Bioinformatics scientist positions at the postdoctoral level are available in the lab of Dr. Sabine Dietmann at Washington University School of Medicine in St. Louis, Missouri, USA.  Our research program is dedicated the development of multi-omics and machine learning approaches to the data sets generated in stem cell-based model systems for embryonic development and organoids. (https://informatics.wustl.edu/research-lab-sabine-dietmann). The candidate’s independent research will benefit from our lab’s extensive collaborative network in the Department of Developmental Biology and the Division of Nephrology at Washington University in St Louis and at international institutions. Projects are available in the following areas: (1) comparing developmental trajectories across species (2) machine learning models for cell fate decisions and gene regulatory networks (3) epitranscriptomics in single cells (https://profiles.wustl.edu/en/persons/sabine-dietmann).

 

We are seeking enthusiastic and talented candidates with high proficiency in scientific programming languages, such as R and Python/PERL. A good understanding of machine learning frameworks in Python (Keras/Tensorflow), experience with creating packages in R or some experience with single cell data analysis and genomics would be very beneficial.

 

Applicants should have a Ph.D. or master’s degree in Biology, Computer Science, Bioinformatics, Physics or related field plus 2 years of demonstrated relevant research experience.

 

Consistently ranked among the top 10 US medical schools, Washington University School of Medicine offers a highly interactive and stimulating academic environment for scientists in training, a place where you can be an individual and achieve exceptional things. Washington University in St. Louis is an equal opportunity employer and committed to providing a comprehensive and competitive benefits package. Our lab is located in the Central West End of St. Louis, a vibrant neighborhood adjacent to major cultural institutions.

 

For further information please contact sdietmann@wustl.edu.

 

To apply for this position please submit a CV, a cover letter describing your research interests and contact information for two references no later than March 14 to sdietmann@wustl.edu.

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The Tavosanis lab welcomes applications for a post-doc position to study the cellular mechanisms of neuronal dendrite differentiation in Drosophila.

For reference, please, see: Stuerner et al., Development 2019 https://doi.org/10.1242/dev.171397; Castro et al. Elife 2020 doi: 10.7554/eLife.60920; Stuerner et al., Biorxiv https://www.biorxiv.org/content/10.1101/2020.10.01.322750v1; Baltruschat et al., Biorxiv https://www.biorxiv.org/content/10.1101/2020.07.07.191064v1).

This project will combine the generation of molecular tools for acute manipulation of protein activity with high-resolution in vivo microscopy.

For more details, please, contact Gaia Tavosanis directly at: gaia.tavosanis@dzne.de

To apply, you can follow the link: https://jobs.dzne.de/en/jobs/50653/postdoctoral-researcher-fmd-1871202011

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Position Summary:
The Paul Lab at the MBL seeks a highly motivated individual to join the Josephine Bay Paul Center for Comparative Molecular Biology and Evolution as a Research Assistant (Level I). The successful candidate will be responsible for carrying out routine laboratory work as outlined below. Our research group is looking at the processes that diversify microbial genes, to better understand the functional significance of protein variation in cells and viruses from a variety of biomes.

 

Additional Information:
The primary aim of the position is to maintain the molecular lab facilities and to assist in developing genetic experiments with bacteria/archaea primarily derived from marine and freshwater ecosystems. Responsibilities will include establishing and monitoring cell cultures, maintaining lab equipment, ordering lab supplies, and conducting basic molecular experiments.

Basic Qualifications:
A Bachelor’s degree in biology, molecular biology or a related discipline is required. This position requires an independent, organized, and self-motivated individual with strong problem-solving skills and the ability to multitask. Prior experience in a research lab and applying basic molecular biology techniques is required. Excellent written, verbal, and interpersonal skills; attention to detail; and a strong work ethic are essential. Position level and salary will depend upon education and experience.

 

Preferred Qualifications:
The ideal candidate will have prior experience with nucleic acid purification, PCR, and maintaining (bacterial/archaeal) cell cultures.  An understanding of basic molecular biology concepts is important.

 

Physical Requirements:
Minimal exposure to biohazardous chemicals. Occasional lifting of heavy objects.

 

Required documents:
Apply on the MBL website and include the following documents in your application package: cover letter, resume/CV, copies of most recent transcripts (unofficial is acceptable), and contact details of 3 references.

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By Oriana Q. H. Zinani, Kemal Keseroğlu, Ahmet Ay & Ertuğrul M. Özbudak:

Gene expression is an inevitably stochastic process (Ozbudak et al., 2002). In contrast, embryonic development and homeostasis require cells to coordinate the spatiotemporal expression of large sets of genes. Many mechanisms are known to orchestrate this coordination, such as operons, bidirectional promoters, enhancer sharing, 3-D DNA looping, topologically associated domains, transcription factories or hubs, and shared upstream regulators.

In metazoans, pairs of co-expressed genes often reside in the same chromosomal neighborhood, with gene pairs representing 10 to 50% of all genes, depending on the species (Adachi and Lieber, 2002; Arnone et al., 2012). Although many paired genes encode for essential housekeeping proteins, some encode for signaling regulators and transcription factors (such as CYP26A1–CYP26C1, ETS1–FLI1, MRF4–MYF5, MESP1–MESP2, SIX1–SIX4–SIX6, and STAT1–STAT4), which have transcription start sites that are 9–516 kb apart. Because various other mechanisms can ensure correlated gene expression, the selective advantage of maintaining adjacent gene pairs remains unknown.

To address this question, in Zinani et al, we used two linked zebrafish segmentation clock genes, her1–her7, as the testbed. The subdivision of the anterior–posterior axis into a fixed number of somites is a landmark example of how coordinated gene expression patterns the vertebrate embryo. During somitogenesis, groups of cells synchronously commit to segmentation in a notably short time frame. The pace of segmentation is set by the period of an oscillator, the segmentation clock, in cells of the unsegmented presomitic mesoderm (PSM). Oscillatory expression of the Hes or her clock genes is conserved in vertebrates; disruptions of their oscillations lead to vertebral segmentation defects (i.e., congenital scoliosis in humans). Approximately every 30 min in zebrafish, around 200 cells bud from the PSM to form a new somite. Segmentation is carried out for a species-specific number of cycles (33 in zebrafish). Her1 and Her7 are basic helix-loop-helix (bHLH) proteins that dimerize to bind DNA. The zebrafish segmentation clock relies on a transcriptional negative-feedback loop in which Her7-Hes6 hetero- or Her1-Her1 homodimers repress transcription of her1 and her7 (Ay et al., 2013; Giudicelli et al., 2007; Schroter et al., 2012). In zebrafish, two paired clock genes (her1 and her7) are separated by a 12-kb regulatory intervening sequence. her1 and her7 have similar transcriptional time delays (Hanisch et al., 2013) and RNA half-lives (Giudicelli et al., 2007); therefore, the transcription of her1 and her7 is mainly concomitant in the tissue. To achieve the rapid tempo and reproducible precision of segmentation, the transcription of her1 and her7 should be tightly coordinated.

Chromosomal adjacency was previously shown to cause correlated expression of synthetic reporters (Becskei et al., 2005; Fukaya et al., 2016; Raj et al., 2006). To test the role of gene pairing on transcriptional co-firing, we detected nascent transcription loci in the nucleus of single cells with single-molecule fluorescence in situ hybridization (smFISH) (Keskin et al., 2018; Zinani et al., 2021). We found that the probability of transcriptional co-firing of paired her1 and her7 genes on the same chromosome is significantly higher than the two unpaired her1 genes on homolog chromosomes. This finding demonstrated that gene pairing augments correlated transcription of the two clock genes by triggering transcriptional co-firing.

Co-firing of two paired clock genes could be advantageous for somite segmentation as it would coordinate transcript levels. To test this hypothesis, we generated cis and trans double heterozygous embryos by using CRISPR/Cas9 (Figure). The cis heterozygous mutants carried two mutant genes in one chromosome and two wild-type genes on the homologous chromosome (Figure, top row). In contrast, the trans mutants carried a mutant her1 gene adjacent to a wild-type her7 gene on one chromosome, and a mutant her7 gene adjacent to a wild-type her1 gene on the other chromosome (Figure, bottom row). Hence, fish that are compound heterozygous for these alleles will have the same functional gene dose as the previously described double heterozygous embryos with paired her1 and her7 genes (Figure, left column). We next raised the gene-paired and gene-unpaired embryos at 21.5 °C, where wild-type embryos successfully form somites. Gene-unpaired embryos had reduced success in somite segmentation as compared to gene-paired embryos (Figure, right column). These results revealed that maintaining paired genes in the genome is beneficial for successful pattern formation during embryonic development.

We next investigated the mechanism by which gene pairing is beneficial for clock oscillations. Although negative-feedback loops are widespread in gene regulatory networks, they usually do not give rise to oscillations, but instead act as a rheostat to tightly maintain gene expression around a steady-state. For a negative-feedback loop to generate oscillations, several important criteria need to be satisfied. Previous studies revealed the importance of time delays and short RNA or protein half-lives to generate sustained oscillations. However, another important criterion needed to generate oscillations is that the rate of transcription needs to be high enough to push the system into an unstable steady-state, establishing a limit cycle (Lewis, 2003; Novak and Tyson, 2008). We found that when genes are paired on the same chromosome, co-transcription happens more frequently. We hypothesized that co-firing of transcription results in a high rate of RNA production, and thereby overshoots the limit-cycle threshold. Simulations of our stochastic model agreed with our hypothesis.

To assess the function of gene pairing in the segmentation clock in real-time, we imaged transgenic Tg(her1:her1-Venus) (Delaune et al., 2012) zebrafish embryos along the entire PSM. We quantified the amplitude of oscillations in the next presumptive somites for 11 somite cycles. We found that the average amplitude was decreased in gene-unpaired embryos compared to gene-paired embryos. The amplitudes of oscillations preceding disrupted boundaries were significantly lower than the ones preceding the successful ones in a given genetic background.

Our results demonstrate that the prevention of gene pairing disrupts oscillations and segmentation in zebrafish embryos. We predict that gene pairing is similarly advantageous in other biological systems, and our findings could inspire engineering of precise synthetic clocks in embryos and organoids.

References:

Adachi, N., and Lieber, M.R. (2002). Bidirectional gene organization: a common architectural feature of the human genome. Cell 109, 807-809.

Arnone, J.T., Robbins-Pianka, A., Arace, J.R., Kass-Gergi, S., and McAlear, M.A. (2012). The adjacent positioning of co-regulated gene pairs is widely conserved across eukaryotes. Bmc Genomics 13.

Ay, A., Knierer, S., Sperlea, A., Holland, J., and Özbudak, E.M. (2013). Short-lived Her Proteins Drive Robust Synchronized Oscillations in the Zebrafish Segmentation Clock. Development 140, 3244-3253.

Becskei, A., Kaufmann, B.B., and van Oudenaarden, A. (2005). Contributions of low molecule number and chromosomal positioning to stochastic gene expression. Nature genetics 37, 937-944.

Delaune, E.A., Francois, P., Shih, N.P., and Amacher, S.L. (2012). Single-cell-resolution imaging of the impact of notch signaling and mitosis on segmentation clock dynamics. Dev Cell 23, 995-1005.

Fukaya, T., Lim, B., and Levine, M. (2016). Enhancer Control of Transcriptional Bursting. Cell 166, 358-368.

Giudicelli, F., Ozbudak, E.M., Wright, G.J., and Lewis, J. (2007). Setting the Tempo in Development: An Investigation of the Zebrafish Somite Clock Mechanism. PLoS Biol 5, e150.

Hanisch, A., Holder, M.V., Choorapoikayil, S., Gajewski, M., Ozbudak, E.M., and Lewis, J. (2013). The elongation rate of RNA Polymerase II in the zebrafish and its significance in the somite segmentation clock. Development 140, 444-453.

Keskin, S., Devakanmalai, G.S., Kwon, S.B., Vu, H.T., Hong, Q., Lee, Y.Y., Soltani, M., Singh, A., Ay, A., and Ozbudak, E.M. (2018). Noise in the Vertebrate Segmentation Clock Is Boosted by Time Delays but Tamed by Notch Signaling. Cell reports 23, 2175-2185 e2174.

Lewis, J. (2003). Autoinhibition with transcriptional delay: A simple mechanism for the zebrafish somitogenesis oscillator. Current Biology 13, 1398-1408.

Novak, B., and Tyson, J.J. (2008). Design principles of biochemical oscillators. Nat Rev Mol Cell Biol 9, 981-991.

Ozbudak, E.M., Thattai, M., Kurtser, I., Grossman, A.D., and van Oudenaarden, A. (2002). Regulation of noise in the expression of a single gene. Nat Genet 31, 69-73.

Raj, A., Peskin, C.S., Tranchina, D., Vargas, D.Y., and Tyagi, S. (2006). Stochastic mRNA synthesis in mammalian cells. Plos Biology 4, 1707-1719.

Schroter, C., Ares, S., Morelli, L.G., Isakova, A., Hens, K., Soroldoni, D., Gajewski, M., Julicher, F., Maerkl, S.J., Deplancke, B., et al. (2012). Topology and dynamics of the zebrafish segmentation clock core circuit. PLoS Biol 10, e1001364.

Zinani, O.Q.H., Keseroglu, K., Ay, A., and Ozbudak, E.M. (2021). Pairing of segmentation clock genes drives robust pattern formation. Nature 589, 431-436.

(6 votes)
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In our third SciArt Profile we meet Sydney Wyatt, a PhD student based at the University of California, Davis.

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Where are you originally from, where do you work now, and what do you work on?

