In a new study, Joshua Gendron and colleagues find that plants can measure two different photoperiods to independently control seasonal flowering and growth, and the vegetative growth is partially dependent on the production of myo-inositol, a precursor required in many processes that control growth (1). First author Qingqing Wang takes us through the story behind the paper.

After earning my PhD in fish reproductive physiology from a laboratory in China, I ventured to the US and secured a postdoctoral position in the Gendron lab, initiating my journey into the field of botany. While transitioning from zoology to botany presented significant hurdles, my background in biology, which encompassed genes, molecules, and proteins, eased the process of assimilating knowledge into the botanical sphere. Fortunately, the steadfast support of my lab colleagues, along with Josh Gendron’s encouragement, fostered within me the belief that creativity and problem-solving acumen are indispensable in scientific research, igniting a fervent passion for botanical pursuits.

In our laboratory, we have elucidated a metabolic daylength measurement (MDLM) system that is crucial for regulating plant growth under short winter photoperiod conditions. Notably, the post-dusk induction of one gene, PHLOEM PROTEIN 2-A13 (PP2-A13), in short days is pivotal for sustaining plant growth in winter but not summer photoperiod (2). This led me to speculate about the existence of a contrasting pathway that is regulated by MDLM system controlling plant summer growth. My exploration of photoperiod-related literature primarily uncovered research focused on the CONSTANS- FLOWERING LOCUS T (CO-FT) module’s role in regulating flowering, leaving much unknown about other pathways controlling plants’ summer growth.

MIPS1 as a model to study photoperiod-controlled growth.

Delving into the RNA-seq database curated by Gendron lab (3), I meticulously examined gene expression profiles from RNA-seq, seeking candidates exhibiting heightened expression under summer long day conditions. Amidst the constraints of Covid-induced isolation, devoid of laboratory benchwork, I seized the opportunity to immerse myself in extensive literature reviews pertaining to each intriguing gene. I came across a gene called MYOINOSITOL-1-PHOSPHATE SYNTHASE 1 (MIPS1), which plays a pivotal role in myo-inositol biosynthesis. Myo-inositol is an essential sugar that governs various cellular processes crucial for growth regulation. Notably, MIPS1 displayed elevated expression under summer long-day photoperiods, and we discovered that its mutant counterpart, mips1, exhibited specific growth defects under summer long-day conditions but not winter short-day conditions, contrasting with the pp2-a13 mutant. We observed that MIPS1 has a long-day-specific growth effect, prompting us to investigate whether growth is photoperiod-controlled and how MIPS1 responds. To address this, I cultivated both wild type and mips1 mutant plants under critical photoperiod conditions and monitored their growth. As the daytime lengthened, wild type growth was minimal in photoperiods less than 12 hours light to 12 hours dark (12L:12D). However, in photoperiods of 12L:12D or longer, wild type growth accelerated significantly, while the mips1 mutant exhibited clear growth defects. Upon seeing these results, I was excited to share the findings with everyone. The two years of effort dedicated to growing plants under various conditions in the same growth chamber proved worthwhile. These results indicate that growth is indeed controlled by photoperiod and requires MIPS1.

Those findings prompted us to investigate the potential involvement of the CO-FT mechanism in regulating MIPS1 expression. Interestingly, genetic data indicated that MIPS1 expression is not controlled by the CO-FTpathway, which led us to wonder a pivotal question: What regulatory network governs MIPS1 expression, thereby determining plant summer growth rate? 

Parallel control by MDLM for MIPS1 required for long day rapid growth, and CO-FT for photoperiod flowering.

We employed a starch-less pgm mutant with a dysfunctional MDLM system to examine the regulatory effect of MDLM on MIPS1 expression. As expected, the photoperiodic expression of MIPS1 was absent in the pgm mutant, confirming our hypothesis that MDLM system regulates MIPS1 expression. Then I think about how to design an experiment to decouple photoperiodic growth and photoperiodic flowering. Exposing the plant to low light intensity, nearing the compensation point where photosynthesis equals respiration, could exhaust starch and sucrose reserves and therefore impeding MDLM but not CO-FT system. I grew plants in low light intensity condition and found that the mips1 mutant phenotype disappeared, while flowering time remained consistent with long-day conditions, which is making us exciting. This sustained our model that MDLM regulates plant growth in parallel to CO-FT regulated flowering. To further test this model, I propose a classic experiment akin to the “night break” experiments used to test photoperiodic flowering. In “night break” flowering experiments, long day plant flowers in long day but not short day photoperiod. However, introducing short pulses of light during the night in short-day conditions promotes flowering. Similarly, to assess whether photoperiod regulates rapid growth, we propose dividing the daytime in long-day conditions into two segments: one exposed to high light intensity and the other to low intensity. We found that the mips1 mutant phenotype would manifest in the segment under intense light, while the wild-type size would exceed that of the segment under light exposure during the initial portion. Moreover, flowering timing in both scenarios would mirror that of long-day conditions. This suggests that plants can discern an absolute photoperiod using low light-sensing photoreceptor mechanisms to regulate flowering time. Concurrently, they can gauge the photosynthetic duration as a metabolic day length to govern growth.

