Ion channels are famous for their roles in neurons and muscles, but the spectrum of phenotypes seen in ion channel mutants indicate a diversity of roles in development; the underlying mechanisms, however, have remained opaque. This week we feature a paper published in the latest issue of Development that reveals a link between potassium channels and morphogen signalling during epithelial morphogenesis. Co-first-authors Giri Dahal and Sarala Pradhan, and their PI Emily Bates of the University of Colorado Denver, told us more.
Giri, Sarala and Emily
Emily, can you give us your scientific biography and the main questions your lab is trying to answer?
EB My long term goal as a high school student was to understand the mechanism behind migraine headaches and I thought that genetics would be the best tool to do that. The ACCESS program for women in science at the University of Utah placed me in Dr. Anthea Letsou’s lab and that was a great head start for my career. Dr. Letsou introduced the powerful tools available in Drosophila genetics and BMP/Dpp signalling. I stayed in her lab for four years working on defining the role of Punt, a type II Dpp receptor. I then went on to Harvard Medical School for my PhD in Dr. Anne Hart’s laboratory to focus on genetic neurological disease. I took classes about ion channels at Harvard, getting me closer to my goal. Then I joined Dr. Louis Ptacek’s lab at UCSF to study a genetic link to migraine. Dr. Ptacek’s lab focuses on episodic disorders including migraine and Anderson Tawil Syndome, caused by mutations in Kir2.1, a potassium channel. When I saw that in addition to periodic paralysis, mutations in Kir2.1 cause birth defects in people and that the phenotypes in model organisms look like the BMP signalling mutants, I became intrigued. That brought me to one of the central questions my lab is trying to answer: How do ion channels and electrical activity influence developmental signalling? We also have project that are trying to figure out how properties of the cytoskeleton influence neurodevelopment and neurodegeneration.
Giri and Sarala – how did you come to join Emily’s lab?
GD I came to the USA in the fall of 2008 to pursue graduate study at Brigham Young University. Emily was an Assistant Professor there. She had a positive outlook towards life and her views in science were inspiring. She wanted to pursue two projects, both were interesting but something about this project caught my attention. I was intrigued to find that we do not know why Kir channels cause dysmorphic features in Andersen-Tawil Syndrome even though scientists have been studying the channels for a long time. I liked both her personality and the project so decided to join her lab. I went with her to Colorado when she started her position at the University of Colorado.
SP Two ‘D’s attracted me, Drosophila and Denver, but certainly the research that was happening in the lab was key in my decision.
Wing phenotypes following Irk2DN expression, from Figure 1, Dahal, et al. 2017
Can you give us key results of the paper in a paragraph?
EB/GD/SP We knew that Irk channels played a role in Dpp signalling from our first paper that was also published in Development: Dahal et al 2012. The goal of our work since then has been to determine the molecular mechanism. We found that human Kir2.1 could substitute for fly Irk channels, showing that the developmental role of Irk/Kir channels is conserved between flies and humans. We found that Irk channels are important in the cells that produce Dpp and not in the cells that receive the signal. Inhibition of Irk channels in the Dpp-producing cells does not decrease the amount of Dpp that is made, but it changes the temporal dynamics of Dpp release. Irk channels modulate intracellular calcium levels to influence releases of insulin from pancreatic beta cells and neurotransmitter from neurons, so we hypothesized that Irk channels could regulate Dpp release via the same mechanism. Therefore, we looked for calcium activity in the wing disc. We found native transient increases in intracellular calcium that were altered by inhibition of Irk channels. Lastly, we found that depolarizing cells by applying a potassium solution to the extracellular bath caused transient increases in intracellular calcium and Dpp release.
Why might the timing, and not just the bulk amount, of Dpp release be important to development?
EB/GD/SP The timing of exposure to Transforming Growth Factor-beta (TGF- β) impacts the transcriptional response in tissue culture. For example pulsed exposure to TGF-B had a much greater transcriptional response than constant exposure to the same concentration of the ligand (See Sorre and Warmflash 2014). Dpp belongs to the TGF- β superfamily. Perhaps exposure to these ligands must be pulsed to signal efficiently. There are other examples of this in biology such as insulin signalling affecting metabolism and neurotransmitter affecting neurons. Similarly, the timing of notch signalling in somitogenesis is essential for its effect on the development of somites.
Clones in the wing disc, from Figure 2, Dahal, et al. 2017
How similar is Dpp release from wing cells to neurotransmitter release from synapses?
EB/GD/SP Irk channels help to maintain resting membrane potential in neurons and therefore help to determine when a neuron will “fire” or undergo an action potential, increase intracellular calcium, and release neurotransmitter. In the context of the wing disc, we have shown that Irk channels influence calcium activity and Dpp release. We do not yet know if the release machinery is the same for neurotransmitter release and Dpp release.
When doing the research, did you have any particular result or eureka moment that has stuck with you?
GD I would rather like to say that I have experienced surprising moments instead of a eureka because when it happens my first inclination is to think it is a fluke, which is true most of the time. By the time you confirm the result with enough samples and rule out other possible explanations the prospective eureka moment disappeared long ago because there is no element of surprise. I had small eureka moments with each new channel tested during the rescue experiment.
