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Pioneering new strategy lengthens limbs to treat skeletal disorder

Posted by , on 15 February 2023

A Press Release from Development

Robinow Syndrome is the best known of a set of genetic disorders that affect the growth and development of the skeletal system. Patients with these conditions have facial abnormalities, such as cleft palate, and develop short-limb dwarfism by around 18 months. Now, in a study published in Development, scientists from Nationwide Children’s Hospital in Ohio, USA, and the Van Andel Research Institute in Michigan, USA have shown the first successful correction of limb length in a mouse model of a very similar disorder known as FZD2-associated autosomal dominant Robinow Syndrome, providing hope for future therapies.

The forelimb (top) and hindlimb (bottom) of a mouse embryo, stained to reveal the bones (purple) and cartilage (blue). Image credit: Sanika Vaidya.

Although autosomal dominant Robinow Syndrome disorders are extremely rare (affecting around 50 families worldwide), they’re associated with genetic variations (mutations) in a group of genes that can be inherited from one parent or arise spontaneously, meaning diagnosis is not always trivial. Professor Rolf Stottmann who led the study said, “we began the project by studying the genomes of families with structural birth differences of the brain and face who had not yet received a genetic diagnosis. We identified that one of the initial families in this cohort had a mutation in the FZD2 gene.”

FZD2 is now known to be one of the known genes linked to autosomal dominant Robinow Syndrome. Like the other genes in this group, FZD2 makes a protein involved in sending signals that cells use to organise themselves into tissues. In their study, Professor Stottmann and colleagues used CRISPR/Cas9 genome-editing technology to induce mutations in a precise region of Fzd2, reproducing the specific types of mutations found in human patients. The researchers found that mice with these mutations had facial and skeletal malformations resembling those seen in the patients, including cleft palates and limbs less than half the normal size.

The researchers predicted that these types of Fzd2 mutations would disrupt signalling and hinder skeletal growth. To rescue the missing signals, the scientists intervened by treating pregnant mice with a drug that stimulates the signalling pathway. “This drug is an attractive option because we think we know how it works and previous work had shown that it could rescue cleft palates in a mouse model,” Professor Stottmann explained. Strikingly, they found that the pups exposed to the drug had significantly longer limbs than the untreated model mice.

The success of these experiments in mice suggests the drug could also be used as a therapeutic treatment in human patients. “The idea of treating the limb bones medically rather than surgically is a really important proof of principle, which we demonstrate in this study,” said Professor Stottmann, “we are very excited to test if this could work in the context of other genes associated with autosomal dominant Robinow Syndrome.”


Liegel, R.P., Michalski, M.N., Vaidya, S., Bitterman, E., Finnerty, E., Menke, C.A., Diegel, C.R., Zhong, Z.A., Williams, B.O., Stottmann, R.W. (2023). Successful therapeutic intervention in novel mouse models of Frizzled 2-associated congenital malformations. Development, 150, dev201038. doi:10.1242/dev.201038

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SciArt profile: Julie Gamart

Posted by , on 9 February 2023

In our February SciArt profile we feature Julie Gamart. In her illustrations, Julie seeks to combine the scientific topic with the personal preferences of the scientist(s) to create beautiful and playful artworks that communicate with her audience.

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

I was born in Saint-Martin-Boulogne, on the sea coast in the North of France. I stayed at the University of Lille (USTL, France) as a graduate student. As I wanted to work on genetics, I moved to Paris for the Master’s degree ‘Magistère Européen de Génétique’ where I had the opportunity to do a research internship at the University of New York (NYU Langone Health, USA) and then my master’s thesis in the laboratory of Professor Frédéric Relaix in the Institut of Myology in Paris. I was supervised by Dr Vanessa Ribes, and she gave me her passion for developmental genetics, working on the spinal cord development. I did my PhD in Basel in Switzerland in the Laboratory of Professor Rolf Zeller. I was using developmental genetics to decipher the roles of the BMP signalling pathway during the outgrowth of the limb bud. During my career, I have come to realise how a good illustration can improve scientific communication. Today, I draw for scientists and I like to translate a scientific message with an artistic angle.

Were you always going to be a scientist?

Not really. When I was a child my wishes were split between my desire to work on the art field, since I have this gift of drawing transmitted by my family, or my curiosity to understand how genetics works because my family has a hereditary disease. I finally chose the scientific path thinking that one day I would be able to reconnect with art.

Genetics & Cardiac Development
This heart is used as a background on the website of the lab of Professor Marco Osterwalder
(DBMR, Bern, Switzerland) to illustrate the research topic about Genetics & Cardiac Development. The drawing style is inspired by metal music.
Link: https://www.osterwalderlab.com/

And what about art – have you always enjoyed it?

Yes, I managed to reconnect with art. After my PhD, I started to draw again, making artistic and scientific illustrations to communicate my research. I got a lot of good feedback, so I started to make illustrations and figures for my friends. Now I enjoy working with scientists from different fields to build unique illustrations that translate the scientific topic and reflect the tastes and preferences of researchers.

The Faces of a Brain Cancer Cell
This illustration was submitted for the journal cover for the publication Parmigiani, et al. (2022). Based on an idea of a famous movie, it shows the two faces of a brain cancer cell interacting with immune cells: the one with the Notch pathway, being attacked by T cells (T shaped ships) and the one without Notch, recruiting immunosuppressive macrophages (M shaped ships).

What or who are your most important artistic influences?

I have no specific artistic influences. I learned to draw with several techniques when I was young, thanks to Jean-Francis Mulier’s classes (in Seclin in the North of France) that I followed from 10 to 16 years old. My main influence comes from my mother, Christine Gamart, and my aunt, Catherine Gamart, who support me in my decisions and give me very constructive advice and criticism. They draw wonderfully, their expert eye is essential for me.

How do you make your art?

The most important thing for me is the communication with the researchers. The illustration is a construction that we make together: it must translate a scientific message in a playful way and correspond to the personality of the scientist(s) to reflect his or her tastes and preferences. After that, I begin by choosing a drawing technique (acrylic, watercolour, charcoal, pastels, pencil). The technique will help to define the style of the drawing. Depending on the request, I use the computer to create a digital montage of the different drawings. For other realizations, I make the figures directly on the computer.
I share my work on the networks (Facebook, Instagram, LinkedIn and Twitter) and my website.

