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Postdoctoral position studying the role of extracellular matrix in cardiovascular development

Posted by , on 5 September 2017

Closing Date: 15 March 2021

A postdoctoral position is available in the laboratory of Dr. Sophie Astrof at Thomas Jefferson University to study roles of cell-extracellular matrix (ECM) interactions in cardiovascular development and congenital heart disease. We have recently discovered that progenitors within the second heart field (SHF) give rise to endothelial cells composing pharyngeal arch arteries. Projects in the lab focus on the role of ECM in regulating cell fate and migration of SHF-derived cells, and in the regulation of signaling between endoderm-, mesoderm-, and ectoderm-derived tissues during the morphogenesis of the pharyngeal vasculature. The project will combine genetic manipulation, embryology, cell biology, and confocal imaging. My laboratory is a part of a modern and well-equipped Center for Translational Medicine at Jefferson Medical College (http://www.jefferson.edu/university/research/researcher/researcher-faculty/astrof-laboratory.html) located in the heart of Philadelphia. For further information on our work, please see the following publications: Wang et al., Development, 143:88-100, 2016 and Wang et al, Developmental Biology 421:108-217, 2017. To apply, please send a letter of interest detailing your expertise, CV and names and contact information of three references to sophie.astrof@gmail.com

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Research Associate in Cell and Developmental Biology

Posted by , on 5 September 2017

Closing Date: 15 March 2021

This post, funded by The Leverhulme Trust (grant RPG-2017-249) “Dynamic Self-Organisation of Stochastic Intracellular Transport”, is available to study the transport of E-cadherin on microtubule cytoskeleton in the group led by Dr Natalia Bulgakova: www.sheffield.ac.uk/bms/research/bulgakova.

Cell-cell adhesion plays a vital role during the development and adult life of multicellular organisms. The focus of the Bulgakova group is on discovering roles and regulation of cell-cell adhesion using Drosophila as a model organism. We have recently discovered that microtubule organization in epithelial cells is driven by cell shape, and is required for distribution of E-cadherin, a key cell-cell adhesion molecule, around cell periphery. The successful applicant will study the mechanisms of how E-cadherin is transported along a dynamic network of microtubules to achieve correct and reproducible E-cadherin distribution. The project will employ a combination of molecular genetics, immunohistochemistry and live imaging. The work will be a part of collaboration with the group of Dr Lyubov Chumakova, University of Edinburgh, who will complement and support experimental findings by creating a mathematical model of E-cadherin transport.

The successful applicant will have a PhD or equivalent experience relevant to studying cell-cell adhesion or intracellular trafficking, knowledge of working with genetic model systems and be highly motivated. Experience in using Drosophila, molecular biology, confocal microscopy, and live imaging, and knowledge of cell-cell adhesion, cell polarity and intracellular trafficking will be an advantage. The successful candidate will be expected to have excellent interpersonal and communication skills, be highly independent, and committed to research in a fast-moving and competitive field.

 

For more information and to apply, please see http://www.jobs.ac.uk/job/BEA999/research-associate-in-cell-and-developmental-biology/

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PhD position

Posted by , on 5 September 2017

Closing Date: 15 March 2021

My lab has a PhD position on Cell and Developmental Biophysics for UK/EU students. For details please go to https://www.findaphd.com/search/ProjectDetails.aspx?PJID=88173

Thanks

Isa

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The evolution from mouse to human models of lung development

Posted by , on 4 September 2017

The story behind our eLife paper: Nikolić, M. Z., Caritg, O., Jeng, Q., Johnson, J.-A., Sun, D., Howell, K. J., Brady, J. L., Laresgoiti, U., Allen, G., Butler, R., Zilbauer, M., Giangreco, A., Rawlins E.L. (2017). Human embryonic lung epithelial tips are multipotent progenitors that can be expanded in vitro as long-term self-renewing organoids. Elife 6, e26575.

 

As a medical doctor specialising in respiratory diseases, with limited experience in real lab-based research, I was disappointed how little could be done for patients with end-stage lung disease (ESLD). Although respiratory diseases account for the third highest mortality of non-infectious disease deaths worldwide and lung cancer is the most common cancer (World Health Organization, 2011), treatment is largely supportive and lung tissue destruction is irreversible.

I started my PhD with Emma Rawlins at the Gurdon Institute, University of Cambridge, as part of the Wellcome PhD Programme for Clinicians by looking at human induced pluripotent stem cells (hiPSCs). These seemed to provide an opportunity to apply the discoveries of developmental biology to treat disease (Takahashi and Yamanaka, 2006). Differentiating patient-specific iPSCs into any relevant cell type could potentially be used for disease modelling and drug screening, and also bring us a step closer to cell-based therapies including personalised organogenesis. Research on murine lung development as a model for human lung development has been crucial to current protocols for differentiating human iPSCs into lung (Firth et al., 2014; Firth et al., 2015; Ghaedi et al., 2013; Huang et al., 2015; Huang et al., 2013; Longmire et al., 2012; Mou et al., 2012; Wong et al., 2012; Wong et al., 2015). I initially started work on iPSC directed differentiation to lung and wanted to use human embryonic lungs simply for validation purposes. However, it became evident very quickly that little developmental biology had been done on human embryonic lungs and it was not clear how closely the published step-wise iPSC differentiation protocols actually reflect human embryonic and foetal lung development.

Characterising the different progenitor populations in both the developing mouse and human embryonic lung seemed to me an essential part of regenerative medicine. The molecular understanding of developing human lungs was inadequate, as human lung development had not been characterised using cells derived from the human embryonic lung itself, but only using iPS-derived lung cells.

 

Mouse lung development

In parallel to my human work, I also worked on mouse lung development since it has been so extensively used as a model for human lung development. Considering the various anatomical and molecular differences already known between mouse and human lungs, I felt it was important to understand both mouse and human lung development more fully in order to ascertain to what extent the mouse findings could indeed be applied to human lungs. In both species, the lung develops as a blind-ending tube which branches multiple times, a process which results in the production of gas-delivering bronchioles and gas-exchanging alveoli. We know from lineage tracing experiments that the most important epithelial progenitor population in the developing mouse lung is found in the branching tips, giving rise to all the various epithelial cell types in the adult lung, both bronchiolar and alveolar cells (Rawlins et al., 2009). In mice, these epithelial tip cells are classically Sox9+ and initially give rise to the neighbouring Sox2+ stalk cells which are bronchiolar progenitors and give rise to the future airway (Fig.1 A). Using technically challenging grafting experiments I showed, among other things, that extrinsic signalling is the key in determining the tip and stalk progenitor cell fate, but that a significant degree of plasticity is present and that this gradually decreases throughout development (Fig.1 B) (Laresgoiti et al., 2016). I got a lot of practice in dissecting the epithelium free from any mesenchyme, which was very useful later on for the human work (Fig. 3B).

The finding that the environment is crucial in determining distal tip progenitor fate suggested that it would be possible to define in vitro culture conditions for human embryonic lung epithelium, both for the self-renewal of tip cells and their differentiation towards alveolar and bronchiolar lineages. This was an exciting realization as successful identification of culture conditions for developing human lungs would make molecular genetics possible.

 

Figure 1 A. Branching mouse lung is characterised by Sox9+ tips and Sox2+ stalks (reproduced from (Wang et al., 2013). B. Epithelial tip progenitors were microdissected from donor E12.5 (A) or E16.5 (B) Tomato (Rosa26RmTmG/+) lungs and grafted into the mesenchyme of unlabelled E12.5 hosts. Hosts/grafts were cultured for 8 days. Tip grafts grew (shown), integrated into the host lung and formed a lumen (not shown).

 

Main challenges of working on human embryonic lungs

One of the main limitations of working with human tissue is the lack of continuous tissue supply. This changed quickly and unexpectedly when I went to one of the Cambridge pubs to discuss my research plans and get some advice from a post-doctoral friend. He mentioned the “TransEuro” trial going on at the University of Cambridge – a clinical trial in which brain tissue from terminations of pregnancies is used for neurosurgical transplantation into treatment-resistant Parkinson’s patients. This meant that developing lung tissue was regularly discarded without any scientific benefit. This seemed to be the ideal source of human lung tissue for validation of my attempts at iPS-derived directed differentiation, but it quickly became clear what a huge potential an in-depth molecular characterisation of human embryonic lungs would have for the entire lung developmental and stem cell biology community. Additionally, the Joint MRC/Wellcome Human Developmental Biology Resource (www.HDBR.org) coordinated tissue harvesting from all over the UK via London and Newcastle. This meant that we had lung tissue provided to us multiple times per month from all over the country. The developmental age ranged from 5 to 20 weeks’ developmental age (7-22 weeks’ gestational age) and the samples used had no known genetic abnormalities.

Another challenge was that tissue used for sequencing and in vitro culture had to be as fresh as possible. Initially, we did not want to take any chances and dissection usually occurred as soon as possible after tissue was obtained, which was often late in the day. Experiments frequently continued until the early hours of the morning. I must say I was grateful once it became clear that overnight storage in specifically designed embryonic tissue storage medium did not affect gene expression, reproducibility and viability!

Since this was an exciting new area with huge potential, I was very grateful for the help I received from two amazing undergraduate/masters students, Oriol Caritg and Dawei Sun, who assisted me with my human work, as well as another PhD student, Jo Johnson.

 

Main achievements

Molecular comparison of human and mouse embryonic lungs

Molecular characterisation of human embryonic and foetal lungs using immunostaining, qRT-PCR and RNAseq transcriptome analysis revealed both major similarities and differences between mouse and human lung epithelial progenitors (Nikolić et al., 2017). Interestingly, 96% of orthologous genes that were expressed in human tips were also present in mouse.

The most important difference was the discovery that the classical stalk marker SOX2 is expressed in the human SOX9+ distal tip progenitors (Fig. 2), in stark contrast to the expression pattern in mice. We showed that this is a true interspecies difference and cannot be explained by relative age. This is an exciting finding, since Sox9 has been used as a classical mouse tip marker and Sox2 as a classical mouse stalk marker, with a clear demarcation between them (Chang et al., 2013; Liu and Hogan, 2002). My work suggests that SOX2 cannot be used as a unique stalk marker in human embryonic lungs and for validation during iPS-derived directed differentiation. Furthermore, there were more subtle differences in tip signalling pathways between mouse and human (Figure 3). The same signalling pathways were present, but these were wired in fundamentally different ways. For example, BMP2 and BMP7 were highly enriched in human tips, whereas Bmp4 was enriched in the mouse (Bellusci et al., 1996); IHH was expressed in human lungs whereas mouse lungs express Shh  (Bellusci et al., 1997).

 

Figure 2. In the early stages of lung development, Sox2 is only expressed in the stalk in mouse (E11-15), whereas in human SOX2 expression extends into the tip (weeks 5-16).

 

On the one hand these data provide support for the use of mouse as a model for human lung development, but on the other hand they question its applicability in view of the many genetic differences, the functional consequences of which are not yet known. Therefore, to study the functional consequences of manipulating these genes, a genetically modifiable system for studying human lung development is required.

 

Figure 3 A-C. 6-7 post-conception week (pcw) human embryonic lung was incubated in dispase for 2 minutes, upon which the epithelium was microdissected free from any macroscopically obvious mesenchyme. The epithelium was further microdissected into tips and stalk, and then processed for RNAseq. D. Bright field images of one tip taken every 24 hours for 12 days cultured in self-renewing media (R-SPONDIN1, EGF, Noggin, FGF10, FGF7, CHIR99021, SB431542).

 

 

Self-renewing 3D organoid culture of human tip progenitors

We therefore developed culture conditions which have the ability to expand human embryonic lung epithelial stem cells as an indefinitely self-renewing, expanding population of undifferentiated cells with a organoid forming efficiency of 100% (Figure 3). The concept is similar to capturing the inner cells mass of a blastocyst as a self-renewing embryonic stem cell line. Our lung organoids could also be frozen and thawed, and the technical advice obtained from Meritxell Huch’s lab within the Gurdon Institute was immensely helpful. This now allows the in vitro study of human embryonic lung development without the need to obtain fresh tissue for every experiment.

However, in mouse, the same culture conditions were not sufficient to maintain mouse lung epithelial progenitor cells after several passages. This suggests that acquiring a self-renewing state is possible with further optimisation of the culture conditions, but the required signalling mechanisms are likely to be different. This was not surprising based on the transcriptome comparison between mouse and human tip progenitors.

RNAseq of cultured tips and stalks further validated my self-renewing culture conditions, since key genes are shared by cultured tip, cultured stalk and fresh tip cells without expression of differentiation markers. This suggests that the in vitro conditions mimic the in vivo conditions very closely.

Furthermore, single cell efficiency was high at about 35% and unpublished results showed that we were able to genetically manipulate human epithelial tip progenitors using CRISPR-Cas9. Knocking out SOX9 led to loss-of-self-renewing state phenotype, showing that SOX9 expression is essential for organoid maintenance. What this means is that we can now study human lung progenitor self-renewal in vitro in a genetically modifiable system which is extremely efficient without introducing chromosomal abnormalities, and which reproduces what is happening in vivo. This opens up a whole new research field of studying the mechanism of self-renewal and differentiation.

 

In vivo and in vitro differentiation as proof for a self-renewing state

One of the most important proofs that we had actually achieved a self-renewing state was the ability to differentiate our expanded organoid cells towards both bronchiolar and alveolar lineages. If real stem cells do it, then our expanded ones should do it do. Indeed, human embryonic epithelial lung progenitors, which had been expanded as 3D organoids, could be differentiated in vitro towards both alveolar and bronchiolar lineages. Similarly, xenotransplantation of organoid cells mixed with E13.5 dissociated mouse lungs, into the mouse kidney capsule led to efficient bronchiolar differentiation and the appearance of ciliated cells, mucus cells and basal cells, although alveolar differentiation was much less efficient. This strongly supported our hypothesis that a self-renewing state had been achieved.

