The discipline “Evo-devo” studies the developmental basis of morphological evolution. In the field, some original animal models are emerging as interesting model organisms, enriching the knowledge in the field more and more.
In the DECA team (Développement et évolution du cerveau antérieur, in French) we use an Evo-devo approach to study the developmental mechanisms responsible for brain evolution. Adaptation to new environments brings along changes in brain morphology and function, and these changes are more striking in organisms adapted to extreme environments. A beautiful example that illustrates this topic is the model species used in our lab, the Mexican fish Astyanax mexicanus (teleost). Within the same species there are several river-dwelling populations (surface fish) and other populations adapted to caves (cavefish), living in absolute darkness. Evolution in the caves have led to the total loss of eyes and pigmentation, similarly to many other cave organisms. Since the cavefish embryos initially develop a small eye primordium that then degenerates at larval stages, Astyanax mexicanus has become an attractive model to study the genetic and developmental causes of eyes loss and the mechanisms of sensory compensation.
Figure 1.- Adult cavefish and surface fish morphotypes of Astyanax mexicanus (top left and right, respectively). Chica cave (bottom left) and Micos river (bottom right) in Mexico.
In our lab some hypotheses have been tested in order to explain the regression of the eyes in cavefish, including modifications of midline signaling centers important for eye induction, or “trade-offs” within the neural plate between the eye field and other neural tissues.
Recently we started to wonder how early in embryogenesis we were able to find differences between the two eco-morphotypes. We decided to compare the process of gastrulation in the two Astyanax morphs, to look at the establishment of the axial signaling centers important for brain development. By comparing systematically the expression of key genes involved in gastrulation we found important heterochronic differences in terms of internalization and migration of the precursors of axial mesoderm, the embryonic organizer. At this point we were very proud of ourselves, because we were able to discriminate between surface fish and cavefish embryos already at the onset of gastrulation, just by looking at in situ hybridizations.
We realized that at the end of gastrulation the anterior axial mesoderm, also called prechordal plate, was different in several aspects, particularly when we looked at the expression of dkk1b (an inhibitor of the WNT pathway). In cavefish embryos, expression of dkk1b occurs in cells that were more dispersed than in surface fish, with lower levels of transcripts and with an earlier off-set of expression, suggesting a globally reduced repression of WNT compared to the surface morphotype. In vertebrates, WNT repression is fundamental for the normal development of the forebrain, including the eyes. Through functional test we showed that modified WNT modulation is indeed implicated in the cavefish eye phenotype.
Next, we reasoned that if at the onset of gastrulation there is already a morphotype-specific embryonic patterning, there might be something different even before this step. Since embryogenesis before gastrulation, including the induction of the organizer, is controlled by determinants present in the oocyte before fertilization occurs, we made the hypothesis that differences from gastrulation onwards are could be due to modified synthesis of maternal determinants. Thus we decided to compare through RNAseq the transcriptomes in embryos just after fertilization, when only maternally-provided mRNAs are present (maternal transcriptomes). When we got the first results we were quite surprised: more than 30% of the maternally-expressed genes were differentially expressed in the two morphs, and around 6600 different loci were de-regulated!
Figure 2.- Schematic diagram of Astyanax mexicanus embryonic development (top). From left to right: 2 cell stage, onset of gastrulation, mid-gastrulation, tailbud, somitogenesis, hatched larvae. Comparative analyses during Astyanax mexicanus embryogenesis (bottom). From left to right: volcano plot showing the distribution of differentially expressed genes relative to cavefish, downregulated in blue, upregulated in red (first panel), expression of dkk1b during gastrulation (second panel), expression of dkk1b at the end of gastrulation and somitogenesis (third panel), expression of hcrt in the hypothalamus at 24hpf and pax2a in the optic fissure at 48hpf (fourth panel, top and bottom respectively).
Then of course we wanted to test the maternal contribution to the cavefish phenotypic evolution. One of the greatest advantages of Astyanax mexicanus as a model is the interfertility between the different populations. In fact, in nature there are some geographic spots where hybridization of cave and river populations occurs nowadays. This unique feature allowed us to test the maternal contribution to a given phenotype by comparing F1 hybrids obtained by reciprocal crosses (hybrids obtained from surface fish eggs versus hybrids obtained from cavefish eggs). If the phenotype under study in the hybrids resembles the phenotype of the female morphotype, then we can say that there is a maternal effect on that trait. The results obtained here were also striking. We found that the patterns of gene expression in hybrids up to the end of gastrulation were exactly the same as those of their maternal morph. These results show first, that the morphotype-specific pattern of gastrulation is determined by maternal factors, and second, that maternal determinants influence embryonic development until stages much later than the maternal-to-zygotic transition.
After gastrulation, as development continues, all phenotypes analyzed became progressively similar between the reciprocal hybrids, and intermediate between the two pure eco-morphotypes. However, some of these morphotype-specific phenotypes at larval stages (hypothalamic patterning and eye regionalization) showed clear differences in the reciprocal hybrids, with a tendency towards the maternal morphs. This indicates that, when the zygotic genome (in a hybrid condition) takes over the control of development, it tends to homogenize the phenotypes, making less clear the full maternal effect observed at earlier stages.
