In the May Development presents… webinar, we celebrated the winners of Development’s 2023 Outstanding Paper Prize. Catch up on the recordings of the talks from the authors of the two winning papers.
Ling Loh (The George Washington University) & Joe Hanly (The George Washington University and Duke University)
Do you know about Development’s ‘at a glance’ article types? These articles comprise a short text document highlighting the fundamental aspects of a developmental biology topic, which is accompanied by a large poster schematic that illustrates all you need to know ‘at a glance’.
Development has published a number of these articles over the years, ranging on topics from somitogenesis to gibberellin signaling, branching morphogenesis to the peripheral nervous system. To view the full collection, visit this page.
Some of most recent, free-to-read articles are included below; to download the high-resolution image, click on the link in the ‘High-resolution poster’ or ‘Supplementary Information’ section of the online article. If you’d like your own physical copy of a poster to hang in your lab or office, look out for The Company of Biologists’ exhibit at the upcoming Society for Developmental Biology meeting (Atlanta, GA, USA) or the ISSCR annual meeting (Hamburg, Germany).
This Development at a glance article summarizes insulin hormone family signaling and highlights the roles of individual hormones in regulating growth, cell proliferation and differentiation.
This Development at a Glance article provides up-to-date basic knowledge of the anatomical and functional organization of the peripheral nervous system (PNS), with additional insights into the development and cell-type heterogeneity underlying its different roles.
A brief overview of the Notch signaling pathway and its molecular activation mechanism, discussing different examples of Notch-mediated coordination of differentiation between neighboring cells during development and homeostasis.
A survey of germ granules across organisms and developmental stages, highlighting emerging themes regarding granule regulation, dynamics and proposed functions.
This Development at a Glance article provides an overview of the genomic organization, protein structure and regulation of Hox genes and our current understanding of their roles both during and after embryogenesis..
This Development at a Glance article describes how a cells’ limited repertoire of behaviours provide the basis for quantifying morphogenetic phenotypes.
This Development at a Glance article gives an overview of the potential of assembloids – three-dimensional, self-organizing in vitro cell culture systems constructed by integrating organoids or organoids and other cell lineages.
This Development at a Glance article gives an overview of the ontogeny, maintenance and unique tissue adaptions of macrophages, and highlights their role in development, homeostasis and dysfunction.
In the paper “Distinct stem-like cell populations facilitate functional regeneration of the Cladonema medusa tentacle”, Fujita and colleagues found that the mechanism of tentacle regeneration in jellyfish is more similar to how salamanders regenerate their limbs than how other cnidarians regenerate. First author Sosuke Fujita and corresponding author Yuichiro Nakajima tell us more about the story behind the paper.
How did the project get started?
It has long been known that jellyfish organs like the manubrium and the tentacle can regenerate, but the detailed mechanisms at the cellular and molecular levels remain unclear. Using the hydrozoan jellyfish Cladonema pacificum (Figure 1), we began this study by examining the regenerative potential of each organ and found that tentacles have a high regenerative capacity, functionally regenerating within 2-3 days, which exceeded our expectations. We anticipated that the Cladonema tentacle would be a useful model for studying appendage regeneration and aimed to comprehensively understand its mechanism. To this end, we decided to monitor regeneration processes including wound healing, cell proliferation, stem cell distribution, and the timing of cell differentiation over time. In particular, we found that cell proliferation occurs intensively at the site of injury in the early phase of regeneration after wound healing completes. Based on these observations, we asked the simple question, “How do proliferating cells appear at the site of injury?”
Figure 1. Medusa of Cladonema pacificum.Cladonema tentacles exhibit a characteristic branching pattern.
What is known about blastema formation during regeneration before your work?
Blastema is an aggregate of cells that includes undifferentiated cells like stem cells, serving as a cellular source for regeneration. Blastema formation is a critical step for regeneration, occurring in regenerative animals like planarians, salamanders, and cnidarians, which are among the early-branching animals. However, methods of blastema formation, particularly the way of supplying undifferentiated cells, vary among regenerative animals, and the evolutionary aspects of the process remain unknown. While it is ideal to understand the mechanism of blastema formation across diverse animals, our knowledge about it in basal metazoans is mainly limited to a few polyp-type models, such as Hydra and Hydractinia (Bradshaw et al., 2015; Chera et al., 2009). We thus focused our attention on blastema formation during organ/appendage regeneration in jellyfish. Understanding this mechanism in jellyfish allows us to compare it with cnidarian polyps as well as some regenerative bilaterians.
Why did you choose the jellyfish Cladonema pacificum as your research organism?
Cladonema pacificum is a small jellyfish (less than 1 cm in height) widely found along the coast of Japan with a typical hydrozoan life cycle including the polyp and medusa stages (Figure 2). The Cladonema medusa is basically benthic, and all the stages are easily kept in small containers without any special equipment. This organism can be stored at 4°C for years as stolons (structures connecting polyps) as a dormant stage, which can reproduce polyps and medusae once returned to a warm temperature (e.g., 22°C), making maintenance easier. We are able to keep this jellyfish in our laboratory, which is located far from the sea. Importantly, Cladonema has the ability to regenerate organs, especially lost tentacles, in just a few days (Fujita et al., 2019). These factors made Cladonema an ideal model for studying organ regeneration in jellyfish.
