For other posts in this series click here

Welcome back to #DevBiolWriteClub.  Let’s review the rules:

1. Do the work.
2. Do the work.
3. Revise and edit.  Again, and again, and again.
4. Read with intent.
5. You can’t do it alone.

Last time, I hammered away at Rule #4, Read with Intent.  Today, I’ll return to Rule #4, and I’ll make some preliminary comments on Rule #5.  Rule #5 is mostly about being brave enough to show your writing to your peers, and even your mentors.  But it’s also about taking advice where you can get it.

Thankfully, you are not alone in your struggles with writing.  I’m right there with you, and so are hordes of other aspirants.  So many, in fact, that there’s a brisk market in books about writing.  So, let’s look at this:  If you take the time to carefully read a book (or two, or three) about writing, you are hitting rules #1, #2, #4, and #5. Wow.

So, because books are always the best Christmas presents, here are #DevBiolWriteClub’s favorite books about writing.

If you’re only going to read one book about writing, read:  The Scientist’s Guide to Writing, by Stephen Heard.  This is unquestionably the best book for science writing.  Stephen is a biologist, and he’s a delightful presence on Twitter (@StephenBHeard).  He also has an awesome blog, where he frequently writes about writing.  His book has everything:  A brief and fun history of science writing, some big picture psychology at the start, then excellent “brass tacks” advice on writing scientific papers.  I recommend this one especially to anyone following #DevBiolWriteClub and looking for new ways to “do the work.”  Each chapter ends by suggesting helpful exercises.

If you write, but don’t really like what you write, read: Writing Science in Plain English, by Anne Greene, also a biologist.  This very slim book (the core of it is 85 short pages) will likely do more to improve the sentences and paragraphs you write over the short term than any other book I’ve read.  It’s a straight-up style manual focused on how to turn your scientific writing into simple prose and thus to communicate more effectively.  Not surprisingly, this book’s simple, actionable advice is crystal clear.  It also provides a series of short exercises to drive home the key points.

If you have trouble getting that first draft written, read: How to Write a Lot, by Paul Silvia.  This is another little book, but it’s all about the big picture.  Silvia is an academic psychologist, and his book is aimed at fixing bad habits of mind and creating new ones.  Since scientist’s intellectual lives are complex enough already, an important asset is that while Silvia’s book attacks very high level issues, it offers remarkably simple and practical advice on improving your practice as a writer, the core goal of #DevBiolWriteClub.  One of the best aspects of this book is an explicit description of various types of writing groups that help to address subtly different hurdles that writers may face.  This really helps with Rule #5.  This one is also just a fun read.

Ok, those are the Big Three, and any scientist wanting to improve their writing should read all three of these books.

Of course, we can always improve more, so here are some more recommendations:

The Sense of Style, by Steven Pinker.  I read somewhere -possibly in this book- that every writer should read a style manual once per year, whether they need to or not.  If you’re a working scientist, that book probably should be Writing Science in Plain English, above.  But if you want to dive in a little deeper, there are tons of great style books.  The canonical style manual is Strunk and White’s Elements of Style, but with apologies to essentially all of my mentors, I find it too stuffy and rather boring. Pinker’s book, which he freely offers as an update to that classic, is far more fun to read.  This quip from the prologue really spoke to me:  “You can write with clarity and with flair, too.”

The War of Art, by Steven Pressfield.  Ok, this one is really just a self-help book.  But if you’ve read How to Write a Lot, above, and you still have trouble sitting down and doing the work, read this.

Writing Your Journal article in Twelve Weeks, by Wendy Laura Belcher.  Ok, it’s hard to say I “like,” this 400+ page book, but it does offer something none of the others do:  Step-by-step instructions on writing a paper in a reasonable, totally defined time frame.  It presents clear goals each day and each week.  If you are serious about a 12-week, self-taught crash course in writing a scientific paper, pick this one up.

Bird by Bird, Some Instructions on Writing and Life, by Anne Lamott.  This gem of a book is really targeted for aspiring poets and novelists, but since poets and novelists are often good writers (duh), there’s a lot here for us scientists.  Chapter Three is entitled “Shitty First Drafts.”  Need I say more?

On Writing, A Memoir of the Craft, by Stephen King.  Yes, that Stephen King.  Writing advice from one of the most successful authors in history?  Of course, you should read it.  If you’re in a hurry, you can skip the autobiography and go right to the writing advice about 100 pages in.  But then you’d miss learning about his hardscrabble upbringing and the depth of his struggles even as a successful writer.  Writing is hard, reading this book will help you really know that.

The Joy of Drinking by Barbara Holland.  Ok, not a writing book.  But, c’mon!  It’s an hilarious history of drinking written by one of America’s best writers.  If drinking is not your thing, read her equally excellent, They Went Whistling, Women Wayfarers, Warriors, Runaways and Renegades.  Or her fantastic, Gentleman’s Blood, A History of Dueling.  Anyway, read some Barbara Holland.

So, that’s it: If you’re serious about becoming a better writer, go buy some books about writing and read them.

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Understanding brain circuit evolution at single-cell resolution using comparative connectomics and transcriptomics

A position for a postdoc is available in the Kebschull Lab at the Department of Biomedical Engineering at the Johns Hopkins School of Medicine in Baltimore, MD. We develop and apply cutting edge molecular and neuroanatomical tools to study how primordial circuits expanded in evolution to form the complex brains that exist today. We have a special focus on barcode sequencing-based high-throughput connectomics (BRICseq, MAPseq) and in situ sequencing, which we apply in the cerebellar nuclei and brain-wide in different vertebrates. Recent relevant papers include Kebschull et al. 2020 Science, Huang et al. 2020 Cell, Han et al. 2018 Nature, and Kebschull et al. 2016 Neuron.