We have also performed xenotransplantation into bleomycin-injured adult mouse lungs which showed highly efficient integration and proliferation of intratracheally administered single organoid cells. It also showed that the organoid cells can differentiate into bronchiolar cells, suggesting that lung identity is retained within the organoids. Such efficient engraftment has not been achieved previously. This is an exciting new model with many future possibilities.

 

Impact and future directions

In conclusion, the platform that we have developed for in vitro analysis of the embryonic human lung will be the first system available for functional experiments on human embryonic lungs. It will allow human embryonic lung development to be studied using modern molecular genetic techniques. The fact that we can genetically modify our organoid system also means that we can use CRISPR-Cas9 to identify novel genes required for alveolar and bronchiolar differentiation. This has been done in pancreatic development using iPS-derived cells (McGrath et al., 2015). However, our approach would be more reliable, as we would be doing this with real lung progenitors, albeit expanded ones, rather than iPS-derived ones. This research has the long-term potential to be transformative for lung regeneration by disease modelling, specifically by determining the role of genetic variants associated with lung diseases, by developing improved therapies for premature neonatal lung maturation, and also for in vitro differentiation of iPS cells. It has been claimed that iPSCs offer unparalleled opportunities to model lung development and disease using human cells. I would argue that our culture system using real human embryonic lung cells provides a more authentic and reliable platform to model lung development and disease.

From a clinical point of view, I hope that the work will make a difference to at least three groups of patients:

  • Patients with end-stage lung disease: our work will guide iPS-derived directed differentiation, which could then be used to recellularise a decellularised lung or lobar scaffold to be used for lung transplantation without the need for immunosuppression.
  • Premature neonates with lung failure due to immaturity: the 3D organoid culture system we developed will allow the study of late foetal development using real lung progenitors rather than iPS-derived ones. Understanding how the lung matures in these final stages of lung development will be crucial to improve survival for babies born prematurely.
  • Patients with rare congenital lung conditions. Gene editing in our 3D culture system will enable disease modelling of conditions such as surfactant protein B and C deficiencies.

 

Publishing first and fast versus publishing “big”

Every scientist would like their work to be recognised as important and groundbreaking by those in their field. However, as far as career progression is concerned, the journal chosen often appears to be far more important than the actual quality of the work. It seems to me that journal impact factor is used as a substitute for quality by those who are not experts in a particular field, or who do not understand the impact of the work. In my experience, important factors in choosing a journal include the speed of the review process, the availability of person-power to do the revision work, the awareness of competitors, and related guesswork of what stage those competitors have reached and whether their work is yet of a standard suitable for publication. During our paper revision period, I was in full-time clinical training and I was reliant on the goodwill of my colleagues for the revision experiments, especially Oriol Caritg and Quitz Jeng. On reviewing all these aspects, we chose a journal known for its efficient and fair review process rather than focusing simply on journal impact factor. Put differently, we chose to publish first and fast, rather than attempting to publish “big”. I remain hopeful that our work (as well as that of others) will be judged purely by its contents and the impact it has on the field, rather than by the impact factor of the journal in which it was published.

 

Marko Nikolić

Wellcome Trust/CRUK Gurdon Institute & Wellcome Trust/MRC Stem Cell Institute,

University of Cambridge, Cambridge, UK

 

REFERENCES

Bellusci, S., Furuta, Y., Rush, M. G., Henderson, R., Winnier, G. and Hogan, B. L. (1997). Involvement of Sonic hedgehog (Shh) in mouse embryonic lung growth and morphogenesis. Development 124, 53–63.

Bellusci, S., Henderson, R., Winnier, G., Oikawa, T. and Hogan, B. L. (1996). Evidence from normal expression and targeted misexpression that bone morphogenetic protein (Bmp-4) plays a role in mouse embryonic lung morphogenesis. Development 122, 1693–1702.

Chang, D. R., Martinez Alanis, D., Miller, R. K., Ji, H., Akiyama, H., McCrea, P. D. and Chen, J. (2013). Lung epithelial branching program antagonizes alveolar differentiation. Proc. Natl. Acad. Sci. U.S.A. 110, 18042–18051.

Firth, A. L., Dargitz, C. T., Qualls, S. J., Menon, T., Wright, R., Singer, O., Gage, F. H., Khanna, A. and Verma, I. M. (2014). Generation of multiciliated cells in functional airway epithelia from human induced pluripotent stem cells. Proc. Natl. Acad. Sci. U.S.A.

Firth, A. L., Menon, T., Parker, G. S., Qualls, S. J., Lewis, B. M., Ke, E., Dargitz, C. T., Wright, R., Khanna, A., Gage, F. H., et al. (2015). Functional Gene Correction for Cystic Fibrosis in Lung Epithelial Cells Generated from Patient iPSCs. Cell Rep 12, 1385–1390.

Ghaedi, M., Calle, E. A., Mendez, J. J., Gard, A. L., Balestrini, J., Booth, A., Bove, P. F., Gui, L., White, E. S. and Niklason, L. E. (2013). Human iPS cell-derived alveolar epithelium repopulates lung extracellular matrix. J. Clin. Invest. 123, 4950–4962.

Huang, S. X. L., Green, M. D., de Carvalho, A. T., Mumau, M., Chen, Y.-W., d’Souza, S. L. and Snoeck, H.-W. (2015). The in vitro generation of lung and airway progenitor cells from human pluripotent stem cells. Nat Protoc 10, 413–425.

Huang, S. X. L., Islam, M. N., O’Neill, J., Hu, Z., Yang, Y.-G., Chen, Y.-W., Mumau, M., Green, M. D., Vunjak-Novakovic, G., Bhattacharya, J., et al. (2013). Efficient generation of lung and airway epithelial cells from human pluripotent stem cells. Nat. Biotechnol.

Laresgoiti, U., Nikolić, M. Z., Rao, C., Brady, J. L., Richardson, R. V., Batchen, E. J., Chapman, K. E. and Rawlins, E. L. (2016). Lung epithelial tip progenitors integrate Glucocorticoid and STAT3-mediated signals to control progeny fate. Development 143, 3686–3699.

Liu, Y. and Hogan, B. L. M. (2002). Differential gene expression in the distal tip endoderm of the embryonic mouse lung. Gene Expr. Patterns 2, 229–233.

Longmire, T. A., Ikonomou, L., Hawkins, F., Christodoulou, C., Cao, Y., Jean, J. C., Kwok, L. W., Mou, H., Rajagopal, J., Shen, S. S., et al. (2012). Efficient derivation of purified lung and thyroid progenitors from embryonic stem cells. Cell Stem Cell 10, 398–411.

McGrath, P. S., Watson, C. L., Ingram, C., Helmrath, M. A. and Wells, J. M. (2015). The Basic Helix-Loop-Helix Transcription Factor NEUROG3 Is Required for Development of the Human Endocrine Pancreas. Diabetes 64, 2497–2505.

Mou, H., Zhao, R., Sherwood, R., Ahfeldt, T., Lapey, A., Wain, J., Sicilian, L., Izvolsky, K., Musunuru, K., Cowan, C., et al. (2012). Generation of multipotent lung and airway progenitors from mouse ESCs and patient-specific cystic fibrosis iPSCs. Cell Stem Cell 10, 385–397.

Nikolić, M. Z., Caritg, O., Jeng, Q., Johnson, J.-A., Sun, D., Howell, K. J., Brady, J. L., Laresgoiti, U., Allen, G., Butler, R., et al. (2017). Human embryonic lung epithelial tips are multipotent progenitors that can be expanded in vitro as long-term self-renewing organoids. Elife 6, e26575.

Rawlins, E. L., Clark, C. P., Xue, Y. and Hogan, B. L. M. (2009). The Id2+ distal tip lung epithelium contains individual multipotent embryonic progenitor cells. Development 136, 3741–3745.

Takahashi, K. and Yamanaka, S. (2006). Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676.

Wang, Y., Tian, Y., Morley, M. P., Lu, M. M., Demayo, F. J., Olson, E. N. and Morrisey, E. E. (2013). Development and regeneration of Sox2+ endoderm progenitors are regulated by a Hdac1/2-Bmp4/Rb1 regulatory pathway. Dev. Cell 24, 345–358.

Wong, A. P., Bear, C. E., Chin, S., Pasceri, P., Thompson, T. O., Huan, L.-J., Ratjen, F., Ellis, J. and Rossant, J. (2012). Directed differentiation of human pluripotent stem cells into mature airway epithelia expressing functional CFTR protein. Nat. Biotechnol. 30, 876–882.

Wong, A. P., Chin, S., Xia, S., Garner, J., Bear, C. E. and Rossant, J. (2015). Efficient generation of functional CFTR-expressing airway epithelial cells from human pluripotent stem cells. Nat Protoc 10, 363–381.

World Health Organization (2011). Global Status Report on Noncommunicable Diseases 2010.

 

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Categories: Research

August in preprints

Posted by , on 4 September 2017

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


It all went very meta this month with Matthew Cobb’s PeerJ preprint about a forgotten experiment in preprints from the 1960s. The story was highlighted in Science, a journal, Cobb explains, whose editor disparaged the initial preprint experiment in the 60s. Elsewhere, doubts were raised about last month’s headline-making human embryo CRISPR paper, as highlighted on the Niche (which also highlighted Shoukhrat Mitalipov’s response to the prepint).

And I have to share the start to an abstract from Javier Quilez and colleagues’ preprint on what makes large sequencing projects successful:

 

“T47D_rep2 and b1913e6c1_51720e9cf were two Hi-C samples. They were born and processed at the same time, yet their fates were very different. The life of b1913e6c1_51720e9cf was simple and fruitful, while that of T47D_rep2 was full of accidents and sorrow…”

 

The preprints were hosted on bioRxivPeerJ  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

Evo-devo & evo
Cell biology
Modelling
Tools & resources

| Imaging etc.

| Genome tools

Research practice
Why not…

 

Developmental biology

| Patterning & signalling

Drosophila neural stem cells are polarized by their daughter cells. Nicolas Loyer, Jens Januschke

 

Neuromesodermal progenitors from Verrier, et al.’s preprint

 

Generation, selection and transcriptomic profiling of human neuromesodermal and spinal cord progenitors in vitro. Laure Verrier, Lindsay Davidson, Marek Gierliński, Kate G. Storey

 

Satellite-like cells in Drosophila muscles, from Boukhatmi & Bray’s preprint

 

A population of adult satellite-like cells in Drosophila is maintained through a switch in RNA-isoforms. Hadi Boukhatmi, Sarah Bray

 

Programming of neural progenitors of the adult subependymal zone towards a glutamatergic identity by neurogenin2. Sophie Peron, Leo M. Miyakoshi, Monika S. Brill, Felipe Ortega, Marisa Karow, Sergio Gascon, Benedikt Berninger

 

The effect of Wnt signaling on the localization, molecular size and activity of the beta-catenin destruction complex in vivo. Kristina Schaefer, Shiping Zhang, Teresa Bonello, Clara Williams, Daniel McKay, Mark Peifer

 

The BMP2/4 ortholog Dpp functions as an inter-organ signal that regulates developmental timing in Drosophila. Linda Setiawan, Alexis L Woods, Iswar K Hariharan

 

The effect of sonic hedgehog on motor neuron positioning in the spinal cord during chicken embryo development. Ciqing Yang, Xiaoying Li, Qiuling Li, Qiong Li, Han Li, Bichao Zhang, Juntang Lin

 

ShhN-mediated activation of Smo in the absence of Ptch1/2 function. Catalina Casillas, Henk Roelink

 

Copb2 Is Essential For Embryogenesis And Hypomorphic Mutations Cause Human Microcephaly. Andrew DiStasio, Ashley Driver, Kristen Sund, Milene Donlin, Ranjith M. Muraleedharan, Shabnam Pooya, Beth Kline-Fath, Kenneth Kaufman, Cynthia Prows, Elizabeth Schorry, Biplab DasGupta, Rolf Stottmann

 

Ttc21b is required in Bergmann glia during postnatal cerebellar development. Ashley M. Driver, Christopher Shumrick, Rolf Stottmann

 

A mitotic wave passing over the Drosophila embryo, from Liu, et al.’s preprint

 

Protein phosphatase V ensures timely cell cycle remodeling during the mid-blastula transition in Drosophila. Boyang Liu, Hung-wei Sung, Ingo Gregor, Arno Müller, Joerg Grosshans

 

UNC-5 (UNC5) mediates neuronal outgrowth patterning in Caenorhabditis elegans by regulating UNC-40 (DCC) asymmetric localization. Gerard Limerick, Xia Tang, Won Suk Lee, Ahmed Mohamed, Aseel Al-Aamiri, William G. Wadsworth

 

Cdx4 regulates the onset of spinal cord neurogenesis. Piyush Joshi, Andrew J. Darr, Isaac Skromne

 

Sagittal section of a mouse
pallium from Baumgartner, et al.’s preprint

 

Minor spliceosome inactivation in the developing mouse cortex causes self-amplifying radial glial cell death and microcephaly. Marybeth Baumgartner, Anouk M. Olthof, Katery C. Hyatt, Christopher Lemoine, Kyle Drake, Nikita Sturrock, Nhut Nguyen, Sahar Al Seesi, Rahul N. Kanadia

 

PI3K regulates intraepithelial cell positioning through Rho GTP-ases in the developing neural tube. Blanca Torroba, Antonio Herrera, Anghara Menendez, Sebastian Pons

 

Embryonic lethality in mice lacking Trim59 due to impaired gastrulation development. Xiaomin Su, Chenglei Wu, Xiaoying Ye, Ming Zeng, Zhujun Zhang, Yongzhe Che, Yuan Zhang, Lin Liu, Yushuang Lin, Rongcun Yang

 

Time-resolved Interaction Proteomics of the Putative Scaffold Protein GIGANTEA in Arabidopsis thaliana. Johanna Krahmer, Greg Goralogia, Akane Kubota, Richard S. Johnson, Young Hun Song, Karen Halliday, Michael J. MacCoss, Thierry LeBihan, Takato Imaizumi, Andrew Millar

 

Barley leaf explants from Selvaraj, et al.’s preprint

 

Cpk2, a catalytic subunit of cyclic AMP-PKA, regulates growth and pathogenesis in rice blast. Poonguzhali Selvaraj, Qing Shen, Yang Fan, Naweed I. Naqvi

 

 

| Morphogenesis & mechanics

Live imaging of heart tube development in mouse reveals alternating phases of cardiac differentiation and morphogenesis. Kenzo Ivanovitch, Susana Temino, Miguel Torres

 

Modelling Volvox epithelial folding, from Haas, et al.’s preprint

 

Mechanics and Variability of Cell Sheet Folding in the Embryonic Inversion of Volvox. Pierre A. Haas, Stephanie S.M.H. Höhn, Aurelia R. Honerkamp-Smith, Julius B. Kirkegaard, Raymond E. Goldstein

 

Visualising cell movements in gastrulating zebrafish, from Shah, et al.’s preprint.