Figure 2. The life cycle of Cladonema pacificum.(A) Photos of the Cladonema medusa and polyps. (B) Schematic of the Cladonema life cycle.
Can you summarize the key findings of the paper in one paragraph?
Based on previous studies using polyp models, blastema formation in cnidarians was thought to utilize the recruitment of resident pluripotent/multipotent stem cells. In contrast, we found that repair-specific proliferative cells (RSPCs) with stem cell characteristics appear upon amputation and are mainly involved in blastema formation during tentacle regeneration. Additionally, RSPCs preferentially differentiate into epithelial cells in the newly regenerating tentacle, while resident stem cells supply all the cell types including cnidocytes, promoting functional tentacle regeneration. These results suggest that blastema formation during Cladonema tentacle regeneration is analogous to limb regeneration in newts, rather than cnidarian polyps (Figure 3; Fujita et al., 2023). Our findings imply a common mechanism for supplying repair-specific blastema cells for complex organ regeneration that has independently evolved in each animal phylum.
Figure 3. A model of Cladonema tentacle regeneration and evolutionary history of appendage regeneration. Upon amputation, Repair-specific proliferative cells (RSPCs) appear and contribute to the newly regenerating tentacle by differentiating into epithelial cells while resident homeostatic stem cells (RHSCs) give rise to all the cell types in the tentacle. Repair-specific stem/progenitor cells also appear during salamander limb regeneration.
Were you surprised to find that most blastema cells do not come from resident stem cells but instead from repair-specific proliferative cells (RSPCs)?
Yes, we were surprised. We had initially expected resident stem cells to migrate and form blastema as seen in other cnidarian polyp systems during whole-body regeneration. We were puzzled when the nucleoside chase experiments showed unexpected results. We thus needed additional evidence to clarify this: for example, we found that RSPCs can still appear even after eliminating resident stem cells with X-ray irradiation or drugs. During the revision process of the paper (Fujita et al., 2023), we addressed numerous concerns related to this issue with further experiments, which strengthened our observations.
Can you postulate the cellular origins of the RSPCs?
Yes, we believe there are at least two possibilities: one is the reactivation of quiescent stem cells and the other is dedifferentiation. Similar to satellite cells in vertebrate muscle, damage can reactivate their cell cycle to become RSPCs, giving rise to differentiated cells. Alternatively, upon injury stimulus, differentiated cells can revert to RSPCs with an undifferentiated state via dedifferentiation, becoming able to proliferate. We are trying to figure out which is the case for tentacle regeneration.
Were there any other unexpected results and challenges, especially associated with working with a non-model research organism?
Working with non-model animals presented various challenges. Existing protocols for other models, even cnidarians, often require modification, and establishing experimental methods can be time-consuming (Fujita et al., 2022; Masuda-Ozawa et al., 2022). Additionally, some common knowledge does not apply to specific animals and contexts: for instance, some marker genes are not expressed in expected cell types, and their expression can be heterogeneous among tissues and locations, which initially became an issue. After rounds of investigation and consideration, these unexpected results eventually provide insights into the differences between what we observe and what is already known. Overall, the experience of working with a non-model research organism has been more enjoyable than challenging.
What are the implications of your findings in understanding regeneration in other organisms?
Our findings (Figure 3) imply that blastema can be supplied by repair-specific stem cell populations, similar to those observed in salamander limb regeneration (Sandoval-Guzman et al., 2014), rather than by resident stem cells, which previous cnidarian studies had focused on (Amiel et al., 2019; Bradshaw et al., 2015; Chera et al., 2009). Furthermore, the heterogeneity of stem cells discovered in the context of regeneration might also be identified during development and homeostasis in cnidarians or basal metazoans. Investigating how stem cells contribute to regeneration and how blastema forms during regeneration across different cnidarians will enhance our understanding of the evolutionary trajectory of the blastema formation program.
What’s next for this story and your lab?
We want to understand how the two stem cell populations we identified are regulated differently during regeneration. Our lab is currently identifying the signaling pathways that control cell proliferation and differentiation in each cell population. We also aim to determine how RSPCs emerge, especially their cellular origin. To distinguish different possibilities, we are designing new experiments and developing genetic tools in Cladonema. These approaches will provide a better understanding of regenerative processes at the molecular level and enhance our ability to explore diverse phenomena in jellyfish.