Figure 3.- Schematic diagram of the crosses performed to test the maternal effect (first row). Expression of dkk1b at 50% epiboly (second row), expression of notail at 70% epiboly (third row) and expression of pax2a at 48hpf (fourth row).
Our work provided clear evidence that changes in the composition of the oocytes can modify the developmental trajectories, thereby contributing to phenotypic evolution. In this sense, the maternal transcriptome could react under specific environmental conditions, modifying subsequent interdependent developmental events, leading finally to a particular phenotypic outcome, in a way similar to a domino effect.
This work offers a new field for us to dig in. There are some questions we started to ask ourselves, for example could maternal genes be under selective pressure? Which mechanisms could account for their regulation within the ovary? How different is the maternal-to-zygotic transition in Astyanax morphs?
Research done by Jorge Torres-Paz, Julien Leclercq and Sylvie Rétaux at the Paris-Saclay Institute of Neuroscience, CNRS UMR9197, Université Paris-Sud, Université Paris-Saclay, France.
Due to the Coronavirus, Translational Immunology and the satellite BIS meeting were postponed from 26-27 March 2020 to the end of the year. We are happy to confirm the new date: 8-9 December 2020.
The aim of this conference is to bridge the translational gap in immunopathology, bringing together clinicians, research scientists and industry partners to discuss prominent advances from the bench to the clinicimmune The different sessions will have a particular focus on precision medicine in general, starting from disease-oriented cases and lessons learned. Innovative and alternative therapeutic strategies in immune-mediated disorders will be presented, besides the regulatory challenges that companies and researchers are dealing with.
Deadlines:
Abstract submission: 5 October 2020
Early Bird deadline: 27 October 2020
Late Registration deadline: 24 November 2020
Speakers:
Rosa Bacchetta- Stanford Medicine, US
Dirk Elewaut- VIB-UGent Center for Inflammation Research, BE
Alain Fischer – Assistance publique – Hôpitaux de Paris, FR
Martin Guilliams – VIB-UGent Center for Inflammation Research, BE
Pleun Hombrink – Sanquin, NL
Bengt Hoepken – Clinical Program Director, UCB Pharma, DE
Isabelle Huys – KU Leuven, BE
Christophe Lahorte – National Innovation Office & Scientific-Technical Advice Unit – (Famhp), BE
Bart Lambrecht – VIB-UGent Center for Inflammation Research, BE
Antonio Lanzavecchia – Institute for Research in Biomedicine, CH
Sophie Lucas – de Duve Institute, UCLouvain, BE
Bénédicte Machiels – FARAH Center, ULiège, BE
Melanie Matheu – CEO, Founder at Prellis Biologics, Inc., US
Massimiliano Mazzone – VIB-KU Leuven Center for Cancer Biology, BE
Kathy McCoy – University of Calgary, CA
Eoin McKinney – University of Cambridge, UK
Fiona Powrie – Kennedy Institute of Rheumatology, University of Oxford, UK
Federica Sallusto – Institute for Research in Biomedicine, CH
Georg Schett – Friedrich-Alexander University Erlangen-Nürnberg, DE
Marvin van Luijn – Erasmus MC, University Medical Center Rotterdam MS Center ErasMS, NL
Suzanne Eaton, Professor at the Technical University Dresden and Group Leader at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, tragically died on 2 July 2019. Suzanne was a remarkable person, both as a scientist and as a human being. Having worked closely with Suzanne for many years, I remember here some of her key scientific contributions.
Suzanne truly loved science and was driven by a deep curiosity for nature. She was an exceptional scientist with a taste for profound and fundamental problems in biology, and she embraced novel, original and interdisciplinary approaches. Indeed, Suzanne was a pioneer in quantitative approaches to tissue morphogenesis and a leader in the field, bridging scales from cell biology to tissue dynamics. With her fast wit and broad knowledge, she inspired colleagues, co-workers and students alike. Working with her was always a joyful experience, playful and deeply enlightening. Suzanne was also a sophisticated piano player and she had a black belt in Taekwondo. As one of Suzanne’s close collaborators over the past 15 years, it has been a true privilege for me to have interacted with her on a number of exciting problems and to have had weekly joint group meetings with a broad and interdisciplinary spirit.
Born in Oakland, California, Suzanne did her PhD at UCLA in the group of Kathryn Calame. During her PhD, Suzanne worked on the transcriptional regulation of immunoglobulin heavy chain genes (Eaton and Calame, 1987). She then moved to the lab of Tom Kornberg at UCSF, where she worked on the fruit fly Drosophila melanogaster and began to investigate fundamental aspects of Hedgehog signalling. Suzanne discovered that Hedgehog is a membrane-associated signalling molecule and that its expression is confined to posterior compartment cells (Tabata et al., 1992). In 1993, Suzanne moved to EMBL in Heidelberg to the lab of Kai Simons. There, she investigated planar cell polarity in epithelial tissues and revealed how Rho family GTPases play a role in polarizing the actin cytoskeleton and regulating cell shape changes in the fly wing epithelium (Eaton et al., 1995).
