In this episode we’re digging into some of the mysteries around what’s often seen as the ultimate genetic disease: cancer.

We talk to Phil Jones at the Sanger Institute in Cambridge to unpack his latest research showing that low doses of X-rays – similar to what someone might receive from a few CT scans – can trigger the growth of potentially cancerous cells. And we sit down with Steve Elledge from Harvard Medical School to hear how he and his team are using their Cancer Research UK Grand Challenge Award to understand why tumours tend to arise in some tissues and not others. Plus, the evolutionary genetics of rats leaving a sinking ship.

Listen and download now from GeneticsUnzipped.com, plus full show notes and transcripts.

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This obituary by Sonia Sen and K. VijayRaghavan was recently published in Development

Heinrich Reichert, Professor Emeritus at the University of Basel, Switzerland, passed away on the 13th of June 2019 after a prolonged illness. Heinrich described himself as ‘a hedonist when it came to science’ because he said it gave him great pleasure. It was this quality that made working with Heinrich thrilling and deeply fulfilling. Heinrich’s long and versatile career spanned the breadth of neuroscience – from development, to evolution and behaviour. In his passing we have lost not just an astute scientist, but also an impassioned educator and an adventurer of science.

Heinrich grew up in Southern California, to where his parents had moved from Austria. He did his schooling there, but moved back to Europe to study Physics, Biology and Chemistry at the University of Karlsruhe, before doing his Masters at the neighbouring University of Freiburg. These were stimulating years for Heinrich. Inspired by Seymour Benzer’s work on genes and behaviour, he and colleagues established a behavioural paradigm for aversive learning in the fruit fly Drosophila – versions of this assay are standard in many laboratories today (Spatz et al., 1974). He continued on at Freiburg for his PhD in this productive period and collaborated extensively to combine electrophysiological recordings, genetics and behavioural approaches to understand the sensitivities of the photoreceptor neurons in Drosophila. These were also some of the rare years in recent history when it was possible to travel relatively easily from Europe to India by road. So, throwing life and science in a heady mix, Heinrich took a backpacking holiday from southwestern Germany, through Turkey, Iran, Afghanistan and Pakistan all the way into India in the middle of his PhD. Despite this long sojourn, he completed his PhD with three papers on visual perception and learning in Drosophila (Bicker and Reichert, 1978; Hu et al., 1978; Reichert and Bicker, 1979).

Heinrich was then on the lookout for new adventures. Jeffery Wine’s lab, in balmy Stanford, and the electrophysiologically accessible neurons of the crayfish caught his attention. How do nervous systems generate the different components of a behaviour in an orderly fashion? Heinrich decided to tackle this question in the crayfish escape response and spent three intense years unravelling the circuitry underlying it. Crayfish escape threatening stimuli by a near-instantaneous flick of the tail followed by a rapid burst of backward swimming. The initial flick is mediated by the giant fibre neurons and the swimming by a central pattern generator composed of non-giant fibre neurons. Combining direct electrical stimulation of the giant neurons with tactile stimulation of the crayfish in various ways, Heinrich and Wine showed that activation of the giant fibres did not initiate swimming. This ruled out the possibility that an early circuit (giant neurons) activated the later circuit (the central pattern generator). They went on to show that the same sensory stimulus activates both the giant fibre and the non-giant fibre circuits, but with different latencies, allowing the robustly ordered sequence of events that constitutes the stereotypical escape response (Reichert and Wine, 1982, 1983; Reichert et al., 1981, 1982). During this time, Heinrich also made his initial foray into insect flight in a collaboration with Mel Robertson at the University of Alberta in Canada. Together, they identified segmentally homologous interneurons in the locust that were active during flight and argued that this segmental homology reflected an appendage-like evolutionary origin of the wings (the contrary idea was that wings were an extension of the thorax) (Robertson et al., 1982).

Even before he completed his time at Stanford, Heinrich was offered an assistant professorship in the Zoological Institute at the University of Basel, Switzerland. When he got there, he dove straight into solving the circuitry of locust flight, much like he had the crayfish escape response in Stanford. In Basel, his group shifted organisms, but the central questions remained the same – how do interneurons integrate sensory inputs to modulate motor outputs? Over the period of his habilitation (qualification as a Professor) at Basel, Heinrich’s group made important contributions and published steadily – a salt-and-pepper mix of crayfish and locust stories around this idea.

He then moved to the University of Geneva where he found himself facing a new challenge. In Basel, Heinrich had been teaching undergraduate courses in German – a language he was fluent in. He now had to teach the same courses in French – a language he barely knew! But Heinrich had an uncanny flair for teaching. He could effortlessly distil complex ideas and weave them into conversational language. So, teaching in any language came easily to him. By this time, Heinrich was married to Dominique, herself a scientist, whose first language was French. In their first year of marriage, it was Dominique who helped Heinrich translate all his neurobiology lectures into French.

In 1991, Heinrich and Dominique moved back to Basel, where he was appointed an Associate Professor. This period saw a shift in Heinrich’s science. An underlying thread in his work had been the question of evolution, and of how neural circuitry was established during development. So, in Basel, Heinrich’s group began to look at the developmental origins of muscles and the nervous system in the grasshopper embryo. But it was soon clear that the grasshopper was not appropriate for this – this problem needed to be tackled in Drosophila. The way Heinrich told it, he only had a passive role to play in this decision – he was away on holiday, and when he came back, Drosophila had been smuggled into the lab. This was largely modesty. While Heinrich was certainly the sort of mentor who nurtured creative, independent pursuits from people in his group, he was also keenly aware of the workhorse that was Drosophila. Besides, there was a revolution underway. Following work by Michael Bate in the grasshopper, Corey Goodman and colleagues were beginning to look at the establishment of neural circuits during development and demonstrating the striking similarity in the ground-plan of grasshopper and Drosophila nervous systems. What was more, they were showing how genes coding for cell-surface proteins, transcription factors and signalling molecules were orchestrating its precise assembly. In Basel, Heinrich took this same approach and applied it to the central brain – a far more complex part of the nervous system that was, for all practical purposes, uncharted. But he stretched the argument further. If the circuits were evolutionarily conserved, maybe the genes that built them were too. Over the next few years, Heinrich’s group showed that this was indeed the case. You could swap the coding sequences of genes between species as far removed as Drosophila, mouse, human and even corals and achieve functional replacements – in most cases, and for the most part (Nagao et al., 1998). The implications of this are deep: if the circuits are conserved, and so are the genes, it would suggest that these vastly different extant nervous systems shared common evolutionary origins.

Heinrich’s second and far longer association with India came at this point – though it wasn’t Heinrich himself who initiated it. Robert Lichtneckert, who was doing his PhD with Heinrich at the time, was looking at the early embryonic patterning gene empty spiracles (ems) in the development of central brain when he stumbled into the olfactory circuit. ems seemed to be involved in both the central and peripheral neurons of the olfactory circuit – a system whose development Veronica Rodrigues had been studying in Mumbai. Lichtneckert wrote to Veronica, and so began a collaboration that lasted beyond ems and the olfactory system, beyond Veronica’s life, and even beyond Drosophila biology. Veronica fell ill shortly after this. It was to the credit of both Heinrich and Veronica that the science on which Robert Lichtneckert, Beate Hartmann, Abhijit Das and one of us (S.S.) collaborated continued seamlessly. Heinrich would visit the National Centre for Biological Sciences – Tata Institute for Fundamental Research (NCBS-TIFR) in Bangalore (where Veronica had since moved) twice, sometimes three times, a year for prolonged periods. He had become an integral part of the community. When Veronica passed away two years later, Heinrich became the adopted co-mentor of many of Veronica’s PhD students and he generously took them on. He naturally connected with students, which made his presence on campus invaluable – and not just for Veronica’s students. It was a common sight to see Heinrich in the bustling, sunny NCBS canteen, surrounded by students from different labs, sharing meals and science alike. Working with him was an absolute pleasure – he brought clarity to complex data and let the path ahead emerge from there. He was generous with his time and his intellect and met with everyone and anyone who wanted to discuss their work with him, without making any demands.

