Let’s welcome the three new Node correspondents – Dosh Whye, Mariia Golden and Shefali! We look forward to working with them to bring you a wide range of content and perspectives for the Node. Stay tuned for their posts over the coming year.
Dosh Whye serves as the assistant director of the Human Neuron Core, where he leads the cell development and differentiation efforts to build complex 3D neural organoid models using induced pluripotent stem cells (iPSCs) from pediatric patients with rare genetic neurodevelopmental disorders. Dosh has close to 20 years in the stem cell field, and he continues to be fascinated by the power of pluripotent cells and the technological advancements of stem cell applications in the fields of science & medicine. He plans to serve as a correspondent for several international stem cell research conferences, and he’s also inspired to write a Q&A blog series profiling many brilliant scientists in the stem cell field.
Mariia Golden is a third-year PhD student moving from Goethe University Frankfurt to Marburg University, Germany. She investigates dynamical morphogenetic events in insect development. She is passionate about live imaging and working with non-model organisms. As a Node correspondent, Mariia wants to promote diversity among the organisms we choose for our research questions through a series of interviews with established scientists who are enthusiastic about the topic. She also would like to highlight the topic of motherhood and scientific career, because she truly believes that the status quo should change in order to put a stop to the “brain drain” through female scientists.
Shefali is a fifth-year PhD student in the Tennessen Lab at Indiana University, Bloomington. She is broadly interested in inter-organ metabolic signaling, and her current research focuses on how glucose metabolism coordinates the brain-body growth signaling axis during Drosophila melanogaster brain development. Shefali also serves as the elected graduate student representative on the FlyBoard, where she has been working towards creating more mentoring opportunities for early career scientists. Beyond work, she enjoys learning various Latin-style dances and singing classic Hindi songs (which is her mother tongue). As a Node correspondent, she is eager to combine her scientific interests with her commitment towards building a strong and empowered scientific community. She looks forward to writing not only about the emerging field of inter-organ metabolic signaling, but also about unconventional scientific journeys, community resources, importance of mentoring, and bring in her perspective as a trainee to support incoming graduate students.
The Research Training Group: Neurodevelopment and Vulnerability of the Central Nervous System (GRK2162) is excited to host its 3rd International Symposium: Developmental Processes in CNS Plasticity and Pathogenesis. The program will bring together junior scientists with experts in neurodevelopmental biology, stem cell biology and translational neurobiologists. Next to a great set of lectures, the program offers ample opportunities for scientific networking and presentation of your scientific work including round tables / meet the expert sessions, interactive poster sessions, flash talks and short talk opportunities.
Researchers in developmental neuroscience, neurobiology, and related fields—including PhD students, postdocs, and principal investigators—are encouraged to participate!
Date: April 9-11, 2025 Location: Max-Planck-Institute for the Science of Light, Erlangen, Germany
You can register here until 15th February 2025 or until all spots are taken. There is no registration fee but the number of participants is limited by the space we are using. EXTENDED DEADLINE: 28th February 2025
Join us for stimulating discussions and networking opportunities in the vibrant research environment of FAU Erlangen-Nürnberg!
By Claudio Hernández-López and Aditya Singh Rajput
This is one of three reports about the “Physics of the Early Embryonic Divisions” Workshop, organised by The Company of Biologists. Read the other two reports for different perspectives on the science that was discussed:
After a taxi ride from Heathrow to Buxted Park, the first day of the conference started on a high note as everyone was treated to a hearty lunch with a view of the sprawling gardens. Later, having found our way through the many corridors of the hotel, we had a few words from the organizers of the conference, Lendert Gelens and Julia Kamenz, and also from Laura Hankins on behalf of The Company of Biologists. All the speakers introduced themselves and pitched their research interests and out-of-the-lab hobbies. And so, the stage was set for the first session of the conference: actin and its biochemical regulation
Actin I: Swirling biochemical waves in natural and artificial cortices
Andrew Goryachev, professor at the University of Edinburgh, introduced everyone to Rho-Actin (RhoA) waves in the cortex of Starfish oocytes. A critical part of the cell cycle is cytokinesis, i.e. the ability of the cell to constrict its membrane and form two separate cells. These waves are a result of cortical excitability before this process. Andrew showed us their mesmerizing spatio-temporal evolution in fluorescence microscopy movies, displaying correlated activity in regions with sizes of about 10 microns [1]. Biochemical reaction-diffusion systems are able to produce spatio-temporal patterns and spread waves. However, depending on the molecular interactions between the chemical species, the properties of these waves can change. Two competing models have been proposed in the literature to explain these waves, differing in the presence or absence of an explicit chemical species that inhibits RhoA. Current experimental data measures either the total RhoA concentration or active RhoA concentration in space and time, and these two models cannot be distinguished from the observed dynamics of one concentration alone. Andrew presented new experimental data from simultaneous space-time recordings of total and active RhoA. These measurements indicate that changes in active RhoA precede changes in total RhoA, in agreement with a model including an explicit RhoA inhibitor.
A major push in the field is also to study and recapitulate the intrinsic propensity of the actomyosin cortex to form patterns. In this direction, the lab of Jennifer Landino, an assistant professor at Dartmouth College, has been working on developing reconstituted cortices to study the emergence of spatio-temporal patterns by an interplay of F-actin and Rho. These Supported Lipid Bilayers (SLBs) [2] display waves and localized oscillations that have previously been observed in frog and starfish oocytes. This provides strong evidence of the self-organized nature of these patterns, with the mutual feedback between F-actin and Rho rendering the cortex excitable. The observed dynamics in SLBs present crucial differences compared to living cells, in particular, lacking periodic traveling waves. Changes in material properties after Xenopus extract addition allowed more than a single wavefront to propagate, thus bringing attention to the importance of the composition and design of these reconstituted systems.
