All the world’s a metabolic dance, and we are merely moving to the rhythm !

Emerging perspectives in metabolism

This week we will get to know insights from Dr. Eudald Pascual-Carreras, who is a postdoctoral researcher in the Multicellgenome lab at IBE Barcelona where he’s studying how metabolism regulates the cell cycle at the origin of animal multicellularity. Before joining IBE, he conducted postdoctoral work in the Steinmetz Group at the Michael Sars Centre, University of Bergen, Norway. Eudald has long been fascinated by how nutrient-dependent signaling influences stem cell proliferation and growth, approaching these questions using unique model systems like the planarian flatworms and the sea anemones. Keep reading to learn about his journey through the
world of metabolism—and why curiosity driven basic science remains at the heart of it all. Along the way, he’s embraced the value of mentorship, stayed motivated through scientific challenges, and remained rooted in a deep curiosity for basic biology. Discover his journey through metabolism and learn about the mindset that keeps him going. Give him a follow over twitter or bluesky and check out his work here .

What was your first introduction to the field of metabolism? What inspired you to specialize in metabolic studies using two incredibly unique systems – the planaria flatworms and the sea anemones ?

I can clearly remember my first introduction to metabolism during high school biology class. My teacher explained how glucose is broken down, the Krebs cycle, how ATP is generated. I was fascinated by the intricated biochemical pathways that sustain life. Later, in university, I took an animal physiology course that provided a broader biochemical perspective.
For my PhD, I decided to study planarians due to their remarkable body plasticity. These animals can regenerate and modulate their body size depending on the nutrient availability. Initially, my research focused on regeneration, and metabolism wasn’t my main area of interest. However, over time, my focus shifted toward understanding the regulation of animal growth. This eventually led me to pursue a postdoctoral position in a Nematostella lab, where I kept exploring how nutritional changes influence organismal growth.
Classic research organisms such as Drosophila, C. elegans and mice have a predetermined, fixed body size. In contrast, the unique organisms I study can grow and shrink throughout their lifetime, a trait common among many non-bilaterian animals, including sponges, corals, sea anemones and ctenophores. This suggests that body plasticity is likely ancestral to all animals. Studying these organisms has allowed me to explore fundamental questions about the evolution of animal growth, the mechanisms that regulate it and the intricate interplay between metabolism and genetics.   

What sparked your interest in exploring nutritional and metabolic aspects of animal development through the lens of cell cycle and cell fate? Your work intersects metabolism, development and evolution. How do you integrate these disciplines in your research, and what unique insights have emerged from this approach?

Planarians and Nematostella can rapidly adjust their body size in response to nutrient availability. In both cases, cell number drives organismal growth, making the regulation of cell proliferation a crucial factor. This sparked my interest in understanding the cellular and molecular mechanisms that enable these animals to adapt. Therefore, I began studying the cell cycle, which I consider a fundamental cornerstone of this process. I found it fascinating that a such a highly conserved process as cell cycle can exhibit remarkable plasticity – pausing or adjusting its duration to accommodate different nutrient conditions.
Trained as a developmental biologist, I became increasingly interested in evolutionary questions during my PhD. Deciphering how developmental processes have evolved has always been on my interest. Integrating a metabolic perspective into this field adds a new layer of complexity that has been overlooked in evolutionary developmental biology. I believe this perspective has the potential to reshape fundamental concepts in cell biology, physiology and developmental biology.

Can you briefly summarize how you’re using Nematostella to uncover unique mechanisms by which body plasticity responds to environmental inputs, particularly how stem or progenitor cell populations driving this plasticity adapt to nutritional cues?

Nematostella vectensis has emerged as a powerful research organism for studying body plasticity in response to environmental changes, including
nutrient availability and temperature. Nematostella polyps exhibit a remarkable resilience during starvation conditions, capable of surviving over 200 days without food. In Steinmetz lab, we observed that after
prolonged starvation, these animals can be refed and return to their original body size within two weeks.
Our research demonstrated that changes in cell
number and cell proliferation directly correlated with organismal growth (doi: 10.1242/dev.202926). This led us to ask a fundamental question: which cells
contribute to this remarkable organismal growth? At
the same time, the lab was also investigating the identification and characterization of a multipotent stem/progenitor population that contributes to both germline and somatic tissues (doi: 10.1038/s41467-024-52806-4). My project naturally evolved from these findings – I studied how this multipotent stem/progenitor population behaves under starvation and refeeding conditions. Essentially, my goal was to move from the organismal level to the cellular and molecular level, dissecting how this specific population adapts to the extreme nutritional shifts (doi: 10.1101/2025.02.27.640509).

Tell us about your work on nutritional control of cellular quiescence and how Nematostella  is a unique model to answer questions about nutrient dependent quiescence. Summarize your key findings on cell cycle dynamics, the signaling pathways involved, and how these insights differ from known mechanisms in yeast and mammals.

When we began studying how starvation affects this stem/progenitor population, we considered different hypotheses based on observation in planarians and Hydra. In these organisms, stem cell populations (neoblast for planarians and i-cells for Hydra) continue dividing even under starvation. However, in Nematostella, we observed that the stem/progenitor population exhibited a low division rate, suggesting that these cells might enter a state of cellular quiescence.
We then found differences in cell cycle phase distribution depending on the duration of the starvation. The longer the starvation period, the deeper the quiescent state these cells entered! This progressive deepening of quiescence following nutrient withdrawal had only been observed in yeast and cell culture models, never in an organismal level! What is fascinating is that after refeeding, these cells are primed to re-enter the cell cycle in short-term condition while the re-entry was delayed following prolonged starvation.
Our findings position Nematostella as a unique in vivo model to study nutrient-dependent quiescence, and all it requires is subjecting animals to different starvation durations. Surprisingly simple yet incredibly powerful!
Specifically, we have found that starvation induces a G1/G0 quiescence state. During short-term starvation, some cells remain cycling, and after refeeding, quiescent cells rapidly re-enter the cell cycle. However, after long term starvation, the majority of the cells have entered a deep quiescent state, and their cell cycle re-entry is delayed upon refeeding! While we are still investigating the molecular mechanisms underlying quiescence acquisition, we have identified that TOR signalling is essential for feeding-dependent cell cycle re-entry!

Tell us about the experimental challenges you encountered during this project?