In the end…

This journey has taught me that in scientific research, one must be passionate, diligent, possess problem-solving skills, embrace teamwork, and be willing to challenge and follow classic principles. This model has filled and expanded our understanding of plant regulation by photoperiod, which extends beyond just flowering time; there are many other processes for photoperiodic regulation. Moreover, by utilizing different durations and intensities of light exposure, we can achieve separate regulation of flowering and growth in crops, leading to conservation of energy resources for crops in the future.

References

1. Q. Wang, W. Liu, C. C. Leung, D. A. Tarté, J. M. Gendron, Plants distinguish different photoperiods to independently control seasonal flowering and growth. Science 383, eadg9196 (2024). https://doi.org/10.1126/science.adg9196; PMID: 38330117
2. W. Liu, A Feke, C. C. Leung, D. A. Tarte´, W Yuan, M. Vanderwall, G. Sager, X. Wu, A. Schear, D. A. Clark, B. C. Thines, and J. M. Gendron, Ametabolic daylength measurement system mediates winter photoperiodism in plants. Dev. Cell 56, 2501–2515.e5(2021). doi: 10.1016/j.devcel.2021.07.016; pmid: 34407427
3. C. C. Leung, D. A. Tarté, L. S. Oliver, Q. Wang, J. M. Gendron, Systematic characterization of photoperiodic gene expression patterns reveals diverse seasonal transcriptional systems in Arabidopsis. PLOS Biol. 21, e3002283 (2023). doi: 10.1371/journal.pbio.3002283; pmid: 376990558. T. C. Mockler et al., The DIURNAL project: DIURNAL
4. J. M. Gendron, D. Staiger, New Horizons in Plant Photoperiodism. Annu. Rev. Plant Biol. 74, 481–509 (2023). doi: 10.1146/annurev-arplant-070522-055628; pmid: 36854481
5. J. M. Gendron, C. C. Leung, W. Liu, Energy as a seasonal signal for growth and reproduction. Curr. Opin. Plant Biol. 63, 102092(2021). doi: 10.1016/j.pbi.2021.102092; pmid: 34461431

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The Young Embryologist Network conference 2024 (YEN24) is the 16th iteration of the network’s renowned yearly Developmental Biology meeting. This hybrid conference will take place at the Francis Crick Institute on Tuesday 28^thMay 2024, and will be streamed worldwide over Zoom. The YEN conference is a unique opportunity for early career researchers in Developmental Biology to share their research, network, and interact with peers and pioneers in the field.

This year, we will bring together a global audience. We are actively recruiting local representatives from universities and institutes worldwide to establish remote hubs for participants to gather, watch talks and engage in the conversation. We are also awarding travel grants, generously supported by the Company of Biologists. 

YEN24 features a diverse line-up of invited speakers, covering a wide spectrum of topics in Developmental Biology. We will hear from Aydan Bulut Karslioglu (MPI-MG) on environmental regulation of embryonic gene expression and cell fate specification, and Kristian Franze (University of Cambridge, FAU Erlangen-Nürnberg) on the mechanical control of vertebrate neural development. This year, we are delighted to host Pavel Tomancak (MPI-CBG, CEITEC) as keynote speaker, whose lab uses an interdisciplinary toolkit and comparative approach to understand the evolution of tissue morphogenesis.  

We are also excited to host three speakers engaging with the social, legal and ethical implications of biological research in ‘Science in Society’ perspectives talks. Naomi Moris (The Francis Crick Institute) uses synthetic embryos to understands fundamental principles of human development, and recently contributed to a re-evaluation of the term ‘embryo’, defining a roadmap for the use of in vitro embryo models in research. Laurence Lwoff (Council of Europe) is head of the Human Rights and Biomedicine Division at the Council of Europe, and works on an intergovernmental steering committee advising on the protection of human rights in biomedical research. Steve Crabtree (BBC Science Unit) is an award-winning executive producer at BBC Studios, and former series editor for the flagship science series Horizon, where he commissioned and produced over 70 episodes. 

We are also inviting abstracts from early career researchers to highlight a cross-section of research in the field in short talks and posters.

Registration for the YEN Conference 2024 is now open! Use our google form to sign up and send in your abstract: tinyurl.com/YENMeeting24.

We hope to see you there!