The Mouse Heart Development
This figure was used for the ‘Night of Research 2022’ organised by the University of Bern, where the general public was invited to meet scientists to talk about their research. The figure explains how the heart develops in mouse embryos during the 20 day of gestation period.

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

Both worlds are linked: I adapt and use art as a tool to communicate, to popularise and share a scientific message.

You recently created the visual identity for the Franco-Japanese, New Frontiers in Developmental Biology meeting. Can you tell us a little about your brief and how you can up with the concept?

It was a great adventure to participate in this congress. The SFBD committee came to me and asked me to create a poster mixing developmental biology, Japan and the organising city, Strasbourg. The idea of creating the skyline of Strasbourg made of embryos from different species came quite quickly, in agreement with the team. To bring more poetry and softness, I proposed making the drawings using watercolour. The sun and the dominance of light pink colour also represents Japan and the flower of the Japanese cherry tree. From the style of the poster, we have created derivatives for different media (indication panels, presentation slides, name tag booklets) and some illustrations were used to create the website of the meeting. I also did the illustrations for the developmental biology games as part of the outreach programme that was running alongside the meeting. I really enjoyed adapting the drawing to a childlike style to explain developmental biology to little ones.

The 3rd Franco-Japanese Developmental Biology Meeting
Poster of the 3rd Franco-Japanese Developmental Biology Meeting. It shows developmental biology, Japan and the city of Strasbourg in an original and artistic way

What are you thinking of working on next?

I hope it is the beginning of a big adventure. I would like to help many scientists communicate their research and make a difference with illustrations that reflect their personality and transmit a scientific knowledge in a creative and playful way. I will soon be organizing a scientific illustration workshop for a laboratory’s anniversary in Paris. I hope this event will be a success, and will add another string to my bow to share my work and initiate new collaborations.
In the future, I would like to adapt scientific illustration to different events and different media to allow a better popularisation of science and share its beauty with a large and diverse audience..

Twitter: @gamartjulie

Instagram: @gamartjulie

http://www.jgamart.com

Thanks to Julie and all the other SciArtists we have featured so far. We’re looking for new people to feature in this series – 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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Genetics Unzipped: Confident, competent or confused: What do you think you know about genetics?

Posted by , on 9 February 2023

Person filling in a survey

Extreme self-confidence is found, but not warranted for the most part, for those who are objecting to science. But it’s also found amongst those who are highly in favour of science. And the neutrals are: they know they don’t know.

Prof Laurence Hurst

In the latest episode of the Genetics Unzipped podcast, we’re sharing the results of a large survey asking the UK public what their opinions are, what they know, or more importantly, what they think they know about genetics and what that means for society.

Genetics Unzipped is the podcast from The Genetics Society. Full transcript, links and references available online at GeneticsUnzipped.com.

Subscribe from Apple podcasts, Spotify, or wherever you get your podcasts.

Head over to GeneticsUnzipped.com to catch up on our extensive back catalogue.

If you enjoy the show, please do rate and review on Apple podcasts and help to spread the word on social media. And you can always send feedback and suggestions for future episodes and guests to podcast@geneticsunzipped.com Follow us on Twitter – @geneticsunzip

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Development presents… January videos

Posted by , on 7 February 2023

On Wednesday 25 January, Development hosted three talks on the topic of theoretical and computational modelling of development and stem cells.

Below you’ll find each of the talks and Q&As hosted by our Associate Editor, Paul François (who recently moved to the University of Montreal from McGill University).

Simon Freedman (Senior Bioinformatics Scientist at Illumina presenting Postdoctoral work from Madhav Mani‘s group at Northwestern University)
‘A dynamical systems approach to cell fate decisions’

You can read the preprint here.

Mindy Liu Perkins (Postdoctoral Fellow in Justin Crocker‘s lab at EMBL presenting work from Hernan Garcia‘s lab)
‘A bistable autoregulatory module in the developing embryo commits cells to binary fates’

You can read the preprint here.

Kirsten ten Tusscher (Professor of Computational Developmental Biology at Utrecht University)
‘Reverse engineering lateral root formation’

You can read the Research Article here.

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Petition to remove academic age limits on ERC grants

Posted by , on 7 February 2023

Motion to ask ERC council to remove ‘academic age limits’ on ERC Starting and Consolidator grants.

https://www.change.org/p/remove-academic-age-limits-on-erc-grants

We would like to ask the ERC council to consider removing the ‘academic age limits’ as an eligibility criterion for applying for ERC Starting and Consolidator grants. The current “post 7 years” and “post 12 years” after PhD limits are extremely limiting and not in line with current timelines of research, especially in the Life Sciences. There are multiple reasons to ask for this (see examples below), but the main consensus is that such age limits select against social, economic, gender, ethnic and scientific diversity as it promotes people from privileged backgrounds, with straight forward and fast career paths, who are not necessarily the best scientists and mentors of future scientists. Scientific career paths are diverse, so putting one set of absolute time frames on different fields and different personal circumstances does not make sense. Experiments in animal models take much longer than theory. There may be delays due to different caring duties (of which child-birth is only one), illness, moving countries, changing fields, etc. With the current ‘age limits’, especially in countries where the ERC grants are the main source of large funding, once you ‘miss the boat’, you will never catch up, and your scientific career is severely impacted or prematurely ended. Should we be selecting scientific excellence based on speed, or quality?

We understand that to try to limit proposals submitted, and to have categories /cut offs to reflect career stage, there should be some ‘time-based’ criteria. Many countries, such as the UK, have removed these ‘absolute post PhD academic age limits’ on grants, and has thrived on new systems based on ‘new’, ‘mid’, or ‘senior’ investigators. If the ERC insists on having some time limits, we propose that a system such as this will be more inclusive:

– Starting Grant: up to 5 years since independence (defined as starting own group, faculty position, able to supervise PhD students independently, etc).