This project was a major challenge from the start. I spent my first year establishing quantitative flow cytometry analysis in Nematostella. Since the stem/progenitor population is located deep with the tissue and cannot not be imaged directly, I quickly realized that understanding cell cycle dynamics would require a tightly controlled time course experiments. This meant meticulous planning, and of course, having the support of colleagues and undergrads was essential.
To optimize time course experiments, I decided to try something slightly different. From T0 to 12 hours post feeding (hpf), I could sample continuously, which meant spending at least 14 hours in the lab. However, for the later time points (15, 18 and 21 hpf), instead of staying up all night, I strategically delayed the last feeding 3, 6 or 9 hours, allowing me to collect the samples the following morning. Naturally, I ensured that this adjustment had no circadian effects.
This approach not only made the experiment more manageable but also allowed me to generate high-resolution temporal data without requiring overnight shifts. Though long hours were certainly still part of the process!

Before this, you worked on planaria and identified a novel gene family – blitzschnell, which coordinates cell proliferation and differentiation in response to nutritional availability. Please tell us about your exciting findings.  

This was a truly unique project. Characterizing the function of a novel gene family came with significant challenges, as we had no reference to guide our understanding of the phenotype. It took time to piece everything together, but our findings were exciting!
One of our key discoveries was that the transcription of this gene family, blitzschnell, is directly regulated by nutrient intake! Moreover, its function is critical for controlling the cell number by balancing cell proliferation and cell death. In planarians, this regulation may be linked to the requirement for continuous and rapid modulation of cell numbers in response to nutrient availability (doi: 10.1242/dev.184044)

How do you think the fields of studying evolution and metabolism overlap? How do the two model systems you worked with differ in terms of nutrient-dependent regulation ?

Evolution and metabolism are deeply intertwined! Nutritional regulation is likely one of the most ancient evolutionary mechanisms. In unicellular eukaryotes, one of the earliest forms of cellular regulation is nutrient-dependent division: cells divide when food is available, and halt division when it is scarce. In multicellular organisms, this regulation has become more complex due to cell type and tissue specialization, certain tissues sense the nutrients and signal other cells to divide.
While nutrient-dependent growth regulation has been well studied in some animal tissues and cell cultures, we still lack a broader understanding from an organismal perspective. Using planarians and Nematostella as models, we can explore how stem cell populations that drive organismal growth respond to nutritional cues. One of the key differences we have observed is that in Nematostella, stem cells enter a quiescent state during starvation, whereas in planarians, this is less clear. Neoblasts continue proliferating even in the absence of food. The cell cycle dynamics of neoblasts during starvation remain poorly understood, with some results suggesting that starvation prolongs the G2 phase, allowing some neoblast to re-enter the cycle upon refeeding. However, this has not been definitively proven.
To gain a more comprehensive understanding of how nutrient-dependent regulation evolved, more organisms with body plasticity, such as ctenophores, Ciona, and sponges, should be studied. These models could provide crucial insights into the cellular mechanisms underlying metabolic control of animal growth.

How have different animals evolved to respond to nutritional and metabolic stresses? TOR signaling is conserved from yeast to humans, but are there organism specific differences in which the pathway is utilised ?

Yes, the signalling pathways are highly conserved across species. TOR signalling is required for organismal growth and cell proliferation in both Nematostella and planarians. What is particularly interesting is how these different animals utilize the same conserved pathway in distinct ways. While both rely on TOR signalling, they employ different strategies to cope with nutrient availability. As I mentioned earlier, Nematostella stem cells enter a quiescent state during starvation, while planarian neoblasts continue proliferating, even under nutrient-deprived conditions. Despite these differences, both organisms use the same fundamental molecular toolkit, illustrating the remarkable versatility of conserved signalling mechanisms across evolution.

What role does curiosity play in your life, both within and outside of science? How important it is for you to answer basic science questions on metabolic signaling and how do you see its impact on human health/relevance ?

Curiosity is at the core of my scientific journey. I am deeply interested in basic science, particularly in understanding how developmental processes are regulated, how cells integrate surrounding signals, and how the metabolome interacts with the transcriptome and signalling pathways. These fundamental questions drive my research, as uncovering mechanisms not only expands our knowledge of biology but also lays the groundwork for better understanding of human biology and health.
Although my research is not explicitly focused on human biology, I believe that the questions I explore have significant implications for human health. Fundamental discoveries in model organisms often provide insights into conserved biological processes, ultimately influencing biomedical research and our understanding of disease mechanisms.

What are your upcoming plans? What metabolic pathways or signals you aim to investigate further to understand their role in stem cell regulation?

The Steinmetz group at the Michael Sars Center (UiB, Bergen, Norway), where I conducted my postdoc, remains deeply interested in studying the metabolic regulation of this stem/progenitor cell population. Our ongoing work aims to uncover the transcriptomic and epigenetic changes these cells can undergo in response to nutritional shifts. Additionally, the group is exploring metabolic changes at the organismal level.
Personally, I am about to start a new postdoctoral position, where I will investigate the metabolic regulation of the cell cycle in the context of the transition of animal multicellularity. As mentioned, nutritional regulation is likely one of the most ancient evolutionary mechanisms. I plan to leverage a facultative multicellular organism, whose life cycle includes distinct unicellular and multicellular stages. I am particularly curious to understand how metabolism influences multicellularity transition, whether nutritional gradients are generate within cell aggregates and whether shifts in metabolic state serve as prerequisites for multicellularity.

What changes have you seen in the scientific community in regard to studying these unique aspects of metabolic signaling in unconventional systems? How do you think scientific paradigms around gaining new insights from non-model organisms will evolve in the coming decades? Are we moving toward a more nuanced understanding, or do you see potential pitfalls?

The scientific community is increasingly recognizing that non-classic research organisms can provide valuable insights into the more fundamental questions. As a developmental biologist, I am well aware of the critical role that non-classic research organisms have played in advancing our understanding of core processes. For example, the discovery of cyclins in sea urchins. Similarly, I believe that studying unconventional model can unveil new and extraordinary metabolic processes that may have previously been thought to exist only in unicellular eukaryotes.
Moreover, one aspect that has often been overlooked in recent years is the metabolic state of organisms when designing experiments. As we gather more data, it will become increasingly important for each scientific community to establish standardized protocols to improve reproducibility and ensure more meaningful interpretations of results. By integrating a more nuanced understanding of metabolic context, we can refine experimental approaches and uncover deeper insights into the fundamental principles of biology.