In 2000, Suzanne moved to Dresden to help set up the newly founded Max Planck Institute of Molecular Cell Biology and Genetics. In this environment, her research flourished as she became a leader in a new field that brought together cell and developmental biology. She was curious about how morphogens such as Hedgehog and Wnt/Wingless that spread in a tissue over distances could be found tightly associated with membranes. She discovered that these morphogens travel while associated with membranous particles, which move between cells and act as vehicles for morphogen transport (Greco et al., 2001). She further established that these membranous particles are lipoprotein particles (Panáková et al. 2005).
Suzanne then became fascinated by the geometry of cell packing, which appears to be random but at the same time exhibits different types of order and structural features. She thus investigated the mechanisms that govern cell neighbour numbers and the establishment of hexagonal packing in epithelia, revealing a role for planar cell polarity proteins in this process (Classen et al., 2005). This interest in cell packing geometries and cell polarity patterns triggered stimulating discussions about the role of forces and cell mechanics in morphogenesis, which in turn brought about a fruitful, long-lasting and inspiring collaboration between our research groups. A first step in this collaboration was the development of vertex models that capture the forces that define cell shapes. By comparing experiment and theory, key parameters that characterize biophysical properties of cells could be inferred and a general mechanism for the emergence of hexagonal cell packing was identified (Farhadifar et al., 2007). Live imaging over extended periods of time then permitted Suzanne to quantify cell movements, cell flow patterns and dynamic patterns of planar cell polarity over time during Drosophila pupal development. These observations revealed that planar cell polarity patterns in the tissue are reoriented by cell flow and tissue shear. This provided new insights into the role of cell flow in shaping patterns during morphogenesis (Aigouy et al., 2010). Looking at cell polarity patterns at early and late time points in the wing imaginal disc revealed how planar cell polarity patterns that are aligned over large distances could emerge in a tissue. At early time points, cell polarity is oriented in random directions. Groups of cells then locally align their polarity with the help of signals at compartment boundaries, while the tissue is still small. This aligned pattern is then extended over larger scales by tissue growth (Sagner et al., 2012).
Another key question that Suzanne addressed is how the fly wing takes on its final shape. Interestingly, mutants of the protein Dumpy, which links the tissue to the extracellular matrix, exhibit strongly misformed wings. Live imaging of wing development in dumpy mutants revealed that mechanical attachments at the tissue margin have a direct and strong influence on final tissue shape. It was shown that the wing is shaped inside the pupa by an active mechanical process that involves tissue contraction and tissue flow, which depend on patterns of mechanical boundary attachments (Etournay et al., 2015).
Suzanne’s discovery that signalling molecules such as Hedgehog are transported over distances by lipoprotein particles, which are also carriers of lipids, led her to bridge the field of morphogenesis with that of metabolism. She therefore started a research programme to investigate metabolic regulation and the complex interplay between metabolism, growth and development. She discovered that Drosophila lipoproteins generated in the fat body (a structure playing a role similar to that of the liver) provide signals about the nutritional status of the organism that are sent to the brain where they accumulate. In the brain, in turn, insulin-like peptides are secreted to regulate insulin signalling. Surprisingly, lipoproteins accumulate in the brain if the fly is on a yeast diet but not when it is on a plant-based diet. In this case, flies develop and grow more slowly, and live longer, as a consequence of different insulin signalling despite the calorimetric food content being the same. This work thus provided fascinating insights into the regulation of metabolism under varying diets (Brankatschk et al., 2014).
What could be the adaptive roles of different diets? In a very beautiful paper, Suzanne and her team investigated the effects of plant food compared with yeast food on the survival of Drosophila larvae and adults at different temperatures (Brankatschk et al., 2018). They showed that whereas flies growing in warm temperatures prefer yeast food, they prefer plant food when they are maintained at cold temperatures. Furthermore, flies on a plant diet can survive cold temperatures at which flies that are kept on a yeast diet will die. Thus, the choice of the appropriate food is important for survival during winter periods in temperate climates. A key difference between plant and yeast food is the ability of plants to produce polyunsaturated fatty acids. Suzanne and colleagues showed that the difference in diet leads to different lipid composition of membranes. Membranes of larvae on a plant diet maintain fluid properties and exhibit disordered membrane organization at lower temperatures, suggesting that these membrane biophysical properties are modulated by nutrition and are important for survival in the cold.
Remembering her contributions reveals the immense breadth of Suzanne’s work and her ability to bridge different fields and disciplines when addressing important questions in biology. Her work is characterized by very original and deep studies using strong quantitative approaches. She always looked at fundamental problems from new angles and thus made important and surprising discoveries. Her loss leaves a gaping void, and her sharp intellect and warm personality are missed tremendously.
The Blythe Lab at Northwestern University seeks to recruit a motivated postdoctoral fellow to investigate chromatin dynamics in early Drosophila embryogenesis.