References:
Amiel, A. R., Foucher, K., Ferreira, S. and Röttinger, E. (2019). Synergic coordination of stem cells is required to induce a regenerative response in anthozoan cnidarians. bioRxiv, 2019.2012.2031.891804. 10.1101/2019.12.31.891804
Bradshaw, B., Thompson, K. and Frank, U. (2015). Distinct mechanisms underlie oral vs aboral regeneration in the cnidarian Hydractinia echinata. Elife4, e05506. 10.7554/eLife.05506
Chera, S., Ghila, L., Dobretz, K., Wenger, Y., Bauer, C., Buzgariu, W., Martinou, J. C. and Galliot, B. (2009). Apoptotic cells provide an unexpected source of Wnt3 signaling to drive hydra head regeneration. Dev Cell17, 279-289. 10.1016/j.devcel.2009.07.014
Fujita, S., Kuranaga, E., Miura, M. and Nakajima, Y. I. (2022). Fluorescent In Situ Hybridization and 5-Ethynyl-2′-Deoxyuridine Labeling for Stem-like Cells in the Hydrozoan Jellyfish Cladonema pacificum. J Vis Exp. 10.3791/64285
Fujita, S., Kuranaga, E. and Nakajima, Y. I. (2019). Cell proliferation controls body size growth, tentacle morphogenesis, and regeneration in hydrozoan jellyfish Cladonema pacificum. PeerJ7, e7579. 10.7717/peerj.7579
Fujita, S., Takahashi, M., Kumano, G., Kuranaga, E., Miura, M. and Nakajima, Y. I. (2023). Distinct stem-like cell populations facilitate functional regeneration of the Cladonema medusa tentacle. PLoS Biol21, e3002435. 10.1371/journal.pbio.3002435
Masuda-Ozawa, T., Fujita, S., Nakamura, R., Watanabe, H., Kuranaga, E. and Nakajima, Y. I. (2022). siRNA-mediated gene knockdown via electroporation in hydrozoan jellyfish embryos. Sci Rep12, 16049. 10.1038/s41598-022-20476-1
Sandoval-Guzman, T., Wang, H., Khattak, S., Schuez, M., Roensch, K., Nacu, E., Tazaki, A., Joven, A., Tanaka, E. M. and Simon, A. (2014). Fundamental differences in dedifferentiation and stem cell recruitment during skeletal muscle regeneration in two salamander species. Cell Stem Cell14, 174-187. 10.1016/j.stem.2013.11.007
A section of a mouse juvenile brain (cerebral cortex) showing cell nuclei (blue), microglia (red) and the activation of a specific gene called Hes1 (white).
No parent wants to risk their child having a serious infection, least of all while still in the womb, but did you know that the immune response to a viral infection during pregnancy could also affect the development of the unborn offspring? Scientists from Harvard University in Cambridge, USA, have shown that immune reactions in pregnant mice are detected by a specific type of brain cell in the developing embryo and alter how genes are regulated in the brain – a change that persists in juvenile mice. Published today in the journal Development, this study provides new insights into how the maternal immune response might influence brain development in embryos and could help researchers understand the origins of neurodevelopmental disorders such as autism.
Scientists have long suspected that fetal exposure to infectious bugs may increase the risk of developing neurological conditions such as schizophrenia and autism spectrum disorders. There is also evidence that fighting infection while pregnant might affect the growth of offspring in the uterus, even if embryos do not become infected themselves. However, it has been unclear how embryos recognise their parent’s immune response and the exact consequences for their development.
In their latest study, a group at Harvard University led by Professor Paola Arlotta have identified a specific cell type in the mouse embryonic brain that responds to an immune response in the mother. The researchers used a compound that mimics a virus to stimulate an immune response in pregnant mice without causing an actual infection. They then characterised how cells in the embryonic brain respond by assessing which genes were turned on or off. Using this approach, the scientists showed that cells called ‘microglia’ can sense the maternal immune response. “Microglia are the immune cells of the brain. They play a critical role during inflammation and infection and also have fundamental functions in healthy brain development,” explained Arlotta.
Following the mother’s immune response, embryonic microglia change which genes are activated or inactivated, which also occurs in the surrounding brain cells, such as neurons. Interestingly, the change of gene regulation in neighbouring cells depends on microglia being present in the brain; when the researchers repeated the experiments using mice without microglia, the other brain cells did not react to the maternal immune response.
Although most viral infections are often short-lived, the scientists found that the changes that the maternal immune system causes in embryonic brain cells persist well after the immune reaction has subsided. “Based on previous studies demonstrating that microglia exposed to early infections respond differently to stimuli in adulthood, we hypothesized that the maternal immune response could induce changes in microglial gene regulation that persist postnatally” said Dr. Bridget Ostrem, co-author of the study.
This research enhances our understanding of the cellular basis of neurodevelopmental disorders in humans. “Our results suggest a potential role for microglia as therapeutic targets in the setting of maternal infections,” said Ostrem, although there is still more work to be done. Harvard researcher Dr. Nuria Domínguez-Iturza added, “next, it will be crucial to determine the long-term behavioral implications of the changes we observed in this study.”
Ostrem, B. E. L., Domínguez-Iturza, N., Stogsdill, J. A., Faits, T., Kim, K., Levin, J. Z. and Arlotta, P. (2024). Fetal brain response to maternal inflammation requires microglia. Development, 151, dev202252. doi:10.1242/dev. 202252
This is part of the ‘Lab meeting’ series featuring developmental and stem cell biology labs around the world.
Where is the lab?
Daniel Kierzkowski: Our lab is part of the Plant Science Research Institute (fr. Institut de Recherche en Biologie Végétale – IRBV) established through a partnership between the University of Montréal and the City of Montréal. We are located in the beautiful Montréal Botanical Garden.
