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
In the recent BSDB-the Node virtual art exhibition, Christoph Markus Haefelfinger’s ‘The backbone of stem cell derived embryos’ was selected as the Judges’ Choice runner-up in the ‘Scientific images’ category. We briefly caught up with Christoph to find out more about his research and the story behind the image.
The backbone of stem cell derived embryos Christoph Markus Haefelfinger (California Institute of Technology)
The cytoskeletal structure of preimplantation embryos demonstrated in a reconstruction of a stem cell derived mouse blastoid. After fixation, the structure was immunostained for f-actin (phalloidin, grey) and the inner cell mass (Oct4, red), then imaged.
What is your background? I am a final year medical Student from Switzerland, currently applying for a PhD in developmental and stem cell biology in the UK. At the time I took my confocal image, I was a Summer Undergraduate Research Fellow in the laboratory of Professor Magdalena Żernicka-Goetz at the California Institute of Technology.
What are you currently researching on? I am continuing my work at the Żernicka-Goetz lab at the University of Cambridge in parallel to clinical placements at the Universities of Cambridge and Oxford, researching preimplantation development using a mouse stem cell derived embryo model. More precisely, I aim to help solidify the scientific confidence in utilising bioengineered embryo models to study specific developmental questions.
Can you tell us more about the story behind your image ‘The backbone of stem cell derived embryos’? To me, the image signifies the culmination of my ten week fellowship at Caltech learning the ins and outs of stem cell derived embryos, and is one of my proudest achievements. I had a truly wonderful and eye-opening experience grounded in cutting-edge research and exploring the Western USA with amazing friends and colleagues, and many of these emotions are strongly tied to my picture. I am therefore even more proud and grateful for the amazing feedback by the jury and the public – it is truly a fantastic feeling to have so many of you appreciate my image which is so close to my heart!
What is your favourite technique? Choosing from the techniques I had the chance to learn and apply myself as an undergraduate researcher, I must go for live imaging using fluorescent reporters. I believe there are few techniques that hold the promise to not only provide quantifiable data, but to spatiotemporally visualize highly complex processes in an unparalleled beauty. Especially in the context of developmental biology, I know of no other method that could capture the dance of life in a more mesmerizing way, making it an easy choice for me.
What excites you the most in the field of developmental and stem cell biology? I am captivated by the fact that we all originate from a single cell. To me it sometimes still is an abstract thought, and seeing an embryo develop – human, mouse, or stem cell derived – excites me every time. This enthusiasm translates into my strong curiosity for cell fate acquisition, and how it interrelates with self-organisation, spatiotemporal crosstalk, and its regulatory foundation on an omics level. I am therefore truly excited to continue researching development in my PhD.
Castle of Dreaming Dragons This began as a small pencil sketch in May 2019 and went through a series of transitions to the final piece, which was finished in June 2020. It ended up being inked digitally, and painted with watercolours, which was an odd combination to choose but I was pleased with how it turned out. I was really pleased to be able to exhibit it in the BSDB virtual art exhibition this year.
Can you tell us about your background and what you work on now?
I’m from the UK, and I study the genetics of progressive hearing loss in the lab of Professor Karen Steel at King’s College London. The project I have been working on most recently involved analysing sequence data from several large human cohorts and developing different methods to identify genes and variants which might be contributing to the different types of hearing loss observed in the participants.
This is one of the rare images directly based on my research. It shows SNPs from a region on chromosome five from a mouse of unknown background (leftmost column), 15 inbred strains and 7 wild-derived strains. Inbred and wild-derived strain data was obtained from Jax (Center for Genome Dynamics (CGD). SNP data from Mouse Diversity Genotyping Array, 582,000 locations for 72 strains of mice. MPD:CGD2. Mouse Phenome Database web site, The Jackson Laboratory, Bar Harbor, Maine USA. http://phenome.jax.org, Nov, 2010.). The image was generated using perl (green=G, red=A, blue=C, yellow=T). It was exhibited at the the BSDB/GenSoc art exhibition in 2021, which I very much enjoyed being part of.
Were you always going to be a scientist?
I remember not knowing what I wanted to do when I grew up, but I studied the subjects I enjoyed most and I’m pretty happy with where I ended up. I did take a side trip through computer science between my undergraduate degree and my PhD, which turned out to be very useful further down the line.
