Biology Open (BiO) has appointed a new Editor-in-Chief, Daniel Gorelick. Dan is currently Associate Professor in the Center for Precision Environmental Health, and Department of Molecular and Cellular Biology at the Baylor College of Medicine in Houston, Texas, USA. He is also Director of the Zebrafish Advanced Technology Core Facility. Dan’s lab studies how endocrine-disrupting chemicals and related toxicants influence embryonic development.
In this interview, Rachel, the Manager Editor of BiO, talks to Dan about his background in development biology, his views on open access publishing, and his vision for BiO as the new Editor-in-Chief. Dan also mentions that one of his scientific heroes is Cassandra Extavour, who many of the Node and Development readers will be familiar with!
Dan was very excited when he found the elusive zebrafish special issue of Development in the head office of The Company of Biologists! (No Ratings Yet) Loading...
In this SciArt profile, we spoke to Deepti Trivedi, who has a background in neurogenetics in flies and mice, and does drawings inspired by Drosophila research.
Can you tell us about your background and what you work on now?
I grew up in Delhi, where my parents had set up a life, moving from rural part of central India, right around the time I was born. My dad was an ecotoxicologist working for the Government and mom a homemaker. Growing up I was a shy, yet confident kid. After my schooling, I took up Biochemistry at University of Delhi. My first experience with real research happened, when by alignment of several coincidences, I ended up in Bangalore to do Masters by research in a Drosophila neurogenetics lab. I can safely say, this was the first time, I knew that I wanted to be a researcher. This was a really exciting time for me to be able to ask open ended questions and wonder how they could be answered through experiments.
I was one of the beneficiaries of the travel award that The Company of Biologists offers to young researchers, using which I went to USA (SUNY, Buffalo and CSHL) for 6 months to learn electrophysiology. I used this in my Masters’ thesis work. By this time, I knew I wanted to do a PhD. I did a PhD from University of Cambridge as a Gates Cambridge Scholar where I studied phototransduction in flies. After PhD, I went to USA for a postdoctoral training (UCLA and UTMB) further studying neurogenetics in flies and mice. For past 9 years, back in India, at National Centre for Biological science, Bangalore, I set up CRISPR Cas9 based genome engineering services in flies and have been managing a core research facility.
Morgan and flies In 2021, the twitterverse decided to celebrate November 18th as Fly day, owing to the fact that w1118 fly mutant was isolated on this day. Deepti did a series of art work on this day, one of them is “Morgan and Flies” depicted here.
Were you always going to be a scientist?
Although I don’t really recall how I got interested in “science”, I feel it seamlessly integrated into the fabric of my life. Growing up, a lot of discussions at home surrounded topics of nature, plants, animals and habitats. There was a general tendency to approach regular life discussion, such as cooking or exercising, with scientific logic. There wasn’t much discussion about religion, politics, history, business, money or any other topics. So, looking back, the general outlook was already quite skewed towards science. However, taking it seriously as a career choice did not come that obviously. In fact, it was drawing and art that I spent a lot of time in. I remember wanting to be an architect, an artist or a fashion designer at some point. All these interests were deeply rooted in the fact that I really enjoyed the process of drawing and working with my hands, crafting little knick-knacks. In India, at that time, the path to pursuing art as a subject lay solely within the humanities program. This meant delving into social sciences like history, geography, economics, politics, and languages, in which I had no interest, at that time. On the other hand, I loved maths and sciences. It also helped that I had fantastic science teachers in school and then in college. Although it was no brainer to take up sciences for higher studies, I was not sure what exactly I wanted to do in sciences.
Looking back, most of my life decisions have been on the go, with no long term career goals that I have passionately pursued. However, I have always gotten extremely excited about short term goals and have pursued them with great rigour and enthusiasm. As a scientist who runs a core research facility, a shared resource for many scientist, I feel, I have found exactly the kind of work that I like. I help scientists in their passionate pursuits to scientific discovery by making a small contribution to their research programs.
Sensory drosunculus Just like how sensory homunculus is topographic representation of sensory neuronal distribution, Deepti made a “Sensory Drosunculus” that represents that distribution of sensory neurons on Drosophila body.
And what about art – have you always enjoyed it?
As I said, I remember doing art much more vividly from my childhood than science, perhaps because there are no artists in the family. The feeling that you are doing something unique and getting appreciated for it, is kind of nice for a little kid. I doodled all the time – while studying, while listening to radio, while watch television, while on holidays with parents, inside text books, everywhere. I took part in all the art activities at school, and in the community. However, at some point during my late teens (as I picked up science that I suddenly became too passionate about), I stopped doing art completely. I picked it up again only towards the end of my PhD at Cambridge.
