We currently have an opening for a Reviews Editor as a maternity cover position on Development. As this is a temporary position, we are specifically looking for candidates with editorial experience.
Core responsibilities of the position include:
Commissioning, handling peer review and developmental editing of material for the front section of the journal
Representing the journal at international conferences and within the wider scientific community
Writing press releases, article highlights and material for Development’s community website ‘the Node’
Creative involvement in the journal’s development
For further details and instructions on how to apply, please see the full job advert here. If you are interested in applying, but would like further information or have any questions, please feel free to drop me an email.
Naa12 rescues embryonic lethality in Naa10-Deficient Mice in the amino-terminal acetylation pathway
Hyae Yon Kweon, Mi-Ni Lee, Max Dörfel, Seungwoon Seo, Leah Gottlieb, Thomas Papazyan, Nina McTiernan, Rasmus Ree, Andrew Garcia, Michael Flory, Jonathan Crain, Alison Sebold, Scott Lyons, Ahmed Ismail, Elaine Marchi, Seong-keun Sonn, Se-Jin Jeong, Sejin Jeon, Shinyeong Ju, Simon J. Conway, TaeSoo Kim, Hyun-Seok Kim, Cheolju Lee, Tae-Young Roh, Thomas Arnesen, Ronen Marmorstein, Gholson J. Lyon, Goo Taeg Oh
Serine Palmitoyltransferase Controls Stemness of Intestinal Progenitors
Ying Li, Bhagirath Chaurasia, Vincent Kaddai, Joseph L. Wilkerson, J. Alan Maschek, James Cox, Peng Wei, Claire Bensard, Peter J Meikle, Hans Clevers, James A Shayman, Yoshio Hirabayashi, William L. Holland, Jared Rutter, Scott A. Summers
CTCF is a Barrier for Totipotent-like Reprogramming
Teresa Olbrich, Maria Vega-Sendino, Desiree Tillo, Wei Wu, Nicholas Zolnerowich, Andy D. Tran, Catherine N. Domingo, Mariajose Franco, Marta Markiewicz-Potoczny, Gianluca Pegoraro, Peter C. FitzGerald, Michael J. Kruhlak, Eros Lazzerini-Denchi, Elphege P. Nora, Andre Nussenzweig, Sergio Ruiz
Robust integrated intracellular organization of the human iPS cell: where, how much, and how variable?
Matheus P. Viana, Jianxu Chen, Theo A. Knijnenburg, Ritvik Vasan, Calysta Yan, Joy E. Arakaki, Matte Bailey, Ben Berry, Antoine Borensztejn, Jackson M. Brown, Sara Carlson, Julie A. Cass, Basudev Chaudhuri, Kimberly R. Cordes Metzler, Mackenzie E. Coston, Zach J. Crabtree, Steve Davidson, Colette M. DeLizo, Shailja Dhaka, Stephanie Q. Dinh, Thao P. Do, Justin Domingus, Rory M. Donovan-Maiye, Tyler J. Foster, Christopher L. Frick, Griffin Fujioka, Margaret A. Fuqua, Jamie L. Gehring, Kaytlyn A. Gerbin, Tanya Grancharova, Benjamin W. Gregor, Lisa Harrylock, Amanda Haupt, Melissa C. Hendershott, Caroline Hookway, Alan R. Horwitz, Chris Hughes, Eric J. Isaac, Gregory R. Johnson, Brian Kim, Andrew N. Leonard, Winnie Leung, Jordan J. Lucas, Susan A. Ludmann, Blair M. Lyons, Haseeb Malik, Ryan McGregor, Gabe E. Medrash, Sean L. Meharry, Kevin Mitcham, Irina A. Mueller, Timothy L. Murphy-Stevens, Aditya Nath, Angelique M. Nelson, Luana Paleologu, T. Alexander Popiel, Megan M. Riel-Mehan, Brock Roberts, Lisa M. Schaefbauer, Magdalena Schwarzl, Jamie Sherman, Sylvain Slaton, M. Filip Sluzewski, Jacqueline E. Smith, Youngmee Sul, Madison J. Swain-Bowden, W. Joyce Tang, Derek J. Thirstrup, Daniel T. Toloudis, Andrew P. Tucker, Veronica Valencia, Winfried Wiegraebe, Thushara Wijeratna, Ruian Yang, Rebecca J. Zaunbrecher, Allen Institute for Cell Science, Graham T. Johnson, Ruwanthi N. Gunawardane, Nathalie Gaudreault, Julie A. Theriot, Susanne M. Rafelski
Dog color patterns explained by modular promoters of ancient canid origin
Danika L. Bannasch, Christopher B. Kaelin, Anna Letko, Robert Loechel, Petra Hug, Vidhya Jagannathan, Jan Henkel, Petra Roosje, Marjo K. Hytönen, Hannes Lohi, Meharji Arumilli, DoGA consortium, Katie M. Minor, James R. Mickelson, Cord Drögemüller, Gregory S. Barsh, Tosso Leeb
Molecular topography of an entire nervous system