How do you see the future of metabolism evolve with the new upcoming techniques  – what are you most excited about ?

I would love to establish metabolic sensing lines, as my work over the past few years primarily relied on fixed tissue, making it challenging to assess the dynamic nature of metabolic processes. Having live metabolic sensor lines would be a game-changer, allowing us to directly observe and analyze the metabolic state of a cell under the microscope in real time! Additionally, I believe it is crucial to move beyond relying solely on metabolomics. While metabolomic profiling provides valuable insights, integrating real-time metabolic imaging with other approaches will offer a more comprehensive understanding of cellular metabolism and its regulation. These advancements will open new avenues for studying metabolism in a more dynamic and physiologically relevant context.

Were there any pivotal moments that shaped your career path? What’s an unexpected place you’ve found inspiration for your work?

I don’t think I’ve had a single pivotal moment that shaped my career. Instead, I see my scientific journey as continuous progression. However, one thing I am certain of is that having good professors and mentors was essential in building my scientific confidence, which, in itself, is crucial for a successful career. Equally important is making time to disconnect and relax. Some of my ideas have come not while working in the lab, but while running, hiking, spending time with my family, or even having a beer with friends, often in moments when I wasn’t thinking about science at all. Stepping away from research can provide the mental space needed for creative problem-solving.

What advice would you offer to students and early career scientists interested in exploring the intersections of nutrition/metabolism and cell fate decisions ?

For early-career scientists interested in exploring the intersections of nutrition, metabolism, and cell fate, my advice would be to choose an organism with a significant body or developmental plasticity. These are the most fascinating systems, and there is still so much to learn from them!

How do you maintain a balance between your rigorous research activities and personal life? Are there hobbies or practices you find particularly rejuvenating?

Finding balance isn’t easy, and I’ve learned mostly through trial and error. I try to be as focused and productive as possible while I’m in the lab, but once I leave, I make a conscious effort to disconnect. That doesn’t mean I never check an email or skim through a paper in the evenings, but I don’t make it a habit. Setting boundaries has helped me maintain a healthier work-life balance.
I also make time to run at least once a week. It’s a great way to clear my mind, organize my thoughts, and stay active. At the end of the day, having a fulfilling life outside of academia is essential for me. It keeps me motivated and ultimately makes me a better scientist.

If you hadn’t embarked on a career in biological research, what other profession might you have pursued, and why?

I would be a high school science teacher. Over the past few years, I’ve had the opportunity to teach both high school and undergraduate students, and I’ve genuinely enjoyed the experience. Teaching allows me to share my passion for science while inspiring the next generation of students.
I also had an incredible high school biology teacher who played a significant role in shaping my path. His enthusiasm and teaching style sparked my interest in biology, and I wouldn’t be where I am today without that influence.

(No Ratings Yet)
Loading...

Emerging perspectives in metabolism

#MetabolismMondays begin on April 28^th 2025.

From the flicker of a dividing cell to the sweeping arc of evolutionary adaptation, metabolism drives cell behavior and shapes organismal function — choreographing life at every scale. Metabolism is no longer confined to textbook pathways of energy production, today it takes a center stage in driving decisions of cell fate, growth, development, immunity, adaptation and evolution. It is an exciting time to study metabolism, as the field is wide open — metabolic signals are now recognized for their capacity to drive gene regulatory networks, enabling organisms to adapt and survive across different environments. This dynamic interplay offers new opportunities to explore the mechanisms that sustain life in ways previously unimagined.

A field is shaped as much by its discoveries, as by the early career scientists who ask new questions and chart innovative directions. In this new #MetabolismMondays series, we highlight early career scientists including graduate students, postdocs, and new faculty — who are pioneering metabolism research. Through a series of interviews, they share what drew them to metabolism, they reflect not only on their work, but also on the personal and professional moments that shaped their paths, and what continues to excite them into future. Their insights not only illuminate the vibrant energy of this scientific community but also reflect how metabolism, in all its complexity, continues to surprise and inspire.

In #MetabolismMondays, alongside their research, we aim to personify their scientific journey — capturing their perspectives on curiosity, unexpected sources of inspiration, work-life integration, and moments of growth that shaped their path as scientists. They also shed light on the importance of basic science in uncovering metabolism’s role in both animal and human health. The early career scientists featured in this series work across a remarkable range of model systems — including fruit flies, zebrafish, planarians, sea anemones, butterflies, mosquitoes, cavefish, mice, mammals, human organoids, and cell culture. Each model offers distinct advantages for probing key questions in metabolism. In this series, we will explore topics ranging from cell fate, growth, and patterning, to toxicology, seasonal rhythms, host-pathogen interactions, and the evolutionary impact of habitat change. Their work highlights how studying metabolism in diverse organisms and systems can reveal fresh insights not only into fundamental biological and evolutionary processes, but also in disease occurrence and progression.

As an emerging field, metabolism research is being shaped in real time — by new tools, interdisciplinary approaches, and bold ideas. From studying unconventional model systems to challenging long-standing scientific paradigms, these early career voices offer a fresh lens on where metabolism is headed — and why it resonates across different disciplines within biology.

Get ready to learn — and to become part of these unique journeys, discovery and purpose unfold together, shaping new directions in the field of metabolism. Tune in every Monday morning to begin your week with #MetabolismMondays.

Week 1: If you are interested in how nutrient dependent signaling shapes cell fate decisions and developmental plasticity — or fascinated by aquatic organisms like sea anemones and planarians — this article is for you!
Of Tor and Tide (Eudald Pascual-Carreras)

(No Ratings Yet)
Loading...

After two fulfilling years working at the Node and Development, I have decided to move on and embark on a new adventure. That means, my job is up for grabs! I’ll probably write a more personal reflection closer to my leaving day in mid-July, but for now, I’d like to briefly talk about what this role entails and hopefully persuade some of you to apply!

If you’re interested in science communication and would like to help contribute to the developmental and stem cell biology community in a unique way, this role might be a good fit for you! You’ll still be very much in touch with the scientific community, even if you’ll no longer be running experiments. If you know anyone who might be interested, do share this opportunity with them.