In Bangalore, Heinrich’s office was across from that of K. S. Krishnan, a cell biologist of the synapse and an Emeritus Professor at NCBS-TIFR. The two shared a common love for nature, particularly the ocean. Krishnan, an avid birder, was running an extraordinary project on isolating and characterising the diverse peptides that constitute the venom cocktail of marine cone snail species from coastal India; Heinrich was an avid scuba diver – a ‘birdwatcher of fish’, if you will. For decades he had been diving regularly in the Maldives and the Red Sea. In fact, for many years Heinrich, with others in his lab who were also certified divers, ran a marine biology course that took students to the Maldives to monitor coral reef ecosystems, looking particularly at the effect of and recovery after photobleaching. He also organised and taught two experimental marine biology courses at the marine stations in Roscoff and Banyuls in France every year, and neurobiology courses in Trieste and Cambodia. Krishnan and Heinrich’s common interest sparked a much larger project for India – a proposal for a new marine biology institute. Unfortunately, Krishnan passed away quite suddenly in 2014. But Heinrich threw all his efforts behind this idea. For two years, the Swiss man became part of an Indian delegation to establish formal collaborations with the French Centre National de la Recherche Scientifique (CNRS) and Université Pierre et Marie Curie (UPMC) and their three marine stations in Roscoff, Banyuls and Villefranche. He also travelled extensively within India and explored its islands to assess ideal locations for this new Indian marine institute. As India now considers budgetary allocations for this proposal, we owe Heinrich deeply for his generous, unselfish and tireless support of it.

Heinrich’s passing is a tremendous loss to developmental neuroscience. In the last few years before his retirement in 2015, his lab had begun to systematically take apart how the brain was built – in modules constituted by stem cells and their lineages. They were examining the genes that contributed to the identities of these stem cells, and therefore to the establishment of circuitry in the brain, as well as how faults in this programme could result in disease states such as in cancer. His science over the years constitutes a body of work that has greatly advanced our understanding of the brain, its construction and function. He has written textbooks in English and German that are considered essential reading. But Heinrich’s passing will be a loss to science for much more than that. In the current research environment that places high demands on the proxies of academic success, Heinrich exemplified success without dwelling on such proxies. As a mentor, this stripped the experience of science down to why we pursue it in the first case – the desire to understand something. As a collaborator, this meant a committed, unguarded pursuit of a common goal. Heinrich was a true intellect, a Renaissance human of the 21st century. His approach to science bore the same quality as his appreciation of music, literature, art, languages, or even cuisines. Yet he had no pomp and spoke only of what others did, never placing his own contributions at the centre. He was as willing to engage in discussions with students as he was with stalwarts; he equally appreciated quality street food of questionable provenance as he did fine dining; and he was always ready to roll up his sleeves to get something done. Heinrich will be sorely missed by developmental biologists and his friends alike. We who have benefited so much from his generosity and caring mentorship now have the enormous task to pass on this culture of science that he so carefully cultivated.

Heinrich is survived by Dominique and their three sons, Thomas, Marc and Paul.

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Research Assistant I – Investigating Microbial Protein Evolution with Functional Genomics

Position Summary:
The Paul Lab at the MBL seeks a highly motivated individual to join the Josephine Bay Paul Center for Comparative Molecular Biology and Evolution as a Research Assistant (Level I). The successful candidate will be responsible for carrying out routine laboratory work as outlined below. Our research group is looking at the processes that diversify microbial genes, to better understand the functional significance of protein variation in cells and viruses from a variety of biomes.
This is a year-round, full time, non-exempt position. 

Additional Information:
The primary aim of the position is to maintain the molecular lab facilities and to assist in developing genetic experiments with bacteria/archaea primarily derived from marine and freshwater ecosystems. Responsibilities will include establishing and monitoring cell cultures, maintaining lab equipment, ordering lab supplies, and conducting basic molecular experiments.

Basic Qualifications:
A Bachelor’s degree in biology, molecular biology or a related discipline is required. This position requires an independent, organized, and self-motivated individual with strong problem-solving skills and the ability to multitask. Prior experience in a research lab and applying basic molecular biology techniques is required. Excellent written, verbal, and interpersonal skills; attention to detail; and a strong work ethic are essential. Position level and salary will depend upon education and experience.

Preferred Qualifications:
The ideal candidate will have prior experience with nucleic acid purification, PCR, and maintaining (bacterial/archaeal) cell cultures.  An understanding of basic molecular biology concepts is important.

Physical Requirements:
Minimal exposure to biohazardous chemicals. Occasional lifting of heavy objects.

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By decoding the genetic mechanisms that control the neurons of the visual
system, researchers at UNIGE are unveiling the first steps in the construction of vision, paving the way for regenerative eye medicine. A Press Release from the University of Geneva.

How is the retina formed? And how do neurons differentiate to become individual components of the visual system? By focusing on the early stages of this complex process, researchers at the University of Geneva (UNIGE), Switzerland, in collaboration with the École Polytechnique Fédérale de Lausanne (EPFL), have identified the genetic programmes governing the birth of different types of retinal cells and their capacity to wire to the correct part of the brain, where they transmit visual information. In addition, the discovery of several genes regulating nerve growth allows for the possibility of a boost to optic nerve regeneration in the event of neurodegenerative disease. These results can be discovered in the journal Development.

The visual system of mammals is composed of different types of neurons, each of which must find its place in the brain to enable it to transform stimuli received by the eye into images. There are photoreceptors, which detect light, optic nerve neurons, which send information to the brain, cortical neurons, which form images, or interneurons, which make connections between other cells. Though not yet differentiated in the early stages of embryonic development, these neurons are all produced by progenitor cells that, are capable of giving rise to different categories of specialized neurons. To better understand the exact course of this mechanism and identify the genes at work during retinal construction, researchers studied the dynamics of gene expression in individual cells. “To monitor gene activity in cells and understand the early specification of retinal neurons, we sequenced more than 6,000 cells during retinal development and conducted large-scale bioinformatic analyses,” explains Quentin Lo Giudice, PhD student in the Department of Basic Neurosciences at the UNIGE Faculty of Medicine and first author of this article.

Mapping a system under construction

In collaboration with Gioele La Manno and Marion Leleu of EPFL, the researchers studied progenitor’s behaviour during the cell cycle as well as during their progressive differentiation. The scientists then mapped very accurately the different cell types of the developing retina and the genetic changes that occur during the early stages of this process. “Beyond their “age”—that is, when they were generated during their embryonic life—the diversity of neurons stems from their position in the retina, which predestines them for a specific target in the brain,” explains Pierre Fabre, senior researcher in the Department of Basic Neurosciences at the UNIGE Faculty of Medicine, who directed this work. “In addition, by predicting the sequential activation of neural genes, we were able to reconstruct several differentiation programs, similar to lineage trees, showing us how the progenitors progress to one cell type or another after their last division.”

The researchers also conducted a second analysis. If the right eye mainly connects essentially to the left side of the brain, and vice versa, a small fraction of neurons in the right eye make connections in the right side of the brain. Indeed, all species with two eyes with overlapping visual fields, such as mammals, must be able to mix information from both eyes in the same part of the brain. This convergence makes it possible to see binocularly and perceive depths or distances. “Knowing this phenomenon, we have genetically and individually “tagged” the cells in order to follow each of them as they progress to their final place in the visual system,” says Quentin Lo Giudice. By comparing the genetic diversity of these two neural populations, researchers discovered 24 genes that could play a key role in three-dimensional vision. “The identification of these gene expression patterns may represent a new molecular code orchestrating retinal wiring to the brain,” adds Dr. Fabre.

Towards regenerative medicine

Even before the neurons reach the brain, they must leave the retina through the optic nerve. The last part of this study identified the molecules that guide neurons on the right path. Moreover, these same molecules also allow the initial growth of axons, the part of neurons that transmits electrical signals to the synapses and thus ensures the passage of information from one neuron to another, as well as about twenty genes that control this process. This discovery is a fundamental step forward for regenerative medicine.
The more we know about the molecules needed to appropriately guide axons, the more likely we are to develop a therapy to treat nerves trauma. “If the optic nerve is cut or damaged, for example by glaucoma, we could imagine reactivating those genes that are usually only active during the embryonic development phase. By stimulating axon growth, we could allow neurons to stay connected and survive,” explains Dr. Fabre, who plans to launch a research project on this theme. Although the regeneration capacities of neurons are very low, they do exist and techniques to encourage their development must be found. Genetic stimulation of the damaged spinal cord after an accident is based on the same idea and is beginning to show its first successes.

Check out the paper here:

Single-cell transcriptional logic of cell-fate specification and axon guidance in early-born retinal neurons
Quentin Lo Giudice, Marion Leleu, Gioele La Manno, Pierre J. Fabre
Development 2019 146: dev178103 doi: 10.1242/dev.178103

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Our research investigates the fundamental question of how cardiac cells sense and respond to their environment. We seek to understand the mechanisms underlying the regulation of morphogenetic and identity transformations that occur during development and disease. We use the assembly of the heart tube in zebrafish as our model with which to elucidate these mechanisms. Some of the specific research questions we are interested in include:  How do multiple tissues interact to regulate large movements and biomechanical force? How do dynamic changes in the extracellular matrix regulate cardiac morphogenesis? How is lumen formation intrinsically and extrinsically encoded? and How is the plasticity of cardiovascular identity regulated? To answer these questions, we take an interdisciplinary approach, combining the genetic and live-imaging strengths of zebrafish with both biomechanics and systems-level methodologies.