And what about art – have you always enjoyed it?
I have always enjoyed doodling, to the point where I used to worry about being given a new rough book at school – the teachers always checked to make sure the old one had been used properly and I didn’t think covering the pages with horse doodles counted! And I have always told stories, but usually just to myself.
The chapter title page from another illustrated story I’m working on, “Looking for the Sun”.
What or who are your most important artistic influences?
I would say the most important artistic influences on me are writers such as Lois McMaster Bujold and Martha Wells, and artists like Kaoru Mori and Hitoshi Ashinano, but they are the tip of the iceberg. If I read something I like, it’s hard not to be influenced by it.
How do you make your art?
I mostly make comics, and I use coloured pencils to draw, then I ink over the pencils with a dip pen, brush, and ink. For colour work, I use watercolour paints and alcohol markers. But in both cases, I scan and edit the results digitally.
A page from my illustrated novel “The Emperor’s Hound”, showing the first meeting of the protagonists.
Does your art influence your science at all, or are they separate worlds?
I don’t think my art and science influence each other directly, but I find keeping a good balance between them means I can do both better, if that makes sense. When it comes to preparing figures for papers, or posters for conferences, my experience with making and printing comics is invaluable.
An illustration from my current webcomic, “Nobody’s Library”.
What are you thinking of working on next?
I actually started out wanting to write books rather than comics, because I was a novel reader as a child rather than a comic reader (that came later). I have recently been experimenting with prose again, and have produced an illustrated novel. I’d like to keep doing that, and I have an idea I very much want to develop… when I get some of my existing projects finished!
I read the name of Pere Alberch for the first time while leafing through a collection of articles on Ecology and Evolution edited by the Universidad Autónoma de México [1]. At the time I was a bachelor’s student of Biology at the University of Turin, desperately collecting material for my final dissertation on the role of physical parameters in shaping form during embryo development. In the paper “Evolution and complexity: developmental constrains” by B. Luque & J. Bascompte, I found out that Pere was a “blighted theoretician of development and experimental embryologist” who did seminal work on thedevelopment and evolution of the tetrapod limb. Despite having only recently closed my textbooks of Developmental and Evolutionary Biology, I had no idea that Pere was one of the founding fathers of Evo-Devo, a field that aims to connect evolutionary novelty to developmental dynamics, i.e. “phylogeny” to “ontogeny” [2]. To my surprise, most of his work was indeed rarely cited and his name would have been certainly forgotten were it not for the visionary power of his ideas and the determination of his scientific disciples, who so tenaciously kept those ideas alive.
Almost ten years later, I have had the chance to follow a celebrative symposium on Pere’s work, set in Barcelona, just few kilometres from where he was born. “Genes, cells and embryos in development and evolution: Pere Alberch 25 years on” took place at Barcelona Biomedical Research Park (PRBB), onthe 9th and 10th November 2023, organised by Alfonso Martinez-Arias (Universitat Pompeu Fabra), Denis Duboule (École Polytechnique Fédérale de Lausanne) and James Sharpe (EMBL Barcelona). As the title suggests, the symposium aimed to cover each of the biological scales which are relevant to the study of development and evolution of form (the genetic, cellular and tissue scale), whose tight integration at the embryo level had been so consistently emphasized by Pere. Here is the link to the event: https://eventum.upf.edu/94510/detail/genes-cells-and-embryos-in-development-and-evolution-pere-alberch-25-years-on.html.
Poster of the conference.
Who other than Denis Duboule could kick off the first session, entitled “Constraints and the hourglass”? His talk highlighted how the range of morphologies in the early stages of vertebrate embryonic development, during the so-called “phylotypic stage”, is restricted already at the chromatin level, with the Hox timer being one of the main agents constraining the ‘neck’ of the hourglass model. The presence of phenotypic invariance, of which the “phylotypic stage” is an example, was what intrigued Pere the most, together with the study of abnormal phenotypes or “monsters” as a powerful tool to get a glimpse into otherwise hidden developmental rules [3]. The next speaker, Freiton Gallis (Leiden Biodiversity Center), built her research upon these two aspects, focusing on the conservation of the number of cervical vertebrae in mammals and on the analysis of vertebral defects such as cervical ribs. Arkhat Abzhanov (Imperial College London) illustrated his work on cranial shape variation in amniotes, followed by Michael Richardson (Leiden University) who fascinated the audience with a story of coevolution between a parasitic fish and the mussels that host its peculiarly-shaped eggs.