SP Yes, there were several. The most memorable were being able to see the regulation of calcium transients in the wing disc cells by Irk and the evoked Dpp release in wing disc cells by depolarizing with high extracellular potassium. These kinds of experiments that can be visually examined leaves one with a long lasting excitement.
Changes in GCaMP6s fluorescence, from Figure 5, Dahal, et al. 2017
And what about the flipside: any moments of frustration or despair?
GD Initially, we tried electrophysical approach to study mechanism of the Irk channels I took a course on the topic, and spent months to learn the technique. However, when I tried to express the fly Irk channels in Xenopus egg to measure current these channels did not express well so we abandoned this approach
SP There were many moments of frustration, despair, bruises and cuts. Thankfully these are like labor pains, once the child is born; they seem to fade away and you are ready to start again.
What are your career plans following this work?
GD For my postdoctoral training, I joined Dr. Howard Rockman lab at Duke University, where I worked to develop exosome-mediated drug delivery system to modulate cardiac function. Gradually, my interest shifted towards the downstream process of drug development. I decided to move out from academia. At present, I work in a company as a part of clinical operation team to conduct oncology trials.
SP I have always been ambitious to explore career challenges. As a child in Nepal I envisioned myself in white lab coat being a scientist somewhere. I first set foot in science with a degree in microbiology and taught in a brand new medical school in Nepal. It was a good job but I did not find myself challenged enough, so over-ambitiously I set my foot in USA to pursue my PhD. The day I graduated I felt overwhelmingly happy. Deep in my heart I was bothered with a question….that now I have achieved my life’s biggest goal….. what next? It may not be easy to live rest of my life without a goal. So I thought about it and set myself another goal and this time I did not want to be over ambitious. I just wanted to carry the responsibility and legacy of this degree with dignity for rest of my life. I feel that I have achieved this to some extent with this post doc paper in ‘Development’, and with being a biology faculty in college. So with this, I will continue to pursue a career in science. This may take different directions depending on the opportunities that open up and the different paths of life. I am open to new experiences and challenges that will build on my foundation in science and research.
And what next for the Bates lab?
EB We are now identifying other ion channels and ion channel associated proteins that are important for wing morphology and trying to determine if the SNARE complex is important for release of Dpp. In addition, we have evidence that Kir/Irk channels influence BMP signalling in mammals for craniofacial and limb development. To understand how Kir functions in mammals, we are extending our studies into mice.
Wing discs from Figure 2, Dahal, et al. 2017
Finally, what do you like to do when you are not in the lab?
EB My husband and I have a new baby girl, so currently my favourite thing to do outside the lab is play with her and watch her play with her Dad. I also enjoy family hikes and anything outdoors.
GD I live with my wife and two children. I spend most of our time outside of the lab taking care of our children.
SP Physically and mentally travel to Nepal and elsewhere if I can afford it in terms of time and money. But if you are talking about day-to-day activities, I enjoy playing with my son, being in nature, specially around water. I find the sound of water peaceful. And cooking delightful and delicious food at home.
Our latest monthly trawl for developmental biology (and other cool) preprints. See last year’s introductory post for background, and let us know if we missed anything
This month we found lots of plant preprints and plenty of evo-devo work, as well as a series of preprints characterising features of the genome at distinct stages or places during development. The preprints were hosted on bioRxiv, PeerJ and arXiv. Use these links to get to the section you want:
In vivo validation of predicted E12.5 enhancers, from Gorkin, et al.’s preprint
Systematic mapping of chromatin state landscapes during mouse development. David Gorkin, Iros Barozzi, Yanxiao Zhang, Ah Young Lee, Bin Lee, Yuan Zhao, Andre Wildberg, Bo Ding, Bo Zhang, Mengchi Wang, J. Seth Strattan, Jean M Davidson, Yunjiang Qiu, Veena Afzal, Jennifer A Akiyama, Ingrid Plajzer-Frick, Catherine S Pickle, Momoe Kato, Tyler H Garvin, Quan T Pham, Anne N Harrington, Brandon J Mannion, Elizabeth A Lee, Yoko Fukuda-Yuzawa, Yupeng He, Sebastian Preissl,Sora Chee, Brian A Williams, Diane Trout, Henry Amrhein, Hongbo Yang, J. Michael Cherry, Yin Shen, Joseph R Ecker, Wei Wang, Diane E Dickel, Axel Visel, Len A Pennacchio, Bing Ren
