What is Zebrahub?

Zebrahub is a web-based platform that offers an integrated approach to studying and analyzing cellular lineages during zebrafish embryogenesis at both transcriptional and spatiotemporal levels. It combines single-cell sequencing time course data with lineage reconstructions facilitated by light-sheet microscopy. The scRNAseq gene expression across tissues and time points can be directly visually explored in a web browser.  Additionally, researchers can navigate the complex cellular flows and lineages derived from light-sheet microscopy data using Zebrahub’s online web viewer and desktop interactive tool, enabling exploration of whole timelapse datasets and virtual fate mapping experiments.

What inspired the development of Zebrahub?

When we initiated the project, it was clear that the community was missing a database combining systematic live-imaging-based cell lineages with single-cell sequencing during development. Traditionally these approaches have been used separately, thereby limiting the full understanding of development. We wanted to use the most advanced microscopy and sequencing techniques available to establish a multimodal baseline of zebrafish development.

How can scientists utilize Zebrahub in their research?

Many important discoveries in developmental biology originated from observations; therefore, from the beginning, we wanted to have a fully interactive website to empower scientists by making our data accessible and, more importantly, directly explorable, even to scientists without coding skills.  Thus, concerning our terabyte-scale high-resolution light-sheet imaging time-lapse dataset, we provide both an neuroglancer-based interactive viewer for entire multi-color time-lapse datasets and a napari plugin to perform in silico fate mapping experiments.  Similarly, we allow researchers to effortlessly search for specific gene expressions and the emergence of cell types using CZI’s cell-by-gene platform. Our commitment to accessibility led us to invest substantial effort in ensuring that our data, code, and blueprints are readily available and open source. By doing so, we anticipate an immediate impact on a wide-ranging community, spanning disciplines such as developmental biology, single-cell biology, advanced microscopy, computer vision, tissue morphodynamics, and computational biology.

Who are the people behind this resource?

Supported by the CZ Biohub San Francisco (CZB-SF), Zebrahub is led by Merlin Lange,  senior scientist in the lab of Loic Royer, and results from an interdisciplinary collaboration with CZB’s Data Science and Genomics Platforms, with key contributors among others: Angela Oliveira Pisco, Norma Neff, and Alejandro Granados. Overall, Zebrahub has more than 30 collaborators at CZB-SF collaborating institutions (see picture above). Many are early-career scientists who played a key role in the project. In the following, these young scientists introduce themselves and their contributions:

Shruthi : I am Shruthi VijayKumar, a research associate in the Royer lab. A significant part of my role involved developing and optimizing the single embryo single cell dissociation protocol for the various developmental stages in zebrahub along with Michael Borja (Genomics) and Merlin Lange. Additionally, I contributed to preparing the libraries required for sequencing and helped with cell annotations. This project has been an incredible experience, as it has provided me with the opportunity to work in a multidisciplinary and collaborative environment. This experience has not only given me a better understanding of the entire pipeline but also broadened my expertise through extensive interactions with different teams. The fact that Zebrahub is an expanding resource for the community makes this project even more special and rewarding to be a part of.

Sarah: My name is Sarah Ancheta, and I am an associate Data Scientist. As part of the Zebrahub team, I worked on data processing and analysis of inter-individual transcriptomic variability. Since Zebrahub has single-cell transcriptomic datasets from individually resolved embryos, I was able to dissect the embryo-to-embryo variability by developing a framework to investigate the differences in gene expression between sibling individuals over time. I feel fortunate to work with data of such high quality and resolution and excited to have been among the first to analyze Zebrahub’s data and explore new biological insights into zebrafish development. It has been a wonderful experience to work with such an interdisciplinary team and learn to conduct analyses from both a biological and data-driven perspective.

Mike: My name is Michael Borja, and I am a Senior Research Associate for the Genomics platform. My main role and responsibility is to oversee lab activities regarding Single Cell and Spatial Transcriptomic experiments. When Zebrahub initially started, I was tasked with selecting which single-cell transcriptomic assay to use for our initial experiments. From there, I led the early efforts of processing cell dissociations and library preparation of individual embryos. In addition and in partnership with Shruthi VijayKumar, we developed a robust zebrafish single-cell dissociation protocol from single embryos that is independent of the developmental stage. Being part of this multidisciplinary and innovative team has helped me see how large-scale projects within the realm of science can be idealized and completed. As I continue with my personal growth and path in the field of Genomics, I will absolutely continue to seek large-scale collaborations such as Zebrahub so that I may be able to apply what I’ve learned through this experience. 

