Evolutionary developmental genetics of reptile skin colour

In the context of evolutionary developmental biology analyses of reptilian skin colours and colour patterns, we offer one PhD position for an outstanding, highly motivated, and creative experimental wet-lab biologist with strong skills in developmental biology and cell biology.

Michel Milinkovitch’s group at the University of Geneva (UNIGE) integrates the expertise of developmental biologists, evolutionary biologists, computer scientists and physicists for an improved understanding of the mechanisms generating a diversity of skin colours and colour patterns in reptiles.

We have recently shown (Saenko et al. 2013) that the extensive variation of skin colours and patterns in Sauropsida reptiles is generated by precise co-localisation of interacting pigmentary and nano-structural elements. In this framework, we have also shown (Teyssier et al. 2015) that chameleons shift colour through active tuning of a lattice of guanine nanocrystals, which photonic effect is filtered by a layer of pigments. In addition, we have built extensive transcriptomic and genomic resources (Ullate-Agote et al. 2014; Tzika et al. 2015) for mapping colour mutations in our new model species of snakes and lizards. For example, we recently mapped and identified the mutation responsible for the amelanistic mutation in corn snakes (Saenko et al. 2015).

The successful candidate will (i) participate to linkage mapping of multiple colour and colour pattern mutations in snakes and lizards and (ii) use molecular/cell/developmental biology methods (microscopy, immuno-histochemistry, in-situ hybridisation, transcriptomics, in-vivo assays, ex-vivo cultures, etc.) to characterise the effects of these mutations on neural-crest cell migration, as well as on the physiology of pigmentary and structural-colour cells. The new PhD student will also interact with a physicist PhD student who is mathematically modelling the reaction-diffusion processes that generate colour patterns in snakes and lizards.

Candidates must have a Master in biology or biochemistry. Skills and experience with developmental biology and/or cell biology are mandatory. Skills in biophysics are useful. The successful candidate will have a genuine interest for organismal biology and will appreciate interactions with physicists and computer scientists.

The University of Geneva (UNIGE) is world-renowned for its research in Biology and Physics.  UNIGE is among the top 1% best universities in the world and the Faculty of Sciences is ranked 32^th world best (Shangai Academic Ranking of World Universities).

PhD students are remunerated according to the standards of UNIGE, which are very generous when compared to other international programs.

Geneva is an international city occupying a privileged geographical situation.

Candidates must send their application – in the form of a single PDF file including a brief letter of interest, a CV, as well as contact information (not support letters) of two persons of reference – to:

Prof. Michel Milinkovitch (Michel.Milinkovitch@unige.ch), Laboratory of Artificial & Natural Evolution (www.lanevol.org), University of Geneva, Switzerland.

Refs: Saenko, Teyssier, van der Marel & Milinkovitch. Precise colocalization of interacting structural and pigmentary elements generates extensive color pattern variation in Phelsuma lizards. BMC Biology 2013, 11: 105; Teyssier Saenko van der Marel & Milinkovitch. Photonic Crystals Cause Active Colour Change in Chameleons. Nature Communications 6: 6368 (2015); Tzika, Ullate-Agote, Grbic & Milinkovitch. Reptilian Transcriptomes v2.0: An Extensive Resource for Sauropsida Genomics and Transcriptomics. Genome Biol. Evol.  7: 1827-1841 (2015); Ullate-Agote, Milinkovitch & Tzika. The genome sequence of the corn snake (Pantherophis guttatus), a valuable resource for EvoDevo studies in squamates. Int. J. Dev. Biol. 58: 881-888 (2014); Saenko, Lamichhaney, Martinez Barrio, Rafati, Andersson & Milinkovitch. Amelanism in the corn snake is associated with the insertion of an LTR-retrotransposon in the OCA2 gene. Scientific Reports 5, 17118 (2015) .

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A full 3-year ANR funded postdoctoral position is available at the Centre de Biologie Intégrative Toulouse to study mechanisms by which time is translated into a precise developmental sequence in the context of neocortex development. This position is part of the postdoctoral program of CBI Toulouse (http://cbi-toulouse.fr/eng/). Our research focuses on the role of local cell-to-cell communication via Eph:ephrin signaling in the specification of neural progenitors in the mouse. The specific aim of the proposed project is to identify the cellular and molecular mechanisms linking Eph:ephrin signaling to neural progenitor fate decisions, concentrating on the transcriptional response elicited downstream of Eph activation in neural progenitors.