Head to our website, and follow us on social media for the latest news and announcements

Website: www.youngembryologists.org

Twitter: @YEN_community

Instagram: @youngembryologistsnetwork

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Alex Neaverson is a third-year PhD student at the University of Cambridge, studying regeneration of the Hensen’s Node in chick embryos. Alex is a keen artist and has recently got into scientific illustration while doing an internship at a research charity. As a Node correspondent, she plans to use her artistic skills to create illustrated career timelines of developmental biologists and draw graphical summaries to highlight research conducted by different teams around the world.

Congratulations on being selected as one of our new correspondents! What made you decide to apply to become a Node correspondent?

I’ve known about the Node since I started my PhD in 2021. The Node’s a great resource for bringing developmental biologists together. I really like how there’s a mixture of scientific articles and opinion pieces, and I like the ‘Lab meeting’ posts where you get to know all the different labs. I especially like the SciArt profiles. I love seeing my two big passions — biology and art — mixed together, sometimes in really unusual ways. I’ve always kept art and science separate in my life, where science has been my job and art has been my hobby. But I recently started getting into scientific illustration. I thought considering the Node publishes the SciArt profiles, you might be open to something slightly different from a Correspondent. Maybe you’d like to have someone who can create illustrations as a means of communicating science, instead of purely writing text-based articles. I deliberated over it for a while, but I spoke to my PI and he thought it was a great idea, so I took a chance and clearly it paid off!

How did you get into scientific illustration?

Scientific illustration is something that is very new to me. Art has always been a hobby. I love painting people and animal portraits. I have only started doing scientific illustration during my internship with Alzheimer’s Research UK (ARUK) last year. As part of my PhD course, I had to do a 3-month internship. There was an internship fair and while most organisations had very specific projects in mind, Jorge from ARUK’s Research team was very open to ideas and said that my project could depend on my interests.

My internship ended up being about translating research on dementia prevention into infographics that could be understood by a layperson. I wanted to do this in a more creative way. ARUK was very encouraging, and I was able to get a tablet to do digital illustration and attend online courses for Adobe Illustrator. The resource that I contributed to for ARUK is called the Impact Hub, which is used by the Science communication team and other teams in the charity to communicate the impact of the research funded by the charity. The infographics I created have to clearly communicate the science in a way that can be understood by anybody. That internship was where I started to meld science and art together.

Examples of illustrations Alex did during her internship at Alzheimer’s Research UK (click to enlarge image)

Apart from scientific illustration, have you done much science communication and public outreach?

Before I started my PhD, I worked as a research assistant at the Wellcome Sanger Institute. During the COVID lockdown, I had significantly less lab work to do. I started writing a blog together with a colleague, which was quite fun to do. I also completely revamped my department’s website because it was totally out of date and very boring to look at. I’d like to think I improved it! I’ve also taken part in several outreach activities for children, such as the Big Bang Fair at Birmingham NEC, and the Cambridge Festival last year.

What is your scientific background and what is your current research focus?

I did my undergrad in biomedical sciences in York. I was initially interested in human biology and disease. But it started to change over time as I did my degree. The programme was very open, so I was able to pick a lot of different modules. It was around second or third year when I started to show an interest in developmental biology, which probably had a lot to do with my lecturers. They were very passionate about their subject, and they transferred that passion to me.

In my final year, I did a project with Xenopus embryos, which I really enjoyed. When I finished at York, I thought the one experience that I lacked was with cell culture. I started looking for jobs where I could gain those skills, and ended up joining a core facility at the Sanger Institute where I primarily did stem cell differentiation projects. I learned how to work with iPSCs and differentiate them into neural lineages. But I started to miss working model organisms and I started to realise that I wanted to pursue my own research, which I didn’t have much freedom to do as a research assistant. That was when I decided to take on a PhD at Ben Stevenson’s lab in Cambridge.

Now, I work with very early chick embryos, and I’m interested in the role of Hensen’s Node, the so-called organiser in the chick embryo, during neural development. The node is thought to be responsible for releasing signals that pattern the neural territory. If you cut the node out of the embryo it will completely regenerate itself and the embryo carries on developing. I’m studying this regenerative process and what the triggers for tissue re-specification might be and whether this has knock on effect on the development of the embryo.

You mentioned you plan to create illustrated content for the Node. Can you elaborate on your ideas?

I’d like to use my illustration skills to create new kinds of content. For example, I’d like to interview developmental biologists about their career paths and create illustrated timelines of their scientific life. I think this will be really fun to create and I think people will be interested to learn about how other people in the field got to where they are today.

I’m also thinking about doing graphical research summaries about an individual or a lab’s research, similar to a paper’s graphical abstract. I’m not sure who I’m going to interview yet, but I’ll probably start with my own lab and people that I know and then branch out.

Will you also write for the Node as well?

I’d like to gain skills in writing as well. One of the things I want to improve is how to adapt the way I write for different audiences, which I think is a really important skill as a scientist. I’d like to make content that blends both text writing and illustration.

