“It finally got accepted!”, fol­­lowed by “It’s finally out!” about a month later. I am certain this ‘finally’ feeling about their paper is very familiar to those well-acquainted with the peer review process, and it was no different for our recently published Resource article. The ‘biotagging paper’, as we call it within the Sauka-Spengler lab, is the culmination of several years’ of hard (and often frustrating) work that eventually paid off in more (unexpected) ways than one. Tatjana spearheaded the initial work for biotagging while still at Caltech, by transferring components and approaches she developed in the chicken system into the zebrafish. She worked together with Le and Tatiana, then postdoctoral fellows at Caltech, before the rest of us joined in for the lengthy optimisation, submission and review stage.

Part I: What is “biotagging”?

Biotagging is essentially an encompassing term for our Do-It-Yourself (DIY) in vivo biotinylation system for zebrafish researchers, which can be utilised in creative ways to suit specific biological needs. In vivo biotinylation was first employed in mouse (de Boer et al., 2003) by John Strouboulis when he was in Frank Grosveld’s lab and then applied for use in nuclei isolation from Arabidopsis thaliana by Roger Deal and Steven Henikoff (Deal and Henikoff, 2010). The technique was also applied to the nematode worm at around the same time (Ooi et al. 2009). The core of the technique lies in the ability of bacterial biotin ligase (BirA) to biotinylate an Avi-tagged protein-of-interest. In our binary biotagging system, the researcher decides where BirA will be expressed, which protein is Avi-tagged, and then generates transgenic lines that express these components. Crossing BirA-driver and Avi-effector heterozygous lines will give rise to ~25% of double-alleled offspring, where biotinylation of the Avi-tagged protein product only occurs in cells that also express BirA. The sky is the limit when it comes to the combinations of BirA/Avi that one can use. In the paper, we present a ‘starter’ toolkit consisting of multiple tissue-(neural crest, heart, blood) and cellular compartment-specific (ribosomes, nuclei) transgenic lines, as well as constructs to make your own lines.

Part II: Trials and Tribulations

The deconstruction (and reconstruction) of biotagging

The elegance of in vivo biotinylation means that we are not the only group to perform this method in vertebrates. For example, Michael Housley from Stainier lab (Housley et al. 2014) utilised in vivo biotinylation in zebrafish to apply the TRAP (Translating Ribosome Affinity Purification) method developed by Myriam Heiman and colleagues (Heiman et al., 2008). In vivo biotinylation experiments are not ‘difficult’ per se, but we found that obtaining a clear difference between nuclear and polyribosomal data required a remarkable amount of troubleshooting and optimisation. Our patience paid off, as this was rewarded by a wealth of information provided by a high resolution view into the migratory neural crest nascent (nuclear) and polyribosomal transcriptomes from ~200k cells.

In fact, the entire optimisation process came about by accident. In the paper, we described our surprising results when comparing the nuclear transcriptome of Sox10-positive cells at 16-18ss (migratory neural crest) to a ubiquitous control. By looking at both non-poly and polyadenylated transcripts (whole nuclear transcriptomes), our data did not yield any statistically significant neural crest-specific signature, which is what one would expect, as the enriched transcripts should be neural crest-specific. On the other hand, analysis of polyadenylated nuclear transcripts at 24hpf yielded a neural crest-specific signature. This led to further pain-staking deconstruction of our technique where, months later, we eventually came to the surprisingly simple but crucial element for the protocol to be as consistent as it is today – ensuring the complete lysis of cells (by using hypotonic buffer in excess) to release subcellular compartments into the lysate and minimise the presence of intact cell surface membranes. It is also worth noting, that a key element to the success of our protocol was the usage of an Avi-tagged chicken nuclear envelope protein, RanGAP, to label nuclei. Weirdly enough, chicken RanGAP expressed in zebrafish localised to the nuclei, but zebrafish RanGAP did not.

Having reconstructed the method, we were now eager to repeat the previous 16-18ss neural crest experiment. Imagine our initial dismay when the results were…strikingly similar. However, this was soon replaced by curiosity that drove us to carefully re-examine our results and try to figure out what IS actually going on…

Biotagging of migratory neural crest nuclei transcriptome reveals…what?

The brainstorming sessions were remarkably memorable. They were always long, often ‘lively’ as we picked at each other’s brains, and at times quite outrageous as frustrations ran high. It didn’t take us very long to notice that bidirectional transcription at non-coding regions was enriched in neural crest nuclei. However, it was a long journey after that, as we tried to quantify the phenomenon genome-wide, reproduce what we saw, believe in what we saw, and build our findings into a coherent story. Ultimately, we needed to drive home our main message – that bidirectional transcription at non-coding regions is tissue-specific, thus introducing a new method to detect active regulatory elements. These elements form the molecular signature of neural crest cells, which is traditionally based on the expression of protein-coding genes that are mainly transcription factors. We were also excited to find developmentally regulated long non-coding RNAs and transposable elements.

In short, we are proud of what we have managed to achieve with biotagging. The journey may have been long and arduous, but we have learned a lot from this project.  We hope that we have provided a cool new system that includes a fully optimised tool (plasmids on Addgene) with clean protocols (available on the Resources page of our lab website), handy transgenic lines to get started with, as well as analysis pipelines tailored to biotagging datasets. Having worked out the technical intricacies of this system, this toolkit allows the zebrafish community (including us!) to study specific cellular populations in vivo on the systems level, tackling biological questions that could be important to development and disease.

Le A. Trinh, Vanessa Chong-Morrison, Daria Gavriouchkina, Tatiana Hochgreb-Hägele, Upeka Senanayake, Scott E. Fraser, Tatjana Sauka-Spengler. 2017. Biotagging of Specific Cell Populations in Zebrafish Reveals Gene Regulatory Logic Encoded in the Nuclear Transcriptome. Cell Reports Volume 19, Issue 2, p425–440

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NEUBIAS, the Network of European
BioImage Analysts (www.neubias.org), is delighted to announce two new Training Schools on BioImage Analysis:

• Early Career Investigators (life scientists)
• Facility staff (imaging & analysis staff)

The focus of training will be on construction and automation of image analysis workflows, using as examples more than one toolbox and different exercises. The schools will be held in Gothenburg 11-14th of September 2017, hosted by the Centre for Cellular Imaging – Sahlgrenska Academy, University of Gothenburg, Sweden.

NEUBIAS schools are an excellent opportunity to learn from many experts in bioimage analysis (we are expecting ~40 specialists at the event) and  “….a great mix of intensive learning and community networking” (former trainee testimonial!).

• applications for Gothenburg are now open (each school has 25 available seats and 10-12 trainers).
• Within the COST framework, a few travel grants are offered to applicants who qualify.
• Registration deadline: 26th of May, 2017 (must submit also “letter of motivation”).
• Selection notification: 1st week of June 2017.

More information about schools (programme & trainers) and venue, travel & lodge available at our website (linked above).

On behalf of all NEUBIAS members,
Julien Colombelli, Chair; Kota Miura, Vice-Chair
Julia Fernandez-Rodriguez, Local organizer

Carolina Wählby, Jan Eglinger, Joakim Lindblad & Nuno P Martins, TS4&5 programme organizers

Gaby G Martins & Fabrice Cordelières, WG2-Training leaders

Perrine Paul-Gilloteaux, WG4-Webtool leader
Sébastien Tosi, WG5-Benchmarking & Sample Datasets leader

NEUBIAS is an European network of currently ~180 members and 35 countries, which aims to promote the communication between Life Scientists, Instrumentalists, Developers and BioImage Analysts and to establish and promote the role of Bioimage Analysts in Life Science. Our mission includes:

• A training programme for 3 different target audiences:Early Career researcher, Facility Staff, Analyst (running until 2020 – expected 400 trainees and 15 training schools).
• Promote different yearly events (NEUNIAS2020 Conference, workshops [training schools], Taggathons)
• Online Resources: Repository of tools and workflows, Benchmarking and Sample datasets, Training material and Open Textbook.
• A Short Term Scientific Mission mobility programme for Scientists to visit Host Labs and get in depth insights into cutting edge Image Analysis technology.
• Outreach material.
  