Actin II: Geometry, flows, and deformations in early development
The second part of the session on actin started with Claudio Hernández-López, who recently finished his PhD at ENS Paris and is currently a postdoc in AMOLF Amsterdam, discussing the early development of Drosophila Melanogaster. The pre-gastrulation embryo, i.e. from cell cycles 1-14, is a syncytium: all the nuclei share a common cytoplasm. Before gastrulation, the nuclei migrate towards the cortex, forming their cellular membranes during cell cycle 14. The synchrony of the cell cycle along the 500-micron embryo depends on the nuclear density in space, hence, it is important that the nuclei achieve a uniform distribution in the embryo before cellularization. Previous experiments have shown that the expansion of the nuclear cloud along the anterior-posterior axis is mediated by cytoplasmic flows driven by cortical actomyosin contractions [3]. Claudio presented a new modeling framework comprising two fluids: an active gel (actomyosin), and a passive cytosol [4]. A mechanochemical coupling between the position of the nuclei and localized activation of myosin-II at the cortex reproduced previous experimental measurements on the flows and nuclear positioning. Remarkably, this self-organized positioning is robust, meaning that no matter the location of the initial nucleus after fertilization, the final nuclear distribution will remain uniform.
Aditya Singh Rajput, a PhD student at ICTS-TIFR, Bengaluru, continued the session by discussing asymmetric ingression in embryos. This phenomenon seems to be highly conserved amongst multiple phyla, with comb jellies being one of the major examples. The discussion began by looking at ingression in the nematode C. elegans and highlighting the emergence of myosin inhomogeneities that lead to this asymmetry. He then discussed his work on understanding this from the lens of active matter physics and treating the actomyosin cortex as an active fluid surface. Due to an emergence of differing timescales of ingression and cortical flow, the cytokinesis can be symmetric or asymmetric depending on the cortical contractility. The predictions from this theory also seem to hold true when compared to the dynamics of the first cleavage in the C. elegans embryo.
Hervé Turlier, a research group leader at the Collège de France, discussed his group’s work to build physical and computational models for the early development of multicellular organisms. The group has been developing general computational tools to simulate [5], as well as reconstruct [6] cell and tissue surfaces, which could help understand, for example, cleavage patterns in early embryos. One of the foremost open problems in the field of developmental mechanobiology is the experimental measurement of forces in tissues as they undergo growth and morphogenesis. To this end, Dr. Turlier’s group has been working on analysing fully three-dimensional networks of cellular contacts to infer cellular stresses. This method, called foambryo, relies on mesh reconstruction to accurately capture the cellular geometry and then infer the relative tensions from the junctional lengths. These physical and computational tools not only provide a unique window into the mechanical behavior of early embryos but are also demonstrated to be generalizable and scalable to different species and various stages of development.
Information processing across scales
Switching gears, the session on information was kicked off by Rob Phillips with a discussion on language, words, and the information therein. By comparing the information content in examples from daily life- works of literature, encyclopedias, and entire libraries – with the information content of genomes, Rob brought to light the vast unknown regions of genome sequences that remain understudied till now. With his lab, he has been developing novel tools [7] to understand the transcriptional crosstalk between genes in a high-throughput manner to develop a genomic Rosetta stone that helps to bridge our understanding of the genotype-phenotype map. He talked about how this work attempts to infer the underlying gene regulatory networks by studying thermodynamic interactions and binding affinities and combining this with tools from information theory. In addition to the problem of deciphering the genotype-phenotype map itself, Rob highlighted how the many-to-one nature of this map comes with added complexities of different genes having varying degrees of impact on their associated phenotypes, which is also another aspect this toolbox can help bring to light in a more quantitative manner.
Sophie de Buyl, professor at the Vrije Universiteit Brussel, closed this session by talking about the development of the Ascidian embryo. These filter feeders present two characteristics that make them particularly attractive for experimental studies in developmental biology. First, their cleavage pattern is invariant. Second, there is no cell migration, death, or embryo growth during their development. Previous theoretical work performed in her lab focused on the differentiation of neural tissue in the very early stages of development of this species. This process depends on the activation of ERK, which is regulated by the concentration of external signaling cues. In particular, the ERK activator is localized at the basal side of the outermost cells, and the ERK repressor is localized at the cell-cell junctions. Hence, the geometry of the cells is a relevant variable to study in relation to cell differentiation [8]. One overarching question in developmental biology is how living systems integrate signals from their environment to decide cell fate robustly, and the tools of information theory allow us to cast this problem in a tractable mathematical form. As a key result of this new study, Sophie showed that maximizing the information transmission from the external input to cell expression yields a predicted cell geometry that closely matches experimentally measured values. Furthermore, this maximal information transmission supports reliable differentiation between four different possible cell fates [9].
Finishing thoughts
The early embryonic cell divisions arise from an interplay between biochemical and mechanical cues, spanning multiple temporal and spatial scales. Given that regulatory pathways are generally less active at that stage, we feel that a comprehensive dialogue between theory and experiments on early development can be fertile ground for a broader understanding of not only cell division but also the emergence of complex behaviors in metazoan cells. Going beyond, perhaps a more biophysical understanding of the embryonic divisions can tell us something about the evolution of the diverse regulatory networks that we observe in extant organisms, potentially learning more about cell division in the first multicellular organisms.