– Consolidator Grant: up to 12 years since independence.

– Advanced Grant: more than 12 years since independence.
(the current extensions to the above due to child birth, illness, etc, should still be applied).

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Announcing the Node correspondents

Posted by , on 6 February 2023

At the end of 2022 we launched our Node correspondent programme. We were looking for three researchers to help us develop and write content for the Node in 2023. The quality of the applications was extremely high, which made choosing our final three very difficult! We are delighted to announce that we have appointed Alex Bisia, Brent Foster and Dina Myasnikova as our correspondents for 2023. Our correspondents will benefit from a programme of writing groups, webinars and workshops coordinated by the in-house team at The Company of Biologists and will produce approximately six blog posts over the course of the year. We introduce our correspondents briefly below – stay tuned for longer interviews! 

Alex is completing her DPhil (PhD) at the University of Oxford with Elizabeth Robertson, studying the role of Eomesodermin, a T-box transcription factor, in the trophoblast and definitive endoderm in the early mouse embryo. Alex has a strong interest in science communication; she won the BSCB writing competition in 2020 and has contributed articles to her departmental website. Look out for Alex’s posts on non-model organisms, science history and contributions of developmental and stem cell biology in medicine. 

Brent is a technician at the University of Florida, working at the Whitney Laboratory for Marine Bioscience. Brent uses comb jellies and other marine invertebrates to study the evolutionary origin of nervous systems. He has previously written feature articles for his local newspaper, Society for Integrative and Comparative Biology (SICB) blog posts, and has attended several science writing workshops. Brent has a keen interest in non-model organisms and tool and technique development and will post on these topics. 

Dina is a Project Researcher at the Biohydrid System Laboratory at the University of Tokyo, where she is working on developing an organ-on-a-chip model of peripheral diabetic neuropathy. Having worked in an interdisciplinary team, she is keen to improve communication between scientists from different research backgrounds.  As well as exploring interdisciplinary research, Dina is passionate about helping women in science and will post on this topic. 

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January in preprints

Posted by , on 3 February 2023

Welcome to our monthly trawl for developmental and stem cell biology (and related) preprints. Congratulations to all the researchers who kicked off 2023 by preprinting their research.

The preprints this month are hosted on bioRxiv – use these links to get to the section you want.

Developmental biology

Cell Biology

Modelling

Reviews

Tools & Resources

Research practice & education

Developmental biology

| Patterning & signalling

Mouse intestine sections from Colozza, et al.

Intestinal Paneth cell differentiation relies on asymmetric regulation of Wnt signaling by Daam1/2
Gabriele Colozza, Heetak Lee, Alessandra Merenda, Szu-Hsien Sam Wu, Andrea Català-Bordes, Tomasz W. Radaszkiewicz, Ingrid Jordens, Ji-Hyun Lee, Aileen-Diane Bamford, Fiona Farnhammer, Teck Yew Low, Madelon M. Maurice, Vítězslav Bryja, Jihoon Kim, Bon-Kyoung Koo

Notch1 cortical signaling regulates epithelial architecture and cell-cell adhesion
Matthew J. White, Kyle A. Jacobs, Tania Singh, Matthew L. Kutys

Characterization of 3D organotypic epithelial tissues reveals tonsil-specific differences in tonic interferon signaling
Robert Jackson, Esha V Rajadhyaksha, Reid S Loeffler, Caitlyn E Flores, Koenraad Van Doorslaer

Spatial transcriptomics reveals a conserved segment polarity program that governs muscle patterning in Nematostella vectensis
Shuonan He, Wanqing Shao, Shiyuan (Cynthia) Chen, Ting Wang, Matthew C. Gibson

Foveolar cone subtype patterning in human retinal organoids
Katarzyna A Hussey, Kiara Eldred, Thomas Reh, Robert J. Johnston Jr

Cup is essential for oskar mRNA translational repression during early Drosophila oogenesis
Livia V. Bayer, Samantha Milano, Stephen K. Formel, Harpreet Kaur, Rishi Ravichandran, Juan A. Cambeiro, Lizaveta Slinko, Irina E. Catrina, Diana P. Bratu

Haploid androgenetic development in bovines reveals imbalanced WNT signaling and impaired cell fate differentiation
Luis M. Aguila, Ricardo P. Nociti, Rafael V. Sampaio, Jacinthe Therrien, Flavio V. Meirelles, Ricardo N. Felmer, Lawrence C. Smith

Dynamic fate map of hindbrain rhombomeres in zebrafish
Mageshi Kamaraj, Thierry Savy, Sophie Salomé Desnoulez, Nadine Peyrieras, Monique Frain

Control of gastruloid patterning and morphogenesis by the Erk and Akt signaling pathways
Evan J. Underhill, Jared E. Toettcher

Impact of cell size on morphogen gradient precision
Jan A. Adelmann, Roman Vetter, Dagmar Iber

Wengen, a Tumour Necrosis Factor Receptor, regulates the Fibroblast Growth Factor pathway by an unconventional mechanism
Annalisa Letizia, Maria Lluisa Espinàs, Marta Llimargas

The RALF Signaling Pathway Regulates Cell Wall Integrity during Pollen Tube Growth in Maize
Liang-Zi Zhou, Lele Wang, Zengxiang Ge, Julia Mergner, Xingli Li, Bernhard Küster, Gernot Längst, Li-Jia Qu, Thomas Dresselhaus

Shh and Chordin expression in veiled chameleon embryos from Shylo, et al.

