Developmental Biology Community Research Articles

TubULAR: tracking in toto deformations of dynamic tissues via constrained maps.

A common motif in biology is the arrangement of cells into tubes, which further transform into complex shapes. Traditionally, analysis of dynamic tissues has relied on inspecting static snapshots, live imaging of cross-sections or tracking isolated cells in three dimensions. However, capturing the interplay between in-plane and out-of-plane behaviors requires following the full surface as it deforms and integrating cell-scale motions into collective, tissue-scale deformations. Here, we present an analysis framework that builds in toto maps of tissue deformations by following tissue parcels in a static material frame of reference. Our approach then relates in-plane and out-of-plane behaviors and decomposes complex deformation maps into elementary contributions. The tube-like surface Lagrangian analysis resource (TubULAR) provides an open-source implementation accessible either as a standalone toolkit or as an extension of the ImSAnE package used in the developmental biology community. We demonstrate our approach by analyzing shape change in the embryonic Drosophila midgut and beating zebrafish heart. The method naturally generalizes to in vitro and synthetic systems and provides ready access to the mechanical mechanisms relating genetic patterning to organ shape change.

Automated staging of zebrafish embryos with deep learning.

The zebrafish (Danio rerio) is an important biomedical model organism used in many disciplines. The phenomenon of developmental delay in zebrafish embryos has been widely reported as part of a mutant or treatment-induced phenotype. However, the detection and quantification of these delays is often achieved through manual observation, which is both time-consuming and subjective. We present KimmelNet, a deep learning model trained to predict embryo age (hours post fertilisation) from 2D brightfield images. KimmelNet's predictions agree closely with established staging methods and can detect developmental delays between populations with high confidence using as few as 100 images. Moreover, KimmelNet generalises to previously unseen data, with transfer learning enhancing its performance. With the ability to analyse tens of thousands of standard brightfield microscopy images on a timescale of minutes, we envisage that KimmelNet will be a valuable resource for the developmental biology community. Furthermore, the approach we have used could easily be adapted to generate models for other organisms.

Juan Modolell (1937-2023).