Landino, Jennifer, Marcin Leda, Ani Michaud, Zachary T. Swider, Mariah Prom, Christine M. Field, William M. Bement, Anthony G. Vecchiarelli, Andrew B. Goryachev, and Ann L. Miller. “Rho and F-actin self-organize within an artificial cell cortex.” Current Biology 31, no. 24 (2021): 5613-5621.
Text written by Olga Afonso, Helena Cantwell, and Shuzo Kato
This is one of three reports about the “Physics of the Early Embryonic Divisions” Workshop, organised by The Company of Biologists. Read the other two reports for different perspectives on the science that was discussed:
Microtubules: bridging meiosis to mitosis and cellular differentiation
In a workshop dedicated to early embryonic divisions, we could not miss a session focused on microtubules. The session started with a talk from Helena Cantwell (University of California, Berkeley) who combined two model systems, Ciona robusta and Xenopus laevis to study the molecular mechanisms that mediate the meiotic to mitotic spindle transition. Helena found that Casein Kinase II is as a key regulator of spindle morphology that acts through the Ran-GTP pathway of spindle assembly [1]. Further work on how the Ran-GTP gradient itself changes during the meiotic to mitotic spindle transition would ultimately close the loop. Simone Reber, from the Max-Planck Institute for Infection Biology, showed recent work from the lab, focused on the changes of spindle morphology during cell differentiation. They used optical diffraction tomography to show that differentiated cells have a more dilute cytoplasm resulting in a shift of microtubule mass from the mitotic spindle bulk to centrosomes and astral microtubules [2]. Remaining questions relate to how the cytoplasm is diluted during differentiation and what the biological function of increased astral microtubules is. The session concluded with a presentation from Nicolas Minc, Institute Jaques Monod, Paris. Nicolas Minc uses sea urchin embryos to study how the position of the metaphase spindle is maintained in a large cell, where microtubules are far away from the cell’s boundary. By using a combination of optical tweezers and computational analysis of cytoplasmic flows, Nicolas showed that spindle positioning is maintained by the viscoelastic properties of the cytoplasm [3,4,5]. Overall, this session covered the role of microtubules in every step of embryonic development: from the very first meiosis to mitosis transition to what happens to the spindle morphology when cells start to differentiate.
Opening session with the organizers Lendert Gelens and Julia Kamenz.
Energetics of early development
Cellular processes in embryonic development are powered by energy metabolism. Although the biochemical pathways of metabolism have been characterised in past centuries, how embryos organise limited energy sources for their accurate development is poorly understood [6,7]. Specifically, what are the energetic costs of specific processes such as cytoskeletal assembly and cell cycle regulation? Also, how do intracellular energy fluxes constrain these processes? And, what kind of quantitative tools do we need to measure or infer energy fluxes in development? Qiong Yang (the University of Michigan) addressed these questions by quantifying how energy sources limit spatiotemporal control of the cell cycle in embryos using Xenopus laevis cytoplasmic extracts. Shuzo Kato (TU Dresden) discussed the role of energy fluxes in regulating mitotic spindle organisation using cell-free and embryo systems. Jonathan Rodenfels (the Max Planck Institute of Molecular Cell Biology and Genetics) shared insights into the spatial control of energy metabolism during development, and the possible role energetics play in evolution. Assessing these challenges and questions will advance our understanding of the energetic basis of embryonic development.
Cell fate decisions in early embryos
The focus of the workshop then shifted to cellular differentiation with a group of talks describing work tackling the question of what drives cell fate decisions in early embryos using a range of different systems and approaches. Silvia Santos (The Francis Crick Institute) discussed her lab’s work exploring the interplay between cell cycle signature and cell fate in embryonic stem cells (ESCs) and ESC-based organoid models [8]. Amber Rock (Harvard University) then presented her work using acoel worms [9] to explore the minimum components required for, and contribution of positional information to, viable embryonic development. Jordi Garcia-Ojalvo (Universitat Pompeu Fabra) finished the session with a discussion of his group’s work using physical approaches, in combination with experimental data, to uncover circuits driving cell fate specification in embryogenesis [10]. This session brought together a range of perspectives from experimental embryology and cell biology to modelling based on physical principles and sparked interesting discussions around cell autonomy, identity and decision making in the context of embryogenesis.
Early embryonic cell division is a complex phenomenon involving both physical and biological processes. Overall, the workshop was truly a unique opportunity to sit at the same table established group leaders in the field of early embryonic divisions and young researchers in a relaxed and informal setting that fostered open discussions on longstanding and emerging problems, as well as collaborations across traditional disciplines. Moreover, the meeting gathered experimentalists and theoreticians, a much-needed synergy to tackle complex challenges in the field. As an emerging property of such collaborative atmosphere, we built a robust network among all participants – a network that will undoubtedly strengthen the “early embryo” research community. Exciting times lie ahead, as we uncover the principles of early embryonic development.
The group going for an afternoon walk in the fields near Buxted Park.
References
[1] Cantwell H, Nguyen H, Kettenbach A, Heald R. Spindle morphology changes between meiosis and mitosis driven by CK2 regulation of the Ran pathway. Biorxiv (2024) DOI: 10.1101/2024.07.25.605073.