Jordao: My name is Jordao Bragantini. I am a software engineer in the Royer lab. My primary focus revolves around image processing, cell segmentation, and tracking. The Zebrahub project exposed me to the fascinating world of terabyte-scale microscopy images as well as to the mysteries of Developmental Biology. Handling this vast amount of data acquired on our advanced light-sheet microscopes required implementing specialized algorithms, ranging from GPU-friendly approximate morphological operators to our own distributed tracking software. These analyses require the full capacity of our available computational resources. I could not have wished for a better way to engage with machine learning in the biology domain than working with this multidisciplinary team, where we can learn from each other’s expertise.

What are the next steps for Zebrahub?

We want to expand Zebrahub with more developmental stages, novel multiomic modalities, and more lineage-specific imaging to ultimately reconstruct a digital multimodal embryo. We are also working on integrating existing datasets, including those from diverse species, to create a comprehensive atlas of vertebrate embryogenesis. This ambitious endeavor heralds a transformative era for the fields of developmental and evolutionary biology.

You can read more about Zebrahub in the BioRxiv preprint.

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To showcase the variety of interests and artistic talents among the developmental biology community, the Node and the British Society for Developmental Biology (BSDB) will jointly host a virtual art exhibition, accompanying the upcoming European Developmental Biology Congress (EDBC) in September.  

You may wish to submit a scientific image generated in the lab, craft or artwork inspired by your scientific work, or something completely unrelated to science!

The three categories in the exhibition are:

1. Scientific images
2. Science-inspired art
3. Art by Scientists (artwork unrelated to science)

Laser-cut wooden coasters by Helen Weavers

Entries in each of the three categories will have the chance of winning one of Helen Weavers’ laser-cut wooden coasters depicting BSDB medal designs.

Submission is open to anyone from the developmental biology community, even if not registered to attend EDBC, and the art exhibition will be free and available for anyone to view.

To submit your images, please:

1) Complete this Google form, where you can indicate which category your images are in, and provide a title and short description for each image. Each person can submit up to 5 images. 

2) Email the images to thenode@biologists.com. Please save the images under the same image titles indicated in this Google form. If the sizes of the images are too large to attach to the email, use https://wetransfer.com/ and provide the link to the files in your email.

Deadline for submissions: Sunday 27 August 23:59 BST

Please note that the exhibition organisers reserve the right to select or reject images for the exhibition.

(3 votes)

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Lab website: The Blood Engineering Lab (riosugimura.com)

Where is the lab?

Hong Kong

Research summary

Rio: We work at the intersection of bioengineering, immunology, and stem cell technology to invent new tools for understanding and treating cancers. The mission of The Blood Engineering Lab (BEL) is to define fundamental principles of anti-cancer immune cells and apply these insights toward improving chimeric antigen receptor (CAR) technology and checkpoint immunotherapy. We apply cutting-edge approaches including single-cell RNA sequencing, molecular barcoding, organoids, and stem cell differentiation. The goal is to invent new tools for understanding and treating cancers.  

Can you give us a lab roll call?

Yiming: PhD Candidate. Computational biologist in training at Cambridge University. She is a wizard of single-cell and spatial data analysis.

Sanxing: PhD Candidate. Tissue culture veteran. Cannot think of any cell type he cannot culture. Becoming a synthetic immunologist.

David: PhD Candidate. Chromium, Visium, Multiomics… He became a guru of 10X Genomics techniques. Organs-on-chips and myeloid checkpoint.

Shihui: PhD Candidate. Another computational wizard of BEL. Machine-learning to predict cell fate.

Sophronia: Master student leading an international team within a lab. CAR-macrophages from human pluripotent stem cells.

Alex: Master student. Studying myeloid checkpoint in assembloids.

Daniel: Visiting postdoc. Expert in AAV and gene editing.

Theo: Visiting medical student from Heidelberg, Germany. Making Super-CAR.

Patrick: Visiting PhD Candidate from Pavia, Italy. Expert in antibody engineering.

Favourite technique, and why?

Rio: I grew up with flow cytometry. Still watching FACS plots is the most FAVE time of mine. Used to finish my postdoc day enjoying drinks at my go-to bar with catch-of-the-day FACS plots (I had to stop this nerd habit after having babies…). Now I am shifting my addiction to single-cell data.

Apart from your own research, what are you most excited about in developmental and stem cell biology?

Rio: Engineering stem cell biology. Reconstruction and the endowment of new function.

How do you approach managing your group and all the different tasks required in your job?