On February 28th 2023, Juan Modolell passed away at his home in Madrid aged 85, leaving the developmental biology community bereaved of a pioneer in neural pattern formation. He was an extraordinary scientist who made seminal discoveries in two unrelated fields of work – Escherichia coli protein biosynthesis and Drosophila melanogaster developmental biology. All of us who had the privilege of knowing Juan will remember a brilliant, generous and forward-thinking scientist, who did not stop inventing himself and who left wonderful advice to future generations of young scientists: ‘Have fun doing science and do not be afraid of changing topics, because it is a rejuvenating experience that helps to keep the passion for science.’Juan Modolell was born in Barcelona, Spain, in 1937. From childhood, he was passionate about animals but, unlike most children, he preferred insects to furred animals, being fond of observing, collecting and photographing butterflies and beetles (a hobby that he perfected during his life). Unsurprisingly, he obtained a bachelor's degree in Biological Sciences at the University of Barcelona, Spain, in 1959 but, reasoning that unless he devoted himself to teaching, biology would not serve him to earn his livelihood, he obtained a second degree in Biochemistry at the University of La Laguna (1962) in the Canary Islands, where his family had moved following his father's job as a chemist at an oil refinery. Although his original plan was to become an industrial chemist, he finally enrolled in research at the laboratory of R. O. Moore at the Department of Biochemistry, Ohio State University, USA, characterising an ATPase from rat liver adipose tissue and obtaining a PhD in Biochemistry in 1966. From there, he moved to the laboratory of Bernard Davis, a prominent figure in microbiology at Harvard Medical School (USA), and changed his research topic to the study of the inhibition of E. coli protein biosynthesis by the antibiotic streptomycin (Modolell and Davis, 1969). Juan kept very pleasant memories of this scientifically successful period in Boston, accompanied by his beloved wife Rosa María and their eldest daughter Inés.He came back to Madrid, Spain, in 1970 to join the laboratory of the microbiologist David Vázquez, obtained a second PhD degree (in Chemistry, from the Universidad Complutense de Madrid in 1971), and soon became a staff member of the Spanish National Research Council (CSIC). His work helped to decipher the interaction mechanisms of aminoacyl-tRNA and the elongation factors EF-G and EF-Tu with the ribosome, determined the stoichiometry of ribosomal translocation (Modolell et al., 1973) and revealed the mode of action of several antibiotics that specifically inhibit bacterial protein synthesis.In 1979, Juan was an established researcher in the field of protein biosynthesis when, due to his inclination for addressing developmental problems, he decided to join the emerging community of researchers trying to decipher the molecular basis of development using a combination of genetics and molecular biology. He contacted Antonio García-Bellido, also working at the Centro de Biología Molecular Severo Ochoa, to seek advice on which developmental problem would be best addressed at the molecular level. Antonio was clear, suggesting that Juan work (if he was ambitious enough) on the relevant question of pattern formation (that is, the generation of constant distributions of cell types in a developing tissue or organism), focusing on the molecular analysis of the achaete-scute complex (AS-C).The cuticle of D. melanogaster adults is covered by chaetae, sensory organs (SOs) that develop in a stereotyped pattern, appearing in the same number and at the same positions in all wild-type individuals. Interestingly, some of the chaetae are missing in fly mutants for the achaete (ac) or scute (sc) genes of the AS-C at allele-specific positions. Furthermore, flies carrying Hairy wing mutations, which map at the AS-C, display ectopic SOs. These phenotypes suggested that AS-C genes play a key role in SO patterning (García-Bellido, 1979). After a brilliant presentation by Antonio on all the subtleties and unknowns of the system, Juan took Antonio's advice and was determined to give a definitive turn to his scientific career.To clone AS-C, a technically challenging project in the early 1980s, and much more so in Spain, Juan returned to Boston with his family, which by then had increased to three daughters. There, at Harvard University and with the help of Welcome Bender, Mat Meselson and Victor Corces, he managed to clone a genomic fragment of the AS-C (see Modolell et al., 1983 for details) and returned to Madrid in the summer of 1981. That clone was used as the starting point for a chromosomal walk within the AS-C performed by Modolell's group (initially, a small team of five women including two young predoctoral students, M.R-G. and Laura Carramolino), which led to the cloning of more than 90 kb of contiguous DNA of the AS-C, as well as the mapping of the molecular lesions associated with most of the available ac and sc mutations within the cloned genomic DNA, and the identification of the transcription units of the three components of the AS-C known at that time: ac, sc and lethal of scute. This was the first report of cloning a developmental gene complex (Campuzano et al., 1985, 1986; Carramolino et al., 1982).Although these were very relevant observations, Juan's main concern was to determine the role of the AS-C in the patterning of the adult SOs. Each chaeta is formed by several cells that derive from a SO precursor cell (SOP). Thanks to using one enhancer trap line that accumulates β-galactosidase in the SOPs, it was possible to determine the strict correlation between the position of SOPs in the wing imaginal disc (the precursor of the notum and wing of the adult fly) and that of the adult fly chaetae. Therefore, the problem of how the pattern of SOs was generated shifted to understanding how the pattern of SOPs was established in the wing disc. Modolell's team and others (Cubas et al., 1991; Romani et al., 1989; Skeath and Carroll, 1991) demonstrated that ac and sc are co-expressed in clusters of cells in the wing disc and that SOPs showed an enhanced accumulation of Ac and Sc proteins. Furthermore, ectopic expression of ac or sc led to ectopic SOs (Balcells et al., 1988; Rodríguez et al., 1990). These results, combined with the involvement of the AS-C in the development of the embryonic central nervous system, described by Jiménez and Campos-Ortega (1979), and the in situ hybridization data to visualize the embryonic expression of AS-C genes (Cabrera et al., 1987; Romani et al., 1987), indicated that the AS-C proteins endow ectodermal cells with the ability to become neural precursors (either SOPs or neuroblasts). Accordingly, Juan and Alain Ghysen coined the name ‘proneural’ for these genes, and the clusters of cells expressing proneural genes were called ‘proneural clusters’ (Ghysen and Dambly-Chaudiere, 1989; Romani et al., 1989).The key role of ac-sc in the patterning of the notum external SOs thus relies on their spatially and temporally restricted pattern of expression in the wing disc. Thus, the next relevant question was to understand how this expression is controlled. Modolell's group predicted the existence of cis-regulatory elements (enhancers; first proposed for a developmental gene complex) in the non-transcribed genomic DNA of the AS-C that would drive its expression at precise positions of the wing disc (Ruiz-Gómez and Modolell, 1987). Juan's team demonstrated that these enhancers were present, and an additional enhancer was required to reinforce ac and sc expression in neural precursors, as well as the use of shared enhancers that accounted for the identical expression patterns of ac and sc (Culí and Modolell, 1998; Gómez-Skarmeta et al., 1995; Martínez and Modolell, 1991).The next logical aim was to characterise the genes and signalling pathways that act through those enhancers to control ac/sc expression; the so-called ‘prepattern genes’, based on ideas envisaged by C. Stern 70 years ago (Stern, 1954; reviewed by Ghysen and Dambly-Chaudiere, 1989; Gómez-Skarmeta et al., 2003). The prepattern model predicted that prepattern genes were expressed in the wing disc in domains partially overlapping the proneural clusters. AS-C would act as an integrating device, reading prepattern information and, consequently, allowing ac/sc transcription to take place only in clusters of cells harbouring the adequate combination of prepattern proteins. Several prepattern genes were identified in Juan's lab including pannier, tailup, charlatan and those forming the Iroquois complex (Leyns et al., 1996; García-García et al., 1999; Gómez-Skarmeta et al., 1996; de Navascués and Modolell, 2010; Escudero et al., 2005). Similarly, it was determined that the molecular mechanisms that led to the specific accumulation of Ac and Sc proteins in SOPs involved the action of the proneural proteins, Notch and epidermal growth factor receptor signalling pathways on SOP-dedicated enhances (Culí and Modolell, 1998; Culí et al., 2001).Surprisingly, data from Juan's laboratory showed that transient, generalised expression of sc in wing discs devoid of the endogenous Ac and Sc proteins led to the development of some chaetae at the standard positions (Rodríguez et al., 1990). These findings suggested that SO patterning relies on topological informational in addition to the spatially restricted distribution of Ac/Sc proteins. Again, Juan's team provided a molecular explanation to this puzzling observation that relies on the activity of extra macrochaetae (emc), loss-of-function of which causes the development of extra chaetae. AS-C genes encode transcription factors of the basic-helix-loop-helix (bHLH) family that form heterodimers with the bHLH protein Daughterless (Da) and bind to the DNA through their basic region. Cloning emc (Garrell and Modolell, 1990; Ellis et al., 1990) demonstrated that it encodes an HLH protein devoid of the basic DNA-interacting domain. Emc competes with Da in binding to Ac or Sc, forming Emc/Ac or Emc/Sc dimers unable to bind to DNA and effectively sequestering Ac/Sc proteins. Furthermore, Emc distribution provided positional information in the wing disc, because SOPs appear within proneural clusters in regions with minimal levels of emc expression (Cubas and Modolell, 1992; Van Doren et al., 1992).These discoveries from Juan's group were paradigmatic because they established how hierarchical gene activity generates morphological patterns. Furthermore, they facilitated the identification of proneural genes in other invertebrates and vertebrates, thus demonstrating the universality of the proneural function and marking the beginning of our knowledge of nervous system development (Gómez-Skarmeta et al., 2003). After this pioneering work on pattern formation, Juan continued making important contributions to our understating of other developmental processes in Drosophila. It is common in development for a single protein to control different processes and this is indeed the case for the Iroquois-complex homeodomain proteins. After their discovery as components of the prepattern, Iroquois genes were reported to be involved in the specification of the presumptive notum region of the wing disc and of the dorsal compartment of the eye disc, just to mention two of their functions (Cavodeassi et al., 2000; Diez del Corral et al., 1999; Villa-Cuesta et al., 2007). Iroquois genes are evolutionarily conserved and, from there, Juan and his group embarked on the analysis of the role of these genes in Xenopus development demonstrating that, similar to their Drosophila counterparts, they control the expression of proneural genes and neural plate specification (reviewed by Cavodeassi et al., 2001). Last, but not least, Juan participated in international initiatives such as the sequencing of the Drosophila genome.Juan was a mentor for several generations of researchers. The members of his laboratory, who he considered his second family, as well as many visiting researchers, benefited from the know-how and the excellent scientific environment of Juan's lab. Many of these researchers presently form an active school and all of them were marked to some extent by Juan's approach to scientific research that combined an elegant experimental design (not devoid of risk), the most rigorous execution of the experiments, exhaustive data analyses and concise writing. Once retired, he continued being an active member of the group providing invaluable advice to all who approached him seeking guidance. We were very fortunate to have him as a colleague and friend and will never forget him.The authors thank the family, friends and collaborators of Juan Modolell for their help in the elaboration of this manuscript.