Research in the Blythe Lab focuses on a critical period of embryogenesis termed the maternal-to-zygotic transition (MZT). During this time, embryos establish an initial ‘ground state’ of chromatin structure that defines the initial cis-regulatory landscape underlying the embryo’s first cell fate decisions. We are interested both in how the initial state is established and how this constrains the interpretation of developmental cues during pattern formation. To study this question, we apply a combination of genetic, genomic, and quantitative imaging approaches to understand the mechanisms that shape the embryonic chromatin landscape.
Projects are available in three major areas at the interface of developmental biology, epigenetics, and systems biology: 1) Temporal control of zygotic genome activation; 2) Patterning-dependent chromatin remodeling and gene regulatory network function; 3) Conflicts between DNA replication and transcription.
We are particularly interested in candidates with experience in genomic approaches (RNA-, ChIP-, or ATAC-seq), analysis of genomic data, quantitative confocal microscopy, biophysical approaches, and/or Drosophila genetics. The position available immediately.
We have two fully funded PhD positions in the Wheeler lab at University of East Anglia, Norwich, UK.
NEUcrest is an Innovative Training Network (ITN) project, funded by the European Union Horizon 2020 Programme. The neural crest (NC) is an essential stem cell population of the vertebrate embryos that gives rise to various tissues in the body such as the cranial facial cartilage, peripheral nervous system and the Adrenal Medulla. NEUcrest focuses on integrating academic, clinical and industrial research for a better understanding of neural crest development and neural crest related diseases called Neurocristopathies. These pathologies are a major group of congenital diseases in human, and a heavy societal concern. The NEUcrest network comprises 20 partners in academia, industry and hospitals from seven European countries, gathered in a synergistic effort to advance knowledge and outreach about these diseases.
Modelling Neurocristopathies in Xenopus, mechanisms and drug screening
Micro RNA regulation of neural crest development
Please follow these links for more information:
https://euraxess.ec.europa.eu/jobs/447869
https://www.euraxess.fo/jobs/461086
Or contact Dr. Grant Wheeler for more information: Grant.Wheeler@uea.ac.uk
In this episode we’re bringing you highlights from the Society’s Centenary Conference, held up in Edinburgh last month.
We’ve got stories of sneaky sheep, substandard racing stallions, the Vikings of the Scottish Isles and a ceilidh with a scientific spin. Plus, news from the front lines of the sperm wars.
If you enjoy the show, please do rate and review and spread the word. And you can always send feedback and suggestions for future episodes and guests to podcast@geneticsunzipped.com Follow us on Twitter – @geneticsunzip
In this episode from our centenary series exploring 100 ideas in genetics, we’re uprooting the tree of life – asking whether we should believe our eyes or our sequencing machines when it comes to deciding what makes a species.
Plus, the greatest comebacks of all time – we look at the science of de-extinction and find out whether Jurassic Park could ever become a reality.
If you enjoy the show, please do rate and review and spread the word. And you can always send feedback and suggestions for future episodes and guests to podcast@geneticsunzipped.com Follow us on Twitter – @geneticsunzip
Two weeks ago, we had the opportunity to attend the Company of Biologists Workshop, “Understanding Birth Defects in the Genomic Age”. This workshop brought together a diverse collection of basic developmental biologists, human geneticists and clinicians to discuss the current challenges and opportunities in the field of birth defects research. We can almost guarantee you that none of the groups of attendees would normally overlap at any other meeting. And yet, what quickly became apparent was that there was so much in common between everyone in attendance.
The setting for the meeting was stunning. Set at Wiston House in the English countryside not too far from Brighton, history oozed from every corner of the building. From the delicious catering, to the beautiful (but rainy) countryside walk, to the very interesting talk on the history of the house, this venue provided an epic background for what would be an extremely stimulating three and a half days.
The meeting was unique right from the start. It was definitely the smallest meeting we had ever attended. There were only about 33 people total, and we each had the opportunity to introduce ourselves to the group on the first day. We were asked to give a few slides introducing ourselves as well as a “problem” (a topic that we would like help with) and “solution” (something that we were good at/could use to help others). Right away this encouraged discussion and it became quickly apparent how each of our skillsets would be able to help not just each others’ research, but contribute a unique perspective to the group.
Participants at the Workshop
In addition to traditional scientific talks, we had the opportunity to sit down and talk amongst the group about some of the issues which we would like to address. Collectively, birth defects are the number one cause of infant mortality in the USA, but it is sometimes challenging to justify studying individual rare developmental defects. Many of our discussions centred around how to increase public awareness of our research and to emphasize the huge impact of return of results to families – even if a genetic diagnosis doesn’t lead to a treatment, patients and families can be hugely comforted to know more about the underlying cause. John Wallingford gave a stirring talk about the disturbing history of society’s (including the medical profession’s) poor treatment of individuals with congenital anomalies. There was unanimous agreement amongst the group that we needed a new term for birth defects that was both more sensitive and more inclusive. There was much discussion, but the group was not able to come to a consensus as to a better term moving forward. One of our favourite suggestions was that perhaps we needed to create a new word entirely!