Candidates must hold a PhD degree (or equivalent) in neuroscience, biomedical engineering, molecular biology, or a related field. The ideal candidate should also have some bioinformatics skills and be passionate about brain mapping and evolution. We particularly encourage applications from any underrepresented or minority group.

Our lab is located on the School of Medicine Campus of Johns Hopkins University, surrounded by world-class neuroscience and biomedical engineering labs. We are committed to establishing a first-class, stimulating, diverse, and equitable environment in our new lab to allow you to flourish, achieve your goals, and further your career.

Qualified applicants should send a letter describing their current and future research interests, their CV, and names and contact details for three references to kebschull@jhu.edu. More information is available on https://www.kebschull-lab.org/.

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Journal covers celebrate the aesthetic achievements of researchers and showcase the beauty of science to the wider world. Here are all 24 of Development’s covers for the crazy year that was 2020 – click the images to open the gallery, and you’ll find the cover description. Be sure to check out Development’s review of 2020 over on Twitter.

Which one’s your favourite? Leave a comment and we’ll let the authors know!

Micrographs of C. elegans anchor cells (cdh-3>mCherry::moeABD, magenta) atop the uterine-vulval basement membrane (laminin::GFP, green), expressing endogenously-tagged transcription factors (nuclear, green), grouped by column (left to right: egl-43::GFP, fos-1::GFP, hlh-2::GFP and nhr-67::GFP). Each row represents a different RNAi perturbation [top to bottom: empty vector, egl-43(RNAi), fos-1(RNAi), hlh-2(RNAi) and nhr-67(RNAi)]. See Research article by Medwig-Kinney et al. (dev185850)

Coronal section of a postnatal day 0 mouse brain stained to reveal EGFP from Dlx5/6-CIE cells in green, calbindin in red, and Hoechst in blue. Intact JNK signalling is required for Dlx5/6-CIE-positive interneurons to travel in tangentially oriented migratory streams to their correct positions in the developing cortical wall. See Research article by Myers et al. (dev180646).

Mouse primary cortical neurons cultured for 8 days in microfluidic chambers, which allow the compartmentalisation and fluidic isolation of axons from the cell bodies. Tau-1 immunolabelling (magenta) shows axons crossing via microgrooves into the axon compartment. Immunolabelling of the dendritic marker Map2 (green) shows dendrites and cell bodies restricted to the somatodendritic compartment. See Research article by Lucci et al. (dev180232).

An adult of the basal echinoid (cidaroid) Prionocidaris baculosa. The endomesoderm gene regulatory network (GRN) in cidaroids appears to preserve the ancestral state of echinoids and provides a valuable model for understanding the diversification of the early developmental GRN. See Research article by Yamazaki et al. (dev182139). Picture credit: Makoto Urata (Kanazawa University).

Dorsal view of the abdominal epidermis of a Drosophila pupa stained for E-cadherin to visualize cell junctions (white). The small histoblasts (cyan and black) proliferate and replace the large larval epidermal cells. Larval epidermal cells of one segment are coloured according to their position at the time of their extrusion: at the border of the histoblast nest (yellow), at the dorsal midline (green) or in between (magenta). See Research article by Michel and Dahmann (dev179606).

Artistic rearrangement of leaf confocal micrographs displaying battery of fluorescently tagged cell fate determinants in response to injuries. Images created by Anju P. S., Dhanya Radhakrishnan and Abdul Kareem V. K. Artwork by Mabel Maria Mathew (Indian Institute of Science Education and Research, Thiruvananthapuram, India). See Research article by Radhakrishnan et al. (dev185710).

Metatarsal from an E16.5 Lifeact-EGFP embryo (Lifeact is false coloured in pink, centre), which has been dissected and put into culture. Blood vessels (visualised with CD31, purple) sprout from the metatarsal to form a complex vascular network, allowing for ex vivo analysis of vascular density and sprout dynamics. See Research article by Schimmel et al. (dev185405).

Dorsal view of a Drosophila larval posterior segment, showing the topology of internal organs. The alary muscles (red) connect to the heart (phalloidin, blue; cardioblast nuclei, green) and to pericardiac cells (green) via an extracellular matrix network (pericardin, cyan) and maintain the heart and trachea (cyan) in proper positions. See Research article by Bataillé et al. (dev185645).

Polarising region grafts made to the anterior margin of a wing bud of a host chick embryo produce mirror-image duplications of the feather bud pattern, as shown by the black pigmentation. See Research article by Busby et al. (dev188821).

Proliferating Muller glia-derived progenitor cells in the chick retina. A vertical section of the retina was labeled for Sox2 (red), neurofilament (green) and phospho-histone H3 (blue). Inhibition of NF-κB-signaling stimulates the formation of proliferating Muller glia-derived progenitors. See Research article by Palazzo et al. (dev183418).

Volume rendering of an E16.5 mouse foetus based on X-ray microCT imaging. A novel protocol for staining cartilage matrix with Ruthenium Red is introduced that allows isotropic 3D imaging of the entire developing skeleton at micron resolution. See Research article by Gabner et al. (dev187633).

Line art traced using a real zebrafish retina image for reference and filled with single-cell transcriptome-defined clusters of cells depicted in different colours, representing a unified developmental program shared by embryonic and post-embryonic retinogenesis. See Techniques and Resources article by Xu et al. (dev185660).