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Our 20th instalment of this series comes from South Korea and features an investigation into the molecular basis of how temperature influences developmental transitions in Arabidopsis seedlings, recently published in Developmental Cell. We caught up with joint first authors Jun-Ho Ha and Hyo-Jun Lee, and their supervisor Chung-Mo Park, Professor in the Department of Chemistry, Seoul National University (SNU), to hear the story of the paper.

Chung-Mo, can you give us your scientific biography – I understand you spent some years in the US before returning to South Korea?

CMP I am currently professor in the Department of Chemistry at SNU. I earned my Bachelor of Science in the Department of Science Education from Seoul National University in 1983 and my PhD in molecular virology from State University of New York at Buffalo in 1993 under the supervision of professor Jeremy Bruenn. The topic of my thesis work was identification of killer toxin genes in a double-stranded virus endogenously residing in Ustilago maydis, a corn smut fungus and functional and structural characterization of the killer toxin proteins. After completing my PhD, I worked as a postdoctoral researcher in the same university and the Hauptman-Woodward Medical Research Institute, Buffalo, until I joined the Kumho Life & Environmental Science Laboratory, Korea, as PI in 1996. In the Kumho Laboratory, I worked on the photochemical and photobiological characterization of phytochrome photoreceptors in higher plants and the cyanobacteria Synechocystis PCC6803 and their associated light signal transduction in photomorphogenic responses.

In 2002, I accepted an associate professor position in the Department of Chemistry, SNU, where I have been since that time. While at SNU, my research team has been working on diverse aspects of plant growth and developmental processes, such as seed germination, phase transition and flowering induction, and leaf senescence. I have also been working on plant responses to environmental stresses with emphasis on temperature extremes and drought stresses. In recent years, my research is focused on plant adaptation to high but nonstressful temperatures (warm temperatures) with emphasis on leaf hyponasty, heat dissipation from leaves, and autotrophic development.

And what is South Korea like as a place to do science?

CMP The Korean government and several biotech companies have been investing a huge amount of research fund during the last 30 years. While industrial research and development has been a priority as a potential driving force of economic growth, the Korean government is also spending heavily on basic research. In plant science, there is a national research supporting program, termed New-Generation Biogreen 21, which is organized and supported by the Korean Rural Development Administration.  The Program supports various research on both model plants and crops. It is considered that although not sufficient, enthusiastic plant scientists are able to get enough research funds to perform both basic and applied researches in recent years.

Jun-Ho and Hyo-Jun – how did you come to join Chung-Mo’s lab?

JHH I earned my Bachelor of Science in chemistry. I was also interested in molecular biology with an expectation that combining chemical and biological principles would be exciting in understanding life. While I was looking for an appropriate lab for my graduate study, I met Chung-Mo Park, who is my current thesis advisor. I was greatly impressed by his passion for science and research. It was also impressive that his group is working on plant molecular biology in the Department of Chemistry. I therefore decided to join his laboratory for my graduate study.

HJL Since I was a high school student, I planned to be a scientist with an aim of discovering unknown principles of nature and living organisms. After I entered the Department of Chemistry, Seoul National University, as an undergraduate student, I searched for potential labs in the Department appropriate for my research carrier. I realized that Chung-Mo’ lab is unique among the laboratories in that he is studying plant molecular biology and biochemistry. I thought that understanding molecular biological and biochemical mechanisms underlying plant performance would be helpful for me to find ways to sustain the Earth’s ecosystem. In particular, as a chemist, I thought that applying chemical tools to understanding biological systems would be interesting. I therefore decided to perform my graduate study in his lab.

Before your work, what was known about how plants respond to temperature changes during autotrophic development, and what was the key question you set out to answer?

CMP, JHH & HJL It is well known that extreme temperatures significantly affect plant performance, including autotrophic development. In addition, associated molecular events and signaling schemes are fairly well understood. In nature, the soil temperature is rapidly elevated under warm temperature conditions. Therefore, developing seedlings should cope with high temperatures while they pass through the heat-absorbing soil layer to obtain photosynthetic capacity required for autotrophic growth. However, it is almost unknown how the heat-labile shoot apical meristem tissues of developing seedlings handle the temperature constraints. It has recently been reported that warm temperatures, in a temperature range of 23 – 28^oC in Arabidopsis, accelerate cell elongation during early seedling development. Thus, we were curious about whether and how warm temperatures influence chlorophyll biosynthesis during autotrophic development.

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

CMP, JHH & HJL We demonstrated that developing seedlings are capable of maintaining chlorophyll biosynthesis required for autotrophic development at warm temperature conditions. A group of photooxidoreductase (POR) enzymes is responsible for chlorophyll biosynthesis. Notably, they are susceptible to warm temperatures and thus rapidly inactivated in developing seedlings while they pass through the warm soil layer. We found that an RNA-binding protein FCA maintains the abundance of POR enzymes at warm temperatures in developing seedlings. Without FCA, plants fail to maintain the enzyme abundance, resulting in loss of chlorophyll and thus failure to achieve autotrophic growth. Our work provide a molecular basis for the acquisition of autotrophic growth under fluctuating temperature conditions in plants.

How do have any idea of what is upstream of FCA? How does it sense temperature changes?

CMP, JHH & HJL Our recent findings strongly support that the typical RNA-binding protein FCA plays a critical role through epigenetic control of target genes during high temperature responses and thermomorphogenesis in Arabidopsis. Our data also indicate that FCA sustains the thermos-stable expression of POR enzymes during autotrophic development at warm temperatures. Altogether, these observations suggest that FCA function is thermos-regulated. However, it is current unclear how FCA is activated by ambient temperatures. We found that gene transcription and protein stability of FCA are not altered by temperature changes. Its subcellular localization is also unaltered under fluctuating temperature conditions.

Our preliminary data suggest that warm temperatures activates FCA through post-translational modifications, such as protein phosphorylation. We are currently under way to examine if FCA is differentially phosphorylated or chemically modified in response to temperature changes by employing global-scale proteomics.

Do you think your work will have relevance to agriculture in a warming world?

CMP, JHH & HJL Global warming depicts the gradual elevation of the average temperature of the Earth’s climate system. It is widely documented that under high ambient temperature conditions, plants exhibit distinct morphological and developmental traits, such as accelerated hypocotyl growth, leaf hyponasty, reduction of stomatal density, and early flowering, which profoundly influence crop productivity and commercial values. Our findings on plant thermal responses are closely associated with global warming. We propose that the FCA-mediated thermal adaptation of autotrophic development allows developing seedlings to cope with the heat-absorbing soil surface layer under natural conditions. In particular, we found that a single gene mutation causes a total loss of chlorophyll biosynthesis and autotrophic development at warm temperatures, providing a way of enhancing plant adaptation to thermal fluctuations in crop agriculture.

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

HJL & JHH In the initial stage of the research, we germinated and grew the FCA-defective mutants at normal temperatures for 3 days before transferred to warm temperatures to see if the fca mutations affect seedling growth. However, we did not observe any phenotypic differences in seedling growth and greening patterns in the mutants. A few months later, we anticipated that the fca mutations might affect the earlier stages of seedling growth. To examine the hypothesis, we germinated and grew the mutant seedlings at 28^oC. We were surprised at the albino phenotype of the mutants. This observation triggered the re-examination of the thermal phenotypes of the fca mutants, resulting in the completion of this paper.

At first, we could not figure out why the fca mutants exhibited albinism only when germinated and grown at warm temperatures. As a potential cause of the albino phenotype, we considered several possibilities, such as defects in chloroplast development, chlorophyll biosynthesis, or both. It was found that the expression of POR genes was disrupted in the fca mutants when grown at warm temperatures. Accordingly, the level of chlorophylls was extremely low in the mutants, showing that the thermo-sensitive albino phenotype of the mutants is caused primarily by defects in chlorophyll biosynthesis, consistent with the FCA-mediated stabilization of POR production.

