Two postdoctoral positions are available in the Boavida laboratory in the Department of Botany and Plant Pathology at Purdue University. The lab investigates the molecular mechanisms controlling gamete identity and function and cell-cell signaling in plant fertilization.

We are seeking highly motivated individuals who value achievement, are proactive, creative, detail-oriented, flexible and constructive team players. Candidates should have completed their Ph.D. degree on a relevant area in Biological Sciences within the last 2-3 years. Proven ability to present and publish research data and excellent English communication skills both oral and written are required.

Postdoc A. The recruited researcher will work in two main axes of investigation based on (1) identification of interaction partners of gamete-expressed proteins primarily through a high-throughput proteomic screening (NGS-Y2H); and (2) integration of PPI networks with derived NGS-transcriptomic approaches to establish high-confidence interaction maps for prediction and functional characterization of signaling networks operating in plant gametes and fertilization. The ideal candidate should have experience in molecular biology and protein biochemistry (membrane protein expression and purification from various cellular systems, Y2H, BIFC, co-immunoprecipitation, etc.). Knowledge of integrative computational analysis, structural bioinformatics, protein docking and characterization of regulatory networks is an asset.

Postdoc B. The postdoctoral researcher will use an exciting combination of techniques including flow cytometry (Microfluidics and FACs), genomics, transcriptomics, epigenomics, and molecular biology to study mechanisms underlying cell identity and differentiation of plant gametophytes in a spatiotemporal context. He/she will also be involved in the characterization of a cell-based functional assay to study the cellular functions of candidate genes in plant fertilization. Prior experience in flow cytometry, confocal microscopy, molecular genetics, functional genomics, and bioinformatics is highly desired. Candidates with interest in sexual reproduction and/or documented experience in Arabidopsis, tomato and maize are especially encouraged to apply.

Application

Applications will be accepted until the position is filled and should include CV, contact details of at least 2 references and a cover letter outlining how your previous research experience/contribution integrate with the laboratory research projects. Incomplete applications will not be considered for evaluation. Relevant publications and information can be found here.

Please send your application as a single PDF file to lboavida@purdue.edu. Include in the subject header PlantRepro2018_A (or B) (according to your interest in Postdoc position A or B).  The appointment is initially for 12 months with the possibility of extension depending on research performance and available funds. Starting date is flexible and can be as early as February 1^st, 2019.

Purdue University is an Equal Opportunity Employer, has a strong commitment to diversity and actively encourages applications from candidates from groups underrepresented in higher education.

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A PhD position is available in the laboratory of Néva Meyer at Clark University in Worcester, MA USA. Research in Dr. Meyer’s lab is currently focused on understanding how the central nervous system develops in annelids with the goal of gaining a better understanding of how nervous systems evolved.

The successful applicant will develop a project focused on molecular control of neural fate specification in the annelid Capitella teleta, but this can be expanded to include other spiralians and different avenues of research depending on the applicant’s interests and goals. Additional information is available on the Meyer lab website.

The anticipated start date is late August 2019. Previous experience in molecular biology and working with marine larvae and/or bioinformatics is desirable. The successful applicant will be guaranteed funding for five years through a combination of research assistantships and teaching assistantships; two years of research assistantship for this position are currently available.

Please email a cover letter explaining your interest in the position and qualifications and a CV to: nmeyer[a]clarku.edu.

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When we examined the kinetics of Rho GTPase activity in endothelial cells in response to receptor stimulation (Reinhard, 2017), we noticed considerable cell-to-cell heterogeneity. In the original work we published graphs with the average response, reflecting the response of the whole cell population. However, these graphs fail to show the cellular heterogeneity. What is the best way to visualize these data? I don’t know, but I will explore several options to visualize all individual traces from the experiment.

1. All together

The original paper displayed the average responses of the Rho GTPases RhoA, Rac1 and Cdc42 and the graphs were remade with R/ggplot2 in this blog. Since the Rac1 data showed the largest differences between cells, I took this data to explore different ways of visualizing it. One can simply plot all the individual lines together with the average response in a single graph (figure 1). How this can be achieved with R/ggplot2 is explained in this blog. The graph may look cluttered when there are many lines and therefore it is advisable to use thin gray lines. To enable the identification of individual traces one may use a unique color for each trace. Putting all traces from a single experiment in the same graph is a simple but effective method to depict variability. However, putting all data in a single graph for multiple conditions is usually makes the graph difficult to understand.

Figure 1: Ordinary graphs showing the data from individual cells as thin lines on top of each other. In the left panel the average is shown as a thicker black line. In the right panel the data from each line has a unique color to improve identification of cells.

2. Ridges

Instead of putting all graphs on top of each other, an offset along the y-axis is introduced, which reduces overlap. This type of plot is called a ridgeline plot (formerly known as a joyplot). By adding an increasing offset for the x-axis, the curves are further separated and a 3D effect is generated. This may result in a nicer plot to look at, but it comes at the cost of impeding quantitative interpretation. For example of the use of ridgeline plots fro kymographs see this blog.

Figure 2: Ridgeline plots showing the individual cellular responses with an offset in the vertical direction (left) or an offset in both vertical and horizontal direction (right).

3. Small multiples

Instead of plotting all lines in a single graph, it is also an option to show all lines in individual plots. This type of design is coined the “small multiple” and it was popularized by Edward Tufte. The presentation of small multiples is not limited to line graphs, but be used to depict other types of data, e.g. several still images from a movie.

Small multiples can be reproduced in R/ggplot2 by using ‘faceting’ and this has been briefly highlighted in a previous blog (near the end). Figure 3 (left) shows the standard output of ggplot2, with labels for each plot. In my opinion, the small multiple is at its best when it is trimmed down to the bare minimum. As an example, I made a minimalistic variant with a high data-ink ratio (figure 3, right). Although numbers are absent, this visualization still allows for quantitative comparison and it shows the heterogeneity. In summary, the small multiple is a great way to depict the individual data, but it requires quite some space.

Figure 3: The small multiple presentation of the time-lapse data shown as the standard output of ggplot2 with facets (left) and a minimalistic version (right) with improved data-ink ratio.

4. Heatmap

The ‘heatmap’ is well-known for the visualization of microarray data. It can also be used for different types of data including time-series data. To generate a heatmap, the actual numbers of each of the line graphs are color coded and these are presented as a line. Every line (row) of the heatmap represents a single trace from a time series experiment. The result is an image in that shows the responses encoded by colors (figure 4).

As the data is encoded by color, the quantitative comparison of the data is limited to comparing colors. This comparison is inherently non-quantitative. As such, the downside of a heatmap is that it only allows qualitative interpretation. Still, heatmaps enable the visualization of a lot of data on a relatively small space.

Figure 4: Heatmap style presentation in which each row represents the data from a cell. The response is color coded according to the legend. The data is presented in order of acquisition (left) or clustered based on similarity (right).

Sorting out the mess

The data from single cell experiments can be very heterogeneous (as in this example) and may look like a mess. To structure the data, it can be sorted or grouped. Sorting uses a feature of the data that can be used to rank the individual traces. For instance, for the ridgeline plot (figure 2) the maximum response of every trace was determined. Subsequently, the plots were ordered based on the maximum response (ratio) that was observed. Any other parameter can be used to order the data, e.g. integrated response, timing of the maximum response or noise of the baseline.

Another method to structure the data is grouping or clustering. For the data presented in the heatmap a hierarchical clustering was performed (figure 4, right), which determines the pairwise difference for each of the traces. The ouctome is an order of traces that groups similar responses together. There are many ways to cluster data and information on this topic can be found elsewhere (for instance here, here and here). In the end, the sorting or clustering of the time-lapse data may structure the data and aid interpretation. It can precede any of the visualizations shown above, but it makes most sense for ridgeline plots or heatmaps.

Howto

This blog explores several options to visualize data, but does not go into detail on how to achieve it. The code (and data) that was used to generate the graphs is available at Zenodo (http://dx.doi.org/10.5281/zenodo.2211123) and should give some idea of how to achieve the different visualizations in R/ggplot2. Alternatively, some of the plots shown in this blog (including small multiples and heatmaps) can be made with a web-based tool PlotTwist that uses R/ggplot2 but does not require coding skills. A nice feature of the web tool is that the presentation of the data (e.g. visibility of the lines and their color) can be adjusted in realtime.

Final words

Showing all of the data is important for full appreciation of experimental results.  Since cell-to-cell variability is observed in every single imaging experiment, methods to visualize the heterogeneity are needed. Here, I have highlighted several methods to visualize data from time-lapse imaging. These methods may be combined with some way of sorting or clustering of the data. Which approach works best for your data needs to be examined on a case-by-case basis and will depend on what you want to communicate. The different visualizations shown here may serve as a starting point to explore how to best visualize your data from time-lapse experiments.

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We are seeking outstanding postdoctoral candidates to join the Campas lab at the University of California, Santa Barbara. Our group uses interdisciplinary and quantitative approaches to study the formation of tissues and organs during zebrafish embryonic development. We are interested in connecting the molecular and cellular process that orchestrate embryogenesis with the physical/mechanical processes that sculpt tissues and organs into their functional morphologies. To quantify and perturb local tissue mechanics we employ unique microdroplet techniques that we have recently developed (Campàs et al., Nature Methods, 2014; Serwane et al., Nature Methods, 2017). These techniques offer unprecedented opportunities to study tissue morphogenesis quantitatively (see e.g., Mongera et al., Nature, 2018).

We are specifically seeking independent, passionate, and motivated applicants for a postdoctoral position to study the interplay between the molecular and mechanical processes that shape embryonic tissues in zebrafish. The candidate will be able to work in a collaborative manner with a highly interdisciplinary group of researchers, including physicists, engineers and developmental biologists. A Ph.D. in the biological sciences (or related fields) with at least 3 years of laboratory research experience in zebrafish developmental biology is required. Experience in quantitative biology or biophysics, in addition to experience in zebrafish development, will be considered positively, but is not required.

This is a renewable, two-year position with full benefits, that will be extended as needed upon good performance of the candidate. Salary will be competitive and dependent on the level of experience of the candidate. Applicants should email a CV and a description of research interests to Prof. Campas (campas@ucsb.edu), and should also arrange for at least two references to submit letters of recommendation of their behalf. Applications submitted by February 15th, 2019 will receive priority consideration, but the position will remain open until filled. Start date is flexible.

The University of California, Santa Barbara provides an exceptional, interdisciplinary and collaborative environment for scientists interested in quantitative biology and systems biology (including exposure to the Santa Barbara/KITP Summer School on Quantitative Biology).

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We are seeking independent, passionate and creative students to join the López-Schier group at the Helmholtz Zentrum in Neuherberg/Munich, Germany.

The position is to work, at either experimental or theoretical level, on the cellular, genetic and mechanical aspects of multicellular self-organisation and their relevance to sensory-organ morphogenesis and regeneration. This project is ideal for someone with a strong theoretical background in biology, physics or engineering. Knowledge of computer programming and optics would be ideal but not essential.

Qualifications & skills

– University studies in biology-related sciences, physics or engineering

– A good command of the English language is essential

Please, apply via electronic mail only, including a cover letter with a short statement of research interests and motivation, a Curriculum Vitae including a list of names and email-addresses for two/three academic references, to:

Dr. Hernán López-Schier

Unit Sensory Biology & Organogenesis, Helmholtz Zentrum München

E-mail: hernan.lopez-schier@helmholtz-muenchen.de

http://lopez-schier.strikingly.com

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I am Shinichi Morita, a postdoctoral researcher in Teruyuki Niimi’s lab at the National Institute for Basic Biology, Japan (Fig. 1A, B). Our research interests focus on the evolutionary novelties that insects have acquired, and how various insect morphologies have arisen during evolution (Fig. 1C-P).