The project includes genome-wide gene expression analyses (RNA-Seq and ChIP-Seq) to fully characterize the repertoire of genes downstream of Eph:ephrin signaling in cultured progenitors and the assessment of candidate genes in regulating the production of projection neurons in vitro and in vivo. The succesful candidate should have a PhD and a strong background in genome-wide gene expression analyses. Expertise in cell culture and/or mouse genetics would be a plus. The position is available from october 2016.

Highly motivated candidates should send a brief description of their research interests and career goals, their CV, and contact information for three references to Alice Davy (alice.davyatuniv-tlse3.fr)

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Each adult mammalian skeletal muscle has a unique complement of fast and slow myofibers, a consequence of cell-autonomous and non-cell-autonomous patterning decisions during development. Intriguingly, following either acute muscle regeneration or deinnervation/reinnervation, the proportionality and patterning of muscle fibers is largely preserved, suggesting a mechanism for ongoing maintenance of fiber type specification during homeostasis and regeneration/repair. We have recently reported that interactions between the repulsive guidance ligand ephrin-A3 [which is expressed on all and only slow (Type I) myofibers] and EphA8 [an ephrin receptor expressed by terminal Schwann cells at all and only neuromuscular junctions of fast (Type II) myofibers] promote and preserve slow myofiber identity by preventing stable innervation of slow muscle fibers by fast motor neurons [Stark et al, JCB 211:1077–91 (2015)]. Additional data from our lab suggest that variations on this mechanism may also direct slow fiber type-specific interactions with muscle satellite (stem) cells, and/or promote and preserve fast (Type IIb) myofiber identity during development and regeneration. The future potential of this work includes not only extending our basic understanding of muscle patterning during development, regeneration, neuromuscular disease, and aging but also has implications for targeted gene or cell transplantation therapies.

The Cornelison lab at the University of Missouri is recruiting 1-2 postdoctoral fellows to work on this NIH-funded project, addressing the significant unsolved question of how muscle fiber type is specified, maintained, and recapitulated in each muscle in that muscle’s unique pattern. The project will involve analysis of muscle fiber patterning in wild type, loss-of-function and gain-of-function mouse models during development and following muscle or nerve damage, using section immunohistochemistry, RNA in situ hybridization, timelapse videomicroscopy, flow cytometry, tissue culture and coculture, cell transplantation, and global gene expression and epigenetic profile analysis.

We are looking for highly motivated colleagues, ideally with a background in muscle and/or nerve development and regeneration, who are able to work both independently and collaboratively. A doctoral degree, strong background in cell and molecular biology, and proficiency in spoken and written English are required.

Columbia is a vibrant college town with a low cost of living that consistently appears on ‘Best Places to Live’ lists (Forbes, Livability, Outside). It is only two hours away from either St. Louis or Kansas City, and also has easy access to outdoor activities in-town (biking on the Katy Trail, rock climbing, camping) or nearby (climbing or canoeing in SW Missouri, boating on Lake of the Ozarks). The University of Missouri is a top-ranked public research university with the main undergraduate campus, the medical school, and the veterinary school all on the same campus, facilitating active collaborations in the life sciences. The Bond Life Sciences Center is a new multidisciplinary facility housing 38 labs from 14 different departments, as well as multiple University core facilities.

To apply, please send a CV, cover letter, and the names of three references to cornelisond@missouri.edu.

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Gustafson, T., Wolpert, L. (1967) Cellular movement and contact in sea urchin morphogenesis. Biological reviews of the Cambridge Philosophical Society 42, 442-498.

Recommended by Thomas Lecuit (IBDM- Developmental Biology Institute of Marseille)

In the beginning of his famous 1969 paper on positional information, Lewis Wolpert states that “the central problem of the development of form and pattern is how genetic information can be translated in a reliable manner to give specific and complex multicellular forms and varying spatial patterns of cellular differentiation”. In considering this problem, Wolpert continues, it is important to distinguish between three different, but interdependent, aspects: molecular differentiation (i.e cell fate choice), spatial differentiation and morphogenesis. Most biologists’ first (and maybe only) encounter with Wolpert’s work will be his conceptual contributions to our understanding of spatial differentiation, i.e. “the process by which the individual cells within a population are specified to undergo a particular molecular differentiation, which results in a characteristic spatial pattern”. His solution was positional information, the idea that a cell will differentiate in a specific way by interpreting its position, most famously applied to the French Flag problem.