-More information about the laboratory can be found at thebloomekatzlaboratory.org.

If you are interested in joining our lab as a PhD student, please contact us directly at josh@olemiss.edu.

-Additional positions, including a rotation program, are also available in our interdisciplinary graduate program in the department of Biology at the University of Mississippi. For more information about our graduate program including rotations please see biology.olemiss.edu

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We seek a biocurator to join the FlyBase group at the University of Cambridge, UK. If you are looking for a fulfilling, fly-related career away from the lab, and enjoy the challenge of organizing complex data clearly and concisely, then this is the job for you!

FlyBase curators extract biological information from scientific articles about the model organism Drosophila melanogaster, recording and organizing these data in template forms and graphical interfaces. Phenotype curators focus on data that illuminate the function of genes based on their mutant phenotypes and genetic interactions. All curated data are subsequently integrated into our central database and made freely available via the FlyBase website.

Additional responsibilities of phenotype curators include: developing strategies/tools to improve curation; enhancing data display/querying on the website; and interacting with the research community through HelpMail and presentations/help desks at research conferences. Curators also contribute to FlyBase publications and have the opportunity to develop computational skills (e.g. Unix, scripting, SQL).

More details and a link to the application form are here: http://www.jobs.cam.ac.uk/job/23086/

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Welcome to our monthly trawl for developmental biology (and related) preprints. 

The preprints were hosted on bioRxiv, PeerJ, and arXiv. Let us know if we missed anything, and use these links to get to the section you want:

Developmental biology

| Patterning & signalling

| Morphogenesis & mechanics

| Genes & genomes

| Stem cells, regeneration & disease modelling

| Plant development

Evo-devo & evo

Cell biology

Modelling

Tools & resources

Research practice & education

Why not…

Developmental biology

| Patterning & signalling

In vivo lineage conversion of vertebrate muscle into early endoderm-like cells
Clyde Campbell, Joseph J. Lancman, Raquel Espin Palazon, Jonatan Matalonga, Jiaye He, Alyssa Graves, Xin-Xin I. Zeng, Rashmi Mishra, Jan Huisken, David Traver, P. Duc Si Dong

Emergence and patterning dynamics of mouse definitive endoderm
Maayan Pour, Abhishek Sampath Kumar, Maria Walther, Lars Wittler, Alexander Meissner, Iftach Nachman

A Hedgehog-FGF signaling axis patterns anterior mesoderm during gastrulation
Alexander Guzzetta, Mervenaz Koska, Megan Rowton, Junghun Kweon, Hunter Hidalgo, Heather Eckhart, Rebecca Back, Stephanie Lozano, Anne M. Moon, Anindita Basu, Michael Bressan, Sebastian Pott, Ivan P. Moskowitz

The absence of SOX2 in the anterior foregut alters the esophagus into trachea and bronchi in both epithelial and mesenchymal components
Machiko Teramoto, Ryo Sugawara, Katsura Minegishi, Masanori Uchikawa, Tatsuya Takemoto, Atsushi Kuroiwa, Yasuo Ishii, Hisato Kondoh

NRL- and CRX-guided gene network modulates photoreceptor presynapse size and positioning during retinal development
D. Thad Whitaker, Anupam K. Mondal, Hannah Fann, Passley Hargrove, Matthew J. Brooks, Vijender Chaitankar, Wenhan Yu, Zhijian Wu, Soo-Young Kim, Anand Swaroop

Transcriptome-based molecular staging of human stem cell-derived retinal organoids uncovers accelerated photoreceptor differentiation by 9-cis retinal
Koray D. Kaya, Holly Y. Chen, Matthew J. Brooks, Ryan A. Kelley, Hiroko Shimada, Kunio Nagashima, Natalia de Val, Charles T. Drinnan, Linn Gieser, Kamil Kruczek, Slaven Erceg, Tiansen Li, Dunja Lukovic, Yogita K. Adlakha, Emily Welby, Anand Swaroop

Gli3 regulates vomeronasal neurogenesis, olfactory ensheathing cell formation and GnRH-1 neuronal migration
Ed Zandro M. Taroc, Ankana Naik, Jennifer M. Lin, Nicolas B. Peterson, David L. Keefe Jr., Elizabet Genis, Gabriele Fuchs, Ravikumar Balasubramanian, Paolo E. Forni

GLI transcriptional repression regulates tissue-specific enhancer activity in response to Hedgehog signaling
Rachel K. Lex, Zhicheng Ji, Kristin N. Falkenstein, Weiqiang Zhou, Joanna L. Henry, Hongkai Ji, Steven A. Vokes

A SMAD1/5-YAP signaling module drives radial glial cell expansion and growth of the developing cerebral cortex
Sonia Najas, Isabel Pijuan, Anna Esteve-Codina, Susana Usieto, Juan D. Martinez, An Zwijsen, Mariona L. Arbonés, Elisa Martí, Gwenvael Le Dréau

Siah2 integrates mitogenic and extracellular matrix signals linking neuronal progenitor ciliogenesis with germinal zone occupancy
Taren Ong, Niraj Trivedi, Randall Wakefield, Sharon Frase, David J. Solecki

Modulation of β-catenin levels is critical for cranial neural crest patterning and dispersal into first pharyngeal arch
Alok Javali, Vairavan Laxmanan, Dasaradhi Palakodeti, Ramkumar Sambasivan

Early neuronal processes interact with glia to establish a scaffold for orderly innervation of the cochlea
Noah R Druckenbrod, Evan B Hale, Olubusola O Olukoya, Wynn E Shatzer, Lisa V Goodrich

Directed robust generation of functional retinal ganglion cells from Müller glia
Dongchang Xiao, Suo Qiu, Xiuting Huang, Rong Zhang, Qiannan Lei, Wanjing Huang, Haiqiao Chen, Bin Gou, Xiaoxiu Tie, Sheng Liu, Yizhi Liu, Kangxin Jin, Mengqing Xiang

NF-κB signaling regulates the formation of proliferating Müller glia-derived progenitor cells in the avian retina
Isabella Palazzo, Kyle Deistler, Thanh V. Hoang, Seth Blackshaw, Andy J. Fischer

Multipotent radial glia progenitors and fate-restricted intermediate progenitors sequentially generate diverse cortical interneuron types
Sean M. Kelly, Ricardo Raudales, Monika Moissidis, Gukham Kim, Z. Josh Huang

Experience-dependent structural plasticity at pre- and postsynaptic sites of layer 2/3 cells in developing visual cortex
Yujiao Jennifer Sun, J. Sebastian Espinosa, Mahmood S. Hoseini, Michael P. Stryker

Sex differences in maturation and attrition rate of adult born neurons in the hippocampus of rats
Shunya Yagi, Jared E.J. Splinter, Daria Tai, Sarah Wong, Liisa A.M. Galea

Functional properties of habenular neurons are determined by developmental stage and sequential neurogenesis
Stephanie Fore, Mehmet Ilyas Cosacak, Carmen Diaz Verdugo, Caghan Kizil, Emre Yaksi

LSD1-mediated enhancer silencing enables endocrine cell development through attenuation of retinoic acid signalling
Nicholas K. Vinckier, Nisha A. Patel, Allen Wang, Jinzhao Wang, Hung-Ping Shih, Jianxun Wang, Ulupi S. Jhala, Michael G. Rosenfeld, Christopher W. Benner, Maike Sander

CYLD, a Mechanosensitive Deubiquitinase, Regulates TGFβ Signaling in Load-Induced Bone Formation
Jacqueline Nguyen, Ramin Massoumi, Tamara Alliston

Chemokine receptors CCR1 and ACKR2 coordinate mammary gland development
Gillian J Wilson, Ayumi Fukuoka, Samantha R Love, Jiwon Kim, Marieke Pingen, Alan J Hayes, Gerry Graham

Essential role of Bone morphogenetic protein 15 in porcine ovarian and follicular development and ovulation
Yufeng Qin, Tao Tang, Wei Li, Zhiguo Liu, Xiaoliang Yang, Xuan Shi, Guanjie Sun, Xiaofeng Liu, Min Wang, Xinyu Liang, Peiqing Cong, Delin Mo, Xiaohong Liu, Yaosheng Chen, Zuyong He

Neural tube development depends on notochord-derived Sonic hedgehog released into the sclerotome
Nitza Kahane, Chaya Kalcheim

Hedgehog signaling regulates neurogenesis in the larval and adult zebrafish hypothalamus
Ira Male, A. Tuba Ozacar, Rita R. Fagan, Matthew Loring, Meng-Chieh Shen, Veronica Pace, Chris Devine, Alyssa Lutservitz, Rolf O. Karlstrom