Beetle horns are thought to be an evolutionary novelty and are used as weapons for intraspecific combats between males. Beetle horns display sexual dimorphism in many Scarab beetles, and their shapes, numbers, sizes and forming regions are highly diverged even among closely related species (Fig. 2). Elucidating how these novel traits were acquired in Scarab species will lead to better understanding of the mechanisms of morphological diversification during evolution. My postdoc project is to understand how exaggerated horns are acquired and formed in Japanese rhinoceros beetles (Trypoxylus dichotomus) (Fig. 2A, B).

First, I will introduce T. dichotomus. In Japan, T. dichotomus is a popular and familiar insect to children and adults, and is sold as a pet at department stores and DIY shops during the summer. The Japanese name for T. dichotomus is Kabuto-mushi, and it is also used as one of the season words of “Haiku” (Haiku is a traditional short Japanese poem with seventeen syllables in the pattern of 5-7-5, including a season word in it). T. dichotomus is a holometabolous insect that has egg, larval, pupa and adult stages. Its life cycle is about 12 months (Fig. 3). Adults emerge in early summer and lay eggs in the soil at the end of summer. Larvae hatch from the eggs in about 2 weeks (Fig. 3, Egg) and feed on humus. The larval period is about 8 months and they pupate in the next spring (Fig. 3, First – Third instar larva). At the end of third (last) instar, they make pupal chamber (Fig. 3, Prepupa). During the prepupal period, horn primordia are formed in the head and the thorax. After about 2 weeks of pupal period (Fig. 3, Pupa), they become adults in the early summer (Fig. 3, Adult). T. dichotomus male adults have exaggerated horns on the head and prothorax (Fig. 2A), whereas females do not have these structures (Fig. 2B). The head horn is shaped like a plow with a long stalk, and bifurcated twice at the distal tip, while the prothoracic horn is shorter than the head horn, and bifurcated once at the distal tip.

Here, I share my daily activities in the laboratory. As mentioned above, since the life cycle of T. dichotomus is one year, our daily life differs depending on season. In April, we purchase about 3,000 – 4000 last instar larvae of T. dichotomus from insect supplier (Fig. 4A). With help of our lab members, the sex of these larvae are determined (Fig. 4B) and they are packed individually in a bottle filled with breeding mats (Fig. 4C). They are stored at 10 ° C until use (Fig. 4D). Therefore, we can use T. dichotomus as an experimental material in any season.

The sexual dimorphism of horns first appears in the horn primordia during the prepupal stage (Fig.3, Prepupa). One of my main research aims is to find out which genes control horn formation, so we dissected horn primordia in males and females at this stage and performed comparative transcriptome analysis by RNA-seq. We performed an intersexual comparison between male and female horn primordial transcriptome datasets, and tried to identify genes driving the development of different morphologies between male and female. In addition, we also compared transcriptome data between different horn types (head and prothoracic horns) intersexually in males and females. As a result, we identified 1,553 differentially expressed genes (DEGs) in total. To identify the essential genes for horn formation, we focused on genes encoding 38 transcription factors and 11 signaling molecules included in the 1,553 DEGs, and performed larval RNA interference (RNAi) screening. In beetles including T. dichotomus, larval RNAi experiments is extremely efficient to analyze the function of genes during postembryonic development. Double-stranded RNA (10 – 50 µg) was injected laterally into the T1 segment of each last instar larva before the prepupal stage using a 1 ml syringe with a 30 gauge needle. As a result, 11 genes were newly identified as horn formation genes (Fig. 5A-E). Interestingly, these 11 genes are mostly categorized as larval head- and appendage-patterning genes.

Future perspective of beetle horn studies

In addition to the above 11 genes, we have identified a number of other horn formation genes, but the gene regulatory network for horn formation is still unknown. So far, we have set up various resources and tools necessary for beetle horn research (precise staging of beetle horn formation, larval RNAi, whole mount in situ hybridization, immunostaining etc.). Therefore, it has become possible to analyze the horn formation gene regulatory network through developmental biological approaches. In addition, we are going to test whether novel cis-regulatory elements play a crucial role in acquisitions of horns during evolution. To this end, we are planning to perform ATAC-seq (Assay for Transposase-Accessible Chromatin sequencing), a technique to assess genome-wide chromatin accessibility, as a project to estimate cis-regulatory elements involved in horn formation and acquisition. Through the above approaches, we believe a part of evolutionary mechanisms associated with acquisition of animal diversity will be unravelled at the molecular level.

If you would like any more information about rhinoceros beetles and evo-devo questions in Scarab beetles, please get in touch with me (shinichi@nibb.ac.jp) or Teruyuki Niimi (niimi@nibb.ac.jp).

References

1. Ohde, T., Morita, S., Shigenobu, S., Morita, J., Mizutani, T., Gotoh, H., Zinna, RA., Nakata, M., Ito, Y., Wada, K., Kitano, Y., Yuzaki, K., Toga, K., Mase, M., Kadota, K., Rushe, J., Lavine, LC., Emlen, DJ. and Niimi, T. (2018) Rhinoceros beetle horn development reveals deep parallels with dung beetles. PLOS Genetics, 14: e1007651.
2. Ito, Y., Harigai, A., Nakata, M., Hosoya, T., Araya, K., Oba, Y., Ito, A., Ohde, T., Yaginuma, T. and Niimi, T. (2013) The role of doublesex in the evolution of exaggerated horns in the Japanese rhinoceros beetle. EMBO reports, 14: 561-567.

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Job title:           Laboratory Research Scientists

Location:         The Francis Crick Institute, Midland Road, London

Contract:          Fixed-term, (3-4 months)

Full time

Salary:             Competitive with benefits, subject to skills and experience

Vacancy ID:     9385

Short summary

We are seeking a highly motivated and collaborative Laboratory Research Scientists in the area of human embryology and stem cell biology to join Dr. Kathy Niakan’s laboratory. Our lab seeks to understand gene function and to characterise gene expression during human pre-implantation development. This foundational information not only informs our understanding of human biology but also has clinical importance for infertility treatment and the therapeutic use of embryonic stem cells to treat various diseases.

The successful candidate is likely to be collaborative, energetic, focused, and productive individual. Excellent organisational, analytical, and communication skills are essential.

Project scope

Dr Niakan’s laboratory focuses on understanding the mechanisms of lineage specification in human embryos and the derivation of novel human stem cells. The post holder will report directly to the Group Leader, Kathy Niakan. Details of research projects currently being undertaken can be seen at: http://www.crick.ac.uk/kathy-niakan

The pluripotent epiblast of the early human embryo has the unique potential to give rise to the entire fetus in vivo and can self-renew indefinitely as embryonic stem cells (hESCs) in vitro. Understanding how this lineage is established is of fundamental biological importance and has significant clinical implications for both infertility treatment and the use of hESCs to treat various diseases.

The aim of this project is to further understand fundamental aspects of early human development and to use this knowledge to inform our understanding of existing stem cells and to establish novel alternative stem cells. Research techniques used in the laboratory include: molecular biology, advanced microscopy, human and mouse preimplantation embryo culture and micromanipulation, CRISPR/Cas9-mediated genome editing, genome-wide techniques including single-cell RNA-sequencing combined with DNA-sequencing.

About us

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

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

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

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

• If you are interested in applying for this role, please apply via our website.
• The closing date for applications is 21 December 2018 at 23:30.
• All offers of employment are subject to successful security screening and continuous eligibility to work in the United Kingdom.

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This interview, the 52nd in our series, was the first to be published in Development. We’re aiming for one interview per issue, and will continue to put them up here (once the issue has closed). 

During teleost fertilisation, sperm fertilises the oocyte through the micropyle, a channel traversing the vitelline membrane at the animal pole. This crucial structure is formed by a specialised micropylar cell (MC) in the follicular epithelium that surrounds the oocyte, but many aspects of MC specification and differentiation remain incompletely understood. A paper from the current issue of Development reveals an unexpected role for the Hippo pathway effector Taz in this process, and hence in fertilisation, in zebrafish. First author and PhD student Chaitanya Dingare and his supervisor Virginie Lecaudey, Professor for Developmental Biology of Vertebrates at the Goethe University of Frankfurt in Germany, told us more about the story.

Virginie, can you give us your scientific biography and the questions your lab is trying to answer?

VL I studied Biology in Paris and did my PhD at the Ecole Normale Supérieure in the lab of Sylvie Schneider-Maunoury. We were interested in the mechanisms underlying the segmentation of the vertebrate hindbrain; this is when I started to work with zebrafish. During this time, I developed a solid background in molecular biology and a passion for developmental biology. Then in 2005 I joined Darren Gilmour at the European Molecular Biology Laboratory (EMBL) in Heidelberg as his lab was just starting. There I started to use the zebrafish lateral line primordium as a model of dynamically remodelling epithelium, and truly enjoyed the extraordinary scientific and international environment of the EMBL. These years were influential in my career, not only because of the amount of things I learned, but also because of the amazing people I met there, and who are now my colleagues, my collaborators and my friends. In 2009, I got the opportunity to start my own lab as a Junior Professor at the University of Freiburg, within the BIOSS Centre for Biological Signalling Studies excellence cluster. We started to focus on the mechanisms that underlie cell shape changes in epithelia and how this drives morphogenesis and organogenesis. After spending 5 years in Freiburg, in 2015 I was appointed as a full professor at the Goethe University of Frankfurt.

My lab is still focusing on how cells coordinate their behaviours to assemble coherent and functional tissues and organs during development. For this purpose, we have mainly been using the lateral line primordium, which is a beautiful system to understand how cell proliferation, cell migration, cell shape changes and cell differentiation are orchestrated in a tissue that is undergoing morphogenesis. In addition, as a group of cells that migrate superficially in a transparent embryo, this is also an ideal system to use to follow these processes in real time within a living organism using high-resolution microscopy. More recently, we have started to look at another epithelium, the follicle cell layer that surrounds the oocyte, and in particular one cell within it: the micropylar cell (MC).

Chaitanya, how did you come to join the Lecaudey lab, and what drives your research?

CD After 2 years of research experience at the Tata Institute for Fundamental Research in Mumbai, I was looking for a PhD position involving zebrafish genetics and morphogenesis. Among other places in Europe, I had applied to Virginie’s lab in Freiburg as the focus of the lab was on studying various cellular behaviours in a very dynamic system, the lateral line primordium.

The major force that drives my research is the frequent stimulating and motivating discussions with Virginie, neighbouring lab members, my friends and my colleagues. Another personally important aspect of doing research is to try and look at my results without having any ‘favourite’ hypothesis in mind: this makes a huge difference as it gives some flexibility to explore more options. I also personally believe that collaborations play a major role in research, in particular when you start working on a completely new question and lack some expertise. This is reflected in our current story as well. Finally, the strong support of my supervisor, a productive research environment and, last but not least, extremely supportive colleagues: all of these aspects play a pivotal role in my research.

How did you come to be interested in zebrafish fertilisation?

CD Our current story is all about serendipity. As I joined Virginie’s lab, I started to analyse the role of Yap and Taz in the lateral line primordium. For that, we generated mutants for yap and taz/wwtr1 using TALENs. To our surprise, we found out that the taz mutant females were infertile, and that’s how we started to work on fertilisation and oogenesis. It was a bit challenging for me initially, as this was the first time I was working on adult fish to obtain immature oocytes for my experiments. It was quite exciting as well, as I got to learn a whole new set of techniques. This project has definitely honed my experimental skills, and also trained me to think in a very simple, yet ‘out of the box’, way, as we began with a very simple observation.