I am originally from a small Northern California town, Paradise. I went out of state to get my BS at University of Utah in Salt Lake City, and while I enjoyed my time there, I’m happy to be pursuing my PhD in Integrative Genetics and Genomics at University of California, Davis; it gives me the opportunity to be closer to my parents. My thesis research in Dr. Bruce Draper’s lab currently revolves around interrogating sex determination and early gonad development in zebrafish. Specifically, I am investigating the female sex determination pathway, as well as the role of gap junctions in early germ cell development.

 

Has science always been an important part of your life?

I remember loving dinosaurs growing up: my favorite is still Parasaurolophus. Understandably, I wanted to be a paleontologist for a long time, although it changed to forensic pathologist by the time I went to college. After my first anatomy lab I quickly changed my mind! Instead, I found I loved genetics and developmental biology through my classes and undergraduate research. Despite working on specific projects now, I still enjoy learning about other fields (and still love learning about dinosaurs!).

I was fortunate that STEM was always encouraged by my family, despite limited exposure growing up. I didn’t have access to the opportunities and mentorship I volunteer for today, namely mentoring high school senior research projects and various public science outreach events like the North Bay Science Discovery Day. I think if I had had those opportunities, I might have learned what I wanted out of my education more quickly.

 

And what about art – have you always enjoyed drawing/painting/etc?

I was a ballet dancer for many, many years, so performing arts were important to me. I didn’t start drawing until high school when I needed a new creative outlet after an injury. I took classes from a local oil painter, and he mentored my senior community project. I eventually moved into digital art; it allows me to do my art in short bursts in any location without hauling around a pad of paper and a case of pencils. It’s nice to have that outlet to help me avoid burnout.

 

“Digital art allows me to do my art in short bursts in any location”

 

What or who are your artistic influences?

I have been drawing a lot of fish lately thanks to my pandemic discovery of #SundayFishSketch created by Rene Martin on Twitter.

 

How do you make your art? 

I pick a subject based either on suggestions from friends and family or a color palette. I try to vary the main color to avoid too much repetition. Varying the subject helps too: I rotate between fish, flowers and birds. Once I have my subject and references, I get sketching. For physical pieces, I use a grid technique to help me capture the relative positions of all the details. For digital pieces, I start with basic shapes (and use the eraser and undo button a lot). Color swatching is important. I’ll do a couple practice swatches to warm up and remind myself of what I was thinking when designing the piece. The main colors get lightly blocked first with shadows and highlights, and then I build up from there. I have a tendency to do entire sections in one sitting, like one entire wing of a bird, to keep my technique consistent.

 

Does your art influence your science at all, or are they separate worlds?

I work on fish, so maybe a little influence. There are a couple of zebrafish-themed Sunday fish sketches floating around Twitter. Science I read about influences my art, too. I learned about really interesting killifish genomics research and was inspired to create a whole series of non-traditional model organisms, like killifish or gar or delta smelt. These organisms are so important but not widely heard of outside their niches.

 

What are you thinking of working on next?

I’m excited to keep working on my research projects, as well as continue to build my art and writing portfolios. As far as art goes, I’ve recently been commissioned by friend to help make label for a home-brewed beer called Axolotl Ale. I also manage a sticker shop (mostly fish) based on previous interest in purchasing pieces. My long-term goal is continue to create non-traditional model organism pieces to highlight the diversity in research subjects for the public as part of my science communication efforts.

 

 

 

 

Fish Gallery (click for full size image & caption)

 

 

 

 

 

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We’re looking for new people to feature in this series throughout the year – whatever kind of art you do, from sculpture to embroidery to music to drawing, if you want to share it with the community just email thenode@biologists.com (nominations are also welcome!).

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A postdoctoral position is available in the Scholpp lab at the Living Systems Institute (LSI) at the University of Exeter (https://www.exeter.ac.uk/livingsystems/). The mission of the institute is to study the function of living systems by multi-scale and interdisciplinary approaches. A primary focus of our lab is understanding how cells communicate in a tissue. We focus mainly on signals from the WNT protein family, which regulate fundamental processes including cell proliferation and differentiation, cell polarity and migration. Misregulation of this morphogenetic network causes severe diseases such as neurodegenerative diseases.  We have demonstrated that WNT proteins can be loaded on signalling filopodia known as cytonemes (yellow arrows) to allow paracrine signalling in vertebrates.

In this pilot project, we will study the interplay of WNT and β-amyloid signalling during the formation and maintenance of synapses. We will use hiPSC-derived cortical neurons to study the underlying molecular mechanism controlling WNT cytoneme function and synaptogenesis by in vivo high-resolution imaging.

What we offer:

• A fully-funded position for 12 months (with the possibility of extension, including consumables and travel money) by the Alzheimer’s BRACE Charity  ( https://www.alzheimers-brace.org/ )
• A highly collaborative team and a collegial environment in the LSI

• A stimulating environment with freedom to develop new research directions.
• Supportive mentorship for multi-faceted career development and opportunities tailored towards individual career goals.
• Regular interactions with world-class colleagues through Biosciences and Medical School.
• An institute located in a dynamic city in the South West of England with the affordable cost of living.

What we are looking for:

• Applicants with experience in developmental neuroscience and imaging, preferable in hiPSC culture (incl. maintenance and differentiation, and functionality assessment through cellular and molecular biological assays) and high-resolution imaging (incl. confocal microscopy, SIM, 2-photon)

• Enthusiastic and ambitious individuals with a keen interest in our research and a collaborative and collegial laboratory environment.
• Fearlessness in learning new techniques and designing projects independently.
• Willingness to apply for applicable fellowships and grants
• Interest in working with junior lab members and project students.
• Strong verbal and written communication skills. 

Start date 1.5.2021 (flexible).

Application materials (email to s.scholpp@exeter.ac.uk ):

• Cover letter outlining relevant expertise and scientific interests
• CV

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A joint research team co-led by Prof. Chao Tang (Peking University, PKU), Prof. Zhongying Zhao (Hong Kong Baptist University, HKBU) and Prof. Hong Yan (City University of Hong Kong, CityU) has developed a novel computational tool that can reconstruct and visualize three-dimensional shapes and temporal changes of cells, speeding up the analytical process from thousands of hours by hand to a few hours by computer. Furthermore, a total of 17 C. elegans embryos were fully segmented and normalized, generating a time-lapse 3D (i.e., 4D) morphological atlas from the 4- to 350-cell stages, including cell shape, volume, surface area, migration, nucleus position and cell-cell contact with confirmed cell identities. Both the computational tool and standard dataset can advance further studies in developmental biology, cell biology and biomechanics (Figure 1). This interdisciplinary study has been published in Nature Communications, entitled “Establishment of a morphological atlas of the Caenorhabditis elegans embryo using deep-learning-based 4D segmentation” [1].

 

Figure 1. The concept of 3D cell membrane imaging and segmentation (photo source: DOI number: 10.1038/s41467-020-19863-x).

 

The tool developed by the team is called “CShaper”. “It is a powerful computational tool that can segment and analyze cell images systematically at the single-cell level, which is much needed for the study of cell division (Figure 2), and cell and gene functions,” described Prof. Hong Yan, Chair Professor of Computer Engineering and Wong Chung Hong Professor of Data Engineering in the Department of Electrical Engineering (EE) at CityU.

 

Figure 2. Morphological dynamics of cell division, deformation and migration during C. elegans embryogenesis at single-cell resolution (photo source: DOI number: 10.1038/s41467-020-19863-x).

 

Breakthrough in segmenting cell images automatically

Cell images are usually obtained by laser beam scanning. The existing image analysis systems can only detect cell nucleus well with a poor cell membrane image quality, hampering reconstruction of cell shapes. Also, there is a lack of reliable algorithm for the segmentation of time-lapse 3D images (i.e. 4D images) of proliferating cells. Image segmentation is a critical process in computer vision that involves dividing a visual input into segments to simplify image analysis. Often, researchers have to spend hundreds of hours labeling many cell images manually.

The breakthrough in CShaper is that it can detect cell membranes, build up cell shapes in 3D, and more importantly, automatically segment the cell images at the cell level. “Using CShaper, biologists can decipher the contents of these images within a few hours. It can characterize cell shapes and surface structures, and provide 3D views of cells at different time points (Figure 3),” said Mr Jianfeng Cao, a PhD student in Prof. Hong Yan’s lab and a co-first author of the paper.

To achieve this, the deep-learning-based model DMapNet developed by the team plays a key role in the CShaper system. “By learning to capture multiple discrete distances between image pixels, DMapNet extracts the membrane contour while considering shape information, rather than just intensity features. Therefore CShaper achieved a 95.95% accuracy of identifying the cells, which outperformed other methods substantially,” he explained. CShaper was also tested on plant tissue cells, showing promising results. The team believe the computer tool can be adopted to other biological studies.

 

Figure 3. Fluorescent imaging (cell membrane and cell nucleus) and segmentation pipeline (CShaper) (photo source: DOI number: 10.1038/s41467-020-19863-x).

 

Generating a standard morphological atlas

With CShaper, the team collected 17 C. elegans embryos with fluorescence on both cell membrane and cell nucleus. The segmented regions were subjected to spatial and temporal normalization, producing a set of standardized embryo structures placed in a cuboid framework. The 4D morphological atlas lasts from the 4- to 350-cell stages during C. elegans embryogenesis, and includes quantitative information of cell shape, volume, surface area, migration, nucleus position and cell-cell contact with confirmed cell identities (Figure 4). “The morphological atlas at cellular level is information-rich and allows systematic analysis with cell identity, and is needed by the field of developmental biology,” said Prof. Zhongying Zhao.

“With such accurate data, we can not only develop mathematical model to ‘compute’ embryogenesis, but also search the underlying principles which govern the nematode development,” said Prof. Chao Tang. “Using the standard morphological data, recently we built a phase field model to reconstruct the C. elegans embryonic morphogenetic procedure [2], and uncovered a minimal time principle optimizing the C. elegans embryonic cell lineage [3],” said Mr Guoye Guan, a PhD student in Prof. Chao Tang’s lab and a co-first author of the paper.

 

Figure 4. Standard morphological atlas and multidimensional developmental properties (photo source: DOI number: 10.1038/s41467-020-19863-x).

 

Prof. Chao Tang (PKU), Prof. Zhongying Zhao (HKBU) and Prof. Hong Yan (CityU) are the corresponding authors of the paper; Ph.D students Jianfeng Cao (CityU) and Guoye Guan (PKU) and Dr. Vincy Wing Sze Ho (HKBU) are the co-first authors; Ming-Kin Wong (HKBU) and Lu-Yan Chan (HKBU) provided experimental assistance.

The funding support for this study included the Hong Kong Research Grants Council, the HKBU Interdisciplinary Research Cluster Fund, the Hong Kong Innovation and Technology Commission, the Hong Kong Institute for Data Science, the Ministry of Science and Technology of China, and the National Natural Science Foundation of China.

Part of this article is from the news release in PKU [4] and CityU [5].

 

References

[1] Jianfeng Cao, Guoye Guan, Vincy Wing Sze Ho, Ming-Kin Wong, Lu-Yan Chan, Chao Tang, Zhongying Zhao, Hong Yan. Establishment of a morphological atlas of the Caenorhabditis elegans embryo using deep-learning-based 4D segmentation. Nature Communications, 2020, 11: 6254 (https://www.nature.com/articles/s41467-020-19863-x).
[2] Xiangyu Kuang, Guoye Guan, Ming-Kin Wong, Lu-Yan Chan, Zhongying Zhao, Chao Tang, Lei Zhang. Computable early C. elegans embryo with a data-driven phase field model. bioRxiv, 2020, 422560 (https://www.biorxiv.org/content/10.1101/2020.12.13.422560v2).
[3] Guoye Guan, Ming-Kin Wong, Zhongying Zhao, Lei-Han Tang, Chao Tang. Lineage optimization in nematode’s early embryogenesis. arXiv, 2020, 2007.05723 (https://arxiv.org/abs/2007.05723).
[4] Standard morphological atlas of C. elegans embryo (http://cqb.pku.edu.cn/tanglab/News/shownews.php?id=224&lang=en).
[5] A powerful computational tool for efficient analysis of cell division 4D image data (https://www.cityu.edu.hk/research/stories/2020/12/22/powerful-computational-tool-efficient-analysis-cell-division-4d-image-data).