Hingepoints and neural folds reveal conserved features of primary neurulation in the zebrafish forebrain
Jonathan M. Werner, Maraki Y. Negesse, Dominique L. Brooks, Allyson R. Caldwell, Jafira M. Johnson, Rachel Brewster

Smad4 signaling establishes the somatosensory map of basal vomeronasal sensory neurons
Ankana S. Naik, Jennifer M. Lin, Ed Zandro M. Taroc, Raghu R. Katreddi, Jesus A. Frias, Morgan Sammons, Paolo E. Forni

Crumbs2 mediates ventricular layer remodelling to form the adult spinal cord central canal
Christine Tait, Kavitha Chinnaiya, Mariyam Murtaza, John-Paul Ashton, Nicholas Furley, Chris J. Hill, C Henrique Alves, Jan Wijnholds, Kai S. Erdmann, Raman M. Das, Penny Rashbass, Kate G. Storey, Marysia Placzek

Haploinsufficient maternal effect of Epidermal Growth Factor Receptor A mutation in zebrafish
Margherita Ciano, Paul R. Kemp, S. Amanda Sathyapala, Simon M. Hughes

Developmental stage-specific distribution of macrophages in mouse mammary gland
Teneale A. Stewart, Katherine Hughes, David A. Hume, Felicity M. Davis

Optogenetic inhibition of Delta reveals digital Notch signaling output during tissue differentiation
Ranjith Viswanathan, Aleksandar Necakov, Mateusz Trylinski, Rohit Krishnan Harish, Daniel Krueger, Emilia Esposito, Francois Schweisguth, Pierre Neveu, Stefano De Renzis

BMP-signalling inhibition in Drosophila secondary cells remodels the seminal proteome, and self and rival ejaculate functions
Ben R. Hopkins, Irem Sepil, Sarah Bonham, Thomas Miller, Philip D. Charles, Roman Fischer, Benedikt M. Kessler, Clive Wilson, Stuart Wigby

Notch signaling coordinates ommatidial rotation in the Drosophila eye via transcriptional regulation of the EGF-Receptor ligand Argos
Yildiz Koca, Benjamin E. Housden, William J. Gault, Sarah J. Bray, Marek Mlodzik

Constraints and limitations on decoding positional information: the Bicoid case-study
Huy Tran, Aleksandra M. Walczak, Nathalie Dostatni

Shuttling of Dorsal by Cactus: mechanism and implications
Allison E. Schloop, Sophia Carrell-Noel, Gregory T. Reeves

Robustness of the Dorsal morphogen gradient with respect to morphogen dosage
Hadel Y. Al Asafen, Prasad U. Bandodkar, Sophia Carrell-Noel, Gregory T. Reeves

Caspase-dependent activation of Hedgehog-signalling sustains proliferation and differentiation of ovarian somatic stem cells
Alessia Galasso, Daria Iakovleva, Luis Alberto Baena-Lopez

A Canal-Associated Neuron cAMP signalling pathway that regulates C. elegans larval development
Jason Chien, Fred W. Wolf, Sarah Grosche, Nebeyu Yosef, Gian Garriga, Catarina Mörck

| Morphogenesis & mechanics

The plakin domain of C. elegans VAB-10/plectin acts as a hub in a mechanotransduction pathway to promote morphogenesis
Shashi Kumar Suman, Csaba Daday, Teresa Ferraro, Thanh Vuong-Brender, Saurabh Tak, Sophie Quintin, François Robin, Frauke Gräter, Michel Labouesse

Mechanical Feedback and Robustness of Apical Constrictions in Drosophila Embryo Ventral Furrow Formation
Michael C. Holcomb, Guo-Jie Jason Gao, Mahsa Servati, Dylan Schneider, Presley K. McNeely, Jeffrey H. Thomas, Jerzy Blawzdziewicz

Regionalized tissue fluidization by an actomyosin cable is required for epithelial gap closure during insect gastrulation
A. Jain, V. Ulman, A. Mukherjee, M. Prakash, L. Pimpale, S. Muenster, K.A. Panfilio, F. Jug, S.W. Grill, P. Tomancak, A. Pavlopoulos

Fascin regulates protrusions and delamination to mediate invasive, collective cell migration in vivo
Maureen C. Lamb, Kelsey K. Anliker, Tina L. Tootle

Morphogenesis is transcriptionally coupled to neurogenesis during olfactory placode development
Raphaël Aguillon, Romain Madelaine, Harendra Guturu, Sandra Link, Pascale Dufourcq, Virginie Lecaudey, Gill Bejerano, Patrick Blader, Julie Batut

Deficiency in the endocytic adaptor protein PHETA1/2 impairs renal and craniofacial development
Kristin M. Ates, Tong Wang, Trevor Moreland, Rajalakshmi Veeranan-Karmegam, Priya Anand, Wolfgang Wenzel, Hyung-Goo Kim, Lynne A. Wolfe, Joshi Stephen, David R. Adams, Thomas Markello, Cynthia J. Tifft, William A. Gahl, Graydon B. Gonsalvez, May Christine Malicdan, Heather Flanagan-Steet, Y. Albert Pan

The desmosomal cadherin Desmogon is necessary for the structural integrity of the Medaka notochord
Ali Seleit, Karen Groß, Michaela Wölk, Camilla Autorino, Lazaro Centanin, Jasmin Onistschenko

mRNA compartmentalisation spatially orients tissue morphogenesis
Guilherme Costa, Joshua Bradbury, Nawseen Tarannum, Shane P. Herbert

Cytokinetic abscission dynamics in neuroepithelial stem cells during brain development
Katrina C. McNeely, Jessica Neville Little, Noelle D. Dwyer

Neuroblast sensory quiescence depends of vascular cytoneme contacts and sensory neuronal differentiation requires initiation of blood flow
Laura Taberner, Aitor Bañón, Berta Alsina

Non-junctional Cadherin3 regulates cell migration and contact inhibition of locomotion via domain-dependent opposing regulations of Rac1
Takehiko Ichikawa, Carsten Stuckenholz, Lance A. Davidson

Head Mesoderm Tissue Growth, Dynamics and Neural Crest Cell Migration
Mary Cathleen McKinney, Rebecca McLennan, Rasa Giniunaite, Ruth E. Baker, Philip K. Maini, Hans G. Othmer, Paul M Kulesa

ADAMTS-family protease MIG-17 regulates synaptic allometry by modifying the extracellular matrix and modulating glia morphology during growth
Tingting Ji, Kai Wang, Jiale Fan, Jichang Huang, Mengqing Wang, Xiaohua Dong, Yanjun Shi, Laura Manning, Xumin Zhang, Zhiyong Shao, Daniel A. Colón-Ramos

In-silico definition of the Drosophila melanogaster matrisome
Martin N. Davis, Sally Horne-Badovinac, Alexandra Naba

The versican-hyaluronan complex provides an essential extracellular matrix niche for Flk1+ precursors in vasculogenesis and primitive hematopoiesis
Sumeda Nandadasa, Anna O’Donnell, Ronald J Midura, Suneel S Apte

Mechanically activated Piezo channels modulate outflow tract valve development through Yap1 and Klf2-Notch signaling axis
Anne Laure Duchemin, Hélène Vignes, Julien Vermot

| Genes & genomes

A Single-Cell Transcriptome Atlas for Zebrafish Development
Dylan R. Farnsworth, Lauren Saunders, Adam C. Miller

A single cell transcriptome atlas of the developing zebrafish hindbrain
Monica Tambalo, Richard Mitter, David G. Wilkinson

A single cell atlas of the developing Drosophila ovary identifies follicle stem cell progenitors
Maija Slaidina, Torsten U. Banisch, Selena Gupta, Ruth Lehmann

A single-cell transcriptomics CRISPR-activation screen identifies new epigenetic regulators of zygotic genome activation
Celia Alda-Catalinas, Danila Bredikhin, Irene Hernando-Herraez, Oana Kubinyecz, Fátima Santos, Mélanie A. Eckersley-Maslin, Oliver Stegle, Wolf Reik

The enteric nervous system of the human and mouse colon at a single-cell resolution
Eugene Drokhlyansky, Christopher S. Smillie, Nicholas Van Wittenberghe, Maria Ericsson, Gabriel K. Griffin, Danielle Dionne, Michael S. Cuoco, Max N. Goder-Reiser, Tatyana Sharova, Andrew J. Aguirre, Genevieve M. Boland, Daniel Graham, Orit Rozenblatt-Rosen, Ramnik J. Xavier, Aviv Regev

The molecular anatomy of mouse skin during hair growth and rest
Simon Joost, Karl Annusver, Tina Jacob, Xiaoyan Sun, Unnikrishnan Sivan, Tim Dalessandri, Inês Sequeira, Rickard Sandberg, Maria Kasper