Seth R Taylor, Gabriel Santpere, Alexis Weinreb, Alec Barrett, Molly B. Reilly, Chuan Xu, Erdem Varol, Panos Oikonomou, Lori Glenwinkel, Rebecca McWhirter, Abigail Poff, Manasa Basavaraju, Ibnul Rafi, Eviatar Yemini, Steven J Cook, Alexander Abrams, Berta Vidal, Cyril Cros, Saeed Tavazoie, Nenad Sestan, Marc Hammarlund, Oliver Hobert, David M. Miller III
Automated hiPSC culture and sample preparation for 3D live cell microscopy
Mackenzie E. Coston, Benjamin W. Gregor, Joy Arakaki, Antoine Borensztejn, Thao P. Do, Margaret A. Fuqua, Amanda Haupt, Melissa C. Hendershott, Winnie Leung, Irina A. Mueller, Angelique M. Nelson, Susanne M. Rafelski, Madison J. Swain-Bowden, W. Joyce Tang, Derek J. Thirstrup, Winfried Wiegraebe, Calysta Yan, Ruwanthi N Gunawardane, Nathalie Gaudreault
Scalable production of tissue-like vascularised liver organoids from human PSCs
Sean P Harrison, Richard Siller, Yoshiaki Tanaka, Yangfei Xiang, Benjamin Patterson, Henning Kempf, Espen Melum, Kathrine S Åsrud, Maria E Chollet, Elisabeth Andersen, Per Morten Sandset, Saphira Baumgarten, Flavio Bonanini, Dorota Kurek, Santosh Mathapati, Runar Almaas, Kulbhushan Sharma, Steven R Wilson, Frøydis S Skottvoll, Ida C Boger, Inger L Bogen, Tuula A Nyman, Jun J Wu, Ales Bezrouk, Dana Cizkova, Jaroslav Mokry, Robert Zweigerdt, In-Hyun Park, Gareth J Sullivan
We live in an ageing society with high incidence of cognitive, sensory and motor decline, as well as neurodegenerative diseases such as Alzheimer’s disease (AD) or Fronto-temporal Dementia (FTD). Although decay of synaptic functions is a clear hallmark of the aforementioned conditions, we know too little about the underlying causes. The overarching aim of this project is to study roles of the ageing- and neurodegenerative disease-related factor Tau during the regulation of synapses in health, ageing and disease.
Synapses are specialised neuronal cell junctions which contain complex machinery for rapid transmission of signals to partner cells. This machinery is frequently disrupted during ageing and in neurodegeneration and the resulting synaptic malfunction is an important cause for cognitive, sensory and motor decline. The underpinning mechanisms are poorly understood. To bridge this knowledge gap, we focus on Tau. Tau plays a vital role in the pathogenesis of neurodegenerative disorders and is also linked to physiological ageing. Accordingly, Tau is an important therapeutic target for the development of treatments of AD and FTD.
Considering Tau’s crucial roles during pathogenesis and treatment of dementia, it is vital to understand its physiological function. Tau loss is known to lead to age-related synaptic deficits both in mice and the fruit fly Drosophila, and our work has started to deliver first explanations. Thus, we have shown that Tau loss triggers aberrations of microtubule networks and axonal transport deficits affecting synapse formation and maintenance (Voelzmann et al., 2016, eLife 5, e14694ff.; Hahn et al., 2020, bioRxiv 2020.08.19.257808ff.). We now find from our proteomic and preliminary functional studies that Tau plays even more direct roles by binding to factors that are important for synaptic function. The aim of this project is to understand these synaptic mechanisms of Tau. For this, we will use the model organism Drosophila which harbours Tau and synaptic machinery that is well conserved with humans, but can be studied far more effectively than in other model organisms. Using Drosophila‘s efficient genetics, powerful experimental strategies and simple robust behavioural assays, you will study the functional links between Tau and its synaptic binding partners. This will involve inter-disciplinary approaches using genetics, molecular biology, biochemistry, cell biology, cell culture and in vivo studies, cutting-edge bioimaging of synaptic activity and behavioural studies. You will unravel mechanisms of Tau at synapses as a means to understand neuronal decay during ageing and in neurodegeneration.