Caenorhabditis elegans embryos imaged using single-molecule FISH to detect maternally-loaded mRNAs (clu-1, chs-1, imb-2, erm-1, F40G12.11, lem-3, nos-2 and cpg-2) in combination with cellular markers (PH::GFP, GLH-1::GFP, and DAPI). mRNAs accumulate at cell membranes, nuclear peripheries and within P granules. See Research article by Parker et al. (dev186817).

Root growth trajectories of Arabidopsis mutants in genes encoding RNA-binding proteins with specific N6-methyladenosine (m6A)-binding capacity, showing that a set of m6A-binding proteins controls directionality of root growth, and is required for rapid cellular proliferation during organogenesis, including root formation. See Research article by Arribas-Hernández et al. (dev189134).

Drosophila melanogaster embryos expressing an endogenously tagged EGFR-sfGFP construct showing localization of the EGFR in the developing tissue. Stage 7 (top), 9 (middle) and 11 (bottom) embryos are shown in a lateral view and are co-stained with EGFR-sfGFP (anti-GFP; green) and diphosphorylated ERK (dpERK; blue) antibodies. Images are depicted with anterior to the left and posterior to the right. See Techniques and Resources article by Revaitis et al. (dev183210).

Blood-brain barrier disruption in mice lacking FGFBP1 in endothelial cells. Brain blood vessels lacking FGFBP1 (podocalyxin; magenta) fail to deposit collagen IV (green) in the basement membrane and become permeable to circulating compounds (cadaverin; red). See Research article by Cottarelli et al. (dev185140).

The stereocilia bundles are apical extensions of the sensory cells of the inner ear (hair cells), here labelled with phalloidin in a newborn mouse utricle. The development and survival of the hair cells requires the transcription factor GFI1, which functions to repress a neuronal-associated gene expression profile. See Research report by Matern et al. (dev186015).

Interactive 3D model of an E18.5 typically developing mouse skull based on microCT data. Different colours indicate distinct bones. See Research article by Samuels et al. (dev191213).

An eight-cell embryo cultured within the confines of a cylindrical channel in a biocompatible hydrogel, in order to alter the shape and position of its blastomeres, and test the influence of these parameters on cell specification (magenta, pERM; yellow, F-actin; grey, DAPI). See Research article by Royer et al. (dev189449).

A cross-section of the small intestine in an embryonic day 14.5 Ryk knockout mouse (magenta, F-actin; cyan, nuclei). See Research article by Wang et al. (dev195388).

Dorsal view of the nervous system of a Xenopus tropicalis tadpole following β-tubulin antibody staining and confocal microscopy. X. tropicalis is a valuable model for understanding the function of human neurodevelopmental risk disorder genes due to its conserved diploid genome, the ability to make unilateral mutants, and the wealth of experimental tools and knowledge. See Research report by Willsey et al. (dev189290).

ChIP-seq binding data for HOXC6 (left), HOXC9 (center) and HOXC10 (right) in spinal cord patterning. The image was made by Dylan Iannitelli from experimental ChIP-seq data for Hox binding generated by Milica Bulajić. See Research article by Bulajić et al. (dev194761)

Scanning electron micrograph of the junction of the internal and external jugular vein with the superior vena cava in an E16.5 mouse embryo. Venous valves that guard the jugular veins are highlighted in green. Lymphovenous valves that prevent back flow of venous blood into lymphatic sacs are highlighted in magenta. Development of both types of valve is blocked in embryos that lack the RASA1 Ras-GTPase-activating protein, VEGF-C signalling and the transcription co-factors YAP and TAZ. See Research articles by Chen et al. (dev192351) and Cha et al (dev195453).

An image of the moment the optic fissure fuses to create the eye globe in human embryonic development. A section through the eye globe and lens was labelled for the transcription factor PAX6 (blue) and the actin cytoskeleton (white). Cells at the margins rearrange to form two complete epithelial layers. See Research article by Patel et al. (dev193649)

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From the 18^th to the 20^th of November 2020, the “17th Meeting of the Spanish Society for Developmental Biology” (SEBD2020) took place in virtual format, organized by the Spanish Society for Developmental Biology (SEBD), CIC bioGUNE, the University of the Basque Country and the University of Cantabria. The SEBD was founded in 1994 to promote scientific activities in the field of Developmental Biology and to promote the exchange of knowledge within the community of Spanish Developmental Biologists nationally and internationally.

The meeting was initially planned to take place in Bilbao, Spain, on the same dates, but this was not possible due to the COVID-19 pandemic. It is worth mentioning that the first meeting of the SEBD, organized by Juan Aréchaga, took place close to Bilbao in 1996 (University of the Basque Country, Leioa). Little could they imagine the circumstances we would face in the 2020 meeting organization! So, we missed out on the wonderful city of Bilbao, its cultural and food and drink scene, but we did not miss out on the great science being done by developmental biologists in Spain and abroad. Despite the switch to a non-face-to-face format, it was the aim of the organizers to respect the program that was already prepared. We were fortunate that all the invited speakers accepted to change to the virtual format. We still thank them for that!

In the virtual SEBD2020 meeting, different sessions were organized, that ranged from the study of the most basic processes of development (Self-organization, Growth & Scaling, Cell Biology, Evo-Devo, Genomes), to the consequences of the modulation of these processes, such as developmental disease and regenerative biology (Neurodevelopment, Development & Disease, Regeneration). All sessions were initiated by invited speakers, all internationally renowned researchers in Developmental Biology, who presented their unpublished work to an audience of over 250 people ranging from early career researchers to established project leaders. Furthermore, two short presentations and three or four flash-talks were selected per session from the abstracts received.