[2] Kletter T, Muñoz O, Reusch S, Biswas A, Halavatyi A, Neumann B, Kuropka B, Zaburdaev V, Reber S. Cell State-Specific Cytoplasmic Material Properties Control Spindle Architecture and Scaling. Biorxiv (2024) DOI: 10.1101/2024.07.22.604615
[3] Nommick A, Xie J, Minc N. Manipulation of Spindle Position Using Magnetic Tweezers in Sea Urchin Embyos. Methods Mol Biol. (2025) 2872:87-100.
[4] Tanimoto H, Sallé J, Dodin L, Minc N. Physical Forces Determining the Persistency and Centering Precision of Microtubule Asters. Nat Phys. (2018) 14(8):848-854.
[5] Najafi J, Dmitrieff S, Minc N. Size- and position-dependent cytoplasm viscoelasticity through hydrodynamic interactions with the cell surface. PNAS (2023) 120(9)e2216839120.
[6] Ghosh S, Körte A, Serafini G, Yadav V, Rodenfels J, Developmental energetics: Energy expenditure, budgets and metabolism during animal embryogenesis. Semin. Cell Dev. Biol. (2023) 138, 83–93.
[7] Yang X, Heinemann M, Howard J, Foster P, Physical bioenergetics: Energy fluxes, budgets, and constraints in cells. PNAS (2021) 118(26)e2026786118.
[8] Padgett J, Santos S. From clocks to dominoes: lessons on cell cycle remodelling from embryonic stem cells. FEBS letters (2020) 594(13), 2031-2045.
[9] Srivastava M. Studying development, regeneration, stem cells, and more in the acoel Hofstenia miamia. Curr. Top. Dev. Biol. (2022) 147:153–172.
[10] Saiz N, Mora-Bitria L, Rahman S, George H, Herder J, Garcia-Ojalvo J, Hadjantonakis, AK. Growth Factor-Mediated Coupling between Lineage Size and Cell Fate Choice Underlies Robustness of Mammalian Development. eLife (2020) 9, e56079.
Written by Irene Li, Magdalena Schindler and Isaac Wong
This is one of three reports about the “Physics of the Early Embryonic Divisions” Workshop, organised by The Company of Biologists. Read the other two reports for different perspectives on the science that was discussed:
We recently had the chance to be amongst 30 developmental biologists and theoretical biophysicists who tackled the complex dynamics of early embryonic cell divisions in a workshop organized by The Company of Biologists. This scientifically stimulating event took place at Buxted Park in the picturesque Sussex countryside of England. The small size of the workshop fostered conversations and encouraged sharing of unpublished work, creating an ideal environment for both established and early-career researchers to engage in scientific discourse that wouldn’t have been possible at larger-scale meetings.
The historic Buxted Park Hotel, gracefully overlooking the picturesque countryside
Thanks to the hard work of the organizers Lendert Gelens and Julia Kamenz, scientific conversations flowed seamlessly from morning presentations into afternoon walks around the countryside and evening minglings at the bar. The program’s design struck an excellent balance between structured sessions and informal discussions, while the venue’s inviting spaces encouraged participants to delve deep into scientific exchanges. The atmosphere of openness was further enhanced by the break-out sessions in the evening, where the participants brainstormed on the bigger picture for early embryonic studies. These interactions throughout the workshop laid excellent groundwork for new friendships and exciting future ventures. We summarised here some, to us, outstanding sessions:
Session on cell cycle control
Recent studies are painting a vivid picture of just how finely tuned and adaptable the cell cycle really is. Stefano di Talia opened the session with a fascinating talk on the relationship between nearest-neighbour network topology and spindle packing. He showed that embryonic cells start deciding their future nuclear identities surprisingly early, hinting that fate is determined sooner than we might expect [1]. Next, Julia Kamenz introduced a new sensor that gives us a clearer view of how the cell cycle progresses. Yuting Irene Li’s research uncovers a kind of “tug-of-war” between two mechanisms that keep the meta-synchrony of cell cycles in early embryonic divisions: pre-set gradients of cell cycle lengths and short-range interactions [2]. Finally, Lendert Gelens highlighted how even temperature can influence these delicate processes, showing that environmental factors can shift the gears of cell division [3]. Taken together, these insights reveal just how dynamic and responsive the cell cycle can be.
Session on the cytoskeleton and cytoplasmic flow
Despite many years of research, there are still countless open questions on the interplay of the cell cycle, the cytoskeleton and the cytoplasm. How these components interact within the embryo to achieve proper tissue-scale development is even more elusive. Olga Afonso addressed this problem by analysing how scaling of cytoplasmic flows can happen despite the massive cell size changes throughout the reductive cell cleavages of the embryo. The session concluded with Isaac Wong’s presentation, which examined how variations in the cytoplasmic concentration of centrosomal proteins influence centrosome growth. His findings offered new insights into the mechanisms that enable early embryos to maintain centrosome size homeostasis.
Session on multicellular dynamics
In the last session, the participants explored how one egg cell can give rise to complex multicellular dynamics. Nathan Goehring opened the discussion with exciting research on cell polarity and its propagation during early embryonic divisions in C. elegans [4]. Next, Sebastian Streichan addressed how cytoskeletal anisotropy arises in the first place. Magdalena Schindler then asked the question of how changes in cell cycle synchrony can impact the tissue material state of a developing embryo. She suggested that an optimum level of variability in cell cycle synchronicity driven by cell lineage is key in controlling tissue fluidization, which is essential for developmental progression. Diana Pinheiro’s research then explored how cell fate and macroscopic patterns may be impacted by material properties in Warmflash patterns. Lastly, Nicoletta Petridou’s work showed how cell scale dynamics dictate emergent tissue mechanical properties and how using optogenetics to control those properties revealed unexpected changes in cell signalling. The talks altogether gave a great insight into the impact of cell divisions and other cellular dynamics across scales.