Applications from candidates, ideally with some background in cell biology, genetics, neuroscience and/or biomedical sciences are encouraged to apply. The successful applicant will be based in the Institute of Systems, Molecular & Integrative Biology, University of Liverpool, supervised by Dr Sánchez-Soriano (https://sanchezlab.wordpress.com/research/), whilst working closely with Dr Olena Riabinina (http://insectneurolab.com/) at the Department of Biosciences, Durham University. Interested applicants should contact Dr Sanchez-Soriano to discuss the project: n.sanchez-soriano@liverpool.ac.uk.
A postdoctoral research associate position is available immediately to investigate the role of reactive oxygen species (ROS) as physiological signaling molecules in axonal growth and guidance in the lab of Dr. Daniel M. Suter at Purdue University, West Lafayette, IN https://suterlab.bio.purdue.edu/. Specifically, the work will investigate the molecular and cellular mechanisms of how ROS regulate axonal growth and guidance in vitro and in vivo. The successful applicant has experience in cell biology and molecular biology. Additional expertise in developmental neuroscience, microscopy, and working with zebrafish is desirable but not required. This position is supported through funding from the NIH.
Highly motivated candidates with a PhD in cell biology, molecular biology, or neuroscience who are interested to participate in this exciting project at the interface of cellular and developmental neurobiology are invited to send their CV, a brief statement of research interests and contact information of three referees to Dr. Suter.
Dr. Daniel M. Suter
Department of Biological Sciences
Purdue University
915 West State Street
West Lafayette, IN 47907
USA dsuter@purdue.edu
765-496-1562
The BiOf lab http://biof-lab.org/ has developed a microfluidic technique, the Cellular Capsules Technology, that allows them to produce multicellular spheroids and organoids in a high throughput and controlled format. The applications in tissue engineering, oncology and regenerative medicine and toxicology testing are numerous. The recruited postdocs will be involved in the interdisciplinary projects pursued by the team in engineering multiscale vascularized tissues, reconstructing a functional liver lobule, deciphering the impact of mechanical cues on hepatocarcinoma and glioblastoma progression in vitro models, developing innovative microscopy techniques for thick tissue imaging.
We seek for talented scientists with exceptional motivation and outstanding expertise (i.e. PhD) in biophotonics /image analysis, cancer or stem cell biology, microfluidics, biophysics or tissue engineering.
The proposed funding is for 12 months and can be renewed up to 36 months. The salary will be adapted to the experience of the applicant. Starting date will be between March and June 2021.
A postdoctoral research position is available in the group of Dr. Kristen Panfilio at the University of Warwick, UK, to join our BBSRC-funded project on how polyploid nuclear structure influences cellular function in dynamic epithelial tissues. This is a full-time, fixed-term position for up to 36 months, integrating developmental biology, bioinformatics, cell cycle regulation, genome organization, and 4D live cell imaging.
Polyploidy is hypothesized to aid epithelial barrier formation and its repair after wounding and to rapidly supply gene products by transcription from multiple gene copies. Yet polyploid genomic structure may be unstable and require active inhibition of apoptosis through regulatory processes that are not yet well understood. Investigating the costs and benefits of polyploidy is essential to understand tissue-specific development, homeostasis, and ageing.
The two extraembryonic tissues of insects offer an excellent – and inherently comparative – research model, spanning key developmental stages for morphogenesis and cellular physiology. Our research species is the flour beetle Tribolium castaneum, which offers advanced genetic resources and where we integrate fluorescent live cell imaging and next-generation sequencing approaches (see the lab’s recent publications in eLife 5:e13834, Development 143:3002, Commun. Biol. 3:552). The project uses methods to assess nuclear size and tissue integrity, quantify gene expression, and genetically challenge barrier organization and cell number. Altogether, we will test long-standing hypotheses on polyploidy function and its end-stage implications in animal tissues. A complete description of the project is available at: https://gtr.ukri.org/projects?ref=BB%2FV002392%2F1.