Apart from gaining a bit more writing experience, what else do you hope to gain from being a correspondent?

I’d like to meet other people who have similar interests. I’m thinking about a potential career path into science communication after I finish my PhD. I’d like to get to know people and network and find out more about careers in this area.

Finally, what do you like to do in your spare time?

At the end of my undergraduate degree, I loved cooking and baking so much that I convinced myself that I didn’t want to do science anymore and that I actually wanted to be a recipe developer. I felt very conflicted about this because I just spent four years of my life working towards a career in science. I ended up going to my first job in science anyway at the Sanger Institute. I’m glad I did because it did revive my interest in science.

I still do a lot of baking in my spare time and my lab is more than happy to eat all of my creations. Some of my favourite bakes have been embryo themed. I’ve made some cupcakes for a friend’s viva with the stages of zebrafish development. Another friend is a fellow chick embryologist. When she finished her viva, I made some early chick culture cupcakes that were really realistic. So realistic that maybe they were slightly off putting to some people!

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Dear colleagues,

We are delighted to bring you a 2-day workshop at the Francis Crick Institute that will gather leading experts in the field to break new ground in cell-type evo-devo. This workshop is free and open to all, but you do need to register (link).

Cells are the fundamental building blocks of living systems. Understanding the differentiation of cell types as well as the origin of novel cell types remains a central problem in developmental and evolutionary biology. Today, advances in molecular techniques have enabled the molecular profiling of individual cells, providing fresh opportunities for new insights into cell type development and evolution. This meeting will be of interest to anyone working with single-cell data.

Speakers:

Pawel Burkhardt (University of Bergen): “The deep evolutionary origins of neurons and nervous systems”

Margarida Cardoso-Moreira (Francis Crick Institute): “Origins of cells and organs – the view from the placenta”

Douglas Erwin (Smithsonian Institute): “Alternative models for formation of cells”

Jacob Musser (Yale University): TBA

Joe Parker (Caltech): “The cellular substrate of evolutionary novelty”

Mihaela Pavlicev (University of Vienna): “Cell types as characters”

Arnau Sebé-Pedrós (CRG – Barcelona): “Early animal cell type diversity, evolution, and regulation”

Stefan Semrau (University of Leiden): “How many cell types are there?”

Francesca Spagnoli (Kings College London): “Mapping the emergence of lineage identities in time & space”

Uli Technau (University of Vienna): TBA

Gunter Wagner (Yale University): “How to distinguish cell types from mere similarity clusters? “

There will also be two panel discussions, and there is plenty of time allocated for discussion and mixing within the schedule.

More information can be found here

All the best, 

James DiFrisco and Margarida Cardoso Moreira

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What we see

Approximately 1 in 20 babies are born with severe anatomical malformations. Each year this equates to 8 million affected newborns, of which 300,000 die within the first four weeks of life. With advances in sequencing technology, the identification of possible disease-causing changes in the genetic code of these patients has accelerated. However, it is a major challenge to prove which of these genetic changes, also called variants, cause these malformations, as well as to establish the cellular mechanisms by which these changes disrupt normal development. How do we distinguish problematic inherited or spontaneous variants in DNA from the many benign changes, and prove that they disrupt normal development? Can we better understand why some patients are more affected than others even though they carry similar, if not the same, genetic changes? How do important environmental influences, such as maternal health during pregnancy, modify how these genetic changes exhibit themselves in terms of severity and spectrum of patient presentations? Many genes that are implicated in congenital anomalies play multiple roles in different tissues during prenatal and postnatal development; thus, these genes are difficult to study in humans, even in stem cell ‘disease-in-a-dish’ models.

What we plan to do

Working closely with clinicians and researchers who submit variants of uncertain significance (VUS) via our portal, the Congenital Anomalies Cluster will create precisely engineered mouse models of patient variants, which will:

1. Help clinicians establish genetic diagnoses
2. Drive increased understanding of the molecular and cellular mechanisms underlying congenital anomalies.

Our cluster has broad developmental biology expertise and together with the MRC National Mouse Genetics Network (NMGN) we have built a pipeline to investigate the complex interactions that are disrupted during early life, across multiple organ systems. Through the detection of overlapping phenotypes in F0 embryo screening, we hope to provide clinicians with sufficient evidence to confirm a genetic diagnosis in their families. The generation of clinically relevant mouse lines to study pathogenic mechanisms allows exploration of the consequences of genetic mutations during the critical postnatal period (automated live monitoring), and during disease progression later in life. These models will serve as improved platforms for developing much-needed therapeutic interventions.

The portal

Part of the remit of the Congenital Anomalies Cluster is to help clinicians and researchers establish genetic diagnoses by modelling VUS in mice. Our submissions portal is open to clinicians and researchers worldwide.