Lifting the cloche: Jeroen Bakkers interviews Didier Stainier.

Didier Stainier is Director of the Department of Developmental Genetics at the Max Planck Institute for Heart and Lung Research in Bad Nauheim, Germany. He became acquainted with the zebrafish model as a PhD student in Walter Gilbert's lab at Harvard, which motivated him to champion the use of this powerful model organism to study heart development as a postdoctoral fellow with Mark Fishman at Massachusetts General Hospital. Although his scientific focus has expanded significantly since then, zebrafish modelling and heart development and regeneration remain key topics in his research. The developmental biology and zebrafish modelling communities have embraced him as an inspiring mentor and advocate for basic research. Jeroen Bakkers is a group leader at the Hubrecht Institute for Developmental Biology and Stem Cell Research and Professor of Molecular Cardiogenetics at the University Medical Center Utrecht, The Netherlands. Jeroen did hid PhD with Herman Spaink at Leiden University, The Netherlands. A short visit to Massachusetts Institute of Technology during his doctoral training introduced him to the zebrafish model, which he applied to his PhD project. Zebrafish development remained the focus of his career, including during his postdoctoral training in the lab of Matthias Hammerschmidt at the Max Planck Institute of Immunology and Epigenetics in Freiburg and in his own lab at the Hubrecht Institute, where his group uses this powerful model organism to investigate cardiac development, disease and regeneration. Jeroen and Didier met up at a recent conference to talk about their shared interest in cardiac regeneration, a zebrafish mutant with a curious name and Didier's commitment to mentorship.

Preprint Highlight: ERK-mediated curvature feedback regulates branching morphogenesis in lung epithelial tissue

During development, cells operate in a complex geometrical environment. Geometry can inform morphogenesis by patterning mechanical and chemical signals. Yet, how this feedback occurs remains elusive. Using elegant imaging tools, mechanical perturbation, and modeling, the authors show that positive tissue curvature defines the site of highest ERK activity in lung epithelium. In turn, ERK dampens the curvature by promoting actin-mediated apical extension of cells. This negative feedback loop generates the branching pattern in developing lungs. These findings reinforce the notion that tissue geometry is necessary to comprehensively understand and recapitulate morphogenesis. This study will appeal to the broad cell and developmental biology community, as well as labs focusing on tissue engineering and in vitro organ models.

Preprint Highlight: Dynamic interplay of protrusive microtubule and contractile actomyosin forces drive tissue extension.

Cytoskeletal mechanical forces shape tissues during development. Although the role of the actomyosin machinery is extensively studied, how microtubules actively generate forces to shape tissues remains unknown. Combining in vivo experiments and simulations, this study elucidates that initial cell elongation during fly wing development is not driven by myosin contractility or external forces. Instead, protrusive forces generated by planar polarized noncentrosomal microtubules actively drive cell elongation, while myosin contractility is needed for final cell shape refinement. Thus ordered coordination between microtubules and actomyosin shapes the fly wing. This study will appeal to the broad cell and developmental biology community as it strengthens the growing notion that microtubules are active morphogenetic effectors. Beyond their core functions in cell division and intracellular transport, microtubule-mediated forces can directly dictate cell and tissue shape during development.

Preprint Highlight: Intertissue mechanical interactions shape the olfactory circuit in zebrafish.

How the mechanics of surrounding tissue regulate tissue morphogenesis in vivo is not well known. This study addresses this problem by studying the developing olfactory placodes in zebrafish, a sensory organ which later gives rise to the opening of the nose. Combining this highly tractable system with quantitative live imaging, genetics, and biophysical manipulations, the authors reveal that the extracellular matrix transmits mechanical cues from the developing eye to the adjacent olfactory placode, thereby coupling their morphogenesis. This study will appeal to the broad cell and developmental biology community as it strengthens the fundamental notion that the emergence of form during embryogenesis does not happen in isolation and relies on the surrounding physical cues and interactions with adjacent tissues.