VL Indeed, this is an example of a purely curiosity-driven project. Chaitanya joined the lab as we started to work on the Hippo signalling pathway. The mutant he – together with former bachelor student Svenja Godbersen – generated did not show any obvious phenotype, but when homozygous mutants were incrossed, the eggs were systematically unfertilised. At that point, it was really Chaitanya’s curiosity and perseverance which made the difference, as he was so determined to figure out what was going wrong in the mutant. And then it became so exciting to discover this entirely new field for us. It was totally refreshing!

It became so exciting to discover this entirely new field for us. It was totally refreshing!

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

CD & VL Our study provides a molecular and genetic basis to MC development that has otherwise been studied only at the structural level. We show that the Hippo pathway effector Taz is essential for the differentiation of the MC, and thus for fertilisation in zebrafish. One of our key findings is that Taz enrichment in the MC precursor precedes the drastic changes in shape and size that characterise the differentiated MC. This makes Taz not only the first bona fide marker of the MC, but also the earliest event that distinguishes a unique cell among hundreds within the follicular cell (FC) layer. These findings are supported by our genetic data, which show that in the taz/wwtr1 mutants, no sign of MC differentiation can be detected. As a consequence, the MC and the micropyle fail to form.

What do you think might be upstream of Hippo – how is a single cell specified from the follicular epithelium?

CD & VL This is indeed a very interesting question! We know from previous studies that the polarity of the oocyte is crucial to localise the micropyle facing the oocyte animal pole, but the nature of the signal transmitted from the oocyte to the FC layer is unclear. Our paper shows that a small patch of microvilli at the oocyte animal pole is distinctly lost much earlier than the rest of the microvilli that cover the oocyte, irrespective of the presence or absence of the MC. In wild type, the MC lengthens as the microvilli shorten so that it remains constantly attached to the oocyte surface. This suggests that the microvilli at the animal pole may have distinct properties and could be involved in transmitting a signal, possibly a biomechanical one, leading to modulation of the Hippo pathway in the MC precursor.

Hippo signalling, in both canonical and non-canonical flavours, has been implicated in numerous developmental processes. Have you got any idea how the pathway is directing MC development?

CD Currently, I would give equal importance to both the pathways. Canonical Hippo signalling, by a classical definition, is a kinase cascade, so we need to first find out the phosphorylation status of Taz in the MC in comparison with other cells in the epithelium. This would at least help us to favour one over another.

VL This question remains fully open and, in many cases, it has been shown that canonical and non-canonical Hippo pathways are interconnected. We are just starting to look at whether components of the canonical or non-canonical Hippo pathway are present in the FC layer, and in the MC in particular, so it is too early to rank one pathway over the other.

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

CD Yes. At the time I was still working in Freiburg: I started crossing the Taz mutants, but after three to four crossings, I got only unfertilised eggs. This was a kind of eureka moment for me – it was so unusual that hundreds of eggs were left unfertilised.

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

CD During the initial period of my PhD, the mutants I had generated using reverse genetic approaches did not show any detectable phenotype. Therefore, the candidate-based approach did sometimes leave me frustrated!

So what next for you after this paper?

CD I am currently applying for postdoc positions. I wish to continue in the developmental biology field, with a special emphasis on in vitro systems such as organoids or embryonic stem cells.

Where will this work take the Lecaudey lab?

VL This work establishes the MC as a new and exciting system to dissect the mechanisms that underlie the specification of a unique cell fate in a field of otherwise homogeneous cells. This is what we are particularly interested in and want to focus on in the near future. The two main obvious questions that come out of this work are: what are the mechanisms downstream of Taz that drive the differentiation of the MC and what is the nature of the signal that transmits positional information from the oocyte into the overlying FC layer, leading to the specification of a unique cell within? As mentioned above, this signal could be biochemical, biomechanical or both.

Finally, let’s move outside the lab – what do you like to do in your spare time in Frankfurt?

CD Frankfurt being a very international city, I often go out and try cuisines from different countries.

VL I spend as much time as I can with my husband and our two children. We live just outside Frankfurt in a very nice hilly area called ‘Taunus’. We like to hike and bike there. It does not really matter what we do, we just enjoy the time together.

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

This month’s haul includes a potful of plant development, new ways to mend broken hearts, an Alexa in the lab, and three preprints from Development’s recently appointed Editor Cassandra Extavour.

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

Developmental biology

| Patterning & signalling

| Morphogenesis & mechanics

| Genes & genomes

| Stem cells, regeneration & disease modelling

| Plant development

Evo-devo & evo

Cell biology

Modelling

Tools & resources

Research practice & education

Why not…

Developmental biology

| Patterning & signalling

Intracellular pH controls Wnt signaling downstream of glycolysis in the vertebrate embryo
Masayuki oginuma, yukiko harima, Fengzhu Xiong, Olivier Pourquie

In vitro characterization of the human segmentation clock
Margarete Diaz-Cuadros, Daniel Wagner, Christoph Budjan, Alexis Hubaud, Jonathan Touboul, Arthur Michaut, Ziad Al Tanoury, Kumiko Yoshioka-Kobayashi, Yusuke Niino, Ryoichiro Kageyama, Atsushi Miyawaki, Olivier Pourquie

A Scube2-Shh feedback loop links morphogen release to morphogen signaling to enable scale invariant patterning of the ventral neural tube
Zach Collins, Kana Ishimatsu, Tony Tsai, Sean Megaso

A dual function of FGF signaling in Xenopus left-right axis formation
Isabelle Schneider, Jennifer Kreis, Axel Schweickert, Martin Blum, Philipp Vick

Fgf3 is crucial for the generation of monoaminergic cerebrospinal fluid contacting cells in zebrafish
Isabel Reuter, Jana Jaeckels, Susanne Kneitz, Jochen Kuper, Klaus-Peter Lesch, Christina Lillesaar

Osteocyte death and bone overgrowth in mice lacking Fibroblast Growth Factor Receptors 1 and 2 in mature osteoblasts and osteocytes
Jennifer McKenzie, Craig Smith, Kannan Karuppaiah, Joshua Langberg, Matthew J Silva, David M Ornitz

High-throughput micro-patterning platform reveals Nodal-dependent dissection of peri-gastrulation-associated versus pre-neurulation associated fate patterning
Mukul Tewary, Dominika Dziedzicka, Joel Ostblom, Laura Prochazka, Nika Shakiba, Curtis Woodford, Elia Piccinini, Alice Vickers, Blaise Louis, Nafees Rahman, Davide Danovi, Mieke Geens, Fiona Mary Watt, Peter W Zandstra

Genetic dissection of Nodal and Bmp signalling requirements during primordial germ cell development
Anna D Senft, Elizabeth K Bikoff, Elizabeth J Robertson, Ita Costello

Reevaluation of the Role of ERK3 in Perinatal Survival and Post-Natal Growth Using New Genetically-Engineered Mouse Models
Mathilde Soulez, Marc K Saba-El-Leil, Benjamin Turgeon, Simon Mathien, Philippe Coulombe, Sonia Klinger, Justine Rousseau, Kim Lévesque, Sylvain Meloche

Iron deficiency affects early stages of embryonic hematopoiesis but not the endothelial to hematopoietic transition
Maya Shvartsman, Saygın Bilican, Christophe Lancrin

Germline deletion reveals a non-essential role of the atypical MAPK6/ERK3
Natalia Ronkina, Karin Schuster-Gossler, Florian Hansmann, Heike Kunze-Schumacher, Inga Sandrock, Tatiana Yakovleva, Juri Lafera, Wolfgang Baumgärtner, Andreas Krueger, Immo Prinz, Achim Gossler, Alexey Kotlyarov, Matthias Gaestel

Rgs12 enhances osteoclastogenesis by suppressing Nrf2 activity and promoting the formation of reactive oxygen species
Andrew Ying Hui Ng, Ziqing Li, Megan M Jones, Chengjian Tu, Merry Jo Oursler, Jun Qu, Shuying Yang

Newly developed single-cell computational approach elucidates the stabilization of Oct4 expression in the E3.25 mouse preimplantation embryo
Daniela Gerovska, Marcos J. Araúzo-Bravo

Fetal and trophoblast PI3Kp110α have distinct roles in regulating resource supply to the growing fetus
Jorge Lopez-Tello, Vicente Perez-Garcia, Jaspreet Khaira, Laura C Kusinski, Wendy N Cooper, Adam Andrani, Imogen Grant, Edurne Fernandez de Liger, Myriam Hemberger, Ionel Sandovici, Miguel Constancia, Amanda N Sferruzzi-Perri

ATR function is indispensable to allow proper mammalian follicle development.
Sarai Pacheco, Montserrat Garcia Caldes, Ignasi Roig

Abrogation of Stem Loop Binding Protein (Slbp) function leads to a failure of cells to transition from proliferation to differentiation, retinal coloboma and midline axon guidance deficits.
Kate Turner, Jaqueline Hoyle, Leonardo E Valdivia, Kara Cerveny, Wendy Hart, Maryam Mangoli, Robert Geisler, Michele Rees, Corinne Houart, Richard J Poole, Steve W Wilson, Gaia Gestri

Apical progenitors remain multipotent throughout cortical neurogenesis
Polina Oberst, Sabine Fievre, Natalia Baumann, Cristina Concetti, Denis Jabaudon

Tcf4 encodes cortical differentiation during development
Simone Mesman, Reinier Bakker, Marten Smidt

Notch-Mediated Polarity Decisions in Mechanosensory Hair Cells
Adrian Jacobo, Agnik Dasgupta, Anna Erzberger, Kimberly Siletti, Albert James Hudspeth

The BTB-ZF transcription factor Tramtrack 69 shapes neural cell lineages by coordinating cell proliferation and cell fate
Francoise Simon, Anne Ramat, Sophie Louvet-Vallee, Jerome Lacoste, Angelique Burg, Agnes Audibert, Michel Gho

Detailed analysis of chick optic fissure closure reveals Netrin-1 as an essential and conserved mediator of epithelial fusion during vertebrate embryogenesis.
Holly Hardy, James Prendergast, Aara Patel, Sunit Dutta, Violeta Trejo-Reveles, Hannah Kroeger, Andrea Yung, Lisa V Goodrich, Brian P Brooks, Jane Sowden, Joe Rainger

Oculomotor nerve requires an early interaction with muscle precursors for nerve guidance and branch patterning
Brielle Bjorke, Katherine G Weller, Gregory Eric Robinson, Michelle Vesser, Lisheng Chen, Philip J Gage, Thomas W Gould, Grant S Mastick

Onecut factors and Pou2f2 regulate the distribution of V2 interneurons in the mouse developing spinal cord
Audrey Harris, Gauhar Masgutova, Amandine Collin, Mathilde Toch, Maria Hidalgo-Figueroa, Benvenuto Jacob, Lynn M Corcoran, Cedric Francius, Frederic Clotman

Differential physiological role of BIN1 isoforms in skeletal muscle development, function and regeneration
Ivana Prokic, Belinda Simone Cowling, Candice Kutchukian, Christine Kretz, Hichem Tasfaout, Josiane Hergueux, Olivia Wendling, Arnaud Ferry, Anne Toussaint, Christos Gavriilidis, Vasugi Nattarayan, Catherine Koch, Jeanne Lainné, Roy Combe, Laurent Tiret, Vincent Jacquemond, Fanny Pilot-Storck, Jocelyn Laporte