You will have a Ph.D. or equivalent and good knowledge and experience in genetics, cell and developmental biology, standard molecular biology techniques,and working with NGS data, as evidenced by your Ph.D. thesis and/or authored papers in peer-reviewed journals. Familiarity with the fields of insect developmental genetics and comparative genomics would also be highly advantageous. Practical experience in any of the following is desired: advanced microscopy (including light sheet fluorescence microscopy),RNAi, FACS, RT-qPCR, and computational work with either sequencing or imaging data. We will provide full training in new techniques, supported by the possibility for international travel and collaboration.
Enquiries and expressions of interest directly to Kristen (K.Panfilio@warwick.ac.uk) are welcome, with applications made on-line (post number 103508). Full applications will include contact details for at least two referees, a CV, and covering letter stating why you are interested in the topic and what you would bring to the project. The application closing date is 7th February 2021.
The patterning of stomata – the pores in the plant epidermis that facilitate gas exchange and water control – is regulated by a family of small secreted peptides. A new paper in Development analyses the effective ranges of two such peptides, borrowing a statistical technique used by astrophysicists to investigate the distribution and patterning of galaxies. We caught up with authors Emily Lo, who worked on the project when an undergraduate at the University of Washington (UW), and her supervisor Keiko Torii, who recently moved her lab from UW to The University of Texas at Austin (where she is Professor and Johnson & Johnson Centennial Chair in Plant Cell Biology), to hear more about the story.
Emily (L) and Keiko (R)
Keiko, can you give us your scientific biography and the questions your lab is trying to answer?
KT: As a plant developmental biologist, I was always super fascinated by how dazzling arrays of functional, beautiful patterns emerge during development and how the external environment, where plants thrive, shapes the manifestation of such functional patterns. My main focus is to tackle such observations through understanding the molecular and genetic basis of cell-cell communication, ‘how plant cells talk to each other to generate functional patterns’.
I received my PhD and did my first short postdoc in Japan, where I identified the causal gene for the Arabidopsis mutant, erecta, which exhibits short stature and altered organ shape. It turned out that the ERECTA gene encodes a putative receptor kinase (collectively known as ‘Receptor-like Kinase’ or ‘RLK’), and it was the first report that this type of putative peptide receptor regulates plant growth and development. Later, after I obtained a tenure-track Assistant Professor position at the UW in Seattle, our research elucidated that ERECTA-family RLKs perceive a family of peptides to enforce proper stomatal patterning, which is the basis of this work.
In the Fall of 2019, I accepted the Johnson & Johnson Centennial Chair in Plant Cell Biology at the Department of Molecular Biosciences, The University of Texas at Austin. Currently I am also a Howard Hughes Medical Investigator.
And Emily – how did you come to work in Keiko’s lab on this project?
EL: I was lucky enough to be hired as an undergrad in Keiko’s lab during my freshman year at UW, and I stayed on until I graduated. It’s a rare opportunity to have such a long research experience as an undergrad, so I was able to devote a substantial amount of time to this project. Keiko introduced me to this fascinating project using mosaic fluorescent sectors to track peptide expression, which had been initiated by Dr. Takeshi Kuroha, a previous postdoctoral fellow, and Janelle Sagawa, a previous undergrad researcher (both acknowledged in the manuscript). So right away I could start growing seedlings, generating these mosaic sectors, and imaging on the confocal microscope. It was great fun! I graduated before we were able to complete the project, so Scott [Zeng] developed the majority of the SPACE pipeline after I left the lab.
How has your research been affected by the COVID-19 pandemic?
KT: Unfortunately, my lab and research program got hit really hard by the COVID-19 situation, because we had just relocated from Seattle WA to Austin TX right before the pandemic hit. Our brand-new lab at UT Austin was finally operating in the beginning of 2020 when we had to suddenly shut it down. Like myself, almost all the new lab members were new to Texas (or the Southern part of USA), and many were separated from family. So, staying at home in an unfamiliar city was stressful to everyone, and I truly thank my lab members for being positive and hanging together during this exceptionally difficult time. As for this manuscript, since we were at the phase of drafting a manuscript (lucky us!), Scott and I completed the manuscript during the full shut down phase, with thoughtful inputs from Emily and other co-authors. New online technology, such as Zoom, helped us work together, remotely.