Our group studies the fundamental aspects of plant organogenesis. We aim to understand how tiny primordia, composed of groups of undifferentiated cells, give rise to the amazing diversity of organs found in nature. Using model systems such as Arabidopsis and Physcomitrium, we seek to uncover how fundamental processes of cellular growth, patterning, and differentiation are controlled at the molecular, cellular, and tissue levels to produce specific shapes. We hope that our research will provide a foundation for future crop improvement.
Lab role call
Wenye Lin: I am a Ph.D. student in the lab since 2020. The tiny moss Physcomitrium patens is my best friend. I study the evo-devo aspect of organ development with a focus on the role of auxin in regulating moss leaf (phyllid) morphogenesis.
Elvis Branchini: I am interested in plant development, genetic editing, and synthetic biology. My Ph.D. project aims to uncover the growth dynamics and regulation of primordia initiation in Arabidopsis thaliana.
Amelie Bauer: I am a Post Doc investigating the mechanisms behind the initiation of the valve margin structure in Brassicaceae fruits.
Binghan Wang: My Ph.D. project focuses on studying the gynoecium development of Brassicaceae species. Specifically, I investigate the roles of hormones and mechanical forces in fruit shape establishment.
Benjamin Lapointe: I am a Ph.D. student working on the development of the leaf in Arabidopsis thaliana. I use genetics, novel imaging methods, and mathematical analysis to decipher the processes shaping leaf growth and morphology.
Xuan Zhou: I am a visiting PhD student from Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences. My project investigates the development of leaf shape during primary and secondary morphogenesis.
Sylvia Silveira: I spent four years as a postdoc in the lab and now transitioned into a research professional. While being involved in other projects from the lab, my focus is on exploring how organs get their 3D shapes using stamen as model system.
Rachelle Fontaine: I am a Master 2 internship student in the lab. I work on understanding shoot apical meristem growth in A. thaliana and how it is related to auxin.
Favourite technique, and why?
Daniel: No doubt: confocal microscopy! Our lab specializes in confocal time-lapse imaging, which allows us to follow organ development at cellular resolution for extended periods (up to two weeks of growth). When combined with image analysis software like MorphoGraphX, we can quantify cellular growth dynamics on the organ surface and, more recently, in 3D. This powerful approach helps us precisely understand how molecular and cellular behaviors translate over time into the final organ shape.
Apart from your own research, what are you most excited about in developmental and stem cell biology?
Daniel: Synthetic biology is fascinating. It’s amazing how animal stem cells can self-organize in vitro to spontaneously form early embryos or simple organs. I am also excited to see new model systems emerging in plants, which will allow us to answer important evolutionary questions in the near future.
How do you approach managing your group and all the different tasks required in your job?
Daniel: As a university professor, my job involves constant multitasking, from teaching undergraduates to managing the lab. I try to focus as much as possible on my research group. I want to be directly involved in all research projects while giving the people working with me enough freedom to pursue their own ideas. I strongly believe in teamwork and aim to create a collaborative environment that stimulates scientific interaction within the lab and with collaborators. Home office is not my thing; I try to be in the lab whenever possible. I am convinced that exciting discoveries can be achieved only when people work together to exchange ideas, troubleshoot problems, and support each other.
What is the best thing about where you work?
Benjamin: The multidisciplinary approach to biology, combining molecular tools, microscopy, and a biophysics perspective. Applying mathematics and modeling to extract new information is very exciting. To be at the edge of what has been done and what can be achieved in science.
Wenye: I love the location of the lab in a botanical garden, in our case, the largest one in north America. I am also spoiled by the amicable atmosphere between colleagues and supervisors.
Elvis: The best thing about where I work is the dynamic lab exchanges that keep us always thinking about the common patterns of development in general, how to make better experiments, and how to present it properly and succinctly. Also, the lab being at the Montreal Botanical Garden is a great perk!
Amelie: I like the effervescence of collaborative and interdisciplinary work that is at the root of our laboratory’s scientific dynamism. Fueled by a positive and friendly atmosphere, we can engage in multiple projects aimed at enhancing our understanding of plant morphogenesis.
Sylvia: I appreciate how collaborative everyone in the group is, and I love the inspiring location of the lab, within the Montreal Botanical Garden.
Rachelle: What is amazing in the lab is the collaborative and interdisciplinary work environment. Everyone is always willing to share their knowledge and help, leading to many exciting discussions and reflections.
Daniel: It is not so much about where but with who I work. I am super lucky to work with amazing people that are passionate about science.
What’s there to do outside of the lab?
Daniel: Montreal is a vibrant and multicultural city where everyone can find something interesting to do. We are privileged to have numerous festivals and cultural activities throughout the year, especially in the summer. The surrounding nature is outstanding. Although Canadian winter can be intense, there are plenty of outdoor and indoor activities to help us get through it.
Amelie: We are located in the Botanical Garden, a unique place where you can admire the diversity of the plant world. With its spectrum of sporting, cultural, and intellectual activities, Montreal reveals itself as a vibrant and surprising city. Close to immense natural parks, its location allows easy access to the great outdoors and an easy escape from the city.