The LIM-Only Protein FHL2 is Involved in Autophagy to Regulate the Development of Skeletal Muscle
Zihao Liu, Shunshun Han, Yan Wang, Haorong He, Xiaoxu Shen, Yuqi Chen, Can Cui, Yao Zhang, Lin Ye, Diyan Li, Xiaoling Zhao, Huarui Du, Xiaosong Jiang, Chunlin Yu, Qingyun Li, Qing Zhu, Chaowu Yang, Huadong Yin

Retinoic acid and androgens interact to regulate spermatogenesis in a non-mammalian vertebrate lacking stra8
Diego Crespo, Luiz H.C. Assis, Henk J.G. van de Kant, Sjors de Waard, Diego Alejandro Safian, Moline S. Lemos, Jan Bogerd, Rüdiger W. Schulz

Drosophila anion exchanger 2 is required for proper ovary development and oogenesis
Marimar Benitez, Sumitra Tatapudy, Diane Barber, Todd Nystul

Chondroitin sulfate proteoglycan Windpipe modulates Hedgehog signaling in Drosophila
Masahiko Takemura, Fredrik Noborn, Jonas Nilsson, Eriko Nakato, Tsu-Yi Su, Göran Larson, Hiroshi Nakato

Inter-organ growth coordination is mediated by the Xrp1/Dilp8 axis in Drosophila
Laura Boulan, Ditte Andersen, Julien Colombani, Emilie Boone, Pierre Léopold

A Cyclin A – Myb-MuvB – Aurora B network regulates the choice between mitotic cycles and polyploid endoreplication cycles.
Michael Rotelli, Robert A. Policastro, Anna Bolling, Andrew Killion, Abraham Weinberg, Michael Dixon, Gabriel E Zentner, Claire E. Walczak, Mary A Lilly, Brian R Calvi

Glutamate signaling at cytoneme synapses
Hai Huang, Songmei Liu, Thomas B Kornberg

The Toll pathway inhibits tissue growth and regulates cell fitness in an infection-dependent manner
Federico Germani, Daniel Hain, Denise Sternlicht, Eduardo Moreno, Konrad Basler

Lipid Droplet metabolism dependent microbial defense in pre-immune zebrafish embryos
Asmita Dutta, Sampali Banerjee, Deepak Kumar Sinha

Prolonged quiescence delays somatic stem cell-like division in Caenorhabditis elegans and is controlled by insulin signalling
María Olmedo, Alejandro Mata Cabana, María Jesús Rodríguez Palero, Sabas García-Sánchez, Antonio Fernández Yáñez, Martha Merrow, Marta Artal-Sanz

Repression of an activity-dependent autocrine insulin signal is required for sensory neuron development in C. elegans.
Lauren Bayer Horowitz, Julia P. Brandt, Niels Ringstad

SKN-1/Nrf2 regulation of neuromuscular function in response to oxidative stress requires EGL-15/FGF Receptor and DAF-2/insulin Receptor signaling in Caenorhabditis elegans.
Sungjin Kim, Derek Sieburth

| Morphogenesis & mechanics

E-cadherin endocytosis is modulated by p120-catenin through the opposing actions of RhoA and Arf1
Joshua Greig, Natalia A. Bulgakova

Force inference predicts local and tissue-scale stress patterns in epithelia
Weiyuan Kong, Olivier Loison, Pruthvi Chavadimane Shivakumar, Claudio Collinet, Pierre-François Lenne, Raphaël Clément

Trynity controls epidermal barrier function and respiratory tube maturation in Drosophila by modulating apical extracellular matrix nano-patterning
Yuki Itakura, Sachi Inagaki, Housei Wada, Shigeo Hayashi

Sprouting and anastomosis in the Drosophila trachea and the vertebrate vasculature: similarities and differences in cell behaviour
Maria Paraskevi Kotini, Maarja Andaloussi Mäe, Heinz-Georg Belting, Christer Betsholtz, Markus Affolter

Xenopus hybrids provide insight into cell and organism size control
Romain Gibeaux, Kelly Miller, Rachael Acker, Taejoon Kwon, Rebecca Heald

Desmoplakin is required for epidermal integrity and morphogenesis in the Xenopus laevis embryo
Amanda J.G. Dickinson, Navaneetha Krishnan Bharathan

Wolf-Hirschhorn Syndrome-associated genes are enriched in motile neural crest and affect craniofacial development in Xenopus laevis
Alexandra Mills, Elizabeth Bearce, Rachael Cella, Seung Woo Kim, Megan Selig, Sangmook Lee, Laura A Lowery

A novel photoactivatable tool for intermediate filament disruption indicates a role for keratin filaments in early embryogenesis
Rucha Sanghvi-Shah, Shalaka Paranjpe, Jiyeon Baek, Radek Dobrowolski, Gregory Weber

Probing epithelial tissue rheology with a Stokes experiment
S. Tlili, C. Gay, B. Ladoux, F. Graner, H. Delanoë-Ayari

| Genes & genomes

Organ transformation by environmental disruption of epigenetic memory
Orli Snir, Michael Elgart, Filippo Ciabrelli, Shlomi Dagan, Iris Aviezer, Elizabeth Stoops, Giacomo Cavalli, Yoav Soen

A kinesin Klp10A mediates cell cycle-dependent shuttling of Piwi between nucleus and nuage
Zsolt G Venkei, Charlotte Park Choi, Suhua Feng, Steven E Jacobsen, John K Kim, Yukiko M Yamashita

Differential phase partition of a PICS complex is required for piRNA processing and chromosome segregation in C. elegans
Chenming Zeng, Chenchun Weng, Xiaoyang Wang, Yong-Hong Yan, Wen-Jun Li, Demin Xu, Minjie Hong, Shanhui Liao, Xuezhu Feng, Meng-Qiu Dong, Chao Xu, Shouhong Guang

The Drosophila pioneer factor Zelda modulates the nuclear microenvironment of a Dorsal target enhancer to potentiate transcriptional output
Shigehiro Yamada, Peter H Whitney, Shao-Kuei Huang, Elizabeth C Eck, Hernan G Garcia, Christine A Rushlow

The Drosophila fussel gene is required for bitter gustatory neuron differentiation acting within an Rpd3 dependent chromatin modifying complex
View ORCID ProfileMathias Rass, Svenja Oestreich, Severin Guetter, Susanne Fischer, Stephan Schneuwly

Chromatin Accessibility Plays a Key Role in Selective Targeting of Hox Proteins
Damiano Porcelli, Bettina Fischer, Steven Russell, Robert White

The modular mechanism of chromocenter formation in Drosophila
Madhav Jagannathan, Ryan Cummings, Yukiko M Yamashita

Genetic analysis reveals novel roles for mei-MCMs during meiotic recombination in Drosophila
Talia Hatkevich, Jeff Sekelsky, Michaelyn Ann Hartmann, Kathryn P Kohl

Gene expression atlas of a developing tissue by single cell expression correlation analysis
Josephine Bageritz, Philipp Willnow, Erica Valentini, Svenja Leible, Michael Boutros, Aurelio A Teleman

let-7 controls the transition to adulthood by releasing select transcriptional regulators from repression by LIN41
Florian Aeschimann, Anca Neagu, Magdalene Rausch, Helge Grosshans

The interplay between small RNA pathways shapes chromatin landscapes in C. elegans
Ekaterina Gushchanskaia, Ruben Esse, Qicheng Ma, Nelson Lau, Alla Grishok

Chromatin Compaction by Small RNAs and the Nuclear RNAi Machinery in C. elegans
Brandon D Fields, Scott Kennedy

MicroRNAs modulate alternative splicing in the C. elegans intestine and body muscle tissues
Kasuen Kotagama, Anna L Schorr, Hannah S Steber, Marco Mangone

Pioneer and nonpioneer cooperation drives lineage specific chromatin opening
Alexandre Mayran, Kevin Sochodolsky, Konstantin Khetchoumian, Juliette Harris, Yves Gauthier, Amandine Bemmo, Aurelio Balsalobre, Jacques Drouin

Maintenance of spatial gene expression by Polycomb-mediated repression after formation of a vertebrate body plan
Julien Rougot, Naomi D Chrispijn, Marco Aben, Dei M Elurbe, Karolina M Andralojc, Patrick J Murphy, Pascal WTC Jansen, Michiel Vermeulen, Bradley R Cairns, Leonie M Kamminga

Slow transcriptional elongation causes embryonic lethality and perturbs kinetic coupling of long neural genes
Magdalena M Maslon, Ulrich Braunschweig, Stuart Aitken, Abigail R Mann, Fiona Kilanowski, Chris J Hunter, Benjamin J Blencowe, Alberto R Kornblihtt, Ian R Adams, Javier F. Caceres

Mammalian SWI/SNF collaborates with a polycomb-associated protein to regulate male germ line transcription in the mouse
Debashish U Menon, Yoichiro Shibata, Weipeng Mu, Terry Magnuson

TH2BS12P histone mark is enriched in the unsynapsed axes of the XY body and predominantly associates with H3K4me3-containing genomic regions in mammalian spermatocytes
Aditya Mahadevan, Satyakrishna Pentakota, Raktim Roy, Utsa Bhaduri, Satyanarayana M R Rao

The mouse Klf1 Nan variant impairs nuclear condensation and erythroid maturation
Ileana Cantú, Harmen JG van de Werken, Nynke Gillemans, Ralph Stadhouders, Steven Heshusius, Alex Maas, Zeliha Ozgur, Wilfred van IJcken, Frank Grosveld, Marieke von Lindern, Sjaak Philipsen, Thamar B van Dijk

PETISCO is a novel protein complex required for 21U RNA biogenesis and embryonic viability
Ricardo J Cordeiro Rodrigues, Antonio Miguel de Jesus Domingues, Svenja Hellmann, Sabrina Dietz, Bruno de Albuquerque, Christian Renz, Helle D. Ulrich, Falk Butter, Rene Ketting

Tfap2a is a novel gatekeeper of differentiation in renal progenitors during kidney development
Brooke E. Chambers, Gary F. Gerlach, Karen H. Chen, Eleanor G. Clark, Ignaty Leshchiner, Wolfram Goessling, Rebecca A. Wingert

Cell-type-specific genomics reveals histone modification dynamics in mammalian meiosis
Kwan Wood Gabriel Lam, Kevin Brick, Gang Cheng, Florencia Pratto, R. Daniel Camerini-Otero

The long noncoding RNA Hand2as orchestrates heart development through regulation of precise expression of HAND2
Xue Han, Jiejie Zhang, Yaxi Liu, Xiaoying Fan, Shanshan Ai, Yingjie Luo, Xin Li, Sai Luo, Hui Zheng, Yanzhu Yue, Zai Chang, Zhongzhou Yang, Fuchou Tang, Aibin He, Xiaohua Shen

Genome-wide strategies reveal target genes of Npas4l associated with cardiovascular development in zebrafish
Michele Marass, Arica Beisaw, Claudia Gerri, Francesca Luzzani, Nana Fukuda, Stefan Guenther, Carsten Kuenne, Sven Reischauer, Didier Stainier

Inferring novel lncRNA associated with Ventricular septal defect by DNA methylation interaction network
Min Zhang, Yue Gu, Mu Su, Shumei Zhang, Chuangeng Chen, Wenhua Lv, View ORCID ProfileYan Zhang

Non-monotonic regulation of gene expression, neural progenitor fate and brain growth by the chromatin remodeller CHD8
Shaun Hurley, Conor Mohan, Philipp Suetterlin, Jacob Ellegood, Fabrizio Rudari, Jason P Lerch, Cathy Fernandes, M. Albert Basson