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

HJL & JHH The FCA-defective mutants are well-known late flowering mutants. A set of transgenic fca plants expressing POR genes were required for this study. It needs a lot of time to generate the transgenic plants because it takes 3-4 months to obtain seeds from the transgenic plants. While we were generating transgenic plants, we realized that a wrong expression construct was accidentally used, spending at least 5 additional months to obtain correct transgenic plants.

We also remember the frustrating moment when temperature controllers in the culture room were out of order during last summer, when we experienced a rarely high temperature and thus unstable supply of electricity in Korea. We had to grow a full set of plants again after a period time for fixing the temperature controllers.

What are your career plans following this work?

HJL I am currently a postdoc in Chung-Mo Park’s lab. I will continue studying for a while on molecular and physiological mechanisms underlying plant thermomorphogenesis. I am interested in the as-yet unidentified regulator of POR abundance at warm temperatures. After finishing the experiments, I am planning to find an appropriate postdoc position to extend my research career in environmental control of plant proteomics.

JHH I hope to be able to finish my thesis study in a couple of years, after which I am planning to find postdoc positions in Korea or in USA to extend my research career in the field.

And what next for the Park lab?

CMP We have a well-organized research system with a variety of molecular and biochemical tools, personnel, and facilities. We are specialized in gene regulatory mechanisms with emphasis on induction and activation mechanisms of transcription factors. Using these research tools and system, we will further extend our researches on plant thermomorphogenesis, which is emerging as a hot issue in the field because of the growing concern about global warming. In particular, we are focused on the functional linkage between photomorphogenic responses and growth hormones. We are also preparing a long-term project for engineering crop plants to enhance their adaptation capacity to changing temperature environment.

Jun-Ho Ha, Hyo-Jun Lee, Jae-Hoon Jung and Chung-Mo Park. 2017. Thermo-Induced Maintenance of Photo-oxidoreductases Underlies Plant Autotrophic Development. Developmental Cell 41(2): 170-179.

Browse the People behind the Papers archive here

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Location:          The Francis Crick Institute, Midland Road, London

Contract:          Fixed-term (3 years), Full time

Salary:             Competitive with benefits, subject to skills and experience

Vacancy ID:      5003

SHORT INTRODUCTION/SUMMARY

We seek a talented and motivated postdoc to join a Research Group led by Victor Tybulewicz at the Francis Crick Institute. The Group currently consists of 12 scientists, including 6 postdocs and 4 PhD students. One of the two main research interests of the Group is the study of the genetics underlying Down Syndrome. The Group has previously generated a series of mouse models of Down Syndrome that can be used to map the location of dosage-sensitive genes that cause Down Syndrome phenotypes (Lana-Elola et al, eLife 2016).

PROJECT SCOPE/ DESCRIPTION

The postdoc will study the genetics and developmental biology underlying congenital heart defects in Down Syndrome. The overall aim is to understand how increased dosage of genes on human chromosome 21 leads to heart defects. Specifically, the project aims to identify the dosage-sensitive genes that cause heart defects when present in three copies and to elucidate the mechanism by which the genes cause pathology. The work will involve use of genetic, developmental biology and biochemical techniques including microscopy, image analysis, and RNAseq, and will be supported by the excellent core facilities of the Institute. The work is funded by the Wellcome Trust.

The Francis Crick Institute is a biomedical discovery institute dedicated to understanding the fundamental biology underlying health and disease. Its work is helping to understand why disease develops and to translate discoveries into new ways to prevent, diagnose and treat illnesses such as cancer, heart disease, stroke, infections, and neurodegenerative diseases.

An independent organisation, its founding partners are the Medical Research Council (MRC), Cancer Research UK, Wellcome, UCL (University College London), Imperial College London and King’s College London.

The Crick was formed in 2015, and in 2016 it moved into a brand new state-of-the-art building in central London which brings together 1500 scientists and support staff working collaboratively across disciplines, making it the biggest biomedical research facility under a single roof in Europe.

The Francis Crick Institute will be world-class with a strong national role. Its distinctive vision for excellence includes commitments to collaboration; to developing emerging talent and exporting it the rest of the UK; to public engagement; and to helping turn discoveries into treatments as quickly as possible to improve lives and strengthen the economy.

If you are interested in applying for this role, please apply via our website https://goo.gl/IaFC2r

The closing date for applications is 10 June at 23:30 pm.

Please note: all offers of employment are subject to successful security screening and continuous eligibility to work in the United Kingdom.

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We are pleased to announce the Center for Dental, Oral, Craniofacial Tissue and Organ Regeneration (C-DOCTOR – www.c-doctor.org) RFP that will award funding to promising dental, oral and craniofacial tissue engineering and regenerative medicine technologies and help them advance toward human clinical trials through customized product development advice and core resources. Please see the full RFP below the cut or here for details – deadline June 9, 2017. We ask that you kindly distribute this RFP widely to investigators who may be interested.

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Our latest monthly trawl for developmental biology (and other cool) preprints. See June’s introductory post for background, and let us know if we missed anything

At the end of April, life science preprinting received a boost with the news that the Chan Zuckerberg Initiative will provide funding for the main preprint server, bioRxiv, which had the week before celebrated hosting its 10,000th article.

bioRxiv just passed 10,000 papers! :-)
Huge thanks to all involved https://t.co/xfNeiSBk3v pic.twitter.com/BQhIohafNX

— Richard Sever (@cshperspectives) April 21, 2017

And a good month for bioRxiv was also a good month for developmental biology (and related) preprints. This month we found 115 preprints covering coral regeneration, spider development, a root-on-a-chip, a lot of discussion about publishing in our ‘Research Practise’ section, and a range of stem cell and cell biology, hosted on bioRxiv, F1000Research, PeerJ  and arXiv.

Use these links to get to the section you want –

Developmental biology

| Patterning & signalling

| Morphogenesis & mechanics

| Genes & genomes

| Stem cells, regeneration & disease modelling

Cell biology

Modelling

Evo-devo & evo

Tools & resources

Research practice

Why not…

Developmental biology

| Patterning & signalling

An Embryonic System To Assess Wnt Transcriptional Targets. Jahnavi Suresh, Nathan Harmston, Ka Keat Lim, Prameet Kaur, Helen Jingshu Jin, Jay B. Lusk, Enrico Petretto, Nicholas S. Tolwinski

C. elegans Flavin Monooxygenases Regulate C. elegans Axon Guidance and Growth Cone Protrusion with UNC-6/Netrin signaling and Rac GTPases. Mahekta R. Gujar, Aubrie M. Stricker, Erik A. Lundquist

TGF(beta) Mediated Structural Remodeling Facilitates Optic Fissure Fusion And The Necessity Of BMP Antagonism In This Process. Max D. Knickmeyer, Juan L. Mateo, Priska Eckert, Eleni Roussa, Belal Rahhal, Aimee Zuniga, Kerstin Krieglstein, Joachim Wittbrodt, Stephan Heermann

Alternative cleavage of a bone morphogenetic protein (BMP) produces ligands with distinct developmental functions and receptor preference. Edward N Anderson, Kristi A Wharton

MCAM controls cell autonomous polarity in myogenic and chondrogenic differentiation. Artal Moreno-Fortuny, Laricia Bragg, Giulio Cossu, Urmas Roostalu

The Calcineurin-FoxO-MuRF1 Signaling Pathway Regulates Myofibril Integrity in Cardiomyocytes. Jau-Nian Chen, Hirohito Shimizu, Adam D Langenbacher, Jie Huang, Kevin Wang, Georg Otto, Robert Geisler, Yibin Wang

Secretogranin-II Plays A Critical Role In Zebrafish Neurovascular Modeling. Binbin Tao, Hongling Hu, Kimberly Mitchell, Ji Chen, Haibo Jia, Zuoyan Zhu, Vance Trudeau, Wei Hu

Sympathetic Nerve Activity Promotes Cardiomyocyte Cell-Cycle Arrest And Binucleation. Li Chen, Alexander Y Payumo, Kentaro Hirose, Rachel B. Bigley, Jonathan Lovas, Rejji Kuruvilla, Guo N. Huang

| Morphogenesis & mechanics

Par3/Baz levels control epithelial folding at actomyosin-enriched compartmental boundaries. Jose M Urbano, Huw W Naylor, Elena Scarpa, Leila Muresan, Bénédicte Sanson