Morphological changes and two Nodal paralogs drive left-right asymmetry in the squamate veiled chameleon (C. calyptratus)
Natalia A. Shylo, Sarah E. Smith, Andrew Price, Fengli Guo, Melainia McClain, Paul Trainor

Maternal and intrauterine influences on feto-placental growth are accompanied by sexually dimorphic changes in placental mitochondrial respiration, and metabolic signalling pathways
Esteban Salazar-Petres, Daniela Pereira-Carvalho, Jorge Lopez-Tello, Amanda Nancy Sferruzzi-Perri

The phosphodiesterase 2A regulates lymphatic endothelial development via cGMP-mediated control of Notch signaling
Claudia Carlantoni, Leon Liekfeld, Sandra A. Hemkemeyer, Danny Schreier, Ceren Saygi, Roberta Kurelic, Silvia Cardarelli, Joanna Kalucka, Christian Schulte, Manu Beerens, Reiner Mailer, Tilman Schäffer, Fabio Naro, Manuela Pellegrini, Viacheslav O. Nikolaev, Thomas Renné, Maike Frye

More than germ cells: vascular development in the early zebrafish (Danio rerio) gonad
Michelle E. Kossack, Lucy Tian, Kealyn Bowie, Jessica S. Plavicki

Reduced glycolysis links resting zone chondrocyte proliferation in the growth plate
Tatsuya Kobayashi, Cameron Young, Wen Zhou, Eugene P. Rhee

Establishment of Wnt ligand-receptor organization and cell polarity in the C. elegans embryo
Pierre Recouvreux, Pritha Pai, Rémy Torro, Mónika Ludányi, Pauline Mélénec, Mariem Boughzala, Vincent Bertrand, Pierre-François Lenne

Dally is not essential for Dpp spreading or internalization but for Dpp stability by antagonizing Tkv-mediated Dpp internalization
Niklas Simon, Abu Safyan, George Pyrowolakis, Shinya Matsuda

PRDM16 restricts stem cell proliferation by integrating BMP and Wnt signalling in the developing choroid plexus
Li He, Jiayu Wen, Qi Dai

BMP suppresses WNT to integrate patterning of orthogonal body axes in adult planarians
Eleanor G. Clark, Christian P. Petersen

Wnt signaling regulates ion channel expression to promote smooth muscle and cartilage formation in developing mouse trachea
Nicholas X. Russell, Kaulini Burra, Ronak Shah, Natalia Bottasso-Arias, Megha Mohanakrishnan, John Snowball, Harshavardhana H. Ediga, Satish K Madala, Debora Sinner

Leftward transfer of a chemosensory polycystin initiates left-dominant calcium signaling for lateralized embryonic development
Yosuke Tanaka, Ai Morozumi, Nobutaka Hirokawa

Not all Notch pathway mutations are equal in the embryonic mouse retina
Bernadett Bosze, Julissa Suarez-Navarro, Illiana Cajias, Joseph A. Brzezinski IV, Nadean L Brown

The multimodal action of G alpha q in coordinating growth and homeostasis in the Drosophila wing imaginal disc
Vijay Velagala, Dharsan K. Soundarrajan, Maria F. Unger, David Gazzo, Nilay Kumar, Jun Li, Jeremiah Zartman

Follicle stimulating hormone signaling opposes the DRL-1/FLR-4 MAP Kinases to balance p38-mediated growth and lipid homeostasis in C. elegans
Sarah K. Torzone, Aaron Y. Park, Peter C. Breen, Natalie R. Cohen, Robert H. Dowen

C. elegans SMOC-1 interacts with both BMP and glypican to regulate BMP signaling
Melisa S. DeGroot, Byron Williams, Timothy Y Chang, Maria L. Maas Gamboa, Isabel Larus, J. Christopher Fromme, Jun Liu

Type H vessels in mouse tibia from Lang, et al.

Endothelial SMAD1/5 signaling couples angiogenesis to osteogenesis during long bone growth
Annemarie Lang, Andreas Benn, Angelique Wolter, Tim Balcaen, Joseph Collins, Greet Kerckhofs, An Zwijsen, Joel D. Boerckel

The myocardium utilizes Pdgfra-PI3K signaling to steer towards the midline during heart tube formation
Rabina Shrestha, Tess McCann, Harini Saravanan, Jaret Lieberth, Prashanna Koirala, Joshua Bloomekatz

| Morphogenesis & mechanics

The mechanics of cephalic furrow formation in the Drosophila embryo
Redowan A. Niloy, Michael C. Holcomb, Jeffrey H. Thomas, Jerzy Blawzdziewicz

Mechanical forces in extendable tissue matrix orient cell divisions via microtubule stabilization in Arabidopsis
Lukas Hoermayer, Juan Carlos Montesinos, Leonhard Spona, Saiko Yoshida, Petra Marhava, Silvia Caballero-Mancebo, Eva Benková, Carl-Philip Heisenberg, Jiří Friml

KDM2B regulates hippocampal morphogenesis by transcriptionally silencing Wnt signaling in neural progenitors
Bo Zhang, Chen Zhao, Wenchen Shen, Wei Li, Yue Zheng, Xiangfei Kong, Junbao Wang, Xudong Wu, Ying Liu, Yan Zhou

Temporal variability and cell mechanics control robustness in mammalian embryogenesis
Dimitri Fabrèges, Bernat Corominas Murtra, Prachiti Moghe, Alison Kickuth, Takafumi Ichikawa, Chizuru Iwatani, Tomoyuki Tsukiyama, Nathalie Daniel, Julie Gering, Anniek Stokkermans, Adrian Wolny, Anna Kreshuk, Véronique Duranthon, Virginie Uhlmann, Edouard Hannezo, Takashi Hiiragi

Anoctamin 10/TMEM16K mediates convergent extension and tubulogenesis during notochord formation in the early chordate Ciona intestinalis
Zonglai Liang, Daniel Christiaan Dondorp, Marios Chatzigeorgiou

Mouse pancreatic explants from Darrigrand, et al.