Patrick Lemaire (Centre de Recherche en Biologie Cellulaire de Montpellier) used the “parameter space” proposed by Pere in 1991 [4] to guide us through the world of ascidian embryos which display an incredible invariance in morphologies despite the extreme genetic divergence among species and their phenotypic diversity as adults. Margarita Cardoso Moreira (The Francis Crick Institute), whose recently established lab explores the evolution of sexual dimorphism, highlighted how sex differences can be traced down even to the cellular level! Her talk was followed by Camille Berthelot (Institut Pasteur), whose lab exploits organoid models of the uterine epithelium to study a trait that, similarly to sex differences, evolves quite rapidly: embryo implantation. The session, entitled “Of genes and cells”, was finally closed by the provocative talk of Iñaki Ruiz-Trillo (Universitat Pompeu Fabra) who clearly stated that we are still quite far from understanding what the unicellular ancestor of animals, the source of all the phenotypic diversity we witness at the present day, looked like. We left for lunch with a glimpse of hope that, through the use of metagenomics and the sampling of new taxa of unicellular organisms, we will be able to better address the origins of multicellularity.
The afternoon session was a journey in Pere’s life, fortune and friends. It started with the talk of Gerd Müller (University of Vienna), one of Pere’s closest collaborators. His presentation showcased some of his old work with Pere on the archosaur limb [5] together with some more recent work on polydactyly, and was interspersed with pictures of their fruitful meetings and forays. While the philosopher Laura Nuño de la Rosa (Universidad Complutense de Madrid) explained the reasons why Pere may have been forgotten by the scientific community over the years, despite his relevance for the Evo-Devo field, Diego Rasskin-Gutman (Universitat de València) clearly expressed why he cannot forget his mentor and how Pere’s ideas deeply influenced the work of his own lab, including the development of the Anatomical Network Analysis (AnNA) for topological analysis of organismal form. In the last years of his life, before his premature death in 1998, Pere became director of the Natural History Museum of Madrid. Rafael Zardoya, the current director of the museum, gave the last talk of the session, showing the crucial role that Pere played in restoring the Museum to its former glory and how deeply his decisions are still impacting the organization of the museum today.
Day 1 of the conference closed with a keynote lecture from Neil Shubin, who was one of Pere’s first PhD students at Harvard University. His engaging talk gripped the minds of the audience, who very much enjoyed the narration of the discovery of the Tiktaalik fossil, the first fish venturing onto land. He mostly focused on his work on fin-to-limb transition in vertebrates and hinted to some new work he is envisioning to do on salamander limbs, which relates to his PhD project in Pere’s lab.
Neil Shubin guides the audience through the characteristics of the Tiktaalik (photo credits: Marta Vila Cejudo).
Ricard Solé (Universitat Pompeu Fabra) kicked off Day 2 of the conference, arguing that the logic of life is predictable since life itself has its own constraints: in order for life to exist, even in another planet, certain conditions need to be met. We came back to earth for the rest of the session, in particular to life in the waters: Berta Verd (University of Oxford), Joost Woltering (University of Konstanz) and Emilia Santos (University of Cambridge) each illustrated their research on teleost fishes. Verd and Santos both exploit cichlid fishes as model organisms to study the evolution of two different morphological traits: vertebral counts and pigmentation patterns, respectively. Interestingly, cichlid fishes display a wide phenotypic diversity despite bearing similar genetics, falling on the opposite side of the spectrum with respect to ascidians. Joost Woltering uses a variety of teleost fish models in his lab to look at morphogenesis and evolution of their dermal skeleton, with particular attention to fins. With James Sharpe’s talk we shifted from fins to limbs, having the chance of listening to some new insights on digit pattern formation, an intriguing follow-up to some of Pere’s old work [6].