I now realise that art is not something I like to do all the time. I go through these phases when I do a lot of it, and then I don’t do any. Great that I didn’t choose it as a career, otherwise I would go through a lot of famines.
What or who are your most important artistic influences?
Nature is the greatest influencer. I am also deeply influenced by traditional art making and art practices.
As I mentioned there is always a long pauses which can last up to months before I pick up art and draw or paint something. However, it doesn’t mean that I am not thinking about art or in artistic way. An art process requires a lot of thinking for me and I pick up pen and paper only when an idea has clicked and has made an impact on me for a few days and stayed there and compelled me to go ahead with the idea. I usually have thought through what exactly I want to make, which medium I want to use, what size, what colour scheme etc. The actual work may require just 10 minutes, or 10 hours, but it is an immersive experience and there is enough energy that I can sit through the night finishing a piece if it requires. Once I am done, I am done and may not touch art for several months. I don’t repeat an idea or make several iterations of the same piece. It is usually a one-time process for me as if to go through a once in a life time experience and back. However, it is a deeply satisfying process.
Sometimes, I am asked to do something by friends or colleagues, which requires rounds of corrections or changes. Those are not the things that I enjoy. One more reason why this could not have been a sound career choice for me.
Circle of Life “From the day we arrive on the planet And, blinking, step into the sun There’s more to see than can ever be seen More to do than can ever be done” From “Circle of life” on which this painting is based. Drosophila has certainly been instrumental for us to see more than ever could be done otherwise.
Does your art influence your science at all, or are they separate worlds?
I am sure it does influence, but in a more sublime way rather than tangible. Both art and science, as passionate pursuits of truth, are deeply creative and immersive processes. Both require you to observe something as they are, but also to wonder what could be. I have always used drawing as a tool to understand scientific concepts, and also sometimes to avoid distractions to focus. I am a visual person and so if I am to listen to something, I usually use drawing to understand what is being said.
I feel art is more open, more non-restrictive. There are no rules to follow and so it also gives me a respite when things are not working as one wants in science or life.
What are you thinking of working on next?
There are many ideas, mostly revolving around science outreach for younger audience. I have a preteen kid and I think a lot about catering to that age group kids through art and science. I have still not pinpointed what exactly it is and hence currently going through an artistic lull period.
Jennifer A. Schumacher, Zoë A. Wright, Diandra Rufin Florat, Surendra K. Anand, Manish Dasyani, Laurita Klimkaite, Nina O. Bredemeier, Suman Gurung, Gretchen M. Koller, Kalia N. Aguera, Griffin P. Chadwick, Riley D. Johnson, George E. Davis, Saulius Sumanas
Stefania Tavano, David B. Brückner, Saren Tasciyan, Xin Tong, Roland Kardos, Alexandra Schauer, Robert Hauschild, Carl-Philipp Heisenberg
Mannitol-induced detachment of the blastoderm from the yolk from Tavano et al. This image is made available under a CC-BY-NC 4.0 International license.
Teresa Krammer, Hannah T. Stuart, Elena Gromberg, Keisuke Ishihara, Manuela Melchionda, Jingkui Wang, Elena Costantini, Stefanie Lehr, Dillon Cislo, Laura Arbanas, Alexandra Hörmann, Ralph A. Neumüller, Nicola Elvassore, Eric Siggia, James Briscoe, Anna Kicheva, Elly M. Tanaka
James L. Engel, Xianglong Zhang, Daniel R. Lu, Olaia Fernandez Vila, Vanessa Arias, Jasper Lee, Christopher Hale, Yi-Hsiang Hsu, Chi-Ming Li, Vasanth Vedantham, Yen-Sin Ang
Adriana Migliorini, Sabrina Ge, Michael H. Atkins, Rangarajan Sambathkumar, Angel Sing, Conan Chua, Adam J. Gehring, Gordon M. Keller, Faiyaz Notta, Maria Cristina Nostro
Zaid Muhammad, Phoebe W. Brown, Larema Babazau, Abdulrahman I. Alkhamis, Baba W. Goni, Haruna A. Nggada, Kefas M. Mbaya, Selina Wray, Isa H. Marte, Celeste M. Karch, Louise C. Serpell, Mahmoud B. Maina