Below are my main tasks:

Running the Node

• Commission content: behind the paper stories, interviews, meeting reports, discussions, perspectives… anything you think the community will be interested in reading about
• Provide editorial feedback on drafts from researchers
• Write and produce your own content
• Manage the Node’s social media channels: Bluesky, X, LinkedIn, Facebook
• Maintain and develop the site: make sure the site is up-to-date, provide user support, and steer the development of the site (we are turning 15 this year and as the online environment continues to evolve, there are always opportunities to try out new things)

Working as part of the ‘Community Managers’ team

• Collaborate with the two other community managers of preLights and FocalPlane: we share tips on running our sites, bounce ideas and co-organise webinars and workshops
• Provide cover and support

Working as part of the Development team

• Write Research Highlights: usually once a week
• Conduct interviews: ‘people behind the papers interviews’, longer single-person features of scientists from a variety of career stages
• Manage the journal’s social media channels: Bluesky, X, Facebook, Instagram
• Help out with the Development presents… webinars: promotion, video editing of the recordings
• Write press releases

Attending conferences

• Go to meetings and conferences, both within the UK and abroad, mostly society/community-based meetings: represent the Node/Development, promote our work, network with people, learn about the latest science

Check out the full job advert:

https://www.biologists.com/about-us/work-for-us/

For any informal enquiries, you can get in touch with me (joyce.yu@biologists.com) or with Alex Eve (alex.eve@biologists.com).

(No Ratings Yet)
Loading...

Where is the lab?

In Edinburgh, Scotland, UK: the lab itself is about 5 minutes’ walk from Edinburgh’s historic Royal Mile.

https://discovery-brain-sciences.ed.ac.uk/our-staff/research-groups/jamie-davies

Research summary

Jamie: A bit of a mad mixture. The lab has always worked on organogenesis and self-organization in development, at the bench and at the computer. For around 20 years, we have combined natural development with tissue engineering, with a special interest in 3Rs applications as well as eventual clinical use. We were among the founders of the now burgeoning field of synthetic morphogenesis (our first publication, 2008). Many in the lab want to use it to make useful living materials; the PI has an interest in using synthetic biology ‘re-creating’ developmental mechanisms that we think we understand, in a very simple form, to check that we really do understand them (a bit like testing understanding of aerodynamics by making a paper ‘plane’). We began this by making synthetic patterning systems, and then added creation of shape. The next step is engineering agency and purpose. In addition to this, and almost by accident, we have a strong interest in pharmacoinformatics and run the global drug database for IUPHAR, the International Union of Basic and Clinical Pharmacology, and the antibiotic database for the Global Antibiotic Research and Development Partnership. Sadly, the IUPHAR meetings, which I have to attend, almost always clash with the BSDB spring conference.

Roll call (in order of length of time in the lab):

The lab gremlin, in the lab from time immemorial; spends its time corroding electrical connections, moving critical antibodies to the wrong fridge, and emptying CO₂ cylinders overnight. Like magnetism, it is invisible but we know it to be present by its observable effects.

Jamie Davies, Professor and anyone’s-technician-in-a-crisis (the jobs go together); now grey-haired enough to have made most of the mistakes people make in research, so is able to help young scientists avoid them and instead discover new and exciting mistakes of their own.

Jane Armstrong, Senior Curator, who joined as a wet-lab post-doc over 25 years ago and later discovered the joy of informatics.

Simon Harding, Senior Developer, a molecular biology post-doc turned software wrangler, with the group for over a decade now.

Elena Faccenda, Curator, a pharmacology post-doc turned informatician, also in the group for more than a decade. As well as managing the database, Elena, Simon and Jane write high-profile papers together, and have each acquired h-indices higher than many full professors.

Rhiannon Beadman, a post-doc working on homeorhesis and error-correction in organ development, uses a mix of classic 1920s-style cut-and-paste embryology and up-to-date molecular techniques.

Hüseyin Gül, a PhD student of this lab turned post-doc; works on a new drug target he identified for polycystic kidney disease.

Natalia Penar, a PhD student; combines optogenetics and morphogenetic control to test hypotheses about symmetry-breaking in branching morphogenesis.

Sneha Ravi, a PhD student; uses our new patented biofabrication technique to engineer ureters and similar tubular tissues.

Louise Goossens, a PhD student who will use Sneha’s ureters to model bacteria-tissue interactions, and how they affect antibiotic resistance, in urinary tract infections.

Nick Younger, a post-doc just joining us to work on optogenetics and axioloids.

Wentong Fu, an MSc project student working on dynamics of pattern coarsening following wounding of a synthetic patterning system.

Favourite technique

Jamie: Reading developmental literature from a century or more ago; researchers then did not have our fancy tools, but they had observation, insight and imagination and their work is an unfailing source of inspiration.

Outside your own work, what are you most excited about in developmental or stem cell biology?

Jamie: Evo-devo generally. I have never worked in this area, but seeing links develop between understanding of developmental opportunities and constraints, and the areas of morphospace visited and avoided over phylogenetic evolution, is amazing and is a ‘new’ new synthesis.

How do you manage your group and your various tasks?

Jamie: I ‘manage’ with as light a touch as possible. If you give bright young people the right encouragement, they will ask interesting questions and do interesting things, many of which I would never have imagined. In recruitment, I value diversity, not just in terms of ethnicity, gender and religion, but also in terms of academic culture; my lab has included people with first degrees in philosophy, anthropology, mathematics, and engineering as well as in biological subjects, and has benefited from the different ways of thinking they bring. As for managing my own tasks, the golden rule is not to procrastinate, and to reserve time just to think; I mean actually reserve it in a calendar, with the same non-negotiability as one marks out a timetabled lecture or conference. Thinking is part of a scientist’s job, and it is entirely reasonable to demand time in which it can be done.

What’s the best thing about where you work?

Answers given by members of the lab in general include:
“I like how everyone in the building helps each other….  I love my daily commute to work through the Meadows.”
“It’s a space where complex problems turn into exciting challenges that motivate me to learn, experiment and grow. It’s a mix of curiosity, teamwork, and the occasional lab triumph—it’s never dull!”
“The people! As a biocurator and office-based scientist, it is great to still be part of an academic research laboratory, especially one that is so supportive. Being based on a campus right in the heart of Edinburgh is pretty special as well.”
“The lab is friendly and supportive — and seems to benefit from lots of different experiences.”
“I enjoy the intellectual stimulation that researching for the Guide to Pharmacology brings. A huge bonus is working with competent and friendly colleagues who help you through the days when things aren’t quite going to plan.”
“The best part about working here is the friendly and supportive lab environment, where you can always count on others and never feel like you are asking too much.”
“The best thing is friendly atmosphere and cooperation in our lab. It makes dealing with setbacks easier, celebrating successes even more pleasant, and keeps us motivated.”
“The people—everyone is approachable, motivated, and genuinely passionate about their work”.