The Biological Robots Are Coming! But Note They Have Been Here for ∼3.5 Billion Years

GEN BiotechnologyVol. 1, No. 1 Views & NewsFree AccessThe Biological Robots Are Coming! But Note They Have Been Here for ∼3.5 Billion YearsWilliam C. RatcliffWilliam C. Ratcliff*Address correspondence to: William C. Ratcliff, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA, E-mail Address: william.ratcliff@biology.gatech.eduSchool of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA.Search for more papers by this authorPublished Online:16 Feb 2022https://doi.org/10.1089/genbio.2022.29007.wraAboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail Researchers led by Michael Levin and Josh Bongard cause a stir by investigating multicellular xenobot assemblies that challenge our conventional idea of replication.Where is the line between a robot and an organism? Does such a line even exist? Definitions, even those that are fundamental, have long been problematic in biology. For example, we still argue about how to define species,1 organisms,2 Darwinian fitness,3 or even life itself.4 Don't believe me? Go on Twitter and defend any definition of the mentioned concepts as the One True Definition!It should come as little surprise that pioneering work in biological robotics is as controversial as it is exciting. Take for example the article published in December 2021 in the Proceedings of the National Academy of Sciences by Sam Kreigman and Douglas Blackiston at Tufts University and colleagues.5 This article, entitled “Kinematic self-replication in reconfigurable organisms,”5 is the third installment of the authors' “xenobots” series.In their prior study, this interdisciplinary team of roboticists, developmental biologists, and computer scientists (which makes up the Institute for Computationally Designed Organisms) showed how xenobots can be generated through the self-assembly of pluripotent Xenopus laevis stem cells and programmed through artificial intelligence (AI)-guided design for functions such as walking locomotion.6 Xenobots were next shown to be capable of navigating aqueous environments through ciliary swimming, repair damage, and exhibit novel properties as swarms.7 In the latest report, the Tufts team has extended this model system, showing that xenobots are capable of reproduction.Before describing the article further, it is worth emphasizing that xenobots are an example of what is known in the trade as weird biology. The cells that constitute them do not divide. The only way they can reproduce is by building new xenobots from isolated cells in their environment. In the recent PNAS article, the authors take advantage of this fact. Using AI, the researchers designed xenobots with a crescent shape that leads to them swimming in circles, effectively pushing progenitor cells sitting on the bottom of a culture dish into piles. These piles then self-assemble into new xenobots (Fig. 1). This is not reproduction in the normal vertical manner, yet it is unquestionably reproduction.FIG. 1. Crescent-shaped xenobots swim in circles, sweeping up piles of isolated cells, which then self-assemble into a new xenobot. (Credit: Douglas Blackiston and Samuel Kriegman, Institute for Computationally Designed Organisms.)Such “kinetic” reproduction has its limits. For one thing, the offspring that are generated do not inherit their parents' ability to reproduce. Unlike normal vertical reproduction, where phenotype can be inherited by the transfer of informational polymers (i.e., DNA or RNA) or epigenetic cellular states, there is no material transfer between generations. Offspring xenobots are little more than piles of cells that self-assemble into spherical propagules, and thus lack the crescent shape that allows them to reproduce by swimming in circles and sweeping up piles of cells. I expect this is only a temporary limitation, surmountable by future innovations that allow the traits of daughter propagules to be tuned, perhaps by modifying the types of progenitor cells present and their rules for multicellular self-assembly.X, RobotThis study has generated much excitement in the press and a fair amount of criticism. Although it is easy to dismiss the apocalyptic “Terminator” media takes (even as the authors' YouTube video racks up hundreds of thousands of hits), more serious criticism has been lodged by the developmental biology community. First, many observers on Twitter thought this study was simply a rebranding of “animal caps,” a widely used model system in developmental biology that allows researchers to isolate pluripotent Xenopus cells and induce them to differentiate into different cell types.8 Second, individuals argued that calling xenobots “robots” was disingenuous, and that by the same definition fruit flies, yeast, and prions should be considered robots too.These criticisms miss the mark. Kreigman, Blackiston et al. are not attempting to learn about Xenopus development or claim that they are the first to show that animal caps can exhibit behaviors like swimming. The goal of the study is fundamentally robotic, exploring the rational design of biological machines capable of performing user-directed behaviors. As for the second critique, we come back to a problem of definitions. What is a robot and how does it differ from an organism?This distinction has always been blurry. In his influential 1976 book The Selfish Gene, Richard Dawkins wrote: “We are survival machines—robot vehicles blindly programmed to preserve the selfish molecules known as genes.” Whether you agree with this sentiment, all organisms possess the key trait of a robot: the ability to be programmed to perform autonomous actions. Perhaps the largest difference between biorobots and bog-standard organisms is that the former have behaviors programmed by people, the latter by a process of Darwinian evolution (and in organisms with cognition and memory, with the complex menagerie of behaviors developed over the individual's lifetime). According to this definition, all organisms are robots, although not all robots are organisms.The field of biological robotics is clearly in its infancy. Although I think it is reasonable to ask, “What practical use is there for xenobots?” in truth I do not think they have any immediate utility. The real payoff is the future potential of this approach. Bespoke multicellular construction is a key goal for synthetic biology,9 and currently it is far easier to leverage extant developmental modules (such as Xenopus stem cells) than construct them from scratch.Although the lack of multicellular heredity may seem like a crucial limitation, it can also be extremely valuable. Darwinian systems are inherently dangerous: difficult to control even under the best of circumstances. There may be real value in designing biological machines capable of performing a specific function, and then expiring, with little risk of gaining evolutionary autonomy.

