, Huafeng Wang, Xinbo Zhang, Pablo Fernández-Tussy, Kyung Jo Jeong, Jungmin Choi, Yajaira Suárez, Jeffrey G. McDonald, Carlos Fernández-Hernando, Jean-Ju Chung
Matthew Lefebvre, Jonathan Colen, Nikolas Claussen, Fridtjof Brauns, Marion Raich, Noah Mitchell, Michel Fruchart, Vincenzo Vitelli, Sebastian J Streichan
Quan Xu, Lennard Halle, Soroor Hediyeh-zadeh, Merel Kuijs, Umut Kilik, Qianhui Yu, Tristan Frum, Lukas Adam, Shrey Parikh, Manuel Gander, Raphael Kfuri-Rubens, Dominik Klein, Zhisong He, Jonas Simon Fleck, Koen Oost, Maurice Kahnwald, Silvia Barbiero, Olga Mitrofanova, Grzegorz Maciag, Kim B. Jensen, Matthias Lutolf, Prisca Liberali, Joep Beumer, Jason R. Spence, Barbara Treutlein, Fabian J. Theis, J. Gray Camp
William Dalleywater, Alexander V. Predeus, Batuhan Cakir, Pavel Mazin, Jayakumar Vadakekolathu, Sergio Rutella, Marian L. Meakin, Alison A. Ritchie, Shamir Montazid, Sara Cuevas Ocaña, Nadine Holmes, Victoria Wright, Fei Sang, Adam Bills, Declan Sculthorpe, Rasa Elmentaite, Sarah A. Teichmann, Shazia Irshad, Ian Tomlinson, Andrew Silver, Ricky D. Wildman, Nicholas R.F Hannan, Felicity R.A.J. Rose, Mohammad Ilyas
Mirazul Islam, Yilin Yang, Alan J. Simmons, Vishal M. Shah, Musale Krushna Pavan, Yanwen Xu, Naila Tasneem, Zhengyi Chen, Linh T. Trinh, Paola Molina, Marisol A. Ramirez-Solano, Iannish Sadien, Jinzhuang Dou, Ken Chen, Mark A Magnuson, Jeffrey Rathmell, Ian G Macara, Douglas J Winton, Qi Liu, Hamim Zafar, Reza Kalhor, George M. Church, Martha J. Shrubsole, Robert J. Coffey Jr., Ken Lau
C. Lapoujade, M. Blanco, M. Givelet, A.S Gille, I. Allemand, L. Lenez, N. Thiounn, S. Roux, J.P. Wolf, C. Patrat, L. Riou, V. Barraud-Lange, P. Fouchet
Malgorzata Lagisz, Joanna Rutkowska, Upama Aich, Robert M. Ross, Manuela S. Santana, Joshua Wang, Nina Trubanová, Matthew J. Page, Andrew Adrian Yu Pua, Yefeng Yang, Bawan Amin, April Robin Martinig, Adrian Barnett, Aswathi Surendran, Ju Zhang, David N. Borg, Jafsia Elisee, James G. Wrightson, Shinichi Nakagawa
Melanie M Cooper, Marcos D. Caballero, Justin H. Carmel, Erin M. Duffy, Diane Ebert-May, Cori L. Fata-Hartley, Deborah G. Herrington, James T. Laverty, Paul C. Nelson, Lynmarie A. Posey, Jon R. Stoltzfus, Ryan L. Stowe, Ryan D. Sweeder, Stuart Tessmer, Sonia M. Underwood
To provide more visual content on the Node, we are starting a new series called ‘Show and Tell’. The aim of these short posts is to act as a hook for people to find out more about a paper, a technique or a location that is of interest to the developmental and stem cell biology community.
Write a ‘Show and tell’ post yourself!
Do you have an incredible image or video from one of your recent papers? Are you optimising a technique and want to showcase a piece of equipment you are using? Or perhaps your research involves going to a field site to collect samples?
Post an image, photo, or video of your choice, and answer the questions below. Keep the answers short and snappy, and always include a link at the end for people to find out more. Be as creative as you want with what you show people, as long as it is relevant to #devbio!