One of the goals of the workshop was to generate actual concrete steps to address the above issues. Working groups were established to draft a white paper, review articles, social media campaigns, and other methods to increase the awareness of this very important field of research. One of they key action items became bringing together a similar group of people again to build on the ideas started at this workshop. The Company of Biologists is already planning a meeting on developmental disorders for 2021; hopefully this will provide another opportunity for a meeting of minds to continue to forward the cause.
As two early career researchers funded by the Company of Biologists to attend the workshop, we gained great insight into the diverse approaches being used to study birth defects research. In addition, it provided a unique opportunity to discuss and learn about larger scope projects such as impacting public awareness and advocating for increased funding for a particular area of research.
At the conclusion of the meeting everyone left inspired and ready to act. We are looking forward to 2021!
Find out more about The Company of Biologists’ Workshops, including our 2020 schedule and details of how to apply for funded places, here:
Welcome to our monthly trawl for developmental biology (and related) preprints.
This month we found preprints detailing extensive mouse and fly knockout resources, exploring bacterial influences on development, and investigating mechanics in vivo and in silico. They were hosted on bioRxivandarXiv. Let us know if we missed anything. Use these links to get to the section you want:
Apcdd1 is a dual BMP/Wnt inhibitor in the developing nervous system and skin
Alin Vonica, Neha Bhat, Keith Phan, Jinbai Guo, Lăcrimioara Iancu, Jessica A. Weber, Amir Karger, John W. Cain, Etienne C. E. Wang, Gina M. DeStefano, Anne H. O’Donnell-Luria, Angela M. Christiano, Bruce Riley, Samantha J. Butler, Victor Luria
Syndecan-3 enhances anabolic bone formation through WNT signalling
Francesca Manuela Johnson de Sousa Brito, Andrew Butcher, Addolorata Pisconti, Blandine Poulet, Amanda Prior, Gemma Charlesworth, Catherine Sperinck, Michele Scotto di Mase, George Bou-Gharios, Robert Jurgen van ’t Hof, Anna Daroszewska
A TBX5 dosage-sensitive gene regulatory network for human congenital heart disease
Irfan S. Kathiriya, Kavitha S. Rao, Giovanni Iacono, W. Patrick Devine, Swetansu K. Hota, Michael H. Lai, Bayardo I. Garay, Reuben Thomas, Andrew P. Blair, Henry Z. Gong, Lauren K. Wasson, Piyush Goyal, Tatyana Sukonnik, Gunes A. Akgun, Laure D. Bernard, Brynn N. Akerberg, Fei Gu, Kai Li, William T. Pu, Joshua M. Stuart, Christine E. Seidman, J. G. Seidman, Holger Heyn, Benoit G. Bruneau
A novel microRNA-based strategy to expand the differentiation potency of stem cells
María Salazar-Roa, Marianna Trakala, Mónica Álvarez-Fernández, Fátima Valdés-Mora, Cuiqing Zhong, Jaime Muñoz, Yang Yu, Timothy J. Peters, Osvaldo Graña, Rosa Serrano, Elisabet Zapatero-Solana, María Abad, María José Bueno, Marta Gómez de Cedrón, José Fernández-Piqueras, Manuel Serrano, María A. Blasco, Da-Zhi Wang, Susan J. Clark, Juan Carlos Izpisua-Belmonte, Sagrario Ortega, Marcos Malumbres
PI 3-kinase delta enhances axonal PIP3 to support axon regeneration in the adult CNS
Amanda C Barber, Rachel S Evans, Bart Nieuwenhuis, Craig S Pearson, Joachim Fuchs, Amy R MacQueen, Susan van Erp, Barabara Haenzi, Lianne A Hulshof, Andrew Osborne, Raquel Conceicao, Sarita S Deshpande, Joshua Cave, Charles ffrench-Constant, Patrice D Smith, Klaus Okkenhaug, Britta J Eickholt, Keith R Martin, James W Fawcett, Richard Eva
A cell surface arabinogalactan-peptide influences root hair cell fate
Cecilia Borassi, Javier Gloazzo Dorosz, Martiniano M. Ricardi, Laercio Pol Fachin, Mariana Carignani Sardoy, Eliana Marzol, Silvina Mangano, Diana Rosa Rodríguez Garcia, Javier Martínez Pacheco, Yossmayer del Carmen Rondón Guerrero, Silvia M. Velasquez, Bianca Villavicencio, Marina Ciancia, Georg Seifert, Hugo Verli, José M. Estevez
A simple method for spray-on gene editing in planta
Cara Doyle, Katie Higginbottom, Thomas A. Swift, Mark Winfield, Christopher Bellas, David Benito-Alifonso, Taryn Fletcher, M. Carmen Galan, Keith Edwards, Heather M. Whitney
Lgr5+ telocytes are a signaling hub at the intestinal villus tip