What’s there to do outside the lab?

Answers given by members of the lab in general include:
“Dancing! Edinburgh has a vibrant community for various dancing styles (my pick is Latin dances). It’s amazing for meeting new friends and staying healthy.”
“I like to go for walks in the Pentland Hills followed by a well-deserved beer in one of the many pubs.”
“The Meadows is a great spot to unwind and soak in some greenery or a hike up Arthur’s seat offers stunning views of the city. Plus, the area is filled with great eateries, making it easy to grab a bite between experiments”
“The Scottish Highlands and Islands are all within a half-day of travel. Fantastic if you enjoy epic scenery and being outdoors.”
“Being based in the centre of Edinburgh is great – there’s usually lots going on, especially during the festival. Lots of nice green spaces close by is another positive.”
“There is no shortage of historical, cultural, sporting, entertainment and foody places and events to explore in the heart of Scotland’s capital city. What makes it really special is that beaches, hills and the great outdoors are within very easy reach, whether you’re a thrill seeker or just want to chill.”
“I love exploring Scotland, with its endless hikes and breathtaking scenery, though it is most enjoyable on the rare occasion when the weather is not cold and wet!”
“The best place to go if you find yourself outside the lab is back inside the lab again!”
 

Lab Blog
Waiting for the cells to grow.

(1 votes)
Loading...

The Node is turning 15 this year. If you’ve ever visited the Node to read, write and interact with the global developmental and stem cell biology community – thank you for your support!

We would really appreciate any feedback you have about the Node, to make sure the community site is still relevant and useful for you, our community members.

Please spare around 5 minutes to fill in our survey.

Thank you!

Joyce
Community Manager of the Node

(No Ratings Yet)
Loading...

Where is the lab?

Li-Kun: My lab is located in Kobe, Japan. My lab initially belonged to RIKEN Center for Developmental Biology, which subsequently reformed to become the RIKEN Center for Biosystems Dynamics Research.

Lab website: https://www.bdr.riken.jp/en/research/labs/phng-lk/index.html

Research summary

Li-Kun: My lab aims to understand how blood vessels are built and shaped into a hierarchical tubular network of arteries, veins and capillaries of optimal connections and size. We are particularly interested in endothelial cell mechanobiology – how physical forces and mechanical properties govern their shapes and behaviours to drive distinct steps of vessel morphogenesis, from sprouting angiogenesis to vessel remodelling. We are also keen to elucidate the interplay between endothelial cells and the perivascular environment such as haemodynamic forces (shear stress and pressure) at the apical surface and mural cells on the abluminal surface. In the long term, we aim to uncover whether altered endothelial cell mechanobiology contributes to endothelial dysfunction and vascular anamolies. To address these questions, we employ a spectrum of methodologies such as zebrafish genetics, high resolution time-lapse confocal microscopy, optogenetics, pharmacology, quantitative image analyses, scRNA sequencing and mathematical modelling.

Lab roll call

Li-Kun Phng: We are an internationally diverse lab, and the current lab members are listed from oldest to newest here.

Emi Taniguchi: I have been a lab assistant since 2016. I am doing administrative work and zebrafish system care in the lab. Also, I check the condition of our zebrafish daily to keep them healthy.

Igor Kondrychyn: I am a Research Scientist and am currently working on a project investigating the role of aquaporins in embryonic hematopoiesis.

Yan Chen: I am a postdoctoral researcher investigating vascular remodelling during zebrafish development, with a focus on how endothelial cells regulate vessel size and structure. My research explores how endothelial cells undergo rearrangement and shape changes, particularly through actin-driven constriction, to fine-tune vessel dimensions. Using zebrafish models, molecular genetics, and live imaging, I aim to uncover the cellular mechanisms underlying vascular remodelling.

Haymar Wint: I am a postdoctoral researcher, and my research interest lies in investigating the role of microtubules in mediating endothelial cell responses to fluid shear stress, unveiling its role in vascular development and remodeling.

Mingzhao Hu: I am a PhD student enrolled at the Department of Biological Sciences at Osaka University. I am interested in understanding how mural cells impact vascular remodeling using genetics and high-resolution time-lapse imaging.

Jason da Silva: I am a research technician. I carry out general lab duties and am working on creating knock-in zebrafish lines.

Rajrishi Kumar: As a technical staff member in the lab, I contribute to research on developmental biology and vascular morphogenesis, with a focus on sprouting angiogenesis and mechanobiology using zebrafish as a model organism. My work involves maintaining zebrafish lines, performing genotyping, and assisting with experiments that dive into the molecular and biophysical aspects of blood vessel formation. Along the way, my science toolbelt’s been getting a glow up with hands-on experience in genetic manipulation, molecular biology, and advanced imaging techniques.

Favourite technique, and why?

Li-Kun: Undoubtedly light microscopy – the higher the resolution the better – as it allows us to peer into the dynamics of vascular cell behaviour, enabling us to understand the process of vessel morphogenesis.

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

Li-Kun: I am presently fascinated with the growing prominence of ion channels, osmotic gradient and hydrostatic pressure in regulating tissue morphogenesis.

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

Li-Kun: My job entails juggling research, administrative work and some teaching. It was a steep learning curve starting my lab in Japan without knowing the language. Thankfully, I am lucky to have a very capable assistant who helps me deal with work-related matters in Japanese within and outside the institute, allowing me to focus on the science. A major goal is to provide a good research environment (in terms of infrastructure and opportunities) that is conducive to scientific excellence and efficiency. I firmly believe that communication is crucial not only in keeping up-to-date with scientific progress and shaping research direction, but also in identifying and tackling problems (be it scientific or personal) that surface. As such, I meet researchers every two weeks, encourage open communication in our weekly lab meetings and foster team spirit over meals and lab outings.  I also like to enliven the lab atmosphere by hosting visitors from abroad, which at the same time promotes exchange of ideas and technology as well as fostering collaborations. Another important aspect of my job is to ensure that we stay abreast with current developments in our field and to disseminate our work to the scientific community. In Japan, the JSPS-funded ‘Mechanical Self-transformation of Living Systems’ consortium (https://multicellular-mechanics.org/research) has been a vital platform for networking with scientists in the fields of biomedical sciences, engineering and physics. Beyond Japan, I attend internationally conferences and meetings but this is limited by family commitments. The plus side is that I spend more time with my lab members to develop and complete projects!