In the morning of the first day, a virtual outreach event with schools was organized to talk about research and developmental biology with young students all across Spain. After that we had two workshops. The first, on animal experimentation legislation was organized by Augusto Escalante and gave participants tips and tricks on how to build an evaluation report for ethics committees. The second, organized by Sofia J. Araújo and Teresa Rayon brought together a panel to discuss new initiatives on journal-independent peer review. The panel, composed of representatives from innovative projects such as Preprint Review from eLife, Sciety, Peer Community In (PCI), Review Commons and PREreview as well as long standing representatives in preprint curation such as ASAPbio and PreLights from the Company of Biologists, lead a dynamic discussion on the possibilities of changing the peer review system. Concerns were raised about the validity of the review without the label of the signing publisher, although it was also argued that the same concerns can be raised in the case of established publishers. The workshop ended with the overall feeling that it is worth continuing the discussion on which projects will be more valuable for the community.

The scientific meeting kicked off with a plenary seminar by Maria Leptin (EMBL Heidelberg and EMBO Director), on the recent work of her lab on how cell mechanics can modulate intrinsic genetic programmes. This was followed by a session on Growth and Scaling, sponsored by Developmental Dynamics with Marian Ros (IBBTEC, UNICAN) as an invited speaker. Marian presented recently published work from her lab on how Hoxc genes are activated in a colinear manner in the embryonic limb ectoderm and are subsequently transcribed in developing nails and hairs, modulating their growth and scaling. The second session focused on multicellular self-organization, and started with an invited seminar by Miki Ebisuya (EMBL Barcelona) on recently published work from her group showing an elegant example of how mouse ES cells and human iPS cells can autonomously generate oscillating expression patterns that are faster in mouse than in human cells, reflecting the species specific somitogenesis clock period observed in the embryo.

The second day started with the Neurodevelopment session, with an invited talk by Elisa Martí (IBMB-CSIC, Barcelona) who told us how the caudal part of the spinal cord is generated through secondary neurulation, dependent on cell intercalation driven by SMAD3 and YAP. This gave way to the Genomes session, dedicated to the memory of José Luis Gómez-Skarmeta, who recently left us prematurely, leaving a great sadness in all the community. The session was opened by Tatjana Sauka-Spengler (Oxford University, Radcliffe Dept. of Medicine) who focused on the regulation of FoxD3, a gene encoding a key transcription factor during neural crest development. By studying different FoxD3 cis-regulatory elements and using single-cell approaches in zebrafish, Tatjana discussed the role of FoxD3 in controlling the development of trunk neural crest cells from neuromesodermal progenitors. Furthermore, the SEBD organized a tribute video to José Luis, with testimonies from his closest collaborators and friends, that praised the life and scientific achievements of this extraordinary researcher and captured the essence of what the figure of José Luis represents for us. The video was shared with those outside the meeting by YouTube live.

The afternoon brought us the Cell Biology session, sponsored by the journal Mechanisms of Development, and the talk of Mónica Bettencourt-Dias (Gulbenkian Science Institute Director) on the de novo origin of centrioles, the diversity of centriole structure between species and even within the same organism, and centriole abnormalities in cancer. Later, we had the Development and disease session, sponsored by the journal Developmental Biology. The session opened with an inspiring talk by Ramón Muñoz-Chápuli (University of Málaga), who introduced the audience to the origin and role of endothelial cells in mammals.

The third and last day started with a session in Evo-Devo. The invited speaker Naoki Irie (University of Tokyo, Japan) spoke about the limits that the genetic programs of development impose to the evolution of vertebrates. With an astounding collection of embryos from a plethora of chordate species, Irie presented a comparison of transcriptomes and epigenetic signatures throughout embryonic development and vertebrate species. Last but not least, we had the Regeneration session, representing a growing branch of developmental biology. It started with a seminar by Florenci Serras (University of Barcelona), who shared with us his group results on the mechanisms of sensing and repairing damage in epithelial tissues, using Drosophila wing discs as the model system.

At the end of the meeting, we organized an awards session, where several prizes were announced. The President of the SEBD, Miguel Torres (CNIC), announced the two winners of the “José Luis Gómez-Skarmeta Award to Scientific excellence in Developmental Biology” for young PIs. Alvaro Rada-Iglesias (IBBTEC, UNICAN) and Manuel Irimia (CRG, Barcelona) won this prize ex-aequo for their contributions to genome regulation in development. Also, the “SEBD Awards for scientific excellence in doctoral theses” were announced, and given this year to Diana García Morales (CABD), Pedro Javier Gómez Gálvez (IBiS) and Cristina Sánchez Fernández (UNICAN) for their outstanding Ph.D. work.

Furthermore, during the meeting, there were two science-competitions. The SEBD prizes for the best posters were selected by a scientific committee present at the meeting. The best poster prize went to Carlos Camilleri-Robles from the University of Barcelona, who presented his results on Regeneration of Drosophila wing imaginal discs. The 2^nd prize went to Daniel del Toro also from the University of Barcelona for his poster on migrating neuron guidance. And we had two 3^rd prizes for Cruz Morenilla-Palao from the Neurosciences Institute and José Santos-Pereira from the CABD-CSIC, on the formation of bilateral circuits and zebrafish gene regulation, respectively.