Rio: I have two labs. It is an extra challenge as well as joy. I put most of my effort into two labs communicating smoothly. I shuttle myself between two labs. Very busy, but sitting down with students and discussing data is a rewarding part of my job. Zoom and Slack are great. I cannot imagine how I would operate my labs without these. Besides labs, I always spot myself in a grant-writing seat, namely Starbucks, Pacific Coffee, and Coffee Academics.

What is the best thing about where you work? 

Yiming: The lab is always encouraging knowledge exchange and collaboration inside and outside Hong Kong. Everyone has lots of chances to talk to other people and get feedback on the projects. These are very important for junior students to learn how to do research.

Sanxing: I think our lab combines many different directions and is a big fan of collaboration, which inspires me a lot.

David: I am very lucky to be in Dr. Rio’s lab due to my strong connection with various experts in different labs. I enjoy the FACS machine, BioRad PCR & qPCR machine as well as the services provided by the HKU-Med leaders, and technicians.

Alex: At HKU, the supportive culture encourages shared insights and vibrant discussions about grand theories and passions. Being part of this large institution promotes intellectual cross-pollination with other labs, and the plethora of free seminars and lectures further bolsters our academic growth.

Sophronia: I like the collaborative culture the most in our lab. We don’t solve problems alone, we solve problems together. We also engage with people from different labs with different expertise, and that’s how we come up with new ideas.

Theo: Working at Hong Kong University’s BEL research laboratory is an amazing experience. The lab is a great environment for research, and Rio is one of the best PIs I’ve worked – academically, and also personally. The research topic is fascinating, and our collaborative projects are exciting. However, the best thing about working at the BEL is the outstanding atmosphere with my co-workers. Everyone is friendly and supportive, making it a great place to work. The lab’s culture of collaboration and teamwork is what makes it stand out from other research labs. It’s inspiring to see how everyone works together to achieve common goals and how everyone is willing to help each other out. Additionally, the lab’s location in Hong Kong is a great advantage, as it provides access to a diverse range of resources and opportunities for research and collaboration. Overall, working at the BEL has been an incredible experience, and I feel fortunate to be part of such a dynamic and supportive research team.

Patrick: 1) The lab’s dedication to groundbreaking science. This is amazing from the point of view of the challenges inherent to translational stem cell biology and it’s relevance to cancer therapies 2) Regular meetings. The weekly science meetings to my opinion is an important moment to discuss and share ideas, points of view and strategies about different experiments. This enforces the conception and science methodologies to different experimental protocols, and allows for a solid foundation of the lab’s self-approach in tackling problems 3) The extensive network of collaborations, international seminars, meetings and conferences, to which lab members regularly take part.

What’s there to do outside of the lab?

Yiming: Endless mountain and sea!

Sanxing: Hong Kong is a wonderful city. There are lots of hiking mountains such as Dragon’s Back, Sunset Peak, and Victoria Peak surrounded by beautiful seas and relaxing landscapes. We usually go hiking or swimming to have fun at the weekend

David: I enjoy the hall life, for example, joining Spartan Running, High Table Dinner, and K11 MUSEA with tutors/masters. Now, I, together with an engineering friend, lead the hiking club in the Jockey Club Student Village III. As a captain of the club, I can not only experience a lot of nice sea views but also meet new friends here.

Sophronia: Hong Kong is a food paradise, so tasting food would definitely be one of the best thing to do. The night life in Hong Kong is also really nice where you can hang out with friends, go grab a drink, meet new friends and socialize.

Alex: Outside the lab, Hong Kong presents an abundance of activities. Prime among these is hiking, with the city’s varied landscapes offering everything from rugged peaks to tranquil beaches. Additionally, the Faculty of Medicine houses a nearby swimming pool, a regular haunt of mine. Both provide excellent avenues for unwinding after intense lab sessions.

Theo: Living in Hong Kong is an experience like no other. The city is a perfect blend of chaos and color, making it a fantastic place to live. First, the city is surrounded by nature, with many outlying islands, country parks, and hiking trails. So, there’s always something new to explore. Second, the food here is amazing, with everything from dim sum to noodle shops to oven-baked pizza. Third and last, the skyline and the city vibe are breathtaking. The view from The Peak is one of the most iconic in the world, and from festivals to cultural landmarks, there’s always something to see and do. Overall, whether you’re a nature lover, a foodie, or a culture enthusiast, there’s always something new to discover in this vibrant city.