What is the best thing about where you work?  

LKP: Core funding from RIKEN! And being able to pursue curiosity-driven research.

EM: I enjoy working in multi-cultural environment with the members come from different countries. So far, I have met the lab members from 15 different countries.

IK: Friendly atmosphere.

YC: One of the best aspects of working in our lab is the supportive and collaborative environment. Communication flows easily within our team and across research groups. We also have access to an excellent microscopy facility, where the friendly staff provide invaluable support. 

HW: One of the best things about working at RIKEN BDR is its highly international environment, where researchers from diverse countries come together to collaborate. And, our lab’s warm, supportive, and well-structured team environment accelerates scientific progress, and makes work both productive and enjoyable.

MH: I’m the only student in our lab, so that I often receive helpful suggestions and feedback from other members, who have full experience in this field.

JDS: Everyone is nice and the atmosphere is very relaxed. 

RK: The best part? The people and the place. Sure, RIKEN’s state-of-the-art facilities and cutting-edge instruments are great for high quality research, but it’s the environment and community that make it truly exceptional. From lab members to admin staff, everyone is incredibly friendly, communicative, and genuinely helpful. And then there’s our team leader, high energy, inspiring, and somehow always present when you need a hand, a nudge, or a fresh perspective. Oh, and bonus points for the stunning sea view from the lunch area. Yes, science with a seaside vibe!

What’s there to do outside of the lab?

LKP: I would typically like to recharge my batteries by not doing anything, but this, unfortunately, is not possible because I have two young ones at home to entertain. Kobe is sandwiched between the mountain and the sea, and so we often venture to the beach or forests to appreciate nature. In Spring, we enjoy hanami (cherry blossom viewing); in Autumn, momijigari (viewing of the vibrant autumn colours of maple leaves); in Winter, warming ourselves up by going to onsen (hot springs). And of course, we love trying out new cafes and restaurants.

EM:  I like to travel not only in Japan but also to other countries to learn about cultures and ideas created by each region that has original geographical and historical factors.

IK: Relaxing outdoors (if no rain), cycling and listening to music while drinking wine.

YC: Outside the lab, Japan offers a perfect blend of nature, culture, and city life. Depending on the season, I enjoy hiking in the nearby mountains, visiting historical temples and shrines, or exploring the diverse food options. There are also many festivals throughout the year, offering a chance to experience traditional culture. Within the lab, we often celebrate small victories, birthdays, and milestones with group dinners and relaxed afternoon tea gatherings.

HW: Outside the lab, I enjoy exploring Japan’s rich culture and natural beauty. I visit historical sites, experience seasonal festivals, and try different local foods. Sometimes, I join social gatherings with colleagues or participate in local events to experience Japanese traditions firsthand.

MH: Outside of the lab, we often have a food-themed adventure to explore the local food, from Ramen restaurant to open-air bar. I also spend time in nature to increase feelings of happiness and pay attention to the changing seasons. I really enjoy cherry blossom in spring and Momiji viewing in autumn!

JDS:  Kobe is close to the sea and to mountains so there are a lot of scenic places to visit. There are hundreds of restaurants to try around Kobe too. It’s also easy to visit other cities in Japan by public transport.

RK: I am new to the area, but outside of the lab I usually go for a run or play basketball. Here in Kobe, there are great cafes, cozy izakayas, and lively karaoke spots where we can relax after a long day. The city is also surrounded by mountains, offering plenty of hiking spots with scenic views of both the city and the ocean. And of course, we are in Japan, a hub for shopping and entertainment, so there is always something to do. Also, if you are feeling too adventurous, there are plenty of options for onsens to enjoy a hot spring experience.

(No Ratings Yet)
Loading...

The Company of Biologists is organising an essay competition entitled “Innovative Ideas for the Future of Sustainable Events”.

Participants are invited to write an essay of maximum 1000 words to details how your idea will change the way we organise scientific events and will open the door to a new concept of organising events more sustainably in the next 10 years.

Prizes:

1st place: £250

2nd place: £150

3rd place: £100

The winning essays will be selected by the Sustainability Committee and featured on The Company of Biologists’ website.

This is a fantastic opportunity for anyone passionate about sustainability and writing. For more details, please visit our post here.

If you have any questions, feel free to contact me at sustainability@biologists.com.

(No Ratings Yet)
Loading...

To accompany the Biologists @ 100 conference, we’ve partnered with FocalPlane to bring to you an image competition. We shortlisted 15 images and asked you to vote for your favourite online and in person at the conference. On the final day of the conference, we announced the top3 images of the competition.

In this ‘Featured image’ post, we find out more about the story behind Allan Carrillo-Baltodano’s image, which was one of the runners-up in the competition.

What is your background?

I did my undergrad at the University of Costa Rica, in Costa Rica. Early on, I biased my interests towards invertebrate zoology, and ended up doing an undergrad thesis on marine zooplankton of coral reefs. It was back then when I saw the beauty of marine invertebrate larvae. I have been studying evolution and development (EvoDevo) of marine invertebrates since — first, during my PhD in Néva Meyer’s lab at Clark University in Massachusetts (USA), and currently as a postdoc in Chema Martín-Durán’s lab at Queen Mary University of London in UK.

What are you currently working on?

I study how body plans of marine annelids develop, and try to understand how different modes of development in these and other animals could have evolved.

Can you tell us more about the story behind the image that you submitted to the image competition?

The image shows a larva of a phoronid worm. The larva is commonly known as actinotroch, and it is very conspicuous among other members of the zooplankton community because of the tentacles surrounding the head. To swim the larva propels itself using cilia (shown in the image in magenta) concentrated in a ciliary band on the posterior part of the larva. The big hoodie you see at the top will open slightly so that food can be captured in the mouth. One of the wonderful things of the plankton is that if you are lucky, you can find any stage of development of these and many other amazingly weird invertebrates.

What is your favourite technique?