A novel method for systematic genetic analysis and visualization of phenotypic heterogeneity applied to orofacial clefts
Jenna Carlson, Deepti Anand, Azeez Butali, Carmen Buxo, Kaare Christensen, Frederic Deleyiannis, Jacqueline Hecht, Lina Moreno-Uribe, Ieda Orioli, Carmencita Padilla, John Shaffer, Alexandre Vieira, George Wehby, Seth Weinberg, Jeff Murray, Terri Beaty, Irfan Saadi, Salil Lachke, Mary Marazita, Eleanor Feingold, Elizabeth Leslie

Early divergence of mutational mechanisms drives genetic heterogeneity of fetal tissues
Ewart Kuijk, Francis Blokzijl, Myrthe Jager, Nicolle Besselink, Sander Boymans, Susana Chuva de Sousa Lopes, Ruben van Boxtel, Edwin Cuppen

Single cell transcriptomic analysis of the adult mouse pituitary reveals a novel multi-hormone cell cluster and physiologic demand-induced lineage plasticity
Yugong Ho, Peng Hu, Michael T Peel, Pablo G Camara, Hao Wu, Liehaber A Stephen

Functional heterogeneity within the developing zebrafish epicardium
Michael Weinberger, Filipa C. Simões, Roger Patient, Tatjana Sauka-Spengler, Paul R. Riley

Single-cell RNA-seq of the Developing Cardiac Outflow Tract Reveals Convergent Development of the Vascular Smooth Muscle Cells at the Base of the Great Arteries
Xuanyu Liu, Wen Chen, Wenke Li, James R. Priest, Jikui Wang, Zhou Zhou

Charting the emergent organotypic landscape of the mammalian gut endoderm at single-cell resolution
Sonja Nowotschin, Manu Setty, Ying-Yi Kuo, Vincent Liu, Vidur Garg, Roshan Sharma, Claire S Simon, Nestor Saiz, Rui Gardner, Stéphane C Boutet, Deanna M Church, Pamela A Hoodless, Anna-Katerina Hadjantonakis, Dana Pe’er

Prolactin Receptor Signaling Regulates a Pregnancy-Specific Transcriptional Program in Mouse Islets
Mark E. Pepin, Adam R. Wende, Ronadip R. Banerjee

Normal spermatogenesis in Fank1 (fibronectin type 3 and ankyrin repeat domains 1) mutant mice
Jintao Zhang​, Xin Zhang1, Yue Zhang, Wentao Zeng, Shuqin Zhao, Mingxi Liu​

DAZL is a master translational regulator of murine spermatogenesis
Haixin Li, Zhuqing Liang, Jian Yang, Dan Wang, Hanben Wang, Mengyi Zhu, Baobao Geng, Eugene Y. Xu

Sex differences in gene expression in the human fetal brain
Heath E O’Brien, Eilis Hannon, Aaron R Jeffries, William Davies, Matthew J Hill, Richard J Anney, Michael C O’Donovan, Jonathan Mill, Nicholas J Bray

Genetic control of gene expression and splicing in the developing human brain
Rebecca L Walker, Gokul Ramaswami, Christopher Hartl, Nicholas Mancuso, Michael J Gandal, Luis de la Torre-Ubieta, Bogdan Pasaniuc, Jason L Stein, Daniel H Geschwind

DEAH-box helicase 37 (DHX37) defects are a novel molecular etiology of 46,XY gonadal dysgenesis spectrum
Thatiana Evelin da Silva, Nathalia Lisboa Gomes, Antonio M Lerario, Catherine E Keegan, Mirian Yumie Y Nishi, Filomena M Carvalho, Eric Vilain, Hayk Barseghyan, Alejandro Martinez-Aguayo, Maria Verónica Forclaz, Regina Papazian, Luciani Renata Carvalho, Elaine Frade Costa, Berenice B Mendonca, Sorahia Domenice

Contribution of Retrotransposition to Developmental Disorders
Eugene J Gardner, Elena Prigmore, Giuseppe Gallone, Patrick J Short, Alejandro Sifrim, Tarjinder Singh, Kate E Chandler, Emma Clement, Katherine L Lachlan, Katrina Prescott, Elisabeth Rosser, David R FitzPatrick, Helen V Firth, Matthew E Hurles, Deciphering Developmental Disorders study

High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue-specificity
Kaia Mattioli, Pieter-Jan Volders, Chiara Gerhardinger, James C. Lee, Philipp G. Maass, Marta Mele, John L. Rinn

Long Non-Coding RNA LncKdm2b Regulates Cortical Neuronal Differentiation by Cis-Activating Kdm2b
Wei Li, Wenchen Shen, Bo Zhang, Kuan Tian, Yamu Li, Lili Mu, Zhiyuan Luo, Xiaoling Zhong, Xudong Wu, Ying Liu, Yan Zhou

Landscape of RNA editing reveals new insights into the dynamic gene regulation of spermatogenesis based on integrated RNA-Seq
Xiaodan Wang, Zhenshuo Zhu, Xiaolong Wu, Hao Li, Tongtong Li, Qun Li, Peng Zhang, Leijie Li, Dongxue Che, Xia Xiao, Jinlian Hua, Mingzhi Liao

The landscape of DNA methylation associated with the transcriptomic network in laying hens and broilers get insight into embryonic muscle development in chicken
Zihao Liu, Xiaoxu Shen, Shunshun Han, Yan Wang, Qing Zhu, Can Cui, Haorong He, Jing Zhao, Yuqi Chen, Yao Zhang, Lin Ye, Zhichao Zhang, Diyan Liu, Xiaoling Zhao, Huadong Yin

Exploring differentially expressed key genes related to development of follicle by RNA-seq in Peking ducks (Anas Platyrhynchos)
Jindong Ren, Changsen Sun, Li Chen, Jianhong Hu, Xuetao Huang, Xiaolin Liu, Lizhi Lu

| Stem cells, regeneration & disease modelling

Hierarchical stem cell topography splits growth and homeostatic functions in the fish gill
Lazaro Centanin, Julian Stolper, Elizabeth Mayela Ambrosio, Diana-Patricia Danciu, David Elliott, Kiyoshi Naruse, Anna Marciniak-Czochra

Pluripotent Stem Cell-derived Cerebral Organoids Reveal Human Oligodendrogenesis with Dorsal and Ventral Origins
Hyosung Kim, Ranjie Xu, Padmashri Ragunathan, Anna Dunaevsky, Ying Liu, Cheryl Dreyfus, Peng Jiang

Basal stem cell fate specification is mediated by SMAD signaling in the developing human lung
Alyssa J. Miller, Quanhui Yu, Michael Czerwinski, Yu-Hwai Tsai, Renee F. Conway, Angeline Wu, Emily M. Holloway, Taylor Walker, Ian A. Glass, Barbara Treutlein, J. Gray Camp, Jason R. Spence

Identification of slow-cycling germline stem cells and their regulation by PLZF
Robert E Braun, Manju Sharma, Anuj Srivastava, Heather E Fairfield, David Bergstrom, William F Flynn

Heterochromatin protein 1 (HP1) is intrinsically required for post-transcriptional regulation of Drosophila Germline Stem Cell (GSC) maintenance
Assunta Maria Casale, Ugo Cappucci, Laura Fanti, Lucia Piacentini

Stem cell receptor degradation by niche cells restricts signalling
Sophia Ladyzhets, Mayu Inaba

fruitless functions downstream of doublesex to promote sexual dimorphism of the gonad stem cell niche
Hong Zhou, Cale Whitworth, Caitlin Pozmanter, Megan C. Neville, Mark Van Doren

Glia mediated ionic balance in the stem cell niche is required for the proper proliferation of neurogenic tissues and wiring of neural circuits.
Haritz Plazaola-Sasieta, Qi Zhu, Hector Gaitan-Penas, Martin Rios, Raul Estevez, Marta Morey

X Chromosome Dosage Modulates Multiple Molecular and Cellular Properties of Mouse Pluripotent Stem Cells Independently of Global DNA Methylation Levels
Juan Song, Adrian Janiszewski, Natalie De Geest, Lotte Vanheer, Irene Talon, Mouna El Bakkali, Taeho Oh, Vincent Pasque

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

High Throughput Mechanobiological Screens Enable Mechanical Priming of Pluripotency in Mouse Fibroblasts
Jason Lee, Miguel Ochoa, Pablo Maceda, Eun Yoon, Lara Samarneh, Mitchell Wong, Aaron B Baker

Transient activation of the UPRER is an essential step in the acquisition of pluripotency during reprogramming
Milos Simic, Erica Moehle, Robert Schinzel, Franziska Lorbeer, Damien Jullie, Jonathan Halloran, Kartoosh Heydari, Melissa Sanchez, Dirk Hockemeyer, Andrew Dillin

Non-cell-autonomous promotion of pluripotency induction mediated by YAP
Amaleah Hartman, Xiao Hu, Xinyue Chen, Anna E Eastman, Cindy Yang, Shangqin Guo

TCF7L1 and TCF7 differentially regulate specific mouse ES cell genes in response to GSK-3 inhibition
Steven Moreira, Caleb Seo, Enio Polena, Sujeivan Mahendram, Eloi Mercier, Alexandre Blais, Bradley Doble

Environmental Optimization Enables Maintenance of Quiescent Hematopoietic Stem Cells Ex Vivo
Hiroshi Kobayashi, Takayuki Morikawa, Ayumi Okinaga, Fumie Hamano, Tomomi Hashidate-Yoshida, Shintaro Watanuki, Daisuke Hishikawa, Hideo Shindou, Fumio Arai, Yasuaki Kabe, Makoto Suematsu, Takao Shimizu, Keiyo Takubo

Genome-wide screens in accelerated human stem cell-derived neural progenitor cells identify Zika virus host factors and drivers of proliferation
Michael F Wells, Max R Salick, Federica Piccioni, Ellen J Hill, Jana M Mitchell, Kathleen A Worringer, Jospeph J Raymond, Sravya Kommineni, Karrie Chan, Daniel Ho, Brant K Peterson, Marco T Siekmann, Olli Pietilainen, Ralda Nehme, Ajamete Kaykas, Kevin Eggan

Human Dental Pulp Stem Cells Grown In Neurogenic Media Differentiate Into Endothelial Cells And Promote Neovasculogenesis In The Mouse Brain.
Jon Luzuriaga, Oier Pastor-Alonso, Juan Manuel Encinas, Fernando Unda, Gaskon Ibarretxe, Jose R. Pineda

The iPSC proteomic compendium
Alejandro Brenes, Dalila Bensaddek, Jens Hukelmann, Vackar Afzal, Angus I Lamond

Neuropilin 1 mediates epicardial activation and revascularization in the regenerating zebrafish heart
Vanessa Lowe, Laura Wisniewski, Jacob Sayers, Paul Frankel, Nadia Mercader, Ian C Zachary, Caroline AP Pellet-Many

Distinct progenitor populations mediate regeneration in the zebrafish lateral line.
Eric D Thomas, David Raible

Effects of BMP-2 on neovascularization during large bone defect regeneration
Hope B Pearson, Devon E Mason, Christopher D Kegelman, Liming Zhao, James Dawahare, Melissa A Kacena, Joel D Boerckel

Scleraxis Lineage Cells Contribute to Organized Bridging Tissue During Tendon Healing, and Identifies Subpopulations of Resident Tendon Cells
Katherine T Best, Alayna Loiselle