Wenye: Montreal is a green gateway to nature. Besides having the Botanical Garden as our backyard, our lab is also within walking distance of the Olympic Park and the large Maisonneuve Park. The world-famous Niagara Falls and popular whale-watching spots are also nearby. Afraid of the long winter season? You will easily fall in love with the winter sports opportunities Montreal generously offers, such as downhill or cross-country skiing, ice skating, and snowshoeing. Montreal is also rich in cultural events, offering a variety of museums, concerts, and performances.
Binghan: Montreal offers several free public facilities, such as tennis courts in the summer, skating rinks in the winter, and indoor swimming pools available year-round. I appreciate how multicultural this city is, providing a fascinating exploration of diverse histories and food cultures from various nations.
Sylvia: Discover the diverse international culinary scene and local breweries. Go cycling, have picnics in the parks, explore museums, enjoy numerous festivals, hike in nearby national parks, and experience winter sports.
Development’s Deputy Editor Steve Wilson (UCL) hosts three early-career researchers studying brain development
Wednesday 5 June – 15:00 BST
Akanksha Jain (ETH-Zurich) ‘Unveiling the choreography of human brain development: Longterm lightsheet imaging reveals patterning morphodynamics in human brain organoids’
Noelia Antón-Bolaños (Harvard University) ‘Multi-donor human cortical Chimeroids reveal individual susceptibility to neurotoxic triggers’
Yuxiang Liu (UT Southwestern Medical Center) ‘Function of human CLOCK during embryonic development of neocortex’
At the speakers’ discretion, the webinar will be recorded for viewing on demand. To see the other webinars scheduled in our series, and to catch up on previous talks, please visit: thenode.biologists.com/devpres
Introducing the Node’s new search and filter function.
Just over a year ago, I was applying to become the Node’s Community Manager. One of the pre-interview tasks was to come up with ideas for the Node, so I wanted to look back at what’d been done already. While I enjoyed discovering random posts from the early days of the Node, I quickly realised that the search function was rather limited: I could only filter by date or category, and it wasn’t possible to filter by date and category.
Now, I’m delighted to introduce our brand new ‘Advanced search’ function, where you can search and filter by category, tag, author and date. Thank you to the team working behind the scenes to push out this new search tool!
As the Node approaches its 15th anniversary in 2025, we hope this new search function will allow long-time and new readers alike to enjoy all the weird and wonderful posts the Node has put out since 2010.
Have a go and let us know what you think! What else would be useful to you, our dear Node readers, to include in the search functionality?
Do you know
… we have a new Search button:
Click the Search button in the menu bar to go to the ‘Advanced search’ page.
… you can filter by category, tag, author and date:
For example, I wanted to search for ‘behind the paper’ stories that mention Wnt signalling, my favourite signalling pathway. I can type ‘Wnt’ in the search bar and filter in Tags by ‘behind the paper’.
… you can search for all the posts someone has written:
I found out the first ever Community Manager of the Node, Eva Amsen, wrote a total of 141 posts!
Authors: Sandra Franco-Iborra (ASAPbio Community Lead), Pablo Ranea-Robles (Postdoctoral Fellow, Novo Nordisk Foundation Center for Basic Metabolic Research at the University of Copenhagen), Lonni Besancon (Assistant Professor, Linköping University) & Jonathon Alexis Coates (Assoicate Director, ASAPbio; jonny.coates@asapbio.org)
Scientific publishing is experiencing a reckoning; scientists are resigning across a wide range of editorial boards, the dominance of traditional publishers has been successfully challenged, open access has revolutionized publishers’ business models, there’s a lack of trust in science and preprints are on the rise. Preprints (manuscripts shared prior to journal-organised peer review) offer an opportunity to transform scholarly communication into a system that places science and society first in addition to alleviating many of the issues we currently face.
Brief history of preprints in the life sciences
Although the fields of physics and mathematics are often credited as the origins of preprinting, the practice actually began in the 1960’s with biology focussed NIH information exchange groups (IEGs). However, this initiative faced opposition from publishers and scientific societies who effectively ended the IEGs by 1969. In 1991, arXiv launched and the physics community rapidly adopted preprinting. It was not until the launch of bioRxiv in 2013 that biology began to accept preprints. More recently, some funders such as the Chan Zuckerberg Initiative and Bill & Melinda Gates Foundation have begun to mandate preprints. We’ve also witnessed governmental declarations that support a not-for-profit, no cost to authors or readers system of academic publishing; a system that has preprints at the beating heart. There are now over 750,000 life science preprints (Fig 1A), representing approximately 12% of the literature in 2023 (Fig 1B). Of these 750,000, over 220,000 are hosted on bioRxiv alone (Fig 1C) and have been downloaded over 150 million times (Fig 1D).
Fig 1. Preprints in the life sciences. A) Preprints indexed on Europe PMC. B) Preprints indexed on Europe PMC as a percentage of published articles on Europe PMC. C) Cumulative bioRxiv submissions since 2013. D) Cumulative PDF downloads for bioRxiv preprints. Thanks to Europe PMC for the code and data to produce panels A & B and Nicholas Fraser for the code used to produce panels C & D.