The future of conferences.

One of the many great things about being a developmental biologist is our strong sense of community. Conferences of all shapes and sizes reinforce these bonds between us and yet, even before the pandemic, scientists were becoming increasingly reluctant to travel to conferences due to concerns about climate change:‘Don't think I will travel to conferences as delegate again. Cutting down as speaker a lot.’Prof. Michael Stumpf (@theosysbio). Twitter; December 2019.Younger scientists in particular expressed concerns about the environmental impact of their travel, but also worried about how not travelling might affect their career:‘I know many senior scientists who are reducing attendance, but for someone like me without that recognition, how do I get my name out there without physically attending? Would love other options!’Dr Louise Stephen (@ciliaNcilia). Twitter; December 2019.Concerns about the changing climate were not the only problem. Traditional conference models also tend to exclude people with caring duties and those who can't travel due to lack of funding or difficulties obtaining visas (Sarabipour, 2020; Sarabipour et al., 2021). As we approached 2020, it became increasingly clear that things needed to change.Then came the pandemic. We got used to connecting with people, sharing and discussing data, and even socialising and networking, all through a computer screen. For many people, the online format has brought benefits even beyond the improvements in sustainability and accessibility:‘For the first time, I actually mustered up the courage to ask a question in a talk at ISSCR! The chat is helpful for introverts like me.’Mary Heather Celine Florido (@KiwiFlorido). Twitter; June 2020.There are, however, downsides to the new online world: awkward online poster sessions, unsatisfactory online networking and, at least for some, a sense that they were becoming disconnected from their scientific community. As we emerge into 2022, things are changing again and our new normal is characterised by hybrid conferences, for example the upcoming joint Spring Meeting of the British Societies for Developmental Biology and Cell Biology, which will adopt a hybrid format for the first time. This, in some ways, gives us the best of both worlds, but also shares some of the same problems as fully remote conferences. Hybrid meetings create an additional risk that remote attendees may feel like second-class citizens (Parncutt et al., 2021). Getting the balance right between in-person and online also creates uncertainty for organisers: will there be enough in-person attendees for the meeting to work successfully? If a high proportion of delegates decide to switch from in-person to online at short notice, then will the online provision be sufficient to sustain the conference?All of this leaves us with a problem. We urgently need to change the way we run our conferences, but many of us worry we might be losing too much if we limit ourselves to the existing remote and hybrid conference models.Scientists do experiments. When things are not working optimally we try again, we fail again, we fail better. Eventually, we improve things. Yet, before the pandemic the traditional conference model remained, well… traditional, with little innovation. The pandemic has forced us into new ways of coming together to share our science: if we are not completely happy with them, should this drive us back to our old ways? We propose that we should instead embark upon a period of experimentation with conference models.One particularly promising experimental approach is represented by ‘spatially distributed’ international conferences (Abbott, 2020; Parncutt et al., 2021). These bring people together in-person while limiting long-distance travel by organising into a number of hubs, linked together through streaming technologies. Such multi-hub conferences have already proved successful in other fields (Parncutt et al., 2021). This model could work particularly well for fields such as developmental biology, where many countries already have thriving national societies or regional meetings that could form local hubs within international spatially distributed conferences.We'd suggest that some travel between hubs should be encouraged. In particular, cohorts of younger delegates might be keen to travel beyond their own country to expand their networks, and a few well-established international scientists might also switch places between hubs. This would enrich the experience for those who wish to (or need to) stay closer to home, while still greatly reducing overall air travel compared with a typical large international meeting.By breaking large meetings up into multiple smaller hubs, we could encourage a more retreat-like atmosphere, perhaps with core workshop-like sessions on specific topics, giving opportunities for early career researchers (ECRs) to get focused feedback. These smaller sessions may also provide an ideal setting for productive discussions with remote contributors to the conference. This format would be a refreshing contrast to the typical traditional large international conference, which can be intimidating for younger researchers or those new to the field. So many of us have had the experience of arriving hopefully at these huge meetings, excited about meeting new colleagues, only to leave disappointed.Multi-hub conferences could therefore solve a number of problems, but they could also bring new problems of their own. The organisation of these meetings could be complicated and potentially expensive. We sorely need reliable sources of information, particularly on logistics and technologies, in order to bring this promising new conference model within the grasp of the typical academic organiser.Scientific meetings can be distributed in time as well as in space. A number of excellent field-specific online seminar series (webinars) have sprung up during the COVID-19 pandemic, with one particularly successful example being the Virtual Gastrulation Zoom Talks (VGZT; Twitter: @VGZT2020_21; see https://thenode.biologists.com/webinar-list/ for more examples). Such ventures can be more than just a series of talks; VGZT has fostered ongoing lively discussion and networking through asynchronous discussions on Slack between participants, many of whom return week after week. Other webinars have a broader scope. Development's own ‘Development presents…’ series showcases the recently published or unpublished work of ECRs with a monthly menu of three short talks, often around a theme, followed by online small group discussions and socialising using Remo software (https://thenode.biologists.com/devpres/). Overall, webinars have been extremely helpful for keeping us in touch with each other in recent times, although most people would think of them as a complement to, rather than a replacement for, conferences. Plus, of course, they still lack the personal face-to-face interactions that so many people have missed.Scientists are creative people. Ideas must be out there that can overcome or bypass some of the problems discussed above. For example, how about visiting conferences around the world in the form of a holograph or avatar (Le et al., 2020) (Box 1)? Or, maybe the traditional scientific talk, which can be delivered successfully online, could be completely separated from the free-flowing discussion of science, which tends to happen best in person. To take this second idea to its extreme, we could imagine one single large event each year that brings together all developmental biologists (or – let's think big – all biologists) into an Expo-like festival with a varied menu of scientific and social activities. These activities could include lightning talks, poster sessions and focused workshops to provide a platform for ECRs and kick-start