 

Pan-embryo cell dynamics of germlayer formation in zebrafish. Gopi Shah, Konstantin Thierbach, Benjamin Schmid, Anna Reade, Ingo Roeder, Nico Scherf, Jan Huisken

 

Asymmetric cell volume changes regulate epithelial morphogenesis in zebrafish Kupffer’s vesicle. Agnik Dasgupta, Matthias Merkel, Andrew E. Jacob, Jonathan Edward Dawson, Jeffrey D. Amack, Lisa Manning

 

Decoupling the roles of cell shape and mechanical stress in orienting and cueing epithelial mitosis.Alexander Nestor-Bergmann, Georgina A Stooke-Vaughan, Georgina K Goddard, Tobias Starborg, liver E Jensen, Sarah Woolner

 

Bimodal Spindle Orientation Drives Tissue Regularity in a Proliferating Epithelium. Tara M. Finegan,Daxiang Na, Austin V. Skeeters, Nicole S. Dawney,Patrick W. Oakes, Alexander Fletcher, Dan T. Bergstralh

 

 

Dividing intestinal cells, from McKinley, et al.’s preprint

 

The actin cytoskeleton governs apical mitosis and daughter cell dispersion in intestinal epithelia. Kara L. McKinley, Nico Stuurman, Ophir D. Klein, Ron D. Vale

 

Modelling cell divisions in epithelial tubes, from Hirashima, et al.’s preprint

 

Anisotropic Cellular Mechanoresponse for Radial Size Maintenance of Developing Epithelial Tubes. Tsuyoshi Hirashima, Taiji Adachi

 

YAP and TAZ regulate adherens junction dynamics and endothelial cell distribution during vascular development. Filipa Neto, Alexandra Klaus-Bergmann, Yu-Ting Ong, Silvanus Alt, Anne-Clemence Vion, Anna Szymborska, Joana R. Carvalho, Irene Hollfinger, Eireen Bartels-Klein, Claudio A. Franco, Michael Potente, Holger Gerhardt

 

Neurexin and Neuroligin-based adhesion complexes drive axonal arborisation growth independent of synaptic activity. William D. Constance, Amrita Mukherjee, Yvette E. Fisher, Sinziana Pop, Eric Blanc, Yusuke Toyama, Darren W. Williams

 

The RacGAP βChimaerin is essential for cerebellar granule cell migration. Jason A. Estep, Wenny Wong, Yiu-Cheung E. Wong, Brian M. Loui, Martin M. Riccomagno

 

Functional limb muscle innervation prior to cholinergic transmitter specification during early metamorphosis in Xenopus. Francois M. Lambert, Laura Cardoit, Elric Courty, Marion Bougerol, Muriel Thoby-Brisson, John Simmers, Hervé Tostivint, Didier Le Ray

 

A migrating chick neural crest cell, from Genuth, et al.’s preprint

 

Chick cranial neural crest cells migrate by progressively refining the polarity of their protrusions. Miriam A Genuth, Christopher DC Allen, Takashi Mikawa, Orion Weiner

 

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

 

Clearance of senescent decidual cells by uterine natural killer cells drives endometrial remodeling during the window of implantation. Paul J. Brighton, Yojiro Maruyama, Katherine Fishwick, Pavle Vrljicak, Shreeya Tewary, Risa Fujihara, Joanne Muter, Emma S. Lucas, Taihei Yamada, Laura Woods, Raffaella Lucciola, Yie Hou Lee, Satoru Takeda, Sascha Ott, Myriam Hemberger, Siobhan Quenby, Jan J. Brosens

 

Flavonol rhamnosylation indirectly modifies the cell wall defects of RHAMNOSE BIOSYNTHESIS1 mutants by altering rhamnose flux. Adam Saffer, Vivian Irish

 

Dlic1 deletion impaired cerebellar development in mouse. Shanshan Kong, Wufan Tao

 

 

| Genes & genomes

Local and global chromatin interactions are altered by large genomic deletions associated with human brain development. Ying Zhang, Xianglong Zhang, Xiaowei Zhu, Carolin Purmann, Michael Haney, Thomas Ward, Jie Yao, Sherman Weissman, Alexander Urban

 

Nonparametric Bayesian inference of transcriptional branching and recombination identifies regulators of early human germ cell development. Christopher Andrew Penfold, Anastasiya Sybirna, John Reid, Yun Huang, Lorenz Wernisch, Zoubin Ghahramani, Murray Grant, M. Azim Surani

 

Epigenetic memory via concordant DNA methylation is inversely correlated to developmental potential of mammalian cells. Minseung Choi, Diane P Genereux, Jamie Goodson, Haneen Al-Azzawi, Shannon Q. Allain, Noah Simon, Stan Palasek, Carol B. Ware, Chris Cavanaugh, Daniel G. Miller, Winslow C. Johnson, Kevin D. Sinclair, Reinhard Stöger, Charles D. Laird

 

Transient Reduction of DNA Methylation at the Onset of Meiosis in Male Mice. Valeriya Gaysinskaya, Brendan F. Miller, Godfried W. van der Heijden, Kasper D. Hansen, Alex Bortvin

 

IVF human embryos, from McCoy, et al.’s preprint

 

Tripolar mitosis drives the association between maternal genotypes of PLK4 and aneuploidy in human preimplantation embryos. Rajiv C. McCoy, Louise J. Newnham, Christian S. Ottolini, Eva R. Hoffmann, Katerina Chatzimeletiou, Omar E. Cornejo, Qiansheng Zhan, Nikica Zaninovic, Zev Rosenwaks, Dmitri A. Petrov, Zachary P. Demko, Styrmir Sigurjonsson, Alan H. Handyside

 

Spermatocyte meioses from Jain, et al.’s preprint

 

ketu mutant mice uncover an essential meiotic function for the ancient, putative RNA helicase YTHDC2. Devanshi Jain, M. Rhyan Puno,Kathryn V. Anderson, Scott Keeney

 

rahu is a mutant allele of Dnmt3c, encoding a DNA methyltransferase homolog required for meiosis and transposon repression in the mouse male germline. Devanshi Jain, Cem Meydan, Julian Lange, Corentin Claeys Bouuaert, Christopher E Mason, Kathryn V Anderson, Scott Keeney

 

Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic. Peter A. Combs, Hunter B. Fraser

 

A non-catalytic role of TET3 promotes open chromatin and enhances global transcription. Christel Krueger, Julian R. Peat, Melanie A. Eckersley-Maslin, Timothy A. Hore, Hisham Mohammed, Simon R. Andrews, Wendy Dean, Wolf Reik

 

Model for cohesin and chromosome smoothening from Gassler, et al.’s preprint

 

 

A Mechanism of Cohesin-Dependent Loop Extrusion Organizes Zygotic Genome Architecture. Johanna Gassler, Hugo B. Brandao, Maxim Imakaev, Ilya M. Flyamer, Sabrina Ladstatter, Wendy A. Bickmore, Jan-Michael Peters, Leonid A. Mirny, Kikue Tachibana-Konwalski

 

Cyclin G And The Polycomb Repressive Complexes PRC1 And PR-DUB Cooperate For Developmental Stability. Delphine Dardalhon-Cumenal, Jerome Deraze, Camille A. Dupont, Valerie Ribeiro, Anne Coleno-Costes, Juliette Pouch, Stephane Le Crom, Helene Thomassin-Bourrel, Vincent Debat, Neel B. Randsholt, Frederique Peronnet

 

Cftr Modulates Wnt/β-Catenin Signaling and Stem Cell Proliferation in Murine Intestine. Ashlee M. Strubberg, Jinghua Liu, Nancy M. Walker, Casey D. Stefanski, R. John MacLeod, Scott T. Magness, Lane L. Clarke

 

CTCF mediated genome architecture regulates the dosage of mitotically stable mono-allelic expression of autosomal genes. Keerthivasan Raanin Chandradoss, Kuljeet Singh Sandhu

 

Cryo-ET reveals nucleosome reorganization in condensed mitotic chromosomes in vivo. Shujun Cai, Chen Chen, Zhi Yang Tan, Jian Shi, Lu Gan

 

Maternal RNA-directed DNA methylation is required for seed development in Brassica rapa. Jeffrey Grover, Timmy Kendall, Abdul Baten, Graham J. King, Rebecca A. Mosher

 

Frequent paramutation-like features of natural epialleles in tomato. Quentin Gouil, David Baulcombe

 

Regulatory divergence of flowering time genes in the allopolyploid Brassica napus. Marc Jones, Nick Pullen, Rachel Wells, Martin Trick, Judith Irwin, Richard Morris

 

The roles of Conserved Domains in DEMETER-Mediated Active DNA Demethylation in planta. Changqing Zhang, Yu-Hung Hung, Xiang-Qian Zhang, Dapeng Zhang, Wenyan Xiao, Lakshminarayan M. Iyer, L. Aravind, Jin Hoe Huh, Tzung-Fu Hsieh

 

Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat. Jemima Brinton, James Simmonds, Cristobal Uauy

 

The genetic architecture of the network underlying flowering time variation in Arabidopsis thaliana. Eriko Sasaki, Florian Frommlet, Magnus Nordborg

 

Somatic developmental defects in dmrad51/spnA mutant show low temperature sensitivity with enhanced genomic damages and cell death. Chaitali Khan, Sonia Muliyil,Champakali Ayyub, Basuthkar J. Rao

 

Induction of X-chromosome Inactivation by the Histone Demethylase SMCX/KDM5C. Srimonta Gayen, Emily Maclary, Yumie Murata-Nakamura, Christina N. Vallianatos, Robert S. Porter, Patricia M. Garay, Shigeki Iwase, Sundeep Kalantry

 

Incomplete MyoD-induced transdifferentiation is associated with chromatin remodeling deficiencies. Dinesh Manandhar, Lingyun Song, Ami Kabadi, Jennifer Kwon, Lee Edsall, Melanie Ehrlich, Koji Tsumagari, Charlie Gersbach, Gregory Crawford, Raluca Gordan

 

Heterogeneity and Intrinsic Variation in Spatial Genome Organization. Elizabeth Finn, Gianluca Pegoraro, Hugo B. Brandao, Anne-Laure Valton, Marlies E. Oomen, Job Dekker, Leonid Mirny, Tom Misteli

 

Assessing eRNAs associated with a cytokine-sensing mammary super-enhancer. Chaochen Wang, Tyler Kuhns, Christian Reinbold, Michaela Willi, Lothar Hennighausen

 

Mitotic chromosomes fold by condensin-dependent helical winding of chromatin loop arrays. Johan H. Gibcus, Kumiko Samejima, Anton Goloborodko, Itaru Samejima, Natalia Naumova, Masato Kanemaki, Linfeng Xie, James R. Paulson, William C. Earnshaw, Leonid A. Mirny, Job Dekker

 

Inbred or Outbred? Genetic diversity in laboratory rodent colonies. Thomas D. Brekke, Katherine A. Steele, John F. Mulley

 

| Stem cells, regeneration & disease modelling

Inter-homologue repair in fertilized human eggs? Dieter Egli, Michael Zuccaro, Michal Kosicki, George Church, Allan Bradley, Maria Jasin

 

Committed hemopoietic progenitors, not stem cells, are the principal responders to Hox gene transduction. Harvey Lim, Salima Janmohamed, Patricia Benveniste, Robert Herrington, Mary Barbara, Catherine Frelin, Deborah Hyam, Christopher Paige, Juan-Carlos Zuniga-Pflucker, Carol Stocking, Jana Krosl, Guy Sauvageau, Norman Iscove

 

BMP signalling is critical for maintaining homeostasis of hair follicles and intestine in adult mice. Aditi Nag, Pallavi Nigam, Abhishek L. Narayanan, Megha Kumar, Ritika Ghosal, Jonaki Sen, Amitabha Bandyopadhyay

 

Accelerated human liver progenitor generation from pluripotent stem cells by inhibiting formation of unwanted lineages. Lay Teng Ang, Antson Tan, Matias Ilmari Autio, Joanne Su-hua Goh, Siew Hua Choo, Kian Leong Lee, Bangfen Pan, Jianmin Tan, Jane Jia Hui Lee, Isabelle Kai Xin Yeo, Chloe Jin Yee Wong, Jen Jen Lum, Chet Hong Loh, Christina Ying Yan Lim, Jueween Ling Li Oh, Cheryl Pei Lynn Chia, Angela Chen, Qing Feng Chen, Irving Weissman, Kyle M. Loh, Bing Lim