Development of the Mouse and Human Cochlea at Single Cell Resolution
Kevin Shengyang Yu, Stacey M. Frumm, Jason S. Park, Katharine Lee, Daniel M. Wong, Lauren Byrnes, Sarah M. Knox, Julie B. Sneddon, Aaron D. Tward

A molecular cell atlas of the human lung from single cell RNA sequencing
Kyle J. Travaglini, Ahmad N. Nabhan, Lolita Penland, Rahul Sinha, Astrid Gillich, Rene V. Sit, Stephen Chang, Stephanie D. Conley, Yasuo Mori, Jun Seita, Gerald J. Berry, Joseph B. Shrager, Ross J. Metzger, Christin S. Kuo, Norma Neff, Irving L. Weissman, Stephen R. Quake, Mark A. Krasnow

Single Cell RNAseq Reveals A Critical Role of Chloride Channels in Airway Development
Mu He, Bing Wu, Daniel D. Le, Wenlei Ye, Adriane W. Sinclair, Valeria Padovano, Yuzhang Chen, Kexin Li, Rene Sit, Michelle Tan, Michael J. Caplan, Norma Neff, Yuh Nung Jan, Spyros Darmanis, Lily Y. Jan

Generation of human neural retina transcriptome atlas by single cell RNA sequencing
Samuel W. Lukowski, Camden Y. Lo, Alexei Sharov, Quan H. Nguyen, Lyujie Fang, Sandy S.C. Hung, Ling Zhu, Ting Zhang, Tu Nguyen, Anne Senabouth, Jafar S. Jabbari, Emily Welby, Jane C. Sowden, Hayley S. Waugh, Adrienne Mackey, Graeme Pollock, Trevor D. Lamb, Peng-Yuan Wang, Alex W. Hewitt, Mark Gillies, Joseph E. Powell, Raymond C.B. Wong

Single-cell transcriptomics reveals temporal dynamics of critical regulators of germ cell fate during mouse sex determination
Chloé Mayère, Yasmine Neirijnck, Pauline Sararols, Isabelle Stévant, Françoise Kühne, Anne Amandine Chassot, Marie-Christine Chaboissier, Emmanouil T. Dermitzakis, Serge Nef

Integrated single-cell transcriptomics and chromatin accessibility analysis reveals novel regulators of mammary epithelial cell identity
Nicholas Pervolarakis, Quy Nguyen, Guadalupe Gutierrez, Peng Sun, Darisha Jhutty, Grace XY Zheng, Corey M Nemec, Xing Dai, Kazuhide Watanabe, Kai Kessenbrock

The gastrointestinal development ‘parts list’: transcript profiling of embryonic gut development in wildtype and Ret-deficient mice
Sumantra Chatterjee, Priyanka Nandakumar, Dallas R. Auer, Stacey B. Gabriel, Aravinda Chakravarti

Developmental gene expression differences between humans and mammalian models
Margarida Cardoso-Moreira, Britta Velten, Matthew Mort, David N. Cooper, Wolfgang Huber, Henrik Kaessmann

Transcriptional control of cardiac neural crest cells condensation and outflow tract septation by the Smad1/5/8 inhibitor Dullard
Jean-François Darrigrand, Mariana Valente, Pauline Martinez, Glenda Comai, Maxime Petit, Ryuichi Nishinakamura, Daniel S. Osorio, Vanessa Ribes, Bruno Cadot

MACF1 Facilitates SMAD7 Nuclear Translocation to Drive Bone Formation in Mice
Fan Zhao, Xiaoli Ma, Wuxia Qiu, Pai Wang, Ru Zhang, Zhihao Chen, Peihong Su, Yan Zhang, Dijie Li, Jianhua Ma, Chaofei Yang, Lei Chen, Chong Yin, Ye Tian, Lifang Hu, Yu Li, Ge Zhang, Xiaoyang Wu, Airong Qian

MIR3607 regulates cerebral cortex development via activation of Wnt/βCat signaling
Kaviya Chinnappa, Ángel Márquez-Galera, Anna Prieto-Colomina, Yuki Nomura, Adrián Cárdenas, José P. López-Atalaya, Víctor Borrell

The homeoprotein ENGRAILED-1 promotes motoneuron survival and sustains motor functions
Stephanie E. Vargas Abonce, Mélanie Lebœuf, Kenneth L. Moya, Alain Prochiantz

Role of the imprinted allele of the p57Kip2 gene in mouse neocortical development
Yui Imaizumi, Shohei Furutachi, Tomoyuki Watanabe, Hiroaki Miya, Daichi Kawaguchi, Yukiko Gotoh

CRISPR/Cas9 interrogation of the mouse Pcdhg gene cluster reveals a crucial isoform-specific role for Pcdhgc4
Andrew M Garrett, Peter J Bosch, David M Steffen, Leah C Fuller, Charles G Marcucci, Alexis A Koch, Preeti Bais, Joshua A Weiner, Robert W Burgess

The transcription factor E2A drives neural differentiation in pluripotent cells
Chandrika Rao, Mattias Malaguti, John O. Mason, Sally Lowell

DUX4 regulates oocyte to embryo transition in human
Sanna Vuoristo, Christel Hydén-Granskog, Masahito Yoshihara, Lisa Gawriyski, Anastassius Damdimopoulos, Shruti Bhagat, Kosuke Hashimoto, Kaarel Krjutškov, Sini Ezer, Priit Paluoja, Karolina Lundin, Pauliina Paloviita, Gaëlle Recher, Vipin Ranga, Tomi Airenne, Mahlet Tamirat, Eeva-Mari Jouhilahti, Timo Otonkoski, Juha S. Tapanainen, Hideya Kawaji, Yasuhiro Murakawa, Thomas R. Bürglin, Markku Varjosalo, Mark S. Johnson, Timo Tuuri, Shintaro Katayama, Juha Kere

Developmental Genome-Wide DNA Methylation Asymmetry Between Mouse Placenta and Embryo
LM Legault, K Doiron, A Lemieux, M Caron, D Chan, FL Lopes, G Bourque, D Sinnett, S McGraw

Cables2 Is a Novel Smad2-Regulatory Factor Essential for Early Embryonic Development in Mice
Tra Thi Huong Dinh, Hiroyoshi Iseki, Seiya Mizuno, Saori Iijima-Mizuno, Yoko Tanimoto, Yoko Daitoku, Kanako Kato, Yuko Hamada, Ammar Shaker Hamed Hasan, Hayate Suzuki, Kazuya Murata, Masafumi Muratani, Masatsugu Ema, Jun-dal Kim, Junji Ishida, Akiyoshi Fukamizu, Mitsuyasu Kato, Satoru Takahashi, Ken-ichi Yagami, Valerie Wilson, Ruth M. Arkell, Fumihiro Sugiyama

Nf1 deletion results in depletion of the Lhx6 transcription factor and a specific loss of parvalbumin+ cortical interneurons
Kartik Angara, Emily Ling-Lin Pai, Stephanie M Bilinovich, April M Stafford, Julie T Nguyen, Anirban Paul, John L Rubenstein, Daniel Vogt

Screening and identification of MicroRNAs expressed in perirenal adipose tissue during rabbit growth
Guoze Wang, Guo Guo, Xueting Tian, Shenqiang Hu, Kun Du, Jingxin Mao, Xianbo Jia, Shiyi Chen, Jie Wang, Songjia Lai

Developmental regulation of Canonical and small ORF translation from mRNA
Pedro Patraquim, Jose I. Pueyo, M. Ali Mumtaz, Julie Aspden, J.P. Couso

Identification of genes involved in the differentiation of R7y and R7p photoreceptor cells in Drosophila
James B Earl, Lauren A Vanderlinden, Laura M Saba, Steven G Britt

Low Affinity Binding Sites in an Activating CRM Mediate Negative Autoregulation of the Drosophila Hox Gene Ultrabithorax
Rebecca K Delker, Vikram Ranade, Ryan Loker, Roumen Voutev, Richard S Mann

Enhancer architecture sensitizes cell specific responses to Notch gene dose via a bind and discard mechanism
Yi Kuang, Ohad Golan, Kristina Preusse, Brittany Cain, Joseph Salomone, Ian Campbell, FearGod V. Okwubido-Williams, Matthew R. Hass, Natanel Eafergan, Kenneth H. Moberg, Rhett A. Kovall, Raphael Kopan, David Sprinzak, Brian Gebelein

The Impact of Genetic Background and Cell Lineage on the Level and Pattern of Position Effect Variegation
Sidney H. Wang, Sarah C.R. Elgin