PDGFRα signaling in cardiac fibroblasts modulates quiescence, metabolism and self-renewal, and promotes anatomical and functional repair
Naisnana S Asili, Munira Xaymardan, Elvira Forte, Ashley J Waardenberg, James Cornwell, Vaibhao Janbandhu, Scott Kesteven, Vashe Chandrakanthan, Helena Malinowska, Henrik Reinhard, Sile F Yang, Hilda A Pickett, Peter Schofield, Daniel Christ, Ishtiaq Ahmed, James Chong, Corey Heffernan, Joan Li, Mary Simonian, Romaric Bouveret, Surabhi Srivastava, Rakesh K Mishra, Jyotsna Dhawan, Robert Nordon, Peter Macdonald, Robert M Graham, Michael Feneley, Richard P Harvey

Deriving Cardiomyocytes from Human Amniocytes
Colin T. Maguire, Ryan Sunderland, Bradley L Demarest, Bushra Gorsi, Joshua Jackson, ANGELICA LOPEZ-IZQUIERDO, Martin Martin Tristani-Firouzi, H. Joseph Yost, Maureen L Condic

In vivo generation of post-infarct mouse cardiac muscle by cardiomyocyte progenitors produced with a reproducible laminin-promoted human stem cell differentiation system
Lynn Yap, Jiong-Wei Wang, Aida Moreno-Moral, Li Yen Chong, Yi Sun, Nathan Harmston, Xiaoyuan Wang, Suet Yen Chong, Miina K. Ohman, Heming Wei, Ralph Bunte, Sujoy Ghosh, Stuart Cook, Outi Hovatta, Dominique P.V. de Kleijn, Enrico Petretto, Karl Tryggvason

Active Receptor Tyrosine Kinases, but not Brachyury, are sufficient to trigger chordoma in zebrafish
Gianluca D’Agati, Elena M. Cabello, Karl Frontzek, Elisabeth J. Rushing, Robin Klemm, Mark Robinson, Richard M. White, Christian Mosimann, Alexa Burger

Culling less fit neurons protects against amyloid-β induced brain damage and cognitive and motor decline
Dina S Coelho, Silvia Schwartz, Marisa M Merino, Barbara Hauert, Barbara Topfel, Colin Tieche, Christa Rhiner, Eduardo Moreno

Chondrocyte-specific RUNX2 Overexpression Causes Chondrodysplasia During Development, but is Not Sufficient to Induce OA-like Articular Cartilage Degeneration in Adult Mice Without Injury
Sarah E. Catheline, Donna Hoak, Martin Chang, John P Ketz, Matthew J Hilton, Michael J Zuscik, Jennifer H Jonason

Spinocerebellar ataxia type 11-associated alleles of Ttbk2 dominantly interfere with ciliogenesis and cilium stability.
Emily Bowie, Ryan Norris, Kathryn V Anderson, Sarah Goetz

Cytoneme-mediated signaling essential for tumorigenesis
Sol Fereres, Ryo Hatori, Makiko Hatori, Thomas B Kornberg

A giant ankyrin-B mechanism for neuro-diversity/divergence through stochastic ectopic axon projections
Rui Yang, Kathryn K Walder-Christensen, Namsoo Kim, Danwei Wu, Damaris Lorenzo, Alexandra Badea, Shen Gu, Haley Streff, Claudia Soler-Alfonso, Linyan Meng, William C Wetsel, Yong-Hui Jiang, Henry Yin, Vann Bennett

Behavioral changes and growth deficits in a CRISPR engineered mouse model of the schizophrenia-associated 3q29 deletion
Timothy P. Rutkowski, Ryan H. Purcell, Rebecca M. Pollak, Stephanie M. Grewenow, Georgette M. Gafford, Tamika Malone, Uswa Khan, Jason P. Schroeder, Michael P. Epstein, Gary J. Bassell, Stephen T. Warren, David Weinshenker, Tamara Caspary, Jennifer Gladys Mulle

Re-expression of SynGAP Protein in Adulthood Improves Translatable Measures of Brain Function and Behavior in a Model of Neurodevelopmental Disorders
Thomas Creson, Camilo Rojas, Ernie Hwaun, Thomas Vaissiere, Murat Kilinc, J. Lloyd Holder Jr., Jianrong Tang, Laura Lee Colgin, Courtney A. Miller, Gavin Rumbaugh

661W photoreceptor cell line as a cell model for studying retinal ciliopathies
Gabrielle Wheway, Liliya Nazlamova, Dann Turner, Stephen Cross

Reversing Abnormal Neural Development by Inhibiting OLIG2 in Down Syndrome Human iPSC Brain Organoids and Neuronal Mouse Chimeras
Ranjie Xu, Andrew Brawner, Shenglan Li, Hyosung Kim, Haipeng Xue, Zhiping Pang, Woo-Yang Kim, Ronald Hart, Ying Liu, Peng Jiang

| Plant development

A stress-response-related inter-compartmental signalling pathway regulates embryonic cuticle integrity in Arabidopsis
Audrey Creff, Lysiane Brocard, Jerome Joubes, Ludivine Taconnat, Nicolas M Doll, Stéphanie Pascal, Roberta Galletti, Anne-Charlotte Marsollier, Steven Moussu, Thomas Widiez, Frédéric Domergue, Gwyneth Christina Ingram

The Flowering Hormone Florigen Accelerates Secondary Cell Wall Biogenesis to Harmonize Vascular Maturation with Reproductive Development
Akiva Shalit-Kaneh, Tamar Eviatar-Ribak, Guy Horev, Naomi Suss, Roni Aloni, Yuval Eshed, Eliezer Lifschitz

Effects of FLOWERING LOCUS T on FD during the transition to flowering at the shoot apical meristem of Arabidopsis thaliana
Silvio Collani, Manuela Neumann, Levi Yant, Markus Schmid

PERPETUAL FLOWERING2 coordinates the vernalization response and perennial flowering in Arabis alpina
Ana Lazaro, Yanhao Zhou, Miriam Giesguth, Kashif Nawaz, Sara Bergonzi, Ales Pecinka, George Coupland, Maria C Albani

Spatiotemporal expression of FRIGIDA modulate flowering time in Arabidopsis thaliana
Xiangxiang Kong, Jinjie Zhao, Landi Luo, Qian Chen, Guanxiao Chang, Jingling Huang, Yongping Yang, Xiangyang Hu

Epigenetic signatures associated with imprinted paternally-expressed genes in the Arabidopsis endosperm
Claudia Kohler, Jordi Moreno-Romero, Gerardo Del Toro De León, Vikash Kumar Yadav, Juan Santos-González

Differences in effective ploidy as drivers of genome-wide endosperm expression asymmetries and seed failure in wild tomato hybrids
Morgane Roth, Ana M Florez-Rueda, Thomas Staedler

CrRLK1L receptor-like kinases HERK1 and ANJEA are female determinants of pollen tube reception
Sergio Galindo-Trigo, Noel Blanco-Tourinan, Thomas A DeFalco, Cyril Zipfel, Julie E Gray, Lisa M Smith

In vivo phosphatidylserine variations steer Rho GTPase signaling in a cell-context dependent manner
Matthieu Pierre Platre, Vincent Bayle, Laia Armengot, Joseph Bareille, Maria Mar Marques-Bueno, Audrey Creff, Lilly Maneta-Peyret, Jean-Bernard Fiche, Marcelo Nolmann, Christine Miege, Patrick Moreau, Alexandre Martiniere, Yvon Jaillais

From spatio-temporal morphogenetic gradients to rhythmic patterning at the shoot apex
Carlos Samuel Galvan-Ampudia, Guillaume Cerutti, Jonathan Legrand, Romain Azais, Géraldine Brunoud, Steven Moussu, Christian Wenzl, Jan Lohmann, Christophe Godin, Teva Vernoux

A SOSEKI-based coordinate system interprets global polarity cues in Arabidopsis
Saiko Yoshida, Alja van der Schuren, Maritza van Dop, Luc van Galen, Shunsuke Saiga, Milad Adibi, Barbara Moller, Peter Marhavy, Richard Smith, Jiri Friml, Dolf Weijers

The AGC protein kinase UNICORN controls planar growth by attenuating PDK1 in Arabidopsis thaliana
Sebastian Scholz, Janys Plessmann, Regina Huettl, Katrin Wassmer, Balaji Enugutti, Kay Schneitz

WUSCHEL acts as a rheostat on the auxin pathway to maintain apical stem cells in Arabidopsis
Yanfei Ma, Andrej Miotk, Zoran Sutikovic, Anna Medzihradszky, Christian Wenzl, Olga Ermakova, Christophe Gaillochet, Joachim Forner, Goedze Utan, Klaus Brackmann, Carlos S. Galvan-Ampudia, Teva Vernoux, Thomas Greb, Jan U. Lohmann

Effect of simulated microgravity on gene expression during embryogenesis of Arabidopsis thaliana
Michaela Švecérová, Markéta Kovalová, Vladan Ondřej

Remote control of alternative splicing in roots through TOR kinase
Ezequiel Petrillo, Stefan Riegler, Armin Fuchs, Lucas Servi, Micaela A. Godoy Herz, Maria Guillermina Kubaczka, Peter Venhuizen, Alois Schweighofer, Alberto R Kornblihtt, Craig Simpson, John W.S. Brown, Christian Meyer, Maria Kalyna, Andrea Barta

ARF5/MONOPTEROS directly regulates miR390 expression in the Arabidopsis thaliana primary root meristem
Mouli Ghosh Dastidar, Andrea Scarpa, Ira Maegele, Paola Ruiz Duarte, Patrick von Born, Lotte Bald, Virginie Jouannet, Alexis Maizel

Systems approaches provide new insights into Arabidopsis thaliana root growth under mineral nutrient limitation
Nadia Bouain, Arthur Korte, Santosh B. Satbhai, Seung Y. Rhee, Wolfgang Busch, Hatem Rouached

The embryonic transcriptome of Arabidopsis thaliana
Falko Hofmann, Michael A Schon, Michael D Nodine

Transcriptome dynamics in developing leaves from C3 and C4 Flaveria species reveal determinants of Kranz anatomy
Kumari Billakurthi, Thomas Jan Wrobel, Andrea Braeutigam, Andreas Weber, Peter Westhoff, Udo Gowik

A wheat/rye polymorphism affects seminal root length and is associated with drought and waterlogging tolerance
Tyson Howell, Jorge I. Moriconi, Xueqiang Zhao, Joshua Hegarty, Tzion Fahima, Guillermo Santa-Maria, Jorge Dubcovsky

The interaction between genotype and maternal nutritional environments affects tomato seed and seedling quality
Nafiseh Geshnizjani, Saadat Sarikhani Khorami, Leo A.J. Willems, Basten L. Snoek, Henk Hilhorst, Wilco Ligterink

Mechanisms driving endosperm-based hybrid incompatibilities: insights from hybrid monkeyflowers
Taliesin J Kinser, Ronald D Smith, Amelia H Lawrence, Arielle M Cooley, Mario Vallejo-Marín, GD Conradi Smith, Joshua R Puzey

Transcriptomic response to divergent selection for flowering time in maize reveals convergence and key players of the underlying gene regulatory network
Maud I Tenaillon, Khawla Seddiki, Maeva Mollion, Martine Le Guilloux, Elodie Marchadier, Adrienne Ressayre, Christine Dillmann

A genome-wide analysis of the cellulose synthase-like (Csl) gene family in maize (Zea mays)

Yongkai Li​, Xiaojie Cheng​, Yaqin Fu, Qinqin Wu, Yuli Guo, Jiayu Peng, Wei Zhang​, Bin He​