 

Transgene-free hematopoietic stem and progenitor cells from human induced pluripotent stem cells. Laurence Guyonneau-Harmand, Bruno L’Homme, Brigitte Birebent, Christophe Desterke, Nathalie Chevallier, Loic Garcon, Helene Lapillonne, Marc Benderitter, Francois Delhommeau, Thierry Jaffredo, Alain Chapel, Luc Douay

 

In situ’d Xenopus from Ciau-Utix, et al.’s preprint

 

CBFβ initiates the hematopoietic stem cell program without obligatory binding to RUNX. Aldo Ciau-Uitz, Philip Pinheiro, Arif Kirmizitas, Claire Fernandez, Roger Patient

 

Single-cell RNA-Sequencing uncovers transcriptional states and fate decisions in haematopoiesis. Emmanouil I Athanasiadis, Jan Botthof, Helena Andres, Lauren Ferreira, Pietro Lio, Ana Cvejic

 

Assessment of clonal kinetics reveals multiple trajectories of dendritic cell development. Dawn Lin, Andrey Kan, Jerry Gao, Edmund Crampin, Philip D. Hodgkin, Shalin H. Naik

 

Regulation of mesenchymal stem cell function by TGFβ-1 on mast cell extracellular vesicles — role of endosomal retention. Yanan Yin, Ganesh Vilas Shelke, Su Chul Jang, Cecilia Lasser, Stefan Wennmalm, Hans Jurgen Hoffmann, Jonas Nilsson, Li Li, Yong Song Gho, Jan Lotvall

 

Transitioning chromatin states in stem cells, from Battle, et al.’s preprint

 

Epigenomic and 3D genome architecture in naïve and primed human embryonic stem cell states. Stephanie Battle, Naresh Doni Jayavelu, Robert N. Azad, Jennifer Hesson, Faria N. Ahmed, Joseph A. Zoller, Julie Mathieu, Hannele Ruohola-Baker, Carol B. Ware, Raymond Hawkins

 

Resolution of Reprogramming Transition States by Single Cell RNA-Sequencing. Lin Guo, Xiaoshan Wang, Mingwei Gao, Lihui Lin, Junqi Kuang, Yuanbang Mai, Fang Wu, He Liu, Jiaqi Yang, Shilong Chu, Hong Song, Yujian Liu, Jiadong Liu, Jinyong Wang, Guangjin Pan, Andrew P. Hutchins, Jing Liu, Jiekai Chen, Duanqing Pei

 

Delayed activation of the DNA replication licensing system in Lgr5(+) intestinal stem cells. Thomas Carroll, Ian Newton, Julian J. Blow, Inke Nathke

 

Expression of lamina proteins Lamin Dm0 and Kugelkern suppresses stem cell proliferation. Roman Petrovsky, Joerg Grosshans

 

BCL-3 enhances β-catenin signalling in colorectal tumour cells promoting a cancer stem cell phenotype. Danny N. Legge, Alex P. Shephard, Tracey J. Collard, Alexander Greenhough, Adam C. Chambers, Richard W. Clarkson, Christos Paraskeva, Ann C. Williams

 

Acquisition of cell migration defines NK cell differentiation from hematopoietic stem cell precursors. Barclay J. Lee, Emily M. Mace

 

Induction of differentiation and metabolic reprogramming in human hepatoma cells by adult human serum. Rineke H. Steenbergen, Martin Oti, Rob ter Horst, Wilson Tat, Chris Neufeldt, Alexandr Belovodskiy, Tiing Tiing Chua, Woo Jung Cho, Michael Joyce, Bas E. Dutilh, D. Lorne Tyrrell

 

On the numbers and division rates of stem cells in human tissues. Augusto Gonzalez

 

Activating the regenerative potential of Müller glia cells in a regeneration-deficient retina. Katharina Lust, Joachim Wittbrodt

 

Inhibition of granulocyte ROS production by opioids prevents regeneration. Elodie Labit, Lise Rabiller, Christophe Guissard, Mireille Andre, Christine Rampon, Corinne Barreau, Beatrice Cousin, Audrey Carriere, Margaux Raffin, Gilles Mithieux, Mohamad Ala Eddine, Bernard Pipy, Anne Lorsignol, Sophie Vriz, Cecile Dromard, Louis Casteilla

 

Tracking ectopic vertebra formation in injured zebrafish, from Lopez-Baez, et al.’s preprint

 

Wilms Tumor 1b defines a wound-specific sheath cell subpopulation associated with notochord repair. Juan Carlos Lopez-Baez, Zhiqiang Zeng, Witold Rybski, Leonie F. A. Huitema, Alessandro Brombin, Rodney M. Dale, Koichi Kawakami, Christoph Englert, Stefan Schulte-Merker, Nicholas D. Hastie, E. Elizabeth Patton

 

Loss of lrrk2 impairs dopamine catabolism, cell proliferation, and neuronal regeneration in the zebrafish brain. Stefano Suzzi, Reiner Ahrendt, Stefan Hans, Svetlana A. Semenova, Saygin Bilican, Shady Sayed, Sylke Winkler, Sandra Spiess, Jan Kaslin, Pertti Panula, Michael Brand

 

Replication of early and recent Zika virus isolates throughout mouse brain development. Amy B. Rosenfeld, David J. Doobin, Audrey L. Warren, Vincent R. Racaniello, Richard B. Vallee

 

Human macrophages survive and adopt activated genotypes in living zebrafish. Colin D. Paul, Alexus Devine, Kevin Bishop, Qing Xu, Kathryn M. Daly, Chaunte Lewis, Daniel S. Green, Jack R. Staunton, Swati Choksi, Zheng-Gang Liu, Raman Sood, Kandice Tanner

 

A transgenic zebrafish model for the in vivo study of the blood and choroid plexus brain barriers using claudin 5. Lisanne van Leeuwen, Robert Evans, Kin Ki Jim, Theo Verboom, Xiaoming Fang, Aleksandra Bojarczuk, Jarema Malicki, Simon Johnston, Astrid van der Sar

 

A Zebrafish Model For Ocular Tuberculosis. Kevin Takaki, Lalita Ramakrishnan, Soumyava Basu

 

Whole exome sequencing of ENU-induced thrombosis modifier mutations in the mouse. Kärt Tomberg, Randal Westrick, Emilee Kotnik, David Siemieniak, Guojing Zhu, Thomas Saunders, Audrey Cleuren, VDavid Ginsburg

 

Asleep at the Wheel: Forward Genetic ENU Mutagenesis Screen for Mouse Models of Chronic Fatigue Identifies a Mutation in Slc2a4 (GLUT4). Marleen H. M. de Groot, Carlos M. Castorena, Vivek Kumar, Jennifer A. Mohawk, Newaz I. Ahmed, Joseph S. Takahashi

 

Assaying protocadherins and cell mixing, from Pederick, et al.’s preprint.

 

Abnormal cell sorting underlies the unique X-linked inheritance of PCDH19 Epilepsy. Daniel Pederick, Kay Richards, Sandra Piltz, Simone Mandelstam, Russell Dale, Ingrid Scheffer, Jozef Gecz, Steve Petrou, James Hughes, Paul Thomas

 

Post-transcriptional remodelling is temporally deregulated during motor neurogenesis in human ALS models. Raphaelle Luisier, Giulia E. Tyzack, Claire E. Hall, Jernej Ule, Nicholas M. Luscombe, Rickie Patani

 

A Caenorhabditis elegans model of adenylosuccinate lyase deficiency reveals neuromuscular and reproductive phenotypes of distinct etiology. Adam R. Fenton, Haley N. Janowitz, Melanie R. McReynolds, Wenqing Wang, Wendy Hanna-Rose

 

Whole chromosome loss in tetraploid cells confers tumorigenic potential in a mouse allograft model. Rozario Thomas, Daniel H. Marks, Yvette Chin, Robert Benezra

 

Zinc detoxification: a functional genomics and transcriptomics analysis in Drosophila melanogaster cultured cells. Stephanie Mohr, Kirstin Rudd, Yanhui Hu, Wei Roc Song, Quentin Gilly, Michael Buckner, Benjamin E. Housden, Colleen Kelley, Jonathan Zirin, Rong Tao, Gabriel Amador, Katarzyna Sierzputowska, Aram Comjean, Norbert Perrimon

 

Expanding primary cells from mucoepidermoid and other salivary gland neoplasms for genetic and chemosensitivity testing. Ahmad M. Alamri, Xuefeng Liu, Jan K. Blancato, Bassem R. Haddad, Weisheng Wang, Xiaogang Zhong, Sujata Choudhary, Ewa Krawczyk, Bhaskar V. Kallakury, Bruce J. Davidson, Priscilla A. Furth

 

Monsters in the uterus: A parthenogenetic quasi-program causes teratoma-like tumors during aging in wild-type C. elegans. Hongyuan Wang, Yuan Zhao, Marina Ezcurra, Ann Gilliat, Josephine Hellberg, Alexandre Benedetto, Trin Athigapanich, Johannes Girstmair, Max Telford, Zhizhou Zhang, David Gems

 

Mitochondrial sirtuins sir-2.2 and sir-2.3 regulate lifespan in C. elegans. Sarah M. Chang, Melanie R. McReynolds,Wendy Hanna-Rose

 

Global accumulation of circRNAs during aging in Caenorhabditis elegans. Mariela Cortés-López, Matthew Gruner, Daphne A. Cooper, Hannah N. Gruner, Alexandru-Ioan Voda, Alexander van der Linden, Pedro Miura

 

Evo-devo & evo

Insulin resistance in cavefish as an adaptation to a nutrient-limited environment. Ariel Aspiras, Misty Riddle, Karin Gaudenz, Robert Peuss, Jenny Sung, Brian Martineau, Megan Peavey, Andrew Box, Julius A. Tabin, Suzanne McGaugh, Richard Borowsky, Clifford J. Tabin, Nicolas Rohner

 

Whole-mount in situ hybridization in planarians, from Cheng, et al.’s preprint

 

Cellular, ultrastructural and molecular analyses of epidermal cell development in the planarian Schmidtea mediterranea. Li-Chun Cheng, Kimberly C. Tu, Chris W. Seidel, Sofia M. C. Robb, Fengli Guo, Alejandro Sánchez Alvarado

 

Differences in the genetic control of early egg development and reproduction between C. elegans and its parthenogenetic relative D. coronatus. Christopher Kraus, Philipp H. Schiffer, Hiroshi Kagoshima, Hideaki Hiraki, Theresa Vogt, Michael Kroiher, Yuji Kohara, Einhard Schierenberg

 

Dramatic evolution of body length due to post-embryonic changes in cell size in a newly discovered close relative of C. elegans. Gavin C. Woodruff, Patrick C. Phillips, Natsumi Kanzaki

 

Insights into regeneration from the genome, transcriptome and metagenome analysis of Eisenia fetida. Aksheev Bhambri, Neeraj Dhaunta, Surendra Singh Patel, Mitali Hardikar, Nagesh Srikakulam, Shruti Shridhar, Shamsudheen Vellarikkal, Hemant Suryawanshi, Rajesh Pandey, Rijith Jayarajan, Ankit Verma, Vikram Kumar, Abhishek Bhatt, Pradeep Gautam, Manish Rai, Jameel Ahmed Khan, Bastian Fromm, Kevin J. Peterson, Vinod Scaria, Sridhar Sivasubbu, Beena Pillai

 

Argentinian pearlfish embryos from Van Dooren & Varela-Lasheras’ preprint

 

Desiccation plasticity and diapause in the Argentinian pearlfish Austrolebias bellottii. Tom Van Dooren, Irma Varela-Lasheras

 

Maternal X chromosome upregulation in both sexes initiates dosage compensation evolution. Aline Muyle, Niklaus Zemp, Cecile Fruchard, Radim Cegan, Jan Vrana, Clothilde Deschamps, Raquel Tavares, Franck Picard, Roman Hobza, Alex Widmer, Gabriel Marais

 

Natural variation at FLOWERING LOCUS T2 mediates local adaptation in a key life history trait in European aspen. Jing Wang, Jihua Ding, Biyue Tan, Kathryn M. Robinson, Ingrid H. Michelson, Anna Johansson, Björn Nystedt, Douglas G. Scofield, Ove Nilsson, Stefan Jansson, Nathaniel R. Street, Pär K. Ingvarsson

 

Hemimetabolous genomes reveal molecular basis of termite eusociality. Mark C. Harrison, Evelien Jongepier, Hugh M. Robertson, Nicolas Arning, Tristan Bitard-Feildel, Hsu Chao, Christopher P. Childers, Huyen Dinh, Harshavardhan Doddapaneni, Shannon Dugan, Johannes Gowin, Carolin Greiner, Yi Han, Haofu Hu, Daniel S. T. Hughes, Ann-Kathrin Huylmans, Carsten Kemena, Lukas P. M. Kremer, Sandra L. Lee, Alberto Lopez-Ezquerra, Ludovic Mallet, Jose M. Monroy-Kuhn, Annabell Moser, Shwetha C. Murali, Donna M. Muzny, Saria Otani, Maria-Dolors Piulachs, Monica Poelchau, Jiaxin Qu, Florentine Schaub, Ayako Wada-Katsumata, Kim C. Worley, Qiaolin Xie, Guillem Ylla, Michael Poulsen, Richard A. Gibbs, Coby Schal, Stephen Richards, Xavier Belles, Judith Korb, Erich Bornberg-Bauer

 