(5 votes)
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CONTACT

Frank Schnorrer ; Pierre Mangeol

frank.schnorrer@univ-amu.fr ; pierre.mangeol@univ-amu.fr

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

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The preprints this month are hosted on bioRxiv, arXiv and, for the first time, preprints.org (check out our new ‘Reviews’ section!) – 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

Reviews

Tools & resources

Research practice & education

 

 

Developmental biology

| Patterning & signalling

Fatty acid metabolic reprogramming promotes C. elegans development
Xuwen Cao, Yusu Xie, Beining Xue, Hanwen Yang, L. Rene Garcia, Liusuo Zhang

 

 

Nuclear translocation of tagged endogenous ERK/MPK-1 MAP Kinase denotes a subset of activation events in C. elegans development
Neal R. Rasmussen, David J. Reiner

 

Neuronal post-developmentally acting SAX-7S/L1CAM can function as cleaved fragments to maintain neuronal architecture in C. elegans
V.E. Desse, C.R. Blanchette, P. Perrat, C.Y. Bénard

 

Amnion signals are essential for mesoderm formation in primates
Ran Yang, Alexander Goedel, Yu Kang, Chenyang Si, Chu Chu, Yi Zheng, Zhenzhen Chen, Peter J. Gruber, Yao Xiao, Chikai Zhou, Nevin Witman, Chuen-Yan Leung, Yongchang Chen, Jianping Fu, Weizhi Ji, Fredrik Lanner, Yuyu Niu, Kenneth Chien

 

Glycogen Synthase Kinase 3 regulates the genesis of the rare displaced ganglion cell retinal subtype
Elena Kisseleff, Robin J Vigouroux, Catherine Hottin, Sophie Lourdel, Parth Shah, Alain Chédotal, Muriel Perron, Anand Swaroop, Jerome E Roger

 

Rostrocaudal patterning and neural crest differentiation of human pre-neural spinal cord progenitors in vitro
Fay Cooper, George E Gentsch, Richard Mitter, Camille Bouissou, Lyn Healy, Ana Hernandez Rodriguez, James C Smith, Andreia S Bernardo

 

 

Quantitative analysis of signaling responses during mouse primordial germ cell specification
Sophie M. Morgani, Anna-Katerina Hadjantonakis

 

Cell competition acts as a purifying selection to eliminate cells with mitochondrial defects during early mouse development
Ana Lima, Gabriele Lubatti, Jörg Burgstaller, Di Hu, Alistair Green, Aida Di Gregorio, Tamzin Zawadzki, Barbara Pernaute, Elmir Mahammadov, Salvador Perez Montero, Marian Dore, Juan Miguel Sanchez, Sarah Bowling, Margarida Sancho, Mohammad Karimi, David Carling, Nick Jones, Shankar Srinivas, Antonio Scialdone, Tristan A. Rodriguez

 

Cell-to-cell heterogeneity in Sox2 and Brachyury expression ratios guides progenitor destiny by controlling their motility.
Michèle Romanos, Guillaume Allio, Léa Combres, Francois Médevielle, Nathalie Escalas, Cathy Soula, Ben Steventon, Ariane Trescases, Bertrand Bénazéraf

 

 

Δ9-tetrahydrocannabinol inhibits Hedgehog-dependent patterning during development
Hsiao-Fan Lo, Mingi Hong, Henrietta Szutorisz, Yasmin L. Hurd, Robert S. Krauss

 

A small increase in CHEK1 activity leads to the arrest of the first zygotic division in human
Beili Chen, Jianying Guo, Ting Wang, Qianhui Lee, Jia Ming, Fangfang Ding, Haitao Li, Zhiguo Zhang, Lin Li, Yunxia Cao, Jie Na

 

 

Cardiac progenitors auto-regulate second heart field cell fate via Wnt secretion
Matthew Miyamoto, Suraj Kannan, Hideki Uosaki, Tejasvi Kakani, Sean Murphy, Peter Andersen, Chulan Kwon

 

Multiple sources of Shh are critical for the generation and scaling of ventral spinal cord oligodendrocyte precursor populations
Lev Starikov, Miruna Ghinia-Tegla, Andreas H. Kottmann

 

 

Scx-positive tendon cells are required for correct muscle patterning
Yudai Ono, Tempei Sato, Chisa Shukunami, Hiroshi Asahara, Masafumi Inui

 

Gradual differentiation uncoupled from cell cycle exit generates heterogeneity in the epidermal stem cell layer
Katie Cockburn, Karl Annusver, Smirthy Ganesan, Kailin R. Mesa, Kyogo Kawaguchi, Maria Kasper, Valentina Greco

 

The role of Gdf5 in the development of the zebrafish fin endoskeleton
Laura Waldmann, Jake Leyhr, Hanqing Zhang, Amin Allalou, Caroline Ohman-Magi, Tatjana Haitina

 

 

Dual expression of Atoh1 and Ikzf2 promotes transformation of adult cochlear supporting cells into outer hair cells
Suhong Sun, Shuting Li, Zhengnan Luo, Minhui Ren, Shunji He, Guangqin Wang, Zhiyong Liu

 

Slit2 is necessary for optic axon organization in the zebrafish ventral midline
Camila Davison, Flavio R. Zolessi

 

Neuroepithelial organoid patterning is mediated by Wnt-driven Turing mechanism
Abdel Rahman Abdel Fattah, Sergei Grebenyuk, Idris Salmon, Adrian Ranga

 

GATA2 deficiency during embryogenesis elevates Interferon Regulatory Factor-8 to subvert a progenitor cell differentiation program
Emery H Bresnick, Kirby D Johnson

 

KIT is required for fetal liver erythropoiesis but dispensable for angiogenesis
Alessandro Fantin, Alice Plein, Carlotta Tacconi, Emanuela Villa, Elena Ceccacci, Laura Denti, Christiana Ruhrberg

 

Microglial Neuropilin-1 trans-regulates oligodendrocyte expansion during development and remyelination
Amin Sherafat, Friederike Pfeiffer, Alexander M. Reiss, William M. Wood, Akiko Nishiyama

 

BMP pathway antagonism by Grem1 regulates epithelial cell fate in intestinal regeneration
Martijn AJ Koppens, Hayley Davis, Gabriel N Valbuena, Eoghan J Mulholland, Nadia Nasreddin, Mathilde Colombe, Agne Antanaviciute, Sujata Biswas, Matthias Friedrich, Lennard Lee, Oxford IBD cohort investigators, Lai Mun Wang, Viktor H Koelzer, James E East, Alison Simmons, Douglas J Winton, Simon J Leedham

 

Differential requirement of NPHP1 for compartmentalized protein localization during photoreceptor outer segment development and maintenance
Poppy Datta, J. Thomas Cribbs, Seongjin Seo

 

Wnt target enhancer regulation by a CDX/TCF transcription factor collective and a novel DNA motif
Aravinda-Bharathi Ramakrishnan, Lisheng Chen, Peter Burby, Ken M. Cadigan

 

 

Zebrafish spinal cord oligodendrocyte formation requires boc function
Bruce Appel, Christina A Kearns, Macie Walker, Andrew M Ravanelli, Kayt Scott, Madeline R Arzbecker

 

FOXO1 and FOXO3 cooperatively regulate innate lymphoid cell development
Thuy T. Luu, Jonas Nørskov Søndergaard, Lucía Peña-Pérez, Shabnam Kharazi, Aleksandra Krstic, Stephan Meinke, Laurent Schmied, Nicolai Frengen, Yaser Heshmati, Marcin Kierczak, Thibault Bouderlique, Arnika Kathleen Wagner, Charlotte Gustafsson, Benedict J. Chambers, Adnane Achour, Claudia Kutter, Petter Höglund, Robert Månsson, Nadir Kadri

 

PEDF and Derived Peptides Prevent Apoptosis and Promote Differentiation of Retinal Photoreceptors
Germán Michelis, Olga Lorena German, Rafael Villasmil, Nora P. Rotstein, Luis Politi, S Patricia Becerra

 

Cep55 regulation of PI3K/Akt signaling is required for neocortical development and ciliogenesis
Behnam Rashidieh, Belal Shohayeb, Amanda Louise Bain, Patrick R. J. Fortuna, Debottam Sinha, Andrew Burgess, Richard Mills, Rachael C. Adams, J. Alejandro Lopez, Peter Blumbergs, John Finnie, Murugan Kalimutho, Michael Piper, James Edward Hudson, Dominic Ng, Kum kum Khanna

 

Hyperoxia Inhibits the Growth of Mouse Forebrain Oligodendrocyte Progenitors
Lisamarie Moore, Lauren E. McLane, Stacey Wahl, Isis M. Ornelas, Teresa L. Wood, Peter Canoll, Steven W. Levison

 

PTEN regulates adipocyte progenitor growth, differentiation and cellular aging
Anna S. Kirstein, Stephanie Kehr, Michèle Nebe, Judith Lorenz, Melanie Penke, Jana Breitfeld, Diana Le Duc, Peter Kovacs, Peter F. Stadler, Wieland Kiess, Antje Garten

 

Vangl2, a core component of the WNT/PCP pathway, regulates adult hippocampal neurogenesis and age-related decline in cognitive flexibility
M Koehl, E Ladevèze, M Montcouquiol, DN Abrous

 

Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons
Laurence Cathala, Celia Biane, Florian Rückerl, David DiGregorio, Ryuichi Shigemoto, Therese Abrahamsson, Cécile Saint-Cloment, Jean Mariani, Rachel M Sherrard

 

Intrinsic network activity in human brain organoids
Tal Sharf, Tjitse van der Molen, Elmer Guzman, Stella M.K. Glasauer, Gabriel Luna, Zhouwei Cheng, Morgane Audouard, Kamalini G. Ranasinghe, Kiwamu Kudo, Srikantan S. Nagarajan, Kenneth R. Tovar, Linda R. Petzold, Paul K. Hansma, Kenneth S. Kosik

 

mTOR inhibition represses transcription of cholesterol biosynthesis genes and alters cholesterol levels in primary neurons and in the developing brain
Martin Schüle, Tamer Butto, Sri Dewi, Susanne Strand, Susanne Gerber, Kristina Endres, Susann Schweiger, Jennifer Winter

 

Mitochondrial fusion regulates proliferation and differentiation in the type II neuroblast lineage in Drosophila
Dnyanesh Dubal, Prachiti Moghe, Bhavin Uttekar, Richa Rikhy

 

Gelsolin and dCryAB act downstream of muscle identity genes and contribute to preventing muscle splitting and branching in Drosophila
Benjamin Bertin, Yoan Renaud, Teresa Jagla, Guillaume Lavergne, Cristiana Dondi, Jean-Philippe Da Ponte, Guillaume Junion, Krzysztof Jagla

 

AP2 regulates Thickveins trafficking through Rab11 to attenuate NMJ growth signaling in Drosophila
Manish Kumar Dwivedi, Saumitra Dey Choudhury, Abhinandan Patnaik, Shirish Mishra, Raghu Padinjat, Vimlesh Kumar

 

Bazooka/Par3 cooperates with Sanpodo for the assembly of Notch signaling clusters following asymmetric division of Drosophila sensory organ precursor cells
Elise Houssin, Mathieu Pinot, Karen Bellec, Roland Le Borgne

 

 

 

| Morphogenesis & mechanics

 

Cell shape anisotropy and motility constrain self-organised feather pattern fidelity in birds
Camille Curantz, Richard Bailleul, Magdalena Hidalgo, Melina Durande, François Graner, Marie Manceau

 

The Biomechanical Basis of Biased Epithelial Tube Elongation in Lung and Kidney Development
Lisa Conrad, Steve Runser, Harold Gomez, Christine Lang, Mathilde Dumont, Aleksandra Sapala, Laura Kramps, Odysse Michos, Roman Vetter, Dagmar Iber

 

Subcellular tube guidance requires anchoring of the apical and basal actin cortices through late endosomes
LD Rios-Barrera, M Leptin

 

Actin dependent membrane polarization reveals the mechanical nature of the neuroblast polarity cycle
Bryce LaFoya, Kenneth E. Prehoda

 

Pulsatile actomyosin contractions underlie Par polarity during the neuroblast polarity cycle
Chet Huan Oon, Kenneth E. Prehoda

 

Septate junction proteins are required for egg elongation and border cell migration during oogenesis in Drosophila
Haifa Alhadyian, Dania Shoaib, Robert Edwin Ward

 

Invivo and systematic analysis of random multigenic deletions associated with human diseases during epithelial morphogenesis in Drosophila
Usha Nagarajan, Shanmugasundaram Pakkiriswami, Sandiya Srinivasan, Niveditha Ramkumar, Rajeswari Rajaraman, Kumarasamy Thangaraj

 

 

Moving patronin foci and growing microtubule plus ends direct the spatiotemporal dynamics of Rho signaling and myosin during apical constriction
Anwesha Guru, Surat Saravanan, Deepanshu Sharma, Maithreyi Narasimha

 

20-hydroxyecdysone (20E) signaling regulates amnioserosa morphogenesis during Drosophila dorsal closure: Ecdysone receptor modulates gene expression in a complex with the AP-1 component, Jun
Byoungjoo Yoo, Hae-yoon Kim, Xi Chen, Weiping Shen, Ji Sun Jang, Olga Cormier, Charles Krieger, Bruce Reed, Nicholas Harden, Simon Ji Hau Wang

 

Mechanical control of morphogenetic robustness in an inherently challenging environment
Emmanuel Martin, Sophie Theis, Guillaume Gay, Bruno Monier, Christian Rouvière, Magali Suzanne

 

Ataxin-2 is essential for neurodevelopment in Drosophila and is a major regulator of the cytoskeleton
Urko del Castillo, Rosalind Norkett, Anna Serpinskaya, Vladimir I. Gelfand

 

Eya1-dependent homeostasis of morphogenetic territories during collective cell migration
Hernan Lopez-Schier, Matthias Hammerschmidt, Koichi Kawakami, Filipe Pinto Teixeira, Jeronimo R Miranda Rodriguez, Augusto Borges, Indra Wibowo

 

Functional plasticity of polarity proteins controls epithelial tissue architecture
Cornélia Biehler, Katheryn E. Rothenberg, Alexandra Jetté, Hélori-Mael Gaudé, Rodrigo Fernandez-Gonzalez, Patrick Laprise

 

Rapid assembly of a polar network architecture drives efficient actomyosin contractility
Vlad Costache, Serena Prigent Garcia, Camille N. Plancke, Jing Li, Simon Begnaud, Shashi Kumar Suman, Anne-Cécile Reymann, Taeyoon Kim, François B. Robin

 

Yolk platelets impede nuclear expansion in Xenopus embryos
Sora Shimogama, Yasuhiro Iwao, Yuki Hara

 

 

Physically asymmetric division of the C. elegans zygote ensures invariably successful embryogenesis
Radek Jankele, Rob Jelier, Pierre Gönczy

 