Meiotic effects of MSH4 copy number variation support an adaptive role for post-polyploidy gene loss
Adrian Gonzalo, Marie-Odile Lucas, Catherine Charpentier, Andrew H Lloyd, Eric Jenczewski

Transcriptional landscape of soybean (Glycine max) embryonic axes during germination in the presence of paclobutrazol, a gibberellin biosynthesis inhibitor
Rajesh Kumar Gazara, Eduardo A. G. de Oliveira, Antonia Elenir A. Oliveira, Thiago M. Venancio

Epigenetics of floral homeotic genes in relation to sexual dimorphism in the dioecious plant Mercurialis annua
Janardan Khadka, Narendra Singh Yadav, Micha Guy, Gideon Grafi, Avi Golan-Goldhirsh

Physiological regulation of bud burst in grapevine
Santiago Signorelli, Jeremy Shaw, Dina Hermawaty, Zi Wang, Pieter Verboven, John Anthony Considine, Michael J Considine

Determining targeting specificity of nuclear-encoded organelle proteins with the self-assembling split fluorescent protein toolkit
Mayank Sharma, Carola Kretschmer, Christina Lampe, Johannes Stuttmann, Ralf Bernd Klosgen

Phosphoproteomics of Arabidopsis Highly ABA-Induced1 identifies AT-Hook Like10 phosphorylation required for stress growth regulation
Min May Wong, Govinal Badiger Bhaskara, Tuan-Nan Wen, Wen-Dar Lin, Thao Thi Nguyen, Geeng Loo Chong, Paul Verslues

HNI9 and HY5 maintain ROS homeostasis under high nitrogen provision in Arabidopsis
Fanny Bellegarde, Amel Maghiaoui, Jossia Boucherez, Gabriel Krouk, Laurence Lejay, Lien Bach, Alain Gojon, Antoine Martin

Excess light priming in Arabidopsis thaliana with altered DNA methylomes
Bethany AB Stone, Diep R Ganguly, Steven R Eichten, Barry J Pogson

Functional dissection of the ARGONAUTE7 promoter
J Steen Hoyer, Jose L Pruneda-Paz, Ghislain Breton, Mariah A Hassert, Emily E Holcomb, Halley Fowler, Kaylyn M Bauer, Jacob Mreen, Steve A Kay, James C Carrington

A novel model plant to study the light control of seed germination
Zsuzsanna Merai, Kai Graeber, Per Wilhelmsson, Kristian K. Ullrich, Waheed Arshad, Christopher Grosche, Danuse Tarkowska, Veronika Tureckova, Miroslav Strnad, Stefan A. Rensing, Gerhard Leubner-Metzger, Ortrun Mittelsten Scheid

Single-cell transcriptome analysis of Physcomitrella leaf cells during reprogramming using microcapillary manipulation
Minoru Kubo, Tomoaki Nishiyama, Yosuke Tamada, Ryosuke Sano, Masaki Ishikawa, Takashi Murata, Akihiro Imai, Daniel Lang, Taku Demura, Ralf Reski, Mitsuyasu Hasebe

Evo-devo & evo

Functional role of pax6 in eye and central nervous system development in the annelid Capitella teleta
Marleen Klann, Elaine C Seaver

Stem cell differentiation trajectories in Hydra resolved at single-cell resolution
Stefan Siebert, Jeffrey A. Farrell, Jack F. Cazet, Yashodara Abeykoon, Abby S. Primack, Christine E. Schnitzler, Celina E. Juliano

tartan underlies the evolution of male genital morphology
Joanna F. D. Hagen, Claudia C. Mendes, Kentaro M. Tanaka, Pedro Gaspar, Maike Kittelmann, Alistair P. McGregor, Maria D. S. Nunes

Convergent recruitment of life cycle regulators to direct sporophyte development in two eukaryotic supergroups
Alok Arun, Susana M. Coelho, Akira F Peters, Simon Bourdareau, Laurent Pérès, Delphine Scornet, Martina Strittmatter, Agnieszka P Lipinska, Haiqin Yao, Olivier Godfroy, Gabriel J Montecinos, Komlan Avia, Nicolas Macaisne, Christelle Troadec, Abdelhafid Bendahmane, J. Mark Cock

Plastic multicellular development of Myxococcus xanthus: genotype-environment interactions in a physical gradient
Natsuko Rivera-Yoshida, Alejandro Vasquez Arzola, Juan Antonio Arias Del Angel, Alessio Franci, Michael Travisano, Ana Elena Escalante, Mariana Benitez

Modular co-option of cardiopharyngeal genes during non-embryonic myogenesis
Maria Mandela Pruenster, Lorenzo Fabrice Ricci, Federico Brown, Stefano Tiozzo

Analysis of sea star larval regeneration reveals conserved processes of whole-body regeneration across the metazoa
Gregory Cary, Andrew Wolff, Olga Zueva, Joseph Pattinato, Veronica Hinman

ABC-transporter activity and eicosanoid-signaling are required for germ cell migration a basal chordate
Susannah H Kassmer, Delany F Rodriguez, Anthony W De Tomaso

Evolution of ovipositor length in Drosophila suzukii is driven by enhanced cell size expansion and anisotropic tissue reorganization
Jack E Green, Matthieu Cavey, Emmanuelle Caturegli, Nicolas Gompel, Benjamin Prud’homme

Insect egg size and shape evolve with ecology, not developmental rate
Samuel H. Church, Seth Donoughe, Bruno A. S. de Medeiros, Cassandra G. Extavour

Reproductive capacity evolves in response to ecology through common developmental mechanisms in Hawaiian Drosophila
Didem Pelin Sarikaya, Samuel H. Church, Laura P. Lagomarsino, Steven Montgomery, Karl N. Magnacca, Donald K. Price, Kenenth Y. Kaneshiro, Cassandra G. Extavour

A database of egg size and shape from more than 6,700 insect species
Samuel H. Church, Seth Donoughe, Bruno A. S. de Medeiros, Cassandra G. Extavour

Occurrence and predictive utility of isochronal, equiproportional, and other types of development among arthropods
Brady Quinn

Transcriptome landscape of the developing olive fruit fly embryo delineated by Oxford Nanopore long-read RNA-Seq
Anthony Bayega, Spyros Oikonomopoulos, Eleftherios Zorbas, Yu Chang Wang, Maria-Eleni Gregoriou, Konstantina T Tsoumani, Kostas D Mathiopoulos, Jiannis Ragoussis

Functional lability of RNA-dependent RNA polymerases in animals
Natalia Pinzón, Stéphanie Bertrand, Lucie Subirana, Isabelle Busseau, Hector Escrivá, Hervé Seitz

Drift and directional selection are the evolutionary forces driving gene expression divergence in eye and brain tissue of Heliconius butterflies
Ana Catalan, Adriana D. Briscoe, Sebastian Hoehna

Evolutionary transition in accessible chromatin landscapes during vertebrate embryogenesis
Masahiro Uesaka, Shigeru Kuratani, Hiroyuki Takeda, Naoki Irie

Evolution of Nodal and Nodal-related genes and the putative composition of the heterodimer that triggers the Nodal pathway in vertebrates
Juan C. Opazo, Shigehiro Kuraku, Kattina Zavala, Jessica Toloza-Villalobos, Federico G. Hoffmann

Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard
Pedro Andrade, Catarina Pinho, Guillem Perez i de Lanuza, Sandra Afonso, Jindrich Brejcha, Carl-Johan Rubin, Ola Wallerman, Paulo Pereira, Stephen J. Sabatino, Adriana Bellati, Daniele Pellitteri-Rosa, Zuzana Bosakova, Miguel A. Carretero, Nathalie Feiner, Petr Marsik, Francisco Pauperio, Daniele Salvi, Lucile Soler, Geoffrey M. While, Tobias Uller, Enrique Font, Leif Andersson, Miguel Carneiro

Chromosome-wide evolution and sex determination in a nematode with three sexes
Sophie Tandonnet, Georgios Koutsovoulos, Sally Adams, Delphine Cloarec, Manish Parihar, Mark Blaxter, Andre Pires da Silva

A clinal polymorphism in the insulin signaling transcription factor foxo contributes to life-history adaptation in Drosophila
Esra Durmaz, Subhash Rajpurohit, Nicolas Betancourt, Daniel K. Fabian, Martin Kapun, Paul Schmidt, Thomas Flatt

Selection at behavioral, developmental and metabolic genes is associated with the northward expansion of a successful tropical colonizer
Yann Bourgeois, Stephane Boissinot

Behavioral evolution drives hindbrain diversification among Lake Malawi cichlid fish
Ryan York, Allie Byrne, Kawther Abdilleh, Chinar Patil, J. Todd Streelman, Thomas Finger, Russell Fernald

Analysis of structural variants in four African cichlids highlights an association with developmental and immune related genes
Luca Penso Dolfin, Angela Man, Wilfried Haerty, Federica Di-Palma

Selection, linkage, and population structure interact to shape genetic variation among threespine stickleback genomes
Thomas C Nelson, Johnathan G Crandall, Catherine M Ituarte, Julian M Catchen, William Cresko

Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks.
Jukka-Pekka Verta, Felicity Jones

Evolution of the D. melanogaster chromatin landscape and its associated proteins
Elise Parey, Anton Crombach

Rampant hybrid misexpression in craniofacial tissues within a recent adaptive radiation of Cyprinodon pupfishes
Joseph Alan McGirr, Christopher Herbert Martin

A phylogenomic framework, evolutionary timeline, and genomic resources for comparative studies of decapod crustaceans
Joanna M. Wolfe, Jesse W. Breinholt, Keith A Crandall, Alan R. Lemmon, Emily Moriarty Lemmon, Laura E. Timm, Mark E. Siddall, Heather D. Bracken-Grissom

Size, shape and structure of insect wings
Mary K Salcedo, Jordan Hoffmann, Seth Donoughe, Lakshminarayanan Mahadevan

Reorganization of 3D Genome Structure May Contribute to Gene Regulatory Evolution in Primates
Ittai E Eres, Kaixuan Luo, Chiaowen Joyce Hsiao, Lauren E Blake, Yoav Gilad

Widespread conservation of chromatin accessibility patterns and transcription factor binding in human and chimpanzee induced pluripotent stem cells
Irene Gallego Romero, Shyam Gopalakrishnan, Yoav Gilad

The convergent evolution of eusociality is based on a shared reproductive groundplan plus lineage-specific sets of plastic genes
Michael R Warner, Lijun Qiu, Michael J Holmes, Alexander S Mikheyev, Timothy A Linksvayer

Evolution of limb development in cephalopod mollusks
Oscar A. Tarazona, Davys H. Lopez, Leslie A Slota, Martin J. Cohn

Cell biology

An F-actin shell ruptures the nuclear envelope by sorting pore-dense and pore-free membranes in meiosis of starfish oocytes
Natalia Wesolowska, Pedro Machado, Celina Geiss, Hiroshi Kondo, Masashi Mori, Yannick Schwab, Peter Lenart

Mammalian kinetochores count attached microtubules in a sensitive and switch-like manner to control cell cycle progression
Jonathan Alexander Kuhn, Sophie Dumont

Differential requirement for centriolar satellites in cilium formation among different vertebrate cells
Ezgi Odabasi, Signe K Ohlsen, Seref Gul, Halil I Kavakli, Jens S Andersen, Elif N Firat-Karalar

YAP independently regulates cell size and population growth dynamics via non-cell autonomous mediators
Douaa Mugahid, Marian Kalocsay, Scott Gruver, Leonid Peshkin, Marc W Kirschner