Reduced function of the RNA export factor, Nxt1, in Drosophila causes muscle degeneration and lowers expression of genes with long introns and circular RNA
Kevin van der Graaf, Katia Jindrich, Robert Mitchell, Helen White-Cooper

Dynamics of activating and repressive histone modifications in Drosophila neural stem cell lineages and brain tumors
Merve Deniz Abdusselamoglu, Lisa Landskron, Sarah K. Bowman, Elif Eroglu, Thomas Burkard, Robert E. Kingston, Juergen A. Knoblich

| Stem cells, regeneration & disease modelling

Imp/IGF2BP levels modulate individual neural stem cell growth and division through myc mRNA stability
Tamsin J Samuels, Aino I Järvelin, David Ish-Horowicz, Ilan Davis

IRBIT Directs Differentiation of Intestinal Stem Cell Progeny to Maintain Tissue Homeostasis
Alexei Arnaoutov, Hangnoh Lee, Karen Plevock Haase, Vasilisa Aksenova, Michal Jarnik, Brian Oliver, Mihaela Serpe, Mary Dasso

Ureteric Bud Cells Programmed from Embryonic Stem Cells Obtain Competence for Secondary Induction in the Kidney
Zenglai Tan, Aleksandra Rak-Raszewska, Ilya Skovorodkin, Seppo J. Vainio

Release of stem cells from quiescence reveals multiple gliogenic domains in the adult brain
Ana C. Delgado, Angel R. Maldonado-Soto, Violeta Silva-Vargas, Dogukan Mizrak, Thomas von Känel, Alex Paul, Aviv Madar, Henar Cuervo, Jan Kitajewski, Chyuan-Sheng Lin, Fiona Doetsch

CHD8 regulates the balance between proliferation and differentiation of human iPSCs in neural development
Wenzhong Liu, Weilai Dong, Ellen J. Hoffman, Thomas V. Fernandez, Abha R. Gupta

Aging induces aberrant state transition kinetics in murine muscle stem cells
Jacob C. Kimmel, Ara B. Hwang, Wallace F. Marshall, Andrew S. Brack

Interactome comparison of human embryonic stem cell lines with the inner cell mass and trophectoderm
Adam Stevens, Helen Smith, Terence Garner, Ben Minogue, Sharon Sneddon, Lisa Shaw, Maria Keramari, Rachel Oldershaw, Nicola Bates, Daniel R Brison, Susan J Kimber

Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of mouse hematopoietic cells
Ross C. Hardison, Yu Zhang, Cheryl A. Keller, Guanjue Xiang, Elisabeth Heuston, Lin An, Jens Lichtenberg, Belinda M. Giardine, David Bodine, Shaun Mahony, Qunhua Li, Feng Yue, Mitchell J. Weiss, Gerd Blobel, James Taylor, Jim Hughes, Doug Higgs, Berthold Gottgens

An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis
Guanjue Xiang, Cheryl A. Keller, Elisabeth Heuston, Belinda M. Giardine, Lin An, Alexander Q. Wixom, Amber Miller, April Cockburn, Jens Lichtenberg, Berthold Göttgens, Qunhua Li, David Bodine, Shaun Mahony, James Taylor, Gerd A. Blobel, Mitchell J. Weiss, Yong Cheng, Feng Yue, Jim Hughes, Douglas R. Higgs, Yu Zhang, Ross C. Hardison

Single-cell tracing of the first hematopoietic stem cell generation in human embryos
Yang Zeng, Jian He, Zhijie Bai, Zongcheng Li, Yandong Gong, Chen Liu, Yanli Ni, Junjie Du, Chunyu Ma, Lihong Bian, Yu Lan, Bing Liu

Proliferative behavior of hematopoietic stem cells revisited: No evidence for mitotic memory
Mina N. F. Morcos, Thomas Zerjatke, Ingmar Glauche, Clara M. Munz, Yan Ge, Andreas Petzold, Susanne Reinhardt, Andreas Dahl, Natasha Anstee, Ruzhica Bogeska, Michael Milsom, Petter Säwén, Haixia Wan, David Bryder, Axel Roers, Alexander Gerbaulet

Function of Pumilio Genes in Human Embryonic Stem Cells and Their Effect in Stemness and Cardiomyogenesis
Isabelle Leticia Zaboroski Silva, Anny Waloski Robert, Guillermo Cabrera Cabo, Lucia Spangenberg, Marco Augusto Stimamiglio, Bruno Dallagiovanna, Daniela Fiori Gradia, Patrícia Shigunov

NCOR1 and OCT4 Facilitate Early Reprogramming by Co-Suppressing Fibroblast Gene Expression
Georgina Peñalosa-Ruiz, Klaas W. Mulder, Gert Jan C. Veenstra

Distinct features of nucleolus-associated domains in mouse embryonic stem cells
Aizhan Bizhanova, Aimin Yan, Jun Yu, Lihua Julie Zhu, Paul D. Kaufman

Map3k2-Regulated Intestinal Stromal Cells (MRISC) Define a Distinct Sub-cryptic Stem Cell Niche for Damage Induced Wnt Agonist R-spondin1 Production
Ningbo Wu, Hongxiang Sun, Xiaoyun Zhao, Lei Chen, Yuanyuan Qi, Yuheng Han, Xianan Liu, Caixia Gao, Qun Wang, Lingjuan He, Xiaoyin Niu, Zhiduo Liu, Hua-Bing Li, Yi Arial Zeng, Manolis Roulis, Dou Liu, Zhengfeng Yang, Bin Zhou, Richard A. Flavell, Bing Su

Short and long TNF-alpha exposure recapitulates canonical astrogliosis events in human induced pluripotent stem cells-derived astrocytes
Pablo Trindade, Erick Correia Loiola, Juciano Gasparotto, Camila Tiefensee Ribeiro, Pablo Leal Cardozo, Sylvie Devalle, José Alexandre Salerno, Isis Moraes Ornelas, Pitia Flores Ledur, Fabiola Mara Ribeiro, Ana Lucia Marques Ventura, José Claudio Fonseca Moreira, Daniel Pens Gelain, Lisiane Oliveira Porciúncula, Stevens Kastrup Rehen

Ephrin-B1 blocks adult cardiomyocyte proliferation and heart regeneration
Marie Cauquil, Céline Mias, Céline Guilbeau-Frugier, Clément Karsenty, Marie-Hélène Seguelas, Gaël Genet, Edith Renaud-Gabardos, Anne-Catherine Prats, Véronique Pons, Maxime Branchereau, Christophe Heymes, Denis Calise, Olivier Lairez, Danièle Daviaud, Benjamin Honton, Céline Frongia, Bernard Ducommun, Marie-Bernadette Delisle, Dina N. Arvanitis, Atul Pathak, Jean-Michel Sénard, Céline Galés

Regenerative neurogenesis is induced from glia by Ia-2 driven neuron-glia communication
Neale Harrison, Elizabeth Connolly, Alicia Gascón Gubieda, Zidan Yang, Benjamin Altenhein, Maria Losada-Perez, Marta Moreira, Alicia Hidalgo

ZIP-5/bZIP transcription factor regulation of folate metabolism is critical for aging axon regeneration
Vanisha Lakhina, Melanie McReynolds, Daniel T. Grimes, Joshua D. Rabinowitz, Rebecca D. Burdine, Coleen T. Murphy

Signaling gradients in surface dynamics as basis for planarian regeneration
Arnd Scheel, Angela Stevens, Christoph Tenbrock

TRiC activates the unfolded protein response and protects starved stem cells by modulating energy and lipid metabolism during planarian regeneration
Óscar Gutiérrez-Gutiérrez, Daniel A. Felix, Alessandra Salvetti, Anne Thems, Stefan Pietsch, Andreas Koeberle, K. Lenhard Rudolph, Cristina González-Estévez

Cellular heterogeneity and lineage restriction during mouse digit tip regeneration at single cell resolution
Gemma L. Johnson, Erick J. Masias, Jessica A. Lehoczky

Regeneration in the absence of a blastema requires cell division but is not tied to wound healing in the ctenophore Mnemiopsis leidyi
Julia Ramon-Mateu, Tori Ellison, Thomas E. Angelini, Mark Q. Martindale

Cellular reprogramming for successful CNS axon regeneration is driven by a temporally changing cast of transcription factors
Sumona P. Dhara, Andrea Rau, Michael J. Flister, Nicole M. Recka, Michael D. Laiosa, Paul L. Auer, Ava J. Udvadia

Transcriptional profiling of non-injured nociceptors after spinal cord injury reveals diverse molecular changes
Jessica R. Yasko, Isaac L. Moss, Richard E. Mains

Catecholaminergic axons in the neocortex of adult mice regrow following brain injury
Sarah E. Dougherty, Tymoteusz J. Kajstura, Yunju Jin, Michelle H. Chan-Cortés, Akhil Kota, David J. Linden