Matēj Drs, Samuel Haluška, Eliška Škrabálková, Pavel Krupař, Lucie Brejšková, Karel Muller, Natalia Serrano, Andrea Potocká, Aline Voxeur, Samantha Vernhettes, Jitka Ortmannová, George Caldarescu, Matyas Fendrych, Martin Potocký, Viktor Žárský, Tamara Pečenková
Avilash S. Yadav, Lilan Hong, Patrick M. Klees, Annamaria Kiss, Xi He, Iselle M. Barrios, Michelle Heeney, Anabella Maria D. Galang, Richard S. Smith, Arezki Boudaoud, Adrienne H.K. Roeder
Victoria E. Deneke, Andreas Blaha, Yonggang Lu, Jonne M. Draper, Clara S. Phan, Karin Panser, Alexander Schleiffer, Laurine Jacob, Theresa Humer, Karel Stejskal, Gabriela Krssakova, Dominik Handler, Maki Kamoshita, Tyler D.R. Vance, Elisabeth Roitinger, Jeffrey E. Lee, Masahito Ikawa, Andrea Pauli
Francesca Zappa, Daniela Intartaglia, Andrea M. Guarino, Rossella De Cegli, Cathal Wilson, Francesco G. Salierno, Elena Polishchuk, Nicolina Cristina Sorrentino, Ivan Conte, Maria Antonietta De Matteis
Jared A Tangeman, Sofia M Rebull, Erika Grajales-Esquivel, Jacob M Weaver, Stacy Bendezu-Sayas, Michael L Robinson, Salil A Lachke, Katia Del Rio-Tsonis
Joshua Hislop, Amir Alavi, Qi Song, Rayna Schoenberger, Kamyar Keshavarz F., Ryan LeGraw, Jeremy Velazquez, Tahere Mokhtari, Mohammad Nasser Taheri, Matthew Rytel, Susana M Chuva de Sousa Lopes, Simon Watkins, Donna Stolz, Samira Kiani, Berna Sozen, Ziv Bar-Joseph, Mo R. Ebrahimkhani
Chloe Santos, Ailish Murray, Abigail R. Marshall, Kate Metcalfe, Priyanka Narayan, Sandra C. P. de Castro, Eirini Maniou, Nicholas D. E. Greene, Gabriel L. Galea, Andrew J. Copp
Patrick D. Brandt, Dawayne Whittington, Kimberley D. Wood, Chris Holmquist, Ana T. Nogueira, Christiann H. Gaines, Patrick J. Brennwald, Rebekah L. Layton
Matthew A.T. Elliott, Hunter E. Schweiger, Ash Robbins, Samira Vera-Choqqueccota, Drew Ehrlich, Sebastian Hernandez, Kateryna Voitiuk, Jinghui Geng, Jess L. Sevetson, Yohei M. Rosen, Mircea Teodorescu, Nico O. Wagner, David Haussler, Mohammed A. Mostajo-Radji
I’m a trained PhD cell biologist (University of Alberta 2019), where I spent days and days locked in a dark closet taking confocal microscopy photos of fluorescently labelled organelles (my whole thesis was basically quantifying green and red dots).
Somehow, after a brief stint as a postdoc, I stumbled into entrepreneurship. I started a biotech company, called Future Fields. We utilize genetically engineered Drosophila (yes, fruit flies) to mass manufacture growth factors and other recombinant proteins for supporting the growth of stem cells. We’ve grown to 35 people in just over 3 years, commercialized our first few products, and have our own 20,000 sf facility in the heart of Edmonton, Canada.
Starting the lab in my basement in 2019. Back then it was just me in the lab.
Shortly after starting the company, I put the pipette down and hopped into the hot seat as CEO and what a wild ride it’s been. While I certainly miss being in the lab, I’m having a whole lot more fun learning how to operate a high growth business. Plus, I still get to talk science from time to time. And if I’m really getting sick of investor meetings, I can still go for a stroll through the lab and surround myself with really cool science.
Anyways. I wanted to share this because I wasn’t exposed to many alternative career paths in my academic journey and I wish I had been. Starting a biotech company has been insanely rewarding and fun and if I can inspire just 1 more scientist to take the leap into entrepreneurship, that’d make me happy.
The Future Fields team today!
If you wanna chat about anything biotech or entrepreneurship – hit me up! My email is matt@futurefields.io
Attending the Society for Developmental Biology (SDB) Annual Meeting this July for the first time, I was blown away by the wide variety of approaches and model organisms employed to unravel all the fascinating questions in developmental biology.
As a developmental biologist by training who has been working in science communication for the past few years, it’s hard for me not to notice a common theme throughout the conference — communication, be it researcher-facing or public-facing. Science communication comes in many shapes and forms, and this SDB meeting demonstrated the importance of communicating clearly and accurately to different audiences about the exciting research happening in a field that is close to all our hearts.