conversations, but would not include standard conference talks. Instead, we'd have watched these talks in our favourite online seminar series over the preceding year. Could the ‘Biology Expo’ give us all the benefits of traditional conferences at the bargain cost – in both money and carbon – of no more than one journey each year? Box 1. From Altspace to the Metaverse: a holographic space between traditional and hybrid?Holograms provide a way to ‘be in the room’ without being there and have captured imaginations and conveyed important messages ever since Princess Leia appeared as a hologram in Star Wars. Their use for major events, such as concerts (think 2022 ABBA tour), are making them more mainstream and there are companies (e.g. ARHT Media, Spatial) currently making 3D holographic displays for workplace meetings that could transform scientific events. Imagine each hub at a multi-hub conference with the ability to ‘beam’ their speakers to plenary stages across space and time so that those physically there listening feel connected to the virtual holographic speaker.Alternatively, we can give up the physical and go completely virtual. Virtual (VR) and augmented (AR) reality have been connecting people (well, their avatars) in virtual space for decades, but adopting their use for scientific meetings, workshops and conferences could provide additional ways for scientists to connect without being physically together.Microsoft already offers AltspaceVR (https://altvr.com/), where users across AR/VR space can interact and attend or host meetings, events and workshops. The utility of the platform for scientists is growing as AltspaceVR aligns with ‘Mesh’, Microsoft's mixed reality platform, providing VR avatars, holographic avatars and 2D PC users a space to come together ‘with a feeling of presence’. Facebook's Horizon is a similar idea whereby meetings and events occur in the ‘Metaverse’ (https://www.wired.com/story/what-is-the-metaverse/). Online meetings and events in virtual space, or in real space with holographic attendees, are already happening. As mixed-reality technology improves, the utility of these environments for scientific conferences will grow.Smaller, but equally creative, ideas pop up from time to time in blogs and on social media. For example, how about the ‘poster bot’, an interactive mobile video-conferencing interface that could be based on ‘Meeting Owl’ technology (https://sustainability.biologists.com/blog/meeting-Owls-and-Poster-Bots-2/). We imagine the poster bot might resemble a friendly species of Dalek that has somehow acquired a surprisingly broad grasp of developmental biology. Your poster bot would roam around a poster session – or even a bar or coffee room – and allow you to join conversations from the comfort of your own sofa at home.These ideas are not presented here as ready-to-use solutions. Rather, our point is that we don't have all the solutions right now, so we must all think outside the box and share our suggestions. From this melting pot of ideas new solutions will emerge. But what is the mechanism for capturing and developing new ideas?Experiments are always a step into the unknown. A great conference should spark transformative ideas and collaborations and can be a life-changing experience, particularly for early career researchers. No conference organiser wants to risk all this by adopting an experimental conference design that might fall flat. There is also a financial risk in moving away from established conference models. New technology costs money, and delegates may be unwilling to pay the true cost for remote access to a conference. It can also be difficult for organisers to predict how many delegates will register for a meeting that adopts an unfamiliar format.We propose that we need three types of resource to limit these risks: 1. Information about what worked and what failed for others.2. Discussion of new ideas.3. Funding to pay for new technologies and to mitigate financial risk.Some excellent sources of information are already available online. These include: The Company of Biologists Sustainable Conferencing initiative (https://sustainability.biologists.com); the ‘Flying Less’ initiative to reduce academia's carbon footprint (https://sites.tufts.edu/flyingless/multi-site-low-carbon-conferences-mulch/); resources from EMBL to help design virtual conferences (https://blogs.embl.org/events/2020/04/09/how-to-turn-your-conference-into-a-virtual-event/); ‘the Green Room’, a discussion forum for event planners to chat about sustainable events (https://forum.legacy-events.com/); and the YouTube channel of the Max Perutz Labs Climate Group (https://www.youtube.com/channel/UCwxfXV1iY2ROr6hf3zDH5JQ).In particular, The Company of Biologists Sustainable Conferencing website aims to be a one-stop shop, collecting together information sources, summarising new developments through a series of blogs, and allowing anyone to feed in their own ideas through a discussion board or on Twitter (follow @COB_Sustainable and use #Sustainable_Conferencing to share your own thoughts). Importantly, they also provide grants to support new conference models and ask grantees to report back on what worked well and what worked less well in their particular experiment (Box 2). Box 2. Sustainable Conferencing GrantsThe Company of Biologists offer Sustainable Conferencing Grants to fund innovative ideas that enable biologists to collaborate productively while minimising their impact on the environment. Applications are invited from the organisers of a wide range of virtual activities, including – but not limited to – meetings, workshops, conferences, seminars, training and networking in the fields covered by The Company of Biologists journals. Organisers are encouraged to come forward with innovative ideas, for example: Ideas that will reduce travel requirements and increase accessibility and inclusivity.Ideas that will improve interaction opportunities for geographically diverse participants.Ideas that will improve the ‘human’ experience of virtual meetings.In return, they ask for feedback on the tools used/support provided, describing what did and did not work, value for money and any ideas for future improvement, which they share on their website.For more information, see https://www.biologists.com/sustainable-conferencing-grants/.There will be no single ‘one size fits all’ solution to creating conferences fit for our new future. Pre-pandemic, most conferences tended to adopt a standard structure with very little evolution or experimentation. In the future, we envisage a ‘mix and match’ model based on a library of solutions that can be adapted to the particular needs of each conference.This is not just a problem to be solved by conference organisers: everyone has a part to play. As Steve Royle puts it:‘We can choose which meetings we attend. As a community, we can support meetings that are organised by organisations whose mission is to support science.’(Steve Royle; https://quantixed.org/2021/10/29/pleased-to-Meet-Me-Returning-to-in-Person-Meetings/)As he points out elsewhere in his article, we can also choose meetings organised with sustainability and accessibility in mind (see also Hamant et al., 2019; Sarabipour et al., 2021). In addition, we can all help by generating and discussing creative ideas and suggestions. What do you think would make conferences better for you? If you have an idea, we encourage you to discuss it with your colleagues and with the wider developmental biology community – who knows where it might lead. Let's work together for a better future for conferences.We thank Viktoria Lamprinaki for useful discussions. We are grateful to Michael Stumpf, Louise Stephen and Mary Heather Celine Florido for giving permission to quote their tweets, and Steve Royle for permission to quote from his blog.