Acinar-ductal cell rearrangement drives pancreas branching morphogenesis in an IGF/PI3K-dependent manner
Jean-Francois Darrigrand, Anna Salowka, Francesca M. Spagnoli

YAP and TAZ couple osteoblast precursor mobilization to angiogenesis and mechanoregulated bone development
Joseph M. Collins, Annemarie Lang, Cristian Parisi, Yasaman Moharrer, Madhura P. Nijsure, Jong Hyun (Thomas) Kim, Greg L. Szeto, Ling Qin, Riccardo L. Gottardi, Nathanial A. Dyment, Niamh C. Nowlan, Joel D. Boerckel

Mechanical models affecting beetle horn remodeling
Keisuke Matsuda, Haruhiko Adachi, Hiroki Gotoh, Yasuhiro Inoue, Shigeru Kondo

Spatio-temporal remodeling of extracellular matrix orients epithelial sheet folding
Alice Tsuboi, Koichi Fujimoto, Takefumi Kondo

Information integration during bioelectric regulation of morphogenesis in the embryonic frog brain
Santosh Manicka, Vaibhav P. Pai, Michael Levin

Durotaxis bridges phase transition as a function of tissue stiffness in vivo
Min Zhu, Bin Gu, Evan Thomas, Hirotaka Tao, Theodora M. Yung, Kaiwen Zhang, Janet Rossant, Yu Sun, Sevan Hopyan

| Genes & genomes

Modulating the epigenetic state promotes the reprogramming of transformed cells to pluripotency in a line-specific manner
Xiuling Fu, Qiang Zhuang, Isaac A. Babarinde, Liyang Shi, Gang Ma, Haoqing Hu, Yuhao Li, Jiao Chen, Zhen Xiao, Boping Deng, Li Sun, Ralf Jauch, Andrew P. Hutchins

Genomic resources enable insight into the developmental transcriptome of the blastoclad fungus, Coelomomyces lativittatus, an obligate parasite of mosquitoes and microcrustaceans
Cassandra L. Ettinger, Talieh Ostovar, Mark Yacoub, Steven Ahrendt, Robert H. Hice, Brian A. Federici, Jason E. Stajich

An epigenetic basis of adaptive plasticity in Drosophila melanogaster
Abigail DiVito Evans, Regina A. Fairbanks, Paul Schmidt, Mia T. Levine

Spatial enhancer activation determines inhibitory neuron identity
Elena Dvoretskova, May C. Ho, Volker Kittke, Ilaria Vitali, Daniel D. Lam, Irene Delgado, Chao Feng, Miguel Torres, Juliane Winkelmann, Christian Mayer

scMultiome analysis identifies embryonic hindbrain progenitors with mixed rhombomere identities
Yong-Il Kim, Rebecca O’Rourke, Charles G. Sagerström

ChIP-seq heatmaps from Mancheno-Ferris, et al.

Crosstalk between chromatin and the transcription factor Shavenbaby defines transcriptional output along the Drosophila intestinal stem cell lineage
Alexandra Mancheno-Ferris, Clément Immarigeon, Alexia Rivero, David Depierre, Nicolas Chanard, Olivier Fosseprez, Gabriel Aughey, Priscilla Lhoumaud, Julien Anglade, Tony Southall, Serge Plaza, Olivier Cuvier, François Payre, Cédric Polesello

Eomes restricts Brachyury functions at the onset of mammalian gastrulation
Katrin M. Schüle, Jelena Weckerle, Simone Probst, Alexandra E. Wehmeyer, Lea Zissel, Chiara M. Schröder, Mehmet Tekman, Gwang-Jin Kim, Inga-Marie Schlägl, Sagar, Sebastian J. Arnold

Single cell transcriptomics of human prenatal anterior foregut-derived organs identifies distinct developmental signatures directing commitment and specialization of the thymic epithelial stroma
Abdulvasey Mohammed, Benjamin Solomon, Priscila F. Slepicka, Kelsea M. Hubka, Hanh Dan Nguyen, Michael G. Chavez, Christine Y. Yeh, Virginia D. Winn, Casey A. Gifford, Purvesh Khatri, Andrew Gentles, Katja G. Weinacht

Cellular remodeling and JAK inhibition promote zygotic gene expression in the Ciona germline
Naoyuki Ohta, Lionel Christiaen

A transcriptional and regulatory map of mouse somitogenesis
Ximena Ibarra-Soria, Elodie Thierion, Gi Fay Mok, Andrea E. Münsterberg, Duncan T. Odom, John C. Marioni

YTHDC2 serves a distinct late role in spermatocytes during germ cell differentiation
Alexis S. Bailey, Margaret T. Fuller

Mitochondrial citrate metabolism and efflux regulates trophoblast differentiation
Renee M. Mahr, Snehalata Jena, Sereen K. Nashif, Alisa B. Nelson, Adam J. Rauckhorst, Ferrol I. Rome, Ryan D. Sheldon, Curtis C. Hughey, Patrycja Puchalska, Micah D. Gearhart, Eric B. Taylor, Peter A. Crawford, Sarah A. Wernimont

Whole transcriptome profiling of placental pathobiology in SARS-CoV-2 pregnancies identifies a preeclampsia-like gene signature
Nataly Stylianou, Ismail Sebina, Nicholas Matigian, James Monkman, Hadeel Doehler, Joan Röhl, Mark Allenby, Andy Nam, Liuliu Pan, Anja Rockstroh, Habib Sadeghirad, Kimberly Chung, Thais Sobanski, Ken O’Byrne, Patricia Zadorosnei Rebutini, Cleber Machado-Souza, Emanuele Therezinha Schueda Stonoga, Majid E Warkiani, Carlos Salomon, Kirsty Short, Lana McClements, Lucia de Noronha, Ruby Huang, Gabrielle T. Belz, Fernando Souza-Fonseca-Guimaraes, Vicki Clifton, Arutha Kulasinghe

Determinants of renin cell differentiation: a single cell epi-transcriptomics approach
Alexandre G Martini, Jason P. Smith, Silvia Medrano, Nathan C. Sheffield, Maria Luisa S. Sequeira-Lopez, R. Ariel Gomez

NuRD independent Mi-2 activity represses ectopic gene expression during neuronal maturation
Gabriel N Aughey, Elhana Forsberg, Krista Grimes, Shen Zhang, Tony D Southall

Dbx2, an aging-related homeobox gene, inhibits the proliferation of adult neural progenitors
Andrea Giuliani, Valerio Licursi, Paola S. Nisi, Mario Fiore, Stefano Biagioni, Rodolfo Negri, Peter J. Rugg-Gunn, Emanuele Cacci, Giuseppe Lupo

Nr5a2 is essential for morula development
Nicola Festuccia, Sandrine Vandormael-Pournin, Almira Chervova, Anna Geiselman, Francina Langa-Vives, Rémi-Xavier Coux, Inma Gonzalez, Michel Cohen-Tannoudji, Pablo Navarro

DMRT1 is a Testis Determining Gene in Rabbits and is Also Essential for Female Fertility
Emilie Dujardin, Marjolaine André, Aurélie Dewaele, Béatrice Mandon-Pépin, Francis Poulat, Anne Frambourg, Dominique Thépot, Luc Jouneau, Geneviève Jolivet, Eric Pailhoux, Maëlle Pannetier

Summary profiles of H3K27ac histone mark from Riesle, et al.

