Developmental Biology

Tracking cell lineages in 3D by incremental deep learning

1. Ko Sugawara
2. Çağrı Çevrim
3. Michalis Averof

• Curated by eLife

  Evaluation Summary:

  Sugawara et al describe a new interactive tool for 3D cell tracking in time that allows the user to retrain models quickly with updated labels. The utility of a tool like this for biologists is great: many experiments require tracking cell division over time or cell movements. With clear comparison to the latest developments in cellular segmentation and an improved procedure enabling the use of the tool, this paper would make an interesting contribution to the image analysis field.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #3 agreed to share their names with the authors.)

Reviewed by eLife

Emergence of a geometric pattern of cell fates from tissue-scale mechanics in the Drosophila eye

1. Kevin D Gallagher
2. Madhav Mani
3. Richard W Carthew

• Curated by eLife

  Evaluation Summary:

  This paper will have a high impact for all developmental and cell biologists who are interested in tissue patterning and organogenesis. It provides unexpected insights into the problem of regular spacing of sub-organ structures. The study is based on innovative live imaging technology with state of the art analysis tools.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript.)

Reviewed by eLife

Supracellular organization confers directionality and mechanical potency to migrating pairs of cardiopharyngeal progenitor cells

1. Yelena Y Bernadskaya
2. Haicen Yue
3. Calina Copos
4. Lionel Christiaen
5. Alex Mogilner

• Curated by eLife

  Evaluation Summary:

  In this study, the authors develop a model to understand the simplest form of collective migration represented by a pair of cardiopharyngeal progenitor cells. They propose that the collective migrates as a "supracell", with leader cells assuming a greater protrusive capability and trailer cells assuming greater retractive capability. They meticulously study the effects of leader-trailer and cell-matrix adhesivity, intracellular force distributions and noise on robustness of cell migration. They corroborate their simulation results with experiments. Overall, this study comprehensively demonstrates that migrating as a collective leads to more mechanically efficient and persistent migration than as a single motile cell.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Reviewed by eLife

Positive feedback regulation of frizzled-7 expression robustly shapes a steep Wnt gradient in Xenopus heart development, together with sFRP1 and heparan sulfate

1. Takayoshi Yamamoto
2. Yuta Kambayashi
3. Yuta Otsuka
4. Boni A Afouda
5. Claudiu Giuraniuc
6. Tatsuo Michiue
7. Stefan Hoppler

• Curated by eLife

  Evaluation Summary:

  Regulation of morphogen diffusion that controls tissue patterning is an important issue in developmental biology. The study deals with the mechanisms that establishes the Wnt gradient combining a mathematical model and experiments considering multiple extracellular components such as receptor and diffusible antagonist. The study revealed that the ligand/receptor feedback enables robust and quick formation of the morphogen gradient and that the diffusible antagonist also plays a role in this process. With some strengthening of experimental data and better explanation of the modeling, this study will be a useful contribution to the field.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Reviewed by eLife

Renal interstitial cells promote nephron regeneration by secreting prostaglandin E2

1. Xiaoliang Liu
2. Ting Yu
3. Xiaoqin Tan
4. Daqing Jin
5. Wenmin Yang
6. Jiangping Zhang
7. Lu Dai
8. Zhongwei He
9. Dongliang Li
10. Yunfeng Zhang
11. Shuyi Liao
12. Jinghong Zhao
13. Tao P Zhong
14. Chi Liu

• Curated by eLife

  eLife assessment

  This fundamental work substantially advances our understanding of the kidney interstitium and how it influences kidney development focusing on zebrafish as a model organism. The evidence supporting the conclusions is compelling, using single-cell analysis combined with in vivo zebrafish studies to mechanistically explore the functional importance of the discovery. The work will be of broad interest to cell and developmental biologists as well as the kidney community.