A Photography Competition was sponsored by the journal Developmental Biology. In this SciArt competition there were many beautiful images from different developmental biology models and methods. Victor Borrell (Neurosciences Institute, Alicante) authored the winning image, a ferret kid brain section named “Ferret Butterfly”. The second prize went to Veronica Murcia from the same institute, with a growth cone image she entitled “Flower Thistle”. And, last but not least, Ettore de Giorgio (IBMB-CSIC, Barcelona) got the third prize with a photo of a Drosophila embryonic trachea entitled “Roots and Branches”. There were many other beautiful pictures, which unfortunately could not be selected, but we have been posting them in the SEBD Twitter and Instagram accounts.

Notwithstanding the virtual format, we decided to pursue initial plans for poster presentations and side-activities, aiming to promote as much interaction as possible among participants. Posters were visible in pdf format at the virtual platform and, in many cases, were accompanied by explanatory audio or video. Most of the presentations, were live and followed by a live Q&A session by the audience. This made the sessions highly interactive, dynamic and participative, with lively discussions. Oral presentations were recorded and made available for up to one week after the meeting finished. Discussions in the poster sessions were done through the Slack channels or (virtual) face-to-face in Remo.

Virtual meetings lack human contact and networking which is so important for science advancement. An extra effort from the organizing and scientific committees was done to facilitate computer-based communication tools, including online platforms for live presentations and discussions, Slack channels for specific discussion on each poster and scientific talk, and Remo sessions for informal discussions among participants. Slack channels were also used for putting adds and general information about the meeting. All together these channels helped fill in the gap left by the lack of real-life contacts.

We were very fortunate to count on sponsorship from the Company of Biologists, Developmental Biology, Mechanisms of Development, Developmental Dynamics and Development. This financial support was used to waive the registration fee for undergraduate and PhD students, which benefitted students not only form the SEBD, but also from abroad (other European countries, and other as far as Brazil, Mexico and Australia). Opinion polls were performed at the end of the meeting, where most of the participants manifested that the meeting was better or much better than they anticipated! And nobody complained about the catering…

You can read more here!

The SEBD2020 Scientific Committee: Isabel Almudi, Sofia J. Araújo, Rosa Barrio, Laura Bozal, Augusto Escalante, Fernando Garcia-Moreno, Maria Losada-Perez, Ignacio Maeso, Luciano Marcon, Oscar Ocaña, Olatz Pampliega

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This interview, the 85th in our series, was published in Development earlier this year. 

The enteric nervous system (ENS) derives from the neural crest and innervates the gastrointestinal system, in which it is essential for gut function throughout life. A new paper in Development uses zebrafish to investigate the poorly understood process of post-embryonic ENS neurogenesis, in both development and injury contexts. To find out more, we met the paper’s two authors, Wael Noor El-Nachef, Assistant Clinical Professor of Medicine at UCLA, and Marianne Bronner, Albert Billings Ruddock Professor of Biology and Biological Engineering at Caltech.

Marianne, can you give us your scientific biography and the questions your lab is trying to answer?

MB: When I started graduate school, I thought that I wanted to do structural biology, but then I took a course in developmental biology and found my passion. I learned about Nicole Le Douarin’s work on the neural crest and it blew me away. I immediately knew that I wanted to work on neural crest cells and be just like her. To this day, she remains my role model. I was fortunate enough to get my first faculty position at the University of California Irvine right out of graduate school. I then moved to Caltech in 1996, where my lab grew larger but continued working on the same types of problems, while adapting new and exciting technologies to help solve them.

My lab pursues diverse questions in neural crest biology, ranging from how and when neural crest cells are induced to how they may have arisen and changed during vertebrate evolution. How and why have neural crest cells continued to acquire new traits? How do they migrate, find their proper sites and differentiate into a diverse array of cell types? Most recently, we have become fascinated by their potential role in tissue regeneration. Wael’s work on de novo neurogenesis in the ENS fits perfectly into these areas of interest.

And Wael – how did you come to work in Marianne’s lab and what drives your research today?

WE-N: I have had somewhat of a non-traditional path into basic science research in that I didn’t get serious about research until after medical school. During my clinical training, I was frequently frustrated by so many ‘idiopathic’ diseases in gastroenterology that are difficult to treat and terrible for the patient, and the most challenging of those conditions often involve the ENS. Rather than wait around for someone else to figure out these problems, I decided to pursue research training in regenerative medicine, initially studying cultured enteric neuronal progenitors in a tissue-engineered intestine construct. Although that was a rewarding experience, I quickly realized that there are many fundamental issues that we do not yet understand about ENS development and homeostasis. And without establishing some of these basics, regenerative medicine approaches to enteric neuropathies will be stymied.

My big revelation came when I realized that ‘developmental biology’ is not limited to embryogenesis, but rather includes postnatal development and growth, aging and senescence, and homeostasis and regeneration. Or, in the words of John Wallingford, ‘we are all developmental biologists’. This perspective expanded my views of the field I wished to join and I reached out to Marianne (I cold called her, and she surprisingly took me on). Training in her lab seems like an obvious choice in retrospect, but in our sometimes cloistered research niches it initially felt a bit mavericky. Luckily, UCLA, my home institution, has an established affiliation with Caltech and has been extremely supportive of my research pursuits.

How has your research been affected by the COVID-19 pandemic?