Comprehensive phylogenomic analyses resolve cnidarian relationships and the origins of key organismal traits. Ehsan Kayal, Bentlage Bastian, M Sabrina Pankey, Aki Ohdera, Monica Medina, David C Plachetzki​, Allen Collins, Joseph F Ryan

 

Gene markers for exon capture and phylogenomics in ray-finned fishes. Jiamei Jiang, Hao Yuan, Xin Zheng, Qian Wang, Ting Kuang, Jingyan Li, Junning Liu, Shuli Song, Weicai Wang, Fangyaun Cheng, Hongjie Li, Junman Huang, Chenhong Li

 

Opsin phylogenomic tree from Lowe, et al.’s preprint

 

The crowns have eyes: Multiple opsins found in the eyes of the Crown-of-Thorns Starfish Acanthaster planci. Elijah K. Lowe, Anders Garm, Esther Ullrich-Luter, Maria Ina Arnone

 

EVOLUTIONARY ANALYSIS OF CANDIDATE NON-CODING ELEMENTS REGULATING NEURODEVELOPMENTAL GENES IN VERTEBRATES. Francisco J. Novo

 

Gene expression drives the evolution of dominance. Christian D. Huber, Arun Durvasula, Angela M. Hancock, Kirk E. Lohmueller

 

On somatic constraints in the evolution of multicellularity. Andrii Rozhok, James DeGregori

 

Towards physical principles of biological evolution. Mikhail I Katsnelson, Yuri I. Wolf, Eugene V. Koonin

 

 

Cell biology

Size control in mammalian cells involves modulation of both growth rate and cell cycle duration. Clotilde Cadart, Sylvain Monnier, Jacopo Grilli, Rafaele Attia, Emmanuel Terriac, Buzz Baum, Marco Cosentino-Lagomarsino, Matthieu Piel

 

Positive Feedback Between Contractile Ring Myosin and Ring-Directed Cortical Flow Drives Cytokinesis. Renat Khaliullin, Rebecca Green, Linda Shi, Michael Berns, J. Sebastian Gomez-Cavazos, Arshad Desai, Karen Oegema

 

PCM assembly and disassembly in c. elegans embryos, from Enos, et al.’s preprint

 

Phosphatase PP2A and microtubule pulling forces disassemble centrosomes during mitotic exit. Stephen J. Enos, Martin Dressler, Beatriz Ferreira Gomes, Anthony A. Hyman, Jeffrey B. Woodruff

 

Kif2 microtubule depolymerase is required for unequal cell division and localizes to a subdomain of cortical endoplasmic reticulum. Vlad Costache, Celine Hebras, Gerard Pruliere, Lydia Besnardeau, Margaux Failla, Richard R. Copley, David Burgess, Janet Chenevert, Alex McDougall

 

Rapid degradation and 3D CLEM of condensin reveal chromatin compaction uncoupled from chromosome architecture in mitosis. Kumiko Samejima, Daniel G. Booth, Hiromi Ogawa, James R. Paulson, Linfeng Xie, Cara A. Watson, Melpomeni Platani, Masato T. Kanemaki, William C. Earnshaw

 

Spindle asymmetry drives non-Mendelian chromosome segregation. Takashi Akera, Lukáš Chmátal, Emily Trimm, Karren Yang, Chanat Aonbangkhen, David M. Chenoweth, Carsten Janke, Richard M. Schultz, Michael A. Lampson

 

Kinesin-6 KIF20B is required for efficient cytokinetic furrowing and timely abscission in human cells. Kerstin M Janisch, Katrina C McNeely, Joseph M Dardick, Samuel H Lim, Noelle D Dwyer

 

Conformational states during vinculin unlocking differentially regulate focal adhesion properties. Dror Shlomo Chorev, Tova Volberg, Ariel Livne, Miriam Eisenstein, Bruno Martins, Zvi Kam, Brigitte Jockusch, Ohad Medalia, Michal Sharon, Benjamin Geiger.

 

The PtdIns3P-binding protein Phafin2 escorts macropinosomes through the cortical actin cytoskeleton. Kay Oliver Schink, Kia Wee Tan, Helene Spangenberg, Domenica Martorana, Marte Sneeggen, Coen Campsteijn, Camilla Raiborg, Harald Stenmark

 

Mitosis in the Drosophila brain, from Blum, et al.’s preprint

 

Lhr and Hmr are required for sister chromatid detachment during anaphase but not for centromere function. Jacob A. Blum, Silvia Bonaccorsi, Marta Marzullo, Valeria Palumbo, Yukiko Yamashita, Daniel Barbash, Maurizio Gatti

 

Systematic analysis of atx-2 suppressors reveals a novel regulator of PAR-5/14-3-3sigma function during mitosis in Caenorhabditis elegans. Megan M. Gnazzo, Alex R. Villarreal, Ahna R. Skop

 

Microtubule dynamics regulates mitochondrial fission. Kritika Mehta, Manjyot Kaur Chug, Siddharth Jhunjhunwala, Vaishnavi Ananthanarayanan

 

TRIP6 inhibits the Hippo signaling pathway in response to tension at adherens junctions. Shubham Dutta, Sebastian Mana-Capelli, Murugan Paramasivam, Ishani Dasgupta, Heather Cirka, Kris Billiar, Dannel McCollum

 

The contributions of the actin machinery to endocytic membrane bending and vesicle formation. Andrea Picco,Wanda Kukulski, Hetty E. Manenschijn, Tanja Specht, John A. G. Briggs, Marko Kaksonen

 

Modelling

Memory effects in gene regulatory networks reveal key properties of dynamical spatial patterning. Edgar Herrera-Delgado, Ruben Perez-Carrasco, James Briscoe, Peter Sollich

 

Modelling migration in the neural crest, from Merchant, Edelstein-Keshet & Feng’s preprint

 

A Rho-GTPase based model explains spontaneous collective migration of neural crest cell clusters. Brian Merchant, Leah Edelstein-Keshet, James Feng

 

Spontaneous Chiral Symmetry Breaking in Planar Polarized Epithelia. Jeremy Hadidjojo, David K. Lubensky

 

The Role of Criticality of Gene Regulatory Networks in Morphogenesis. Hyobin Kim, Hiroki Sayama

 

SOMSC: Self-Organization-Map for High-Dimensional Single-Cell Data of Cellular States and Their Transitions. Tao Peng, Qing Nie

 

Compartmental and spatial rule-based modeling with Virtual Cell (VCell). Mikhail L. Blinov, James C. Schaff, Dan Vasilescu, Ion I. Moraru, Judy E. Bloom, Leslie M. Loew

 

Tools & resources

| Imaging etc.

Magnetised zebrafish, from Berndt, et al.’s preprint

 

Dynamic, non-contact 3D sample rotation for microscopy. Frederic Berndt, Gopi Shah, Jan Brugues, Jan Huisken

 

Brillouin imaging from Schlüßler, et al.’s preprint

 

Mechanical mapping of spinal cord development and repair in living zebrafish larvae using Brillouin microscopy. Raimund Schlüßler, Stephanie Möllmert, Shada Abuhattum, Conrad Möckel, Conrad Zimmermann, Jürgen Czarske, Jochen Guck

 

A scheme for 3-dimensional morphological reconstruction and force inference in the early C. elegans embryo. Muzhi Xu, Yicong Wu, Hari Shroff, Min Wu, Madhav Mani

 

Spatial protein analysis in developing tissues: a sampling-based image processing approach. Karolis Leonavicius, Christophe Royer, Antonio M. A. Miranda, Richard Tyser, Annemarie Kip, Shankar Srinivas

 

Structural and functional diversity of a dense sample of retinal ganglion cells. J. Alexander Bae, Shang Mu, Jinseop S. Kim, Nicholas L. Turner, Ignacio Tartavull, Nico Kemnitz, Chris S. Jordan, Alex D. Norton, William M. Silversmith, Rachel Prentki, Marissa Sorek, Celia David, Devon L. Jones, Doug Bland, Amy L. R. Sterling, Jungman Park, Kevin L. Briggman, H. Sebastian Seung, the EyeWirers

 

Leaf-GP: An Open and Automated Software Application for Measuring Growth Phenotypes for Arabidopsis and Wheat. Ji Zhou, Christopher Applegate, Albor Dobon Alonso, Daniel Reynolds, Simon Orford, Michal Mackiewicz, Simon Griffiths, Steven Penfield, Nick Pullen

 

An ensemble learning approach to auto-annotation for whole-brain C. elegans imaging. Stephen Wu, Yu Toyoshima, Moon Sun Jang, Manami Kanamori, Takayuki Teramoto, Yuishi Iwasaki, Takeshi Ishihara, Yuichi Iino, Ryo Yoshida

 

Labeling RNAs in live cells using malachite green aptamer scaffolds as fluorescent probes. Venkata Siddartha Yerramilli, Kyung Hyuk Kim

 

OptoGap: an optogenetics-enabled assay for quantification of cell-cell coupling in multicellular cardiac tissue. Jinzhu Yu, Patrick M. Boyle, Aleksandra Klimas, John C. Williams, Natalia A. Trayanova, Emilia Entcheva

 

X10 Expansion Microscopy Enables 25 nm Resolution on Conventional Microscopes. Sven Truckenbrodt, Manuel Maidorn, Dagmar Crzan, Hanna Wildhagen, Selda Kabatas, Silvio O. Rizzoli

 

3D Single-Molecule Super-Resolution Microscopy With A Tilted Light Sheet. Anna-Karin Gustavsson, Petar N. Petrov, Maurice Y. Lee, Yoav Shechtman, W. E. Moerner

 

Single-shot super-resolution total internal reflection fluorescence microscopy. Min Guo, Panagiotis Chandris, John Paul Giannini, Adam J. Trexler, Robert Fischer, Jiji Chen, Harshad D. Vishwasrao, Ivan Rey-Suarez, Yicong Wu, Clare M. Waterman, George H. Patterson, Arpita Upadhyaya, Justin Taraska, Hari Shroff

 

Intra-voxel incoherent motion magnetic resonance imaging of the living human fetus: the technique and within-subject reproducibility. Andras Jakab, Ruth Tuura, Raimund Kottke, Christian Kellenberger, Ianina Scheer

 

Ultra-fast super-resolution imaging of biomolecular mobility in tissues. Helen Miller, Jason Cosgrove, Adam J. M. Wollman, Peter J. O’Toole, Mark Coles, Mark C. Leake

 

A dual-mode mobile phone microscope using the onboard camera flash and ambient light. Antony Orth, Emma R Wilson, Jeremy Thompson, Brant C Gibson

 

Fast and Powerful Genome Wide Association Analysis of Dense Genetic Data with High Dimensional Imaging Phenotypes. Habib Ganjgahi, Anderson M. Winkler, David C. Glahn, John Blangero, Brian Donohue, Peter Kochunov, Thomas E. Nichols

 

Systematic analysis of cell phenotypes and cellular social networks in tissues using the histology topography cytometry analysis toolbox (histoCAT). Denis Schapiro, Hartland Warren Jackson, Swetha Raghuraman, Vito Riccardo Tomaso Zanotelli, Jana R Fischer, Daniel Schulz, Charlotte Giesen, Raul Catena,Zsuzsanna Varga, Bernd Bodenmiller

 

| Genome tools

Deeper sequencing at unexpected CRISPR/Cas9 off-target sites in vivo : A response to Editas, Intellia, Beacon, ToolGen and others. Kellie A. Schaefer, Wen-Hsuan Wu, Benjamin W. Darbro, Diana F. Colgan, Stephen H. Tsang, Alexander G. Bassuk, Vinit B. Mahajan

 

Inhibition of p53 improves CRISPR/Cas-mediated precision genome editing. Emma Haapaniemi, Sandeep K. Botla, Jenna Persson, Bernhard Schmierer, Jussi Taipale

 

The effect of sequence mismatches on binding affinity and endonuclease activity are decoupled throughout the Cas9 binding site. Liyang Zhang, Hans Tomas Rube, Harmen J. Bussemaker, Miles A. Pufall

 

NmeCas9 is an intrinsically high-fidelity genome editing platform. Nadia Amrani, Xin D. Gao, Pengpeng Liu, Ankit Gupta, Alireza Edraki, Raed Ibraheim, Kanae E. Sasaki, Lihua Julie Zhu, Scot A. Wolfe, Erik J. Sontheimer

 

Endogenous gene tagging from Li, et al.’s preprint

 

Design and specificity of long ssDNA donors for CRISPR-based knock-in. Han Li, Kyle A. Beckman, Veronica Pessino, Bo Huang, Jonathan S. Weissman, Manuel D. Leonetti

 

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. M. Ryan Corces, Alexandro E. Trevino, Emily G. Hamilton, Peyton G. Greenside, Nicholas A. Sinnott-Armstrong, Sam Vesuna, Ansuman T. Satpathy, Adam J. Rubin, Kathleen S. Montine, Beijing Wu, Arwa Kathiria, Seung Woo Cho, Maxwell R. Mumbach, Ava C. Carter, Maya Kasowski, Lisa A. Orloff, Viviana I. Risca, Anshul Kundaje, Paul A. Khavari, Thomas J. Montine, William J. Greenleaf, Howard Y. Chang

 

High resolution annotation of Zebrafish transcriptome using long-read sequencing. German Nudelman, Antonio Frasca, Brandon Kent, Kirsten Edepli-Sadler, Stuart C. Sealfon, Martin J. Walsh, Elena Zaslavsky

 

Transcriptomes of major renal collecting-duct cell types in mouse identified by single-cell RNA-Seq. Lihe Chen, Jae Wook Lee, Chung-Lin Chou, Anilkumar Nair, Maria Agustina Battistone, Teodor Paunescu, Maria Mekulova, Sylvie Breton, Jill W. Verlander, Susan Wall, Dennis Brown, Maurice B. Burg, Mark A. Knepper.