Patrick: Hong Kong is an amazing City, with beautiful landscapes, and many places to visit. There are always many places to visit, good food to discover and sports to practice around

Rio: gosh, I should do hiking…

(2 votes)

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In recognition of the Genetics Society of America 24th International C. elegans Conference at the end of June 2023, Disease Models & Mechanisms (DMM) celebrated worm research with specially commissioned open-access articles, including an Editorial from DMM Editorial Board member Guy Caldwell, an interview with Piali Sengupta and a Review from Julián Cerón. The GSA worm meeting was exuberantly welcomed by the C. elegans community, who had been deprived of an in-person meeting since 2019. The meeting was kicked off with a plenary session that was sponsored by DMM and included a fantastic talk from Julie Ahringer on how the genome directs development. The engaging plenary and break-out sessions journeyed through a wide range of topics from genomics and epigenetics to the cytoskeleton and intracellular trafficking, to metabolism and neuronal cell biology, many in the context of development and human disease. The attendees were entranced by a keynote address from Oliver Hobert, aptly titled ‘Why C. elegans remains special’, and many whole-heartedly embraced the Scottish Ceilidh dancing at the conference dinner. The conference maintained an energic buzz throughout, with animated discussions following speaker sessions and clustered around the posters. It was wrapped up with a thought-provoking ‘Inclusivity Session’ led by organiser Miriam Goodman and others, and in the closing remarks organiser Sander van den Heuvel left us with the fitting statement that C. elegans is “not just a model system, but a pioneering system”.
Sander’s comments, along with the energy at GSA worm, echoed Guy Caldwell’s editorial that highlighted the model organism as a robust and translational model of disease. Guy discussed advances in genomic data and the progress of the model over the past 15 years, highlighting the power of genetic screens and CRISPR gene editing. He expanded by stating that the use of this technology in cell-based or invertebrate models have not been supplanted but are instead joined by voluminous datasets of human genomic variation. C. elegans researchers are now increasingly able to face the staggering task of parsing function from human disease-associated variants. Away from genetic screening, Guy continues by highlighting that C. elegans studies have also been applied to deep phenotyping, where research has provided a higher level of detail of disease characterisation.

DMM’s focus on C. elegans also featured ‘See[ing] elegance in sensory biology: an interview with Piali Sengupta’. Piali is a prominent researcher in the field of sensory biology and in this interview emphasises the use of C. elegans in neurology, stating that the model is ideal to assess the role of specific neurons in behaviour. She also states that, “Forward genetic screens are also very easy because most of the worm population in the lab are hermaphrodites. If you have a mutant hermaphrodite, you just put it on a plate, and it reproduces”

“You can kill most neurons in the worm, and they will normally survive in the lab”, Piali Sengupta

The final piece of literature that DMM included in this C. elegans focus, was a review by Julián Cerón; ‘Caenorhabditis elegans for research on Cancer hallmarks’. Julián emphasises the use of C. elegans as a robust translational model of cancer that can recapitulate ten of the major hallmarks of cancer. Julián emphasises how C. elegans can be used to study hallmarks ranging from the regulation of apoptosis to the activation of invasion.

DMM is honoured to support the C. elegans community by publishing cutting-edge science that provides mechanistic and translational insights to benefit human health and welcome your next C. elegans paper to wriggle into their dedicated collection. We hope you enjoyed #Worm23 and we look forward to the next C. elegans conference in 2025!

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Last week, I attended the LMB-VBC Graduate Life Sciences Symposium in Cambridge, UK. Besides its wonderful academic programme, this symposium also included a workshop and panel discussion that touched on the societal impact of science. During the workshop, participants were challenged to think about different ways to connect with (non-specialist) communities, enthuse audiences and create memorable engagement experiences.

This ‘Public Engagement’ workshop was led by Dr Jamie Gallagher, an award-winning engagement professional specialising in impact narratives and evaluation. The fact that Jamie is also a comedian became quite clear when he took the stage – as well as his love for the fantasy genre! In an engaging and entertaining workshop, Jamie used pop culture references – including the Lord of the Rings and Game of Thrones – to introduce and guide us through the four key questions you need to consider when setting up any public engagement activity. In short, these where the following:

• What would you like to achieve with your proposed activity?
• Who would you like to get on board to reach your goals?
• How will you make sure that you achieve your goals?
• What does success look like?

And to answer these for Frodo Baggins of the Shire (spoiler alert!)

• I’d like to destroy the One Ring.
• I’ll join a fellowship of skilled individuals to get me to Mount Doom.
• I’ll take the shortest road through Middle Earth (and will go through the mines of Moria).
• I’ll throw the one ring into the fiery chasm from whence it came, so that Sauron can never rule Middle Earth again.