EL: For this project, it was fortunate in that all experiments were completed and we were at the data analysis phase before COVID hit, so we were able to complete it through online communication (and because I’m located in Baltimore, I’d been communicating solely online anyway). For my current research at Hopkins, we were in an Essential-Only phase from March to June, in which no new experiments were allowed to begin; luckily, at that point I did have some computational analysis to catch up on. In mid-June we had our Phase-I reopening, so I’ve been able to resume many of my experiments, though of course progress is still limited by how much time we’re allotted in the lab.
Why have the signalling ranges of peptides like EPF1 and Stomagen been hard to assess, prior to your paper?
EL & KT: Whether secreted peptides or small chemical hormones, how far the signal moves is a fundamental question of pattern formation in development. But precisely quantifying the distance is not trivial. For direct observation, one could tag fluorescent proteins (or exogenously synthesize a peptide conjugated with a fluorophore). In a strict sense, however, such modifications change the size and property of peptides or chemical signals. Alternatively, one could develop sensors (such as a FRET sensor) that detect the existence of peptides or chemical signals.
We have previously shown that EPIDERMAL PATTERNING FACTOR (EPF) family members of secreted peptides fine-tune patterning of stomata on the plant epidermis by competitive binding to the same receptor. Because of the flat, two-dimensional nature of the developing leaf epidermis, we thought that our system would be a great model for understanding how far the secreted peptides influence tissue patterning, rather than directly observing its movement.
Can you give us the key results of the paper in a paragraph?
EL & KT: Using recombination-based mosaic sectors to overexpress signaling peptides EPF1 and Stomagen, which inhibit and promote stomatal development, respectively, we determined the effective ranges of these peptides in Arabidopsis cotyledons. We developed a quantitative pipeline to model stomatal distributions across the cotyledon in response to peptide overexpression, which we named SPACE (stomata patterning autocorrelation on epidermis), an homage to the astrophysics origin of the autocorrelation approach. We found that the inhibitor peptide EPF1 has a longer effective range than the activator peptide STOMAGEN, and that the patterning effects of peptide overexpression are limited to a local range rather than the global cotyledon.
Tile scan of Arabidopsis thaliana cotyledon with mosaic sectors simultaneously overexpressing GFP, retained in the endoplasmic reticulum, and secreted peptide EPF1, an inhibitor of stomatal differentiation.
How did you come upon the idea of borrowing an astrophysical technique to look at stomatal patterning?
KT: At the initial stage of our research, we were able to produce chimeras via heat-shock Cre/lox recombination, but we could not think of how to actually ‘calculate’ the effective distance of the peptides. Initially, we tried to set bin range (such as 100 μm, 200 μm, etc.) from each sector border. However, because of the complex geometry of pavement cells as well as the unique size, shape and location of individual sectors, we could not figure out how to normalize stomatal distribution surrounding each sector.
One morning in the kitchen, I was talking about this problem to my spouse, who is a theoretical physicist studying String Theory. When I was drawing a cartoon of a simple leaf (essentially an oval) with lots of stomata (essentially dots inside the oval), he told me, ‘this sounds familiar to me. I think my colleague, Miguel, is addressing the exact same problem – except that in his case, it’s the distribution of galaxies in the Universe’. I immediately e-mailed Prof. Miguel Morales of UW Physics. I thought that he might think I was crazy, but to my pleasant surprise, Miguel and his postdoc Dr Bryna Hazelton were very excited to hear about our research and the potential of the spatial autocorrelation statistics that they utilize for astrophysics in solving questions in plant development. Bryna mentored Emily in programming for the spatial autocorrelation analysis.
My Physics colleagues generously gave me the opportunity to give a 15 min talk to incoming Physics Graduate Students. I discussed the principles of spatial patterning in biological systems and introduced Alan Turing’s reaction-diffusion model; luckily, Scott remembered my brief talk and was curious enough to join my lab to tackle this problem after Emily’s graduation.