Wolpert did not centre his attentions exclusively on spatial control of differentiation though. In fact, just two years earlier, he published another work, in collaboration with Tryggve Gustafsson, where he focuses on morphogenesis. At 57 pages, one would assume this to be a long review on morphogenesis (and this is indeed how it is classified on PubMed). In reality, the article is somewhere between a review, a paper and a hypothesis. It is an overview of Gustafson and Wolpert’s thoughts on the mechanisms underlying morphogenesis, in the context of other work published in the field and their own careful and detailed observations of sea urchin development.

Gustafson and Wolpert explain their motivation in the introduction. By the late 60s much was already known about how information encoded in DNA is translated into proteins, as well as other biochemical processes in cells. But how do these processes ultimately determine and influence morphogenesis? Part of the problem was that both biochemistry and genetics were seen as separate fields from development. This paper attempted to bridge the gap. As the authors state “our purpose is to reduce the complex processes at the organ level to activities of the individual cells […] that may be more meaningful for the biochemist than concepts such as gastrulation, mesenchymal patterns and coelom”. To do this, they “reduce the complex morphogenic events […] into a question about the cellular forces involved.” They argue that much of early morphogenesis depends on only two cellular activities: adhesiveness and motility. They show how these determine each morphogenetic step of early development, using the sea urchin as their model.

Reproduced with permission of Wiley

By today’s standards this paper might be considered ‘too descriptive’. Gustafson and Wolpert are basically just using a microscope to observe sea urchin development. But this paper shows that you don’t necessarily need fancy techniques to provide ‘mechanistic insight’. With detailed observations and clear thinking, the authors argue that most of morphogenesis, regardless of organ or developmental stage, can be explained by a few simple mechanisms. In an age when labs dedicate decades of work to a single gene in a specific tissue system, it is surprising and refreshing to read a paper that tries to identify overall principles and puts the big picture at the forefront. Of course, this paper was just the beginning and, as the authors admit themselves, further work was necessary, e.g. more direct measurements of the forces involved and additional ultrastructural information. Maybe your own research is trying to fill some of these gaps? Either way, next time you come across Wolpert’s positional information paper, spare a thought (and some reading time) for his 1967 paper on sea urchin morphogenesis. As Thomas Lecuit put it, this largely unknown paper is “a must read […] [which] lays down the foundation of tissue morphogenesis in all animals”. In fact, why not read both? “Together these two papers cover most of the important concepts in morphogenesis, including cellular behaviour, physical forces and regulatory information.”

Further thoughts from the field

Gustafson and Wolpert’s 1967 paper was a landmark in the field of developmental biology. The paper summarized many of the cell behaviors that these two biologists described in a series of earlier publications (published in the 1950s and 1960s), all of which were based on time-lapse, light microscopic observations of transparent sea urchin embryos. The 1967 paper had a tremendous impact when it was published because it revealed a whole new world of remarkable cell behaviors that accompany embryonic development. The paper remains highly relevant today. It highlights the power of observing the behavior of living cells in intact embryos by time-lapse imaging. In fact, many of the cell behaviors Gustafson and Wolpert described are still being deciphered at the molecular/genetic levels. The paper also described simple mechanical models of tissue morphogenesis based on a small number of cell-level properties, such as cell adhesion, cell division, and cell contractility. These models remain relevant today, but more importantly they highlight the critical importance of integrating information at multiple levels of biological organization in order to understand morphogenesis.

Chuck Ettensohn (Carnegie Mellon University)

Wiley has kindly provided free access to this paper until  June 2016!

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by Cat Vicente

This post is part of a series on forgotten classics of developmental biology. You can read the introduction to the series here and read other posts in this series here.

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The laboratory of Jianjun Sun at the University of Connecticut Department of Physiology and Neurobiology is inviting applications for a postdoctoral researcher to work on a NIH-funded project.

Our group studies female reproductive organ formation and function. We recently developed a Drosophila model to investigate the conserved mechanism of ovulation and its contribution to ovarian cancer (Sun and Spradling, Curr Biol, 2012; Sun and Spradling, eLife, 2013; Deady et al., PLoS Genet, 2015; Deady and Sun PLoS Genet, 2015). We are working to identify the signaling network that control the spatiotemporal activation of matrix metalloproteinase in Drosophila ovary, which is essential for ovulation and cancer metastasis. Please see our website (sunlab.pnb.uconn.edu) for more information.