Submitted VUS will be assessed by our Clinical Advisory Board who will meet at least twice a year.

They will consider and rank the submitted VUS based on the following Congenital Anomalies Cluster priorities (in order of importance): 1) New disease gene. 2) Known disease gene, but new phenotype association or novel allelic disorder. 3) Known disease gene with difficult-to-interpret VUS; e.g., nearby significant variants such as structural variants, or deep intronic single nucleotide variants. 4) Known disease genes where broader investigation of the mouse model could lead to new insights into pathogenic mechanism and/or therapy development.

Considerations:

Contributing teams are ideally clinically led or have strong clinical engagement, to efficiently return diagnostic information and enable further assessment of patient phenotypes. The clinical features of your patient should be present at birth and should overlap with the specialities of our developmental biology team: craniofacial, skeletal, heart, neural tube, kidney, and ciliopathies. More weight will be given to syndromic conditions to enable the simultaneous study of multiple systems in the mouse.

Please follow this link to the submission portal and feel free to download and share the flyer above.

For further information please email Karen Liu karen.liu@kcl.ac.uk or Stephen Twigg stephen.twigg@imm.ox.ac.uk

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In the last of the series of speakers from Development’s 2023 Pathway to Independence programme, we hear from two researchers studying the role of RNA biology in development.

Wednesday 6 March – 16:00 GMT

At the discretion of the speakers, the webinar will be recorded for viewing on demand. To see the other webinars scheduled in our series, and to catch up on previous talks, please visit: thenode.biologists.com/devpres

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A press release related to the Research Article in Development “Developmental regulation of cellular metabolism is required for intestinal elongation and rotation“.

How does our intestine, which can be at least 15 feet long, fit properly inside our bodies? As our digestive system grows, the gut tube goes through a series of dramatic looping and rotation to package the lengthening intestine. Failure of the gut to rotate properly during development results in a prevalent, but poorly understood, birth anomaly called intestinal malrotation. Now, in a study published in the journal Development, scientists from North Carolina State University have uncovered a potential cause of this life-threatening condition.

Intestinal malrotation affects 1 in 500 births but the underlying causes are not well understood. To find out why gut revolution could go amiss, scientists need to first understand intestinal rotation during normal development, a complex process that still baffles biologists.

The team of scientists, led by Dr Nanette Nascone-Yoder, decided to make use of a well-established system in frogs. “As vertebrates, frogs and humans share a common ancestor and have many similar anatomical features, including an intestine that rotates in a counter-clockwise direction,” explained Dr Nascone-Yoder. “Because frog embryos develop in only a few days and are highly experimentally accessible, they allow us to quickly test new hypotheses about how and why development goes awry during malrotation.”

“Frog embryos develop in a petri dish and are transparent when the intestine is developing, so they can be exposed to drugs or environmental chemicals to screen for substances capable of producing malrotation,” said Dr Nascone-Yoder. One of the compounds the team screened was the herbicide atrazine. They found that exposure to atrazine greatly increased the frequency at which frog intestines rotated in the reverse (clockwise) direction and decided to focus on atrazine to further investigate intestinal malrotation.

Dr Julia Grzymkowski, who led the experimental work of this study, found that exposure to atrazine disrupted metabolism (chemical reactions that provide energy for biological processes) in the frog embryos. Metabolic imbalance in the embryos derailed a series of cellular processes in the gut — cells could not grow, divide and rearrange appropriately to drive the proper intestinal elongation and rotation.

“Although we found that atrazine causes malrotation in frogs, these results do not necessarily mean that this herbicide causes malrotation in humans, because, in our screen, the tadpoles were exposed to 1000-fold higher levels than are typically found in the environment,” Dr Nascone-Yoder emphasised, “but our findings do strongly suggest that disturbing the same cellular metabolic processes affected by atrazine, for example, via exposure to other chemicals in the environment and/or genetic variations that affect metabolism, could contribute to intestinal malrotation in humans.”

This study is just beginning to unravel what happens during embryonic development that leads to intestinal malrotation. Dr Nascone-Yoder’s team hopes to extend this work: “Our results have provided new avenues to explore the underlying causes of this prevalent birth anomaly. We are now starting to dive deeper into the cellular events that coordinate the complicated process of intestinal elongation and rotation.”

———-

To find out more about the story behind the paper, check out this interview we did with first author Julia Grzymkowski and corresponding author Nanette Nascone-Yoder.

———-

Reference: Grzymkowski, J.K., Chiu, M.Y., Jima, D.D., Wyatt, B.H., Jayachandran, S.M., Stutts, W.L., Nascone-Yoder, N.M. (2024) Developmental regulation of cellular metabolism is required for intestinal elongation and rotation. Development, 151, dev202020. doi:10.1242/dev.202020

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What is Daniocell?