I like mostly confocal microscopy, although if a sample is nice enough, you can get some very beautiful images with DIC microscopy as well.

What excites you the most in the field of developmental and stem cell biology?

The breakthrough in technologies has really opened the door for many of us who like to study development in unusual research organisms. In combination with the EvoDevo field being more open and the growing interest in comparative biology across many species and many scales, we are creating a great environment for anyone to make new discoveries.

(1 votes)
Loading...

Abstract submission to the Young Embryologist Network Conference closes this week on the 13^th April 2025. Please share!

This is a great opportunity for PhD students and postdocs working on differentiation, stem cells, embryonic development, IVF or organoids to present a short talk or a poster. YEN2025 will take places at the Francis Crick Institute on the 19^th May and is free to attend.

Register here: https://forms.gle/fxtmNHjEziVTFprN6

YEN 2025 Image Competition

Exiting news! We have revived our tradition of the YEN Image Competition. Please submit your science images and art by the 1st May 2025 and follow us to get updates on where to vote!

Check out our YEN2025 Image Competition: https://bsky.app/profile/yen-network.bsky.social/post/3lloc7ppldc2w

To learn more about the conference head to: https://thenode.biologists.com/yen-2025-conference-registration-is-open/

(No Ratings Yet)
Loading...

An easily-consumable recap of the latest happenings in the #zebrafish community!

Use these links below to get to the section you want:

Community news

Zebrafish careers

Publications

Preprints

Reviews

Protocols and tools

Link to Bluesky post: https://bsky.app/profile/zebrafishrock.bsky.social/post/3lmfpzcvve42s

Community News:

Dr. Brant Weinstein at NIH named a Fellow of the American Association for the Advancement of Science (AAAS). 

Prof. Robyn Tanguay at Oregon State University awarded the 2025 @sotoxicology.bsky.social‬ Leading Edge in Basic Science Award. 

PhDs awarded to:
Dr. Tom Rappol of Elisa Vilardo (@vilardoelisa.bsky.social‬) Lab. 

Dr. Phoebe Reynolds (@pheereynolds.bsky.social‬) of Robert Hindges Lab.

Do you have news or research that you want to add to the next digest? Use the submission form at our website:

https://linktr.ee/zebrafishrock

#ZebrafishCareers posted by: 

@benjhogan.bsky.social‬ 🇦🇺 (Group Leader)– Deadline: May 9

https://careers.petermac.org/job/MELBOURNE-Group-Leader-VIC-3000/1062003466

‬@dvalenzano.bsky.social‬ 🇩🇪 (Postdoc) #Killifish – Deadline: April 30

https://jobs.leibniz-fli.de/jobposting/a7a7e53e0d339c74d9c64d73dab1332087b57f935

@bensimonbrito.bsky.social‬ 🇫🇷 (Two Postdocs)– See Images Below

#KrishnanLab at OMRF 🇺🇸 (Postdoc) #Cavefish

https://omrf.org/about-omrf/human-resources/?jobId=C13CA7EA-2C1B-4BBC-9EEA-818D866D8FEC

@rashmi-priya.bsky.social‬ 🇬🇧 (Postdoc)– Deadline: April 29

https://crick.wd3.myworkdayjobs.com/External/job/London/Postdoctoral-Fellow_R1957-1

‪@seiliez.bsky.social‬ 🇫🇷 (PhD)

https://jobs.inrae.fr/en/ot-25516

@nakamuralab.bsky.social‬ 🇺🇸 (Technician/ Fish Specialist)– Contact directly:

https://nakamuralab.com/

Publications:

Regeneration

#JianlongMaLab (Liver regeneration/ Transdifferentiation/ Sam68) 

10.1242/dev.204266

‪@rmarinjuez.bsky.social‬ (Heart regeneration/ Macrophages/ Gpnmb)

10.1016/j.ydbio.2025.02.011

Disease Models

#DowlingLab @sickkidsvs.bsky.social (Charcot-Marie-Tooth type 4B3/ MTMR5/ Disease model) 

10.1093/braincomms/fcaf077

Metabolism

@mennigenlab.bsky.social (Methylene blue/ Development/ Metabolism)

10.1038/s42003-025-07471-8

Embryogenesis

@heisenbergcplab.bsky.social @stetavano.bsky.social‬ (Cell migration/ BMP/ Lateral mesendoderm) 

10.1016/j.celrep.2025.115387

Toxicity

‪@alliancegenome.bsky.social‬ (ZFIN/ Toxicology data/ Gene-chemical interactions)

10.1093/genetics/iyaf021

#KaiserLab ‪@ceitec.eu‬ (Microplastics/ Tomography/ MicroCT)

10.1016/j.jhazmat.2025.137442

Transcriptomics

@mvargam.bsky.social‬ (snoRNAs/ Zebrafish snoRNAome/ Sequencing) 

10.1093/nargab/lqaf013

@immler.bsky.social @alicegodden.bsky.social (Sperm sRNAs/ Transposable elements)

10.1038/s41437-025-00752-2

Neuroscience

@bruceappel.bsky.social‬ @aineurolab.bsky.social‬ (Amyloid-β/ Brain aging/ Neurodegeneration)

10.1002/glia.70015

#MonkLab @volluminstitute.bsky.social (Schwann cells/ Rac1/ Myelin maintenance)

10.1083/jcb.202311041

@juliesemmelhack.bsky.social‬ (Visual stimulus/ Fear response/ Tectum) 

10.1073/pnas.2416215122

@grzoidl.bsky.social‬ (Pannexin-2/ Ocular defects/ Visual Perception)

10.1016/j.bbadis.2025.167807

Behavior

@mishaahrens.bsky.social (Predator recognition/ Learning/ Noradrenergic circuits)

10.1016/j.cub.2024.11.057

‪@ctudorache.bsky.social‬ (Coping styles/ Risk taking/ Heritability)

10.1186/s12868-025-00944-w

Physiology

@pcraig77.bsky.social‬ (Ectotherms/ Thermal agitation temperature/ Thermal tolerance)

10.1016/j.jtherbio.2025.104094

Vasculature

@sarahdv.bsky.social (Arterial endothelium/ Transcriptional regulators) 

https://elifesciences.org/articles/102440

Cell biology

@dparichy.bsky.social‬ (Chromatophores/ MITF/ Xanthophores)