The task to close the conference was given to another speaker that has been deeply influenced by Pere’s work: Cliff Tabin. He surprised everyone by announcing that his talk would focus on the physical forces shaping gut development, rather than the topic of heterochronic shifts in limb development. As an homage to Pere, he showed how the circular model of morphogenesis Pere proposed in 1989 [3] can elegantly explain the process of villification in chick gut tube, a topic that the Tabin lab has been working on for over 15 years. Pere stated that genes undoubtedly influenced cell properties and thus morphogenesis by contributing to tissue geometry, but that tissue geometry and so the morphogenetic outcome (the ‘structure’ itself), feeds back into gene regulation, making morphogenesis a rather dynamic process and, far less simplistic than what was previously thought. This was my favourite talk of the conference, since it unleashed the true revolutionary power of Pere’s ideas and their relevance in the study of development and evolution.
Cliff Tabin elaborating on the schematic of the circular view of morphogenesis proposed by Pere Alberch (photo credits: Marta Vila Cejudo).
As Laura Nuño de la Rosa explained on Day 1 of the conference, there are a number of reasons for the aura of mystery around Pere’s work, which despite his relevance for the field of Developmental and Evolutionary Biology is very poorly cited. These include the fact that Pere had to close his lab in Harvard for lack of funding, his rather quarrelsome personality that did not make him popular among collaborators, and his premature death in 1998. By the end of the meeting, I understood more clearly why I had only encountered his name in a hidden collection of papers rather than in the textbooks or classes where I had first about Evo-Devo in University. As Alfonso Martinez-Arias stated in his closing remarks, this symposium proved that, despite “the slings and arrows of fortune”, ideas can outlive their creators and do not fade despite their work being ignored by the scientific community. The circular view of causation in morphogenesis, development as a new level of selection between genotype and phenotype, the genotype-phenotype maps, the importance of ‘monsters’: all of this we owe to Pere and we can only thank him for promoting avenues of research that are so relevant today.
References to Pere’s work:
[1] Benítez M. et al., ‘Frontiers in Ecology, Evolution and Complexity’, Copit-arXives, Mexico DF 2014. [2] Alberch et al., ‘Size and shape in ontogeny and phylogeny’, Paleobiology, 1979, 5(3):296-317. [3] Alberch P., ‘The logic of monsters: evidence for internal constraint in development and evolution’, Geobios, 1989, 12:21–57. [4] Alberch P, ‘From genes to phenotype: Dynamical systems and evolvability’, Genetica, 1991, 84: 5–11. [5] Müller G. and Alberch P., ‘Ontogeny of the limb skeleton in Alligator mississippiensis. Developmental invariance and change in the evolution of archosaur limbs’, Journal of Morphology, 1990, 203: 151–164. [6] Alberch P. et al, ‘Size dependence during the development of the amphibian foot: Colchicine-induced digital loss and reduction’, Journal of Embryology and Experimental Morphology, 1983, 76: 177–197.
In my previous article, I discussed the importance of joining communities and finding your crowd. Following my own advice, I have joined the Japan SciComm Forum, the community for English-speaking science communicators in Japan. It is a warm and welcoming community with professional and aspiring science communicators. The community meetings happen once every two months with two speakers (one from Japan and one from abroad) presenting on a wide variety of topics. Some of the ones I attended included how to make science accessible for people of all abilities and the place of AI in science communication. If you are a science communicator from Japan, professional, or just interested in communicating your research, you can join here.
Japan SciComm Forum Conference: overview
One of the events I was looking forward to during this year was the Japan SciComm Forum Conference. You can check out the schedule and speakers here. By the way, you can find YouTube videos from past events there, too. This year’s conference was held in the beautiful Okinawa at the Okinawa Institute of Science and Technology, one of Japan’s most international research centers I know of. I waited for this event both because I wanted to visit Okinawa once again and because it was my first in-person conference in four years. The conference lasted for two days. On the first day, we had a keynote speaker, flash presentations, a workshop, and a networking event in the evening. We had a panel discussion and a second workshop on the second day.
Why do organizations need communication teams?
This year’s keynote speaker was Ali Bailey, Director of Communications and Public Engagement at Francis Crick Institute. The institute has a versatile outreach program and not only shares its research with the scientific community but is also involved in educational programs and engagement with the non-scientific community. It also provides training for scientists to communicate their research. You may have read (and if not, you should!) Alexandra Bisia’s post about Francis Crick’s Cut + Paste exhibition. Ali Bailey’s talk was dedicated to the importance of science communication professionals. Professional science communicators are often met with a question:
Why do organizations or institutes need communication teams?