What is this?
Where can this be found?
How was this taken?
What does it do?
Why should people care about this?
How would you explain this to an 8-year-old?
Where can people find more about it?
(Note: you can choose to answer the questions that apply to you, and feel free to adapt the questions to fit your answers)
Scanning Electron Micrographs (SEM) of a sea anemone stinging cell (F) and change in cell identity following the knockout of a gene called NvSox2 (G). Images are pseudo-colored to highlight characteristics of these cells, collectively called cnidocytes. Taken from Babonis et al. (2023).
What is this?
A sea anemone stinging cell (F; left panel) and change in cell identity following the knockout of a gene called NvSox2 (G; right panel).
How was this taken?
With a Scanning Electron Microscope. Images are pseudo-colored to highlight characteristics of these cells.
What does it do?
Sea anemones have various stinging cells, called cnidocytes, with different functions such as piercing prey for feeding or sticking to surfaces so they don’t get swept away by ocean currents.
Why should people care about this?
Piercing cells come in over 30 different sizes and shapes, all of which were thought to share a single “piercing” ancestor. But at some point in the starlet sea anemone’s evolution, a gene called NvSox2 silenced the molecular decisions that led stinging cells to become “sticky” and instead instructed them to become a specific type of “piercing” cell (F), effectively inventing a new cell type.
When NvSox2 is disabled, these “piercing” cells are restored to their ancestral “sticky” identities (G) that have been forgotten in this particular anemone’s long evolutionary history.
These results suggest that single-gene switches driving cell fate have been around for a long, long time and provide a flexible molecular mechanism for animals to adapt to new and changing environments as needed to survive. It’s plausible — maybe even likely — that other types of “piercing” cells have a similar gene-induced amnesia blocking cellular memories of a distant past.
How would you explain this to an 8-year-old?
Sea anemones (pronounced “uh-neh-moh-nees”) don’t look like you and me. They’re related to jellyfish and have special stinging cells. If you’ve ever been stung by a jellyfish, you know that can hurt!
These are pictures of two cells that come from a sea anemone. Someone has colored the cells for us so we can see them better. They’re very different from each other. Can you see how they’re different?
The smooth yellow cell on the left shoots pointy darts into the sea anemone’s food so it can eat. The dart is colored pink and blue in the picture.
The tan cell on the right has large, sticky strings that keep the sea anemone from being washed away.
When these cells are young, they’re not sure if they’re supposed to shoot small pointy darts or large sticky strings when they grow up. Do you know what you want to be when you grow up? How do you know what to choose?
These cells are told what to do with an on-off switch. When the switch is flipped on, the cell forgets how to be large and sticky and looks like the small pointy cell on the left. That’s what this sea anemone normally does. But when scientists turn the switch off, the cell suddenly remembers it should be large and sticky like the cell on the right.
Wouldn’t you like to have a switch to help you remember something that you forgot?
Switches like this can teach us how animals invent new cells. It also shows us how cells store old memories that might help them survive through hard times. When something works, you don’t want to forget it!
Where can people find more about it?
This paper was featured on Nature Communications Editors’ Highlights page. You can find the full-length article here.
BEE-ST (Bone and tEEth Spatio-Temporal growth monitoring) is a method to monitor mineralization dynamics across species. It is based on the intraperitoneal (abdominal cavity) administration of fluorescent calcium-binding dyes in an animal of interest at the specific time you want to observe newly-forming mineralized tissue. Sequential administration of dyes that fluoresce at different wavelengths (alizarin, red; and calcein, green) enables the observation of bone and tooth mineralization dynamics across time.
Where can this be found?
The technique can be applied to all tissues that undergo mineralization in various species, so the fluorescent dyes will be found in parts of bones and teeth that have developed since the administration of the dyes. The technique was developed by graduate student Marcos González López and his colleagues in Jan Křivánek’s lab at the University of Masaryk in Brno, Czechia.
How was this image taken?