Preprints in Developmental Biology
With the launch of bioRxiv in 2013, Developmental Biology was quick to adopt this new method of scientific communication, posting preprints that same year. As of 2023, Developmental Biology sits in the middle of preprints on bioRxiv, as the 15th largest field with almost 6700 total preprints posted (Fig 2A). This is also true in terms of preprint downloads where Developmental Biology preprints are downloaded slightly less than the mean for bioRxiv. Approximately ~70% of bioRxiv preprints are eventually published, with our data showing that at least 54% of Developmental Biology have been published by the end of 2023 (though this number is likely to be higher due to issues linking preprints to the published version). Additionally, many Developmental Biology preprints are posted with restrictive licenses with only 17% having an open, CC-BY license (Fig 2B). However, this is very similar to the larger bioRxiv corpus where only 18% of preprints have a CC-BY license. Similarly, most Developmental Biology preprints are posted as a single version which negates the benefit of being able to iteratively update a preprint (Fig 2C). Within the field, the University of Cambridge (UK) is one of the largest contributors of preprints, having contributed over 100 Developmental Biology preprints to bioRxiv since 2013.
Interestingly, despite being in the middle of the pack in terms of preprint posting, Developmental Biology is the second biggest category for number of preLights posted (>350). preLights (a preprint highlighting service from CoB) is a platform in which ECRs write news & views style articles of preprints. This highlights the benefits of a strong community-led curation and demonstrates how this can work for other platforms.
Fig 2. Characteristics of Developmental Biology. A) Developmental Biology preprints in bioRxiv over time. B) Licences used for Developmental Biology preprints on bioRxiv. C) Number of versions for Developmental Biology preprints on bioRxiv. Data downloaded using the bioRxiv API.
Develop your use of preprints
Preprints serve multiple purposes. First, they help to shift the power dynamic in academic publishing, placing the power back in the hands of authors. This helps to accelerate the dissemination of scientific knowledge, free from the pressures and delays associated with publishing. The benefits of this open, accelerated system were highlighted during the COVID-19 pandemic when almost 40% of the initial COVID-19 related research was first shared as preprints, directly leading to changes in policy and potentially saving lives. Preprints can appear online within 48 hours of submission, compared to months and years under traditional publishing routes. This also proves particularly useful to publicly rebut published research and avoid the long delays of scientific corrections or the rather unused platforms for post-publication peer review
Preprints also decouple the quality of research from metrics like journal impact factor, promoting fairer, better, evaluation. They also provide a platform for early-career researchers to showcase their work and gain recognition, fostering a more inclusive and diverse research landscape. Additionally, preprints can be used iteratively to share ongoing research and get feedback from the community. However, perhaps the most important benefit of preprints is that they offer a viable route towards meaningful change to scientific communication; one that is free from financial incentives and pressure and that is community-focussed.
The best way to get started with preprints is to use them in your research by citing and reading them. The Node maintains “In preprints” which is a great series for discovering relevant Developmental Biology preprints each month. Going further, you could also discuss preprints in your journal club – or even review them on platforms like PREreview or hypothes.is with support from ASAPbio. For ECRs, preLights is an excellent opportunity to take your first steps into commenting on preprints.
Ready to develop how you share your research, amplify your voice, and contribute to a more open, Developmental Biology community? Grab our checklist (Box 1), explore resources, and join the preprint movement!
As biologists we work regularly with images to collect, interpret and communicate our data, findings and ideas. These days, however, images are almost entirely digital, and it is becoming increasingly uncommon to incorporate manually drawn pictures or 3D hand-crafted models into research, either during experimental observations or to communicate findings. Accurate scientific illustration is an important skill to record anatomical detail during an organism’s life, and realistic drawing was the main working method for early naturalists and anatomists, but drawing and modelling can also be used as a way to develop new ways of thinking about topics and processes from a different perspective1,2. We set out to explore how hand-drawing and 3D modelling could allow researchers today to engage with their research from new perspectives in a collaborative workshop guided by artist Dr Gemma Anderson-Tempini.
On the afternoons of Wednesday December 13th and Thursday December 14th 2023, we held a drawing workshop to bring together participants across three different research groups – (1) the ‘Molecular Marine Systems’ group of Dr Elizabeth Williams in the Faculty of Health and Life Sciences at the University of Exeter, (2) the ‘Micromotility’ group of Dr Kirsty Wan from the Living Systems Institute (LSI) at the University of Exeter, and (3) the ‘Algal Microbiome and Ecophysiology’ group of Dr Katherine Helliwell at the Marine Biological Association (MBA), Plymouth. Although focused on different research questions from different perspectives, the groups share an overlapping interest in understanding how microscopic organisms can sense, respond to, and move through their fluid environment.
Welcome to the workshop. We looked at planktonic larvae and discussed the potential of drawing: to infer or ‘draw hypotheses’, to ‘be like’ a biological process, to select salient information, to show and share understanding, and to constructively collaborate towards a processual view (Photo – Kirsty Wan).