Keren Bahar Halpern, Hassan Massalha, Rachel K. Zwick, Andreas E. Moor, David Castillo-Azofeifa, Milena Rozenberg, Lydia Farack, Adi Egozi, Dan R. Miller, Inna Averbukh, Yotam Harnik, Noa Weinberg-Corem, Frederic J. de Sauvage, Ido Amit, Ophir D. Klein, Michal Shoshkes-Carmel, Shalev Itzkovitz
Novel function of TRIP6, in brain ciliogenesis
Shalmali Shukla, Pavel Urbanek, Lucien Frappart, Ronny Hänold, Sigrun Nagel, Shamci Monajembashi, Paulius Grigaravicius, Woo Kee Min, Alicia Tapias, Olivier Kassel, Heike Heuer, Zhao-Qi Wang, Aspasia Ploubidou, Peter Herrlich
Large-scale transgenic Drosophila resource collections for loss- and gain-of-function studies
Jonathan Zirin, Yanhui Hu, Luping Liu, Donghui Yang-Zhou, Ryan Colbeth, Dong Yan, Ben Ewen-Campen, Rong Tao, Eric Vogt, Sara VanNest, Cooper Cavers, Christians Villalta, Aram Comjean, Jin Sun, Xia Wang, Yu Jia, Ruibao Zhu, Pin Peng, Jinchao Yu, Da Shen, Yuhao Qiu, Limmond Ayisi, Henna Ragoowansi, Ethan Fenton, Senait Efrem, Annette Parks, Kuniaki Saito, Shu Kondo, Liz Perkins, Stephanie E. Mohr, Jianquan Ni, Norbert Perrimon
A resource of targeted mutant mouse lines for 5,061 genes
Marie-Christine Birling, Atsushi Yoshiki, David J Adams, Shinya Ayabe, Arthur L Beaudet, Joanna Bottomley, Allan Bradley, Steve DM Brown, Antje Bürger, Wendy Bushell, Francesco Chiani, Hsian-Jean Genie Chin, Skevoulla Christou, Gemma F Codner, Francesco J DeMayo, Mary E Dickinson, Brendan Doe, Leah Rae Donahue, Martin D Fray, Alessia Gambadoro, Xiang Gao, Marina Gertsenstein, Alba Gomez-Segura, Leslie O Goodwin, Jason D Heaney, Yann Hérault, Martin Hrabe de Angelis, Si-Tse Jiang, Monica J Justice, Petr Kasparek, Ruairidh E King, Ralf Kühn, Ho Lee, Young Jae Lee, Zhiwei Liu, K C Kent Lloyd, Isabel Lorenzo, Ann-Marie Mallon, Colin McKerlie, Terrence F Meehan, Stuart Newman, Lauryl MJ Nutter, Goo Taeg Oh, Guillaume Pavlovic, Ramiro Ramirez-Solis, Barry Rosen, Edward J Ryder, Luis A Santos, Joel Schick, John R Seavitt, Radislav Sedlacek, Claudia Seisenberger, Je Kyung Seong, William C Skarnes, Tania Sorg, Karen P Steel, Masaru Tamura, Glauco P Tocchini-Valentini, Chi-Kuang Leo Wang, Hannah Wardle-Jones, Marie Wattenhofer-Donzé, Sara Wells, Brandon J Willis, Joshua A Wood, Wolfgang Wurst, Ying Xu, IMPC Consortium, Lydia Teboul, Stephen A Murray
Minimal genome-wide human CRISPR-Cas9 library
Emanuel Gonçalves, Mark Thomas, Fiona M Behan, Gabriele Picco, Clare Pacini, Felicity Allen, David Parry-Smith, Francesco Iorio, Leopold Parts, Kosuke Yusa, Mathew J Garnett
A portable and cost-effective microfluidic system for massively parallel single-cell transcriptome profiling
Chuanyu Liu, Tao Wu, Fei Fan, Ya Liu, Liang Wu, Michael Junkin, Zhifeng Wang, Yeya Yu, Weimao Wang, Wenbo Wei, Yue Yuan, Mingyue Wang, Mengnan Cheng, Xiaoyu Wei, Jiangshan Xu, Quan Shi, Shiping Liu, Ao Chen, Ou Wang, Ming Ni, Wenwei Zhang, Zhouchun Shang, Yiwei Lai, Pengcheng Guo, Carl Ward, Giacomo Volpe, Lei Wang, Huan Zheng, Yang Liu, Brock A. Peters, Jody Beecher, Yongwei Zhang, Miguel A. Esteban, Yong Hou, Xun Xu, I-Jane Chen, Longqi Liu
bioRxiv: the preprint server for biology
Richard Sever, Ted Roeder, Samantha Hindle, Linda Sussman, Kevin-John Black, Janet Argentine, Wayne Manos, John R. Inglis
Plagiarism in Brazil: A perspective of 25,000 PhD holders across the sciences
Sonia MR Vasconcelos, Hatisaburo Masuda, Martha Sorenson, Francisco Prosdocimi, Marisa Palácios, Edson Watanabe, José Carlos Pinto, José Roberto Lapa e Silva, Adalberto Vieyra, André Pinto, Jesús Mena-Chalco, Mauricio Sant’Ana, Miguel Roig
Heart development in mammals is a beautifully complex process. Patterning, proliferation and differentiation are all coordinated with cell movements and tissue morphogenesis (for instance elongation, fusion, folding, looping). However, our knowledge of the molecular regulators of heart development currently outstrips what we know about the morphogenetic processes that create the functional structure. A new paper in Development seeks to understand tissue-level morphogenesis – and its molecular control – in the mouse secondary heart field. We caught up with first author Ding Li and his postdoctoral advisor Jianbo Wang, Associate Professor at the University of Alabama at Birmingham, to find out more about the paper.