Large, long range tensile forces drive convergence during Xenopus blastopore closure and body axis elongation. David R Shook, Raymond Keller, Lance Davidson, Eric M. Kasprowicz

Cells From The Same Lineage Switch From Reduction To Enhancement Of Size Variability In Arabidopsis Sepals. Satoru Tsugawa, Nathan Hervieux, Daniel Kierzkowski, Anne-Lise Routier-Kierzkowska, Aleksandra Sapala, Olivier Hamant, Richard S. Smith, Adrienne H. K. Roeder, Arezki Boudaoud, Chun-Biu Li

Cell type boundaries organize plant development. Monica Pia Caggiano, Xiulian Yu, Neha Bhatia, André Larsson, Hasthi Ram, Carolyn K Ohno, Pia Sappl, Elliot M Meyerowitz, Henrik Jönsson, Marcus G Heisler

Distinct effects of tubulin isotype mutations on neurite growth in Caenorhabditis elegans. Chaogu Zheng, Margarete Diaz-Cuadros, Susan Laura Jao, Ken Nguyen, David H Hall, Martin Chalfie

Myomerger Induces Fusion Of Non-Fusogenic Cells And Is Required For Myoblast Fusion. Malgorzata Quinn, Qingnian Goh, Mitsutoshi Kurosaka, Dilani Gamage, Michael Petrany, Vikram Prasad, Douglas Millay

| Genes & genomes

Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos. Shai Joseph, Mate Palfy, Lennart Hilbert, Mukesh Kumar, Jens Karschau, Vasily Zaburdaev, Andrej Shevchenko, Nadine Vastenhouw

Comprehensive Characterization Of The Complex Lola Locus Reveals A Novel Role In The Octopaminergic Pathway Via Tyramine Beta-Hydroxylase Activation. Nadja Dinges, Violeta Morin, Nastasja Kreim, Tony Southall, Jean-Yves Roignant

Genomic and chromatin features shaping meiotic double-strand break formation and repair in mice. Shintaro Yamada, Seoyoung Kim, Sam E Tischfield, Julian Lange, Maria Jasin, Scott Keeney

Germ cell connectivity enhances cell death in response to DNA damage in Drosophila testis. Yukiko M Yamashita, Kevin L Lu

The G-box transcriptional regulatory code in Arabidopsis. Daphne Ezer, Samuel JK Shepherd, Anna Brestovitsky, Patrick Dickinson, Sandra Cortijo, Varodom Charoensawan, Mathew S Box, Surojit Biswas, Philip Wigge

Cross-talk between active DNA demethylation, resetting of cellular metabolism and shoot apical growth in poplar bud break. Daniel Conde, Mariano Perales, Anne-Laure Le Gac, Christopher Dervinis, Matias Kirst, Stephane Maury, Pablo Gonzalez-Melendi, Isabel Allona

A Role For The F-Box Protein HAWAIIAN SKIRT In Plant miRNA Function. Patricia Lang, Michael Christie, Ezgi Dogan, Rebecca Schwab, Joerg Hagmann, Anna-Lena Van de Weyer, Detlef Weigel

Sequence Features Of MADS-Domain Proteins That Act As Hubs In The Protein-Protein Interaction Network Controlling Flower Development. Florian Ruempler, Guenter Theissen, Rainer Melzer

Nuclear Microenvironments Modulate Transcription From Low-Affinity Enhancers. Justin Crocker, Albert Tsai, Anand K Muthusamy, Luke D Lavis, Robert H Singer, David L Stern

Genetical genomics reveals Ras/MAPK modifier loci. Mark G. Sterken, Linda Van Bemmelen van der Plaat, Joost A.G. Riksen, Miriam Rodriguez, Tobias Schmid, Alex Hajnal, Jan E. Kammenga, Basten L. Snoek

5-Hydroxymethylcytosine Is Highly Dynamic Across Human Fetal Brain Development. Helen Spiers, Eilis Hannon, Leonard Schalkwyk, Nicholas Bray, Jonathan Mill

OGT binds a conserved C-terminal domain of TET1 to regulate TET1 activity and function in development. Joel Hrit, Cheng Li, Elizabeth Allene Martin, Mary Goll, Barbara Panning

Transcription Activation Of Early Human Development Suggests DUX4 As An Embryonic Regulator. Virpi Töhönen, Shintaro Katayama, Liselotte Vesterlund, Mona Sheikhi, Liselotte Antonsson, Giuditta Filippini-Cattaneo, Marisa Jaconi, Anna Johnsson, Sten Linnarsson, Outi Hovatta, Juha Kere

Extensive alternative splicing transitions during postnatal skeletal muscle development are required for Ca2+ handling. Tom Cooper

| Stem cells, regeneration & disease modelling

Morphogen And Community Effects Determine Cell Fates In Response To BMP4 Signaling In Human Embryonic Stem Cells. Anastasiia Nemashkalo, Albert Ruzo, Idse Heemskerk, Aryeh Warmflash

A protein phosphatase network controls temporal and spatial dynamics of differentiation commitment in human epidermis. Ajay Mishra, Angela Oliveira Pisco, Benedicte Oules, Tony Ly, Kifayathullah Liakath-Ali, Gernot Walko, Priyalakshmi Viswanathan, Jagdeesh Nijjher, Sara-Jane Dunn, Angus I Lamond, Fiona M Watt

The role of Cdx2 as a lineage specific transcriptional repressor for pluripotent network during trophectoderm and inner cell mass specification. Daosheng Huang, Xiaoping Han, Ping Yuan, Amy Ralston, Lingang Sun, Mikael Huss, Tapan Mistri, Luca Pinello, Huck Hui Ng, Guocheng Yuan, Junfeng Ji, Janet Rossant, Paul Robson, Guoji Guo

A lncRNA/Lin28/Let7 Axis Coupled To DNA Methylation Fine Tunes The Dynamics Of A Cell State Transition. Meng Amy Li, Paulo P. Amaral, Priscilla Cheung, Jan H. Bergmann, Masaki Kinoshita, Tuzer Kalkan, Meryem Ralser, Sam Robson, Ferdinand von Meyenn, Maike Paramor, Fengtang Yang, Caifu Chen, Jennifer Nichols, David L. Spector, Tony Kouzarides, Lin He, Austin Smith

Mouse embryonic stem cells can differentiate via multiple paths to the same state. James Alexander Briggs, Victor C Li, Seungkyu Lee, Clifford J Woolf, Allon Klein, Marc W Kirschner

Pervasive Discordance Between mRNA And Protein Expression During Embryonic Stem Cell Differentiation. Patrick van den Berg, Bogdan Budnik, Nikolai Slavov, Stefan Semrau

Establishment In Culture Of Expanded Potential Stem Cells. Jian Yang, David Ryan, Wei Wang, Cheuk-Ho J Tsang, Guocheng Lan, Xuefei Gao, Liliana Antunes, Adam Clifford Wilkinson, Yong Yu, Aleksandra Kolodziejczyk, Lia Campos, Juexuan Wang, Fengtang Yang, Yosuke Tanaka, Melanie Eckersley-Maslin, Michael Woods, James Bussell, Ramiro Ramirez-Solis, Wolf Reik, Bertie Gottgens, Xiangang Zou, Liming Lu, Cui Wang, Hideki Masaki, Jacqui White, Hiro Nakauchi, Zheng Zhong, Sarah Teichmann, Beiyuan Fu, Zhexin Zhu, Pentao Liu

Fused dorsal-ventral cerebral organoids model human cortical interneuron migration. Joshua A Bagley, Daniel Reumann, Shan Bian, Juergen A. Knoblich