Perhaps a bit silly, but I would argue that the use of analogies and metaphors greatly helped Jamie to get his message across. The power of different presentation techniques was something we analysed further by watching the winner of FameLab 2019: Tim Gordon. We discussed the many ways in which Tim managed to captivate his audiences with his story on climate change and its effects on coral reefs. It turns out Tim used a combination of humour, enthusiasm, analogies, imagination, stories, pop culture references, questions and more to claim his prize – and all of that in just a 3 minute talk! Perhaps take a look at the video yourself and see whether you can spot even more tricks and presentation techniques.

The careful analysis of Tim’s successful talk at FameLab led to one more analogy from Jamie that stuck with me: if your scientific data are raw vegetables, you can imagine that most people don’t want to digest it that way. You will have to clean, process and chop things up before cooking it and making it palatable. Not only this, but to make things really memorable, you need to add spices and flavourings – just like Tim in his FameLab final. So if you’re thinking about setting up a public engagement project, let’s get cooking!

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“I think it’s really important we have to do science that serves all. Because otherwise we’re not going to provide betterment for all, which must be of course, the goal with our science.”

Dr Cecilia Lindgren

In the latest episode of the Genetics Unzipped podcast, we’re chatting with two of this year’s Genetics Society award winners – Cecilia Lindgren, who’s an expert on the genetics of obesity and metabolic disorders, and Lucy van Dorp, who has spent the past three years tracing the spread of SARS-CoV-2 around the world.

Genetics Unzipped is the podcast from The Genetics Society. Full transcript, links and references available online at GeneticsUnzipped.com.

Subscribe from Apple podcasts, Spotify, or wherever you get your podcasts.

Head over to GeneticsUnzipped.com to catch up on our extensive back catalogue.If you enjoy the show, please do rate and review on Apple podcasts and help to spread the word on social media. And you can always send feedback and suggestions for future episodes and guests to podcast@geneticsunzipped.com Follow us on Twitter – @geneticsunzip

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One of the most fascinating observations that comes from comparing mammalian development is the difference in developmental tempo across species (Ebisuya & Briscoe, 2018). Mice and humans develop through a series of stereotypical events requiring conserved molecular pathways. Yet, embryogenesis takes around 60 days in humans and 20 days in mice. How mice generate similar-sized embryos containing the same structures as humans in only half the time remains unknown. Moreover, for other unconventional mammalian species, our knowledge is even more limited.

The Ebisuya lab has been addressing this question using the segmentation clock as a model system. The segmentation clock is the oscillatory gene expression found in the cells of the pre-somitic mesoderm (PSM) that controls the periodic formation of vertebrate body segments. These oscillations are cell-autonomous, and their period differs across species: around 30 min in zebrafish, 90 min in chicken, 100 min in snake, 2 hours in mouse and 5 hours in human (Matsuda et al, 2020b; Gomez et al, 2008). In our past study, in vitro recapitulation of the segmentation clock using mouse and human pluripotent stem cells (PSCs) revealed that differences in the biochemical reaction speeds, including protein degradation rates and gene expression delays, are responsible for the 2-3 times slower tempo of the human clock compared to that of the mouse (Matsuda et al, 2020a). However, whether this constitutes a general mechanism of developmental time control across mammals remained to be determined. In this study, we used PSCs to recapitulate in vitro the segmentation clock of four novel mammalian species in addition to the mouse and human: marmoset, rabbit, cattle and rhinoceros. We then used this “stem cell zoo” platform to systematically investigate the general mechanism behind the interspecies differences in developmental tempo (Lázaro et al, 2023).

The bigger the better?

Based on the results obtained comparing mouse and human developmental time, our first hypothesis was that the slower tempo of human was due to its bigger size. Several biological processes such as metabolic rates or gestation periods are known to scale with body weight. Larger animals tend to have slower metabolism, longer gestation, extended lifespan and scale most of their physical and biological properties to match their big size. Therefore, initially it made sense that developmental tempo could be regulated by similar rules. For this reason, to extend our zoo we wanted to have the largest mammal we could possibly get stem cells from. This animal turned out to be the southern white rhinoceros.

The question most people ask is: how did you manage to get rhinoceros cells? This is thanks to the work of Prof. Thomas B. Hildebrandt and colleagues in trying to save the northern white rhinoceros from extinction. For this, they have derived high quality embryonic stem cell lines of rhinoceros which can now be used for different studies (Hildebrandt et al, 2018). The first thing we did for this project was to obtain the rhinoceros stem cells and differentiate them into PSM. To our surprise, despite rhinoceros being much larger than human, their PSM cells showed a faster tempo. We then thought that maybe the slower tempo of human was due to a primate specific feature. Therefore, we searched the primate literature and found studies describing the very slow development of the common marmoset monkey. Common marmoset is a very small primate with a longer embryogenesis length than human. We obtained marmoset PSCs and, after differentiating them to PSM, we confirmed that their tempo was indeed slower than that of human. With the examples of rhinoceros and marmoset, it started to be evident that early developmental time could be uncoupled from the animal body weight, proving wrong our initial hypothesis.