After all, people do communicate on a daily basis, what can be so difficult that it would require a communication team? And Ali Bailey shared one of her favourite answers:
Even though everyone has a bank account, organizations do prefer to have a professional financial team.
She then shared her career path and especially “the bad day in the office” experiences. I always admire people who share their mistakes. It is inspiring how people turn their mistakes into lessons. Her talk brought a beautiful message that science communication is a craft that requires time and perfection of skillset, not something you will be able to do overnight. I think that although obvious, it is an important reminder, as too often, I see that technological progress gives people the illusion that you can replace experience with automation. Although technology can make different processes more efficient, I also think knowing what you are doing is important to get a worthy result.
Using podcasts for science communication
After the keynote speaker, we had a workshop. There were two options, from which I chose “The Art and Science of Communicating Research through Podcasting” by Andrew MacIntosh, Associate Professor, Kyoto University (check his podcast here; he was lucky enough to interview Jane Goodall at some point!). I discovered podcasting some years ago, but I got into it only recently. As a person for whom talking is the main way to develop ideas, evaluate reality, and find solutions to problems, I have always wanted to try podcasting. There is something so simple and so mysterious about talking with people. Even when you think you know a person, talking to them often brings surprises. The logic or opinions you never thought could coexist. And if we are talking about a fluid and controversial topic such as science, podcasting seems like a natural way to deal with it. The workshop was really lightning speed. We had just enough time to listen to the basics and then develop and record the intro to a model podcast. It was a lot of fun! So, I hope to use these skills to do some science podcasting one day.
Flash talks: Sci-fi and STEM escape rooms
Flash talks at scientific conferences are always controversial to me. I see why they are there, but I am not sure they actually help. Risking stating the obvious, communicators are good at communicating😉, so their flash talks were informative and engaging despite the short time. I will share two of my favorite ones. The first was about using sci-fi to explain complex scientific ideas by Aileen Cooney, PhD Student at Tokyo Tech / Imperial College London. This inspired me to take “The Hitchhiker’s Guide to the Galaxy” from a bookshelf. For some reason, I never thought of sci-fi in that way. I thought of it as a kind of creative outlet from scientist to scientist, or at least people interested in science. The idea that we can use our imagination to create narratives that explain something real in an engaging manner was a surprise to me. Nevertheless, I fully agree with the speaker and made a mental note that if I ever try to be an author, sci-fi is where I can use both my writing and scientific knowledge to create something interesting and educational.
Another was about creating STEM escape rooms by Amanda Mathieson, Education and Public Engagement Manager, University College Dublin. Can you imagine? As a person who loves escape room games, I am thrilled at the possibility of using my knowledge in STEM to escape the room. I wonder how I can use tissue engineering or developmental biology in an escape room. It can be something more obvious, as an escape from a laboratory in the case of an accident; or it can be something more mysterious, connected to the development of the human brain, memories, and emotions! Either way, I hope this kind of escape room will become popular and that they will come to Japan!
The panel discussion “Many Worlds of Science Communicators.”
The panel discussion was facilitated by Heather Young, Vice President of Communication and Public Relations, Okinawa Institute of Science and Technology (OIST). The three amazing panelists were Chibuamam Ilechukwu (Founder, Hypertension Africa), Charmaine Caparas (Communications Manager, Stockholm Environment Institute/ Chulalongkorn University), and Naoki Namba (Director of Public Relations & Communications Division, Hokkaido University/ Director/Professor, Hokkaido University). It was great to see science communicators with different backgrounds sharing how they ended up in this field, their challenges, and their hopes for the future. Charmaine Caparas shared insights from her extensive career in communication on some tough questions, such as “Should science writers be worried about AI?”. Chibuamam Ilechukwu talked about her fight against disinformation and lack of information and her quest to help people live healthier lives. Naoki Namba shared how he shaped his path toward science communication when it didn’t exist as a profession in Japan. When asked about his motivation for choosing science communication after receiving a master’s degree in life sciences, he said something that particularly spoke to me. What he liked about science was knowledge, the excitement of understanding something. But he didn’t care if he was the one who made the discovery or explained the phenomenon first.
