Here are the highlights from the current issue of Development:

SEGGA: new software for analysing cell shape and dynamics

Changes in epithelial cell shape and organisation are essential for tissue morphogenesis, regeneration and repair. In recent years, advances in microscopy have made it possible to capture these changes in living animals, but the quantitative analysis of changes in cell shape, behaviour and polarity in large cell populations remains a significant challenge. Here, on p. 1725, Jennifer Zallen and colleagues describe new image analysis software that allows automated image processing, image segmentation, cell tracking, data analysis and data visualization. Using this software, which they term SEGGA (for image SEGmentation, Graphical visualization and Analysis), the team analysed cell behaviours during convergent extension in the Drosophila embryo. Their analyses reveal that cell intercalation is a key mechanism that drives convergent extension and that planar polarity is rapidly established, prior to the onset of elongation, and is dynamically remodelled as cells intercalate. The researchers also demonstrate the general utility of this software by analysing images of epithelial cells from other tissues and organisms. This software, which is freely available and can run on Mac, Windows and Linux operating systems, promises to be a valuable tool for the community.

CDC42 shapes up the epicardium

The epicardium – a single layer of cells that covers the heart – contributes to multiple cardiac lineages and is essential for heart development and regeneration. During development, the epicardium arises from a transient structure known as the pro-epicardium (PE): pro-epicardial cells (PECs) dissociate from the PE, translocate across the pericardial cavity and attach to the heart surface. The molecular and cellular mechanisms that control this process have thus far been elusive but, now, Mingfu Wu and co-workers reveal four different mechanisms of PEC translocation to myocardium and a key role for the small GTPase CDC42 during epicardial development in mice (p. 1635). They first report that the conditional knockout of Cdc42 in PECs results in epicardial defects, with PECs failing to form villous protrusions and floating cysts and failing to translocate to the myocardium. The authors further demonstrate that Cdc42 null PECs exhibit loss of polarity and impaired cell dynamics. Finally, they reveal that CDC42 also regulates the trafficking of FGFR1 in PECs and hence is likely to be required for FGF2-mediated signalling activity in these cells. Overall, these findings provide new insights into the mechanism by which the epicardium forms and highlight a pivotal role for CDC42 in epicardial development.

Controlling somatic cell NUMB-ers during gonadogenesis

During gonadogenesis in mice, cells within the coelomic endothelium (CE) proliferate to give rise to additional CE cells as well as somatic cells of the gonads. But how is this cell fate decision – CE versus gonadal – determined? In this issue, Blanche Capel and colleagues show that NUMB, a known antagonist of Notch signalling, plays a central role (p. 1607). They show that, during early gonadogenesis in mice, NUMB is asymmetrically localised to the basolateral domain of CE cells, which also exhibit high levels of Notch signalling. Importantly, the authors report that the temporal deletion of Numb results in gonadal defects; mutant gonads contain patches of undifferentiated cells, reduced numbers of differentiated somatic cells and, curiously, reduced numbers of germ cells. The polarity of CE cells in mutant gonads is also disrupted. Finally, the researchers demonstrate that blocking Notch signalling (using the g-secretase inhibitor DAPT) can rescue the somatic cell defects. Based on their findings, the authors propose that asymmetric divisions in the CE give rise to one daughter that remains in the CE, and one daughter that inherits NUMB and the competence to differentiate.

PLUS:

An interview with John Gurdon

John Gurdon is a Distinguished Group Leader in the Wellcome Trust/Cancer Research UK Gurdon Institute and Professor Emeritus in the Department of Zoology at the University of Cambridge. In 2012, he was awarded the Nobel Prize in Physiology or Medicine jointly with Shinya Yamanaka for work on the reprogramming of mature cells to pluripotency. We met John in his Cambridge office to discuss his career and hear his thoughts on the past, present and future of reprogramming. Read the Spotlight article on p. 1581

Human organomics: a fresh approach to understanding human development using single-cell transcriptomics

Innovative methods designed to recapitulate human organogenesis from pluripotent stem cells provide a means to explore human developmental biology. New technologies to sequence and analyze single-cell transcriptomes can deconstruct these ‘organoids’ into constituent parts, and reconstruct lineage trajectories during cell differentiation. In their Spotlight article, J. Gray Camp and Barbara Treutlein summarize the different approaches to performing single-cell transcriptomics on organoids, and discuss the opportunities and challenges of applying these techniques to generate organ-level, mechanistic models of human development and disease.