Daniocell is an exploratory tool that allows users to navigate pre-computed, time-resolved gene expression information for each cell type during zebrafish development. We profiled embryos across the first 5 days of development, as the animal progresses from a field of unpatterned cells to a swimming, feeding, and behaving animal. Daniocell showcases gene expression information for each gene in the zebrafish genome across most zebrafish cell types as they develop. For users interested in specific cell types at different stages of their development, Daniocell also holds cell type-specific pages that contains information on the most specific and most highly expressed genes within each cell type.

What inspired the development of Daniocell?

Single-cell genomics studies generate massive amounts of information, much of which is beyond the authors’ analytical goals, but could be highly useful to other members of the community. For instance, in our study, we focused on two tissues and made discoveries about several under-characterized cell types, but there are 17 other tissues that remain! Not every scientist wants to become an expert in analyzing these types of data. So, we made a list of the questions that we thought were most frequently addressed from these types of data and built a website to answer them. We hope that sharing this data with everyone will accelerate discovery-driven research within the community.

Daniocell was created from the perspective of active developmental biologists; we were hoping to create the resource we wished to have access to while performing our studies. We also tried to address feedback that we received about portals from our previous studies to try to make this one even more useful. We made some trade-offs in its development: the results are all pre-computed, which means that users cannot generate arbitrary plots to address specific questions; on the other hand, it means the website is fast, responsive, and inexpensive to run, hopefully allowing us to fund its support long-term.

How can scientists use Daniocell in their research?

Daniocell was designed to quickly and easily answer the most common questions we expect researchers might want to ask from our data, namely: (1) When and where is any given gene expressed? (2) Which genes have the most similar and dissimilar gene expression patterns? (3) When is each cell type present and undergoing the cell cycle? and (4) Which genes does each cell type express most strongly and most specifically, and how does that compare to related cell types?

To this end, each gene page in Daniocell demonstrates (1) that gene’s expression pattern (as UMAP and dot plot) across each tissue and cell type, resolved by time, and (2) which genes have the most similar and dissimilar expression patterns across all cells and each tissue. Additionally, each cell cluster page demonstrates (1) the developmental stages of cells in the cluster, (2) whether they are undergoing the cell cycle (based on their expression of cell cycle-associated transcripts), and (3) the most specific and most highly expressed genes within each cluster.

Of course, researchers might want to generate plots with curated sets of genes or groups of cells. To facilitate this simple/easy reuse of the data, we have the fully processed Seurat object posted on the Daniocell front page, along with our annotations, so that researchers can jump right in. These data can also be used with label transfer approaches, to transfer our annotations onto newly generated scRNAseq data; this process isn’t perfect, but can accelerate progress through analyzing scRNAseq data generated across similar stages from different perturbation conditions.

Who are the people behind the resource?

This resource was designed by the Farrell Lab at NICHD/NIH. The primary people behind Daniocell were Dr. Jeffrey Farrell (PI) and Dr. Abhinav Sur (postdoc).

Abhinav Sur: I began working on zebrafish in 2020 when I started my postdoc in the Farrell Lab at NICHD. My Ph.D. was on Evodevo where I studied the evolution of nervous systems using an annelid called Capitella teleta. I generated one of the first single-cell atlases in an annelid and first single-cell atlas of Capitella teleta. The most exciting part of working on Daniocell was that it was like a “treasure hunt”, as I dug through this large dataset to uncover hidden biology. The fact that the community have found Daniocell to be a useful resource has made this experience quite rewarding. In future, I hope to continue using single-cell genomics approaches to understand how cell types are constantly produced at the right time and place in constitutively regenerating tissues such as the intestine and how their dysregulation causes disease.

Jeffrey Farrell: I’m the head of the Unit on Cell Specification and Differentiation in the NICHD Intramural Research Program. I’ve been studying developmental biology for 17 years and started using zebrafish as a research model organism a little over a decade ago. Daniocell is a continuation of my long-term efforts to profile zebrafish development using single-cell genomics approaches and to thereby uncover interesting biology that was previously missed to study using both modern and classical approaches. For me, one of the most fun parts of this project has been to hear from many of you how Daniocell has helped you in your own research.

How can researchers help and contribute to the resource?

We are very happy to receive suggestions about improvements to the annotations and metadata from members of the community, based on either newly generated information or other labs’ expertise in particular tissues. These should further increase the value of the gene expression information in Daniocell over time. They can be submitted via email, and there is a template for the information to include on the Daniocell front page.

What are the next steps for Daniocell?

We plan to update Daniocell 1–2 times per year based on community input into cell annotations and to keep it up to date with new releases of the zebrafish genome. Additionally, we hope to add a tutorial to the site demonstrating how to use the Daniocell dataset with label transfer approaches to facilitate draft annotations of newly generated scRNAseq data. We are also exploring the possibility of integrating some additional datasets into the portal or adding a more interactive component that could be used to generate custom visualization figures from the data.