The image was taken by high-resolution confocal laser-scanning microscope. Confocal microscopes use fluorescent lasers to illuminate different depth spots in your sample. By using confocal microscopy, you can obtain several images in different planes that can be put together to recreate a 3D model of your sample, in this case, the mouse molar.
What does it do?
The BEE-ST technique enables researchers to investigate how mineralized tissues (bones and teeth) develop or repair themselves after injury. This is achieved through the binding of dyes to the newly-synthesized or newly-repaired regions of bone or teeth. Once harvested, bones and teeth can be subjected to an optical-clearing protocol, enabling light to pass through them, and a couple of days later the tissue is ready to be imaged by fluorescent laser-scanning microscopy.
Why should people care about this?
The BEE-ST method is a powerful to understand how hard tissues become mineralized.
In the developmental biology and tissue engineering research communities this tool can be utilized to:
Gain a better understanding about how bone and teeth obtain their shape.
Evaluate how changes in the expression of genes, proteins or signalling pathways influence bone or tooth regeneration.
Assess the effectiveness of small molecules or drugs in promoting repair and healing of bones.
How would you explain this to an 8-year-old?
Teeth and bone have a lot of calcium in them. When they grow, or when they break and repair themselves, they add more calcium to themselves. We can use special, coloured dyes that “grab onto” growing teeth and bones to see how fast they grow or repair themselves. This way, when we look at a tooth or bone from an animal that we gave these dyes to, we can see which parts grew recently. Like you can see in the picture, when we switch between red and green dyes, we can find out how long ago each part of the tooth or bone grew, or how quickly. Look at the bones from the front and back leg of the mouse: the red parts grew before the green parts. This way, we can study how teeth and bones grow, and how they repair themselves after they break. We can also test new medicines to see if they can help bones heal more quickly after they break.
Where can people find more about it?
If people want further information on how this method works and its versatile use in all mineralized tissues across species, they can read the recent paper from the Křivánek lab at the Department of Histology and Embryology at Masaryk University in Czechia.
Flipping through the pages of Development Volume 123 Issue 1 (1996) shows the dynamics of zebrafish embryogenesis from the 2-cell stage to the 16-somite stage.
What is this?
A physical copy of Development Volume 123 Issue 1 (1996), with a flipbook at the upper corner of the issue showing zebrafish embryogenesis over 17 hours from the 2-cell stage to the 16-somite stage.
Where can this be found?
The Company of Biologists office in Cambridge, UK
Why should people care about this?
Consisting of 37 papers, this zebrafish special issue presented the results of two large screens for zebrafish mutants. The papers describe about 1500 mutations in more than 400 new genes involved in a wide range of processes that govern development and organogenesis. The mutants described in this issue provide a rich resource for many zebrafish laboratories to study embryogenesis, neuronal networks, regeneration and disease.
How would you explain this to an 8-year-old?
What happens to the first 17 hours of the life of a little zebrafish? In this science book, when you flip through the pages, you can see how the zebrafish grows from just two cells to 16 cells by the end of the book, where you can start to see the shapes of the eyes and brain of the zebrafish.
These zebrafish may look very different from us humans, but they are actually very useful for scientists to learn more about the general rules of how we grow, and what happens to us if something inside us is not working properly.
Where can people find more about it?
For more details about the making of the ‘flipbook’, read this article.
A recent Cell paper finds that proteostasis governs differential temperature sensitivity across cell types in zebrafish embryos. First author Mike Dorrity tells us more about the story behind the paper.
How did you come to join Cole Trapnell’s lab and how did the project get started?
My PhD lab shared a work area with Cole’s in Seattle, so I spent a lot of time chatting with his group. One time, they were all heading out for pizza + drinks, and, being a graduate student, I tagged along hoping for an easy meal. As I was a bit out of place, some jokes were made about me being a new lab member, so Cole played along and asked: “Since you’re joining the lab, what are you going to work on?” He only seemed to be half-joking, so I had no choice but to give a half-serious response: “how temperature influences developmental robustness, something like that.” I believe that got the ball rolling. After discussing with other Trapnell lab folks working on fish, we hatched initial plans for temperature experiments.