Development of the hypothalamus: conservation, modification and innovation

Yuanyuan Xie and Richard Dorsky review the factors involved in the induction, patterning and neuronal differentiation of the hypothalamus, highlighting recent evidence that illustrates how changes in Wnt/β-catenin signaling during development may lead to species-specific form and function of this important brain structure. Read the Review article on p. 1588.

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Or, please stop mixing green/red

Color is a key aspect of graphic design, but for many years was not relevant for scientific figures that were largely black and white. Falling prices for color print and electronic publishing changed this dramatically and scientists now frequently produce multi-colored figures. Using color functionally is not always straightforward but few rules exist: do not combine red and green!

Already in 1939 Willard Brinton advised his readers to not use red letters on a green background as they become invisible to color-blind people (and are hideous for the rest of us!). [his great book on data visualization is available for free here]. A century later, when browsing through figures in scientific periodical, this message has not reached everyone.

Red/Green line chart

Color-blind friendly

Direct data labels abolish color need

In charts, it is very straightforward to avoid mixing red and green. If you want to use red, combine it with blue or cyan, if you want to use green, combine it with magenta or orange. That way also color blind people can distinguish the data points. A side note: try starting a chart in black and white, and only add color if absolutely essential.

Overlapping data is problematic

Color-blind friendly

Alternative without using color

In laser-microscopy green and red fluorophores are widely used, often in combination. But: Simply because a wavelength of your fluorophore is 488nm this does not mean you have to use green for its display! The camera output doesn’t have color anyway, so you are at liberty to choose a suitable lookup table. Why not be color-blind friendly and choose colors visible to your entire audience. Options that still preserve a little information on the wavelength are green/magenta or cyan/red.

Red/green confocal image

Color-blind friendly version

Again, consider if two black and white images instead of a composite color. In fact, the contrast is usually higher in greyscale which benefits the display of structure details and subtle intensity differences.

More detail visible…

…in black/white images

*Rm62 RNA in Drosophila egg chambers part of my postdoc project, find more subcellular RNAs on the Dresden Ovary Table.

Helpful tools:

• Test color-blind visibility for your images here
• Choose color for categorical, quantitative and diverging data in charts using color-brewer.

Comments suggesting more tools very welcome!

(8 votes)

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In this post, I would like to introduce to “The Node” our website, reviewercredits.com, launched last July by myself and my friend Robert Fruscio. We are both physicians (I’m in critical care, he is in Gynecological oncology) and several times we chatted about peer review: we always realized how this activity is poorly recognized, despite its invaluable role. As scientists we felt, often, hard to devote time and energies to something which has no metrics or repository or publicity. Of course, we are not so small-minded to deny that, as part of sciectific community we are all devoted to this “common effort”. At the same time it is tempting to spend an afternoon writing your own paper or preparing lessons or analyzing data (where you are more likely to get an “immediate” reward) rather than peer reviewing someone else’s paper. This is becoming more and more relevant, since scientist are increasingly “metered” in terms of productivity.

So we had the Idea of reviewercredits.com

What is reviewercredits.com?

Scientist and researchers can subscribe to ReviewerCredits.com and get recognition for all the reviews they perform. ReviewerCredits keeps a history of all the reviews performed, assigns an Index and, in the future, will give tangible rewards!

Researchers, after subscribing to the website, can fill a claim for each peer review performed in the previous twelve months. We verify that the review has actually been performed by asking a confirmation from the journal. This step is essential in the process to create a solid and reliable history of reviews performed and is a feature unique to ReviewerCredits.com. Upon confirmation from the Editor, the review is added to the personal account of the reviewer.

We decided to create our own metric, the Reviewer Index, to appraise and quantify the work of reviewers. The reviewers are able to accumulate points towards their Reviewer Index. For each review performed, the reviewer will receive one point. The reliability of this Index is guaranteed by the fact that each single review is verified and certified by the Journals. A high Reviewer Index reflects a very active reviewer. This Index reflects and measures the value created by all the hard work performed with peer reviewing.

Furthermore, subscribers on their profile will be able to keep track of the reviews performed for any Journal, and will be able to download a pdf file with the list of all approved reviews.

Reviewers can also earn credits and redeemed these credits for tangible rewards. One review certified by the journal earns 10 credits for the reviewer (20 if the Journal has an account at reviewercredits.com). Credits can also be earned by inviting colleagues to join ReviewerCredits.

Our vision is to make credits convertible in real, tangible rewards. We would like to offer the possibility to choose between several alternatives, including, for example, discount on publishing fees for articles, free subscription to Journals, gift cards, small reseach grants, or others. The amount of this kind of reward will depend on you, on your activity, and on your willingness to change things that are, apparently, unchangeable.