Visit Daniocell or read the accompanying manuscript.

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Leonora Martínez Nuñez has a background in microbiology and fungal cell biology. She is now a scientific visualization specialist at UMass Chan Medical School. Find out more about Leonora’s artistic influences and her path to a career in scientific illustration.

Can you tell us about your background and what you work on now?
I grew up in Mexico, where I studied Biology and later obtained a PhD in Microbiology. I immigrated to the U.S. in 2017 to train as a postdoctoral researcher studying membrane trafficking and exocytosis in different organisms. However, I’ve always been an artist at heart. In 2020, I decided to pursue a career in Scientific Illustration and started carving a path for myself in the field. I don’t have formal training as an artist, and I learned new skills through tutorials and workshops. In 2023, I left the bench and started working full-time in science communication and outreach, where I had the chance to do creative work as a scientific visualization specialist in the Biochemistry and Molecular Biotechnology Department at UMass Chan Medical School.

Were you always going to be a scientist?
Officially, yes. Growing up, I was interested in viruses, insects, and chemistry. I remember myself, as a kid, telling people I wanted to be a chemist or biologist and find the cure for HIV. I laugh about that nowadays because I didn’t go into virology or immunology; instead, I studied fungi for several years of my training.

And what about art – have you always enjoyed it?
I was always pursuing some artistic or creative endeavors on the side, like contemporary dance, folkloric dance, theater, clay modeling and sculpture, building scale wood boats, painting, or drawing. My hometown, Xalapa in México, is such a cultural hub that it was impossible not to be drawn to these activities.

What or who are your most important artistic influences?
I’d say that my favorite artists are Remedios Varo and Leonora Carrington. I want to portray such magic in my work, but that is a work in progress. In my current style, I think I was significantly influenced by Dr. Verena Resch (Luminous Lab) since I learned a lot from her tutorials. I also admire the work of Olena Shmahalo (Nature in theory). I want to add that Dr. Matteo Farinella significantly influenced me and encouraged me to pursue science illustration as a career.

How do you make your art?
I use a computer and a free program for 3D modeling called Blender. I use a lot of Molecular Nodes (a tool fro Blender created by Dr. Brady Johnston). I mix it up with basic programs for vector and pixel-based design. I extensively use the 3D coordinates deposited in the Protein Data Base (PDB) and chemical formulas in ChemSpider and Chempub. I like to doodle ideas with pen and paper, which I then translate onto the 3D space. So far, I’m mostly doing 3D images (ultimately 2D with 3D elements), short animations, and vector graphics. My first step is always to read the science and do my research. I want to be as scientifically accurate as possible. I read a lot about different fields, and the best part is that I’m learning so much from this job.

Does your art influence your science at all, or are they separate worlds?
While working at a research bench, my art helped me understand my science better. The extensive research done to translate it into a visual with the most accuracy possible makes you question everything. It also helped me present my science in a better light. My whole world is a mix of science and art, so I’d say that science influenced my art and vice versa.

What are you thinking of working on next?
I have many projects in the works, but I want to focus mainly on helping other scientists tell their stories visually. I’m part of a research core at UMass Chan, where I manage the Science Visualization Services, so I can help researchers translate their scientific discoveries into striking visuals. We are open for commissions! Additionally, I want to put more of my energy into community outreach. I want to encourage younger audiences to think about science and art as converging worlds, so I’ll also be working on that.

Find out more about Leonora:

Website: www.leonoramartinez.com
Instagram: radiant_molecules
X: @leonoramtzn
Mastodon: @leonoramtzn@mstdn.social

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James Zwierzynski is currently a first-year PhD student at Stanford University, investigating vascular morphogenesis and growth in the placenta. With a background in humanities, James aims to combine his interests in philosophy and science to write about topics in reproductive biology and philosophy of science. We caught up with James to find out more about his career and his plans as a Node correspondent.

You’ve been selected as one of our new correspondents, congrats! What made you decide to apply?

Development is one of my favourite journals to read and I’m just a giant science nerd. Reading Development meant I very quickly ended up discovering the Node and FocalPlane. I love this broader community of developmental biologists who are really interested in the same things that I am. I also have to admit that I am a huge fangirl for John Wallingford. He’s a PI in Texas and one of the things his lab works on is Shroom3, a gene that my old lab was very interested in. I got introduced to him through his papers and I was like, “Oh my gosh, we’re working on the same gene that nobody works on!” I very quickly discovered that he writes about developmental biology for not only scientists but also for the wider community. His #DevBiolWriteClub posts on the Node advocate that to become a good scientist, you need to build your skills in reading and writing. When I saw the call for new Node Correspondents, I thought this would be a good opportunity to improve my skills in thinking, writing, and communicating about science.