WE-N: Like so many other scientists, our experimental lab work was placed on hold for a few months while we were on lockdown. Luckily, we are currently ramping-up our activity in the lab; we work in shifts, practice physical distancing, wear masks, etc. It’s great to be back in the lab, and I’m sure I’m not the only one who may have gotten a bit misty-eyed pipetting something for the first time in months. I consider myself extremely fortunate in that I didn’t lose anything other than some time; my family and I are healthy, my fish lines are intact, my projects can restart fairly easily, etc. But returning to the lab within this current COVID-19 paradigm, I now realize the importance of those chance collisions with my colleagues when we informally exchange ideas or troubleshoot a problem together during our daily lab tea time. Videoconferencing is no substitute.

Why has the manner (and even the existence) of postnatal enteric neurogenesis been so controversial?

WE-N: It comes down to this: the gastrointestinal tract is difficult to study. It is arguably the largest endocrinologic organ, largest epithelial organ, largest immunologic organ and second largest neurologic organ; it fills up the largest body cavity in a long convoluted bundle; it is constantly moving and is dynamic in several respects; and to top it all off, it is filled with ‘luminal contents’, which include the largest microbiome compartment of our body. Although this amazing complexity is what first attracted me to this field, there are days when I envy those who study the central nervous system.

In model organisms other than zebrafish, one challenge has been how to directly visualize and detect enteric neurogenesis. Simply counting neurons from a representative section and then extrapolating in some way is not reliable. Live imaging the ENS in species such as mouse is possible but technically challenging and often carried out using a few time points rather than a several-hours long time-lapse. Lineage-tracing experiments with murine Cre transgenic lines have been hampered by relatively low recombination rates. Assessing for evidence of enteric neurogenesis with the use of thymidine analogues has also been complicated by unclear optimal pulse/chase duration and timing. Lastly, studies of ENS homeostasis using non-zebrafish models often investigated the intestinal tract divorced from the rest of the body, and thus may have been unable to consider the possibility of a gut-extrinsic source of neuronal precursors using their methods.

Ultimately, new enteric neurons may arise in small numbers over time and over a large area, and thus may be difficult to detect without fully surveying the ENS. It is also important to acknowledge that alternative hypotheses are not necessarily mutually exclusive, and nature may have provided multiple solutions for addressing issues of ENS homeostasis. But, my experience with the zebrafish model has shown me the advantages of using a model that is highly tractable and amenable to live and in toto imaging to allow us to compellingly explore questions of enteric neurogenesis.

Can you give us the key results of the paper in a paragraph?

WE-N & MB: Using a photoconvertible transgenic line to ‘time stamp’ enteric neurons, we found that enteric neurogenesis persists in post-embryonic zebrafish development, despite an apparent absence of enteric neuronal progenitors, including enteric glia. Lineage tracing with carefully timed DiI injections into the neural tube, as well as with an inducible Cre-transgenic line, supported a trunk neural crest origin of these post-embryonic enteric neurons, consistent with them arising from Schwann cell precursors (SCPs). Enteric neurogenesis was also observed after injury, modelled with two-photon laser ablation of individual neurons. The 5-HT4 receptor agonist prucalopride increased enteric neurogenesis during normal development, as well as in pre-treated fish that subsequently underwent neuronal ablation.

Comparing zebrafish with other species, what can you infer about the contribution of SCPs to the ENS during evolution?

WE-N & MB: In the lamprey, an early jawless vertebrate that appears to lack a vagal neural crest, the ENS originates from the trunk neural crest, suggesting that this may have been the original strategy for providing the basal vertebrate intestine with enteric neurons. However, the evolution of jawed vertebrates was accompanied by the appearance of the vagal neural crest, and the initial formation of the ENS in these animals arose from this newer cell population. We suspect that rather than completely losing the trunk crest contribution to the ENS, later vertebrates adapted this cell population of SCPs to act as a reservoir of ENS progenitor cells that contribute enteric neurons as the intestine grows or to maintain enteric neuron number in the case of injury.

Does your work have any implications for the understanding or treatment of human enteric neuropathies?

WE-N & MB: Certainly. As there is evidence of SCP-derived enteric neurogenesis in teleosts, chicks and mice, it is reasonable to consider that this is also conserved in humans. Many acquired enteric neuropathies are thought to be due (at least in part) to a loss of enteric neurons. In such disease states, promoting enteric neurogenesis with agents such as 5HT4 receptor agonists represents a potential therapeutic approach that is much simpler than trying to rebuild the ENS by injecting precursors that were created in a lab.

Stepping aside from treatment, understanding why a patient’s SCPs are unable to maintain enteric neuron number may lead to a deeper understanding of these pathologies. Is the enteric neuron loss too profound for the SCPs to compensate, or does the disease process involve the SCPs directly? Could enteric neuropathies actually be SCP-opathies?

When doing the research, did you have any particular result or eureka moment that has stuck with you?

WE-N: My first time-lapses that captured new enteric neurons arising in the intestine really energized my efforts. To me, it was exciting, aesthetically pleasing to view, and, simply put, cool. That feeling of seeing something that perhaps no one else has observed before is a very special feeling. I did those experiments early on, and it gave me the confidence that I had the right tools and techniques to explore my research questions in fun and interesting ways.

Seeing something that perhaps no one else has observed before is a very special feeling

And what about the flipside: any moments of frustration or despair?

WE-N: I love coffee. But it turns out that too much coffee on the day you need to dechorionate and microinject zebrafish embryos is not a good thing. Suffice to say that day of experiments was an absolute disaster and had to be rescheduled.

What’s next for you after this paper?