We completed the zoo with rabbit and cattle cells to have a more complete phylogenetic representation of our species. Overall, our zoo contains species with adult body weights spanning from 50 grams to 2 tonnes, and gestation lengths ranging from 20 days to 17 months. These species belong to three distinct phylogenetic clades: Primates (marmoset and human), Glires (mouse and rabbit) and Ungulates (cattle and rhinoceros), constituting a diverse sampling of mammalian species unprecedented for developmental studies.

The stem cell zoo

Advancement in PSC technologies opens up new possibilities for broadening our understanding of mammalian development beyond traditional human and mouse models. The utilization of in vitro models representing various species poses a unique opportunity to conduct interspecies comparisons of cell- and tissue-autonomous processes (Figure 1). By recapitulating the segmentation clock of six mammalian species, we observed that the oscillatory period did not scale with the animal body weight but with the embryogenesis length. The biochemical kinetics of the core clock gene HES7 displayed clear scaling with the species-specific segmentation clock period. However, the cellular metabolic rates did not show an evident correlation. Instead, genes involving biochemical reactions showed an expression pattern that scales with the segmentation clock period.

A zoo of possibilities

In this study, we have focused on establishing correlations between developmental time and the different cellular parameters across species. In the future, we would like to test our hypothesis by establishing causal relationships between these processes, trying to better understand the genetic control of species-specific tempo establishment. Additionally, the stem cell zoo opens up possibilities to investigate a plethora of developmental processes across species. Other projects we have ongoing in the lab are the study of interspecies differences in brain development or heart beat rate determination. The use of stem cells allows us to study animals that are normally inaccessible in a lab but have particular features that make them interesting. We hope that the expansion of the stem cell zoo will spark further comparative studies across species.

Access the article

Jorge Lázaro, Maria Costanzo, Marina Sanaki-Matsumiya, Charles Girardot, Masafumi Hayashi, Katsuhiko Hayashi, Sebastian Diecke, Thomas B. Hildebrandt, Giovanna Lazzari, Jun Wu, Stoyan Petkov, Rüdiger Behr, Vikas Trivedi, Mitsuhiro Matsuda, Miki Ebisuya. – A stem cell zoo uncovers intracellular scaling of developmental tempo across mammals. Cell Stem Cell. 2023 Jul 6; 30: 938-949.e7

References

Ebisuya M & Briscoe J (2018) What does time mean in development? Dev 145

Gomez C, Özbudak EM, Wunderlich J, Baumann D, Lewis J & Pourquié O (2008) Control of segment number in vertebrate embryos. Nature 454: 335–339

Hildebrandt TB, Hermes R, Colleoni S, Diecke S, Holtze S, Renfree MB, Stejskal J, Hayashi K, Drukker M, Loi P, et al (2018) Embryos and embryonic stem cells from the white rhinoceros. Nat Commun 9: 1–9

Lázaro J, Costanzo M, Sanaki-Matsumiya M, Girardot C, Hayashi M, Hayashi K, Diecke S, Hildebrandt TB, Lazzari G, Wu J, et al (2023) A stem cell zoo uncovers intracellular scaling of developmental tempo across mammals. Cell Stem Cell 30: 938-949.e7

Matsuda M, Hayashi H, Garcia-Ojalvo J, Yoshioka-Kobayashi K, Kageyama R, Yamanaka Y, Ikeya M, Toguchida J, Alev C & Ebisuya M (2020a) Species-specific segmentation clock periods are due to differential biochemical reaction speeds. Science (80- ) 369: 1450–1455

Matsuda M, Yamanaka Y, Uemura M, Osawa M, Saito MK, Nagahashi A, Nishio M, Guo L, Ikegawa S, Sakurai S, et al (2020b) Recapitulating the human segmentation clock with pluripotent stem cells. Nature 580: 124–129

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Organizing an art exhibition, especially a solo one, is an intimidating but truly exciting experience. For me, as a scientist and artist, the journey of curating a science art exhibition has been a transformative one. I am currently organizing a science art exhibition that will display the intricate world of developmental biology (in zebrafish) through the lens of microscopy and will be hosted from November 2023 to January 2024 in Austria. In this blog post, I will share the challenges, triumphs, and lessons I learned while organizing the exhibition until the time of writing, which is four months before the opening event.