Activator-blocker model of transcriptional regulation by pioneer-like factors
Aileen Julia Riesle, Meijiang Gao, Marcus Rosenblatt, Jacques Hermes, Helge Hass, Anna Gebhard, Marina Veil, Björn Grüning, Jens Timmer, Daria Onichtchouk

DNA elements tether canonical Polycomb Repressive Complex 1 to human genes
Juan I. Barrasa, Tatyana G. Kahn, Moa J. Lundkvist, Yuri B. Schwartz

Single-cell response to Wnt activation in human embryonic stem cells reveals uncoupling of Wnt target gene expression
Simon Söderholm, Amaia Jauregi-Miguel, Pierfrancesco Pagella, Valeria Ghezzi, Gianluca Zambanini, Anna Nordin, Claudio Cantù

Single-cell transcriptomic profiling redefines the origin and specification of early adrenogonadal progenitors
Yasmine Neirijnck, Pauline Sararols, Françoise Kühne, Chloé Mayère, Serge Nef, Andreas Schedl

Modulation of protein-DNA binding reveals mechanisms of spatiotemporal gene control in early Drosophila embryos
Sahla Syed, Yifei Duan, Bomyi Lim

INO80 regulates chromatin accessibility to facilitate meiotic sex chromosome inactivation
Prabuddha Chakraborty, Terry Magnuson

Transient loss of Polycomb components induces an epigenetic cancer fate
V. Parreno, V. Loubière, B. Schuettengruber, M. Erokhin, B. Győrffy, M. Di Stefano, L. Fritsch, J. Moreaux, D. Chetverina, A-M. Martinez, G. Cavalli

Loss of NR5A1 in Sertoli cells after sex determination changes their cellular identity and induces their death by anoikis
Sirine Souali-Crespo, Diana Condrea, Nadège Vernet, Betty Féret, Muriel Klopfenstein, Erwan Grandgirard, Violaine Alunni, Marie Cerciat, Matthieu Jung, Chloé Mayere, Serge Nef, Manuel Mark, Frédéric Chalmel, Norbert B. Ghyselinck

TOBF1 modulates mouse embryonic stem cell fate through co-transcriptional regulation of alternative splicing
Meghali Aich, Asgar Hussain Ansari, Li Ding, Vytautas Iesmantavicius, Deepanjan Paul, Chunaram Choudhary, Souvik Maiti, Frank Buchholz, Debojyoti Chakraborty

| Stem cells, regeneration & disease modelling

IRF1 regulates self-renewal and stress-responsiveness to support hematopoietic stem cell maintenance
Alexandra Rundberg Nilsson, Hongxu Xian, Shabnam Shalapour, Jörg Cammenga, Michael Karin

The Sin3B chromatin modifier restricts cell cycle progression to dictate hematopoietic stem cell differentiation
Alexander Calderon, Tamara Mestvirishvili, Francesco Boccalatte, Kelly V. Ruggles, Gregory David

Cell division tracing combined with single-cell transcriptomics reveals new cell types and differentiation paths in the regenerating mouse lung
Leila R. Martins, Lina Sieverling, Michelle Michelhans, Chiara Schiller, Cihan Erkut, Sergio Triana, Stefan Fröhling, Lars Velten, Hanno Glimm, Claudia Scholl

Zebrafish retina from Konar, et al.

Damage-induced senescent immune cells regulate regeneration of the zebrafish retina
Gregory Konar, Zachary Flickinger, Shivani Sharma, Kyle Vallone, Charles Lyon, Claire Doshier, William Lyon, James G. Patton

Age-dependent structural and morphological changes of the stem cell niche disrupt spatiotemporal regulation of stem cells and drive tissue disintegration
Michelle A. Urman, Nimmy S. John, ChangHwan Lee

TGFB1 Induces Fetal Reprogramming and Enhances Intestinal Regeneration
Lei Chen, Abigail Dupre, Xia Qiu, Oscar Pellon-Cardenas, Katherine D. Walton, Jianming Wang, Ansu O. Perekatt, Wenwei Hu, Jason R. Spence, Michael P. Verzi

Dominant-negative mutations in CBX1 cause a neurodevelopmental disorder
Yukiko Kuroda, Aiko Iwata-Otsubo, Kerith-Rae Dias, Suzanna E.L. Temple, Koji Nagao, Lachlan De Hayr, Ying Zhu, Shin-Ya Isobe, Gohei Nishibuchi, Sarah K Fiordaliso, Yuki Fujita, Alyssa L. Rippert, Samuel W Baker, Marco L. Leung, Daniel C. Koboldt, Adele Harman, Beth A. Keena, Izumi Kazama, Gopinath Musuwadi Subramanian, Kandamurugu Manickam, Betsy Schmalz, Maeson Latsko, Elaine H Zackai, Matt Edwards, Carey-Anne Evans, Matthew C. Dulik, Michael F. Buckley, Toshihide Yamashita, W. Timothy O’Brien, Robert J. Harvey, Chikashi Obuse, Tony Roscioli, Kosuke Izumi

Conditional blastocyst complementation of a defective Foxa2 lineage efficiently promotes generation of the whole lung
Akihiro Miura, Hemanta Sarmah, Junichi Tanaka, Youngmin Hwang, Anri Sawada, Yuko Shimamura, Yinshan Fang, Dai Shimizu, Zurab Ninish, Jake Le Suer, Nicole C. Dubois, Jennifer Davis, Shinichi Toyooka, Jun Wu, Jianwen Que, Finn J. Hawkins, Chyuan-Sheng Lin, Munemasa Mori