Ideal candidates will be accomplished, highly motivated, and creative scientists with a recent Ph.D. in the life sciences (less than 2 years of postdoctoral experience is strongly preferred), or who anticipate completion of their degree prior to starting the position. Previous experience in Drosophila genetics, cell biology, and/or developmental biology is desirable.

Applicants should email a brief cover letter describing research accomplishments and future research goals, current CV with list of publications, and contact information for 3 professional references to: Jianjun.sun[at]uconn.edu in one PDF file. Salary will be commensurate with appropriate experience according to NIH scale.

The University of Connecticut is an EEO/AA employer.

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Are you interested in attending a meeting or course in a DMM-relevant field? Apply for one of our travel grants of up to £600 (or currency equivalent). The first application deadline is 29 April 2016.

Applicants will usually be PhD students and postdoctoral researchers at the beginning of their research careers, who will use the funding to support their travel to relevant scientific meetings. We also welcome applications from independent group leaders and PIs with no independent funding, seeking support to attend meetings, conferences, workshops, practical courses, PI laboratory management courses and courses to re-train.

For further information and to download an application form, go to our travel grant page.

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University College London is one of the world top universities for postdoctoral studies owing to excellent training and its friendly, collaborative, multidisciplinary and scientifically outstanding environment. The UCL Cancer Institute is now recruiting post-doctoral researchers to work on ground-breaking projects in genetics and epigenetics of cancer, as well as ageing, signalling and metabolism as they relate to cancer biology. We offer several individual and collaborative projects led by Dr. Ivana Bjedov (Adv Genet. 2015;90:1-101; Biochem Soc Trans. 2011 Apr;39(2):460-5; Cell Metab. 2010 Jan;11(1):35-46) in collaboration with Prof. Stephan Beck (Nat Rev Genet. 2011 Jul 12;12(8):529-41; Nat Biotechnol. 2008 Jul;26(7):779-85; Nat Genet. 2006 Dec;38(12):1378-85) and Prof. Paolo Salomoni (Proc Natl Acad Sci U S A. 2015 Jan 27;112(4):1059-64; Neuron. 2012 Apr 12;74(1):122-35). To address crucial questions in cancer biology, we use mouse and Drosophila model organisms, as well as a variety of mouse and human cell culture systems, including stem cells. The institute is equipped with cutting-edge equipment and core facilities for bioinformatics, flow cytometry and cell sorting, proteomics, genomics, imaging, in vivo biology and histopathology.

The aim is to select and train excellent scientists and encourage their independent future careers. Therefore, we seek high-achieving postdoctoral candidates, with less than 2 years of postdoctoral experience, who will be competitive in obtaining postdoctoral fellowships. Only candidates with published first-author papers in internationally recognised peer-reviewed journals will be considered. We are interested in hearing from talented PhD students near completion of their PhD that are eager to start their postdoctoral career in outstanding laboratories of the UCL Cancer Institute. This position is available to students having, or being near completion of, a PhD degree in a biological subject, and from any nationality or country. Candidates should have extensive experience in molecular biology techniques, microscopy and tissue culture. We particularly encourage students with Drosophila experience.

Please send one PDF document containing a letter of motivation and your CV, clearly stating all your previous laboratory experience and your supervisors, your publications, and details of 2 referees to CI.Vacancies@ucl.ac.uk with “Postdoc position Bjedov-Beck-Salomoni” in email subject. For any informal inquiries, please feel free to contact Ivana Bjedov (i.bjedov@ucl.ac.uk). For further information regarding the Institute please see: http://www.ucl.ac.uk/cancer and http://www.ucl.ac.uk/cancer/research/department-cancer-biology

The deadline for applications is 20th March 2016.

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LM Escudero lab 

Cell Biology Department

Universidad de Sevilla

• We offer a full-time contract for one year (renewable) to do the PhD in our group. The deadline is Friday 11/03/2016.

• The candidates should have a Physics degree, Mathematics degree, Healthcare Engineering degree, Telecommunications degree, Informatics Engineering degree or Biological related degree with a wide programing background.