The Fascination of Developmental Biology in Zebrafish

Throughout my education, I was fascinated by microscopy and developmental biology. The very fact that it is possible to light up cells in the dark and watch them move, divide, and interact in real-time is still fascinating to me. Thus, to share this fascinating world and discover new things, I shifted my career path in 2022 from academia to having my own company where we combine science and art, creating science communication and art.

For the end of 2023, we are planning a science art exhibition in Austria, where we plan to showcase the breathtaking beauty and complexity of developmental biology. To achieve this, the central artworks are a collection of 12 microscopy science art pieces. These artworks reveal the exquisite details of cells that are smaller than a single spider silk strand on canvases that are up to 1 meter in size. Using vibrant colours on black canvas and frames, I aimed to establish high-contrast works which truly emphasize the detail of the cells and tissues on display.

Exploring Various Artistic Mediums

In addition to the central microscopy science art pieces, the exhibition will feature a diverse range of artworks that have contributed to developing my art style, techniques, palettes, and composition. To offer a modern perspective on the subject matter, five contemporary science art pieces of acrylic on canvas are part of the exhibition. Alongside these, the exhibit will contain ink and watercolour works on paper as the technical requirements for these are very complementary to the acrylics on canvas pieces. The topics explored there, are portrait, landscape, and architecture. By incorporating different visual art mediums, I sought to present a comprehensive exploration of the connection between science and art, and how exploring different avenues of topics and techniques can help fine-tune others.

Establishing the Exhibition Theme

One of the primary challenges I faced was pulling together a cohesive exhibition theme. It required careful consideration and collaboration with the gallery, Hofinger BilderRahmen Tirol. Together, we worked on topics, positioning, and carefully selecting manufactured frames to ensure a seamless presentation. Through numerous discussions and consultations, we aimed to create an immersive experience that would captivate viewers and communicate the essence of developmental biology in zebrafish. My biggest tip here is to trust the expertise and experience of the gallery and framers.

Navigating the Artistic Learning Curve

As an individual with an academic background in science and recently transitioning to a small business owner and artist, the journey from concept to execution was a steep learning curve. Building my own company and transitioning from a scientific mindset to that of an entrepreneur and artist required especially a significant shift in perspective. Be it price negotiation, international logistics, or business networking – it is very different to academia.

The art pieces shown reflect this range, and only by embracing this path of being a scientist and artist I could merge different collections and works harmoniously into one cohesive and impactful exhibition.

Embracing the Art of Science Communication and Marketing

To ensure the success of the exhibition, early collaboration with others was essential. Together, with the gallery, colleagues, and family, we established effective marketing strategies, meticulously handpicked materials, debated font choices, and added personal touches such as handwritten notes. By going above and beyond traditional marketing techniques, we aim to create a unique experience for visitors, drawing them into the captivating world of science art. This is particularly important as we want to reach the wider public, friends, family, and academic colleagues alike. For example, choosing the right balance of science communication language is a challenging task – we want it to be scientifically correct but don’t drown the wider public in unnecessary scientific detail. My biggest tip, let a variety of people read the text and ask them to provide feedback.

Making the Invisible Visible

The process of curating an exhibition from scratch resonated deeply with the essence of microscopy itself—making the invisible visible. As a developmental biologist, my work revolved around uncovering the hidden wonders of life. Similarly, organizing an exhibition allowed me to bring together artworks and showcase the unexplored beauty that lies within the intricate world of zebrafish developmental biology.

But to be honest, it is hard work. For me, defining milestones (such as selecting the art pieces, or sending out the first invitations) is incredibly important to keep up the sense of achievement while working towards the exhibition opening.

We still have about four months before the opening, but the to-do lists seem to get longer than shorter. Why? Because we can now switch from higher level decisions (e.g. art pieces and dates) to smaller level decisions (e.g. organizing beamers and picking out food). Thus, decisions started to fan out like a tree. Where the exhibition is the trunk, the branches are higher-level decisions, and the smaller-level decisions are the leaves.

Pro Tips Summary:

1. Think about your why and hold on to it. E.g. for me, it is the love for sharing microscopy and science art
2. Explore different topics and techniques as they might fine-tune each other. E.g. digital microscopy, acrylics on canvas, watercolour on paper
3. Trust the years of experience a gallery and framers bring to the table. E.g. establishing contrast for microscopy art
4. Embrace that science and art are not exclusive. There will be some challenges and contradictions, but they are not necessarily excluding other things.
5. Marketing is a must, but marketing science art is particularly interesting as you want to speak to a variety of people alike. E.g. carefully consider word choices
6. Enjoy the process! As with every project, there are ups and downs, but that’s why considering your “Why” is so important.