CYK-1/Formin activation in cortical RhoA signaling centers promotes organismal left-right symmetry breaking
Teije C. Middelkoop, Júlia Garcia-Baucells, Porfirio Quintero-Cadena, Lokesh G. Pimpale, Shahrzad Yazdi, Paul Sternberg, Peter Gross, Stephan W. Grill

 

 

The Ran pathway uniquely regulates cytokinesis in cells with different fates in the early C. elegans embryo
Imge Ozugergin, Karina Mastronardi, Chris Law, Alisa Piekny

 

Regulation of apical constriction via microtubule- and Rab11-dependent apical transport during tissue invagination
Thao Phuong Le, SeYeon Chung

 

The recycling endosome protein Rab25 coordinates collective cell movements in the zebrafish surface epithelium
Patrick Morley Willoughby, Molly Allen, Jessica Yu, Roman Korytnikov, Tianhui Chen, Yupeng Liu, Isis So, Neil Macpherson, Jennifer Mitchell, Rodrigo Fernandez-Gonzalez, Ashley E. E. Bruce

 

The Amot/Integrin protein complex transmits mechanical forces required for vascular expansion
Yuanyuan Zhang, Yumeng Zhang, Sumako Kameishi, Giuseppina Barutello, Yujuan Zheng, Nicholas P. Tobin, John Nicosia, Katharina Hennig, David Kung-Chun Chiu, Martial Balland, Thomas H. Barker, Federica Cavallo, Lars Holmgren

 

 

Bulkhead-like apical membrane structures between hepatocytes are required for anisotropic lumen expansion and liver tissue morphogenesis
Lenka Belicova, Urska Repnik, Julien Delpierre, Elzbieta Gralinska, Sarah Seifert, José Ignacio Valenzuela, Hernán Andrés Morales-Navarrete, Christian Franke, Helin Räägel, Evgeniya Shcherbinina, Tatiana Prikazchikova, Victor Koteliansky, Martin Vingron, Yannis Kalaidzidis, Timofei Zatsepin, Marino Zerial

 

Convergent extension requires adhesion-dependent biomechanical integration of cell crawling and junction contraction
Shinuo Weng, Robert J. Huebner, John B. Wallingford

 

A two-phase model of skin epidermal stratification: lessons from centrosomes
Mareike Damen, Lisa Wirtz, Ekaterina Soroka, Houda Khatif, Christian Kukat, Benjamin D. Simons, Hisham Bazzi

 

Endothelial NRP2 influences angiogenesis by regulating actin pattern development and α5-integrin-p-FAK complex recruitment to assembling adhesion sites
Christopher J Benwell, James AGE Taylor, Stephen D Robinson

 

Muscle-specific Cavin4 interacts with Bin1 to promote T-tubule formation and stability in developing skeletal muscle
Harriet P. Lo, Ye-Wheen Lim, Zherui Xiong, Nick Martel, Charles Ferguson, Nicholas R. Ariotti, Jean Giacomotto, James A. Rae, Matthias Floetenmeyer, Shayli Varasteh Moradi, Ya Gao, Vikas A. Tillu, Di Xia, Huang Wang, Samira Rahnama, Susan J. Nixon, Michele Bastiani, Ryan D. Day, Kelly A. Smith, Nathan J. Palpant, Wayne A. Johnston, Kirill Alexandrov, Brett M. Collins, Thomas E. Hall, Robert G. Parton

 

Lrrcc1 and Ccdc61 are conserved effectors of multiciliated cell function
Aude Nommick, Camille Boutin, Olivier Rosnet, Elsa Bazellieres, Virginie Thome, Etienne Loiseau, Annie Viallat, Laurent Kodjabachian

 

Basal epidermis collective migration and local Sonic hedgehog signaling promote skeletal branching morphogenesis in zebrafish fins
Joshua A. Braunstein, Amy E. Robbins, Scott Stewart, Kryn Stankunas

 

Mechanics of the cellular microenvironment as perceived by cells in vivo
Alessandro Mongera, Marie Pochitaloff, Hannah J. Gustafson, Georgina A. Stooke-Vaughan, Payam Rowghanian, Otger Campàs

 

High resolution, dynamic imaging of early mouse and human liver bud morphogenesis in three dimensions
Tala Mon, Ogechi Ogoke, Daniel Guiggey, Claire Shamul, Shatoni Ross, Saroja Rao, Natesh Parashurama

 

 

In-frame deletion of SPECC1L microtubule binding domain results in embryonic tissue movement and fusion defects
Jeremy P. Goering, Luke W. Wenger, Marta Stetsiv, Michael Moedritzer, Everett G. Hall, Dona Greta Isai, Brittany Jack, Zaid Umar, Madison K. Rickabaugh, Andras Czirok, Irfan Saadi

 

Cell cycle-dependent active stress drives epithelia remodeling
John Devany, Daniel M. Sussman, Takaki Yamamoto, M. Lisa Manning, Margaret L. Gardel

 

 

 

| Genes & genomes

 

Unveiling unexpected complexity and multipotentiality of early heart fields
Qingquan Zhang, Daniel Carlin, Fugui Zhu, Paola Cattaneo, Trey Ideker, Sylvia Evans, Joshua Bloomekatz, Neil C Chi

 

Spatiotemporal transcriptional dynamics of the cycling mouse oviduct
Elle C. Roberson, Anna M. Battenhouse, Riddhiman K. Garge, Ngan Kim Tran, Edward M. Marcotte, John B. Wallingford

 

Semi-coordinated allelic-bursting shape dynamic random monoallelic expression in pre-gastrulation embryos
C H Naik, K Hari, D Chandel, S Mandal, M K Jolly, S Gayen

 

 

Hox genes regulate asexual reproductive behavior and tissue segmentation in adult animals
Christopher P. Arnold, Analí Migueles Lozano, Frederick G. Mann Jr., Jeffrey J. Lange, Christopher Seidel, Alejandro Sánchez Alvarado

 

Zebrafish Polycomb repressive complex-2 critical roles are largely Ezh2- over Ezh1-driven and concentrate during early embryogenesis
Gabriel A. Yette, Scott Stewart, Kryn Stankunas

 

Transcriptome profile of the zebrafish atrioventricular canal reveals molecular signatures of pacemaker and valve mesenchyme
Abu Nahia Karim, Migdał Maciej, Quinn T. Alexander, Poon Kar-Lai, Łapinski Maciej, Sulej Agata, Pawlak Michał, Bugajski Łukasz, Piwocka Katarzyna, Brand Thomas, Kohl Peter, Korzh Vladimir, Winata Cecilia

 

Production of functional oocytes requires maternally expressed PIWI genes and piRNAs in golden hamsters
Hidetoshi Hasuwa, Yuka W Iwasaki, Au Yeung Wan Kin, Kyoko Ishino, Harumi Masuda, Hiroyuki Sasaki, Haruhiko Siomi

 

 

Polycomb suppresses a female gene regulatory network in Sertoli cells
So Maezawa, Masashi Yukawa, Kazuteru Hasegawa, Ryo Sugiyama, Mengwen Hu, Miguel Vidal, Haruhiko Koseki, Artem Barski, Tony DeFalco, Satoshi H. Namekawa

 

Altered temporal sequence of transcriptional regulators in the generation of human cerebellar granule cells
Hourinaz Behesti, Arif Kocabas, David E. Buchholz, Thomas S. Carroll, Mary E. Hatten

 

Universal DNA methylation age across mammalian tissues
MAMMALIAN METHYLATION CONSORTIUM, Ake T. Lu, Zhe Fei, Amin Haghani, Todd R. Robeck, Joseph A. Zoller, Caesar Z. Li, Joshua Zhang, Julia Ablaeva, Danielle M. Adams, Javier Almunia, Reza Ardehali, Adriana Arneson, C. Scott Baker, Katherine Belov, Pete Black, Daniel T. Blumstein, Eleanor K. Bors, Charles E. Breeze, Robert T. Brooke, Janine L. Brown, Alex Caulton, Julie M. Cavin, Ioulia Chatzistamou, Hao Chen, Priscila Chiavellini, Oi-Wa Choi, Shannon Clarke, Joseph DeYoung, Christopher Dold, Candice K. Emmons, Stephan Emmrich, Chris G. Faulkes, Steven H. Ferguson, Carrie J. Finno, Jean-Michel Gaillard, Eva Garde, Vadim N. Gladyshev, Vera Gorbunova, Rodolfo G. Goya, Matthew J Grant, Erin N. Hales, M. Bradley Hanson, Martin Haulena, Andrew N. Hogan, Carolyn J. Hogg, Timothy A. Hore, Anna J. Jasinska, Gareth Jones, Eve Jourdain, Olga Kashpur, Harold Katcher, Etsuko Katsumata, Vimala Kaza, Hippokratis Kiaris, Michael S. Kobor, Pawel Kordowitzki, William R. Koski, Brenda Larison, Sang-Goo Lee, Ye C. Lee, Marianne Lehmann, Jean-Francois Lemaitre, Andrew J. Levine, Cun Li, Xinmin Li, David TS Lin, Nicholas Macoretta, Dewey Maddox, Craig O. Matkin, Julie A. Mattison, June Mergl, Jennifer J. Meudt, Khyobeni Mozhui, Asieh Naderi, Martina Nagy, Pritika Narayan, Peter W. Nathanielsz, Ngoc B. Nguyen, Christof Niehrs, Alexander G. Ophir, Elaine A. Ostrander, Perrie O’Tierney Ginn, Kim M. Parsons, Kimberly C. Paul, Matteo Pellegrini, Gabriela M. Pinho, Jocelyn Plassais, Natalia A. Prado, Benjamin Rey, Beate R. Ritz, Jooke Robbins, Magdalena Rodriguez, Jennifer Russell, Elena Rydkina, Lindsay L. Sailer, Adam B. Salmon, Akshay Sanghavi, Kyle M. Schachtschneider, Dennis Schmitt, Todd Schmitt, Lars Schomacher, Lawrence B. Schook, Karen E. Sears, Andrei Seluanov, Dhanansayan Shanmuganayagam, Anastasia Shindyapina, Kavita Singh, Ishani Sinha, Russel G. Snell, Elham Soltanmaohammadi, Matthew L. Spangler, Lydia Staggs, Karen J. Steinman, Victoria J. Sugrue, Balazs Szladovits, Masaki Takasugi, Emma C. Teeling, Michael J. Thompson, Bill Van Bonn, Sonja C. Vernes, Diego Villar, Harry V. Vinters, Mary C. Wallingford, Nan Wang, Robert K. Wayne, Gerald S. Wilkinson, Christopher K. Williams, Robert W. Williams, X. William Yang, Brent G. Young, Bohan Zhang, Zhihui Zhang, Peng Zhao, Yang Zhao, Joerg Zimmermann, Wanding Zhou, Jason Ernst, Ken Raj, Steve Horvath

 

A sexual dimorphic role of the miR-465 cluster in placental development
Zhuqing Wang, Nan Meng, Yue Wang, Tong Zhou, Musheng Li, Shawn Wang, Sheng Chen, Huili Zheng, Shuangbo Kong, Haibin Wang, Wei Yan

 

Meiosis-specific ZFP541 repressor complex promotes meiotic prophase exit during spermatogenesis
Yuki Horisawa-Takada, Chisato Kodera, Kazumasa Takemoto, Akihiko Sakashita, Kenichi Horisawa, Ryo Maeda, Shingo Usuki, Sayoko Fujimura, Naoki Tani, Kumi Matsuura, Ryuki Shimada, Tomohiko Akiyama, Atsushi Suzuki, Hitoshi Niwa, Makoto Tachibana, Takashi Ohba, Hidetaka Katabuchi, Satoshi H. Namekawa, Kimi Araki, Kei-ichiro Ishiguro

 

Codon composition in human oocytes reveals age-associated defects in mRNA decay
Nehemiah S. Alvarez, Pavla Brachova, Lane K. Christenson

 

Multiple RNA regulatory pathways coordinate the activity and expression pattern of a conserved germline RNA-binding protein
Mennatallah M.Y. Albarqi, Sean P. Ryder

 

A miR-124-mediated post-transcriptional mechanism controlling the cell fate switch of astrocytes to induced-neurons
Elsa Papadimitriou, Paraskevi N. Koutsoudaki, Timokratis Karamitros, Dimitra Karagkouni, Dafni Chroni-Tzartou, Christos Gkemisis, Maria Margariti, Evangelia Xingi, Irini Thanou, Socrates J. Tzartos, Artemis G. Hatzigeorgiou, Dimitra Thomaidou

 

Identification of TIA1 mRNA targets during human neuronal development
Loryn P. Byres, Marat Mufteev, Kyoko E. Yuki, Wei Wei, Alina Piekna, Michael D. Wilson, Deivid C. Rodrigues, James Ellis

 

Dnmt3a knockout in excitatory neurons impairs postnatal synapse maturation and is partly compensated by repressive histone modification H3K27me3
Junhao Li, Antonio Pinto-Duarte, Mark Zander, Chi-Yu Lai, Julia Osteen, Linjing Fang, Chongyuan Luo, Jacinta D. Lucero, Rosa Gomez-Castanon, Joseph R. Nery, Isai Silva-Garcia, Yan Pang, Terrence J. Sejnowski, Susan B. Powell, Joseph R. Ecker, Eran A. Mukamel, M. Margarita Behrens

 

Complexity and graded regulation of neuronal cell type-specific alternative splicing revealed by single-cell RNA sequencing
Huijuan Feng, Daniel F Moakley, Shuonan Chen, Melissa G McKenzie, Vilas Menon, Chaolin Zhang

 

 

The chromatin remodelling factor Chd7 protects auditory neurons and sensory hair cells from stress-induced degeneration
Mohi Ahmed, Ruth Moon, Ravindra Singh Prajapati, Elysia James, M. Albert Basson, Andrea Streit