Have you done much science writing or other forms of science communication before?

I think that like so many scientists, I’ve mostly done writing while preparing manuscripts, but I haven’t done writing where I pick a topic and write a long form post. I think that is something I’d like to build on because it’s a skill that will not only help me become better at communicating more broadly but make me a more well-rounded scientist.

This quarter I’m teaching in a course for undergrads called ‘bioBUDS: Building Up Developing Scientists’. It’s a student- and community-oriented course, focused on helping students from underrepresented backgrounds in science thrive through workshops, skills, and resources. I’m giving a lecture later this quarter that I’ve titled ‘Meta-Science’. It’s about what can, should (or even shouldn’t!) science tell us. I plan to go through why the scientific thought process is the way it is. We often think of the scientific method as generating a hypothesis, gathering data, and then reporting your results. But when you look back at the intellectual history of science, there are cultural and political events that have shaped the way that we think about science. Especially in the Interwar period, when logical positivism sought to unite science and philosophy, and proofs and direct observation as “truth” in science. I would argue that maybe we don’t have to think about science in this way – it actually has tough ramifications for the public’s view of science as purely “objective”. I will also explain how science relies upon both revision but also reduction. On the grand scale it’s all just hypotheses; you are never really going to prove anything for sure. That lecture is one of the ways I’m trying to do more science communication and I’d like to do more through other channels too, depending on how busy I am throughout the quarter.

What is your background and what are you currently researching on?

Most of my research experience was at Indiana University School of Medicine; I was there for about two and a half years after I graduated from the University of Notre Dame. I worked on heart development, and the pathways altered in structural heart defects, specifically focusing on non-canonical Wnt signalling. I fell in love with research and decided I was going to apply for a PhD. Now I’m at Stanford and joined Kristy Red-Horse’s lab. I pivoted a little bit from a cardiac lab to a vascular biology lab. I’m specifically interested in vascular morphogenesis and growth in my favourite organ, which is the woefully understudied placenta. There are so many mysteries about it. I’m really excited about finding out more.

What ideas do you have for the Node?

One of my ideas relates to my current research. I consider myself a developmental biologist who’s concerned with vascular biology but also reproduction. I plan to write about reproductive biology, which I think is a really understudied field.

I would also like to delve into the ideas in philosophy of science. One of the things that really inspired me as a scientist is my background in the humanities and my training as a philosopher. I’d like to explore the assumptions behind the way that we do science, and the implications of some scientific work that we don’t often think about. A wonderful example of this that I read recently was the book, Embryos Under the Microscope: The Diverging Meanings of Life, by Jane Maienschein. She traces the history of microscopy and embryology alongside advances in technologies, such as cloning and IVF. She argues that the embryo in many forms has influenced the way in which we culturally and politically think about science itself. Now, her book is approaching a decade old, yet the ideas she presents are perhaps more relevant than ever. I would really love to write about the ways in which the cutting edge of developmental and stem cell biology are still important, even though we’re not cloning Dolly the Sheep. There was controversy this past year over the recent stem cell embryo models; we had research that got picked up by the media and brought into the public realm outside of the scientific community. I think that writing about these things in a really thoughtful way is important. I would like to write about what is developmental biology doing today, what does that mean for the world and how we’re thinking about science.

What do you hope to gain from the experience of being a Node correspondent?

My ultimate goal is to inspire people to read something that I’ve written and be excited about it. I hope other people would be excited about science and science-adjacent topics, specifically related to development because that’s the thing that I love.

My secondary goal, thinking about my own growth, is to grow my skills in writing, take ideas from my head and put them on paper in a cohesive way. I think that it will not only help me to be a better communicator in different ways, but I would argue that would make me a better scientist too.

Is there anything that people might find surprising about you?

Some people are surprised that I studied philosophy for a while. I had kind of an odd path to my PhD. Another surprising fact is that I am a twin, and my oldest brothers are also twins. It’s a little bit weird to have so many twins in the family, but I’m special in that I’m the only scientist!

Outside of the lab, what do you like to do in your spare time?

In my spare time, I spoil my cat and a dog. I read through tonnes of books, and I have an ever-expanding book collection. I also make a lot of pottery – the most recent things I’ve been working on are a series of weird fruits with anthropomorphic facial features on them. I’d like to make science-inspired pottery too; as somebody who is obsessed with the placenta, I think it’s the perfect coaster shape. Kristy, my PI, much of her career on collateral artery development in the heart. I think a heart cross-section would be a great coaster as well. I would also like to make little espresso cups for the espresso machine in the lab and carve something science-related on the side of the cups, like the different stages of embryo development. I have all these ideas, but I just need to take the time to go to the studio, it ends up being really analogous to my work in the lab. I have a whole list on my computer of things to do in the ceramic studio right next to the list of things to do in the lab.

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