Conclusion

Organizing a solo science art exhibition has so far been an unforgettable journey. I am incredibly lucky to be able to blend my passion for science and art and do this in full support of the gallery, family, friends, and colleagues. The challenges faced along the way, from establishing a cohesive theme to navigating the nuances of marketing, only served to enhance the outcome. By merging scientific expertise with artistic expression, I aim to inspire viewers and ignite a sense of wonder about the hidden realms of science and life itself. Through the medium of art, I want to bring the invisible to life, weaving together a collection that celebrates the fascination and beauty of microscopy and science.

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The Inclusive STEM Teaching Project is a 6 week course designed to advance the awareness, self-efficacy, and the ability of faculty, postdocs, and doctoral students to cultivate inclusive STEM learning environments for all their students and to develop themselves as reflective, inclusive practitioners.

This is a free, online course (run through edX) that provides an excellent overview of inclusive STEM teaching. We highly recommend this course to all who teach or might teach.

The course runs from Oct 2 to Nov 21, 2023.

Register here https://www.edx.org/course/the-inclusive-stem-teaching-project.

What you’ll learn

Participants in this course will…

• Examine issues of diversity, equity and inclusion in higher education
• Reflect on their own and their students’ identities and experiences
• Question their assumptions about all aspects of instruction
• Identify and implement learner-centered structures and strategies
• Apply principles of evidence-based inclusive teaching
• Use their student learning data and feedback to inform pedagogical and curricular choices

———-

This article is reposted from the ROOT & SHOOT blog (https://rootandshoot.org/the-inclusive-stem-teaching-project/). ROOT & SHOOT is a NSF-funded Research Coordination Network granted to seven plant science organizations that are seeking to “Root Out Oppression Together & SHare Our Outcomes Transparently”. In other words, we recognize that science as traditionally practiced is inherently exclusionary, and we are exploring strategies to build a more inclusive scientific culture. We invite you to visit our project home page, check out our Resources page, and follow us on Twitter (@RootAndShootRCN).

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Reflections on a social media workshop that was part of the Society for Experimental Biology Centenary Conference 2023.

The use and availability of social media platforms are constantly changing, as the recent launch of Threads by Meta Platforms and our own server on Mastodon – biologists.social – nicely exemplify. For years, Twitter has been the go-to platform for biologists to share and discuss recent scientific advances, but this may well change. Regardless of what may – or may not – happen, a refresher on the different ways to use social media to engage with other scientists (and the public) seemed timely.

At the recent SEB Centenary Conference in Edinburgh (UK), Isabel Mendoza (Global Plant Council), Geraint Parry (Global Plant Council & Association of Applied Biologists) and Mary Williams (American Society of Plant Biology) teamed up to provide a workshop with exactly this in mind. They named it: “Science and Social Media. Are they really compatible? Developing Effective Science Communication Strategies”.  

To start things off, Isabel Mendoza showed us (= the participants) some user statistics in order to rank the available social media platforms. This re-affirmed the notion that the platforms we often use as biologists don’t necessarily have the widest reach. Why not use Pinterest, for example, which may actually be a very efficient platform to reach new audiences?

When reaching out to new (and existing!) audiences, thinking about their needs is crucial. How can you make sure that you communicate in a way that is inclusive? The workshop organisers had plenty of examples – such as the lack of ALT-text, or wrong use of hashtags/emojis – that quickly make things inaccessible to people with marginalized identities. Even with all the right intentions…

The topic of inclusivity was actually discussed in the context of a larger movement that drives a cultural change in the plant sciences, known as the ROOT & SHOOT project. This 5-year project, combining the expertise of seven plant science organisations, aims to “remove barriers for individuals historically excluded from science based on gender, gender identity, disability status, sexual orientation, ethnicity, or race”. The title of the project refers to the goals to “Root Out Oppression Together and SHare Our Outcomes Transparently” (ROOT & SHOOT). A wonderful initiative that will hopefully be followed by many others within and outside the biological community.     

There wasn’t just one take-away message from this SEB workshop. Rather, there were many different things to consider. One particular consideration that struck a chord with the participants was this: if you’re still on the fence about using social media as a scientist, there is never an ideal time to join – so why not just dive in straight away? One of the workshop participants took this advice to heart and created her Twitter profile on the spot – that’s the spirit! 💪

For more detailed information about (part of) this workshop, take a look at this page created by Mary Williams: https://rootandshoot.org/how-can-social-media-to-build-a-more-inclusive-scientific-community/

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