EL: For me it started when Keiko suggested we meet with Miguel and Bryna. When we explained that we were trying to generate a metric of epidermal spatial patterning, they almost immediately suggested looking into autocorrelation, an astrophysics method for analyzing galaxy distributions/patterning. Bryna works at the UW eScience Institute, and has a goal to empower the next generation of researchers and students to answer fundamental questions in complex or noisy data. Working with her to develop code to analyze our epidermal patterning questions was a really wonderful and fruitful experience, and that was the starting point for our collaboration and the development of the SPACE pipeline.
Why do you think the stomatal inhibitor EPF1 is able to travel farther than the activator Stomagen?
EL & KT: To clarify your question, the goal of our study was to determine how far these peptides act or have an effect, not necessarily the physical distance they travel. EPF1 has a longer range in terms of developmental outcome than Stomagen, but not necessarily diffusion distance. The question of their differing ranges is complex because stomatal lineage cells (which are induced by Stomagen) will themselves secrete EPF1, acting as a negative-feedback loop; in other words, the peptides are not acting in isolation. Our quantitative determination of peptide effective range is fascinating because in the Turing theory of pattern formation, a short-range activator often interacts with a longer-range inhibitor to achieve a self-regulating, periodic pattern. The relationship between Stomagen and EPF1 might be one such example of this effect to achieve regular, ordered stomatal spacing across the epidermis.
When doing the research, did you have any particular result or eureka moment that has stuck with you?
EL: After we’d established that the mosaic sector generation system indeed worked, we wanted to observe the potential global effects of peptide overexpression (from within the restricted mosaic sectors) across the entire cotyledon, so I switched to a confocal microscope that had tile-scanning functionality. The stitched image I got of the entire cotyledon surface was very beautiful; getting that first image was a hugely satisfying and validating moment for me.
Getting that first image was a hugely satisfying and validating moment for me
And what about the flipside: any moments of frustration or despair?
EL: The initial months were the most difficult experimentally for me. There were a lot of experimental skills that required finesse, for example sowing tiny Arabidopsis seeds individually on plates or mounting the cotyledons on glass slides completely flat without folding or tearing, etc. The way I overcame these challenges was practice and repetition: those are just skills that are gained slowly over time.
I understand you’ve now left Keiko’s lab – what are you doing now?
EL: I’m currently pursuing my PhD in Biomedical Engineering at Johns Hopkins, in the labs of Prof. Patrick Cahan and Prof. Andrew Feinberg. I study how changes in cell identity relate to cancer initiation in the context of pancreatic ductal adenocarcinoma: one of the most lethal malignancies in the US.
Even though I work on human disease research now, plant research is still very important to me, especially given the adaptations humans will have to make to agricultural practices in response to global climate change. Particularly, I think optimizing crop water consumption will be a key strategy in the next several decades to reach necessary agricultural yields in fluctuating environmental conditions.
Where will this story take the Torii lab?
KT: Stomatal patterning and distribution is critical for plant productivity and water use efficiency, and many different genetic and environmental factors (such as temperature, light, CO2 and drought) influence stomatal number, density and distribution. There is a long history in Plant Physiology of studying these traits. Yet, essentially, there are two ways to quantify these traits: stomata density (number of stomata per given area) and stomatal index (number of stomata per total epidermal cells). Different genetic backgrounds and environmental conditions may influence number, density or distribution in unique ways, but often such information is lost by simply presenting bar graphs of stomatal density and index. So, the natural next direction is to apply SPACE pipelines to describe different patterns of stomata, in different ages of Arabidopsis leaves or under different genetic/environmental conditions. Further harnessing the SPACE pipeline to quantitatively characterize stomatal patterning of agronomically important plant species, such as tomato and cereals, may reveal some important characteristics. Finally, we are looking for developmental biologists studying pattern formation of any systems who are brave enough to try out our SPACE pipeline to quantitatively characterize their systems.
Finally, let’s move outside the lab – what do you like to do in your spare time in Baltimore and Austin?
KT: Well…since I just relocated alone to a small one-bedroom apartment in Austin, and then the COVID-19 stay-at-home order was put in place, I really did not have much time to explore my new city. My spouse and children were supposed to move to Austin from Seattle this summer, but this got postponed due to COVID-19. I really hope that, when we (the USA) manage to get the pandemic under control, I can explore the Texas Hill Country and enjoy its natural beauty, and see bluebonnet wildflowers blooming for the first time in my life!
EL: I’m an avid baker, cook and gardener. During COVID-19, I’ve boarded the sourdough starter bandwagon as an at-home quarantine activity. And as much as possible, I’ve tried to stay in touch with friends and family across the country and the world by video chatting.