RUNX1 is required in granulocyte-monocyte progenitors to attenuate inflammatory cytokine production by neutrophils
Alexandra U. Zezulin, Darwin Ye, Elizabeth Howell, Daniel Yen, Erica Bresciani, Jamie Diemer, Jian-gang Ren, Mohd Hafiz Ahmad, Lucio H. Castilla, Ivo P. Touw, Andy J. Minn, Wei Tong, P. Paul Liu, Kai Tan, Wenbao Yu, Nancy A. Speck

Mutation of gabra1 is associated with hypermotility and abnormal expression of proteins critical for ion homeostasis and synaptic vesicle transport
Nayeli G. Reyes-Nava, Isaiah Perez, Brian Grajeda, Igor L. Estevao, Cameron C. Ellis, Sourav Roy, Anita M. Quintana

Fetal exposure to endocrine disrupting-bisphenol A (BPA) alters testicular fatty acid metabolism in the adult offspring: relevance to sperm maturation and quality
Saikanth Varma, Archana Molangiri, Suryam Reddy Kona, Ahamed Ibrahim, Asim K Duttaroy, Sanjay Basak

scRNAseq unravels the transcriptional network underlying zebrafish retina regeneration
Laura Celotto, Fabian Rost, Anja Machate, Juliane Bläsche, Andreas Dahl, Anke Weber, Stefan Hans, Michael Brand

Nematostella vectensis gonadal mesentery region tissues from Miramón-Puértolas and Steinmetz

An adult stem-like cell population generates germline and neurons in the sea anemone Nematostella vectensis
Paula Miramón-Puértolas, Patrick R.H. Steinmetz

Abnormal chondrocyte intercalation in a zebrafish model of cblC syndrome restored by an MMACHC cobalamin binding mutant
David Paz, Briana E. Pinales, Barbara S. Castellanos, Isaiah Perez, Claudia B. Gil, Lourdes Jimenez Madrigal, Nayeli G. Reyes-Nava, Victoria L. Castro, Jennifer L. Sloan, Anita M. Quintana

Nutrient-regulated dynamics of chondroprogenitors in the postnatal murine growth plate
Takeshi Oichi, Joe Kodama, Kimberly Wilson, Hongying Tian, Yuka Imamura, Yu Usami, Yasushi Oshima, Taku Saito, Sakae Tanaka, Masahiro Iwamoto, Satoru Otsuru, Motomi Iwamoto-Enomoto

Spatiotemporal reconstruction of the origin and assembly of smooth muscles in the intestinal villus
Bhargav D. Sanketi, Madhav Mantri, Mohammad A. Tavallaei, Shing Hu, Michael F. Z. Wang, Iwijn De Vlaminck, Natasza A. Kurpios

Coordinated multiple cellular processes in tongue development
Maiko Kawasaki, Katsushige Kawasaki, Finsa Tisna Sari, Takehisa Kudo, Jun Nihara, Madoka Kitamura, Takahiro Nagai, Vanessa Utama, Yoko Ishida, Fumiya Meguro, Takayuki Nishimura, Yuan Kogure, Satoshi Maruyama, Jun-ichi Tanuma, Yoshito Kakihara, Takeyasu Maeda, Sarah Ghafoor, Roman H. Khonsari, Pierre Corre, Paul T. Sharpe, Martyn T. Cobourne, Brunella Franco, Atsushi Ohazama

Apical expansion of calvarial osteoblasts and suture patency is dependent on graded fibronectin cues
Xiaotian Feng, Helen Molteni, Megan Gregory, Jennifer Lanza, Nikaya Polsani, Rachel Wyetzner, M. Brent Hawkins, Greg Holmes, Sevan Hopyan, Matthew P. Harris, Radhika P. Atit

Biallelic Variants in MAD2L1BP (p31comet) Cause Female Infertility Characterized by Oocyte Maturation Arrest
Lingli Huang, Wenqing Li, Xingxing Dai, Shuai Zhao, Bo Xu, Fengsong Wang, Ren-Tao Jin, Lihua Luo, Liming Wu, Xue Jiang, Yu Cheng, Jiaqi Zou, Caoling Xu, Xianhong Tong, Heng-yu Fan, Han Zhao, Jianqiang Bao

SMIM36, a novel and conserved microprotein, is involved in retinal lamination in zebrafish
Surbhi Sharma, Soundhar Ramasamy, Yasmeen Khan, Dheeraj Chandra Joshi, Beena Pillai

The exon junction complex component EIF4A3 is essential for mouse and human cortical progenitor mitosis and neurogenesis
Bianca M. Lupan, Rachel A. Solecki, Camila Manso Musso, Fernando C. Alsina, Debra L. Silver

Production of β-PheRS fragments correlates with food avoidance and slow growth, and is suppressed by the appetite-inducing hormone CCHa2
Dominique Brunßen, Beat Suter

Maternal exposure to environmental levels of carbamazepine induces mild growth retardation in mouse embryos
Douek-Maba Orit, Kalev-Altman Rotem, Mordehay Vered, Hayby-Averbuch Hilla, Shlezinger Neta, Chefetz Benny, Sela-Donenfeld Dalit

Adult stem cell characterization from the Medial Gastrocnemius and Semitendinosus muscles in early development of cerebral palsy pathology
M Corvelyn, J Meirlevede, J Deschrevel, E Huyghe, E De Wachter, G Gayan-Ramirez, M Sampaolesi, A Van Campenhout, K Desloovere, D Costamagna

Metaphase mitotic spindles in Drosophila larval neuroepithelial cells from Mannino, et al.