The rise of developmental biology in China.

Developmental biology research in China started from experimental embryology, in particular from studies on aquatic and reptile animals. The recent growth of the developmental biology community in China parallels the increased governmental funding support and the recruitment of overseas talents. This flourishing field in China embraces the activities of developmental biology-related societies, national meetings, key research initiatives and talented scientists. The first Development paper from China, published in 2000, marked the beginning of a new era. More recently, the second decade in the 21st century witnessed the blossoming of developmental biology research in China. Significant research spotlights, technical advances, and up-and-coming areas will be discussed in this overview.

Quantitative developmental biology in vitro using micropatterning.

ABSTRACTMicropatterning encompasses a set of methods aimed at precisely controlling the spatial distribution of molecules onto the surface of materials. Biologists have borrowed the idea and adapted these methods, originally developed for electronics, to impose physical constraints on biological systems with the aim of addressing fundamental questions across biological scales from molecules to multicellular systems. Here, I approach this topic from a developmental biologist's perspective focusing specifically on how and why micropatterning has gained in popularity within the developmental biology community in recent years. Overall, this Primer provides a concise overview of how micropatterns are used to study developmental processes and emphasises how micropatterns are a useful addition to the developmental biologist’s toolbox.

Wolpert's French Flag: what's the problem?

Two phrases attributed to Lewis Wolpert - 'positional information' and 'The French Flag Model' - have become so intertwined that they are now used almost interchangeably. Here, I argue that this represents an unfortunate oversimplification of Wolpert's ideas that arose gradually in the developmental biology community, some significant time after his key papers were published. In contrast to common belief, Wolpert did not use the phrase French Flag 'Model' but instead introduced the French Flag 'Problem'. This famous metaphor was not a proposal of how patterning works, but rather an abstraction of the question to be addressed. More specifically, the French flag metaphor was an attempt to de-couple the problem from the multiple possible models that could solve it. In this spirit, Wolpert's first article on this topic also proposed (in addition to the well-known gradient model) an alternative solution to the French Flag Problem that was self-organising and had no gradients, and in which each cell 'cannot compute where it is in the system', i.e. there is no positional information. I discuss the history and evolution of these terms, and how they influence the way we study patterning.

Isolation of nanobodies against Xenopus embryonic antigens using immune and non-immune phage display libraries.

The use of Xenopus laevis as a model for vertebrate developmental biology is limited by a lack of antibodies specific for embryonic antigens. This study evaluated the use of immune and non-immune phage display libraries for the isolation of single domain antibodies, or nanobodies, with specificities for Xenopus embryonic antigens. The immune nanobody library was derived from peripheral blood lymphocyte RNA obtained from a llama immunized with Xenopus gastrula homogenates. Screening this library by immunostaining of embryonic tissues with pooled periplasmic material and sib-selection led to the isolation of several monoclonal phages reactive with the cytoplasm and nuclei of gastrula cells. One antigen recognized by a group of nanobodies was identified using a reverse proteomics approach as nucleoplasmin, an abundant histone chaperone. As an alternative strategy, a semi-synthetic non-immune llama nanobody phage display library was panned on highly purified Xenopus proteins. This proof-of-principle approach isolated monoclonal nanobodies that specifically bind Nuclear distribution element-like 1 (Ndel1) in multiple immunoassays. Our results suggest that immune and non-immune phage display screens on crude and purified embryonic antigens can efficiently identify nanobodies useful to the Xenopus developmental biology community.

Improving the visibility of developmental biology: time for induction and specification.

Developmental biology is a prominent field that has captured the imagination of many scientists. Over the years, research in the area has seen a steady number of amazing accomplishments, with peaks in activity following the development and application of new technologies. Although the field continues to flourish and produce excellent work, I have recently noticed difficulty with its perception and visibility. Having joined the developmental biology community during the early 1990s, and contributing since as a stem cell researcher, cancer biologist and an MD, I have a unique perspective on these challenges. Here, I discuss these issues and challenges and offer potential solutions for a field that is very important to me.

Recovery continues for developmental biology community in Puerto Rico

Recovery continues for developmental biology community in Puerto Rico

A "Brief History" of Developmental Biology in Israel.