In the developing spinal cord, progenitor cells sequentially give rise to motor neurons and precursors of one of the major glial cell types: oligodendrocytes. A new paper in Development unpicks the molecular control of the neuron-glia switch and the differentiation of oligodendrocyte precursors in the zebrafish embryo. To find out more about the work, we met first author and graduate student Kayt Scott and her supervisor Bruce Appel, who holds the Diane G. Wallach Chair of Pediatric Stem Cell Biology and is Professor and Head of the Section of Developmental Biology at the Department of Pediatrics, University of Colorado School of Medicine in Aurora.
Kayt (L) and Bruce (R).
Bruce, can you give us your scientific biography and the questions your lab is trying to answer?
BA: I earned my PhD at the University of Utah under the mentorship of Shigeru Sakonju. My thesis work focused on transcriptional control mechanisms in the context of homeotic genes and developmental patterning, and it was during that time that I became interested in problems of cell fate specification. I then moved to the University of Oregon for postdoctoral training with Judith Eisen. Using zebrafish embryos, Judith had previously performed a brilliant set of experiments that led her to conclude that communication between newly born motor neurons determined their subtype identities. As I worked to try to figure out how those subtype identities were specified, other work in the field began to suggest that the same progenitor population that produces motor neurons also gives rise to oligodendrocytes: the myelinating glial cell type of the CNS. I initially thought oligodendrocytes and myelin were pretty boring but as we developed new tools and learned how to do time-lapse imaging, we discovered that these cells and their ability to form a myelin sheath on an axon is incredibly fascinating. This has spun off into many projects investigating the molecular and cellular mechanisms that regulate developmental myelination and how myelin changes in response to brain activity. However, I still consider the age-old question of cell fate specification to be the foundation of all that we do.
And Kayt – how did you come to work in Bruce’s lab and what drives your research today?
KS: Developmental biology has always been a passion of mine, especially in the context of early nervous system formation. So, before I had even applied to graduate school, I was aware of and intrigued by the work conducted in Dr Bruce Appel’s lab. In fact, I discussed my interest in his research in my application letter. Once I entered graduate school, I did a rotation in Dr Appel’s lab and began the study of Prdm8 function in the zebrafish spinal cord. By the end of my rotation, I was sure I wanted to be part of the lab and further my rotation project. Through my experiences in the lab, I have really become interested in understanding how early tissue structure is organized and how this organization is altered through time and these questions are what drives my research today.
How has your research been affected by the COVID-19 pandemic?
KS: At the time of the pandemic shut down I was working from home already, feverishly compiling this manuscript and working on a fellowship application, so the first couple of months weren’t too disruptive. However, after accomplishing these endeavours, I have been unable to get into the lab and further explore the mechanisms of how Prdm8 regulates Shh signalling response. Fortunately, this has provided me with a unique opportunity to delve into the single cell RNA-seq dataset we had generated and develop my bioinformatic skills. This has opened many new avenues of research in the Appel lab.
I am hopeful that the pandemic is making us more collaborative and communicative
BA: I am hopeful that the pandemic is making us more collaborative and communicative. Although we all miss interacting with our friends, colleagues and trainees, the pandemic is forcing us to find new ways to share information. I have been really impressed by how well the virtual scientific conferences are working. The conferences are now available to so many people who couldn’t afford them or had other barriers to travel. Additionally, distance no longer limits with whom we can share seminars or journal clubs or lab meetings. Consequently, I’m optimistic that our research will actually benefit because we will have better information and shared expertise.
In your efforts to understand the regulation of pMN development, what made Prdm8 a good candidate?
KS: Originally our interest in Prdm8 was motivated by understanding how oligodendrocyte precursor cells (OPCs) are maintained into adulthood. Prdm8 was identified in our bulk RNA-seq data as being highly expressed by OPCs and not expressed in oligodendrocytes, and because Prdm8 was a known transcriptional repressor that can complex with bHLH transcription factors, we predicted that Prdm8 was forming a complex with Olig2 to repress oligodendrocyte differentiation. As we began our investigation of Prdm8 function, we came across some interesting and unexpected phenotypes that transitioned our interests in Prdm8 function within pMN progenitors.
Transverse trunk spinal cord section showing olig2 (cyan), prdm8 (magenta) and nkx2.2a (yellow) mRNA at 24 hpf.