So far, about 2400 scientists joined our community. This number is still very small, if compared to the  total number of the scientist active in the field of peer review, but we need the word to spread, to grow more and more!

At the same time we aim to provide a service for journals, too.

Journal’s editors often struggle to find experts willing to review articles submitted or waste time chasing reviewers whose peer reviews are overdue.

There is the lack of any mechanism by which reviewers can be rewarded for their effort. Reviewercredits wants to become this mechanism to encourage and motivate reviewers easing the job on editors, journals and publishers. Reviewercredits wants to reward reviewer and help them create value for themselves by assigning a reviewer Index for the work performed.

Journals can actively participate in this new direction by opening a profile on our website. Registered journals provide twice the credits for each peer review. This will likely increase the involvement and efficiency of peer-reviewers for these journal.

We met, personally, by email and skype so many people, many liked the idea, others did not, but we always tried to get all the good suggestions to improve ourselves. We received many emails, some nice, some odd, some aggressive. Sometimes there is a natural difference toward new ideas, but we hope that the members of this community will like reviewercredits.com and decide to join us, so that, more and more, the efforts of peer reviewers get the reward which they deserve!

(3 votes)

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A postdoctoral position is available in the Cisse laboratory in the department of neurological surgery, the Brain and Mind Research institute and the Children Brain Tumor Project (CBTP) at Weill Cornell Medicine in New York city.

Our research interest is on the transcriptional control of cell fate in the immune system (e.g. Cissé et al., Cell 2008) and current projects will focus on the transcriptional regulation of brain tumor-associated immune cell functions using mouse models and human brain tumor samples.

We are looking for highly qualified and motivated candidates with strong backgrounds in immunology, developmental biology, molecular biology and/or genetics for a 2-3 year post-doctoral position. Experience with computational biology and bioinformatic tools would be advantageous for the position.

Please submit your CV and a cover letter outlining your research interests, career goals and the names of three referees with contact information to Babacar Cisse at the following address: CisseLab@med.cornell.edu

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Apply here:

https://ki.mynetworkglobal.com/en/what:job/jobID:145599/

Deadline: 2017 May 14

Description:

The environment plays a critical role triggering disease in genetically susceptible individuals. The goal of this project is to generate in vivo models to study the interaction between gene function and environmental factors during the initiation/resolution of intestinal inflammation. We have generated CRISPR mutant zebrafish lines targeting IBD-risk genes with unknown function. The successful candidate will characterize these mutants and validate her/his finding in mouse models and human organoids candidate will also generate IBD reporters to visualize immunological processes associated to IBD in the context of genetic susceptibility and environmental triggers.

Entry requirements:
Our lab has an opening for a highly creative and motivated postdoctoral scientist with an interest in mucosal immunology. We look for a candidate with proficiency and documented laboratory research experience particularly in molecular biology, in vivo imaging and genetic manipulation in zebrafish. The candidate is expected to work with both zebrafish and mouse models of intestinal inflammation. Experience in bioinformatics and RNA-seq analysis would be an advantage. The position will require independent work at the laboratory as well as extensive collaboration with other experimental groups. Fluency in both oral and written English is necessary. Documented ability to analyze and present results orally and written is important.

Type of scholarship
A scholarship for carrying out postdoctoral research can be granted for a maximum of two years within a four year period following the receipt of a doctoral degree or equivalent. This educational scholarship is tax-exempt. The amount is set for twelve months at a time and is paid out on a monthly basis. In exceptional cases, shorter periods may be acceptable.

Publications: Villablanca EJ et al., JLB, 2008; Villablanca EJ et al., J. Immunol, 2008; Peloquin JM., et al., Annu. Rev. Immunol, 2016; Villablanca EJ., et al., Gut, 2014; Gagliani N., et al., Cell, 2014; Huber S., et al Nature, 2012; Villablanca EJ., et al., Gastroenterology, 2011; Villablanca EJ., et al., Nat. Med, 2010

More information about the Villablanca lab:

http://www.cmm.ki.se/en/group/eduardo-villablanca-group/

http://ejvillablanca.wixsite.com/villablancalab

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At Development, we are committed to making submission as easy as possible for our authors. We realise that submitting a paper to any journal can be a lengthy process: authors are asked to comply with detailed journal-specific guidelines without knowing whether the paper will be accepted or even peer-reviewed. We are therefore delighted to announce our new format-free submission policy.