Study organisms across the research groups include marine invertebrate larvae, microalgae, particularly diatoms, and protists. How these organisms transition between distinct phases of their life cycle in response to specific environmental cues is also of common interest across the different groups. We took inspiration from Maria Sibylla Merian, an entomologist, naturalist and illustrator (1647-1717) who was among the first to depict animal life cycles in the context of their specific environments at each different life phase3.
All research group members were invited to participate in the workshop and participants included group leaders, postdoctoral research fellows, graduate students and research technicians. Prior experience with drawing or art ranged from absolute beginner to confident regular practitioner. Workshop participants included scientists from both biology and mathematics backgrounds.
The first day of the workshop started with brief roundtable introductions and an overview of research topics by Liz and the practice of using drawing to represent dynamic biological processes by Gemma. As a drawing ‘warm-up’, we started with a group exercise on the ‘evolution of shape’, based on the drawing process developed by Gemma as part of her previous ‘Isomorphogenesis’ project, a drawing-based enquiry into the shared forms of animal, mineral and vegetable morphologies2.
Each participant was given a 3D object to make an observational drawing. This drawing was then passed to the next participant, who added a connected object with an alteration suggested by selecting an action word at random. We continued the process until everyone’s initial drawing was returned to them, and observed the evolution of our original shapes. This allowed everyone to start drawing without feeling inhibited by the need to draw something perfectly, or the lack of an idea about what to draw.
Examples from the ‘evolution of shape’ group drawing exercise. A trend emerged across the group in that various forms started to accumulate cilia.
After this exercise, each participant was asked to draw a depiction of their own current research project or scientific question, and explain what it is they wanted their drawing to show. Examples of topics discussed included trying to understand how a microscopic organism could coordinate multiple cilia for effective swimming, or finding a new way to depict an organism’s life cycle by using continuous line drawing to highlight the connectivity between different life phases and promote the idea of considering an organism as its whole life cycle.
To conclude the first day of the workshop, participants were then asked to complete a drawing exercise similar to the initial ‘evolution of shape’, in which we imagined our organism of interest as a 3D shape, using questions to guide and direct the drawing: ‘What developmental stage is your organism?’, ‘What kind of environment is your organism in?’, ‘What type of response does your organism show?’. These questions also related to our prior recommended reading on the experience of larvae in flow4. In this exercise participants were encouraged to generate a bold drawing that would take up all the space available on their A3 blank sheet.
The instructions for the final drawing exercise on Day 1 (left), with an example outcome drawing of ‘worm larva movement in light and flow’ demonstrating an attempt to fill all the space on the page (right).
We started the second afternoon of the workshop with a short visualization exercise followed by discussion, to help bring participants into the present, and focus on their research questions. Participants lay or sat in comfortable positions with their eyes closed while Gemma guided them on a journey in the plankton as a microscopic organism, slowly dropping down deeper and deeper into the sea in search of a place to settle down on the sea floor. The effect of this exercise on participants was fascinatingly variable, with responses ranging from finding the experience stressful, busy and complicated, with many organisms jostling for position in the plankton, and the added complications of moving in a big 3D space, with different types of flow that could take an organism anywhere, and the ever-present threat of predators from every side. Other participants found the experience relaxing, due the perceived reduction in the types of decisions and actions they could take as a microscopic member of the plankton – sink or swim? The overall effect was to bring the group closer together and focused on the shared topic of marine microorganisms’ development and navigation.
Following the visualization exercise, participants were offered a choice of activities including free-drawing with or without tracing paper, a paper folding origami activity, or the use of a circular maze template that could be converted from 2D circle into a 3D cone. These activities provided a basis from which participants could develop their own ideas about their research project or question. Examples of projects included using transparent layers to add information about environment and different life stage priorities to a coral life cycle, mapping the settlement journey of planktonic larvae through a circular maze, using the maze to demonstrate the carbon capture process during diatom sinking, or to develop an anatomical map of cell types in a marine larva. Origami structures were used to explore the life cycle of a marine worm, incorporating research goals into different sections, to explore environmental effects on marine larvae with changeable combinations of environmental factors, or to demonstrate biodiversity and morphology of diatom species.
Mapping the planktonic journey of larvae using a maze template (left), and developing an interactive marine invertebrate life cycle in 3D with origami (right).
Following the independent work, we ended the second day with presentations and discussion of each participant’s work in progress. Consensus across the group was that drawing provided a useful way of thinking about research. There was strong interest in finding ways to incorporate drawing more into our research papers or use it as a tool to start thinking about and discussing new projects by drawing what the results could look like, the experimental plan, or the overarching question. This workshop showed us that drawing can be used to stimulate discussion, think about research projects, generate new ideas, images and hypotheses/questions, promote lab group interactions and understanding and collaboration between different research communities. Common themes that emerged from our discussions were the usefulness of drawing and paper craft as a tool for teaching and communicating, and to remind us of the bigger picture and broader impacts of our research.