 

Loss of Foxc1 and Foxc2 function in chondroprogenitor cells disrupts endochondral ossification.
Asra Almubarak, Rotem Lavy, Nikola Srnic, Yawen Hu, Devi P Maripuri, Tsutomo Kume, Fred B Berry

 

Control of neurogenic competence in mammalian hypothalamic tanycytes
Sooyeon Yoo, Juhyun Kim, Pin Lyu, Thanh V. Hoang, Alex Ma, Vickie Trinh, Weina Dai, Lizhi Jiang, Patrick Leavey, Jae-Kyung Won, Sung-Hye Park, Jiang Qian, Solange P. Brown, Seth Blackshaw

 

Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution
Alexandro E. Trevino, Fabian Müller, Jimena Andersen, Laksshman Sundaram, Arwa Kathiria, Anna Shcherbina, Kyle Farh, Howard Y. Chang, Anca M. Paşca, Anshul Kundaje, Sergiu P. Paşca, William J. Greenleaf

 

Cell type resolved co-expression networks of core clock genes in brain development
Surbhi Sharma, Asgar Hussain Ansari, Soundhar Ramasamy

 

Dicer promotes genome stability via the bromodomain transcriptional co-activator Brd4
MJ Gutbrod, B Roche, JI Steinberg, AA Lakhani, K Chang, AJ Schorn, RA Martienssen

 

Single-cell transcriptome lineage tracing of human pancreatic development identifies distinct developmental trajectories of alpha and beta cells
Li Lin, Yufeng Zhang, Weizhou Qian, Yao Liu, Yingkun Zhang, Fanghe Lin, Cenxi Liu, Guangxing Lu, YanLing Song, Jia Song, Chaoyong Yang, Jin Li

 

Single Cell Enhancer Activity Maps Neuronal Lineages in Embryonic Mouse Basal Ganglia
Linda Su-Feher, Anna N. Rubin, Shanni N. Silberberg, Rinaldo Catta-Preta, Kenneth J. Lim, Iva Zdilar, Christopher S. McGinnis, Gabriel L. McKinsey, Thomas E. Rubino Jr., Michael Hawrylycz, Carol Thompson, Zev J. Gartner, Luis Puelles, Hongkui Zeng, John L. R. Rubenstein, Alex S. Nord

 

A Single Cell Atlas of Lung Development
Nicholas M Negretti, Erin J Plosa, John T Benjamin, Bryce A Schuler, A. Christian Habermann, Christopher S Jetter, Chase J Taylor, Peter Gulleman, David Nichols, Brittany K Matlock, Susan H Guttentag, Timothy S Blackwell, Nicholas E Banovich, Jonathan A Kropski, Jennifer MS Sucre

 

Molecular profiling of retinal pigment epithelial cell differentiation for therapeutic use
Sandra Petrus-Reurer, Alex R Lederer, Laura Baqué-Vidal, Iyadh Douagi, Belinda Pannagel, Monica Aronsson, Hammurabi Bartuma, Magdalena Wagner, Helder André, Erik Sundström, Aparna Bhaduri, Arnold Kriegstein, Anders Kvanta, Gioele La Manno, Fredrik Lanner

 

Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process
Keiichiro Koiwai, Takashi Koyama, Soichiro Tsuda, Atsushi Toyoda, Kiyoshi Kikuchi, Hiroaki Suzuki, Ryuji Kawano

 

A single cell atlas reveals unanticipated cell type complexity in Drosophila ovaries
Maija Slaidina, Selena Gupta, Ruth Lehmann

 

Single-cell sequencing of the Drosophila embryonic heart and muscle cells during differentiation and maturation
Georg Vogler, Bill Hum, Marco Tamayo, Yoav Altman, Rolf Bodmer

 

 

Ubx orchestrates tissue identity through regional and bidirectional changes to chromatin accessibility
Ryan Loker, Jordyn E. Sanner, Richard S. Mann

 

 

DamID transcriptional profiling identifies the Snail/Scratch transcription factor Kahuli as Alk target in the Drosophila visceral mesoderm
Patricia Mendoza-Garcia, Swaraj Basu, Sanjay Kumar Sukumar, Badrul Arefin, Georg Wolfstetter, Vimala Anthonydhason, Linnea Molander, Henrik Lindehell, Jan Larsson, Erik Larsson, Mats Bemark, Ruth H. Palmer

 

GAF is essential for zygotic genome activation and chromatin accessibility in the early Drosophila embryo
Marissa M. Gaskill, Tyler J. Gibson, Elizabeth D. Larson, Melissa M. Harrison

 

Genetic variation among wMel strains of Wolbachia pipientis differentially rescues a bag of marbles partial loss of function mutant in Drosophila melanogaster
Jaclyn E. Bubnell, Paula Fernandez-Begne, Cynthia K. Ulbing, Charles F. Aquadro

 

Proapoptotic RHG genes and mitochondria play a key non-apoptotic role in remodelling the Drosophila sensory system
Amrita Mukherjee, Sinziana Pop, Shu Kondo, Darren W Williams

 

High levels of Dorsal transcription factor downregulate, not promote, snail expression by regulating enhancer action
Jihyun Irizarry, James McGehee, Angelike Stathopoulos

 

 

 

| Stem cells, regeneration & disease modelling

Self-organized stem cell-derived human lung buds with proximo-distal patterning and novel targets of SARS-CoV-2
E.A. Rosado-Olivieri, B. Razooky, H.-H. Hoffmann, R. De Santis, C.M. Rice, A.H Brivanlou

 

 

Multiplexed live visualization of cell fate dynamics in hPSCs at single-cell resolution
Sungmin Kim, Edward Ren, Paola Marco Casanova, Eugenia Piddini, Rafael Edgardo Carazo Salas

 

BMP-treated human embryonic stem cells transcriptionally resemble amnion cells in the monkey embryo
Sapna Chhabra, Aryeh Warmflash

 

Cell-cell communication through FGF4 generates and maintains robust proportions of differentiated cell types in embryonic stem cells
Dhruv Raina, Azra Bahadori, Angel Stanoev, Michelle Protzek, Aneta Koseska, Christian Schröter

 

 

Fish primary embryonic stem cells self-assemble into retinal tissue mirroring in vivo early eye development
Lucie Zilova, Venera Weinhardt, Tinatini Tavhelidse, Thomas Thumberger, Joachim Wittbrodt

 

Constitutive high expression of NOXA sensitizes human embryonic stem cells for rapid cell death
Richa Basundra, Sahil Kapoor, Emilie Hollville, Nazanin Kiapour, Adriana Beltran Lopez, Nicole Marie Melchiorre, Mohanish Deshmukh

 

A signaling axis involving CNOT3, Aurora B and ERK promotes mesendodermal differentiation of ES cells
Moumita Sarkar, Matteo Martufi, Monica Roman-Trufero, Yi-Fang Wang, Chad Whilding, Dirk Dormann, Pierangela Sabbattini, Niall Dillon

 

Cell cycle exit and stem cell differentiation are coupled through regulation of mitochondrial activity in the Drosophila testis
Diego Sainz de la Maza, Silvana Hof-Michel, Lee Phillimore, Christian Bökel, Marc Amoyel

 

Human induced pluripotent stem cell-derived three-dimensional cardiomyocyte tissues ameliorate the rat ischemic myocardium by remodeling the extracellular matrix and cardiac protein phenotype
Junya Yokoyama, Shigeru Miyagawa, Takami Akagi, Mitsuru Akashi, Yoshiki Sawa

 

Nuclear m6A reader Ythdc1 regulates the scaffold function of LINE1 in mouse ESCs
Chuan Chen, Wenqiang Liu, Jiayin Guo, Yuanyuan Liu, Xuelian Liu, Jun Liu, Xiaoyang Dou, Rongrong Le, Yixin Huang, Chong Li, Lingyue Yang, Xiaochen Kou, Yanhong Zhao, You Wu, Jiayu Chen, Hong Wang, Bin Shen, Yawei Gao, Shaorong Gao

 

Robust integrated intracellular organization of the human iPS cell: where, how much, and how variable
Matheus P. Viana, Jianxu Chen, Theo A. Knijnenburg, Ritvik Vasan, Calysta Yan, Joy E. Arakaki, Matte Bailey, Ben Berry, Antoine Borensztejn, Jackson M. Brown, Sara Carlson, Julie A. Cass, Basudev Chaudhuri, Kimberly R. Cordes Metzler, Mackenzie E. Coston, Zach J. Crabtree, Steve Davidson, Colette M. DeLizo, Shailja Dhaka, Stephanie Q. Dinh, Thao P. Do, Justin Domingus, Rory M. Donovan-Maiye, Tyler J. Foster, Christopher L. Frick, Griffin Fujioka, Margaret A. Fuqua, Jamie L. Gehring, Kaytlyn A. Gerbin, Tanya Grancharova, Benjamin W. Gregor, Lisa J. Harrylock, Amanda Haupt, Melissa C. Hendershott, Caroline Hookway, Alan R. Horwitz, Chris Hughes, Eric J. Isaac, Gregory R. Johnson, Brian Kim, Andrew N. Leonard, Winnie W. Leung, Jordan J. Lucas, Susan A. Ludmann, Blair M. Lyons, Haseeb Malik, Ryan McGregor, Gabe E. Medrash, Sean L. Meharry, Kevin Mitcham, Irina A. Mueller, Timothy L. Murphy-Stevens, Aditya Nath, Angelique M. Nelson, Luana Paleologu, T. Alexander Popiel, Megan M. Riel-Mehan, Brock Roberts, Lisa M. Schaefbauer, Magdalena Schwarzl, Jamie Sherman, Sylvain Slaton, M. Filip Sluzewski, Jacqueline E. Smith, Youngmee Sul, Madison J. Swain-Bowden, W. Joyce Tang, Derek J. Thirstrup, Daniel M. Toloudis, Andrew P. Tucker, Veronica Valencia, Winfried Wiegraebe, Thushara Wijeratna, Ruian Yang, Rebecca J. Zaunbrecher, Allen Institute for Cell Science, Graham T. Johnson, Ruwanthi N. Gunawardane, Nathalie Gaudreault, Julie A. Theriot, Susanne M. Rafelski

 

Identification of X-chromosomal genes that drive global X-dosage effects in mouse embryonic stem cells
Oriana Genolet, Anna A. Monaco, Ilona Dunkel, Michael Boettcher, Edda G. Schulz

 

 

Neural stem cells alter nucleocytoplasmic partitioning and accumulate nuclear polyadenylated transcripts during quiescence
A. Rossi, A. Coum, M. Madelenat, L. Harris, A. Miedzik, S. Strohbuecker, A. Chai, H. Fiaz, R. Chaouni, P. Faull, W. Grey, D. Bonnet, E. V. Makeyev, A. P. Snijders, G. Kelly, F. Guillemot, R. Sousa-Nunes

 

Standardized quality control workflow to evaluate the reproducibility and differentiation potential of human iPSCs into neurons
Carol X.-Q. Chen, Narges Abdian, Gilles Maussion, Rhalena A. Thomas, Iveta Demirova, Eddie Cai, Mahdieh Tabatabaei, Lenore K. Beitel, Jason Karamchandani, Edward A. Fon, Thomas M. Durcan

 

Dynamic adult tracheal plasticity drives stem cell adaptation to changes in intestinal homeostasis.
Jessica Perochon, Gabriel N Aughey, Tony Southall, Julia B Cordero

 

Pannexin 1 influences lineage specification of human iPSCs
Rebecca J. Noort, Grace A. Christopher, Jessica L. Esseltine

 

HLF Expression Defines the Human Hematopoietic Stem Cell State
Bernhard Lehnertz, Jalila Chagraoui, Tara MacRae, Elisa Tomellini, Sophie Corneau, Nadine Mayotte, Isabel Boivin, Guy Sauvageau

 

Induced neural differentiation of human mesenchymal stem cells affects lipid metabolism pathways
Pnina Green, Inna Kan, Ronit Mesilati-Stahy, Nurit Argov-Argaman, Daniel Offen

 

Engineering a niche supporting haematopoietic stem cell development using integrated single cell transcriptomics
Brandon Hadland, Barbara Varnum-Finney, Stacey Dozono, Tessa Dignum, Cynthia Nourigat-McKay, Dana L Jackson, Tomer Itkin, Jason M. Butler, Shahin Rafii, Cole Trapnell, Irwin D. Bernstein

 

Detection of hematopoietic stem cell transcriptome in human fetal kidneys and kidney organoids derived from human induced pluripotent stem cells (iPSC)
Jin Wook Hwang, Christophe Desterke, Julien Loisel-Duwattez, Frank Griscelli, Annelise Bennaceur-Griscelli, Ali G Turhan

 

Megakaryocyte Progenitor Cell Function is Enhanced Upon Aging Despite the Functional Decline of Aged Hematopoietic Stem Cells
Donna Poscablo, Atesh Worthington, Stephanie Smith-Berdan, Camilla Forsberg

 

Characterization in mice of the stromal niche maintaining AT2 stem cell self-renewal in homeostasis and disease
Sara Taghizadeh, Monika Heiner, Jochen Wilhelm, Susanne Herold, Chengshui Chen, JinSan Zhang, Saverio Bellusci

 

Y705 and S727 are required for mitochondrial import and transcriptional activities of STAT3 and regulate proliferation of embryonic and tissue stem cells
Margherita Peron, Giacomo Meneghetti, Alberto Dinarello, Laura Martorano, Riccardo M. Betto, Nicola Facchinello, Annachiara Tesoriere, Natascia Tiso, Graziano Martello, Francesco Argenton