Transcription Factors Orchestrate Dynamic Interplay Between Genome Topology And Gene Regulation During Cell Reprogramming. Ralph Stadhouders, Enrique Vidal, François Serra, Bruno Di Stefano, François Le Dily, Javier Quilez, Antonio Gomez, Samuel Collombet, Clara Berenguer, Yasmina Cuartero, Jochen Hecht, Guillaume Filion, Miguel Beato, Marc A. Marti-Renom, Thomas Graf

Direct Conversion Of Human Fibroblasts Into Osteoblasts And Osteocytes With Small Molecules And A Single Factor, Runx2. Yanjiao Li, YaoLong Wang, Juehua Yu, Zhaoxia Ma, Qiong Bai, Xingfei Wu, Pengfei Bao, Lirong Li, Daiping Ma, Jingxue Liu, Change Liu, Fangyun Chen, Min Hu

RNA helicase, DDX27 regulates proliferation and myogenic commitment of muscle stem cells. Alexis Bennett, Marie Francoise O’Donohue, Stacey Gundry, Aye Chan, Jeffery Widrick, Isabelle Draper, Anirban Chakraborty, Yi Zhou, Leonard Zon, Pierre-Emmanuel Gleizes, Alan Beggs, Vandana Gupta

Constitutive Immune Activity Promotes Tumorigenesis in Drosophila Intestinal Progenitor Cells. Kristina Petkau, Silvia Guntermann, Edan Foley

Conservation of EMT transcription factor function in controlling pluripotent adult stem cell migration in vivo in planarians. Prasad Abnave, Ellen Aboukhatwa, Nobuyoshi Kosaka, James Thompson, Mark Hill, Aziz Aboobaker

MLL3/4 Prevents Stem Cell Hyperplasia And Controls Differentiation Programs In A Planarian Cancer Stem Cell Model. Yuliana Mihaylova, Damian Kao, Samantha Hughes, Alvina Lai, Farah Jaber-Hijazi, Nobuyoshi Kosaka, Prasad Abnave, Aziz Aboobaker

PHRED-1 Is A Divergent Neurexin-1 Homolog That Organizes Muscle Fibers And Patterns Organs During Regeneration. Carolyn E. Adler, Alejandro Sanchez Alvarado

Post-transcriptional regulation of adult CNS axonal regeneration by Cpeb1. Wilson Pak-Kin Lou, Alvaros Mateos, Marta Koch, Stefan Klussmann, Chao Yang, Na Lu, Stefanie Limpert, Manuel Göpferich, Marlen Zschaetzsch, Carlos Maillo, Elena Senis, Dirk Grimm, Raúl Méndez, Kai Liu, Bassem A Hassan, Ana Martin-Villalba

Exposure to elevated sea-surface temperatures below the bleaching threshold impairs coral recovery and regeneration following injury. Joshua Louis Boness, William Leggat, Tracy Danielle Ainsworth

Necroptosis promotes the Aging of the Male Reproductive System in Mice. Xiaodong Wang, Dianrong Li, Lingjun Meng, Tao Xu, Yaning Su, Xiao Liu, Zhiyuan Zhang

Tissue-specific downregulation of EDTP removes polyglutamine protein aggregates and extends lifespan in Drosophila. Chengfeng Xiao, Shuang Qiu, R Meldrum Robertson, Laurent Seroude

Reversal of cardiac and skeletal manifestations of Duchenne muscular dystrophy by cardiosphere-derived cells and their exosomes in mdx dystrophic mice and in human Duchenne cardiomyocytes. Mark A Aminzadeh, Russell G Rogers, Kenneth Gouin, Mario Fournier, Rachel E Tobin, Xuan Guan, Martin K Childers, Allen M Andres, David J Taylor, Ahmed Ibrahim, Xiang-ming Ding, Angelo Torrente, Joshua I Goldhaber, Ronald A Victor, Roberta A Gottlieb, Michael Lewis, Eduardo Marban

PERTURBATION OF PTEN-PI3K/AKT SIGNALLING IMPAIRED AUTOPHAGY MODULATION IN DYSTROPHIN-DEFICIENT MYOBLASTS. Muhammad Dain Yazid, Janet Smith

Modeling Zika Virus Congenital Eye Disease: Differential Susceptibility of Fetal Retinal Progenitor Cells and iPSC-Derived Retinal Stem Cells to Zika Virus Infection. Deisy Contreras, Melissa Jones, Laura E Martinez, Vineela Gangalapudi, Jie Tang, Ying Wu, Jiagang J. Zhao, Zhaohui Chen, Shaomei Wang, Vaithilingaraja Arumugaswami

Cell biology

Astral microtubule dynamics regulate anaphase oscillation onset and set a robust final position for the Caenorhabditis elegans zygote spindle. Helene Bouvrais, Laurent Chesneau, Sylvain Pastezeur, Marie Delattre, Jacques Pecreaux

Anillin proteins stabilize the cytoplasmic bridge between the two primordial germ cells during C. elegans embryogenesis. Eugenie Goupil, Rana Amini, Jean-Claude Labbe

Local Nucleation Of Microtubule Bundles Through Tubulin Concentration Into A Condensed Tau Phase. Amayra Hernández-Vega, Marcus Braun, Lara Scharrel, Marcus Jahnel, Susanne Wegmann, Bradley T. Hyman, Simon Alberti, Stefan Diez, Anthony A. Hyman

An Arf6- And Caveolae-Dependent Pathway Links Hemidesmosome Remodeling And Mechanoresponse. Naël Osmani, Julien Pontabry, Jordi Comelles, Nina Fekonja, Jacky G Goetz, Daniel Riveline, Elisabeth Georges-Labouesse, Michel Labouesse

Cell size sensing in animal cells coordinates growth rates and cell cycle progression to maintain cell size uniformity. Miriam Bracha Ginzberg, Nancy Chang, Ran Kafri, Marc W Kirschner

Scc2-Mediated Loading Of Cohesin Onto Chromosomes In G1 Yeast Cells Is Insufficient To Build Cohesion During S Phase. Kim Nasmyth

Gradients Of Rac1 Nanoclusters Support Spatial Patterns Of Rac1 Signaling. Amanda Remorino, Simon De Beco, Fanny Cayrac, Fahima Di Federico, Gaetan Cornilleau, Alexis Gautreau, Maria Carla Parrini, Jean-Baptiste Masson, Maxime Dahan, Mathieu Coppey

WASP and SCAR are evolutionarily conserved in actin-filled pseudopod-based motility. Lillian K. Fritz-Laylin, Samuel J. Lord, R. Dyche Mullins

Optogenetic Control of RhoA Reveals Zyxin-mediated Elasticity of Stress Fibers. Patrick W Oakes, Elizabeth Wagner, Christoph A Brand, Dimitri Probst, Marco Linke, Ulrich S Schwarz, Michael Glotzer, Margaret L Gardel

Formin-Dependent Adhesions Are Required For Invasion By Epithelial Tissues. Tim B Fessenden, Yvonne Beckham, Mathew Perez-Neut, Aparajita H Chourasia, Kay F Macleod, Patrick W Oakes, Margaret L Gardel

Fast Activation Cycles Of Rac1 At The Lamellipodium Tip Trigger Membrane Protrusion. Amine Mehidi, Olivier Rossier, Anael Chazeau, Fabien Biname, Amanda Remorino, Mathieu Coppey, Zeynep Karatas, Jean-Baptiste Sibarita, Violaine Moreau, Gregory Giannone

Combinatorial Regulation Of The Balance Between Dynein Microtubule End Accumulation And Initiation Of Directed Motility. Rupam Jha, Johanna Roostalu, Martina Trokter, Thomas Surrey

The Ndc80 complex targets Bod1 to human mitotic kinetochores. Katharina Schleicher, Sara ten Have, Iain M Porter, Jason R Swedlow

Dynactin Binding To Tyrosinated Microtubules Promotes Centrosome Centration In C. Elegans By Enhancing Dynein-Mediated Organelle Transport. Daniel J. Barbosa, Joana Duro, Dhanya K. Cheerambathur, Bram Prevo, Ana X. Carvalho, Reto Gassmann