Breakout sessions
The workshop included 3 breakout sessions, during which the participants were split into subgroups to discuss big-picture questions. The three workshops respectively addressed community building within and across fields, important scientific questions we need answered and the tools we might use to do so. Given the interdisciplinarity of the participants, many different problems and hopes for technologies came up. As young researchers, we really appreciated this opportunity to exchange with leaders in our field and the engagement in this higher-level thinking. Altogether, we may have not been able to agree on one common goal in these sessions, but we are excited to see where our field will be going in the future and how we can shape it.
A sample slide displaying the key questions discussed during one breakout session, focused on building a strong and collaborative scientific community
[1] Xu Y, Chao A, Rinaldin M, Kickuth A, Brugués J, Di Talia S. The cell cycle oscillator and spindle length set the speed of chromosome separation in Drosophila embryos. Curr Biol. 2025 Feb 3;35(3):655-664.e3.
[2] Mishra N, Li YI, Hannezo E, Heisenberg CP. Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo. bioRxiv [Preprint]
[3] Rombouts J, Tavella F, Vandervelde A, Phong C, Ferrell JE Jr, Yang Q, Gelens L. Mechanistic origins of temperature scaling in the early embryonic cell cycle. bioRxiv [Preprint]
[4] Rodrigues NT, Bland T, Ng K, Hirani N, Goehring NW. Quantitative perturbation-phenotype maps reveal nonlinear responses underlying robustness of PAR-dependent asymmetric cell division. PLoS biology. 2024 Dec 9;22(12):e3002437.
Want to organise one of The Company of Biolgists’ Workshops? We’re now accepting topic proposals for Workshops in 2027.
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Arteries are an essential part of any tissue. For the tissue or organ to survive, it needs to be perfused with blood carrying nutrients and oxygen, which gets distributed through capillaries and keep cells alive and healthy. We use artery development as a model to ask questions about cellular responses, interactions, heterogeneity and plasticity. Specifically, we use a special kind of artery¾the collaterals (Figure 1), to ask important questions about biological processes.
Collateral arteries are special because these connect two arterial trees. So, if/when there is a clog in one of the artery branches, the collaterals reroute the blood flow and continue perfusing the underlying tissue without interruption. This ensures healthy and functional organs.
Figure 1: A collateral artery segment connecting two artery trees. Image was taken from an adult mouse brain (pial layer). Red, artery endothelial cells; Green, proliferating nuclei. Arrows point to the direction of blood flow. Image credit: Dr. Suraj Kumar
To date, we have not identified a molecular marker for collaterals, which, prevents us from distinguishing collaterals from conventional arteries on a tissue section or in the cellular clusters obtained via analyses of single cell sequencing data. The only identifying characteristic of collateralsis the fact that they connect two artery trees. So, we use imaging of whole organs (in our case, mouse hearts) to identify the coronary arteries and subsequently, the coronary collateral arteries which connect them together. Along with imaging whole hearts with cellular resolution, we heavily use mouse genetics and gene expression datasets to build hypotheses and test them both in silico and in vivo.
Like all scientific studies, this work went through a number of roadblocks which inspired our team to take up the challenges in a systematic manner and tackle them one at a time. It was not straight forward. In the process, we made some inspiring discoveries, developed some new tools and opened avenues for several questions in the field of vascular biology. Here is our story.
The inspiration: Same but Different
While it seems like the properties of cells which compose vessels within an organism are same, scientific evidence points to the contrary. We and others (Arolkar et al., 2023; McDonald et al., 2018) have time and again shown that, the building block of arteries─artery endothelial cells─can be quite different. Research groups around the world have used a variety of experimental models to highlight the differences in their origin, function, plasticity and regenerative abilities. The molecular heterogeneity of endothelial cells within a given vessel segment is getting more and more attention (Augustin and Koh, 2017; Trimm and Red-Horse, 2022).
When we take a section of any vascularized tissue, and immunostain for arterial markers, like Cx40 or SMA, we cannot distinguish one cell from the other. We also know that these cells are different in their gene expression profiles (Arolkar et al., 2023). So, while the artery cells all look the same, they can be very different from each other (Figure 2). Cellular heterogeneity could be determined by their origin, which, consequently regulates the plasticity. This is a hypothesis, which we would like to test in as many ways as possible.
Figure 2: Heterogeneity of artery endothelial cells. (A) UMAP from single cell RNA sequencing data showing heterogeneity of artery cells. aEC1, aEC2, aEC3 and aEC4 are the mature artery cell clusters. Figure adapted from Arolkar et al. 2023 (B) Tissue section of neonatal heart showing artery (in magenta). Image credit: Bhavnesh Bishnoi
In our prior work we have done in silico and in vivo analyses of molecular properties of cardiac artery endothelial cells. In these studies, we have shown that only a small subset of artery cells is plastic enough to give rise to new cells, and that this plasticity is coupled to age¾the younger the hearts, the more plasticity (Arolkar et al., 2023; Das et al., 2019). That being said, we were always curious to test if this molecular heterogeneity within arteries is also observed in other organs.
The question and where to look
In mouse hearts, induction of myocardial infarction leads to dissociation of individual artery endothelial cells from pre-existing arteries. Only a subset of these dissociated single cells undergo proliferation, which results in massive expansion of this population. Eventually these cells come together and coalesce to build a collateral artery in the heart (Figure 3). We still do not understand what makes a small population (~8.4%) of artery endothelial cells more plastic than its neighbors. What is the relevance of such functional heterogeneity? Can these “plastic” cells, with proliferative properties, be distinguished molecularly from other artery cells? We continue to ask these questions in our lab.