 

ACVR1R206H increases osteogenic/ECM gene expression and impairs myofiber formation in human skeletal muscle stem cells
Emilie Barruet, Steven M. Garcia, Jake Wu, Blanca M. Morales, Stanley Tamaki, Tania Moody, Jason H. Pomerantz, Edward C. Hsiao

 

Histone Deacetylase 2 (HDAC2) influences maturation and mitochondrial dynamics in human induced pluripotent stem cell derived neurons
Harald Frankowski, Fred Yeboah, Bonnie J. Berry, Chizuru Kinoshita, Michelle Lee, Kira Evitts, Joshua Davis, Yoshito Kinoshita, Richard S. Morrison, Jessica E. Young

 

Trajectory reconstruction identifies dysregulation of perinatal maturation programs in pluripotent stem cell-derived cardiomyocytes
Suraj Kannan, Matthew Miyamoto, Brian L Lin, Chulan Kwon

 

In-depth analysis of proteomic and genomic fluctuations during the time course of human embryonic stem cells directed differentiation into beta cells
Bogdan Budnik, Juerg Straubhaar, John Neveu, Dmitry Shvartsman

 

 

Remodeling of oxygen-transporting tracheoles drives intestinal regeneration and tumorigenesis
Vasilia Tamamouna, M. Mahidur Rahman, Monika Petersson, Irini Charalambous, Kristina Kux, Hannah Mainor, Verena Bolender, Buse Isbilir, Bruce A. Edgar, Chrysoula Pitsouli

 

In vivo proximity labeling identifies cardiomyocyte protein networks during zebrafish heart regeneration
Mira I. Pronobis, Susan Zheng, Sumeet P. Singh, Kenneth D. Poss

 

Hydrodynamic stress and phenotypic plasticity of the zebrafish regenerating fin
Paule Dagenais, Simon Blanchoud, David Pury, Catherine Pfefferli, Tinri Aegerter-Wilmsen, Christof M. Aegerter, Anna Jaźwińska

 

Extracellular histones, a new class of inhibitory molecules of CNS axonal regeneration
Mustafa M. Siddiq, Sari S. Hannila, Yana Zorina, Elena Nikulina, Vera Rabinovich, Jianwei Hou, Rumana Huq, Erica L. Richman, Rosa E. Tolentino, Jens Hansen, Adam Velenosi, Brian K. Kwon, Stella E. Tsirka, Ian Maze, Robert Sebra, Ravi Iyengar, Marie T. Filbin

 

 

DDX24, a D-E-A-D box RNA helicase, is required for muscle fiber organization and anterior pole specification essential for head regeneration in planarians
Souradeep R. Sarkar, Vinay Kumar Dubey, Anusha Jahagirdar, Vairavan Lakshmanan, Mohamed Mohamed Haroon, Sai Sowndarya, Ramanathan Sowdhamini, Dasaradhi Palakodeti

 

Formation and Spontaneous Long-Term Repatterning of Headless Planarian Flatworms
Johanna Bischof, Jennifer V. LaPalme, Kelsie A. Miller, Junji Morokuma, Katherine B. Williams, Chris Fields, Michael Levin

 

Neutrophil extracellular traps impair regeneration
Eric Wier, Mayumi Asada, Gaofeng Wang, Martin P. Alphonse, Ang Li, Chase Hintelmann, Christine Youn, Brittany Pielstick, Roger Ortines, Lloyd S. Miller, Nathan K. Archer, Luis A. Garza

 

Ischemic tolerance and cardiac repair in the African spiny mouse
Tim Koopmans, Henriette van Beijnum, Elke F. Roovers, Divyanshu Malhotra, Antonio Tomasso, Jochem Boeter, Danielle Versteeg, Eva van Rooij, Kerstin Bartscherer

 

Inhibition of BMP and FGF signaling prior to wound epithelium formation leads to an aberrant regenerative response in teleost fish Poecilia latipinna
Isha Ranadive, Sonam Patel, Siddharth Pai, Kashmira Khaire, Suresh Balakrishnan

 

Coupled myovascular expansion directs growth and regeneration of the neonatal mouse heart
Paige DeBenedittis, Anish Karpurapu, Albert Henry, Michael C Thomas, Timothy J McCord, Kyla Brezitski, Anil Prasad, Yoshihiko Kobayashi, Svati H Shah, Christopher D Kontos, Purushothama Rao Tata, R Thomas Lumbers, Ravi Karra

 

Midkine-a regulates the formation of a fibrotic scar during zebrafish heart regeneration
Dimitrios Grivas, Alvaro Gonzalez-Rajal, Jose Luis de la Pompa

 

Forebrain Shh overexpression improves cognitive function in a Down syndrome mouse model and euploid littermates
Feng J. Gao, Donna Klinedinst, Bei Cheng, Alena Savonenko, Benjamin Devenney, Yicong Li, Dan Wu, Martin G. Pomper, Roger H. Reeves

 

Efficient GNE myopathy disease modeling with mutation specific phenotypes in human pluripotent stem cells by base editors
Ju-Chan Park, Jumee Kim, Hyun-Ki Jang, Seung-Yeon Lee, Keun-Tae Kim, Seokwoo Park, Hyun Sik Lee, Hee-Jung Choi, Soon-Jung Park, Sung-Hwan Moon, Sangsu Bae, Hyuk-Jin Cha

 

Reduced axon caliber in the associative striatum of the Sapap3 knockout mouse
E. Lousada, M. Boudreau, J. Cohen-Adad, B. Nait Oumesmar, E. Burguière, C. Schreiweis

 

Increased cortical volume without increased neuron number in heterozygous Chd8 mutant mouse cortex
Cesar P. Canales, Samuel Frank, Jeffrey Bennett, Paris Beauregard, Pierre Lavenex, David G. Amaral, Alex. S. Nord

 

An activating mutation in Pdgfrb causes skeletal stem cell defects with osteopenia and overgrowth in mice
Hae Ryong Kwon, Jang H. Kim, John P. Woods, Lorin E. Olson

 

Extracellular Matrix Dysfunction in Sorsby Patient-Derived Retinal Pigment Epithelium
Abbi L. Engel, YeKai Wang, Thomas H. Khuu, Emily Worrall, Megan A. Manson, Kaitlen Knight, Aya Yanagida, Jian Hua Qi, Aravind Ramakrishnan, Richard G Weleber, Michael L. Klein, David J. Wilson, Bela Anand-Apte, James B. Hurley, Jianhai Du, Jennifer R. Chao

 

Myogenesis defects in a patient-derived iPSC model of hereditary GNE myopathy
Rebecca E Schmitt, Douglas Y Smith IV, Dong Seong Cho, Lindsey A Kirkeby, Zachary T Resch, Teerin Liewluck, Zhiyv Niu, Margherita Milone, Jason D Doles

 

Developmental and behavioral phenotypes in a new mouse model of DDX3X syndrome
Andrea Boitnott, Dévina C Ung, Marta Garcia-Forn, Kristi Niblo, Danielle Mendonca, Michael Flores, Sylvia Maxwell, Jacob Ellegood, Lily R Qiu, Dorothy E Grice, Jason P Lerch, Mladen-Roko Rasin, Joseph D Buxbaum, Elodie Drapeau, Silvia De Rubeis

 

 

 

| Plant development

 

A hetero-oligomeric remorin-receptor complex regulates plant development
Nikolaj B. Abel, Corinna A. Buschle, Casandra Hernandez-Ryes, Sandy S. Burkart, Anne-Flore Deroubaix, Julia Mergner, Julien Gronnier, Iris K. Jarsch, Jessica Folgmann, Karl Heinz Braun, Emmanuelle Bayer, Véronique Germain, Paul Derbyshire, Frank L.H. Menke, Birgit Kemmerling, Cyril Zipfel, Bernhard Küster, Sébastien Mongrand, Macarena Marín, Thomas Ott

 

MicroRNA775 targets a β-(1,3)-galactosyltransferase to regulate growth and development in Arabidopsis thaliana
Parneeta Mishra, Akanksha Singh, Ashwani Kumar Verma, Rajneesh Singh, Sribash Roy

 

A conserved regulatory module regulates receptor kinase signaling in immunity and development
Thomas A. DeFalco, Pauline Anne, Sean R. James, Andrew Willoughby, Oliver Johanndrees, Yasmine Genolet, Anne-Marie Pullen, Cyril Zipfel, Christian S. Hardtke, Zachary L. Nimchuk

 

An autoregulatory negative feedback loop controls thermomorphogenesis in Arabidopsis
Sanghwa Lee, Ling Zhu, Enamul Huq

 

The LEAFY floral regulator displays pioneer transcription factor properties
Xuelei Lai, Romain Blanc-Mathieu, Loïc GrandVuillemin, Ying Huang, Arnaud Stigliani, Jérémy Lucas, Emmanuel Thévenon, Jeanne Loue-Manifel, Hussein Daher, Eugenia Brun-Hernandez, Gilles Vachon, David Latrasse, Moussa Benhamed, Renaud Dumas, Chloe Zubieta, François Parcy

 

The lncRNA APOLO interacts with the transcription factor WRKY42 to trigger root hair cell expansion in response to cold
Michaël Moison, Javier Martínez Pacheco, Leandro Lucero, Camille Fonouni-Farde, Johan Rodríguez-Melo, Natanael Mansilla, Aurélie Christ, Jérémie Bazin, Moussa Benhamed, Fernando Ibañez, Martin Crespi, José M. Estevez, Federico Ariel

 

A vacuolar hexose transport is required for xylem development in the inflorescence stem of Arabidopsis
Emilie Aubry, Beate Hoffmann, Françoise Vilaine, Françoise Gilard, Patrick A.W. Klemens, Florence Guérard, Bertrand Gakière, H. Ekkehard Neuhaus, Catherine Bellini, Sylvie Dinant, Rozenn Le Hir

 

Proline-rich Extensin-like Receptor Kinases PERK5 and PERK12 are involved in Pollen Tube Growth
Cecilia Borassi, Ana R. Sede, Martin A. Mecchia, Silvina Mangano, Eliana Marzol, Silvina P. Denita-Juarez, Juan D. Salgado Salter, Silvia M. Velasquez, Jorge P. Muschietti, José M. Estevez

 

 

CTP-Synthase 2 from Arabidopsis thaliana is required for complete embryo development
Daniel Hickl, David Scheuring, Torsten Möhlmann

 

The AFB1 auxin receptor controls rapid auxin signaling and root growth through membrane depolarization in Arabidopsis thaliana
Nelson BC Serre, Dominik Kralík, Ping Yun, Sergey Shabala, Zdeněk Slouka, Matyáš Fendrych

 

 

The PELOTA-HBS1 Complex Orchestrates mRNA Translation Surveillance and PDK1-mediated Plant Growth and Development
Wei Kong, Shutang Tan, Qing Zhao, De-Li Lin, Zhi-Hong Xu, Jiří Friml, Hong-Wei Xue

 

The intrinsic chaperone network of Arabidopsis stem cells confers protection against proteotoxic stress
Ernesto Llamas, Salvador Torres-Montilla, Hyun Ju Lee, María Victoria Barja, Elena Schlimgen, Nick Dunken, Prerana Wagle, Wolfgang Werr, Alga Zuccaro, Manuel Rodríguez-Concepción, David Vilchez

 

Estimation of cell cycle kinetics in higher plant root meristem with cellular fate and positional resolution
Taras Pasternak, Stefan Kircher, Klaus Palme

 

Suberin plasticity to developmental and exogenous cues is regulated by a set of MYB transcription factors
Vinay Shukla, Jian-Pu Han, Fabienne Cl&eacuteard, Linnka Legendre-Lefebvre, Kay Gully, Paulina Flis, Alice Berhin, Tonni Grube Andersen, David E Salt, Christiane Nawrath, Marie Barberon

 

Electrophysiological evidence of synergistic auxin transport by interacting Arabidopsis ABCB4 and PIN2 proteins
Stephen D. Deslauriers, Edgar P. Spalding

 

Redefining the roles of UDP-glycosyltransferases in auxin metabolism and homeostasis during plant development
Eduardo Mateo-Bonmatí, Rubén Casanova-Sáez, Jan Šimura, Karin Ljung

 

 

Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis
Jincheng Long, James Walker, Wenjing She, Billy Aldridge, Hongbo Gao, Samuel Deans, Xiaoqi Feng

 

VISUAL network analysis reveals the role of BEH3 as a stabilizer in the secondary vascular development in Arabidopsis
Tomoyuki Furuya, Masato Saito, Haruka Uchimura, Akiko Satake, Shohei Nosaki, Takuya Miyakawa, Shunji Shimadzu, Wataru Yamori, Masaru Tanokura, Hiroo Fukuda, Yuki Kondo

 

The CLASSY family controls tissue-specific DNA methylation patterns in Arabidopsis
Ming Zhou, Ceyda Coruh, Guanghui Xu, Clara Bourbousse, Alice Lambolez, Julie A. Law

 

Brassinosteroid signaling component SlBES1 promotes tomato fruit softening through transcriptional repression of PMEU1
Haoran Liu, Lihong Liu, Dongyi Liang, Min Zhang, Chengguo Jia, Mingfang Qi, Yuanyuan Liu, Zhiyong Shao, Fanliang Meng, Songshen Hu, Chuanyou Li, Qiaomei Wang

 

 

A ClearSee-Based Clearing Protocol for 3D Visualization of Arabidopsis thaliana Embryos
Ayame Imoto and Mitsuhiro Aida

 

An integrative model of plant gravitropism linking statoliths position and auxin transport
Nicolas Levernier, Olivier Pouliquen, Yoël Forterre