WE-N: I’m very interested in exploring the evolutionary development of enteric glia further. Our results suggest that zebrafish may be missing enteric glia, or at least cells with classical glial properties in the gut. If we can determine when in evolution enteric glia arose, it may help us infer why they arose. Currently, there is some controversy concerning the role of enteric glia in health and disease, and improving our understanding of their function may shine a light on a number of gastrointestinal diseases.

I’m also looking forward to better defining the SCP cell population in zebrafish to aid me in the study of their migration dynamics, and to begin exploring the potential signalling mechanism of 5HT4 receptor agonism in enteric neurogenesis.

Where will this story take the Bronner lab?

MB: We are very interested in evolutionary changes in the ENS and how and when increased complexity arises. Comparing diverse species, such as lamprey, zebrafish and mouse ENS neurons and glia, may offer clues as to how the ENS has become elaborated during the course of vertebrate evolution.

Another direction we are pursuing is using single cell RNA sequencing to examine the heterogeneity of enteric neurons in zebrafish as a function of time. Despite the fact that the zebrafish intestine is comparative simple compared with mouse, there are a diverse array of neurons characterized by different neurotransmitters and neuropeptides. Understanding the molecular underpinnings of how and when these differentiate fascinates me and is a direction we are currently pursuing.

Finally, let’s move outside the lab – what do you like to do in your spare time in California?

WE-N: I have a 1-year-old son, and I’ve recently taken up hiking with him sitting in a special pack that I wear on my back. If I slow down, he’ll bang on my head, so it’s a great workout with very personalized coaching.

MB: I enjoy swimming and hiking, both of which I have been lucky enough to continue during the lockdown. My baking has also improved!

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The Sokol laboratory at the Icahn School of Medicine at Mount Sinai, New York, is looking for a motivated candidate to join our group as a postdoctoral associate. Our laboratory is in the Department of Cell, Developmental and Regenerative Biology, with a number of groups with highly collaborative, developmental and stem cell biology program. Besides high-quality research core facilities, career guidance and professional development training are provided for postdoctoral fellows.

Our group studies how Wnt signaling pathways branch out to control cell lineage and cell movements during vertebrate gastrulation and neurulation.  We are also interested in the regulation of apicobasal and planar cell polarity during neural tissue and neural crest formation.  A successful candidate will use live cell imaging and biochemical/proteomic approaches to identify new molecules regulating cell signaling and polarity in early vertebrate embryos and mammalian progenitor cells.  See the description of our interests at   http://labs.icahn.mssm.edu/sokollab/.

Preference will be given to highly motivated and interactive applicants with strong background in cell biology and biochemistry.  Interested candidates may send their CV, a short description of relevant expertise, list of publications and the names of three references to Dr. Sergei Sokol (sergei.sokol@mssm.edu).

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Closing date for applications 19^th of January 2021

Starting date end of 2021, beginning of 2022

The 2020 call for the Spanish “Juan de la Cierva Postdoctoral Fellowships” is now open. This is a fantastic opportunity to join the Araújo group, who are focused on identifying the molecular mechanisms underlying single-cell branching during development and disease. We study this during morphogenesis of the Drosophila melanogaster tracheal and nervous systems (Ricolo et al. Current Biology 2016 and Ricolo and Araújo, eLife, 2020), and are also interested in knowing how single-cell branching affects the whole organismal behaviour. We are combining cell analysis and confocal tissue live imaging, with genetic approaches and CRISPR/Cas9 technologies.

We are based at the Institute of Biomedicine of the University of Barcelona (IBUB) and are looking for a motivated and enthusiastic candidate who will play a central role in the lab. You must have a Ph.D. in areas relevant to cell/developmental biology and/or in computational biology (and have defended your Ph.D. thesis after the 1^st of January 2016). Applicants are expected to have excellent interpersonal and communication skills, be highly independent and committed to research in a fast-moving and exciting field.

If you’re interested, please write to sofiajaraujo [at] ub.edu

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By Jos Wendrich, Yvan Saeys and Bert De Rybel

Nutrients such as phosphate are limiting in most soils. This has a great impact on crop yield in agriculture. Approaches to overcome these challenges often include using fertilizers, that in turn have a detrimental effect on the environment and our climate. Plants have developed adaptation mechanisms to efficiently forage the soil for phosphate such as modifying root system architecture and root hair density. In Wendrich et al., we unexpectedly identified a vascular transcription factor complex that controls root hair formation in response to limiting phosphate conditions.

One of the main interests of our lab is identifying the molecular pathways controlled by the TARGET OF MONOPTEROS 5 and LONESOME HIGHWAY (TMO5/LHW) transcription factor heterodimer. In the root meristem, this complex is active in the inner most cells of the vasculature called the xylem. Here it controls the expression of LONELY GUY 4, which encodes an enzyme that is rate-limiting for the conversion of the phytohormone cytokinin into its bioactive form. Cytokinin is involved in many aspects of vascular development including patterning and proliferation. Using bulk transcriptomics, we previously revealed 273 target genes of the TMO5/LHW complex, but given the downstream intermediate cytokinin is mobile, we expected that many of these target genes would be expressed outside of the xylem cells. This is where this project started.