Reviewed by eLife

Optogenetic control of the Bicoid morphogen reveals fast and slow modes of gap gene regulation

1. Anand P. Singh
2. Ping Wu
3. Sergey Ryabichko
4. João Raimundo
5. Michael Swan
6. Eric Wieschaus
7. Thomas Gregor
8. Jared E. Toettcher

Reviewed by ASAPbio crowd review

Allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants

1. Richard J White
2. Eirinn Mackay
3. Stephen W Wilson
4. Elisabeth M Busch-Nentwich

• Curated by eLife

  Evaluation Summary:

  Zebrafish strains are typically considerably polymorphic. White and colleagues tested the hypothesis that genes in linkage with a mutant allele might show allele-specific expression differences and thus potentially confound the interpretation of mutant effects. Using a variety of mutant and wild-type alleles with sophisticated analysis of RNA-seq data in zebrafish embryos they demonstrate over-representation of gene expression changes from genes that are in linkage with the mutant allele on the same chromosome. The data are extensive, carefully analyzed and of sufficient depth and quality to support their main claim of frequent occurrence of allele-specific gene expression in outcross experiments. These allele-specific expression differences may impact on the interpretation of differential gene expression caused by a specific mutation. The findings of this study will be of interest to genetics working not only with zebrafish, but potentially also other polymorphic species.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and #3 agreed to share their name with the authors.)

Reviewed by eLife

Paraxial mesoderm organoids model development of human somites

1. Christoph Budjan
2. Shichen Liu
3. Adrian Ranga
4. Senjuti Gayen
5. Olivier Pourquié
6. Sahand Hormoz

• Curated by eLife

  Evaluation Summary:

  Budjan et al. describe an organoid protocol to obtain somite-like structures from human iPSCs. Using defined culture media, the authors describe the formation after 5 days in vitro of organoids that express a variety of PSM differentiation markers, such as the segmentation clock gene Hes7 and Pax3. Optimization of their culture conditions and transcription analyses of what they name their "somitoid" system revealed that their culture system recapitulates the time course of expression markers typically observed along PSM and somite early differentiation. Furthermore, somitoid reacted to Shh activation by activating sclerotomal markers Pax1 and 9.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

Using positional information to provide context for biological image analysis with MorphoGraphX 2.0

1. Sören Strauss
2. Adam Runions
3. Brendan Lane
4. Dennis Eschweiler
5. Namrata Bajpai
6. Nicola Trozzi
7. Anne-Lise Routier-Kierzkowska
8. Saiko Yoshida
9. Sylvia Rodrigues da Silveira
10. Athul Vijayan
11. Rachele Tofanelli
12. Mateusz Majda
13. Emillie Echevin
14. Constance Le Gloanec
15. Hana Bertrand-Rakusova
16. Milad Adibi
17. Kay Schneitz
18. George W Bassel
19. Daniel Kierzkowski
20. Johannes Stegmaier
21. Miltos Tsiantis
22. Richard S Smith

• Curated by eLife

  Evaluation Summary:

  This manuscript reports advances in the image analysis software package MorphGraphX (MGX). designed to capture the developmental dynamics of growing tissues at cellular resolution. This version, MGX2.0, includes new tools for precise quantitation of cellular behaviors, such as cell division and expansion, within the context of positional information in the growing organs. To illustrate multiple functionalities of MGX2.0, various tissues are analyzed. This presentation style highlights the power and broad applicability of MGX2.0, but leads to a somewhat disjointed narrative, and how it can provide insight into specific biological questions is less clear.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)

Reviewed by eLife

Birth of mice from meiotically arrested spermatocytes following biparental meiosis in halved oocytes

1. Narumi Ogonuki
2. Hirohisa Kyogoku
3. Toshiaki Hino
4. Yuki Osawa
5. Yasuhiro Fujiwara
6. Kimiko Inoue
7. Tetsuo Kunieda
8. Seiya Mizuno
9. Hiroyuki Tateno
10. Fumihiro Sugiyama
11. Tomoya S Kitajima
12. Atsuo Ogura

Reviewed by Review Commons