Long-Term Memory In The Migration Movements Of Enucleated Amoeba proteus. Carlos Bringas, Iker Malaina, Alberto Perez-Samartin, Maria Dolores Boyano, Maria Fedetz, Gorka Perez-Yarza, Jesus Cortes, Ildefonso Martinez de la Fuente

Do gametes woo? Evidence for non-random unions at fertilization. Joseph H Nadeau

Modelling

Pairwise hybrid incompatibilities dominate allopatric speciation for a simple biophysical model of development. Bhavin S Khatri, Richard Goldstein

A model for autonomous and non-autonomous effects of the Hippo pathway in Drosophila. Jia Gou, Lin Lin, Hans G Othmer

Single-Cell Genome Dynamics in Early Embryo Development: A Statistical Thermodynamics Approach. Alessandro Giuliani, Masa Tsuchiya, Kenichi Yoshikawa

On The Principles Of Cell Decision-Making: Intracellular Coupling Improves Cell Responses Fidelity Of Noisy Signals. Andreas Reppas, Eduard Jorswieck, Haralampos Hatzikirou

Correlating Cell Shape and Cellular Stress in Motile Confluent Tissues. Xingbo Yang, Dapeng Bi, Michael Czajkowski, Matthias Merkel, M. Lisa Manning, M. Cristina Marchetti

Evo-devo & evo

apterous A Specifies Dorsal Wing Patterns And Sexual Traits In Butterflies. Anupama Prakash, Antonia Monteiro

Sex Differences In 20-Hydroxyecdysone Hormone Levels Control Sexual Dimorphism In Bicyclus anynana Butterfly Wing Patterns. Shivam Bhardwaj, Kathleen L Prudic, Ashley Bear, Mainak Das Gupta, Bethany R Wasik, Xiaoling Tong, Wei Fun Cheong, Markus R Wenk, Antonia Monteiro

A practical guide to CRISPR/Cas9 genome editing in Lepidoptera. Linlin Zhang, Robert Reed

A novel role for Ets4 in axis specification and cell migration in the spider Parasteatoda tepidariorum. Matthias Pechmann, Matthew Alan Benton, Nathan James Kenny, Nico Posnien, Siegfried Roth

Evolution And Multiple Roles Of The Pancrustacea Specific Transcription Factor zelda In Insects. Lupis Ribeiro, Vitoria Tobias-Santos, Danielle Santos, Felipe Antunes, Georgia Feltran, Jackson de Souza Menezes, L Aravind, Thiago M Venancio, Rodrigo Nunes da Fonseca

Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus. Alex S Flynt, Alexandra Panzarino, Md Mosharrof Hossain Mondal, Adam Siepel, Jaaved Mohammed, Eric Lai

Tools & resources

Single Molecule Fluorescence In Situ Hybridisation For Quantitating Post-Transcriptional Regulation In Drosophila Brains. Lu Yang, Josh Titlow, Darragh Ennis, Carlas Smith, Jessica Mitchell, Florence L. Young, Scott Waddell, David Ish-Horowicz, Ilan Davis

A Versatile Compressed Sensing Scheme For Faster And Less Phototoxic 3D Fluorescence Microscopy. Maxime Woringer, Xavier Darzacq, Christophe Zimmer, Mustafa Mir

Three-Dimensional Two-Photon Optogenetics And Imaging Of Neural Circuits In Vivo. Weijian Yang, Luis Carrillo-Reid, Yuki Bando, Darcy S. Peterka, Rafael Yuste

Covalent Protein Labeling By SpyTag-SpyCatcher In Fixed Cells For Super-Resolution Microscopy. Veronica Pessino, Y. Rose Citron, Siyu Feng, Bo Huang

Photoacoustic molecular rulers based on DNA nanostructures. James Joseph, Philipp Koehler, Tim J. Zuehlsdorff, Daniel J Cole, Kevin N. Baumann, Judith Weber, Sarah E. Bohndiek, Silvia Hernandez-Ainsa

Rapid Whole Brain Imaging Of Neural Activities In Freely Behaving Larval Zebrafish. Lin Cong, Zeguan Wang, Yuming Chai, Wei Hang, Chunfeng Shang, Wenbin Yang, Lu Bai, Jiulin Du, Kai Wang, Quan Wen

A general method to fine-tune fluorophores for live-cell and in vivo imaging. Jonathan B. Grimm, Anand K. Muthusamy, Yajie Liang, Timothy A. Brown, William C. Lemon, Ronak Patel, Rongwen Lu, John J. Macklin, Phillip J. Keller, Na Ji,Luke D. Lavis

Real-Time Observation Of Light-Controlled Transcription In Living Cells. Anne Rademacher, Fabian Erdel, Jorge Trojanowski, Karsten Rippe

FiloQuant reveals increased filopodia density during DCIS progression. Guillaume Jacquemet, Ilkka Paatero, Alexandre Carisey, Artur Padzik, Jordan Orange, Hellyeh Hamidi, Johanna Ivaska

An organ-on-a-chip approach for investigating root-environment interactions in heterogeneous conditions. Claire E. Stanley, Jagriti Shrivastava, Rik Brugman, Dirk van Swaay, Guido Grossmann

Disabling Cas9 by an anti-CRISPR DNA mimic. Jiyung Shing, Fuguo Jiang, Jun-Jie Liu, Nicholas L Bray, Benjamin J Rauch, Seung Hyun Baik, Eva Nogales, Joseph Bondy-Denomy, Jacob E Corn, Jennifer A Doudna

Modulation of Genome Editing Outcomes by Cell Cycle Control of Cas9 Expression. Yuping Huang, Caitlin McCann, Andrey Samsonov, Dmitry Malkov, Greg D Davis, Qingzhou Ji

The WPRE Improves Genetic Engineering With Site-Specific Nucleases. Jessica M. Ong, Christopher R Brown, Matthew C. Mendel, Gregory J Cost

A Versatile Genetic Tool For Post-Translational Control Of Gene Expression With A Small Molecule In Drosophila melanogaster. Sachin Sethi, Jing W. Wang

Rapid DNA Re-Identification for Cell Line Authentication and Forensics. Sophie Zaaijer, Yaniv Erlich, Daniel Speyer, Robert Piccone, Assaf Gordon

Reading canonical and modified nucleotides in 16S ribosomal RNA using nanopore direct RNA sequencing. Andrew M Smith, Miten Jain, Logan Mulroney, Daniel R Garalde, Mark Akeson

Single-cell analysis of clonal dynamics in direct lineage reprogramming: a combinatorial indexing method for lineage tracing. Brent A Biddy, Sarah E Waye, Tao Sun, Samantha A Morris

Nanopore sequencing and assembly of a human genome with ultra-long reads. Miten Jain, Sergey Koren, Josh Quick, Arthur C Rand, Thomas A Sasani, John R Tyson, Andrew D Beggs, Alexander T Dilthey, Ian T Fiddes, Sunir Malla, Hannah Marriott, Karen H Miga, Tom Nieto, Justin O’Grady, Hugh E Olsen, Brent S Pedersen, Arang Rhie, Hollian Richardson, Aaron Quinlan, Terrance P Snutch, Louise Tee, Benedict Paten, Adam M. Phillippy, Jared T Simpson, Nicholas James Loman, Matthew Loose

Beyond The Linear Genome: Comprehensive Determination Of The Endogenous Circular Elements In C. elegans And Human Genomes Via An Unbiased Genomic-Biophysical Method. Massa Shoura, Idan Gabdank, Loren Hansen, Jason Merker, Jason Gotlib, Stephen Levene, Andrew Fire

Expression of short hairpin RNAs using the compact architecture of retroviral microRNA genes. James M Burke, Rodney P. Kincaid, Francesca Aloisio, Nicole Welch, Christopher S. Sullivan

Improved maize reference genome with single molecule technologies. Yinping Jiao, Paul Peluso, Jinghua Shi, Tiffany Liang, Michelle C Stitzer, Bo Wang, Michael Campbell, Joshua C Stein, Xuehong Wei, Chen-Shan Chin, Katherine Guill, Michael Regulski, Sunita Kumari, Andrew Olson, Jonathan Gent, Kevin L Schneider, Thomas K Wolfgruber, Michael R May, Nathan M Springer, Eric Antoniou, Richard McCombie, Gernot G Presting, Michael McMullen, Jeffrey Ross-Ibarra, R. Kelly Dawe, Alex Hastie, David R Rank, Doreen Ware