Overall, it was useful to have some templates designed by Gemma to work with, such as mazes, games, or origami structures, which helped those unfamiliar with creative work or processual drawing, as these provided an initial framework from which to develop ideas. Representing biological phenomena such as metamorphosis, behaviour and movement as a process is not easy, but through the workshop interesting ideas emerged regarding both ways to represent a process dynamically, as well as ways to think about the process itself. For example, one participant developed a carousel model or zoetrope with which to demonstrate marine larval behaviours in response to changes in oceanic pressure, while another developed a diatom ‘teaching wardrobe’ with interchangeable layers allowing the demonstration of a diatom’s response to different environmental conditions.
Planning a zoetrope to demonstrate planktonic larval behavioural responses in action (left), and development of a ‘teaching wardrobe’ to demonstrate environmental effects on diatoms (right).
New ways of thinking about life cycles also emerged, in particular the representation of a life cycle as a spiral instead of the classic circle. This idea has an interesting synergism with the recent reflections by Sarah and Scott Gilbert on the prevalence of spiral forms in nature, and the possibility of thinking about the animal holobiont as two interlocking spirals, one representing the microbiome and the other the animal – ‘Circles are complete and perfect; life isn’t. Mathematically, the circle is merely the bounded collapse of the spiral. It is complete, but life goes on’5.
Developing new ways to think about coral (left) and jellyfish (right, digitally inverted for clarity) life cycles, with use of layering, spiral shapes or continuous line drawings.
A final take-away from the workshop was that the process of drawing and expressing ideas with paper crafts also allowed participants to incorporate their own identities and personalities into their work. We generated a space for participants to step away from the regular routine of lab work, experiments and computational data analysis, and take the time to think more deeply about their research questions. Participants were encouraged to leave phones and social media behind, although we allowed their use to access relevant images and videos online, promoting a focused atmosphere throughout the workshop. Slowing down, reflecting and sharing imaginative time with colleagues through drawing, creating and discussion, has strong potential to lead to new insights into scientific questions. Workshops such as this could be one tool to help researchers actively engage with the often microscopic life they are studying, enabling a process-oriented approach to ‘flow, attend and flex’, as recently proposed by James Wakefield6. We recommend this style of workshop to other scientists searching for artistic ways of thinking about and communicating their work.
Acknowledgements
Thanks to the University of Exeter Living Systems Institute, for allowing us to host the workshop in their boardroom space, which was an ideal light-filled environment. This workshop was funded as part of a BBSRC David Phillips Fellowship (BB/T00990X/1) to Elizabeth Williams. We also thank each workshop participant for their valued contribution to this collaborative drawing workshop, which was in itself an experiment. Additional thanks to Dr Luis Bezares Calderónfor helpful comments on the text.
References
Anderson, G. 2014. Endangered: A study of morphological drawing in zoological taxonomy. Leonardo 47(3): 232 – 240.
Anderson-Tempini, G., 2017. Drawing as a Way of Knowing in Art and Science. Intellect Books.
Merian, M.S., Brafman, D. and Schrader, S., 2008. Insects & flowers: the art of Maria Sibylla Merian. Getty Publications.
Hodin, J., Ferner, M.C., Heyland, A., Gaylord, B., Carrier, T.J. and Reitzel, A.M., 2018. I feel that! Fluid dynamics and sensory aspects of larval settlement across scales. Evolutionary ecology of marine invertebrate larvae, 13, pp.190-207.
Gilbert, S.R. and Gilbert, S.F., 2023. “Process Epistemologies for the Careful Interplay of Art and Biology: An Afterword”, in Anderson-Tempini, G. and Dupré, J., 2023. Drawing Processes of Life: Molecules, Cells, Organisms, pg. 295.
Wakefield, James G. 2023. “Flow, Attend, Flex: Introducing a Process-Oriented Approach to Live Cell Biological Research”, in Anderson-Tempini, G. and Dupré, J., 2023. Drawing Processes of Life: Molecules, Cells, Organisms, pg. 280.
Open microscopy projects are flourishing with researchers contributing new technology and accessible workflows with the hope of democratising access to microscopy. In our upcoming webinar on Thursday 16 May at 15:00 BST, we’ll be hearing from Richard Bowman, Jan Huisken and Dumisile Lumkwana about three very different projects, OpenFlexure, Flamingo and VP-CLEM-KIT.
Richard will speak about OpenFlexure Microscopes, which are open-source optical microscopes that are built using 3D printed components and off the shelf components. You can read about the OpenFlexure microscope here.
Jan will discuss the Flamingo project. Flamingos are modular light sheet microscopy setups, which flip the concept of core microscopy facilities allowing the team to move custom advanced microscopes to the samples instead of taking samples to a core facility.
Dumi will discuss VP-CLEM-KIT, a new low-cost pipeline to support users to access high resolution volume correlative light-electron microscopy.
The deadline for entries for the FocalPlane-elmi204 has been extended until 21 May 2024. We would be delighted to receive entries from all imaging modalities, and you don’t need to be attending elmi2024 to enter. The winning entry, which will be selected by public vote following shortlisting by the elmi2024 organising committee, will be featured as the cover image on an upcoming issue of Journal of Cell Science.
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