Figure 3: Schematic diagram of the process of artery reassembly involved in the formation of collateral artery in neonatal heart. Upon myocardial infarction (MI), artery endothelial cells migrate, dedifferentiate, proliferate and coalesce to form collateral arteries (Adapted from Arolkar et al. 2023 with modifications)
We are also curious about the occurrence of this unique biological process elsewhere in the mouse. So, we asked, if other critical (ischemia-prone) organs such as the brain, would demonstrate similar molecular heterogeneity within a given artery cell population. Luckily for us, apart from circle of Willis, which is embedded deep, the brain’s superficial layer, the pial layer, also has an extensive network of collaterals. This collateral network is formed between two major arterial trees, the middle cerebral artery and the anterior cerebral artery (Figure 4).
Figure 4: An embryonic brain vasculature. Arteries are shown in cyan and magenta shows all vessels. Collateral arteries are located between middle cerebral artery (MCA) and anterior cerebral artery (ACA) in each hemisphere of brain. Image credit: Swarnadip Ghosh
At the time, the brain was a new model to work on. The team did a thorough research on the anatomy and structure of mouse brain, especially how the arteries run through different segments of the brain, the time-lines, and the drivers. We read about different structures in the mouse brain and analyzed the gene expression patterns of various anatomic structures. We were surprised how little was known about the brain vasculature. Though stroke is one of the leading causes of deaths world-wide and have been known to us since ages, our approaches in its prevention or treatment is extremely limited (Bam et al., 2022; Grossman and Broderick, 2013). With all this in mind, we set off to ask our question: How do collateral arteries develop in a mouse brain? We chose to study pial collaterals to look for answers.
The hiccups: Mind the brain
While we were excited to start this new venture, we encountered the first bump very early on. A big challenge was to deduce a timeline. From earlier studies, we understood that pial collaterals in mouse brains were present at the time of birth, meaning, these structures developed during embryogenesis. We knew that tracking a developmental process could easily become very tricky. For starters, multiple overlapping cellular events during development could complicate our assessment of the timeline for the origin of pial arteries (middle and anterior cerebral arteries) and pial collateral arteries. Lack of a single molecular marker for collaterals would not let us distinguish arteries from collateral arteries.
The second challenge was more technical. The brain tissue was nothing like the heart¾it was squishy and lost its integrity post-processing. Preserving the integrity of the tissue and the embedded vasculature was a non-trivial task. We tried a variety of approaches, from isolating the pial layer (as a sheet) to sectioning and reconstructing different slices of brain tissue. But nothing worked.
The detours: Bypassing the blocks
None of our (older) tactics allowed us to reliably visualize the collaterals. With time, we realized that we will need to develop new tools to address the questions we were asking. During the late-gestational period, when the pial collateral arteries develop (embryonic day (e) 15.5 to 18.5), the cranium and the skin (with its very own intricate vascular network) grow concurrently. This transformation posed a great obstacle for us to accurately visualize the pial blood vessels across different stages without the interference from surrounding tissue. It took us a year and a half to optimize a method for immunostaining and whole brain imaging of vasculature, with cellular resolution. After many trials and errors, we had a protocol which allowed us to confidently identify pial collaterals in all stages of developing mouse brain. Alongside, we also developed a quantitative method (Figure 5) to distinguish pial arteries from pial collaterals. Eventually, we were able to leverage this quantitative approach to delineate the precise timeline for development of pial arteries vis-à-vis collaterals in the mouse brain. With this, our curiosity deepened. We asked what was the cellular lineage of the pial collaterals. To address these questions, we utilized several transgenic mouse lines which enabled us for genetic fate mapping of the endothelial cells that form collateral arteries. As anticipated, we found a major cellular contribution (77%) from the preexisting artery cells with a smaller but notable contribution (31%) from the capillary cells, resulting in a mixed lineage composition.
Figure 5: A quantitative approach of analyzing complex brain arterial network. (i, ii) Intensity line profile were generated across each hemisphere. (iii) peaks per line profile were plotted along the width of a hemisphere and (iv) fitted with a Gaussian function. The fitted curve shows arterial coverage and the area under the curve within ±500 micron denotes the extent of collateral network. (Figure adapted from Kumar et al. 2024 with modification).
We next asked how pial collaterals form. This led us to embark on a new phase of investigation using in vivo experimentation and whole organ imaging to capture snapshot of the developmental process. Here we encountered one of the most formidable challenges. From immunostaining fixed samples, we realized that pial collaterals develop rapidly during embryogenesis. After a series of unsuccessful attempts to capture the cellular process in action, we refined our work-plan, and pushed the limits. We decided to build a system which allowed us to image brains of live embryos (Kawasoe et al., 2020; Yuryev et al., 2016). From immunostaining whole brains, we already knew that pial collaterals form in a very short time-range of 1-2 days. Hence, we hoped that keeping the embryo alive outside the mother’s womb for 3-4 hours (at the relevant gestational period, i.e., e16-e16.5) and making it accessible to microscopy, would help us capture the cellular dynamics involved in pial collateral artery development. We followed a surgical procedure where the developing embryos were taken out from the anesthetized pregnant dam. The embryos were still connected via umbilical cord and kept within the intact yolk sac. The whole set-up was kept adequately hydrated and temperature was stringently maintained to ensure the survival of the embryos. This set up was coupled with a (stereo and confocal) microscope to capture the vascular dynamics at cellular resolution (Figure 6). By live imaging embryos, we bypassed all biases and concerns, be it technical or biological. And the results were truly surprising and rewarding. The process we captured was distinct from what we observe in the heart. We captured pre-existing artery tips walking on defined microvascular structures (Kumar et al., 2024). It was exciting to observe the collaboration of artery and capillary endothelial cells.