Myogenesis modelled by human pluripotent stem cells uncovers Duchenne muscular dystrophy phenotypes prior to skeletal muscle commitment
Virginie Mournetas, Emmanuelle Massouridès, Jean-Baptiste Dupont, Etienne Kornobis, Hélène Polvèche, Margot Jarrige, Maxime Gosselin, Spiros D. Garbis, Dariusz C. Górecki, Christian Pinset

Primary cilia deficiency in neural crest cells causes Anterior Segment Dysgenesis
Céline Portal, Peter Lwigale, Panteleimon Rompolas, Carlo Iomini

Hyperactive MEK1 signaling in cortical GABAergic interneurons causes embryonic parvalbumin-neuron death and deficits in behavioral inhibition
Michael C. Holter, Lauren T. Hewitt, Kenji J. Nishimura, George R. Bjorklund, Shiv Shah, Noah R. Fry, Katherina P. Rees, Tanya A. Gupta, Carter W. Daniels, Guohui Li, Steven Marsh, David M. Treiman, M. Foster Olive, Trent R. Anderson, Federico Sanabria, William D. Snider, Jason M. Newbern

Human cerebral organoids capture the spatiotemporal complexity and disease dynamics of UBE3A
Dilara Sen, Alexis Voulgaropoulos, Zuzana Drobna, Albert J. Keung

Modeling and treating GRIN2A developmental and epileptic encephalopathy in mice
Ariadna Amador, Christopher D. Bostick, Heather Olson, Jurrian Peters, Chad R. Camp, Daniel Krizay, Wenjuan Chen, Wei Han, Weiting Tang, Ayla Kanber, Sukhan Kim, Jia Jie Teoh, Sabrina Petri, Hunki Paek, Ana Kim, Cathleen M. Lutz, Mu Yang, Scott J. Myers, Subhrajit Bhattacharya, Hongjie Yuan, David B. Goldstein, Annapurna Poduri, Michael J. Boland, Stephen F. Traynelis, Wayne N. Frankel

scribble abrogation induces tumor growth through JNK-Wnt pathways depending on cellular-microenvironment in Drosophila wing imaginal tissue
Amarish Kumar Yadav, Roshan Fatima, Saripella Srikrishna

| Plant development

Dual function of HYPONASTIC LEAVES 1 during early skotomorphogenic growth in Arabidopsis
Juan Manuel Sacnun, Roberta Crespo, Javier Palatnik, Rodolfo Rasia, Nahuel González-Schain

PDK1 has a pleiotropic PINOID-independent role in Arabidopsis development
Yao Xiao, Remko Offringa

Auxin-induced nanoclustering of membrane signaling complexes underlies cell polarity establishment in Arabidopsis
Xue Pan, Linjing Fang, Jianfeng Liu, Betul Senay-Aras, Wenwei Lin, Shuan Zheng, Tong Zhang, Uri Manor, Weitao Chen, Zhenbiao Yang

Coordination of Tissue Cell Polarity by Auxin Transport and Signaling
Carla Verna, Sree Janani Ravichandran, Megan G. Sawchuk, Nguyen Manh Linh, Enrico Scarpella

Sugar availability suppresses the auxin-induced strigolactone pathway to promote bud outgrowth
Jessica Bertheloot, François Barbier, Frédéric Boudon, Maria Dolores Perez-Garcia, Thomas Péron, Sylvie Citerne, Elizabeth Dun, Christine Beveridge, Christophe Godin, Soulaiman Sakr

Trehalose 6-phosphate Controls Seed Filling by Inducing Auxin Biosynthesis
Tobias Meitzel, Ruslana Radchuk, Erin L. McAdam, Ina Thormählen, Regina Feil, Eberhard Munz, Alexander Hilo, Peter Geigenberger, John J. Ross, John E. Lunn, Ljudmilla Borisjuk

Arabidopsis ERF109 regulates auxin transport-related genes in root development
Rui Liu, Xiao-Teng Cai, Ping-Xia Zhao, Ping Xu, Cheng-Bin Xiang

Autophagy mediates temporary reprogramming and dedifferentiation in plant somatic cells
Eleazar Rodriguez, Jonathan Chevalier, Jakob Olsen, Jeppe Ansbøl, Vaitsa Kapousidou, Zhangli Zuo, Steingrim Svenning, Christian Loefke, Stefanie Koemeda, Pedro Serrano Drozdowskyj, Jakub Jez, Gerhard Durnberger, Fabian Kuenzl, Michael Schutzbier, Karl Mechtler, Signe Lolle, Yasin Dagdas, Morten Petersen

Integrated Multi-omic Framework of the Plant Response to Jasmonic Acid
Mark Zander, Mathew G. Lewsey, Natalie M. Clark, Lingling Yin, Anna Bartlett, J. Paola Saldierna Guzmán, Elizabeth Hann, Amber E. Langford, Bruce Jow, Aaron Wise, Joseph R. Nery, Huaming Chen, Ziv Bar-Joseph, Justin W. Walley, Roberto Solano, Joseph R. Ecker

Cut and paste – Efficient cotyledon micrografting for Arabidopsis thaliana seedlings
Kai Bartusch, Jana Trenner, Marcel Quint

Identification of nitrogen-dependent QTL and underlying genes for root system architecture in hexaploid wheat
Marcus Griffiths, Jonathan A. Atkinson, Laura-Jayne Gardiner, Ranjan Swarup, Michael P. Pound, Michael H. Wilson, Malcolm J. Bennett, Darren M. Wells

The maize Hairy Sheath Frayed1 (Hsf1) mutant alters leaf patterning through increased cytokinin signaling
Michael G. Muszynski, Lindsay Moss-Taylor, Sivanandan Chudalayandi, James Cahill, Angel R. Del Valle-Echevarria, Ignacio Alvarez, Abby Petefish, Nobue Makita, Hitoshi Sakakibara, Dmitry M. Krivosheev, Sergey N. Lomin, Georgy A. Romanov, Subbiah Thamotharan, Thao Dam, Bailin Li, Norbert Brugière

Natural genetic variation underlying tiller development in barley (Hordeum vulgare L)
Allison M. Haaning, Kevin P. Smith, Gina L. Brown-Guedira, Shiaoman Chao, Priyanka Tyagi, Gary J. Muehlbauer

NbCycB2 represses Nbwo activity via a negative feedback loop in the tobacco trichome developmemt
Minliang Wu, Yuchao Cui, Li Ge, Lipeng Cui, Zhichao Xu, Hongying Zhang, Zhaojun Wang, Dan Zhou, Shuang Wu, Liang Chen, Hong Cui

Genome-wide analysis of GATA factors in moso bamboo (Phyllostachys edulis) unveils that PeGATAs regulate shoot rapid-growth and rhizome development
Taotao Wang, Yong Yang, Shuaitong Lou, Wei Wei, Zhixin Zhao, Chentao Lin, Liuyin Ma

Temperature dependent sex-biased gene expression in the gametophytes of the kelp Saccharina latissima
Cátia Monteiro, Sandra Heinrich, Inka Bartsch, Klaus Ulrich Valentin, Erwan Corre, Jonas Collén, Lars Harms, Gernot Glöckner, Kai Bischof

Developing a rapid and highly efficient cowpea regeneration and transformation system using embryonic axis explants
Ping Che, Shujun Chang, Marissa K. Simon, Zhifen Zhang, Ahmed Shaharyar, Jesse Ourada, Dennis O’Neill, Mijael Torres-Mendoza, Yinping Guo, Kathleen M. Marasigan, Jean-Philippe Vielle-Calzada, Peggy Ozias-Akins, Marc C. Albertsen, Todd J. Jones

Evo-devo & evo

Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion
Aditya Saxena, Virag Sharma, Mai P Tran, Haydee L Gutierrez, Joel M Erberich, Amanda Birmingham, Michael Hiller, Kimberly L Cooper

Mosaic heterochrony in neural progenitors sustains accelerated brain growth and neurogenesis in the juvenile killifish N. furzeri
Marion Coolen, Miriam Labusch, Abdelkrim Mannioui, Beate Hoppe, Mario Baumgart, Laure Bally-Cuif

Characterization of neurogenic niches in the telencephalon of juvenile and adult sharks
A Docampo-Seara, S Pereira-Guldrís, N Sánchez-Farías, S Mazan, MA Rodríguez, E Candal

Evolved differences in cis and trans regulation between the maternal and zygotic mRNA complements in the Drosophila embryo
Emily L. Cartwright, Susan E. Lott

PIWI-piRNA pathway-mediated transposable element repression in Hydra somatic stem cells
Bryan B. Teefy, Stefan Siebert, Jack F. Cazet, Haifan Lin, Celina E. Juliano