While the history of developmental biology in Israel is relatively short, its impact is far-reaching, so we wanted to present a concise perspective on the Israeli developmental biology community, past-present-future. This community has undergone a wonderful, nearly exponential growth over the last three decades. How exactly did this happen? There are approximately fifty research groups that focus on developmental biology questions in Israel today that are members of the Israel Society of Developmental Biology (IsSDB; http://issdb.org/). The community has representative groups in a plethora of model systems, such as Nematostella, C. elegans, Drosophila, sea urchin, ascidians, zebrafish, Xenopus, chick and mouse, as well as plants, representing all the major universities and their branches, which include Bar-Ilan University, Ben-Gurion University of the Negev, The Hebrew University of Jerusalem, The University of Haifa, Technion - Israel Institute of Technology, Tel Aviv University and the Weizmann Institute of Science.

The Childhood Solid Tumor Network: A new resource for the developmental biology and oncology research communities

Significant advances have been made over the past 25 years in our understanding of the most common adult solid tumors such as breast, colon, lung and prostate cancer. Much less is known about childhood solid tumors because they are rare and because they originate in developing organs during fetal development, childhood and adolescence. It can be very difficult to study the cellular origins of pediatric solid tumors in developing organs characterized by rapid proliferative expansion, growth factor signaling, developmental angiogenesis, programmed cell death, tissue reorganization and cell migration. Not only has the etiology of pediatric cancer remained elusive because of their developmental origins, but it also makes it more difficult to treat. Molecular targeted therapeutics that alter developmental pathway signaling may have devastating effects on normal organ development. Therefore, basic research focused on the mechanisms of development provides an essential foundation for pediatric solid tumor translational research. In this article, we describe new resources available for the developmental biology and oncology research communities. In a companion paper, we present the detailed characterization of an orthotopic xenograft of a pediatric solid tumor derived from sympathoadrenal lineage during development.

StemChecker: a web-based tool to discover and explore stemness signatures in gene sets.

Stem cells present unique regenerative abilities, offering great potential for treatment of prevalent pathologies such as diabetes, neurodegenerative and heart diseases. Various research groups dedicated significant effort to identify sets of genes—so-called stemness signatures—considered essential to define stem cells. However, their usage has been hindered by the lack of comprehensive resources and easy-to-use tools. For this we developed StemChecker, a novel stemness analysis tool, based on the curation of nearly fifty published stemness signatures defined by gene expression, RNAi screens, Transcription Factor (TF) binding sites, literature reviews and computational approaches. StemChecker allows researchers to explore the presence of stemness signatures in user-defined gene sets, without carrying-out lengthy literature curation or data processing. To assist in exploring underlying regulatory mechanisms, we collected over 80 target gene sets of TFs associated with pluri- or multipotency. StemChecker presents an intuitive graphical display, as well as detailed statistical results in table format, which helps revealing transcriptionally regulatory programs, indicating the putative involvement of stemness-associated processes in diseases like cancer. Overall, StemChecker substantially expands the available repertoire of online tools, designed to assist the stem cell biology, developmental biology, regenerative medicine and human disease research community. StemChecker is freely accessible at http://stemchecker.sysbiolab.eu.

Atlas-builder software and the eNeuro atlas: resources for developmental biology and neuroscience.

A major limitation in understanding embryonic development is the lack of cell type-specific markers. Existing gene expression and marker atlases provide valuable tools, but they typically have one or more limitations: a lack of single-cell resolution; an inability to register multiple expression patterns to determine their precise relationship; an inability to be upgraded by users; an inability to compare novel patterns with the database patterns; and a lack of three-dimensional images. Here, we develop new 'atlas-builder' software that overcomes each of these limitations. A newly generated atlas is three-dimensional, allows the precise registration of an infinite number of cell type-specific markers, is searchable and is open-ended. Our software can be used to create an atlas of any tissue in any organism that contains stereotyped cell positions. We used the software to generate an 'eNeuro' atlas of the Drosophila embryonic CNS containing eight transcription factors that mark the major CNS cell types (motor neurons, glia, neurosecretory cells and interneurons). We found neuronal, but not glial, nuclei occupied stereotyped locations. We added 75 new Gal4 markers to the atlas to identify over 50% of all interneurons in the ventral CNS, and these lines allowed functional access to those interneurons for the first time. We expect the atlas-builder software to benefit a large proportion of the developmental biology community, and the eNeuro atlas to serve as a publicly accessible hub for integrating neuronal attributes - cell lineage, gene expression patterns, axon/dendrite projections, neurotransmitters--and linking them to individual neurons.

Zebrafish as a model for the study of neutrophil biology

To understand inflammation and immunity, we need to understand the biology of the neutrophil. Whereas these cells can readily be extracted from peripheral blood, their short lifespan makes genetic manipulations impractical. Murine knockout models have been highly informative, and new imaging techniques are allowing neutrophils to be seen during inflammation in vivo for the first time. However, there is a place for a new model of neutrophil biology, which readily permits imaging of individual neutrophils during inflammation in vivo, combined with the ease of genetic and chemical manipulation. The zebrafish has long been the model of choice for the developmental biology community, and the availability of genomic resources and tools for gene manipulation makes this an attractive model. Zebrafish innate immunity shares many features with mammalian systems, including neutrophils with morphological, biochemical, and functional features, also shared with mammalian neutrophils. Transgenic zebrafish with neutrophils specifically labeled with fluorescent proteins have been generated, and this advance has led to the adoption of zebrafish, alongside existing models, by a number of groups around the world. The use of these models has underpinned a number of key advances in the field, including the identification of a tissue gradient of hydrogen peroxide for neutrophil recruitment following tissue injury and direct evidence for reverse migration as a regulatable mechanism of inflammation resolution. In this review, we discuss the importance of zebrafish models in neutrophil biology and describe how the understanding of neutrophil biology has been advanced by the use of these models.