At that time, single-cell technologies were quickly becoming important in other fields and proved ideal to determine gene expression at unprecedented resolution. We thus decided we needed to get this technology up and running to answer our research question. Our institute had recently invested heavily to establish the technique, with commercial microfluidics systems and custom bioinformatic pipelines, but it remained unclear how reliable and efficient this would work on isolated plant cells. We teamed up with the group of Yvan Saeys in our neighboring VIB research center to generate a reference dataset for the Arabidopsis root meristem. We first needed to optimize the workflow leading up to the microfluidics single cell droplet emulsion. With their tough cell walls, plant cells are not easily dissociated from their tissue, requiring enzymatic digestion of the cell walls, called “protoplasting”. Cells in the outer layers are more accessible for these enzymes and tend to be overrepresented after in protoplast suspensions. We therefore first made sure that our single cell protoplast suspensions contained a good representation of each cell type, inner and outer layers, and was free of most debris and impurities, such as dead cells.

Unfortunately, this was the easy part. Now came the analysis, annotation and, importantly, full validation of the technology. This was where our collaboration effort truly started to pay off. The analysis pipelines were custom redesigned for our plant samples. This included building a visualization tool, for quick access to the data. Endless discussions, quick face-to-face check-ups and back-and-forth emailing ensured that we quickly learned from each other and from the dataset. Because of the rich resources available for Arabidopsis, we were able to annotate the main cell types of the root such as epidermis, ground tissues and vascular tissues. We however decided to take it a step further and zoom in to the level of sub-cell-types. Especially the different cell types of the vascular system were more difficult to annotate, as several cell types, like for example the procambium, only have limited known marker genes that are specifically expressed. Sub-cell-type predictions were confirmed by cell ploidy analysis and an extensive trajectory inference. By iteratively applying these trajectory methods, and having an open communication line between wet- and drylab, we were able to assess the robustness of the predicted trajectories and the resulting predicted subcluster annotations.

We next set out to evaluate the predictive power of this dataset, by construction of promoter reporter lines of genes with hitherto unknown expression patterns. All group members chipped in and a remarkable 100% of the lines with stable expression patterns validated the predicted cell type and developmental states. We were thus eager to apply this rich dataset on the 273 target genes of the TMO5/LHW complex previously identified. We identified an unexpected overrepresentation of genes expressed in root hairs (trichoblasts), suggesting that these vascular transcription factors may play a role in the development of the outermost trichoblast cells. Indeed, when overexpressing TMO5 and LHW in all cells of the root meristem, this dramatically increased the density of root hairs, resembling wild type roots grown in phosphate limiting conditions. Extensive follow-up genetic work allowed us to conclude that cytokinin, produced in inner vascular cells, acts as a mobile intermediate to control root hair response to low phosphate conditions in the outer most epidermal cell.

In our opinion, this is a good example of how collaborations within and between teams with different expertise can lead to new biological insights.

Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions. Science. 13 Nov 2020. Jos R. Wendrich, BaoJun Yang, Niels Vandamme, Kevin Verstaen, Wouter Smet, Celien Van de Velde, Max Minne, Brecht Wybouw, Eliana Mor, Helena E. Arents, Jonah Nolf, Julie Van Duyse, Gert Van Isterdael, Steven Maere, Yvan Saeys, Bert De Rybel

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Recently shared by the British Society for Developmental Biology

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The Max Planck Institute for Heart and Lung Research in Bad Nauheim (near Frankfurt, Germany), Department of Developmental Genetics (Prof. Dr. Didier Stainier) invites applications for a Postdoctoral Fellow (m/f/d) in RNA/Protein Biochemistry and Molecular Biology to study Genetic CompensationReference Number 2020_30.

A highly motivated postdoctoral candidate is invited to lead new projects to address fundamental questions in Genetic Compensation and Transcriptional Adaptation.

We have recently discovered a new form of genetic compensation that we have termed transcriptional adaptation.  Briefly, transcriptional adaptation occurs when a premature termination codon leads to mutant mRNA degradation.  The degradation fragments in turn modulate the expression of related genes, and consequently varying degrees of phenotypic rescue in some cases.  We have observed this phenomenon in zebrafish, mouse, C. elegans, and more recently humans.

This is a novel and quickly developing field of research where many open questions remain to be addressed including 1) the nature and trafficking of the degradation fragments, and 2) the regulation of related genes by the degradation fragments, or their derivatives.  For more detailed information please see our recent publications:

https://www.nature.com/articles/s41586-019-1064-z

https://www.nature.com/articles/nature14580

https://elifesciences.org/articles/50014

Required qualifications:

A Ph.D. in biology, biochemistry, genetics or a similar subject with a focus on molecular biology, cell biology, biochemistry and/or genetics.  Knowledge of RNA and/or protein biochemistry and molecular biology is a plus.

About the employer:

The Max Planck Institute for Heart and Lung Research in Bad Nauheim is an interdisciplinary research institution with international flair.  Our researchers have the opportunity to work on various model systems by making use of the latest cutting-edge technologies.  Researchers are supported by state-of-the-art core facilities which offer services in next generation sequencing, proteomics, bioinformatics, cytometry, microscopy, and small animal imaging.

The Max Planck Society strives for gender and diversity equality; we welcome applications from all backgrounds.  Furthermore, the Max Planck Society is committed to increasing the number of individuals with disabilities in its workforce and therefore encourages applications from such qualified individuals.

How to apply:

For further information, please contact Prof. Dr. Didier Stainier (didier.stainier@mpi-bn.mpg.de).

https://www.mpi-hlr.de/207358/job_full_offer_16142347?c=80167

To apply, please submit the names and contact information for 2-3 references, a CV, and a short statement (2 pages max.) of your research experience and interests to didier.stainier@mpi-bn.mpg.de

Max Planck Institute for Heart and Lung Research
Department of Developmental Genetics
Ludwigstraße 43
61231 Bad Nauheim
Germany

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