Using art to explain science
And finally, the last workshop. I chose “Illustrate to Educate: Simplifying Science through Art and Storytelling” by Nikitaa Sivaakumar, Founder and director of Wonder Yonder Research and Design Pvt Ltd. This was a challenging one! We had about 2 minutes to finish a drawing panel, each panel exploring a certain artistic trick to illustrate a piece of scientific information. The story we were illustrating was about the shape of the shinkansen (bullet train) head, which was designed after the beak of a kingfisher, and how this biomimicking helped to solve the problem of noise caused by airwaves pushed by the high-speed trains. Not only that, but we also got a couple of minutes of masterclass on how to do animation. The exercises were difficult, but they made me think about many things, as I have a bit of experience in creating simple animations to explain my research. And I am definitely practicing them again when I have a bit more time on my hands. One of the exciting ideas Nikitaa Sivaakumar shared was that when you try to explain complicated ideas, you can use drawings that are not perfect, maybe even intentionally simplistic. When you try to understand something you consider difficult, you don’t want to see perfect and complicated pictures; you would instead appreciate something that looks simple! Definitely check out the Wonder Younder Instagram!
And that’s a wrap! It’s amazing how many fascinating conversations you can have in the span of two days. I can’t wait for next year’s conference. But in the meantime, I hope this article will inspire anyone new to science communication to join a community. Here are some links to some of the communities I know:
“Here’s looking at you, kid” is the famous quote from the movie Casablanca (1942) that Humphrey Bogart’s character, Rick, says to Ilsa (Ingrid –Ingr-oid?– Bergman), his love interest. Hopefully the scientific interest in -oids will yield more results than Rick and Ilsa’s doomed love story. Picture credits: https://wordhistories.net/2018/03/21/heres-looking-at-you/; Vincent van Batenburg, Hubrecht Institute
One does not easily pass up the opportunity to attend an ISSCR conference, especially when said conference is in Vienna, in the leadup to Christmas, and the venue is the Hofburg palace. I was really lucky, therefore, to have the opportunity to attend the meeting, held in Vienna this month, from 4-6 December. The theme of the meeting was “Elucidating Principles of Development with Stem Cells,” and boy, were those principles elucidated. With a suite of stem cells from various organisms available to developmental and stem cell biologists, research groups are now developing and refining ever more numerous and sophisticated ways to represent aspects of embryonic development with them. Accordingly, across the three days of the meeting, we were showered with a variety of talks covering every modality of -oid imaginable.
Vienna ISSCR meeting venue in the Hofburg.
As suggested by the title of the meeting, a big focus was the use of stem cell-based or -derived models (with various -oid names, such as gastruloid, chimeroid, organoid, blastoid, cardioid, axioloid…). These are increasingly sophisticated and are being manipulated and studied in a variety of ways, and it is possible they may be able to supplement to a great extend the requirement for real embryos in research. I find it fascinating that we are now so familiar with the various signalling regimes that are required during different stages and in different tissues in development that it’s possible to replicate synthetically specific stages or tissues of development, starting from pluripotent stem cells (and sometimes extraembryonic stem cells too) – for example only preimplantation or post-implantation development, or axial elongation, or heart development, or neural tissues, or the gut. One of the many benefits of these systems is, of course, that these -oids can be reproducibly generated in great numbers, giving researchers an abundance of material on which to carry out experiments.
The inaugural talk of the meeting was delivered by Denis Duboule, an excellent speaker, whose lab’s extensive work on Hox genes is revealing increasing detail on the workings of the Hox cluster. Specifically, his lab has been using “stembryos” that recapitulate Hox gene expression along the anterior-posterior (or rostro-caudal) axis of the embryo. His use of a rope with interspaced knots and clothespins to represent Hox genes and the CTCF sites that ensure the sequential and appropriately-timed expression of genes along the cluster was a personal highlight. And it was still only 9:30 on the Monday!
St Stephen’s Cathedral on a sunny morning.
The meeting had a strong showing of groups that work on ectodermal/neural tissue models. As someone who is not very familiar with these cell types from my own research, I was nonetheless impressed by how interesting I found them. Among others, there were talks by Paola Arlotta, Barbara Treutlein, Madeleine Lancaster, Thomas Vierbuchen, Anna Kicheva, Sharad Ramanathan, Elly Tanaka, Akanksha Jain, and Jürgen Knoblich. A topic which stood out for me was Joanna Wysocka’s talk on DNA-guided transcription factor cooperativity and its functions in cranial neural crest cells (CNCCs). Briefly, her lab identified a novel long consensus DNA motif, dubbed the “Coordinator,” containing a homeobox and an E-box binding motif. The Coordinator is specifically bound by the bHLH transcription factor Twist1 and homeobox factor Alx4. These interact only when bound to the Coordinator via a tiny segment of a loop only found on Twist1 and no other bHLH factors, thus promoting expression of a host of genes associated with CNCC behaviour.