Ding (L) and Jianbo (R)
Jianbo, can you give us your scientific biography and the questions your lab is trying to answer?
JW I have always been fascinated by developmental biology, and how limited sets of highly conserved genetic circuits can be used to create hugely diverse structures and organs in different organisms. I did my PhD with Terry Magnuson, investigating epigenetic regulation in embryonic and extra-embryonic development in the mouse. For my postdoctoral training, I studied mouse dishevelled genes during embryogenesis with Tony Wynshaw-Boris. Dishevelled is a multi-functional, modular protein that is crucial for both canonical and non-canonical Wnt/planar cell polarity (PCP) signalling in flies and frogs. To functionally dissect dishevelled genes in the mouse, I created domain-deletion and point mutations in Dvl2 to specifically block either pathway. It turns out that most of the defects in Dvl2 mutants, from neural tube closure to inner ear and heart development, arise from disruption of PCP signalling. After starting my own lab, I have continued to use the mouse as a model to explore the role of PCP-mediated morphogenesis in different contexts of mammalian development. In addition, we are trying to understand the impact of PCP gene variants on human biology and congenital defects. Finally, in collaboration with my colleague Chenbei Chang, we are also using Xenopus to decipher the mechanisms and logics of PCP during tissue morphogenesis.
Ding, how did you come to work in the Wang lab, and what drives your research today?
DL Back in 2012, I was searching for a postdoc training opportunity in America. Jianbo’s ad caught my attention because I was interested in cardiovascular biology and heart development research. I had a nice interview with Jianbo on the phone, came to his lab in June 2012, and started a seven-year-long journey. I recently started a job in a clinical genomics laboratory, overseeing sequencing of human patient samples. I still however pay attention to the latest developments and advances in the field of cardiovascular development, an interest planted deep inside me.
Why do you think knowledge of heart morphogenesis has lagged behind knowledge of the signalling and transcriptional networks involved in its patterning?
DL & JW This probably has multiple reasons. Historically, our fundamental understanding of how the heart forms is largely from studies of key transcription factors and signalling pathways, so naturally there are more labs and people working on them. This trend has been further fuelled by the rapid advance in genomic technology, which has made it feasible to delineate molecularly how signalling crosstalk acts upon epigenetic and transcriptional hierarchies for cardiac specification and differentiation. The knowledge from these studies holds tremendous potential for translational medicine, such as stem cell-based regenerative approaches for cardiac repair. These studies are exciting and significant. They have been, and will continue to be, one of the main driving forces of the field.
Studies of morphogenesis, on the other hand, require greater attention to biology at the cellular and tissue levels. They are time consuming and labour intensive to carry out, the data tend to be noisier, and the results are more likely to be regarded as ‘descriptive and correlative’ rather than ‘mechanistic and causal’. So there is probably less impetus for these studies. But sometimes detailed descriptions at the cellular and tissue levels are important because they inform us about things that molecular and genomic studies cannot, such as spatial organization and the temporal order of events underlying heart development.
Additionally, compared with other fields, studying heart morphogenesis is uniquely challenging because the rapid beating makes live imaging of the heart and its surrounding cardiac progenitor field quite difficult. Some new technologies, such as light-sheet microscopy and high-resolution episcopic microscopy, will help to overcome the technical hurdles for morphogenesis studies, whereas other technologies, such as single cell RNAseq and spatial genomics, may help to bridge the gap between our knowledge of heart patterning and morphogenesis.
Can you give us the key results of the paper in a paragraph?
DL & JW Our studies first reveal that in the mouse, the secondary heart field population (SHF) in the splanchnic mesoderm (SpM-SHF) normally grows in a polarized fashion to preferentially elongate anteroposteriorly. Loss of Wnt5a, however, leads to isotropic expansion of the SpM-SHF. We provide evidence that Wnt5a may act through PCP effector and formin protein Daam1 to form horizontally oriented actomyosin cables in the medial SpM-SHF, thereby generating the mechanical force to constrict SHF widening and promote its lengthening. Genetic labelling and tracing reveal that the Wnt5a lineage is a unique SHF subpopulation specified as early as embryonic day (E)7.5, and undergoes bi-directional deployment towards both the arterial and venous poles to contribute specifically to the pulmonary trunk and atrial septum, respectively. In Wnt5a null mutants, the Wnt5a lineage fails to extend into the arterial and venous poles, causing both outflow tract and atrial septation defects, both of which can be rescued by an activated form of Daam1. Interestingly, the Wnt5a lineage in the SHF also contributes to the pulmonary mesenchyme and proper morphogenesis of the airway, suggesting the intriguing idea that during the evolution of tetrapods for terrestrial life, Wnt5a/PCP was recruited by the cardiopulmonary progenitors to orchestrate morphogenesis of both the pulmonary airway and cardiac septation necessary for pulmonary circulation.