A Systematic Nomenclature for the Drosophila Ventral Nervous System. Robert Christopher Court, James Douglas Armstrong, Jana Borner, Gwyneth Card, Marta Costa, Michael Dickinson, Carsten Duch, Wyatt Korff, Richard Mann, David Merritt, Rod Murphey, Shigehiro Namiki, Andrew Seeds, David Shepherd, Troy Shirangi, Julie Simpson, James Truman, John Tuthill, Darren Williams

MAPseq: Improved Speed, Accuracy And Consistency In Ribosomal RNA Sequence Analysis. Joao F Matias Rodrigues, Thomas SB Schmidt, Janko Tackmann, Christian von Mering

High Accuracy Base Calls in Nanopore Sequencing. Philippe Christophe Faucon, Robert Trevino, Parithi Balachandran, Kylie Standage-Beier, Xiao Wang

BasePlayer: Versatile Analysis Software For Large-Scale Genomic Variant Discovery. Riku Katainen, Iikki Donner, Tatiana Cajuso, Eevi Kaasinen, Kimmo Palin, Veli Mäkinen, Lauri A Aaltonen, Esa Pitkänen

CiliaCarta: An Integrated And Validated Compendium Of Ciliary Genes. Teunis J. P. van Dam, Julie Kennedy, Robin van der Lee, Erik de Vrieze, Kirsten A. Wunderlich, Suzanne Rix, Gerard W. Dougherty, Nils J. Lambacher, Chunmei Li, Victor L. Jensen, Michael R. Leroux, Rim Hjeij, Nicola Horn, Yves Texier, Yasmin Wissinger, Jeroen van Reeuwijk, Gabrielle Wheway, Barbara Knapp, Jan F. Scheel, Brunella Franco, Dorus A. Mans, Erwin van Wijk, François Képès, Gisela G. Slaats, Grischa Toedt, Hannie Kremer, Heymut Omran, Katarzyna Szymanska, Konstantinos Koutroumpas, Marius Ueffing, Thanh-Minh T. Nguyen, Stef J. F. Letteboer, Machteld M. Oud, Sylvia E. C. van Beersum, Miriam Schmidts, Philip L. Beales, Qianhao Lu, Rachel H. Giles, Radek Szklarczyk, Robert B. Russell, Toby J. Gibson, Colin A. Johnson, Oliver E. Blacque, Uwe Wolfrum, Karsten Boldt, Ronald Roepman, Victor Hernandez-Hernandez, Martijn A. Huynen

Research practice

Looking Into Pandora’s Box: The Content Of Sci-Hub And Its Usage. Bastian Greshake

Anticipated effects of an open access policy at a private foundation. Eesha Khare, Carly Strasser

Gender disparity in computational biology research publications. Kevin S. Bonham, Melanie I. Stefan

Why Do Scientists Fabricate And Falsify Data? A Matched-Control Analysis Of Papers Containing Problematic Image Duplications. Daniele Fanelli, Rodrigo Costas, Ferric C Fang, Arturo Casadevall, Elisabeth M Bik

Addressing the digital divide in contemporary biology: Lessons from teaching UNIX. Serghei Mangul, Lana Martin, Alexander Hoffmann, Matteo Pellegrini, Eleazar Eskin

The appropriation of GitHub for curation. Yu Wu​, Na Wang, Jessica Kropczynski, John M Carroll

The earth is flat (p>0.05): Significance thresholds and the crisis of unreplicable research. Valentin Amrhein​, Fränzi Korner-Nievergelt, Tobias Roth

What is open peer review? A systematic review. Tony Ross-Hellauer

Standardising and harmonising research data policy in scholarly publishing. Iain Hrynaszkiewicz,Aliaksandr Birukou, Mathias Astell, Sowmya Swaminathan, Amye Kenall, Varsha Khodiyar

TOWARDS COORDINATED INTERNATIONAL SUPPORT OF CORE DATA RESOURCES FOR THE LIFE SCIENCES. Warwick Anderson, Rolf Apweiler, Alex Bateman, Guntram A Bauer, Helen Berman, Judith A Blake, Niklas Blomberg, Stephen K Burley, Guy Cochrane, Valentina Di Francesco, Tim Donohue, Christine Durinx, Alfred Game, Eric Green, Takashi Gojobori, Peter Goodhand, Ada Hamosh, Henning Hermjakob, Minoru Kanehisa, Robert Kiley, Johanna McEntyre, Rowan McKibbin, Satoru Miyano, Barbara Pauly, Norbert Perrimon, Mark A Ragan, Geoffrey Richards, Yik-Ying Teo, Monte Westerfield, Eric Westhof, Paul F Lasko

Why not…

Caterpillars lack a resident gut microbiome. Tobin J Hammer, Daniel H Janzen, Winnifred Hallwachs, Samuel L Jaffe, Noah Fierer

Estimating The Extinction Date Of The Thylacine Accounting For Unconfirmed Sightings. Colin J Carlson, Alexander L Bond, Kevin R Burgio

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A postdoctoral position is immediately available to pursue cutting-edge musculoskeletal stem cell research in the laboratory of Kathryn Wagner, MD, PhD at the Center for Genetic Muscle Disorders, Kennedy Krieger Institute and Johns Hopkins School of Medicine,

The Wagner laboratory is a moderate-size laboratory that focuses on translational science to develop novel therapies for muscle disorders. Approaches include small molecules, biologics, stem cells and gene therapy. The laboratory is part of a Senator Paul Wellstone Muscular Dystrophy Cooperative Research Center and has extensive collaboration both within Johns Hopkins and across institutions.  https://www.thewagnerlab.org.

The ideal applicant will have a PhD in molecular or cell biology. Experience in skeletal muscle is a positive but not a requirement. This is a fully funded position to study transplantation of iPSC-derived myogenic progenitors in models of muscular dystrophy and volumetric muscle loss.

Interested applicants should send a cover letter and CV to Dr. Wagner at wagnerk@kennedykrieger.org

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Comment on “Anterior-Posterior Gradient in Neural Stem and Daughter Cell Proliferation Governed by Spatial and Temporal Hox Control”, Current Biology 27, 1161-1172 (2017).

Ignacio Monedero, Behzad Yaghmaeian, Stefan Thor.

Department of Clinical and Experimental Medicine, Linkoping University, Sweden.

How cells are generated in proper numbers in order to form specific structures in an organism has been a subject of interest for many years. This issue is particularly intriguing in in the central nervous system (CNS), where the number of neurons of each type plays a crucial role in neural circuitry and cognitive capabilities in different species across evolution¹. An intriguing feature of the CNS is that different regions have different cell numbers, and the number of neurons along the anterior-posterior (A-P) axis seems to be organized in a wedge-like appearance:  the anterior part contains more neurons than the posterior part. This overall feature of CNS organization holds true for many vertebrate and invertebrate species. So how is the generation of proper number of neurons determined in the different regions of the central nervous system? This was, and still is, one of the questions around when I joined Stefan Thor’s lab in Linkoping, and the one which we try to shed light on in this post.

The total number of cells generated in a certain region is determined by several factors: the initial number of progenitors, the number of divisions that those progenitors go through, the proliferative behavior of the daughter cells produced by progenitors, and programmed cell death (PCD) present within the lineage. Drosophila CNS is subdivided into the brain, and the ventral nerve cord (VNC), equivalent to the mammalian and spinal cord respectively. Recent studies in the Drosophila VNC have provided an essential framework for addressing how the proper number of cells are generated in each segment. First, the recent meticulous mapping of the number of neural progenitors or neuroblasts (NBs) in each of the 13 segments of the VNC ^2–6; second, our previous discovery of different daughter proliferation modes in NB lineages, where NBs initially bud off daughters that divide once, to generate two neurons/glia, denoted Type I, and subsequently switch to generating daughters that do not divide, instead directly differentiating, denoted Type 0 ⁷; third, the identification of mutants that lack PCD in embryonic stages⁸. These findings gave us the opportunity to make a global and systematic study of proliferation in the VNC.