 

Design principles of plant root morphogenesis
Marco Marconi, Marcal Gallemi, Eva Benkova, Krzysztof Wabnik

 

Function of the HYDROXYCINNAMOYL-CoA:SHIKIMATE HYDROXYCINNAMOYL TRANSFERASE is evolutionarily conserved in embryophytes
Lucie Kriegshauser, Samuel Knosp, Etienne Grienenberger, Kanade Tatsumi, Desirée D. Gütle, Iben Sørensen, Laurence Herrgott, Julie Zumsteg, Jocelyn K.C. Rose, Ralf Reski, Danièle Werck-Reichhart, Hugues Renault

 

Enhanced reproductive thermotolerance is associated with increased accumulation of flavonols in pollen of the tomato high-pigment 2 mutant
Nicholas Rutley, Golan Miller, Fengde Wang, Jeffrey F Harper, Gad Miller, Michal Lieberman-Lazarovich

 

All-Flesh Tomato Regulated by Reduced Dosage of AFF Provides New Insights into Berry Fruit Evolution
Lei Liu, Kang Zhang, JinRui Bai, Jinghua Lu, Xiaoxiao Lu, Junling Hu, Chunyang Pan, Shumin He, Jiale Yuan, Yiyue Zhang, Min Zhang, Yanmei Guo, Xiaoxuan Wang, Zejun Huang, Yongchen Du, Feng Cheng, Junming Li

 

CcLBD25 functions as a key regulator of haustorium development in Cuscuta campestris
Min-Yao Jhu, Yasunori Ichihashi, Moran Farhi, Caitlin Wong, Neelima R. Sinha

 

Spatial distribution of rice lectin protein r40g3 determines its dual regulatory role in imparting salinity tolerance while impeding seed development
Chandan Roy, Salman Sahid, Riddhi Datta, Soumitra Paul

 

An early-morning flowering trait in rice helps retain grain yield under heat stress field conditions at flowering stage
Tsutomu Ishimaru, Khin Thandar Hlaing, Ye Min Oo, Tin Mg Lwin, Kazuhiro Sasaki, Patrick D. Lumanglas, Eliza-Vie M. Simon, Tin Tin Myint, Aris Hairmansis, Untung Susanto, Bharathi Ayyenar, Raveendran Muthurajan, Hideyuki Hirabayashi, Yoshimichi Fukuta, Kazuhiro Kobayasi, Tsutomu Matsui, Mayumi Yoshimoto, Than Myint Htun

 

Whole-genome sequence analysis of mutations in rice plants regenerated from zygotes, mature embryos, and immature embryos
Masako Ichikawa, Norio Kato, Erika Toda, Masakazu Kashihara, Yuji Ishida, Yukoh Hiei, Sachiko N. Isobe, Kenta Shirasawa, Hideki Hirakawa, Takashi Okamoto, Toshihiko Komari

 

Maize (Zea mays L.) nucleoskeletal proteins regulate nuclear envelope remodeling and function in stomatal complex development and pollen viability.
Joseph Francis McKenna, Hardeep K. Gumber, Zachary M. Turpin, Alexis M. Jalovec, Andre C. Kartick, Katja Graumann, Hank W. Bass

 

Cell cortex microtubules contribute to division plane positioning during telophase in maize
Marschal A. Bellinger, Aimee N. Uyehara, Pablo Martinez, Michael C. McCarthy, Carolyn G. Rasmussen

 

ENHANCED GRAVITROPISM 2 encodes a STERILE ALPHA MOTIVE containing protein that controls root growth angle in barley and wheat
Gwendolyn K. Kirschner, Serena Rosignoli, Isaia Vardanega, Li Guo, Jafargholi Imani, Janine Altmüller, Sara G. Milner, Raffaella Balzano, Kerstin A. Nagel, Daniel Pflugfelder, Cristian Forestan, Riccardo Bovina, Robert Koller, Tyll G. Stöcker, Martin Mascher, James Simmonds, Cristobal Uauy, Heiko Schoof, Roberto Tuberosa, Silvio Salvi, Frank Hochholdinger

 

STARCH SYNTHASE 4 is required for normal starch granule initiation in amyloplasts of wheat endosperm
Erica Hawkins, Jiawen Chen, Alexander Watson-Lazowski, Jennifer Ahn-Jarvis, J Elaine Barclay, Brendan Fahy, Matthew Hartley, Frederick J Warren, David Seung

 

Serial Section-Based 3D Reconstruction of Anaxagorea (Annonaceae) Carpel Vasculature and Implications on Integrated Axial-Foliar Origin of Angiosperm Carpels
Ya Li, Wei Du, Ye Chen, Shuai Wang, Xiao-Fan Wang

 

Teosinte introgression modulates phosphatidylcholine levels and induces early maize flowering time
Fausto Rodríguez-Zapata, Allison C Barnes, Karla A Blöcher-Juárez, Dan Gates, Andi Kur, Li Wang, Garrett M Janzen, Sarah Jensen, Juan M Estévez-Palmas, Taylor Crow, Rocío Aguilar-Rangel, Edgar Demesa-Arevalo, Tara Skopelitis, Sergio Pérez-Limón, Whitney L Stutts, Peter Thompson, Yu-Chun Chiu, David Jackson, Oliver Fiehn, Daniel Runcie, Edward S Buckler, Jeffrey Ross-Ibarra, Matthew B. Hufford, Ruairidh JH Sawers, Rubén Rellán-Álvarez

 

Resetting of 24-nt siRNA landscape is initiated before the first zygotic division in rice
Chenxin Li, Jonathan I. Gent, Hengping Xu, Hong Fu, Scott D. Russell, Venkatesan Sundaresan

 

THE REGULATORY EFFECT OF LIGHT OVER FRUIT DEVELOPMENT AND RIPENING IS MEDIATED BY EPIGENETIC MECHANISMS
Ricardo Bianchetti, Nicolas Bellora, Luis A de Haro, Rafael Zuccarelli, Daniele Rosado, Luciano Freschi, Magdalena Rossi, Luisa Bermudez

 

 

 

Evo-devo & evo

 

 

A complex genetic architecture in zebrafish relatives Danio quagga and D. kyathit underlies development of stripes and spots
Braedan M. McCluskey, Susumu Uji, Joseph L. Mancusi, John H. Postlethwait, David M. Parichy

 

Evolution of lbx spinal cord expression and function
José L. Juárez-Morales, Frida Weierud, Samantha J. England, Celia Demby, Nicole Santos, Sylvie Mazan, Katharine E. Lewis

 

 

Annelids win again: the first evidence of Hox antisense transcription in Spiralia.
Elena L. Novikova, Nadezhda I. Bakalenko, Milana A. Kulakova

 

Conserved and unique transcriptional features of pharyngeal arches in the skate (Leucoraja erinacea) and evolution of the jaw
Christine Hirschberger, Victoria A. Sleight, Katharine E. Criswell, Stephen J. Clark, J. Andrew Gillis

 

Gene family evolution underlies cell type diversification in the hypothalamus of teleosts
Maxwell E.R. Shafer, Ahilya N. Sawh, Alexander F. Schier

 

 

How to align arthropod leg segments
Heather S. Bruce

 

 

Embryonic development in the acoel Hofstenia miamia
Julian O. Kimura, Lorenzo Ricci, Mansi Srivastava

 

Development of larvae of the Australian blowfly, Calliphora augur (Diptera: Calliphoridae), at constant temperatures
Donnah M. Day, Nathan J. Butterworth, Anirudh Tagat, Gregory Markowsky, James F. Wallman

 

The development and neuronal complexity of bipinnaria larvae of the sea star Asterias rubens
Hugh F. Carter, Jeffrey R. Thompson, Maurice R. Elphick, Paola Oliveri

 

The evolution of Sox gene repertoires and regulation of segmentation in arachnids
Luis Baudouin-Gonzalez, Anna Schoenauer, Amber Harper, Grace Blakeley, Michael Seiter, Saad Arif, Lauren Sumner-Rooney, Steven Russell, Prashant P. Sharma, Alistair P. McGregor

 

The genome of a daddy-long-legs (Opiliones) illuminates the evolution of arachnid appendages and chelicerate genome architecture
Guilherme Gainett, Vanessa L. González, Jesús A. Ballesteros, Emily V. W. Setton, Caitlin M. Baker, Leonardo Barolo Gargiulo, Carlos E. Santibáñez-López, Jonathan A. Coddington, Prashant P. Sharma

 

Structural and functional characterization of a putative de novo gene in Drosophila
Andreas Lange, Prajal H. Patel, Brennen Heames, Adam M. Damry, Thorsten Saenger, Colin J. Jackson, Geoffrey D. Findlay, Erich Bornberg-Bauer

 

The Genetics and Evolution of Eye Color in Domestic Pigeons (Columba livia)
Si Si, Xiao Xu, Yan Zhuang, Xiaodong Gao, Honghai Zhang, Zhengting Zou, Shu-Jin Luo

 

The dynamic ontogenetic patterns of adaptive divergence and sexual dimorphism in Arctic charr
Marina De la Cámara, Lieke Ponsioen, Quentin J.B. Horta-Lacueva, Kalina H Kapralova

 

Continuous cis-regulatory changes in an advantageous gene are linked with adaptive radiation in cichlid fishes
Langyu Gu, Chenzheng Li, Xiaobing Mao, Zongfang Wei, Youkui Huang, Ximin He, Wenjun Zhou, Li Li, Deshou Wang

 

 

Cell biology

 

 

Aurora kinases promote mitotic progression and asymmetric cell division through activation of Polo kinase
Emmanuel Gallaud, Aude Pascal, Mathieu Métivier, Laurent Richard-Parpaillon, Vincent Archambault, Régis Giet

 

Aurora kinase A is essential for meiosis in mouse oocytes
Cecilia S. Blengini, Patricia Ibrahimian, Michaela Vaskovicova, David Drutovic, Petr Solc, Karen Schindler

 

Asymmetric chromatin capture and nuclear envelopes separate chromosomes in fused cells during mitosis
Bharath Sunchu, Nicole Lee, Roberto Carlos Segura, Chantal Roubinet, Clemens Cabernard

 

 

Collective ERK/Akt activity waves orchestrate epithelial homeostasis by driving apoptosis-induced survival
Paolo Armando Gagliardi, Maciej Dobrzynski, Marc-Antoine Jacques, Coralie Dessauges, Pascal Ender, Yannick Blum, Robert M Hughes, Andrew R Cohen, Olivier Pertz

 

Quantitative live-cell imaging and computational modelling yield novel insight into endogenous WNT/CTNNB1 signaling dynamics
S.M.A. de Man, G. Zwanenburg, T. van der Wal, M.A. Hink, R. van Amerongen

 

Dia1 Coordinates Differentiation and Cell Sorting in a Stratified Epithelium
Robert M. Harmon, John Devany, Margaret L. Gardel

 

scATAC-Seq reveals epigenetic heterogeneity associated with an EMT-like process in male germline stem cells and its regulation by G9a
Jinyue Liao, Hoi Ching Suen, Alfred Chun Shui Luk, Annie Wing Tung Lee, Judy Kin Wing Ng, Ting Hei Thomas Chan, Man Yee Cheung, David Yiu Leung Chan, Huayu Qi, Wai Yee Chan, Robin M. Hobbs, Tin-Lap Lee

 

A novel adhesive complex at the base of intestinal microcilli
Klaus T Ebnet, Christian Hartmann, Eva-Maria Thüring, Brigitta E Michels, Denise Pajonczyk, Sophia Leußink, Lilo Greune, Frauke Brinkmann, Mark Glaesner-Ebnet, Eva Wardelmann, Thomas Zobel, M. Alexander Schmidt, Volker Gerke

 

Organization of DNA replication origin firing in Xenopus egg extracts : the role of intra-S checkpoint
Diletta Ciardo, Olivier Haccard, Hemalatha Narassimprakash, Jean-Michel Arbona, Olivier Hyrien, Benjamin Audit, Kathrin Marheineke, Arach Goldar

 

 

 

Modelling

From heterogeneous datasets to predictive models of embryonic development
Sayantan Dutta, Aleena L. Patel, Shannon E. Keenan, Stanislav Y. Shvartsman

 

 

Mathematical modeling of Erk activity waves in regenerating zebrafish scales
Luke Hayden, Kenneth D Poss, Alessandro De Simone, Stefano Di Talia

 

Reaction-diffusion Model for the Arrest of Oscillations in the Somitogenesis Segmentation Clock
Jesús Pantoja-Hernández, Víctor F. Breña-Medina, Moisés Santillán

 

A stochastic model of homeostasis: the roles of noise and nuclear positioning in deciding cell fate
Amit Jangid, Suriya Selvarajan, Ramakrishna Ramaswamy

 

An “individualist” model of an active genome in a developing embryo
Shao-Kuei Huang, Sayantan Dutta, Peter H Whitney, Stanislav Shvartsman, Christine Rushlow

 

Role of cell polarity dynamics and motility in pattern formation due to contact dependent signalling
Supriya Bajpai, Ranganathan Prabhakar, Raghunath Chelakkot, Mandar M. Inamdar

 

Quantifying cell transitions in C. elegans with data-fitted landscape models
Elena Camacho-Aguilar, Aryeh Warmflash, David A. Rand

 

Modelling cell guidance and curvature control in evolving biological tissues
Solene G.D. Hegarty-Cremer, Matthew J. Simpson, Thomas L. Andersen, Pascal R. Buenzli

 

Evolution of irreversible somatic differentiation
Yuanxiao Gao, Hye Jin Park, Arne Traulsen, Yuriy Pichugin

 