What was known about how developing zebrafish embryos respond to temperature stress before your work?
Well, I have to split that one up a bit: (1) I think every zebrafish researcher knows something about how they respond to temperature, since slowing or speeding up development is practically very useful. Do you know what time you have to wake up to study 15-somite stage animals? The relationship between temperature and the rate of development is well-documented, and I refer to the chart in Kimmel et al 1995 constantly. (2) For temperature stress, the outcome is a bit different – there are developmental phenotypes that pop up over and over again. We knew about some of these phenotypes, such as a bend in the body axis, and, from previous work, even knew some of the molecular consequences of temperature stress: heat-shock protein induction, regulation of protein homeostasis.
Can you summarise the findings of the paper in one paragraph?
All in all, I think it can be summarized in one sentence: cell types do not respond equally to temperature. That sounds trivial, but it’s counterintuitive in the context of what we know about the heat shock response (uniform across cells) and of what we know about the acceleration of developmental rate at increased temperature (must be uniform-ish, as embryos are still viable). Basically, when you look closely at all cells at these sub heat-shock temperatures, you can see that temperature destabilizes the fidelity or robustness of development of certain cell types more than others. These cell type-specific sensitivities might not be so obvious when looking at the whole embryo under a stereoscope, but they explain the common failure modes of embryogenesis and the phenotypes that emerge as embryos approach the limits of developmental robustness.
Were you surprised to find that some cell types display accelerated developmental rates more than other cell types in response to the same elevated temperature?
Absolutely, this result completely changed how I thought of the problem. I come from a background informed by the biochemistry and molecular control of the heat shock response – the dogma there, rightfully so, is that all cells more or less mount the same response to stress: stop making proteins and prevent the existing ones from falling into misfolded, non-functional states. That makes good sense, but the embryo context is so different from something like yeast; different cells have drastically different functions and thus express a unique repertoire of proteins to carry out those functions. From that perspective, it’s not so surprising that cells respond differently. Beyond that, cells have many ways to sense temperature that can also vary in the embryo. For example, plasma membrane fluidity increases as a function of temperature, but this increased fluidity is also necessary for migratory cell types.
Can you describe how you captured phenotypic variability across individuals raised at different temperatures?
Yes! This technique is indebted to previous work in the Trapnell lab, [Srivatsan, McFaline-Figueroa, Ramani et al 2020] as well as efforts by Lauren and Sanjay in the “sister” publication to this one [Saunders, Srivatsan et al 2023]. Basically, the trick is: during embryo dissociations, we add barcoded, single-stranded DNA oligos and fix them to nuclei that come from a single embryo. This ensures that we can link all those cells back to the embryo-of-origin after our single-cell RNA-seq library preparation. Our phenotype in this case is actually whole-embryo cell composition, and you can only get measures of variability if you measure many individual fish (n > 100). This molecular trick unlocks individual-level data, and we can then perform statistics on the resulting cell counts, which would be otherwise be challenging to acquire for all cell types.
Can you postulate about the mechanisms through which the UPR controls temperature-induced developmental acceleration?
I would be happy to, and I encourage any potential reader to reach out if they’d like to discuss further, because this is an exciting new direction for us. The unfolded protein response, or the integrated stress response more broadly, has access to global control of protein synthesis in the cell. Under protein folding stress in the ER, UPR will put the brakes on translation. Control of translation rate (as well as protein degradation rate), has been linked to species-specific differences in the control of developmental rate, so I think any mechanism that feeds into protein synthesis rate has the potential to affect timing (we also saw slowdown of development when we inhibited translation). I think the sensing of protein concentration, protein synthesis, and protein folding in the ER is an efficient proxy for temperature. If you take away this sensing apparatus, the embryo doesn’t accelerate like it’s supposed to, despite being raised at a higher temperature.
Did you have any particular result or eureka moment that has stuck with you?