 

Co-detection of circular and linear RNAs, from Zaghlool, et al.’s preprint

 

High throughput expression profiling and in situ screening of circular RNAs in tissues. Ammar Zaghlool,Adam Ameur, Chenglin Wu, Jakub Westholm, Adnan Niazi, Manimozhi Manivannan, Kelli Bramlett, Mats Nilsson, Lars Feuk

 

Scanpy for analysis of large-scale single-cell gene expression data. F. Alexander Wolf, Philipp Angerer, Fabian J. Theis

 

Advanced whole genome sequencing and analysis of fetal genomes from amniotic fluid. Qing Mao, Robert Chin, Weiwei Xie, Yuqing Deng, Huixin Xu, Rebecca Yu Zhang, Quan Shi, Erin E. Peters, Natali Gulbahce, Zhenyu Li, Fang Chen, Radoje Drmanac, Brock A. Peters

 

Active ribosome profiling with RiboLace. Massimiliano Clamer, Toma Tebaldi, Fabio Lauria, Paola Bernabo, Rodolfo F. Gomez-Biagi, Elena Perenthaler, Daniele Gubert, Laura Pasquardini, Graziano Guella, Ewout J. N. Groen, Thomas H. Gillingwater, Alessandro Quattrone, Gabriella Viero

 

Tagmentation-Based Mapping (TagMap) of Mobile DNA Genomic Insertion Sites. David L. Stern

 

A Large-Scale Binding and Functional Map of Human RNA Binding Proteins. Eric L Van Nostrand, Peter Freese, Gabriel A Pratt, Xiaofeng Wang, Xintao Wei, Steven M Blue, Daniel Dominguez, Neal A L Cody, Sara Olson, Balaji Sundararaman, Rui Xiao, Lijun Zhan, Cassandra Bazile, Louis Philip Benoit Bouvrette, Jiayu Chen, Michael O Duff, Keri Garcia, Chelsea Gelboin-Burkhart, Abigail Hochman, Nicole J Lambert, Hairi Li, Thai B Nguyen, Tsultrim Palden, Ines Rabano, Shashank Sathe, Rebecca Stanton, Ashley L Louie, Stefan Aigner, Julie Bergalet, Bing Zhou, Amanda Su, Ruth Wang, Brian A Yee, Xiang-Dong Fu, Eric Lecuyer, Christopher B Burge, Brenton Graveley, Gene W Yeo

 

Detection and removal of barcode swapping in single-cell RNA-seq data. Jonathan A. Griffiths, Aaron T. L. Lun, Arianne C. Richard, Karsten Bach, John C. Marioni

 

Fluorescent roots and leaves from Reynoso, et al.’s preprint

 

Nuclear transcriptomes at high resolution using retooled INTACT. Mauricio A. Reynoso, Germain C. Pauluzzi, Kaisa Kajala, Sean Cabanlit, Joel Velasco, Jeremie Bazin, Roger Deal, Neelima R. Sinha, Siobhan M. Brady, Julia Bailey-Serres

 

In situ genome editing method suitable for routine generation of germline modified animal models. Masato Ohtsuka, Hiromi Miura, Naomi Arifin, Shingo Nakamura, Kenta Wada, Channabasavaiah Gurumurthy, Masahiro Sato

 

TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information. Shubhada R. Kulkarni,Dries Vaneechoutte, Jan Van de Velde, Klaas Vandepoele

 

The Oyster River Protocol: A Multi Assembler and Kmer Approach For de novo Transcriptome Assembly. Matthew D MacManes

 

Characterizing a thermostable Cas9 for bacterial genome editing and silencing. Ioannis Mougiakos, Prarthana Mohanraju, Elleke F. Bosma, Valentijn Vrouwe, Max Finger Bou, Mihris I. S. Naduthodi, Alexander Gussak, Rudolf B. L. Brinkman, Richard van Kranenburg, John van der Oost

 

Nonivasive prenatal diagnosis of single-gene disorders using droplet digital PCR. Joan Camunas-Soler, Hojae Lee, Louanne Hudgins, Susan R Hintz, Yair J Blumenfeld, Yasser Y El-Sayed, Stephen R Quake

 

GIC: A computational method for predicting the essentiality of long noncoding lncRNAs. Pan Zeng, Ji Chen, Yuan Zhou, Jichun Yang, Qinghua Cui

 

Oasis2.0: improved online analysis of small RNA-seq data. Raza-Ur Rahman, Abhivyakti Gautam, Joern Bethune, Abdul Sattar, Maksims Fiosins, Daniel Sumner Magruder, Vincenzo Capece, Orr Shomroni, Stefan Bonn

 

COGEM: A Toolbox for Computational Genomics in Matlab. Theodore J. Perkins

 

Euplotid: A Linux-based platform to physically edit the genome. Diego Borges-Rivera

 

DrImpute: Imputing dropout events in single cell RNA sequencing data. Il-Youp Kwak, Wuming Gong, Naoko Koyano-Nakagawa, Daniel Garry

 

Efficient in situ barcode sequencing using padlock probe-based BaristaSeq. Xiaoyin Chen, Yu-Chi Sun, George M. Church, Je Hyuk Lee, Anthony M. Zador

 

Notos – a Galaxy tool to analyze CpN observed expected ratios for inferring DNA methylation types. Ingo Bulla, Benoît Aliaga, Virginia Lacal, Jan Bulla, Christoph Grunau, Cristian Chaparro

 

Chiron: Translating nanopore raw signal directly into nucleotide sequence using deep learning. Haotian Teng, Michael B. Hall, Tania Duarte, Minh Duc Cao, Lachlan Coin

 

SEA: The Small RNA Expression Atlas. Raza-Ur Rahman, Abdul Sattar, Maksims Fiosins, Abhivyakti Gautam, Daniel Sumner Magruder, Joern Bethune, Sumit Madan, Juliane Fluck, Stefan Bonn

 

Enabling cross-study analysis of RNA-Sequencing data. Qingguo Wang, Joshua Armenia, Chao Zhang, Alexander V Penson, Ed Reznik, Liguo Zhang, Thais Minet, Angelica Ochoa, Benjamin E Gross, Christine A Iacobuzio-Donahue, Doron Betel, Barry S Taylor, Jianjiong Gao, Nikolaus Schultz

 

DEsingle: A new method for single-cell differentially expressed genes detection and classification.Zhun Miao, View ORCID ProfileXuegong Zhang

 

SeedVicious: analysis of microRNA target and near-target sites. Antonio Marco

 

NeatSeq-Flow: A Lightweight Software for Efficient Execution of High Throughput Sequencing Workflows. Menachem Y. Sklarz, Michal Gordon, Vered Chalifa-Caspi

 

SureMap: Versatile, Error Tolerant, and High Sensitive Read Mapper. MohammadJavad Rezaei Seraji, Seyed Abolfazl Motahari

 

Research practice

 

The growth of the Information Exchange Group, from Matthew Cobb’s preprint (credit: Cold Spring Harbor Laboratory Archive)

 

The prehistory of biology preprints: a forgotten experiment from the 1960s. Matthew Cobb

 

Preprints as medium for communicating new ideas, hypotheses, data, analysis and beyond. Wenfa Ng

 

The GSS is an unreliable indicator of biological sciences postdoc population trends. Christopher Pickett, Adriana Bankston, Gary S. McDowell

 

A Data Citation Roadmap for Scientific Publishers. Helena Cousijn, Amye Kenall, Emma Ganley, Melissa Harrison,David Kernohan, Thomas Lemberger, Fiona Murphy, Patrick Polischuk, Simone Taylor, Maryann Martone, Timothy Clark

 

Science with no fiction: measuring the veracity of scientific reports by citation analysis. Peter Grabitz, Yuri Lazebnik, Joshua Nicholson, Sean Rife

 

The State of OA: A large-scale analysis of the prevalence and impact of Open Access articles. Heather Piwowar​​, Jason Priem​​, Vincent Larivière, Juan Pablo Alperin, Lisa Matthias, Bree Norlander, Ashley Farley, Jevin West, Stefanie Haustein

 

Imagining the ‘open’ university: Sharing scholarship to improve research and education. Erin C McKiernan

 

The democratization of data science education. Sean Kross​, Roger D Peng, Brian S Caffo, Ira Gooding, Jeffrey T Leek

 

Parallel sequencing lives, or what makes large sequencing projects successful. Javier Quilez,Enrique Vidal, Francois Le Dily, Francois Serra,Yasmina Cuartero, Ralph Stadhouders, Thomas Graf, Marc A. Marti-Renom, Miguel Beato,Guillaume Filion

 

The harmonic mean p-value and model averaging by mean maximum likelihood. Daniel John Wilson

 

Bioinformatics Core Competencies for Undergraduate Life Sciences Education. Melissa A. Wilson Sayres, Charles Hauser, Michael Sierk, Srebrenka Robic, Anne G. Rosenwald, Todd M. Smith, Eric W. Triplett, Jason J. Williams, Elizabeth Dinsdale, William Morgan, James M. Burnette III, Sam S. Donovan, Jennifer C. Drew, Sarah C. R. Elgin, Edison R. Fowlks, Sebastian Galindo-Gonzalez, Anya L. Goodman, Neal F. Grandgenett, Carlos C. Goller, John Jungck, Jeffrey D. Newman, William R. Pearson, Elizabeth Ryder, Rafael Tosado-Acevedo, William Tapprich, Tammy C. Tobin, Arlín Toro-Martínez, Lonnie R. Welch, Robin Wright, David Ebenbach, Kimberly C. Olney, Mindy McWilliams, Mark A. Pauley

 

Lessons Learned: Recommendations for Establishing Critical Periodic Scientific Benchmarking. Salvador Capella-Gutierrez, Diana de la Iglesia, Juergen Haas, Analia Lourenco, Jose Maria Fernandez Gonzalez, Dmitry Repchevsky, Christophe Dessimoz, Torsten Schwede, Cedric Notredame, Josep Lluis Gelpi, Alfonso Valencia

 

Bringing plants and soils to life through a simple role-playing activity. Michael E. Van Nuland, Miranda Chen, Benjamin J. England

 

Why not…

Horizontal gene cluster transfer increased hallucinogenic mushroom diversity. Hannah T. Reynolds, Vinod Vijayakumar, Emile Gluck-Thaler, Hailee B. Korotkin, Patrick B. Matheny, Jason C. Slot

 

Not such silly sausages: Northern quolls exhibit aversion to toads after training with toad sausages.Naomi Liza Indigo, James Smith, Jonathan Webb, Ben Phillips

 

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POSTDOCTORAL POSITION STUDYING SENESCENCE IN DEVELOPMENT AND REGENERATION

Posted by , on 4 September 2017

Closing Date: 15 March 2021

  1. Post Description

A position for a Postdoctoral Fellow is available in the Department of Development and Stem Cells, in the lab of Bill Keyes, IGBMC, Strasbourg, France (www.igbmc.fr/keyes). Previously, the group discovered roles for cellular senescence during embryonic development, and instructing cell plasticity and stemness in tissue regeneration and cancer. We are seeking a postdoctoral candidate to continue and develop these projects. As such, preference will be given to candidates with a proven record in developmental biology or with animal models of regeneration. These projects will involve the use of tissue culture and animal models coupled with high-throughput genomic analysis and molecular biology approaches.

For further information on the project and the work from the lab in general, see recent publications: Keyes et al, Cell Stem Cell, 2011, 8(2) 164-176; Doles et al, Genes & Development, 2012, 26(19): 2144-53; Storer et al, Cell, 2013, 155(5), 1119–1130; Ritschka et al, Genes & Development, 2017, 31(2):172-183

 

  1. Candidate requirements
  • Ph.D or M.D./Ph.D. (already obtained or soon-to-be), with at least one first author publication.
  • Highly motivated person with strong interest in science research.
  • Interactive person, with ability to work independently.
  • Good communication skills, and fluency in English is required.
  • Previous experience in developmental biology will be heavily favored. Experience in molecular biology is desirable.

 

  1. Work Environment

The candidate will join an international group of scientists, working on highly competitive topics. The candidate will benefit from access to a modern well-equipped laboratory, as well as access to the IGBMC’s renowned Core Facilities and support.

 

  1. Conditions
    • Starting date: January 15th, 2018
    • Salary: salary is available for one year, but additional funding is sought, and the candidate will be supported to apply for competitive external fellowships.

 

  1. Application procedure
    • Deadline: October 1st, 2017
    • All applications must include a CV with a letter describing your motivation and research interests (past and present), and the contact information for 2-3 referees.
    • Please submit your application to the following email addresses: bill.keyes@igbmc.fr
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Group Leader Developmental Biology at EMBL Heidelberg, Germany

Posted by , on 1 September 2017

Closing Date: 15 March 2021

The Developmental Biology Unit studies the development of multicellular organisms. Research in the unit covers all levels, from the cellular to the whole organism, and is highly interdisciplinary, combining a wide range of approaches and innovative techniques. EMBL brings together the most talented biologists empowering them to explore bold new areas of biological inquiry.

Research in the Developmental Biology Unit is firmly embedded within the overall EMBL research environment, with extensive in-house collaborations and support from cutting-edge facilities, including genomics, transgenics, metabolomics, mass- spectrometry, and microscopy. Interdisciplinary research at the interface between development and metabolism, tissue mechanics, single-cell genomics, ecology, evolution, or theoretical biology is welcome, as are candidates using classical genetic models or new developmental model organisms.