10.1111/pcmr.70009

Evolution

#SalzburgerLab @unibas.ch @charlottehuyghe.bsky.social‬ (Metagenomics/ Dietary Diversity/ Adaptive Radiation)

10.1111/mec.17743

#Preprints:

Inflammation/Infection

#SharptonLab @oregonstate.edu @gutmichaelbio.me (Gut microbiome/ Infection/ Parasites) 

https://www.biorxiv.org/content/10.1101/2025.03.28.644597

#MadiganLab @ucsandiego.bsky.social (Tuberculosis Meningitis/ Vascular pathology)

https://www.biorxiv.org/content/10.1101/2025.02.28.640927

Neuroscience

@mishaahrens.bsky.social (Gut interoception/ Whole-brain neuronal imaging) 

https://www.biorxiv.org/content/10.1101/2025.03.26.645305

@sthyme.bsky.social (Trangene insertions/ Neurobehavior/ pIGLET) 

https://www.biorxiv.org/content/10.1101/2025.02.28.640904

#KucenasLab at UVA (Microglia/ Neuronal cell death/ Optic tectum) 

https://www.biorxiv.org/content/10.1101/2025.03.14.643334

@bahllab.bsky.social (Neural circuit structure/ Sensory accumulation) 

https://www.biorxiv.org/content/10.1101/2025.03.14.643363

@arrenberglab.bsky.social (Optokinetic Response/ Vestibulo-Ocular Reflex) 

https://www.biorxiv.org/content/10.1101/2025.03.21.644542

Embryogenesis/Organogenesis

‪@bertaverd.bsky.social‬ @jamesehammond.bsky.social (Somitogenesis/ Axial Skeleton/ Embryonic Development)

https://ecoevorxiv.org/repository/view/8740

@nicolettapetridou.bsky.social‬ @laura-rustarazo.bsky.social‬ (Phase Transitions/ Cell adhesion/ Morphogenesis)

https://www.biorxiv.org/content/10.1101/2025.03.18.644006

‪@zkrna.bsky.social‬ (Germline development/ Germ plasm dynamics) 

https://www.biorxiv.org/content/10.1101/2025.02.26.640298

@obog.bsky.social @anaburgos.bsky.social‬ (Spermatogenesis/ Multiomics/ Epigenetics)

https://www.biorxiv.org/content/10.1101/2025.03.12.642371

DNA elements/ structure

@mvargam.bsky.social‬ (Ichabod/ B-catenin 2/ Transposon insertion) 

https://www.biorxiv.org/content/10.1101/2025.02.28.640854

@smburgess.bsky.social (Meiotic checkpoints/ Chromosome synapsis) 

https://www.biorxiv.org/content/10.1101/2025.03.18.644038

Disease Models

#MadelaineLab @mdibiolab.bsky.social (Neuromuscular degeneration/ Atrogin-1) 

https://www.biorxiv.org/content/10.1101/2025.03.07.642048

#HaroldBurgessLab at NICHD (Timothy syndrome/ Arrhythmia/ Calcium channels)

https://www.biorxiv.org/content/10.1101/2025.03.11.642683

Regeneration/ Wound Healing

@jraslab.bsky.social @errricpeterman.bsky.social‬ (Cell migration/ Injury response/ Macrophages) 

https://www.biorxiv.org/content/10.1101/2025.03.13.642867

#DrummondLab @mdibiolab.bsky.social (Wnt signaling/ Kidney/ Regeneration)

https://www.biorxiv.org/content/10.1101/2025.03.26.645545

Tools

@erezraz.bsky.social (Light-induced protein translation control) 

https://www.biorxiv.org/content/10.1101/2025.02.17.638581

Physiology

@haesemeyerlab.bsky.social‬ (Thermoregulation/ Calcium imaging/ Markov models) 

https://www.biorxiv.org/content/10.1101/2025.03.17.643749

Cancer

@robertkelsh.bsky.social (lncRNAs/ Melanoma/ DANCR/ Gene regulation)

https://www.biorxiv.org/content/10.1101/2025.03.21.644561

Ageing

#TenaLab @cabd-upo-csic.bsky.social ‪@anaburgos.bsky.social‬ (Killifish/ scRNAseq/ Aging) 

https://www.biorxiv.org/content/10.1101/2025.03.24.645095

Special Topics

@aburger2009.bsky.social (Data Reporting/ Metadata/ AI)

https://osf.io/preprints/osf/kvn2x

Back to top

#Reviews:

@gbdownes.bsky.social‬ (Neurogenetic disorders/ FERRY Complex) 

10.1242/bio.061808

@bbparis1984.bsky.social‬ (Sexual dimorphism/ Brain/ Aging) 

10.1016/j.tig.2025.02.001

@mirimiam.bsky.social‬ @fedemantica.bsky.social (Gene duplication/ Splicing/ Evolution)

10.1002/bies.202400202

@lkremer1.bsky.social‬ (Drug discovery/ Non-tuberculous mycobacteria)

https://perspectivesinmedicine.cshlp.org/content/early/2025/03/27/cshperspect.a041832

@nvastenhouw.bsky.social‬ (Transcription bodies/ Gene expression) 

10.1042/BST20240599

#Protocols and Tools:

‪@mauramcgrail.bsky.social‬ (CRISPR knock-ins/ Cre drivers/ Hand2 lineage) 

10.1101/2024.12.04.626907

#YunYangLab (Cycling Gal4-UAS/ Endodermal cell tracing) 

10.1242/dev.204289

@crisprscan.bsky.social‬ (CRISPR-Cas13d optimization/ RNA targeting)

10.1101/2024.10.08.617220

@varshneylab.social‬ @sheng-jia.bsky.social (gRNA selection/ Phenotypic penetrance/ Neurodevelopmental disorders)

10.1093/nar/gkaf180

‪@jutfelt.bsky.social Version 2 Husmorph (Image Analysis/ Landmarking) 

https://github.com/HenHus/Husmorph

Special thanks to Maddie Ryan, Charli Corcoran & Michaela Noskova Fairley for putting this digest together! If you would like to thank the Zebrafish Rock! team for their time & effort, you can buy us a strong cuppa at the link below. Every little bit keeps us caffeinated and motivated! We appreciate your support 🙂

Link to buy the ZR! team a caffeinated beverage: https://buymeacoffee.com/zebrafishrock 

Fin!

(1 votes)
Loading...