Chytrid rhizoid morphogenesis is adaptive and resembles hyphal development in ‘higher’ fungi
Davis Laundon, Nathan Chrismas, Glen Wheeler, Michael Cunliffe

Laboratory biases hinder Eco-Evo-Devo integration: hints from the microworld
Natsuko Rivera-Yoshida, Alejandra Hernandez-Teran, Ana E. Escalante, Mariana Benitez

The crustacean Armadillidium vulgare, a new promising model for the study of cellular senescence
Charlotte Depeux, Ascel Samba-Louaka, Thomas Becking, Christine Braquart-Varnier, Jérôme Moreau, Jean-François Lemaître, Tiffany Laverre, Hélène Paulhac, François-Xavier Dechaume-Moncharmont, Jean-Michel Gaillard, Sophie Beltran-Bech

Mutation accumulation in chromosomal inversions maintains wing pattern polymorphism in a butterfly
Paul Jay, Mathieu Chouteau, Annabel Whibley, Héloïse Bastide, Violaine Llaurens, Hugues Parrinello, Mathieu Joron

A chronology of multicellularity evolution in cyanobacteria
Katrin Hammerschmidt, Giddy Landan, Fernando Domingues Kümmel Tria, Tal Dagan

Evolution of imprinting via lineage-specific insertion of retroviral promoters
Aaron B. Bogutz, Julie Brind’Amour, Hisato Kobayashi, Kristoffer N. Jensen, Kazuhiko Nakabayashi, Hiroo Imai, Matthew C. Lorincz, Louis Lefebvre

Cell biology

Isolation of an archaeon at the prokaryote-eukaryote interface
Hiroyuki Imachi, Masaru K. Nobu, Nozomi Nakahara, Yuki Morono, Miyuki Ogawara, Yoshihiro Takaki, Yoshinori Takano, Katsuyuki Uematsu, Tetsuro Ikuta, Motoo Ito, Yohei Matsui, Masayuki Miyazaki, Kazuyoshi Murata, Yumi Saito, Sanae Sakai, Chihong Song, Eiji Tasumi, Yuko Yamanaka, Takashi Yamaguchi, Yoichi Kamagata, Hideyuki Tamaki, Ken Takai

Extraction of active RhoGTPases by RhoGDI regulates spatiotemporal patterning of RhoGTPases
Adriana Golding, Ilaria Visco, Peter Bieling, William Bement

Transient primary cilia mediate robust Hedgehog pathway-dependent cell cycle control
Emily K. Ho, Anaïs E. Tsai, Tim Stearns

Recruitment of mRNAs to P granules by gelation with intrinsically-disordered proteins
Chih-Yung S. Lee, Andrea Putnam, Tu Lu, Shuaixin He, John Paul T. Ouyang, Geraldine Seydoux

Chemotaxis and topotaxis add vectorially for amoeboid cell migration
Joeri A. J. Wondergem, Maria Mytiliniou, Falko C. H. de Wit, Thom G. A. Reuvers, David Holcman, Doris Heinrich

In vivo characterisation of endogenous cardiovascular extracellular vesicles in larval and adult zebrafish
Aaron Scott, Lorena Sueiro Ballesteros, Marston Bradshaw, Ann Power, John Love, Danielle Paul, Andrew Herman, Costanza Emanueli, Rebecca J. Richardson

Cep97 Is Required For Centriole Structural Integrity And Cilia Formation In Drosophila
Jeroen Dobbelaere, Marketa Schmidt-Cernohorska, Martina Huranova, Dea Slade, Alexander Dammermann

A G1 sizer mechanism coordinates growth and division in the mouse epidermis
Shicong Xie, Jan M Skotheim

Traction forces control cell-edge dynamics and mediate distance-sensitivity during cell polarization
Zeno Messi, Alicia Bornert, Franck Raynaud, Alexander Verkhovsky

Cell culture dimensionality influences mesenchymal stem cell fate through cadherin-2 and cadherin-11
Fiona R Passanha, Thomas Geuens, Simon Konig, Clemens A van Blitterswijk, Vanessa LS LaPointe

Intra-Nuclear Tensile Strain Mediates Reorganization of Epigenetically Marked Chromatin During Cardiac Development and Disease
Benjamin Seelbinder, Soham Ghosh, Alycia G. Berman, Stephanie E. Schneider, Craig J. Goergen, Sarah Calve, Corey P. Neu

The CHORD protein CHP-1 regulates EGF receptor trafficking and signaling in C. elegans and in human cells
Andrea Haag, Michael Walser, Adrian Henggeler, Alex Hajnal

LINC complexes are mechanotransducers that discriminate Epithelial-Mesenchymal Transition programs
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The importance of barrier-free use of colors in images and graphs has been highlighted in letters to editors (Miall, 2007), papers (Geissbuehler and Lasser, 2013, Levine, 2009), editorials (anonymous, 2007), columns (Wong, 2011) and on numerous web pages. One of the recommendations is to use a color blindness simulator. Having a color vision deficiency myself, I cannot judge whether these tools work well. Nevertheless, a trial-and-error based approach seems rather inefficient. Instead, the use of (a number of) default color blind friendly palettes would be much more straightforward. For instance, green and magenta colors are the default choice for the production of color blind friendly overlays of fluorescence images. Below, I discuss a number of color palettes that are suitable for coloring graphical elements in plots. I think that people with a color vision deficiency would benefit from the implementation of these palettes in software for data visualization.

Qualitative color schemes

A quantitative color scheme is used when numbers need to be represented by colors. This conversion is done with a Look-Up Table (LUT). For more information on (colorblind-friendly) LUTs see this blog and this paper. Here, I talk about qualitative color schemes, which use colors to label different categories. The number of distinct categories define the number of unique colors that are needed. Ideally, these color can be distinguished by everybody.

For up to four categories, it is rather straightforward to come up with a set of colors that are easy to distinguish. Still, it does make sense to choose the colors from a color blind friendly color scheme. When 5-8 colors are needed to uniquely label different categories, it is a considerable challenge to find a suitable color palette. Beyond 8, it is close to impossible to find colors that can be readily distinguished. In these cases, alternative labeling methods are recommended. Below, several color blind friendly qualitative color schemes are described and four of those are shown in figure 1.

Color blind friendly palettes

Masataka Okabe and Kei Ito have proposed a palette of 8 colors on their website Color Universal Design (CUD). This palette is a “Set of colors that is unambiguous both to colorblinds and non-colorblinds”. The use of this palette is supported by others (Wong, 2011; Levine, 2009) and it is the default scale for the book “Fundamentals of Data Visualization” by Claus Wilke.

Martin Krzywinski has a website with 12- and 15-color palettes that offer more choices. Personally, I have difficulty with distinguishing several of these colors. Also, it is recommended to use no more than 8 different colors. Therefore, these palettes will not be taken along.

Paul Tol has created several qualitative color schemes that are color blind friendly. These palettes have 5-10 colors (including grey) and vary in darkness.

Figure 1: An overview of qualitative, color blind friendly palettes. The figure was produced with an R-script that defines and plots the palettes (doi: 10.5281/zenodo.3381072).

Choosing a color scheme

Which of the palettes is the best? This is hard to say for several reasons. Colors look different when printed, shown on a screen, or projected with a beamer. Next to this, size, structure and position of the objects will determine whether the categories can be distinguished. As a consequence, it is probably impossible to come up with a single universal color palette. I think that the palette designed by Okabe&Ito is a good first choice. Still, it is a good idea to see how different palettes perform when they are used in realistic data visualizations. As an example, figure 2 shows four plots in which the different color blind friendly palettes are used to label 6 lines.

Figure 2: The color palettes shown in figure 1 are used to uniquely label 6 different lines in a realistic data visualization. The graphs are with made with PlotTwist.

The palettes shown in figure 1 are implemented in the webtool PlotTwist (Goedhart, 2019). PlotTwist is a freely available online tool for plotting and annotating time-series data. It enables anyone to experiment with the color blind friendly palettes and apply them to lineplots. I encourage you to share your opinion on these (or any other) palettes and how they perform (especially if you have a color vision deficiency). To do so, you may leave a reply below or share your thoughts on twitter. Ultimately, I hope to see more data visualizations that pass a color blindness test with flying colors.

Recommendations

I will end with some recommendations aimed at improving graphs that use color:

-Use a color blind friendly palette by default.

-Use thick lines or large symbols to make it easier to correctly identify and map the color to a legend.

-In addition to colors, consider the use of patterns or labels to distinguish between categories.

-Use a maximum of 8 different colors for the labeling of different categories.

-Use a legend that shows the colors, instead of referring to the colors by their name.

-Keep the legend that explains the mapping of the colors close to the actual data.

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