Topological data analysis distinguishes parameter regimes in the Anderson-Chaplain model of angiogenesis
John T. Nardini, Bernadette J. Stolz, Kevin B. Flores, Heather A. Harrington, Helen M. Byrne

 

Contact-mediated cellular communication supplements positional information to regulate spatial patterning during development
Chandrashekar Kuyyamudi, Shakti N. Menon, Sitabhra Sinha

 

 

Tools & resources

In Vivo Subcellular Mass Spectrometry Enables Proteo-Metabolomic Single-cell Systems Biology in a Chordate Embryo Developing to a Normally Behaving Tadpole (X. laevis)
Camille Lombard-Banek, Jie Li, Erika P. Portero, Rosemary M. Onjiko, Chase D. Singer, David Plotnick, Reem Q. Al Shabeeb, Peter Nemes

 

 

Rapid fabrication of hydrogel micropatterns by projection stereolithography for studying self-organized developmental patterning
Ye Zhu, Daniel Sazer, Jordan Miller, Aryeh Warmflash

 

Bioengineered embryoids mimic post-implantation development in vitro
Mehmet Girgin, Nicolas Broguiere, Sylke Hoehnel, Nathalie Brandenberg, Bastien Mercier, Alfonso Martinez-Arias, Matthias P Lutolf

 

Monitoring the promoter activity of long noncoding RNAs and stem cell differentiation through knock-in of sgRNA flanked by tRNA in an intron
Yu-Ting Zhao, Yangming Wang

 

Manipulating the murine Lgr5 locus using a rapid, efficient and flexible CRISPR/Cas9 pipeline
Jan Reichmuth, Johannes vom Berg, Michael Brügger, George Hausmann, Tomas Valenta, Konrad Basler

 

A quick and versatile protocol for the 3D visualization of transgene expression across the whole body of larval Drosophila
Oliver Kobler, Aliće Weiglein, Kathrin Hartung, Yi-chun Chen, Bertram Gerber, Ulrich Thomas

 

AGES: An auxin-inducible, GAL4-compatible, gene expression system for Drosophila
Colin D. McClure, Amira Hassan, Aneisha Duggal, Chee Ying Sia, Tony D. Southall

 

A Practical Guide to Sparse Clustering for Studying Molecular Development of the Human Brain
Justin L. Balsor, Keon Arbabi, Dezi Ahuja, Ewalina Jeyanesan, Kathryn M. Murphy

 

TopoStats – a program for automated tracing of biomolecules from AFM images
Joseph G. Beton, Robert Moorehead, Luzie Helfmann, Robert Gray, Bart W. Hoogenboom, Agnel Praveen Joseph, Maya Topf, Alice L. B. Pyne

 

Easymap: a user-friendly software package for rapid mapping by sequencing of point mutations and large insertions
Samuel Daniel Lup, David Wilson-Sánchez, Sergio Andreu-Sánchez, José Luis Micol

 

 

Pipeline for generating stable large genomic deletions in zebrafish, from small domains to whole gene excisions
Alisha Tromp, Kate Robinson, Thomas E Hall, Bryan Mowry, Jean Giacomotto

 

Generation of a New Frizzled 2 Flox Mouse Model to Clarify Its Role in Development
Megan N. Michalski, Cassandra R. Diegel, Zhendong A. Zhong, Kelly Suino-Powell, Levi Blazer, Jarrett Adams, VAI Vivarium and Transgenics Core, Ian Beddows, Karsten Melcher, Sachdev S. Sidhu, Stephane Angers, Bart O. Williams

 

Generation of a novel Nkx6-1 Venus fusion reporter mouse line
Ingo Burtscher, Marta Tarquis-Medina, Ciro Salinno, Julia Beckenbauer, Mostafa Bakhti, Heiko Lickert

 

Optical Tissue Clearing Enables Rapid, Precise and Comprehensive Assessment of Three-Dimensional Morphology in Experimental Nerve Regeneration Research
Simeon C. Daeschler, Jennifer Zhang, Tessa Gordon, Gregory H. Borschel

 

A mesh microelectrode array for non-invasive electrophysiology within neural organoids
Matthew McDonald, David Sebinger, Lisa Brauns, Laura Gonzalez-Cano, Yotam Menuchin-Lasowski, Michael Mierzejewski, Olympia-Ekaterini Psathaki, Angelika Stumpf, Jenny Wickham, Thomas Rauen, Hans Schöler, Peter D. Jones

 

Adult porcine (Sus scrofa) derived inner ear cells possessing multipotent stem/progenitor cell characteristics in in vitro cultures
Printha Wijesinghe, Anand Sastry, Elizabeth Hui, Tristan A. Cogan, Boyuan Zheng, Germain Ho, Juzer Kakal, Desmond A. Nunez

 

CiliaQ – a simple, open-source software for automated quantification of ciliary morphology and fluorescence in 2D, 3D, and 4D images
Jan Niklas Hansen, Sebastian Rassmann, Birthe Stüven, Nathalie Jurisch-Yaksi, Dagmar Wachten

 

Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science
Mick A Phillips, David Miguel Susano Pinto, Nicholas Hall, Julio Mateos-Langerak, Richard M Parton, Josh Titlow, Danail V Stoychev, Thomas Parks, Tiago Susano Pinto, John W Sedat, Martin J Booth, Ilan Davis, Ian M Dobbie

 

CRISPR Del/Rei: A simple, flexible and efficient pipeline for scarless genome editing
Marah H. Wahbeh, Kyra L. Feuer, Sara Abdollahi, Christian Yovo, Eman Rabie, Anh-Thu N. Lam, Lindsay J. Young, Dimitrios Avramopoulos

 

Split-wrmScarlet and split-sfGFP: Tools for faster, easier fluorescent labeling of endogenous proteins in Caenorhabditis elegans
Jérôme Goudeau, Catherine S. Sharp, Jonathan Paw, Laura Savy, Manuel D. Leonetti, Andrew G. York, Dustin L. Updike, Cynthia Kenyon, Maria Ingaramo

 

 

Using zebrafish to elucidate glial-vascular interactions during CNS development
Robyn A. Umans, Carolyn Pollock, William A. Mills III, Harald Sontheimer

 

Minimal genetically encoded tags for fluorescent protein labeling in living neurons
Aleksandra Arsić, Cathleen Hagemann, Nevena Stajković, Timm Schubert, Ivana Nikić-Spiegel

 

Imaging cytoplasmic lipid droplets in vivo with fluorescent perilipin 2 and perilipin 3 knockin zebrafish
Meredith H. Wilson, Stephen C. Ekker, Steven A. Farber

 

QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy
Glyn Nelson, Ulrike Boehm, Steve Bagley, Peter Bajcsy, Johanna Bischof, Claire M Brown, Aurelien Dauphin, Ian M Dobbie, John E Eriksson, Orestis Faklaris, Julia Fernandez-Rodriguez, Alexia Ferrand, Laurent Gelman, Ali Gheisari, Hella Hartmann, Christian Kukat, Alex Laude, Miso Mitkovski, Sebastian Munck, Alison J North, Tobias M Rasse, Ute Resch-Genger, Lucas C Schuetz, Arne Seitz, Caterina Strambio-De-Castillia, Jason R Swedlow, Ioannis Alexopoulos, Karin Aumayr, Sergiy Avilov, Gert-Jan Bakker, Rodrigo R Bammann, Andrea Bassi, Hannes Beckert, Sebastian Beer, Yury Belyaev, Jakob Bierwagen, Konstantin A Birngruber, Manel Bosch, Juergen Breitlow, Lisa A Cameron, Joe Chalfoun, James J Chambers, Chieh-Li Chen, Eduardo Conde-Sousa, Alexander D Corbett, Fabrice P Cordelieres, Elaine Del Nery, Ralf Dietzel, Frank Eismann, Elnaz Fazeli, Andreas Felscher, Hans Fried, Nathalie Gaudreault, Wah Ing Goh, Thomas Guilbert, Roland Hadleigh, Peter Hemmerich, Gerhard A Holst, Michelle S Itano, Claudia B Jaffe, Helena K Jambor, Stuart C Jarvis, Antje Keppler, David Kirchenbuechler, Marcel Kirchner, Norio Kobayashi, Gabriel Krens, Susanne Kunis, Judith Lacoste, Marco Marcello, Gabriel G Martins, Daniel J Metcalf, Claire A Mitchell, Joshua Moore, Tobias Mueller, Michael S Nelson, Stephen Ogg, Shuichi Onami, Alexandra L Palmer, Perrine Paul-Gilloteaux, Jaime A Pimentel, Laure Plantard, Santosh Podder, Elton Rexhepaj, Arnaud Royon, Markku A Saari, Damien Schapman, Vincent Schoonderwoert, Britta Schroth-Diez, Stanley Schwartz, Michael Shaw, Martin Spitaler, Martin T Stoeckl, Damir Sudar, Jeremie Teillon, Stefan Terjung, Roland Thuenauer, Christian D Wilms, Graham D Wright, Roland Nitschke

 

 

Reviews

Hormonal Regulation of Oligodendrogenesis I: Effects across the Lifespan
Kimberly Long, Jocelyn Breton , Matthew Barraza, Olga Litvin, Daniela Kaufer

 

Hormonal Regulation of Oligodendrogenesis II: Implications for Myelin Repair
Jocelyn Breton, Kimberly Long, Matthew Barraza, Olga Litvin , Daniela Kaufer

 

Zebrafish as a Biomedical Model for Stem Cells Research in Hearing Impairment
Salma Hafeez

 

 

Research practice & education

Randomized controlled studies comparing traditional lectures versus online modules
Kiran Musunuru, Zarin P. Machanda, Lyon Qiao, William J. Anderson

 

Intelligence and academic performance: Is it all in your head?
Katherine L. Bottenhorn, Jessica E. Bartley, Michael C. Riedel, Taylor Salo, Elsa I. Bravo, Rosalie Odean, Alina Nazareth, Robert W. Laird, Erica D. Musser, Shannon M. Pruden, Eric Brewe, Matthew T. Sutherland, Angela R. Laird

 

Oncofly: A CURE for Cancer
Floyd A. Reed, H. Gert de Couet

 

Alignment of biomedical data repositories with open, FAIR, citable and trust-worthy principles
Fiona Murphy, Michael Bar-Sinai, Maryann E. Martone

 

Evaluating features of scientific conferences: A call for improvements
Sarvenaz Sarabipour, Aziz Khan, Samantha Seah, Aneth D. Mwakilili, Fiona N. Mumoki, Pablo J. Sáez, Benjamin Schwessinger, Humberto J. Debat, Tomislav Mestrovic

 

An open-source tool to assess the carbon footprint of research
Jérôme Mariette, Odile Blanchard, Olivier Berné, Tamara Ben-Ari

 

Overburdening of peer reviewers. A multi-disciplinary and multi-stakeholder perspective on causes, effects and potential policy implications
Anna Severin, Joanna Chataway

 

Comprehensive mapping of local and diaspora scientists: a database and analysis of 63951 Greek scientists
John P.A. Ioannidis, Chara Koutsioumpa, Angeliki Vakka, Georgios Agoranos, Chrysanthi Mantsiou, Maria Kyriaki Drekolia, Nikos Avramidis, Despina G. Contopoulos-Ioannidis, Konstantinos Drosatos, Jeroen Baas

 

Mentorship as a strategy to improve research ability of students and young researchers in Africa: an exploratory study and initial findings on the CORE Africa Research Mentorship Scheme
Lem Ngongalah, Ngwa Niba Rawlings, James M. Musisi, Kimonia Awanchiri, Emmanuella Akwah, Etienne Ngeh, Andrew Ssemwanga

 

 

 

 

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The Sozen laboratory is looking for talented postdoctoral associates with a background in mammalian developmental stem cell biology to join our team. We conduct research in early mouse/human embryogenesis with the goal of understanding the mechanisms that underlie developmental programming in human health and disease.

 

Our laboratory in the Department of Genetics, Yale School of Medicine, is a part of a highly collaborative, translational developmental biology program that includes stem cell biology, reproductive biology, genetics and computational biology.

 

The candidate will lead a project to participate in our larger efforts to unravel how the developmental environment impacts on physiologic, metabolic, transcriptomic and epigenomic landscapes during embryo implantation and gastrulation, the time when the maternal-fetal interface is established. The project will integrate cutting-edge technologies such as the in vitro reconstitution of development in 3D with stem cells (Harrison et al. Science 2017, Sozen et al. Nature Cell Bio. 2018, Sozen et al. Dev. Cell 2019), advanced imaging techniques and transcriptomic profiling to map developmental trajectories and cellular function during tissue patterning under environmental challenges.

The postdoctoral candidate will have the opportunity to work in collaboration with a team of world-leading researchers, clinicians, and bioinformaticians, and there will be opportunities to develop additional independent projects with clinical collaborators at Yale University.

 

In addition to high-quality research facilities, career and professional development training for postdoctoral researchers is provided. Additional information on being a postdoc at Yale University School of Medicine can be found at https://postdocs.yale.edu/

 

Qualified candidates should have a PhD in Developmental Biology, Stem Cell Biology, Reproductive Biology, Bioengineering or a relevant field. The candidate must have hands-on experience with mammalian embryo culture and/or mammalian stem cell culture. Expertise in 3D cell culture techniques and gene editing methods (e.g. Crispr-Cas9, to engineer stem cell lines with multiple fluorescent reporters) are highly desirable. Experience in transcriptomic profiling techniques (e.g. single-cell RNA-seq) and bioinformatics analyses are desirable but not essential. Please respond with a cover letter that includes a short description of relevant expertise, a CV with publication list, and the names of two references by email to: berna.sozen@yale.edu

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