The successful candidate should have a strong motivation to work in the multidisciplinary and collaborative environment of EMBL, grasping the opportunity to interact with many other research groups. In general, EMBL appoints group leaders early in their career and offers a highly collaborative and uniquely international culture. It fosters top quality, interdisciplinary research by promoting a vibrant environment consisting of independent research groups with access to outstanding graduate students and postdoctoral fellows. Significant core funding and limited teaching responsibilities allow EMBL group leaders to undertake ambitious, farsighted research programs and provides a scientific environment that is particularly attractive for researchers with families.

Further information about the position can be obtained from the Head of Unit Anne Ephrussi (anne.ephrussi@embl.de).

Further information about research in the Developmental Unit and at EMBL can be found at www.embl.org.

Application closing date: 8 October 2017.
Interviews are planned for 18, 19 and 20 December 2017.

An initial contract of 5 years will be offered to the successful candidate. This is foreseen to be extended to a maximum of 9 years, subject to an external review.

APPLICATION INSTRUCTIONS

Please apply online through www.embl.org/jobs and include a cover letter, CV and a concise description of research interests and future research plans. Please also arrange for 3 letters of recommendation to be emailed to: references@embl.de at the latest by 1 October 2017.

ADDITIONAL INFORMATION

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation with a very collegial and family friendly working environment.

The remuneration package comprise a competitive salary, a comprehensive pension scheme, medical, educational and other social benefits, as well as financial support for relocation and installation, including your family, and the availability of an excellent child care facility on campus.

EMBL is committed to achieving gender balance and strongly encourages applications from all under-represented groups. Appointment will be based on merit alone. Further details on Group Leader appointments can be found under www.embl.org/gl_faq.

www.embl.org

The European Molecular Biology Laboratory (EMBL) is one of the highest ranked scientific research organisations in the world. The Headquarters Laboratory is located in Heidelberg (Germany), with additional sites in Barcelona (Spain), Grenoble (France), Hamburg (Germany), Hinxton near Cambridge (UK) and Rome (Italy).

 

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PhD and Postdoc positions – Zaidel-Bar group in Tel-Aviv University

Posted by , on 31 August 2017

Closing Date: 15 March 2021

The Zaidel-Bar group studies Actomyosin Contractility and Tissue Morphogenesis from single proteins to the organism level.

After seven successful years at the Mechanobiology Institute in Singapore the lab is moving to Tel-Aviv university in October 2017. This is an exciting opportunity for highly motivated young scientists to join as MSc, PhD or Postdoctoral fellows.

Tel-Aviv University is a top research and teaching institution in the most vibrant and cosmopolitan city in Israel (https://english.tau.ac.il/ and https://international.tau.ac.il/)

If you are interested in working on a project related to the regulation of actomyosin during cell and tissue morphogenesis (http://celladhesionlab.com/) send a letter of motivation and your CV to zaidelbar@gmail.com.
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Developmental Biologists meet in the Lion City

Posted by , on 30 August 2017

 

Meeting Report: Congress of the International Society for Developmental Biology (ISDB 2017)

 

Singapore, the Lion City, attracted hundreds of developmental biologists from around the world to attend the 18th Congress of the International Society for Developmental Biology (ISDB 2017), June 18-22, at the National University of Singapore (NUS). The meeting takes place every 4 years, and gathers those fascinated by the early steps in life. I had the intention to attend one of the ISDB meetings since my early PhD months, but for different reasons it ended up not being possible – this year (already as a post-doc), I managed to join the international community in ‘the Garden of Asia’, and really enjoyed a vibrant and diverse program.

 

 

The opening ceremony kicked-off to welcome everyone with the traditional Lion dance. The main local host (and Singapore enthusiast) Phil Ingham, together with other members of the vibrant scientific community in Singapore, put together a phenomenal program that included 6 Nobel laureate lectures and many talks covering a variety of topics and (model) organisms. Based on my notes from the meeting, I will give an overview of the diverse sessions and highlight some talks – thus, my own personal bias to select certain topics will likely emerge.

 

The D’Arcy Thompson Symposium

The first day included the D’Arcy Thompson Symposium, celebrating 100 years since the publication of the landmark ‘On Growth and Form’ (a topic that was already highlighted in previous posts on the Node). The symposium, naturally, focused on physical and quantitative approaches in developmental biology. It was a great way to start the meeting, reminding us all about the benefits of talking to scientists in other field and join efforts to address important questions from different angles. Speakers included James Briscoe (The Francis Crick Institute, London, UK), employing experimental and computational modelling of transcription networks in neural tube cell fate specification; Thomas Gregor (Princeton University, USA), visualizing long-range promoter-enhancer interactions and transcription regulation in the fly embryo; Hiroshi Hamada (RIKEN CDB, Japan), addressing symmetry breaking in the mouse embryo; Tim Saunders (Singapore), exploring the zebrafish myotome as a model in addition to his work in the fly embryo (and who co-edited, with Phil Ingham, a special issue of MoD that also celebrated the topics covered in the symposium); Olivier Hammant (ENS Lyon, France), exploring the effects of forces and tension on tissue shape; and Carl-Philip Heisenberg (IST, Austria), who also focuses on how forces are generated and propagated in tissues using zebrafish as a model.

 

Nobel Lectures

We were all lucky to have a stellar selection of speakers and participants in all sessions of the meeting, and the organizers could additionally go the extra mile and gather 6 Nobel laureates all under the same roof (an organizational achievement in itself, as we know agendas do not often allow it). Unfortunately, we learned the one of the lectures had to be cancelled due to health issues (Sydney Brenner), but all other laureates gave fantastic talks: Christiane Nüsslein-Volhard (from fly and zebrafish early development to skin colours), Eric Betzig (beautiful movies of unmatched resolution that will surely inspire generations of developmental biologists), John Gurdon (from somatic cell nuclear transfer to cellular memory and histone modifications), Martin Chalfie (Hox genes as guarantors of cell fate specification in C. elegans), and Eric Wieschaus (Interpretation of the bicoid gradient and the role of chromatin accessibility).

 

On a personal account, as my current projects lie at the intersection of developmental biology and chromatin regulation, I have particularly enjoyed two of the talks that focused on these aspects. Sir John Gurdon, always with an inspiring clarity, showed us recent data about resistance to reprogramming by oocyte factors, not only identifying genes resistant to transcriptional reactivation but also by using chromatin modifiers to erase several histone modifications. Eric Wieschaus, in a talk that I have particularly enjoyed, explored how the maternal bicoid gradient is differentially interpreted by the genome of cells in different regions of the embryo. One of the key aspects is the regulation of chromatin accessibility, and one of the conclusions is that chromatin structure, rather than the underlying sequence, is what determines the concentration-dependent cohort of bicoid enhancers, with different degrees of affinity along the embryonic anterior-posterior axis. It was nice to hear another example of how chromatin remodelling is crucial during early development.

 

The Ross Harrison Medal Lecture

The prize is awarded every four years at the ISDB and is named after the American biologist who pioneered experimental embryology, and ‘applied tissue culture techniques to the study of embryonic tissue development and axon outgrowth’. The prize was awarded this year to Claudio Stern (UCL, London), who gave a talk on the fascinating links between twinning and the pathways that regulate asymmetry. With a well-balanced mix between the classical experiments that are always inspiring, and modern studies on human genetics, Claudio covered a range of the research in his lab over several years. I found it particularly interesting to see how topics connected from the early days to the current times, with very curious aspects that are more than coincidence!…

 

 

In general, the meeting had a wonderful mix of topics as well as model systems. From well-established model organisms to exquisite animals that are now becoming more amenable to use experimentally, of course due to the potentials of genome editing brought by the CRISPR/Cas9 technologies. In particular, I enjoyed the work from Antonia Monteiro’s lab (Singapore) on the evo-devo aspects of Butterfly eyespot formation and wing patterning; an amazing variety of fly species and other diptera resulted in a phenomenal talk by Claude Desplan (NYU) on the visual system and its evolution. It was also cool to hear about using Emu embryos as models (Craig Smith, Australia), or even about turtle shell development (Shigeru Kuratani, Japan)!

 

To highlight a few more speakers, I was marvelled with the identification of multinucleated cells during regeneration in the zebrafish heart (Ken Poss, Duke University, USA), which are temporarily generated and migrate to cover the wound. Norbert Perrimon (Harvard) explored inter-organ communication, giving several examples of how tissues send signals to each other within the organism, making us all aware that the processes we may be interfering with can have impact at distant target organs or tissues. François Schweisguth (Institut Pasteur, Paris) employed experimental and modelling approaches to beautifully tackle a long-lasting question about patterning: how stereotyped sensory organ patterns are self-organized (through Notch dynamics) in the developing fly notum. Finally, Denis Duboule (EPFL, Switzerland) gave an overview of limb development from the point of view of chromatin organization and genome topology. Given my own interests, I found it fascinating as work from his lab could uncover how enhancer regions may activate certain Hox genes in the forelimb or the digits, starting to reveal how development is orchestrated in connection with the structural organization of the genome in topological-associated domains (TADs).

 

 

There would certainly be more to tell, and I have really enjoyed the opportunity to meet some of my scientific heroes and openly discuss science with old colleagues and meet new students/post-docs from all over the world! It was also great for me to meet the Portuguese community (and make me feel at home even half a world away), who were also representing the Portuguese Developmental Biology Society (SPBD).

 

 

 

I can only look forward to the next ISDB, in 4 years’ time…! We already know it will take place in Vancouver, Canada (Summer 2021), and it will surely be a calendar highlight for all of us developmental biologists! Also, a new ISDB President will be in charge over the next 4 years up to the meeting – Angela Nieto (Alicante, Spain) is the newly elected ISDB President. Angela has committed to increase the interactions among developmental biologists around the world, as well as making funding agencies and the lay public aware of the importance of basic research in these fields to further the understanding of mechanisms that will be relevant other fields. This is certainly a point of view that I also share, so we can all hope Angela has a successful term!

 

 

Jorge Beira

ETH Zurich

 

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Categories: Events, Research, Societies

Advocacy for Developmental Biology

Posted by , on 30 August 2017

BSDBlogoTo promote Developmental Biology and bring across the importance of fundamental research in this field, we all should have our elevator pitches ready at all times – whenever there is an opportunity to engage with audiences about our discipline – be it with the public, students, fellow scientists or policy makers. This is a first attempt at providing a concise rationale and ideas that can be woven into such conversations. The arguments presented can and must still be improved and complemented. Therefore, we would like to invite you to send in your thoughts and ideas, potential corrections, suggestions for improvement, additions, new arguments and/or potential links to supporting resources – all with the aim of further strengthening the message that we need to bring across (please, send to Andreas.Prokop@manchester.ac.uk). In particular those working in evo-devo or plant development, please come forward and make your contributions by helping us explain the importance of your subjects and extend this resource for the benefit of all.
If you would like to use some of the ideas currently presented, please download PowerPoint slides with the advocacy information here. If you are already active in science communication or plan to do so, please, also have a look at our public engagement outreach collection which can be found on the BSDB site and in revised form on The Node, at a special issue on science communication in “Seminars in Cell & Developmental Biology” (Box 5) and a recent PLoS Blog post.

If you are a Developmental Biology society, lab, researcher or aficionado and have a website: are you actively advocating the importance of our discipline? Feel free to copy out or use ideas and materials presented here. Vice versa, please share your links, your improved, complementary or additional arguments, and your advocacy strategies and resources. We aim to improve advocacy strategies across the globe and form a powerful network communicating the importance of Developmental Biology!

 

Why should we engage in Developmental Biology?

Developmental Biology enquires about the fundamental processes that underpin the fertilisation of an egg cell and its step-by-step transformation into the fascinating complexity of a whole organism (Box 1).

Box 1:

Some definitions of Developmental Biology

  • Developmental Biology is the study of the processes by which organs grow and develop. Modern developmental biology studies the genetic control of cell growth, differentiation and morphogenesis, which is the process that gives rise to tissues, organs and anatomy, but also regeneration and ageing (after L. Wolpert)
  • Developmental biology is the study of the process by which animals and plants grow and develop, and is synonymous with ontogeny (Wikipedia).
  • Developmental Biology is the causal analysis of the cellular mechanisms that drive processes of growth, pattern formation and morphogenesis (A. Martínez Arias)

Further advocacy articles

  • Development special advocacy articles
    • Maartens, A., Prokop, A., Brown, K., Pourquié, O. (2018). Advocating developmental biology (Editorial). Development 145 — [LINK]
    • Ebisuya, M., Briscoe, J. (2018). What does time mean in development? Development 145 — [LINK]
    • Wiese, K. E., Nusse, R., van Amerongen, R. (2018). Wnt signalling: conquering complexity. Development 145 — [LINK]
    • Philip W. Ingham. (2018). From Drosophila segmentation to human cancer therapy. Development 145 — [LINK]
  • Prokop, A. (2018). What is Developmental Biology – and why is it important? Open Access Govern, in press — [LINK]
  • Duronio, R. J., O’Farrell, P. H., Sluder, G., Su, T. T. (2017). Sophisticated lessons from simple organisms: appreciating the value of curiosity-driven research. Disease Models & Mechanisms 10, 1381-1389 — [LINK] – comment by A Martínez Arias [LINK2]
  • Gilbert, S. F. (2017). Developmental biology, the stem cell of biological disciplines. PLoS Biology 15, e2003691 — [LINK] – comment by A Martínez Arias [LINK2]
  • Zhang, F. (2017). A new age of discovery for biology. In “The World in 2018”. The Economist — [LINK]
  • St Johnston, D. (2015). The renaissance of Developmental Biology. PLoS Biol 13, e1002149 — [LINK]
  • Wassarman, P. M. (2016) Essays on Developmental Biology. Current Topics in Developmental Biology — [PartA] [PartB]
  • Hines, P. J., Marx, J., Parks, S. (1994). Frontiers in development. Science 266, 561-564 — [LINK]
  • Crick, F. (1977). Developmental biology. In “The encyclopedia of ignorance – life sciences” (R. Duncan, M. Weston-Smith, Eds.), Vol. 2, pp. 299-303. Pergamon Press, Oxford, New York, Toronto, Sydney, Paris, Frankfurt — [LINK]

At first sight, Developmental Biology could be viewed as an academic discipline driven by mere curiosity and, hence, to be of little relevance to the big challenges of population health or sustainability. On the contrary, Developmental Biology – along with Physiology[1] – is arguably the most important biological discipline we have. Here we will explain and substantiate this statement[2].