Spatiotemporal DNA Methylome Dynamics of the Developing Mammalian Fetus. Yupeng He, Manoj Hariharan, David U Gorkin, Diane E Dickel, Chongyuan Luo, Rosa G Castanon, Joseph R Nery, Ah Young Lee, Brian A Williams, Diane Trout, Henry Amrhein,Rongxin Fang, Huaming Chen, Bin Li, Axel Visel, Len A Pennacchio, Bing Ren, Joseph R Ecker
Genetic variation and gene expression across multiple tissues and developmental stages in a non-human primate. Anna J. Jasinska, Ivette Zelaya, Susan K. Service, Christine Peterson, Rita M. Cantor, Oi-Wa Choi, Joseph DeYoung, Eleazar Eskin, Lynn A. Fairbanks, Scott Fears, Allison Furterer, Yu S. Huang, Vasily Ramensky, Christopher A. Schmitt, Hannes Svardal, Matthew J. Jorgensen, Jay R. Kaplan, Diego Villar, Bronwen L. Aken, Paul Flicek, Rishi Nag, Emily S. Wong, John Blangero, Thomas D. Dyer, Marina Bogomolov, Yoav Benjamini, George M. Weinstock, Ken Dewar, Chiara Sabatti, Richard K. Wilson, J. David Jentsch, Wesley Warren, Giovanni Coppola, Roger P. Woods, Nelson B. Freimer
An Algorithm for Cellular Reprogramming. Scott Ronquist, Geoff Patterson, Markus Brown, Stephen Lindsly, Haiming Chen, Lindsey Muir, Max Wicha, Anthony Bloch, Roger Brockett, Indika Rajapakse
Speed breeding: a powerful tool to accelerate crop research and breeding. Amy Watson, Sreya Ghosh, Matthew Williams, William S. Cuddy, James Simmonds, Maria-Dolores Rey, M. Asyraf Md Hatta, Alison Hinchliffe, Andrew Steed, Daniel Reynolds, Nikolai Adamski, Andy Breakspear, Andrey Korolev, Tracey Rayner, Laura E. Dixon, Adnan Riaz, William Martin, Merrill Ryan, David Edwards, Jacqueline Batley, Harsh Raman, Christian Rogers, Claire Domoney, Graham Moore, Wendy Harwood, Paul Nicholson, Mark J. Dieters, Ian H. DeLacy, Ji Zhou, Cristobal Uauy, Scott A. Boden, Robert F. Park, Brande B. H. Wulff, Lee T. Hickey
Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes. David Thybert, Maša Roller, Fábio C. P. Navarro, Ian Fiddes, Ian Streeter, Christine Feig, David Martin-Galvez, Mikhail Kolmogorov, Václav Janoušek, Wasiu Akanni, Bronwen Aken, Sarah Aldridge, Varshith Chakrapani, William Chow, Laura Clarke, Carla Cummins, Anthony Doran, Matthew Dunn, Leo Goodstadt, Kerstin Howe, Matthew Howell, Ambre-Aurore Josselin, Robert C. Karn, Christina M. Laukaitis, Lilue Jingtao, Fergal Martin, Matthieu Muffato, Michael A. Quail, Cristina Sisu, Mario Stanke, Klara Stefflova, Cock Van Oosterhout, Frederic Veyrunes, Ben Ward, Fengtang Yang, Golbahar Yazdanifar, Amonida Zadissa, David Adams, Alvis Brazma, Mark Gerstein, Benedict Paten, Son Pham, Thomas Keane, Duncan T. Odom, Paul Flicek
Signatures of the evolution of parthenogenesis and cryptobiosis in the genomes of panagrolaimid nematodes. Philipp H. Schiffer, Etienne Danchin, Ann M. Burnell, Anne-Marike Schiffer, Chris Creevey, Simon Wong, Ilona Dix, Georgina O’Mahony, Bridget A. Culleton, Corinne Rancurel, Gary Stier, Elizabeth A. Martinez-Salazar, Aleksandra Marconi, Urmi Trivedi, Michael Kroiher, Michael A. S. Thorne, Einhard Schierenberg, Thomas Wiehe, Mark Blaxter
Genome expansion and lineage-specific genetic innovations in the world’s largest organisms (Armillaria). Gyorgy Sipos, Arun N Prasanna, Mathias C Walther, Eoin O’Connor, Balazs Balint, Krisztina Krizsan, Brigitta Kiss, Jaqueline Hess, Jason Slot, Robert Riley, Bettina Boka, Daniel Rigling, Kerrie Barry, Juna Lee, Sirma Mihaltseva, Kurt Labutti, Anna Lipzen, Rose Waldron, Nicola Moloney, Christoph Sperisen, Laszlo Kredics, Csaba Vagvolgyi, Andrea Patrigniani, David Fitzpatrick, Istvan Nagy, Sean Doyle, James B Anderson, Igor V Grigoriev, Ulrich Guldener, Martin Munsterkotter, Torda Varga, Laszlo G Nagy
Loss Of PTEN Promotes Formation Of Signaling-Capable Clathrin-Coated Pits. Luciana K. Rosselli-Murai, Joel A. Yates, Sei Yoshida, Julia T. Bourg, Kenneth K. Y. Ho, Megan White, Julia Prisby, Xinyu Tan, Megan Altemus, Liwei Bao, Zhi-Fen Wu, Sarah L. Veatch, Joel A. Swanson, Sofia D. Merajver, Allen P. Liu
Versatile open software to quantify cardiomyocyte and cardiac muscle contraction in vitro and in vivo. Luca Sala, Berend J. van Meer, Leon G. J. Tertoolen, Jeroen Bakkers, Milena Bellin, Richard Davis, Chris Denning, Michel A. E. Dieben, Thomas Eschenhagen, Elisa Giacomelli, Catarina Grandela, Arne Hansen, Eduard R. Holman, Monique R. M. Jongbloed, Sarah M. Kamel, Charlotte D. Koopman, Quentin Lachaud, Ingra Mannhardt, Mervyn P. H. Mol, Valeria V. Orlova, Robert Passier, Marcelo C. Ribeiro, Umber Saleem, Godfrey L. Smith, Christine L. Mummery, Francis L. Burton
Traction force screening enabled by compliant PDMS elastomers. Haruka Yoshie, Newsha Koushki, Rosa Kaviani, Kavitha Rajendran, Quynh Dang, Amjad Husain, Sean Yao, Chuck Li, John K. Sullivan, Magali Saint-Geniez, Ramaswamy Krishnan, Allen Ehrlicher
One of Zimmerman, et al.’s antibodies and its target