Celebrating early-career science communicators
The nature of a conference is talks, lots of them. How does one convey the essence of their research and condense years of work down to 15 minutes? The SDB meeting was full of engaging speakers from different career stages, but a standout was Bonnie Kircher, who took home the Best Postdoc Presentation Award. Bonnie captivated the audience with her talk about female reproductive organ anatomy in the brown anole.
Another award given out each year by the SDB is the Science Communication Award. This year’s award recipient is Kevin Thiessen, the person behind the popular Twitter account @ZebrafishRock. We interviewed Kevin back in 2021 to find out more about him and ZebrafishRock. In his award talk at the meeting, Kevin revealed the reason behind the name ‘ZebrafishRock’ (hint: not the musical genre, but the Zebrafish inner ear structure), introduced the information ZebrafishRock puts out, and stressed the significance of supporting model organism databases (a shoutout to ZFIN — read their ‘Featured resource’ post).
As the Community Manager of the Node, Kevin’s talk made me think about how the Node can learn from ZebrafishRock’s success in community building. Could we do more in terms of highlighting early-career researchers and their work? Any thoughts or suggestions welcome in the comments below!
If you are an early-career researcher interested in science communications, do check out SDB’s SciComm Internship program.
Becoming a better writer: #DevBiolWriteClub workshop
To complement the scientific talks, the meeting also featured a few workshops, including a ‘Communication Workshop’ led by John Wallingford (Professor at University of Texas at Austin) and Pamela Hines (former Senior Editor at Science Magazine).
Through highly interactive and engaging activities, John and Pam took the participants through the questions of ‘what’ and ‘how’ to write as a scientist and provided an abundance of practical tips to become a better writer. From the five rules of #DevBioWriteClub to book recommendations about science writing, most of what John said during the workshop can be found on the Node. Head over to John’s author page to see a list of his #DevBiolWriteClub posts.
As I’m writing this post, I’m very self-conscious about you, the reader, judging this piece of writing, but as John said, there’s no shortcut — it’s all about practise, practise, practise. Let’s get writing and start using the hashtag #DevBiolWriteClub!
SciComm is not just about writing
A wonderful feature at the SDB meeting was the lunchtime theme tables, which allowed people to connect and talk about topics ranging from mentoring, grant writing, to managing a scientific career with disability.
One of the theme tables was on the topic of ‘Communications as an alternative career’. The table facilitator was Ana Beiriger, a scientist and medical illustrator, who communicates science through graphic design, illustration, animation, and 3D modeling. The table included PhD students and postdocs interested in SciComm, as well as Marsha Lucas, the Publications and Communications Director of SDB. Throughout the hour, we discussed the different approaches and pathways to a SciComm career, and the pros and cons of freelancing versus working for a company. Watch out for a SciArt post about Ana on the Node soon, but in the meantime, check out other scientists making amazing SciArt work.
Ethical issues special symposium: talking to the public about our research
It’s all well and good that we talk about our exciting findings to fellow scientists, but scientific research does not exist in a silo. With technology advancing rapidly and guidelines changing accordingly, how do we convey our exciting research to the public without overhyping and allowing the story to spiral out of control in the news? How do we keep the public’s expectations realistic? How can we use our research to inform and influence policies?
These are among the many questions raised during the special symposium on ethical issues in developmental biology research. With research continuing to push the boundaries of what is possible, it is vital that scientists put more thought into communicating our research to different audiences. A few suggestions by the panel include providing more media training for scientists and working with mediators from trusted organisations such as science museums.
A summary of the talks and discussion from the panel, which included viewpoints from bioethics, medicine and basic science, can be found in this Twitter thread (click on link to expand the thread).
Important discussion now #2023SDB on the ethical issues surrounding human embryo and embryo model research.
At the end of her Conklin Medal award talk, Lila Solnica-Krezel stated, “we are all ambassadors for developmental biology.” Indeed, it is up to us to talk about our research responsibly and spread our excitement for this field to others.
To the developmental biology community, how do you approach talking about your research to different audiences? Do you know any developmental biologists who are doing great things in science communication?
Comment below!
Taken on a morning run along the Chicago lakefront, with a group of fellow conference attendees. Thanks for the company! (1 votes) Loading...
“When the first draft of the Human Genome Project was completed, I was thinking, “Oh great, we’re probably gonna now be able to cure cancer!” But of course, as soon as you get to a major scientific milestone, it just opens the door to another series of really exciting and enticing corridors“
Dr Cordelia Langford, Sanger Institute
In the latest episode of the Genetics Unzipped podcast, we’re going behind the scenes at the Sanger Institute with Cordelia Langford, Director of Scientific Operations, to find out what it takes to make Big Science happen, and hear the stories behind the sequencing.