BA: Whereas much of the myelin field focuses on how oligodendrocytes make myelin, we have been curious about why so many OPCs persist without differentiating. Prdm8 jumped out of our RNA-seq data because OPCs expressed it at very high levels compared with myelinating oligodendrocytes. Because Prdm8 can function as a transcriptional repressor, the initial hypothesis was obvious. As Kayt notes, however, her work revealed that Prdm8 has an earlier function in regulating progenitor fate specification.
Can you give us the key results of the paper in a paragraph?
KS: We set out to understand the potential function Prdm8 plays in pMN cell fate. Detailed expression analysis revealed that pMN progenitors express prdm8 through development and that differentiating oligodendrocytes downregulate prdm8 expression, whereas OPCs maintain expression. We then learned that prdm8 mutant embryos have an excess of oligodendrocytes and a deficit in motor neurons as a result of a premature motor neuron-oligodendrocyte fate switch. This premature switch in cell fate was accompanied by a premature increase in nkx2.2a expression and ventral neural tube Shh activity with Prdm8 loss of function. By suppressing Shh signalling in prdm8 mutants, we were able to restore the motor neuron population but were not able to reduce the excess oligodendrocyte phenotype observed in mutants. In all, these data support the hypothesis that Prdm8 prevents the neuron-glia switch in pMN progenitors by suppressing Shh signalling activity, and, independently of Shh activity, Prdm8 regulates the balance of OPCs and oligodendrocytes.
Do you have any clues as to how, at the molecular level, Prdm8 inhibits Shh signalling?
KS & BA: One possibility we have entertained is that Prdm8 might form a complex with Olig2 to suppress transcription of genes that promote cellular response to Shh. Figuring this problem out will be the next big push for the Prdm8 project.
When doing the research, did you have any particular result or eureka moment that has stuck with you?
KS: I would have to say the most striking result I came across in this project was that Shh repression was only able to rescue motor neuron populations, but resulted in a total oligodendrocyte lineage deficit while maintaining excess oligodendrocytes in mutant embryos. This was the point where it really sunk in that Prdm8 function was more complex than I imagined, and appeared to have temporal and spatially distinct functions even within a single lineage.
And what about the flipside: any moments of frustration or despair?
KS: The most frustrating part of this project was that I had started it as a rotation student and hadn’t quite honed my organizational skills. This resulted in having to redo several of the first experiments, because I had not kept good enough documentation of my methods or results. A lesson that will never leave me!
What’s next for you after this paper?
KS: Moving forward, I have been working on a scRNA-seq paper, characterizing pMN cell populations through time and have plans to graduate in the summer of 2021. Following graduation, I hope to obtain an IRACDA fellowship to receive comprehensive training in undergraduate education and develop my own research projects in the field of developmental biology.
Where will this story take the Appel lab?
BA: There is an old joke that, in the absence of good ideas, do a genetic screen. A modern-day version of that is to do single cell RNA-seq. We have been stumped about the earliest molecular events that specify neural progenitors for oligodendrocyte fate, so we carried out a series of single cell RNA sequencing experiments. The data are incredibly exciting and appear to match our previous fate-mapping studies suggesting that motor neurons and oligodendrocytes arise from distinct progenitors. We now have many new ideas to pursue in our attempt to gain a comprehensive understanding of the gene regulatory network that specifies oligodendrocyte fate.
Finally, let’s move outside the lab – what do you like to do in your spare time in Colorado?
KS: Outside of the lab, I never waste an opportunity to enjoy the beautiful state we live in. You will find me camping, hiking and fishing almost every weekend during the warmer months; in the winter, I am hitting the slopes on my snowboard or gliding through the woods on some cross-country skis.
BA: Now that our daughters are pretty much on their own, my wife and I try to spend as much time as possible at our place in the mountains. It’s off-grid and fairly remote, and a great jumping-off spot for hiking, backpacking, skiing and snowshoeing. I am also very slowly and ineptly trying to restore a 1942 Ford tractor that my parents had on their farm.
Welcome back to #DevBiolWriteClub. Let’s review the rules:
Do the work.
Do the work.
Revise and edit. Again, and again, and again.
Read with intent.
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.
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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Understanding brain circuit evolution at single-cell resolution using comparative connectomics and transcriptomics