P53 toxicity is a hurdle to CRISPR/CAS9 screening and engineering in human pluripotent stem cells. Robert J. Ihry, Kathleen A. Worringer, Max R. Salick, Elizabeth Frias, Dan Ho, Kraig Theriault, Sravya Kommineni, Julie Chen, Marie Sondey, Chaoyang Ye, Ranjit Randhawa, Tripti Kulkarni, Zinger Yang, Gregory McAllister, Carsten Russ, John Reece-Hoyes, William Forrester, Gregory R. Hoffman, Ricardo Dolmetsch, Ajamete Kaykas
Genome-wide genetic data on ~500,000 UK Biobank participants. Clare Bycroft, Colin Freeman, Desislava Petkova, Gavin Band, Lloyd T Elliott, Kevin Sharp, Allan Motyer, Damjan Vukcevic, Olivier Delaneau, Jared O’Connell, Adrian Cortes, Samantha Welsh, Gil McVean, Stephen Leslie, Peter Donnelly, Jonathan Marchini
Soon to be dosed fish from Monstad-Rios, Watson & Kwon’s preprint
Best Practice Data Life Cycle Approaches for the Life Sciences. Philippa C. Griffin, Jyoti Khadake, Kate S. LeMay, Suzanna E. Lewis, Sandra Orchard, Andrew Pask, Bernard Pope, Ute Roessner, Keith Russell, Torsten Seemann, Andrew Treloar, Sonika Tyagi, Jeffrey H. Christiansen, Saravanan Dayalan, Simon Gladman, Sandra B. Hangartner, Helen L. Hayden, William W. H. Ho, Gabriel Keeble-Gagnère, Pasi K. Korhonen, Peter Neish, Priscilla R. Prestes, Mark F. Richardson, Nathan S. Watson-Haigh,Kelly L. Wyres, Neil D. Young,Maria Victoria Schneider
Designing an intuitive web application for drug discovery scientists. Nikiforos Karamanis, Denise Carvalho-Silva, Jennifer A. Cham, Luca Fumis, Samiul Hasan, David Hulcoop, Gautier Koscielny, Michael Maguire, William Newell, ChuangKee Ong, Eliseo Papa, Andrea Pierleoni, Miguel Pignatelli, Sangya Pundir, Francis Rowland, Jessica Vamathevan, Xavier Watkins, Jeffrey C. Barrett, Ian Dunham
The York Gospels: a one thousand year biological palimpsest. Matthew D. Teasdale, Sarah Fiddyment, Jiří Vnouček, Valeria Mattiangeli, Camilla Speller, Annelise Binois, Martin Carver, Catherine Dand, Timothy P. Newfield, Christopher C. Webb, Daniel G. Bradley, Matthew J. Collins
Here are the highlights from the current issue of Development:
X-citing insights into dosage compensation
The non-coding RNA Xist plays a key role in the process of X chromosome inactivation (XCI) and is thus essential for dosage compensation of X-linked genes in females. The 5′ region of Xist RNA contains a conserved element termed the A-repeat that is required for the silencing function of Xist in embryonic stem cells, but how this region functions during development is unclear. Now, Takashi Sado and co-workers explore this by introducing into mice a mutated Xist allele that produces Xist RNA lacking the A-repeat region (p. 2784). They first report that imprinted XCI is compromised upon paternal transmission of this allele. The authors further show that the mutant form of Xist is able to coat the X chromosome but fails to silence it in embryonic and extraembryonic tissues. Surprisingly, however, mutant Xist RNA is still able to silence a subset of genes in the trophoblast. Finally, the authors reveal that the failure of imprinted XCI has a more significant impact on genome-wide gene expression than expected; changes in the expression of both X-linked and autosomal genes are observed. Together these findings provide new insights into Xist-mediated gene silencing but also raise the intriguing possibility that dosage compensation regulates X-linked genes as well as gene expression more globally.
Non-neural roles for acetylcholinesterase
Acetylcholinesterase (AChE) is a highly conserved protein that is known for its essential role in degrading the neurotransmitter acetylcholine at neural synapses. However, it is expressed more broadly, outside the nervous system, suggesting that it may carry out additional functions. Now, on p. 2764, Nanette Nascone-Yoder and colleagues reveal that AChE plays an essential non-classical role in Xenopus gut morphogenesis. By exposing tailbud stage Xenopus embryos to AChE inhibitors, or by injecting embryos with morpholinos to knock down AChE in the intestinal endoderm, they show that AChE is required for proper intestinal morphogenesis; in the absence of AChE function, intestines are short/malrotated and exhibit a disorganised epithelium. This function of AChE , they report, is independent of its cholinesterase activity. Further analyses demonstrate that AChE is required for endoderm cell rearrangement and polarisation – events that drive gut lengthening and morphogenesis – as well as endoderm cell differentiation. Finally, the researchers demonstrate that AChE regulates cell-substrate but not cell-cell adhesion. Overall, these results provide direct in vivo evidence for a morphogenetic function for AChE in non-neuronal tissues and suggest that AChE may function in other aspects of development and physiology, a find that has important implications given the widespread use of cholinesterase inhibitors in the treatment of human diseases.