Working in academia can be a wonderful experience, being surrounded by highly inspirational people, full of excitement for science and working together to unlock secrets of the natural world. However, as a work environment, it is not free from challenges and difficulties that many workplaces face. The high prevalence of bullying, harassment and abuses of power has recently been a topic of several articles1-3 which highlight the importance of addressing this issue, discussing it on a public forum and implementing real changes to the structure of our academic system with the goal of minimizing the tolerance for such behavior and the permissiveness of toxic environments. To address this important topic, we hosted a virtual seminar at the Center for Molecular and Cellular Bioengineering (CMCB) of the Technische Universität Dresden (TU Dresden) on the topic of “Bullying and harassment in academia – definitions, prevalence and consequences for our scientific community” on the 28.03.2023.
The first speaker was Dr. Petra Boynton (Twitter – @drpetra), a social psychologist who supports universities, charities, research organisations and government departments to undertake and use research in inclusive, accessible, ethical and safe ways, with a key focus on mental health and wellbeing. Her background is in International Health Services Research, and she has applied her work through working as an Agony Aunt (advice columnist) for print, broadcast and online publications. She discussed the reasons for the high incidence of bullying in academia and what bullying involves, as well as why it is wrongly assumed that it is difficult to record or measure the effects of such behaviours both on affected individuals as well as on research integrity and quality. An important point was made that anyone on any level of the University or Institute structure, be it students, administration, junior or even senior group leaders, can both be the victim or the perpetrator of bullying. Research shows that approximately 1/5 postgraduates and 1/3 academic staff record being bullied themselves and around 40% have witnessed bullying, and approximately 75% of staff are aware bullying is a problem in their university4. Interestingly, the internal poll of the participants in the virtual seminar showed similar numbers with 46% of respondents having witnessed bullying or harassment at the TU Dresden and 89% of respondents saying there is a general problem of bullying in academia (Figure 1).
As the poll indicated, many people could not exactly identify which behaviors fall into the categories of bullying (Figure 1). Dr. Boynton then proceeded to outline these in detail, for example verbal abuse, punishing trivial mistakes, humiliating, setting people up to fail, or intruding into people’s personal lives. Dr. Boynton then expanded on how victims can be affected by experiencing this, many of the aspects aligning with what many wrongly assume to be a “normal” part of doing a PhD – changes to mood and sleep patterns, loss of concentration, feeling muddled, reduced self-esteem, self-doubt, overworking, feeling hopeless. Additionally, bullying can lead to a reduced output caused by inability to focus, being more prone to making mistakes, being scared to take action or progress. Dr. Boynton then outlined the importance of self-care, but also the importance of taking action, including as a bystander.
We also discussed slides created by Anja Wiede who is the contact person of the Complaints Office in cases of harassment, discrimination and violence at the TU Dresden. This part of the session outlined the internal policies of the University, the regulations and guidelines that are in place as well as numerous counselling and support systems that the University offers in cases of bullying. Importantly, the TU Dresden Compliance Management System was introduced, which also includes the possibility to report incidents of scientific or personal misconduct anonymously. Although the system is relatively new and not fully integrated University-wide, it will in the future be a platform for building a trust-worthy tool for elucidating the legal foundations and TU Dresden regulations, prevention measures, reporting concerns and evaluation. Over 50% of respondents in the poll felt that bullying is taken seriously here at TU Dresden (Figure 1), which hopefully can be further improved by the implementation of these measures.
This meeting has been the first in hopefully a series of educational seminars and workshops that we will try to organise here at CMCB to lead the way in creating a professional environment where people feel respected, valued, and supported. Ultimately, an academic environment where mutual respect, good mentorship, professional conduct and healthy communication are prioritised will result not only in happier students and staff, but also more motivated scientists, higher research integrity and quality. I would recommend every university and scientific institute to organise this type of seminar and encourage all scientific staff (especially those in power – group leaders) to attend. Engage your local Equal Opportunity officers, Ombudspersons and Directors to discuss the availability of support measures as well as structures for compliance and official complaints. Here at TU Dresden, it was refreshing to see an academic institution actively implementing ways of tackling inappropriate behaviours and scientific misconduct and I look forward to seeing those in practice.
Figure 1: Zoom seminar poll with questions related to bullying and harassment experience in academia based on responses from 54 participants from the CMCB.
For more information on the topic please have a look at the following resources:
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 performin 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.
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:
Scientific images
Science-inspired art
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.
The 2021 BSDB virtual art exhibition (3 votes) Loading...
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.
The Sugimura Lab
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…
Browse through other ‘Lab meeting’ posts featuring developmental and stem cell biology labs around the world.
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