For me, it’s that an enormous amount of variation in the developmental-series scRNA-seq data is explained by the time or stage of the embryo. Again, this may sound trivial – of course gene expression patterns change over time! What has really stuck with me is how developmental timing, cell composition and transcription go hand-in-hand, even down to timescales of minutes (see Figure). Being immersed in the quantitative/statistical thinking of Cole’s lab made me realize how this simple observation can profoundly affects interpretation of your results; many factors (time, temperature, cell type..) are squabbling over the variation in your data, and it’s up to you to break them up and see what all the fuss is about.
And the flipside: were there any moments of frustration or despair?
Much of this project was completed between the peaks of the initial strain and Delta variant of SARS-CoV-2; despair was unavoidable. On the other hand, the constant questioning during those months was balanced by the task of being a scientist. I was very lucky to have co-authors with me at 2am in N95s, wearing headlamps (I cannot remember why) to dissociate embryos. The ensuing virtual meetings, discussions, optimizations, and laughs were essential in reminding me how science feels at its best: a community of people finding answers in the face of uncertainty.
What’s next for this story? And what’s next for you personally?
What’s next is: why are some cells more sensitive to temperature? Is this at all meaningful in the evolutionary context of temperature adaptation? Thankfully, I just started my group at the EMBL (https://www.dorrity-lab.com/) in Heidelberg, Germany surrounded by amazing colleagues and fellows to pursue these questions. If these questions sound exciting to you, reach out!
Hi! My name is Teodora and I am the new Sustainable Conferencing and Communications Officer from The Company of Biologists.
Since I joined The Company of Biologists, I have worked to improve the sustainability strategy of our events in order to decrease our carbon footprint. If you are interested in making your events with a lower environmental impact, we are happy to support you on this journey as well!
Feel free to email me at sustainability@biologists.com if you do not know where to start, and I am happy to help you start building your sustainable strategy for your events.
We are also keen to support your sustainability progress in event organising with our Sustainable Conferencing Grant. If you have any innovative idea on how decreasing the carbon footprint of your next scientific event, we would like to see your application. Here is a compete list of what we fund with the Sustainable Conferencing Grant:
Measures to reduce the carbon footprint of travel (up to £1,000)
for example, removing the necessity to fly by asking speakers to present virtually, or maximising the number of non-local speakers travelling by train or other relatively low-carbon transport
Additional cost of technology (up to £2,500)
for example, rental of a virtual platform or equipment to host a virtual element, IT and associated support/services
we are particularly keen to fund innovative technologies or innovative uses of existing technologies
Innovative feature (up to £2,500)
for example, the development of an app to enhance the experience of virtual attendees
Other (up to £1,000)
measures to improve sustainability that are not covered by any of the other categories
As we get to the end of 2023, the Node, preLights and FocalPlane, the three community sites of The Company of Biologists, would like say a massive thank you to everyone who have read and contributed to the three sites in the past year!
To share some festive fun, and to encourage you to revisit some of the content we put out in 2023, we’ve come up with an end-of-year quiz.
Complete the quiz for a chance to win a goodie bag prize consisting of the Node postcards, the Node Network jigsaw puzzle, FocalPlane notebook, preLights and Biology Open highlighters, a Foldscope and more!
All the answers can be found on the three community sites or in our journals.
Have fun and see you in 2024, Joyce (Community Manager of the Node)
Finish our end-of-year quiz for a chance to win a goodie bag prize including the Node postcards, preLgihts highlighters, FocalPlane notebooks, a Foldscope and more. (Christmas tree in photo not included, unfortunately shipping costs will be over our budget!) (No Ratings Yet) Loading...
“We’ve wrapped up these conversational crackers into a scientific smorgasbord, an allelic amuse-bouche, a genetic gallimaufry, if you will, into this bonus episode!”
If you enjoy the show, please do rate and review on Apple podcasts and help to spread the word on social media. And you can always send feedback and suggestions for future episodes and guests to podcast@geneticsunzipped.com Follow us on Twitter – @geneticsunzip
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