A chemical reset for pluripotency
Pluripotency in mammalian stem cells is thought to pass through two phases – an initial naïve phase and a later primed phase, mimicked in vitro by mouse embryonic stem cells and human pluripotent stem cells (hPSCs), respectively. Much effort has gone into converting hPSCs to a more naïve state, but current methods are not always reliable or broadly applicable across cell lines. On p. 2748, Ge Guo, Austin Smith and colleagues provide a simple and efficient method for resetting human pluripotency based on transient inhibition of histone deacetylases (HDACs) with chemical inhibitors. HDAC inhibition leads to increased expression of naïve markers in a variety of different hPSC lines, and cells can be expanded in naïve culture conditions without requiring feeders. Chemically reset cells show a marked transcriptional difference to primed hPSCs and a similarity to epiblast cells of the preimplantation inner cell mass. Reset cells undergo global reduction in DNA methylation, have two active X chromosomes, and can differentiate into multiple lineages. This work provides a protocol for efficient resetting of hPSC pluripotency, and a transcription and methylation resource for further interrogation of the human naïve state.
Morphogen signalling: Dpp gets Irked
Mutations in genes encoding ion channels cause severe defects in development across species but the underlying mechanisms, particularly in tissues other than neurons and muscle, have remained unclear. On p. 2771, Emily Anne Bates and colleagues describe a role for Irk2, an inwardly rectifying potassium channel in Drosophilaorthologous to Kir2.1 in vertebrates, in regulating the release of the BMP family morphogen Dpp during development of the wing epithelium. Building on their previous finding that a dominant-negative Irk2 reduces Dpp signalling and causes wing defects, they now show that human KIR2.1 can substitute for inhibited DrosophilaIrk2, and that Irk2’s role is restricted to the cells that produce, rather than just transduce, the Dpp signal. Surprisingly, inhibiting Irk2 broadens the distribution of Dpp in the wing, but also alters the dynamics of Dpp release from cells, suggesting that Irk2 controls the timing of Dpp secretion. Irk2 inhibition reduces the amplitude of calcium spikes in wing cells, and depolarising the membrane with extracellular potassium leads to an overall increased release of Dpp, implicating Irk2’s regulation of membrane potential in Dpp release. Together, these results suggest that ion channels influence tissue morphogenesis by regulating the release of morphogens from the membrane.
Development announces changes to the editorial team and invites community input in choosing a new Editor in Chief and in suggesting future areas for the journal to explore
Jim Smith, recently knighted for services to medical research and science education, talks about his research career and his hopes for the future of biomedical science.
New, freely available illustrations of developing Xenopus laevis, drawn by Natalya Zahn, provide a resource for teaching and research, especially in the field of craniofacial biology.
This Meeting Review discusses recent progress in our understanding of neuronal programming, highlighting some of the common features of cell fate determination during development and directed reprogramming.
This Primer summarises our current understanding of the intriguing family of KRAB-ZFP transcriptional regulators and its contribution to the control, evolution and co-option of transposable elements.
We are seeking a highly motivated and talented postdoctoral researcher initially for 1 year, starting 1 October 2017, to develop nanomaterial-based gene delivery strategies for the topical treatment of genetic skin conditions. We are looking for someone with experience in gene transfer and cell biology. Further experience with optical microscopy and drug delivery would be advantageous.
New fellowships from SDB for students from USA and Canada to attend the International Course on Developmental Biology on January 9-21, 2018 in Quintay Chile. Fellowship for Latin American students will be available as well.
Nipam Patel, Alejandro Sanchez-Alvarado, Ray Keller, Claudio Stern, Corinne Huart, Maria Leptin, Andrea Streit, among other will teach, hands-on, the paradigms, problems and technologies of modern Developmental Biology.
More Information here:
DEADLINE 31st August 2017
For the student opinion’s about previous version of the course: 2014 2012
Post doctoral and/or Research Associate position available to study the genetic and epigenetic control of stem cell attributes and pluripotency, focusing on the neural crest gene regulatory network (NC-GRN). Neural crest cells are stem cell-like progenitors that migrate extensively and whose genesis was central to the evolution of vertebrates. Misregulation of components of the NC-GRN underlies numerous human diseases and congenital disorders.
Candidates should have a background in bioinformatics and/or computational biology, strong analytical skills, and significant experience in the analysis of NGS data (ChIP-seq, RNA-seq, ATACseq etc) and proficiency in programming languages (R, Python, PERL etc). Projects may also involve quantitative image analysis. Candidates should be highly motivated, detail oriented, possess excellent communication skills and the ability to work collaboratively as part of an interdisciplinary team. The LaBonne lab is located on Northwestern University’s beautiful lakeside campus close to the amazing city of Chicago.