Authors can now submit a paper to Development in any format. We will only ask what is absolutely necessary at submission. What this means is that as long as an article adheres to our guidelines on length and the text and figures are easily viewable by reviewers, we only require information that is necessary to confirm the identities of all authors. This does mean that other requirements, such as file formats and sizes, our submission checklist, and provision of funding information, will move to the revision stage – at which point over 95% of papers will be accepted for publication.

As part of this change, and recognising the importance of comprehensive Materials and Methods sections to aid transparency and reproducibility, we are also removing the Materials and Methods section from our length limit to an article. The aim is to allow authors the space they need to describe their methods in sufficient detail for readers to fully understand and replicate the experiments conducted. In exceptional cases where the Materials and Methods are particularly lengthy, more detailed experimental protocols, descriptions of computational analyses or lists of primers and other reagents may still be included as Supplementary Materials and Methods.

For further details, please refer to our Manuscript Preparation guidelines, or get in touch with any queries.

(2 votes)

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Our aim is to build an expandable open-access atlas over brain morphogenesis – the digital Z-hindbrain atlas – containing data from gene expression, transcriptional dynamics, clonal growth, cell lineages, and definitions of anatomical regions. This open-access IT resource will help us to expand our knowledge on how the brain is functionally organized, and therefore for advancing brain research, medicine, and brain-inspired information technology.

The fellow will work in collaboration between two groups: Piella’s lab at Department of Engineering and Information and Communication Technologies (DTIC, Campus Poble Nou, https://www.upf.edu/web/simbiosys), and Pujades’ lab at Department of Experimental and Health Sciences (DCEXS, http://pujadeslab.upf.edu) that is located within the PRBB, a vibrant research park harboring several research institutions.

CANDIDATE REQUIREMENTS:

We are seeking for highly motivated and enthusiastic candidates with background in biological/medical image analysis and, in particular, in image registration, and spatiotemporal alignment techniques such as statistical atlases. Programming experience is required.

Candidates must have good English communication skills. The fellowship covers the salary for 1 year, with the possibility of being extended.

The fellow will benefit from working in two dynamic groups, at university departments that recently received the Maria de Maetzu Award for their scientific excellence.

Interested candidates are encouraged to send a letter of interest, CV, and contact details of 2 referees either to Gemma Piella (gemma.piella@upf.edu) or Cristina Pujades (cristina.pujades@upf.edu).

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The votes are in for our latest Development cover competition with entries from the 2015 class of the Woods Hole Embryology Course. 

With 578 votes counted, a winner emerged with 40% of the vote –

4^th Place (72 votes) – Clathria

3^rd Place (136 votes) – Mice

2^nd Place (138 votes) – Jellyfish

1^st Place (232 votes) – Chicken

This planetary image is a Stage 10 chick embryo with noggin coated beads taken by Theodora Koromila (CalTech, USA), and will probably be the first Development cover to have been taken with a phone through the eyepiece of a microscope!

Congratulations to Theodora, and thanks to Shun Sogabe
, Chiara Sinigaglia
 and Martin Minařík for the other beautiful entries.

Look out for Round 2 in the coming weeks.

(2 votes)

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The laboratory of Zebrafish Neurogenetics, led by Dr. Laure Bally-Cuif at the Pasteur Institute in Paris, is seeking an outstanding and highly motivated Postdoctoral Research Associate to contribute to our ongoing research on adult neurogenesis in zebrafish. Our lab is interested in the molecular and cellular mechanisms underlying basic adult neural stem cell properties, including the control of their quiescence, their interactions with other neural stem cells of the germinal niche, and their recruitment towards neuron generation. The project will involve characterizing how the neurogenic activity of individual neural stem cells is controlled, and how neuronal identities are encoded and used to build a continuously growing but functional brain. Analyses will involve genetic approaches, whole-mount imaging and cell tracing in the adult animal, and will include tool development for conditional functional assays in adult neural stem cells.

Candidates must hold a Ph.D. in biology, and a strong interest and background in molecular and cellular neuroscience, in any model system. Previous experience with imaging and genomic techniques is preferred. Proficiency in English is required.

The position is funded by the European Research Council and Labex Revive.

The Bally-Cuif team is one of the 16 research groups of the “Developmental and Stem Cell Biology” Department of the Pasteur Institute, focusing on evolutionary, developmental and stem cell biology in various animal models. It is also co-affiliated with the Pasteur “Neuroscience” Department.

To apply, please submit your CV and the name of three references to:

laure.bally-cuif@pasteur.fr

Institut Pasteur, CNRS UMR3738

Dept of Developmental and Stem Cell Biology

25 rue du Dr Roux

75015 Paris France

Zebrafish Neurogenetics

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