3D reconstruction of a wild-type heart at E13.5.
Is Wnt5a acting locally or at a distance in the SHF?
DL & JW This is a question that we debated a lot in the lab. The conventional wisdom in the Wnt field seems to be that the Wnt ligand does not travel very far, probably less than ten cell diameters away from the source. Our anti-Wnt5a antibody staining also shows a very restricted distribution in the caudal SHF, largely overlapping with the domain of Wnt5a mRNA expression. But we need to be cautious about the sensitivity of antibody staining. The fact that the SHF deployment defect in Wnt5a null mutants is not restricted to the Wnt5a lineage per se raises the possibility that Wnt5a may signal at some distance. In the limb, we have very strong genetic evidence that Wnt5a produced at a defined location can signal hundreds of microns away. The action of Wnt5a could be tissue specific though, so to address this question, we will need to tag Wnt5a and visualize its distribution.
Does your data have any relevance to the idea of cardiopulmonary progenitors?
DL & JW The idea of ‘cardiopulmonary progenitors’ was initially proposed by Ed Morrisey’s group to explain co-development of the heart and lung during the evolutionary adaptation to terrestrial life. They had found that the posterior SHF contains multipotent progenitors contributing to both the venous pole of the heart and pulmonary mesoderm. Our Wnt5a lineage-tracing data support this idea, and further demonstrate that the cardiopulmonary progenitors may also contribute to pulmonary trunk at the arterial pole, in addition to the dorsal mesenchymal protrusion (DMP) at the venous pole. Formation of the pulmonary trunk and DMP-mediated septation of the atria are both necessary to fully separate pulmonary from systemic circulation.
Recent studies from Ivan Moskowitz’s group further demonstrated that expression of Tbx5 in cardiopulmonary progenitors initiates a signalling cascade to specify pulmonary fate in the adjacent endoderm. We found that deleting Wnt5a using SHF-specific Mef2cCre causes not only cardiac septation but also airway morphogenesis defects. Therefore, we speculate that in addition to adopting the Tbx5 transcription network for pulmonary fate specification, the cardiopulmonary progenitors may have also recruited Wnt5a/PCP as a genetic circuit to orchestrate morphogenesis of the heart and lung during their co-evolution in tetrapods.
When doing the research, did you have any particular result or eureka moment that has stuck with you?
DL I would say the most exciting moment during this project was when I finished the first 3D reconstruction of E10.5 wild-type and Wnt5a null mutant embryos. For the first time I was able to turn around and really see the whole heart in relation to the SHF on the computer display, not just a series of individual sections. That feeling was indescribable and the memory will definitely stay with me forever.
That feeling was indescribable and the memory will definitely stay with me forever
And what about the flipside: any moments of frustration or despair?
DL I have never had a project completely free of frustration, so of course this project was no exception. Here and there, we had big or small troubles with techniques, but somehow found ways to overcome and move on. The biggest frustration came from the clonal analysis. We tried to genetically label a few Wnt5a lineage cells by using our Wnt5aCreER mouse line and R26R-confetti (Brainbow) mouse line, and to test whether their deployment to the arterial and venous poles of the heart would change over time. However, the labelling efficiency of Wnt5aCreER with the confetti reporter was extremely low and we could not get any interpretable result after many tries. Finally, we gave up and had to submit the manuscript without this piece of data.
So what next for you after this paper?
DL After finishing the revision of this manuscript, I accepted a job offer from a clinical genomics laboratory, and started a career path in medical genetics and diagnosis. Although not dealing with embryos anymore, I do benefit a lot at work from my past life in research.
Where will this work take the Wang lab?
JW There are several things that we would like to pursue. First, we want to examine further the role of Wnt5a and PCP signalling in the co-morphogenesis of the heart and lungs. Second, we want to define further the action of Wnt5a by determining its signalling range, and whether it functions in a permissive or instructive fashion. Finally, we want to understand how the human WNT5A point mutations perturb its function during development and result in congenital birth defects.
Finally, let’s move outside the lab – what do you like to do in your spare time in Birmingham?
DL I like hiking. My favourite trail is on the top of the Red Mountain, where Birmingham’s famous Vulcan statue stands. Walking along the trail and overlooking downtown Birmingham is just really relaxing.
JW I was surprised to find how liveable Birmingham was when I first moved here from San Diego, and discovered a large number of fantastic restaurants of different cuisines. When my kids were younger, I hiked and mountain biked a lot with them in the nearby mountains, and practiced karate with them. Now I tend to do activities that are more relaxing, like yoga and golf. The Robert Trent Jones golf trail is a series of world-class golf courses built throughout the state of Alabama, and there are two of them within a 10 minute drive from my house.
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