Please send a CV, brief description of research interests, and the names of three references to:
Carole LaBonne, PhD (clabonne@northwestern.edu)
Department of Molecular Biosciences
Northwestern University, Evanston, IL 602028
Last month I went to Boston for the Annual Meeting of the International Society for Stem Cell Research (ISSCR), which was celebrating its 15th birthday. Sally Temple handed over the Presidential reins to Hans Clevers with a reminder of what a remarkable 15 years it had been for the field – induced pluripotent cells (iPSCs), an explosion of differentiation protocols, the arrival of organoids, CRISPR and single cell sequencing, new windows onto human development, clinical trials and drug screening. She encouraged the audience to think “This is our century” – that is, the century of harnessing the power of stem cells in tackling disease. She also reiterated the ISSCR’s commitment to keep basic science at the core of what it does (you can hear more of her thoughts on the ISSCR in Caroline Hendry’s video interview for Development). In fact the whole meeting (or at least what I got out of it) was a healthy mix of basic and applied, from model organisms to drug trials, and developmental biology was repeatedly heralded as a vital foundation for any future clinical advance; my worries about wandering into a wall-to-wall differentiation protocol fest turned out to be unfounded.
So here’s my belated diary of highlights and impressions from the meeting. There were a thousand talks and posters so of course I missed a lot: if you went and want to write something about the meeting, just register and you’re free to post. Also check out the highlights from Agnes Soos, Cátia Bandeiras and RegenMedNet.
Tuesday, 13th June
Over the Atlantic the in-flight pasta meal tasted like it was cooked in popcorn butter. In Boston it was sweltering until out of nowhere a storm cooled the air down, and in the evening I went to a basement bar where Twitter had assembled a dozen strangers going to the meeting to meet in real life (a ‘Tweet Up’). For someone who knew hardly anyone at the meeting, it was a great way to meet new people and something I’ll try to do again (thanks to Samantha Yammine for instigating this!). After some local IPAs packed with enough hops to blow your head off, I stopped in at a Wallgreen’s on my way back to the hotel and had one of the more depressing late night dinners of my life: Salsitas followed by a flapjack.
Wednesday, 14th June
In the morning I went to a focus session on the ethics of organoids, which was chaired by Megan Munsie (more on Megan’s work below) and paired scientists with ethicists to discuss the impact and meaning of this new technology on wider society.
On the scientific side of things, Hans Clevers gave us the latest update on how organoids derived from adult (often patient) stem cells were helping to understand various pathologies and inform treatments. In an almost throwaway comment he told us that he could make lung organoids from patients’ sputum, and kidney organoids from their urine; you just need to spin the cells down and start the protocol. It struck me as one of those ‘living in the future’ moments. Melissa Little reminded us how critical an understanding normal development is for organoid derivation – you need a guide for which factors to add and in which order, something echoed for iPSC differentiation later in the meeting by George Daley. Indeed most iPSC-derived organoids are models for embryonic rather than mature tissues, which can complicate interpretations. Where the technology is particularly helping Little’s lab is to validate variants of unknown function in genetic kidney diseases – derive iPSCs from patients, ‘fix’ the sequence with gene editing, and see if organoids can form normally; this is such a cool clinical use of organoids that I hadn’t appreciated before.
On the ethics side, Annelien Bredenoord emphasised the inevitable collision of organoid technology and ethics – we have to decide what the moral and legal status of organoids are. Do we treat organoids like any other patient-derived tissue? Are they most akin to cell lines, or something else? What types of consent do we expect patients to give? How do patients see their own oragnoids? And what about if private companies seek to use organoids?
How we answer these questions might really depend on definitions: for Melissa Little, organoids are really just an extension of iPSC differentiation protocols, and if so we need not radically rethink the guidelines that exist for iPSCs (for instance, those written up by the ISSCR). There is also a lot of difference between different kinds of organoids, depending on how complex an organ they are modelling. Plus, according to Jeurgen Knoeblich, the ethical concerns around those most provocative of organoids, cortical ones – “when will they think?” – are based on a perceived rather than a real risk to societal ethics, given that we are light years away from making something capable of a thought or a feeling. Later in the meeting Knoeblich told us about his lab’s efforts to make more complex and representative brain organoids. You can dorsalise one organoid, and ventralise another, culture them together until they fuse, and then observe neural migration from ventral to dorsal, a feature that previous cortical organoids lacked.
Bredenoord’s work involves asking patients what they think about organoids derived from their cells, and revealed ambivalence in one particular cystic fibrosis patient community. Melissa Little had a different experience with kidney patients: they want the opportunity to donate tissue or cells to any initiative that might help them, and organoids are no different; I heard similar things from Jayaraj Rajagopal. Bredenoord also described a reluctance to donate tissue if it was to be commercialised by a private company, and this was echoed by others and presumably a feeling not unique to organoids. Hans Clevers described a fix for this, which was to establish not-for-profits to run the biobanks and profit from commercial customers. The question of consent in biobanking has recently been explored by Tim Caulfield and Blake Murdoch in PLoS Biology.