Project description:

We are focused in the analysis of biological and biomedical images using System Biology methods.

We combine Computerized Image Analysis and mathematical concepts to investigate different biological and biomedical questions. Extracting the defining signature of complex images we obtain objective and quantitative information that help to interpret biological processes in development and disease.

This project is related to the analysis of tissue organization. This is a funded project by the Fundación Asociación Española Contra el Cancer in collaboration with the lab of Dr. Rosa Noguera from INCLIVA (Valencia, Spain). The contract is cofounded by the Fundación Asociación Española Contra el Cancer and Seville University.

You can find more information visiting http://lmescudero.blogspot.com.es/

If you are interested, send me and email with your CV and background to lmescudero-ibis@us.es

In addition, it is necessary to officially apply to Seville University. I will send instructions to preselected candidates.

Thank you!

Luis M. Escudero

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I’ve just finished reading ‘Raw Data’ by Pernille Rørth. As a disclaimer, Pernille ran the lab next door to me when I was a postdoc, and as Editor in Chief at The EMBO Journal helped train me up as an editor – I’ve got a huge amount of respect and liking for her as a scientist and person. I was surprised and somewhat saddened when I heard she was no longer in active research, but intrigued to find out what she was going to do instead. Well, what she has done is written a highly readable novel about research ethics, and I’d really recommend it – both as an abject lesson in how things can go horribly wrong in the lab, and as an enjoyable way to spend a few evenings (I was hooked and read it in a couple of sittings!).

The plot of the novel is one that seemed to me, as someone who has to deal with ethics issues and potential scientific misconduct on a not infrequent basis, all too realistic. Chloe, a talented and successful postdoc in a prestigious Boston-based lab, has just had a Nature paper accepted for publication, and this gives her the kudos she needs to go on the job market. But when Karen, another postdoc in the lab who is struggling with her own project, uncovers potential problems with some of Chloe’s data in the paper, a lab investigation is initiated and – without giving away any of the plot details – things don’t end well for one of them.

As you’d expect from someone who’s spent many years in academia, Pernille’s writing gives an accurate impression of what life in the lab is like – the long hours, the tedious nature of routine experiments, the frustration when things don’t work, the excitement when you get the first sign of the ‘big result’, the friendly banter and petty rivalries between lab mates… The unfolding events, from the  discovery of the problems and the dilemma this creates for Tom (the PI), to the painful and laborious investigation and the inevitable unravelling of a career, are revealed in a highly believable fashion. Tom’s conduct interested me – while he seems to have the best intentions, his claims to be only interested in the scientific truth don’t really hold up in the end, and his man- (or, to be more accurate, woman-) management skills clearly need brushing up! And while you can’t in any way condone what the postdoc did, you can almost understand how she could have ended up there. The fear (and reality) of getting scooped, the certainty that a result must be right, the envy at someone else’s success – some or all of these are emotions we’ve all felt in our research careers. The ending of the book is perhaps all a bit too neat: in many cases of potential research misconduct, I’m not convinced we ever really learn ‘the truth’, whereas things do get fairly well resolved here – but the story certainly echoes with cases I’ve come across.

The book also highlights some of the major flaws in the current system, primarily in terms of the way that a Cell/Science/Nature paper can make or break a career – make if you’re the one to get the paper, or break if you’re scooped by one. The ambitious Chloe was scooped during her PhD (though ended up publishing that work in Development – which I would argue can only be a good thing!) and it’s her determination to avoid this happening again that drives many of the events in the novel. We all know that there’s too much emphasis put on where you publish, and on being first, but it’s much harder to know how to change the system for the better in a practical way. Pernille’s novel doesn’t offer any help on that front, but it exposes the problem in a story that you can almost imagine being played out in labs across the world. And imagining that is scary…

My only criticism – if criticism it is – of Pernille’s book is that I suspect that the non-scientific reader would be put off by the jargon that pervades this novel. In her Q&A at the end (which you should definitely read: Pernille gives thoughtful and insightful answers to important questions about the state of our field), Pernille implies that the novel is aimed at the general public, but I’m not convinced she’ll reach that audience – though I might test this out by lending it out and I’d be happy to be proved wrong! But for the scientifically literate, particularly those just starting out in their research career, this book is a beautifully crafted cautionary tale about life in the lab that will get you thinking about the subtleties and temptations underlying ethical conduct in research.

(16 votes)

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