(1) Developmental defects in humans are very abundant (Box 2). By studying the underlying mechanisms and causes, Developmental Biology addresses the key challenge of population health. Sustaining food resources is another major global challenge, and Developmental Biology can provide key strategies to improving crop and plant cultivation (see Mathan et al., 2016, Development 143, 3283ff. — LINK; further arguments will follow – please help us by contributing your ideas!).

Box 2: Statements from the literature illustrating the abundance of developmental defects in humans

  • The frequency at which all classes of developmental defects occur is thought to be … exceeding half of initial pregnancies.
  • Major developmental defects … occur in approximately 3% of live births.
  • In 1995, major developmental defects accounted for approximately 70% of neonatal deaths (occurring before 1 month of age) and 22% of the 6,500 infant deaths (before 15 months of age) in the US.
  • Approximately 30% of admissions to pediatric hospitals are for health problems associated with such defects.

source: Scientific Frontiers in Developmental Toxicology and Risk Assessment, 2000, National Academic Press, Washington DC, pp.354; edited by the National Research Council (LINK)

(2) Developmental Biology (like Physiology) is asking fundamental questions at the level of whole organisms, organs or tissues (Box 3). Notably, this is the level at which diseases become manifest. For this reason, Developmental Biology has been, and continues to be, most effective in delivering explanations for diseases or medically relevant processes including infertility, neonatal death, birth defects (e.g. deformation, body growth abnormalities, developmental brain disorders, blindness, deafness), cancer, wound healing, tissue regeneration (regenerative medicine including stem cell biology), etc.

Box 3: Fundamental questions asked by developmental biologists – and how they translate into biomedical application

  • What processes lead to fertilisation and the initiation of development? How can we overcome infertility and childlessness?
  • How do single fertilised egg cells, or later on groups of progenitor cells, generate the enormous cellular diversity of an organism and its organs and tissues? How do stem/progenitor cells generate whole tissues or organs – for example in regeneration or tissue engineering, and how does wound healing work?
  • How do cells, which originate from common ancestors and contain the same genetic information, adopt different fates? How do cells change their identities and behaviours – for example in cancer?
  • How do tissues and their cells know when to stop growing? How can cells evade growth control – for example in tumour growth?
  • How is the formation of different cells/tissues coordinated in space and time? What are the patho-mechanisms underlying birth disorders?

(3) By asking fundamental questions at the level of organisms, organs and tissues, Developmental Biology-related research is a generator of new ideas and concepts (Box 4). These concepts essentially underpin the modern biomedical sciences and include cell signalling, tissue and body patterning, growth regulation, cell migration or morphogenesis; they form the basis for contemporary research into stem cells, cancer, wound healing, regeneration or ageing.

(4) Developmental Biology is exciting and powerful because it reaches across the different levels of biological complexity and explanation; phenomena at the level of organisms, organs or tissues can ultimately be understood only by tracing them back to events at the level of genes and cells. Consequently, Developmental Biology embraces disciplines such as genetics, molecular biology, (stem) cell biology, biochemistry, biophysics as well as evolutionary biology.

(5) Developmental Biology capitalises on the principle of evolutionary conservation of genes, mechanisms and concepts by making informed and strategic uses of suitable model organisms, down to experimentally and genetically amenable invertebrates. The use of invertebrate model organisms provides an efficient and powerful strategy to generate new ideas, concepts and understanding which can then be tested (and often validated) in higher organisms, eventually leading to medical applications in humans (LINK). This discovery pipeline has been a central driver for the enormous contributions that Developmental Biology has made and continues to make to the biomedical sciences.

Box 4: A metaphor explaining how Developmental Biology works

Understanding a combustion engine requires investigating its single parts, such as the sparking plug, cylinder or crank shaft. However, for a developmental biologist it is not sufficient to find out how each of these parts works, but this new knowledge needs to be linked back into the mechanistic framework that constitutes the entire engine and explains its function. Linking detailed findings back to the bigger question of understanding the engine is an important validation and filter step that reveals whether the detailed findings are actually relevant and make deeper sense. Only through such systematic and holistic “reverse enginieering” can the necessary systemic and conceptual understanding be achieved which is required to diagnose and eventually repair a faulty engine.

By executing all research work with the ultimate aim of understanding the bigger question (e.g. how to make an organ, appendix or entire body), Developmental Biology has become such an important contributor of concepts and understanding in the field of the biomedical and medical sciences.

As an interesting side note: already in the late 18th century, Johann Wolfgang von Goethe understood that it is not enough to “have the pieces in your hand” but that they need to be connected and “woven” together to “recognise and describe the living”.

These are only some thoughts (still incomplete and in need of further optimisation) about the importance of Developmental Biology as a discipline. If we want to improve the standing of our discipline, we MUST embrace these ideas with passion, help to complement and further improve them and, most importantly, use them whenever possible and adequate to advocate our discipline with self-confidence and enthusiasm. To do this with impact, we need to acknowledge that communicating science is a difficult task which requires belief, love for our subject, stamina, and efficient strategies that enable us to engage with a wide spectrum of target audiences. Such target audiences include the general public and schools, fellow scientists and clinicians, as well as politicians and other decision makers. But we need to be realistic and accept that most members of these target audiences will, by default, show little interest to engage with us. Therefore, intelligent and strategic long-term approaches – ideally shared within networks of scientists – likely provide the most promising path of engagement – as is explained in greater detail in the editorial of a special issue on science communication (published in Sem Cell Dev Biol; Box 5). For those who take an interest, this special issue provides many ideas of how long-term strategies for the communication of biomedical research can be implemented successfully – and can then even become rewarding for our own science and career. Please, also have a look at our link list of public engagement outreach resources which will provide you with further ideas and useful support materials.

Box 5:

Science communication in the field of fundamental biomedical research

(Vol. 70; Oct. 2017, free access for one year)

edited by Sam Illingworth & Andreas Prokop

The aim of this special issue is to provide concise and accessible advice on how to engage effectively, as well as share valuable practice gained from successful long-term science communication initiatives – thus providing ideas to all those who want to participate in dialogue with the public, policy makers or other scientists, or are participating already. This issue is primarily written for scientists working in the field of the biomedical sciences (and beyond), but will hopefully also be seen as a helpful resource for academic & professional science communicators. To appeal to both groups and hopefully stimulate impact-enhancing interdisciplinary collaborations, the issue is an unprecedented experiment written at the interface of both disciplines. The enormous opportunities of long-term approaches and the formation of interdisciplinary science communication networks are explained in great detail in our editorial. Further explanations about this issue were given in the recent NCCPE and PLoS|BLOGS posts.

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Cover art by Matt Girling. See figure legend in the editorial.

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1. EDITORIAL: Science communication in the field of fundamental biomedical research (Sam Illingworth, Andreas Prokop) – This article provides a critical assessment of the current state of science communication in the field of fundamental biomedical science, including lists of existing science communication initiatives, as well as a conceptual overview of the articles in the special issue [PDF] [see also].

2. Delivering effective science communication: advice from a professional science communicator (Sam Illingworth) – From his experience as Senior lecturer in Science communication, Sam Illingworth  writes about important considerations for all who want to participate in active science communication. His tips and tricks for science fairs, school visits or many other forms of dialogue are provided in plain language.  [PDF] [YouTube]

3. The nuts and bolts of evaluating science outreach (Suzanne Spicer) – From her experience as specialist for science communication at the Manchester Museum, Suzanne Spicer writes about the importance and practical implementation of project/event evaluation as an important means to improve quality and demonstrate impact. [PDF]

4. EuroStemCell: A European infrastructure for communication and engagement with stem cell research (Jan Barfoot, Kate Doherty, C. Clare Blackburn) – EuroStemCell is the flagship of non-commercial science communication in the area of the biomedical sciences, centred around their website with over a million annual visitors. The initiative was born out of an EU grant consortium and has developed into an interdisciplinary network that promotes responsible dialogue about stem cells, also through developing outreach resource and providing training. [PDF]

5. The Manchester Fly Facility: Implementing an objective-driven long-term science communication initiative (Sanjai Patel, Andreas Prokop) – The Manchester Fly Facility is an excellent example of an initiative communicating the importance of model organism biology. They promote Drosophila research through improved research training, school projects, science fair programs, and the development of publicly shared resources and strategies. Furthermore, they address Drosophila researchers to stimulate wider participation in science communication. [PDF]

6. Building dialogues between clinical and biomedical research through cross-species collaborations (Hsiao-Tuan Chao, Lucy Liu, Hugo J. Bellen) – Clinicians and biologists do not necessarily share a common scientific culture and way of thinking, but they share the common scientific goal of understanding and treating diseases. To this end, they can complement each other in powerful ways. This article by the Bellen lab provides helpful tools and successful strategies towards interdisciplinary collaboration between biologists working on model organisms and clinicians. [PDF]

7. DrosAfrica: Establishing a Drosophila community in Africa (Maria Dolores Martín-Bermudo, Luka Gebel, Isabel M. Palacios, I. M.) – DrosAfrica is an excellent example of how cost-effective, yet cutting edge research – as it is possible with Drosophila – can be used to free resources and promote active science and science education in disadvantaged countries. This article describes the origins of the DrosAfrica initiative and provides detailed insights into how their activities are organised. [PDF] [YouTube]

 

8. Engaging with primary schools: supporting the delivery of the new curriculum in evolution and inheritance (Paula Kover, Emily Hogge) – The “Teaching Evolution for Primary Children” initiative is an excellent example of successful dialogue with schools. The key strategy explained here is to research curricular and teacher requirements first, to then decide on suitable contents and develop useful resources in close collaboration with schools. This ensures influence of scientists on the correctness and quality of content and the influence of teachers on the way of presentation – in sum an excellent way to engage audiences at young age with science. [PDF]

 

9. The droso4schools project: long-term scientist-teacher collaborations to promote science communication and education in schools (Sanjai Patel, Sophie DeMaine, Joshua Heafield, Lynne Bianchi, Andreas Prokop) – Analogous to the previous article, the droso4schools initiative by the Manchester Fly Facility seeks true dialogue with teachers in that students are placed as teaching assistants in schools to learn about teaching strategies and teacher requirements. These experiences are then turned into sample lessons that use Drosophila as a teaching tool to explain curriculum-relevant concepts of biology, spiced up with micro experiments that are possible with flies even in classrooms. [PDF]

 

10. Science Communication at Scientific Societies (Jeanne Braha) – As former member of the AAAS science communication team, Jeanne Braha explains how societies can help their communities to improve science communication through offering advice, providing resources and training, connecting scientists to audiences, making information available to the public, and awarding prizes for outstanding science communication work. [PDF]

 

11. The Node and beyond – using social media in cell and developmental biology (Catarina Vicente, Aidan Maartens, Katherine Brown) – This article describes The Node as a unique communication platform for biomedical researchers, in particular from the fields of Cell and Developmental Biology. The Node does not only collate event and advocacy information, publish job vacancies and report about science-relevant topics, but it is also a blog site with international outreach where members of the science community can share news, thoughts or experiences. As such it acts as a modern electronic newsletter. [PDF]

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[1] In the sense used here, Physiology comprises disciplines like immunology or functional studies in the field of neurobiology

[2] Arguments and examples given so far concern studies of animal development, and those for plant development will follow soon

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Appendix: Societies promoting Developmental Biology (DB)

APDBN Asian-Pacific DB Network
ABCD Associazione di Biologia Cellulare e del Differenziamento (@Abcdsciencenews)
ANZSCDB Australia & New Zealand Soc. for Cell & DB (@ANZSCDB)
BSCDB Belgian Soc. for Cell & DB
BSDB British Soc. for DB
CSDB Colombian Soc. for DB (@ColSDB)
DSDB Dutch Soc. for DB
EED European Soc. for Evolutionary DB
FSDB Finnish Soc. for DB (Suomen kehitysbiologian yhdistys ry)
GfE Gesellschaft für Entwicklungsbiologie (@GfEeV)
HKSDB Hong Kong Soc. for DB
InSDB Indian Soc. for DB
ISDB Internatnl. Soc. for DB (@IntSocDevBiol)
ISD Internatnl. Soc. of Differentiation
IsSDB Israeli Soc. for DB
JSDB Japanese Soc. for DB
KSDB Korean Soc. of DB
LASDB Latin American Soc. for DB (@LASDB_DevBiol)
PASEDB Pan American Soc. for Evolutionary DB (@EvoDevoPanAm)
RiBiD Red de Investigadores en Biología del Desarrollo (@RiBiD_Chile)
SMBD Sociedad Mexicana de Biología del Desarrollo
SPBD Sociedade Portuguesa de Biologia do Desenvolvimento (@SPBioDev)
SEBD Sociedad Española de Biología del Desarrollo (@SEBiolDev)
SIERR Societa’ Italiana Embriologia Riproduzione e Ricerca
SEDBO Swedish DB Organization (@swedbo)
SFBD Société Française de Biologie du Développement (@sfbd_biodev)
SDB Soc. for DB (@___SDB___)
TSDB Taiwanese Soc. of DB
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Categories: Education, Outreach, Resources, Societies