Insoo Hyun, who sits on the ISSCR’s ethics committee, made the distinction between two types of research ethics: philosophical and practical. Philosophical ethics cover the questions of “should we be doing this?” and “is it wise?”, while practical ethics emphasises the regulatory guidelines in place once we’ve said yes to the philosophical questions. I guess we’ve pretty much gone into the practical side of things – no one in the session questioned the use or potential of organoids, though some thought the hype might catch up with us soon – but he reminded us of the need to really educate the public and justify what we are doing to cover the philosophical part. To paraphrase Hyun, “don’t just forget the public and leave it to committee”.
It was quite a compelling session, though I didn’t exactly come out of it with a clear feeling for where organoids stand from an ethical perspective; I guess that was the point of the session, perhaps the field is too young. For a more coherent discussion of the various ethical issues in hand I’ll send you to a couple of reviews by the speakers, one in Development and one in Science.
The rest of the day was spent in the aircraft-hangar-sized hall where the plenaries were held. It was funny seeing the great and the good walk up to the podium to the snippets of EDM bangers or Coldplay, though I was disappointed that none of them danced their way up. A series of research talks was followed by Sanford Greenberg, who, as a roommate of Art Garfunkel in college (we can thank Greenberg for financing Art’s initial union with Paul Simon), went blind and has since dedicated much of his life to ending blindness, “this wretched curse”. You can check out the website detailing his 3 million dollar prize for blindness research at endblindnessby2020.com.
That evening I actually managed to have dinner, at the Barking Crab – a raucous place on the water, with snow crab and another great IPA (Boston’s a wonderful place for a beer drinker).
Thursday 15th June
In the afternoon I had the mindhurt of trying to choose from one of seven (!) concurrent sessions. The ‘Single Cell Heterogeneity’ session featured so much single cell sequencing of organs and organoids that one almost came out of it feeling blasé about the whole enterprise – just to think of telling a developmental biologist from the eighties that she could sequence the genome of every cell in a developing organ! It wasn’t all sequencing though: David Scadden explored the role of the stem cell niche in blood development, starting with some history (read more here). In the seventies, Raymond Schofield had proposed the niche hypothesis but apparently was at loggerheads with Ernest McCulloch about it – he ended up leaving science and becoming a sheep farmer in Wales, where Scadden met him for a pint in the village pub to discuss his ideas. Scadden’s approach was to test the role of the niche by taking stem cells from one animal and place them into another. Under these new conditions, they behaved pretty much the same. HSCs are very heterogeneous, but this is intrinsic rather than defined by the niche, and Scadden used a game-ey metaphor: rather than highly adaptive ‘transformers’, HSCs are like a collection of chess pieces with distinct functional attributes.
In the evening, dinner at an oyster restaurant with the Twitterati, and my first taste of these opinion-splitting molluscs (verdict: yup, with some hot sauce and lemon juice).
Friday 16th June
The highlight of the day was interviewing George Daley and Jayaraj Rajagopal for Development. Both are residents of Boston who come from clinical backgrounds but are in love with research, and are truly optimistic and excited about the wave of clinical translation of research into treatments. Both are also wonderful people who were generous in conversation with me; watch out for the final interviews in the coming months.
In a stimulating ‘Tissue Regeneration and Homeostasis’ session, Ben Simons began by apologising for being a physicist (though later he proudly showed us some of the first wet data from his lab). Simons uses mathematical approaches to understand developmental problems, and his talk focussed on the statistics of proliferation versus termination in mammary epithelial stem cells during pubertal morphogenesis. I’ve previously talked to Bill Harris about how Simons’ approach helped him understand the retina, and like the idea that sometimes we can be too burdened by knowledge, so a clear eye from a different field is needed to look at a problem. Given the number of collaborations Simons is involved in, his eye is in high demand.
In the evening I took the metro up to Cambridge though it was too rainy really to see much of it, and ate at a Tex Mex place with an old friend from old Cambridge (accompanied this time by Margaritas).
Saturday 17th June
I’d never been so moved at a scientific meeting – in the ‘Road to the Clinic’ session, Michele De Luca, well known for his promotion of responsible stem cell treatments and efforts to shut down charlatans, told us about epidermolysis bullosa, a terrible disease caused by a defective link between the dermis and the epidermis that can lead to skin blistering at even the slightest touch. De Luca described a patient with a severe genetic form of the disease, a child refugee from Syria who on his arrival to Germany had lost much of his epidermis to an infection and was in effect skinless, and placed in an induced coma for the pain it caused. De Luca’s solution was to grow skin from gene-corrected epidermal stem cells, and then graft this skin onto the child’s body (these were really huge grafts). And a couple of years on it seems to have worked – essentially the entire body is covered by transgenic skin that is now functioning like normal skin (faring better, indeed, than skin grafts used to treat burns, as the disease does not affect the underlying dermis like burns do). He ended his talk with a picture of the boy – standing slightly awkwardly in an ill-fitting suit in a hospital corridor, the most heart-wrenching contrast to the pre-treatment images De Luca had shown before. A kid in a coma to a kid standing and smiling.