Figure 6: Schematic diagram of the intravital time lapse imaging set up to capture collateral artery development during embryogenesis. (Figure adapted from Kumar et al. 2024)
We also systematically tested the role of CXCL12 and VEGF pathways in pial collateral development and remodeling. We chose these molecules as they are already known to perform critical functions during coronary collateral development, post-MI. Remarkably, in contrast to the heart, CXCL12 was dispensable for the development of pial collaterals during embryogenesis. While VEGF pathway was critical, it performed a very different function─helping in artery tip extension. We also performed longitudinal imaging of adult pial layer, and assessed the effects of hypoxia on individual artery cells which make up pial collaterals. Together, using a combination of mouse genetics and intravital/longitudinal imaging we showed organ-specific mechanisms drive collateral development in the brain and heart (compare Figure 3 with Figure 7).
Figure 7: Schematic diagram of the process of artery tip extension involved in the formation of pial collateral artery in mouse brain. VegfR2+ artery tips (in red) grows along microvascular (MV) track (in green) to form pial collaterals. (Figure adapted from Kumar et al. 2024, with modification)
This study was a result of combined output from a post-doctoral work, a part of doctoral research work and three master’s theses. It, indeed, was a team-driven pursuit and a notable example of curiosity-driven science. Many of the authors have moved on to their next stage of careers, continuing to explore multiple aspects of neuroscience and vascular biology. We anticipate amazing outcome from their works in near future.
References:
Arolkar, G., Kumar, S. K., Wang, H., Gonzalez, K. M., Kumar, S., Bishnoi, B., Rios Coronado, P. E., Woo, Y. J., Red-Horse, K. and Das, S. (2023). Dedifferentiation and Proliferation of Artery Endothelial Cells Drive Coronary Collateral Development in Mice. Arterioscler Thromb Vasc Biol 43, 1455–1477.
Augustin, H. G. and Koh, G. Y. (2017). Organotypic vasculature: From descriptive heterogeneity to functional pathophysiology. Science (1979) 357,.
Bam, K., Olaiya, M. T., Cadilhac, D. A., Donnan, G. A., Murphy, L. and Kilkenny, M. F. (2022). Enhancing primary stroke prevention: a combination approach. Lancet Public Health 7, e721–e724.
Das, S., Goldstone, A. B., Wang, H., Farry, J., D’Amato, G., Paulsen, M. J., Eskandari, A., Hironaka, C. E., Phansalkar, R., Sharma, B., et al. (2019). A Unique Collateral Artery Development Program Promotes Neonatal Heart Regeneration. Cell 176, 1128-1142.e18.
Grossman, A. W. and Broderick, J. P. (2013). Advances and challenges in treatment and prevention of ischemic stroke. Ann Neurol 74, 363–372.
Kawasoe, R., Shinoda, T., Hattori, Y., Nakagawa, M., Pham, T. Q., Tanaka, Y., Sagou, K., Saito, K., Katsuki, S., Kotani, T., et al. (2020). Two-photon microscopic observation of cell-production dynamics in the developing mammalian neocortex in utero. Dev Growth Differ 62, 118–128.
Kumar, S., Ghosh, S., Shanavas, N., Sivaramakrishnan, V., Dwari, M. and Das, S. (2024). Development of pial collaterals by extension of pre-existing artery tips. Cell Rep 43, 114771.
McDonald, A. I., Shirali, A. S., Aragón, R., Ma, F., Hernandez, G., Vaughn, D. A., Mack, J. J., Lim, T. Y., Sunshine, H., Zhao, P., et al. (2018). Endothelial Regeneration of Large Vessels Is a Biphasic Process Driven by Local Cells with Distinct Proliferative Capacities. Cell Stem Cell 23, 210-225.e6.
Trimm, E. and Red-Horse, K. (2022). Vascular endothelial cell development and diversity. Nature Reviews Cardiology 2022 1–14.
Yuryev, M., Pellegrino, C., Jokinen, V., Andriichuk, L., Khirug, S., Khiroug, L. and Riverat, C. (2016). In vivo calcium imaging of evoked calcium waves in the embryonic cortex. Front Cell Neurosci 9, 173603.
In this SciArt profile, we find out more about B. Duygu Özpolat, an assistant professor whose research focuses on germ cell regeneration in segmented worms. Duygu enjoys creating pottery pieces of worms, bugs, and other “creepy” animals to show people the beauty and wonders of these organisms.
This drawing combines a few embryos and larvae from research organisms used in Developmental Biology! The blood vessels in the background are inspired by chicken embryos.
Can you tell us about your background and what you work on now?
I am an assistant professor of biology and a visual artist currently living in Saint Louis, Missouri. I earned my Ph.D. in Cell and Molecular Biology from Tulane University in New Orleans, and my B.Sc. in Biology from Middle East Technical University in Ankara, Türkiye. I primarily study stem cells and regeneration, with a specific focus on germ cell regeneration, using segmented worms as a model. Here is a great article about my lab’s work.
A seaslug (nudibranch) dish. Inspired by the species Hypselodoris confetti.
Were you always going to be a scientist?