With this set up, our first challenge was to establish just how different the anterior segments are from the posterior ones, and that was one of the most exciting parts in the project. The 13 segments of the VNC are generated by a similar number of progenitors, about 64 per segment, in each segment. Our cell number analysis at the end of neurogenesis revealed that these 64 NBs generate different numbers of cells in different segments, with more cells in anterior segments than posterior ones. Based upon this finding we postulated two main processes that could contribute to this wedge-like appearance: removal of excess cells, by PCD, in posterior segments, and/or increased proliferation in anterior segments. Looking at PCD mutants, the A-P differences in numbers were still noticeable, suggesting PCD could not explain the difference. In contrast, we observed increased proliferation, of both NBs and daughters, in anterior segments, which pointed to proliferation as the main contributor to the A-P differences. To further address this notion, we analyzed proliferation in specific NB lineages, serially presented in all VNC segments. Whereas in anterior segments, NBs undergo more rounds of division and display a late or absent Type I->0 daughter proliferation switch, in the posterior segments NBs undergo  fewer rounds of divisions and display an earlier Type I->0 switch. The combination of cell number analysis with global and single-lineage proliferation analysis allowed us to extract an average lineage behavior for thoracic segments versus posterior segments.

The next goal was to begin identifying some of the players controlling this gradient in proliferation behavior. The A-P axis differences obviously pointed to homeotic domains, and our previous work has identified the Hox gene Antennapedia (Antp) as one of the main triggers of the Type I->0 daughter proliferation switch in the thoracic segments⁷. Therefore, we analyzed the role of the more posteriorly acting Hox genes of the Bithorax-Complex (BX-C); Ultrabithorax (Ubx), abdominal-A (abd-A), and Abdominal-B (Abd-B). Strikingly, we indeed observed that BX-C genes were important for the earlier Type I->0 daughter proliferation switch and NB proliferation exit observed in posterior segments. However, the triggering of the Type I->0 switch during later stages of lineage progression implied that the action of BX-C was gated in a temporal manner. Our previous studies of Antp had revealed that its expression in thoracic NBs commences during later stages. Studying this, we found that although Hox genes are indeed expressed in an A-P manner during early embryonic stages, early NBs display little if any BX-C protein expression. As NBs lineage progression proceeds, we observed onset of Hox protein expression, establishing the characteristic overlapping domains along the A-P axis, and this late onset in NBs then promotes the Type I->0 daughter proliferation switch. Based upon these findings we propose a model where at early stages NBs  progress in  a Hox-free “ground state”, allowing for high proliferative modes, whereas at later stages, the onset of Hox expression in NBs promotes the Type I->0 daughter proliferation switch, and eventually NBs stop dividing. This action of Hox genes establishes a gradient in NB lineage size, and results in the A-P wedge appearance.

The hypothesis of the ground state is not new in Drosophila, and has been proposed by Fernando Casares and Richard Mann for appendages⁹. This idea proposes a “default” program, that we believe applies also to NB proliferation behavior, in thoracic segments, which is modified along the A-P axis by the same cues that determine the body plan. This program allows for homologous NBs in different segments to modify their proliferation behavior to generate the proper number of cells needed for that specific segment.

Since Hox genes are evolutionary conserved, establishing the body plan of invertebrates and vertebrates equally, it is reasonable to envision that they may have a conserved function in proliferation control in the nervous system. Indeed, several studies have identified Hoxc6, Hoxb9 and Hoxb13 related to suppression of proliferation in the vertebrate CNS^10,11. Most intriguingly, while our current study was focused on the VNC, the most obvious wedge-like appearance in nervous systems is brain size when compared to nerve cord. Given that we have shown that Hox expression suppresses neural progenitor and daughter proliferation, and that the brain is a Hox free region, it seems reasonable to think that Hox genes could be one of the motors of the evolutionary expansion of the brain.

We are now very enthusiastic about the open possibilities of what is happening in the brain. The work is now focused on addressing how proliferation is controlled in the brain, and to what extent could alternate neural progenitor and daughter cell proliferation modes be a common feature, using similar or homologous tools, to establish A-P differences across different species.

1. Herculano-Houzel, S. Not All Brains Are Made the Same: New Views on Brain Scaling in Evolution. Brain. Behav. Evol.78, 22–36 (2011).
2. Birkholz, O., Rickert, C., Berger, C., Urbach, R. &Technau, G. M. Neuroblast pattern and identity in the Drosophila tail region and role of doublesex in the survival of sex-specific precursors. Development 140, 1830–1842 (2013).
3. Schmid, A., Chiba, A. & Doe, C. Q. Clonal analysis of Drosophila embryonic neuroblasts: neural cell types, axon projections and muscle targets. Development 126, 4653–4689 (1999).
4. Schmidt, H. et al. The Embryonic Central Nervous System Lineages ofDrosophila melanogaster. Dev. Biol. 189, 186–204 (1997).
5. Bossing, T., Udolph, G., Doe, C. Q. &Technau, G. M. The Embryonic Central Nervous System Lineages ofDrosophila melanogaster. Dev. Biol. 179, 41–64 (1996).
6. Wheeler, S. R., Stagg, S. B. & Crews, S. T. MidExDB: A database of DrosophilaCNS midline cell gene expression. BMC Dev. Biol. 9, 56 (2009).
7. Baumgardt, M. et al. Global Programmed Switch in Neural Daughter Cell Proliferation Mode Triggered by a Temporal Gene Cascade. Dev. Cell 30, 192–208 (2014).
8. Tan, Y. et al. Coordinated expression of cell death genes regulates neuroblast apoptosis. Development 138, 2197–2206 (2011).
9. Casares, F. & Mann, R. S. The Ground State of the Ventral Appendage in Drosophila. Science 293, 1477–1480 (2001).
10. Epstein, M., Pillemer, G., Yelin, R., Yisraeli, J. K. &Fainsod, A. Patterning of the embryo along the anterior-posterior axis: the role of the caudal genes. Development 124, 3805–3814 (1997).
11. Economides, K. D., Zeltser, L. &Capecchi, M. R. Hoxb13 mutations cause overgrowth of caudal spinal cordand tail vertebrae. Dev. Biol. 256, 317–330 (2003).

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We are looking for a motivated, ambitious and collegial person interested in joining us as a postdoc to pursue projects centered around host-pathogen interaction in human stem cell derived macrophages. Prior exprience with stem cells or high throughput microscopy is required. Please contact Eva directly with your CV or with queries if you are interested.

eva.frickel@crick.ac.uk

frickellab.com

This project will dive into regulation of host immunity to infection or infectious stimuli using macrophages derived from human stem cells. More emphasis will be put on deciphering molecular signaling or cellular response pathways than the actual stimuli/infection under study. This will require efficient gene editing approaches for stem cell derived macrophages (CRISPR, siRNA) and the ability to work with high throughput analysis (image based) as well as handling large datasets (RNASeq, proteomic or metabolomic analysis). Thus I believe a person with an interest in using human stem cells to study intracellular mechanisms is best suited for this post.

https://jobs.crick.ac.uk/pls/corehrrecruit//erq_jobspec_version_4.display_form?p_company=1&p_internal_external=E&p_display_in_irish=N&p_applicant_no=&p_recruitment_id=004926&p_process_type=&p_form_profile_detail=&p_display_apply_ind=Y&p_refresh_search=Y

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Please consider visiting us in Sheffield for this exciting symposium this September (register at lifecourse.group.shef.ac.uk). The symposium is being organised by Marysia Placzek, Stephen Renshaw and David Strutt on behalf of the Bateson Centre at the University of Sheffield (https://www.sheffield.ac.uk/bateson). There is an array of outstanding external speakers already confirmed and the opportunity to present your own work (abstract deadline is 15th June). Sign up by 28th July! We look forward to welcoming you to Sheffield!

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