An uplifting, miraculous story such as this shows us the potential of stem cells and gene therapy for treatment. As Megan Munsie then described, shadowing these remarkable advances is the growth of unregulated stem cell treatments. I remember a few years ago hearing that Texas Governor and GOP presidential candidate Rick Perry had had stem cells injected for back pain, and since we’ve seen an explosion in the number of clinics in the US and beyond offering stem cell treatments for just about anything (these are often covered by Paul Knoepfler’s excellent blog, the Niche). Not only might such treatments be expensive, and useless, they could of course also be dangerous. Munsie interviewed a number of patients who had sought such treatment – even if they understood the risk, for some it was really about the hope that it gave them, however small. Many of the patients (all based in Australia) felt let down by their own health care practitioners, which suggests we could do more to engage with patients who see no other way out than unregulated treatments.
A brief trip to see the tall ships that had gathered in the harbour, and that was that – back on the night flight to Heathrow, with the image of de Luca’s patient, smiling awkwardly, still in my head.
A 3-year funded PhD position is available at the Institut de Biologie Paris Seine to investigate the role of mechanical forces in the construction of a neuronal circuit in vivo.
During neuronal circuit formation, neurons move towards their final location while growing axons towards their target. While the biochemical guidance cues involved in neuronal migration and axon elongation are extensively studied, the contribution of mechanical forces in these processes remains largely unexplored in vivo.
In the lab we address this question using the zebrafish olfactory circuit as a model system. Its location underneath the skin of the embryo makes it amenable to live imaging and mechanical perturbation. We already obtained imaging and functional data suggesting an important function for mechanical cues in the formation of the circuit: olfactory axons extend through the effect of extrinsic mechanical forces that drive the passive displacement of neuronal cell bodies away from their axon tips (Breau et al., Nat Comm, in press).
The purpose of the PhD project is to further identify the origin and contribution of mechanical forces in the construction of the circuit, and the molecular mechanisms involved in force propagation and sensing. To achieve this goal, the student will use a pluridisciplinary strategy combining multiscale live imaging, genetic/optogenetic tools and physical approaches to measure and perturb forces in vivo.
We are looking for a highly motivated student willing to join an interdisciplinary environment involving strong interactions between biologists and physicists.
Requirements:
– Master degree in cell/developmental biology or in biophysics
– Strong interest towards interdisciplinary work
Additional beneficial skills:
– Experience with zebrafish
– Skills in confocal, biphoton or light sheet microscopy
– Experience in image analysis (Image J, Matlab)
Starting date: between October 2017 and January 2018. To apply, please send your CV and references to Marie Breau, Institut de Biologie Paris Seine:
A Postdoctoral Research Associate position is available in the Hoffman Lab at Yale University (www.hoffmanlab.net). We use zebrafish as a translational tool to investigate the function of genes that are strongly associated with autism spectrum disorders (Hoffman et al. 2016 Neuron). Specifically, we use CRISPR-generated zebrafish mutants to study how disruption of autism risk genes affects the developing brain and the neural circuitry underlying simple behaviors. Our goal is to utilize this system to identify basic mechanisms underlying autism and potential new pharmacotherapies.
Candidates must have a Ph.D., M.D., or M.D./Ph.D. in Neuroscience, Genetics, or Cell and Developmental Biology. The ideal candidate will have demonstrated expertise in standard and advanced molecular biology techniques, developmental neurobiology, and microscopy. Special consideration will be given to applicants with experience using animal models of human genetic disorders.
Candidates should be highly motivated, enthusiastic, learn quickly, have a strong work ethic, and a high degree of independence.
Please send your CV, a cover letter stating your research interests and professional goals, and the contact information for three (3) references to:
Ellen J. Hoffman, M.D., Ph.D.
Assistant Professor
Yale Child Study Center and Department of Neuroscience
General Purpose: Function as a Lab Manager overseeing a Molecular Biology Lab using a zebrafish model system. Research in the Hoffman Lab at Yale focuses on using zebrafish as a model system for the functional analysis of autism risk genes (www.hoffmanlab.net). Work on an independent research project, master generation of zebrafish mutants using CRISPR/Cas9 technique, maintain wild-type and mutant fish lines, characterize new mutant fish lines by genotypic and phenotypic analysis, supervise undergraduates and post-graduate associates in the laboratory and fish facility.
Required Education and Experience: Master’s Degree in a scientific discipline and one year experience or an equivalent combination of education and experience.
Qualifications:
Demonstrated knowledge and ability with zebrafish husbandry and maintenance.
Demonstrated proficiency in molecular biology, including cloning, PCR, in vitro transcription, in situ hybridization, western blotting, and immunohistochemistry.
Demonstrated ability in zebrafish analysis and mRNA injection.
Demonstrated excellent interpersonal skills.
Demonstrated strong work ethic.
Preferred Education, Experience and Skills: Master’s Degree in the Biological Sciences, Neuroscience, Genetics or a related discipline, and one year experience or an equivalent combination of education and experience. 5 or more years of experience. Ability to lead and provide oversight in a lab setting.
Application: For more information and immediate consideration, please apply online at http://bit.ly/2txRpIY. Please be sure to reference this website when applying for this position.
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The 5′ region of Xist RNA contains a conserved element termed the A-repeat that is required for the silencing function of Xist in embryonic stem cells, but how this region functions during development is unclear. Now, Takashi Sado and co-workers explore this by introducing into mice a mutated Xist allele that produces Xist RNA lacking the A-repeat region (p. 
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