Kind of! I grew up with a mother who was an arts teacher. So, art was in my life from early ages. But then when I started primary school and started getting exposure to science topics, and simple home experiments, similar to making a battery from potatoes or baking powder and vinegar volcano experiments, I fell in love with science. My mom loves telling the story that one day while in primary school, I asked her whether I could become a tailor and a scientist when I grow up, to which she replied, “Of course honey!”. I think of this as one of the defining moments in my life because I was so lucky to have a mother who believed I could be whatever I wanted to be. I got no discouraging, gender-stereotyped messages from her.
A membracid insect. Membracids are amazing insects that come in crazy shapes and I love recreating these fun insects using ceramics.
And what about art – have you always enjoyed it?
There are many layers to this for me: Art, just like science, is the exploration of the unknown, which is one of the main reasons I am also drawn to art. But unlike science, art for me has less anxiety and planning around it. I like mindlessly losing myself in a piece of artwork, and not worrying about what people will think about it, whether anyone will like it. I enjoy the process of creating, the tactile aspect of it, and how making art keeps me present in the moment.
What or who are your most important artistic influences?
Like any biologist, I have been absolutely charmed by the German zoologist Ernst Haeckel’s illustrations (but have been disappointed to find out about his racist ideology). When I visited Harvard Museum of Natural History and saw Leopold and Rudolf Blaschka’s glass flowers I was blown away! Some contemporary Scientist-Artists who inspire me are Steph Nowotarski and Bob Goldstein. Bob does screen printing, him and I collaborated on a poster project for a seminar series, which was great fun. It is encouraging for me to see full-time scientists like Steph and Bob make such great art inspired by science.
Meanwhile, my work could not exist without people who go out and document these amazing creatures. My husband Ryan Null is the person who taught me so much about insects and other arthropods. It is amazing to have somebody so knowledgeable around you. He is able to find all kinds of insects just in our backyard and photograph them, and sometimes I help him with his photography. We took the candy-striped leafhopper photo together while living on Cape Cod and later I made the ceramics piece inspired by it.
I also follow quite a few macro and wildlife photographers’ works such as Markus Kam and Alexander Semenov (who is also a scientist).
Finally, I am a huge fan of contemporary art and related museums. When I lived in Paris, I visited Palais de Tokyo often and was introduced to Marguerite Humeau’s work there for the first time. The exhibition at the time included her work called FOXP2, which is a gene associated with language ability in vertebrates. Another contemporary art museum experience that I cannot forget is Mark Dion’s “Misadventures of a 21st-Century Naturalist” exhibition at ICA in Boston, which left me absolutely speechless. I would love to be able to make artwork at the scale Mark Dion works one day.
Since moving to Saint Louis, I have been mostly making my pottery in my basement, and I take the pieces to be fired in a kiln at a pottery shop. I would like to go back to taking classes at a pottery studio at some point because I like the communal aspects of studios, and having made a commitment to taking a class makes it harder to procrastinate on my arts projects.
A nereidid polychaete worm with some artistic license. Ceramic jar at Duygu’s office (it usually has candies inside). Photo credit: Whitney Curtis. (video: https://www.instagram.com/p/Cb5SaX6lKhY/)
Does your science influence your art at all, or are they separate worlds?
Yes, my science influences my art very much. I am on a mission to get worms, bugs, and other “creepy” animals more appreciated! It is very important to me to invite people to leave their preconceived notions about these animals aside and open their minds to the beauty and wonders of them. We see only a handful of animals (usually vertebrates) celebrated in popular culture when there are literally millions of amazing species out there. I have given SciArt talks at conferences, and would like to use my pieces for science outreach projects in the future.
The photo of the actual animal is by my husband Ryan Null. The second photo is the ceramics piece I made inspired by this colorful bug.
What are you thinking of working on next?
I am very excited about building my own plaster molds to use in slip casting. This is a ceramics technique where clay in liquid form is used to cast a piece using a mold. I trained with Mary Rhein (an amazing local Saint Louis area artist). The process of making molds is very technical, you definitely need a “protocol” for this practice which makes me feel like I am at the lab bench. I am currently working on making molds for some of the insect figures such as the membracids and candy-striped leafhopper I made in the past, so I can focus on painting and decorating pieces.
I also love my most recent collaboration with my husband Ryan Null, who is also a scientist. Ryan loves leeches (so do I!). Leeches have been an amazing developmental biology model, and we finally got some from David Weisblat’s lab. Ryan came up with the design of a leech ice cream dish, with small baby leeches as the ice cream spoons. I want to make a few more variations of this piece.
This is a collaboration with my husband Ryan Null, who adores leeches. He designed this plate with the spoons (the baby leeches), and I built it from clay. We picked the glazes together. This is Helobdella austinensis. They are hermaphrodites, and when they have babies, the babies live attached to the parent’s belly by their suckers. Whenever the parent goes feeding, the babies can reach for the food and feed as well. This species doesn’t suck blood. It eats other animals like insect larvae etc.
Find out more about Duygu:
www.ozpolatlab.org – mostly science and my lab’s news, academic self-help resources, and some science-art
In 2022, Biology Letters launched the Early Career Researcher Competition to highlight the best research papers published in the journal by early career researchers (ECRs). We are delighted to announce that the 2025 competition is now open until Wednesday 30 April. The overall winner will receive £1000 and two runners-up will receive £500 each (or currency equivalent). We hope the prizes are particularly helpful for funding new research and/or attending conferences. Please see our terms and conditions before entering or contact the editorial office with your questions.
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