Another talk on a much less common model organism was by Ali Elagoz, a doctoral student who works on the embryonic development of octopus nervous systems, in a broader effort to identify the evolutionary mechanisms by which cephalopods (octopuses, nautiluses, cuttlefish, and squids) have succeeded in evolving the largest nervous system of all invertebrates. For those not familiar with octopus nervous systems, you might be delighted to find out that only about 1/3 of octopus neurons are actually found in their brains, which, by the way, are wrapped around their oesophagus. Rapid reogranisation of the cephalopod genome and expansion of their suite of protocadherin genes may have contributed to the innovations that permitted the cephalopod brain to dramatically expand in size.
That said, fans of other germ layers were not disappointed, with talks on mesodermal and endodermal specification and derivatives by André Diaz from Universitat Pompeu Fabra (gastruloids), Sasha Mendjan (cardioids), Aryeh Warmflash (2D ESC patterning to study Wnt and Nodal/Activin signalling gradients), Cantas Alev (axial development), Katharina Sonnen (timing of somitogenesis), and Sarah Bowling (hematopoietic stem cells).
Another thematic arc highlighted during the meeting was the novel quantitative aspects that developmental and stem cell biology are being explored from, and which, until very recently, were almost exclusively assessed from a qualitative point of view. Ewa Paluch’s lab, for instance, is studying how epithelial-to-mesenchymal transition, a process essential in multicellular development, can be approached from the perspective of cell shape. Her lab has developed a “morphospace analysis” pipeline whereby cell shape is segmented and many variables quantified, finally undergoing dimensionality reduction to create a 2D “grid” of possible cell shape phenotypes. Cell shapes were then quantified before, during, and at the end of EMT, with cells undergoing EMT having a much “noisier” cell shape than epithelial cells, in other words exploring more of the morphospace. This suggests an instance of noise-driven transitions, where noise may actually help to overcome a barrier, in this case from an epithelial to a mesenchymal state.
View of the Rathaus (City Hall) on an overcast morning after a fresh layer of snow.
Finally, I would be remiss if I didn’t highlight some methods development talks that really captivated me. Alexdander van Oudenaarden detailed a new method, developed by his postdoc Michael VanInsberghe, for profiling both single cells’ full complement of RNA (as single-cell RNA-seq already does), and their ribosome-bound RNA (like single-cell Ribo-seq) in a single experiment, in order to elucidate gene regulation at the transcriptional vs translational level. This is achievable by titrating MNase (micrococcal nuclease), an enzyme that can digest single-stranded nucleic acids, and that can function both as an endonuclease and exonuclease in a concentration-dependent manner. It’s amazing how such a simple concept can yield such rich data at the single-cell level!
I was also blown away by Kate McDole’s talk on imaging in developmental biology. Her unparalleled skills in custom-building microscopes are a boon to developmental and stem cell biologists who want to image samples that are rapidly growing, undergoing morphogenesis and constantly changing optical properties. Her “event-driven microscopy” platform is designed to assist users in imaging their organisms or organoids in a way that accounts for changes in the sample that are going to be happening in the future, without requiring the constant direct supervision of the user.
There was a broad and interesting array of posters at the meeting, and as always at a conference it was great to have the opportunity to meet researchers at all stages of their career, from many institutes and countries. As I mentioned, the venue was spectacular, and since it was literally a room in the former imperial palace, it was quite easy to become distracted by the numerous chandeliers, marble columns, and the stuccoed ceiling. As a bonus, every morning what I assume was a military band would parade past one of the windows, inadvertently serenading the first speaker of the day with some drumming.
One of the many chandeliers I found distracting during the meeting.
Overall, the conference was a great experience. Nothing quite beats the excitement of hearing scientists talk about their work in person, especially about results that are often fresh out of the oven. And it’s always inspiring to meet new scientists with different interests and approaches to conducting research – you never know where a novel idea for your own work may come from, and which technique or new finding will form the basis for a new avenue of scientific exploration!
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