Cell growth dilutes the cell cycle inhibitor Rb to trigger cell division
Evgeny Zatulovskiy, Daniel F. Berenson, Benjamin R. Topacio, Jan M. Skotheim

A spatially regulated GTPase cycle of Rheb controls growth factor signaling to mTORC1
Marija Kovacevic, Christian H Klein, Lisaweta Rossmannek, Antonios D Konitsiotis, Angel Stanoev, Astrid U Kraemer, Philippe Bastiaens

Precursor miRNAs are trafficked along axons associated with vesicles and locally processed to regulate growth cone steering
Eloina Corradi, Antoneta Gavoci, Stephanie Strohbuecker, Michela Roccuzzo, Irene Dalla Costa, Archana Iyer, Simone Bridi, Gabriela Santoz Rodriguez, Cei Abreu-Goodger, Marie-Laure Baudet

Enhanced cell-cell contact stability upon Fibroblast Growth factor Receptor/N-cadherin cross-talk
Thao Nguyen, Laurence Duchesne, Nicole Bogetto, David Fernig, Chandra Murade, Benoit Ladoux, Rene-Marc Mege

The interaction between the tumour suppressor Dlg1 and the MAGUK protein CASK is required for oriented cell division in mammalian epithelia
Andrew Phillip Porter, Gavin White, Natalie A Mack, Angeliki Malliri

Rapid Whole Cell Imaging Reveals An APPL1-Dynein Nexus That Regulates Stimulated EGFR Trafficking
Harrison York, Amandeep Kaur, Abhishek Patil, Aditi Bhowmik, Ullhas K Moorthi, Geoffrey J Hyde, Hetvi Gandhi, Katharina Gaus, Senthil Arumugam

The voltage sensing phosphatase (VSP) localizes to the apical membrane of kidney tubule epithelial cells
Wil Ratzan, Vamsee Rayaprolu, Scott E Killian, Roger Bradley, Susy Kohout

The repressive genome compartment is established early in the cell cycle before forming the lamina associated domains
Teresa Romeo Luperchio, Michael E.G. Sauria, Victoria E Hoskins, Wong Xianrong, Emily DeBoy, Marie-Cecile Gaillard, Peter Tsang, Katja Pekrun, Robert A Ach, Alice Yamada, James Taylor, Karen L Reddy

Modelling

Using a continuum model to decipher the mechanics of embryonic tissue spreading from time-lapse image sequences: An approximate Bayesian computation approach
Tracy Stepien, Holley E. Lynch, Shirley X. Yancey, Laura Dempsey, Lance A. Davidson

Entropic forces drive cellular contact guidance
Gitta Buskermolen, Hamsini Suresh, Siamak Shishvan, Andrea Vigliotti, Antonio deSimone, Nicholas Kurniawan, Carlijn Bouten, Vikram Deshpande

Field induced cell proliferation and death in a thick epithelium
Niladri Sarkar, Jacques Prost, Frank Julicher

Discrete Mechanical Growth Model for Plant Tissue
Louis Daniel Weise, Kirsten H.W.J. ten Tusscher

Quantifying the mechanics and growth of cells and tissues in 3D using high resolution computational models.
Paul Van Liedekerke, Johannes Neitsch, Tim Johann, Enrico Warmt, Steffen Grosser, Ismael Gonzales Valverde, Josef Kaes, Stefan Hoehme, Dirk Drasdo

Towards control of cellular decision-making networks in the epithelial-to-mesenchymal transition
Jorge Gómez Tejeda Zañudo, M. Tyler Guinn, Kevin Farquhar, Mariola Szenk, Steven N. Steinway, Gábor Balázsi, Réka Albert

Maintaining the stem cell niche in multicellular models of epithelia
Claire Miller, Edmund Crampin, James Osborne

Reconstructing probabilistic trees of cellular differentiation from single-cell RNA-seq data
Miriam Shiffman, William T. Stephenson, Geoffrey Schiebinger, Jonathan Huggins, Trevor Campbell, Aviv Regev, Tamara Broderick

Theory of mechano-chemical patterning in biphasic biological tissues
P. Recho, A. Hallou, E. Hannezo

Biophysics and population size constrains speciation in an evolutionary model of developmental system drift
Bhavin S Khatri, Richard Goldstein

Ring shape Golden Ratio multicellular structures are algebraically afforded by asymmetric mitosis and one to one cell adhesion
William Butler, T. Bernard Kinane

Tools & resources

Science Family skills: An Alexa Assistant Tailored for Laboratory Routine
Tiago Lubiana-Alves, Helder I Nakaya

Multi-sample SPIM image acquisition, processing and analysis of vascular growth in zebrafish
Stephan Daetwyler, Ulrik Günther, Carl D. Modes, Kyle Harrington, Jan Huisken

Fast, multicolor 3-D imaging of brain organoids with a new single-objective two-photon virtual light-sheet microscope
Irina Rakotoson, Brigitte Delhomme, Philippe Djian, Andreas Deeg, Maia Brunstein, Christian Seebacher, Rainer Uhl, Clement Ricard, Martin Oheim

Low-cost, sub-micron resolution, wide-field computational microscopy using opensource hardware
Tomas Aidukas, Regina Eckert, Andrew R Harvey, Laura Waller, Pavan Chandra Konda

A genetically encoded probe for imaging HA-tagged protein translation, localization, and dynamics in living cells and animals
Ning Zhao, Kouta Kamijo, Philip Fox, Haruka Oda, Tatsuya Morisaki, Yuko Sato, Hiroshi Kimura, Timothy J. Stasevich

Induction of Interferon-Stimulated Genes and Cellular Stress Pathways by Morpholinos
Jason Kuan Han Lai, Kristina Gagalova, Didier Y. R. Stainier

Swift Large-scale Examination of Directed Genome Editing (SLEDGE Hammer)
Omar T. Hammouda, Thomas Thumberger, Joachim Wittbrodt

Flexible, fast and selective genetic manipulation of the vertebrate CNS with misPiggy
Michal Slezak, Filip de Vin, Yohei Shinmyo, Mykhailo Y Batiuk, Melvin Y Rincon, Carmen Menacho Pando, Johann Urschitz, Stefan Moisyadi, Frank Schnuetgen, Hiroshi Kawasaki, Matthew G Holt

Generation of Cynomolgus Monkeys (Macaca fascicularis) Embryos with ICSI Based on the MII-Stage Oocytes Acquired by Personalized Superovulation Protocol
Kaili Ma, Zhangqiong Huang, Yun Li, Qinfang Jiang, Yixuan Wang, Qihan Li

Deep Phenotyping Enhances Somatic Mutant Detection and Mosaic Pattern Recognition in the Zebrafish Skeleton
Claire J. Watson, Adrian T. Monstad-Rios, Rehaan M. Bhimani, Charlotte Gistelinck, Andy Willaert, Paul J. Coucke, Yi-Hsiang Hsu, Ronald Y. Kwon

Strategies For Efficient Genome Editing Using CRISPR-Cas9
Barbara J. Meyer, Behnom Farboud, Aaron Severson

Cell-specific CRISPR/Cas9 activation by microRNA-dependent expression of anti-CRISPR proteins
Mareike Daniela Hoffmann, Sabine Aschenbrenner, Stefanie Grosse, Kleopatra Rapti, Claire Domenger, Julia Fakhiri, Manuel Mastel, Roland Eils, Dirk Grimm, Dominik Niopek

CRISPR/Cas12a-assisted PCR tagging of mammalian genes
Julia Fueller, Matthias Meurer, Konrad Herbst, Krisztina Gubicza, Bahtiyar Kurtulmus, Julia D. Knopf, Daniel Kirrmaier, Benjamin Buchmuller, Gislene Pereira, Marius K. Lemberg, Michael Knop

BAPC-assisted CRISPR/Cas9 System: Targeted Delivery into Adult Ovaries for Heritable Germline Gene Editing (Arthropoda: Hemiptera)
Wayne B. Hunter, Maria T. Gonzalez, John Tomich

CRISPR-TSKO facilitates efficient cell type-, tissue-, or organ-specific mutagenesis in Arabidopsis
Ward Decaestecker, Rafael Andrade Buono, Marie L. Pfeiffer, Nick Vangheluwe, Joris Jourquin, Mansour Karimi, Gert Van Isterdael, Tom Beeckman, Moritz K. Nowack, Thomas B. Jacobs

Comparison of efficiency and specificity of CRISPR-associated (Cas) nucleases in plants: An expanded toolkit for precision genome engineering
Oleg Raitskin, Christian Schudoma, Anthony West, Nicola J Patron

Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair
Wei Chen, Aaron McKenna, Jacob Schreiber, Yi Yin, Vikram Agarwal, William Stafford Noble, Jay Shendure

Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq
Beeke Wienert, Stacia K Wyman, Christopher D Richardson, Charles D Yeh, Pinar Akcakaya, Michelle J Porritt, Michaela Morlock, Jonathan T Vu, Katelynn R Kazane, Hannah L Watry, Luke M Judge, Bruce R Conklin, Marcello Maresca, Jacob E Corn

aFARP-ChIP-seq, a convenient and reliable method for genome profiling in as few as 100 cells with a capability for multiplexing ChIP-seq
Wenbin Liu, Sibiao Yue, Xiaobin Zheng, Jia Cao, Yixian Zheng

RNA sequencing data: hitchhiker’s guide to expression analysis

Koen Van Den Berge​, Katharina Hembach​, Charlotte Soneson​, Simone Tiberi​, Lieven Clement, Michael I Love, Rob Patro, Mark Robinson​

Linked-read sequencing of gametes allows efficient genome-wide analysis of meiotic recombination
Hequan Sun, Beth A Rowan, Pádraic J Flood, Ronny Brandt, Janina Fuss, Angela M Hancock, Richard W Michelmore, Bruno Huettel, Korbinian Schneeberger

PlotsOfData – a web app for visualizing data together with its summaries
Marten Postma, Joachim Goedhart

Research practice & education

Developing Future Biologists: creating and assessing a portable short course to engage underrepresented undergraduate students in developmental biology
Justine M. Pinskey, Eden A. Dulka, Andrea I. Ramos, Martha L. Echevarría-Andino, David S. Lorberbaum, Brandon S. Carpenter, Jorge Y. Martinez-Marquez, Breane G. Budaitis, Emily M. Holloway, Samhitha Raj, Alana M. Chin, Edu Suarez, Laura A. Buttitta, Deb L. Gumucio, Deneen M. Wellik, Ryan Insolera, Leilani Marty-Santos, Benjamin L. Allen, Scott Barolo

Building a local community of practice in scientific programming for Life Scientists
Sarah L.R. Stevens, Mateusz Kuzak, Carlos Martinez, Aurelia Moser, Petra M. Bleeker, Marc Galland

Ten Simple Rules for Scientific Fraud & Misconduct

Nicolas P Rougier​​, John Timmer​

Departmental-level approaches to gender equity in biology

Christiana J McDonald-Spicer​, Benjamin Schwessinger, Susan Howitt

Participation and Motivations of Grant Peer Reviewers: A Comprehensive Survey of the Biomedical Research Community
Stephen A Gallo, Lisa A Thompson, Karen B Schmaling, Scott R Glisson

Why not…

The impact of modern jazz dance on the electrical brain activity
Johanna Wind, Wolfgang Schöllhorn

Followers of honey bee waggle dancers change their behavior when dancers are sleep-restricted or perform imprecise dances
Barrett Anthony Klein, Michael Vogt, Keaton Unrein, David M. Reineke

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