The neurodevelopmental transcriptome of the Drosophila melanogaster microcephaly gene abnormal spindle reveals a role for temporal transcription factors and the immune system in regulating brain size
Maria C. Mannino, Mercedes Bartels Cassidy, Steven Florez, Zeid Rusan, Shalini Chakraborty, Todd Schoborg

Six3 acts independently of Pax6 to provide an essential contribution to lens development
Sumanth Manohar, Takuya Nakayama, Marilyn Fisher, Robert M. Grainger

Macrophage activation drives ovarian failure and masculinization
Paloma Bravo, Yulong Liu, Bruce W. Draper, Florence L. Marlow

Directed differentiation of human hindbrain neuroepithelial stem cells recapitulates cerebellar granule neurogenesis
Biren M. Dave, Xin Chen, Fraser McCready, Jignesh K. Tailor, James Ellis, Xi Huang, Peter B. Dirks

Defining Cardiac Nerve Architecture During Development, Disease, and Regeneration
Rebecca J. Salamon, Poorva Halbe, William Kasberg, Jiyoung Bae, Anjon Audhya, Ahmed I. Mahmoud

| Plant development

Three-dimensional morphological analysis revealed the cell patterning bases for the sexual dimorphism development in the liverwort Marchantia polymorpha
Yihui Cui, Tetsuya Hisanaga, Tomoaki Kajiwara, Shohei Yamaoka, Takayuki Kohchi, Tatsuaki Goh, Keiji Nakajima

AGAMOUS mediates timing of guard cell formation during gynoecium development
Ailbhe J. Brazel, Róisín Fattorini, Jesse McCarthy, Rainer Franzen, Florian Rümpler, George Coupland, Diarmuid S. Ó’Maoiléidigh

Establishment of cell transcriptional identity during seed germination
Lim Chee Liew, Yue You, Marina Oliva, Marta Peirats-Llobet, Sophia Ng, Muluneh Tamiru-Oli, Oliver Berkowitz, Uyen Vu Thuy Hong, Asha Haslem, Tim Stuart, Matthew E. Ritchie, George W. Bassel, Ryan Lister, James Whelan, Quentin Gouil, Mathew G. Lewsey

Sugar signaling modulates SHOOT MERISTEMLESS expression and meristem function in Arabidopsis
Filipa L. Lopes, Pau Formosa-Jordan, Alice Malivert, Leonor Margalha, Ana Confraria, Regina Feil, John E. Lunn, Henrik Jönsson, Benoît Landrein, Elena Baena-González

Cellular growth along mediolateral axes of the Arabidopsis gynoecium from Gómez-Felipe, et al.

Competing differentiation gradients coordinate fruit morphogenesis
A. Gómez-Felipe, M. Marconi, E. Branchini, B. Wang, H. Bertrand-Rakusova, T. Stan, J. Burkiewicz, S. de Folter, A-L. Routier-Kierzkowska, K. Wabnik, D. Kierzkowski

Microbe-induced plant drought tolerance by ABA-mediated root morphogenesis and epigenetic reprogramming of gene expression
Khairiah M. Alwutayd, Anamika A. Rawat, Arsheed H. Sheikh, Marilia Almeida-Trapp, Alaguraj Veluchamy, Rewaa Jalal, Michael Karampelias, Katja Froehlich, Waad Alzaed, Naheed Tabassum, Thayssa Rabelo Schley, Anton R. Schaeffner, Ihsanullah Daur, Maged M. Saad, Heribert Hirt

| Evo-devo

Wolbachia is a nutritional symbiont
Amelia RI Lindsey, Audrey J Parish, Irene LG Newton, Jason M Tennessen, Megan W Jones, Nicole Stark

Systemic orchestration of cell size throughout the body: Influence of sex and rapamycin exposure in Drosophila melanogaster
Ewa Szlachcic, Anna Maria Labecka, Valeriya Privalova, Anna Sikorska, Marcin Czarnoleski

Evolutionary history of the Brachyury gene in Hydrozoa: duplications, divergence and neofunctionalization
Alexandra A. Vetrova, Daria M. Kupaeva, Tatiana S. Lebedeva, Peter Walentek, Nikoloz Tsikolia, Stanislav V. Kremnyov

Cell Biology

Spontaneous rotations in epithelia as an interplay between cell polarity and boundaries.
Simon Lo Vecchio, Olivier Pertz, Marcela Szopos, Laurent Navoret, Daniel Riveline

Nhsl1b regulates mesodermal cell migration by controlling protrusion dynamics during zebrafish gastrulation
Sophie Escot, Amélie Elouin, Lucille Mellottee, Nicolas B David

Newly born mesenchymal cells disperse through a rapid mechanosensitive migration
Jon Riddell, Shahzeb Raja Noureen, Luigi Sedda, James D. Glover, William K. W. Ho, Connor A. Bain, Arianna Berbeglia, Helen Brown, Calum Anderson, Yuhang Chen, Michael L. Crichton, Christian A. Yates, Richard L. Mort, Denis J. Headon

A planar-polarized MYO6-DOCK7-RAC1 axis promotes tissue fluidification in mammary epithelia
Luca Menin, Janine Weber, Stefano Villa, Emanuele Martini, Elena Maspero, Valeria Cancila, Paolo Maiuri, Andrea Palamidessi, Emanuela Frittoli, Fabrizio Bianchi, Claudio Tripodo, Kylie J. Walters, Fabio Giavazzi, Giorgio Scita, Simona Polo

The Shot CH1 domain recognises a distinct form of F-actin during Drosophila oocyte determination
D. Nashchekin, I. Squires, A. Prokop, D. St Johnston

hESCs from Meyer, et al.

Arp2/3 Complex Activity Enables Nuclear YAP for Naïve Pluripotency of Human Embryonic Stem Cells
Nathaniel P. Meyer, Tania Singh, Matthew L. Kutys, Todd Nystul, Diane L. Barber

SCAR and the Arp2/3 complex polarise the actomyosin cortex and plasma membrane organization in asymmetrically dividing neuroblasts
Giulia Cazzagon, Chantal Roubinet, Buzz Baum

Sperm-contributed centrioles segregate stochastically into blastomeres of 4-cell stage C. elegans embryos
Pierre Gönczy, Fernando R. Balestra

Intrinsic microtubule destabilization of multiciliated choroid plexus epithelial cells during postnatal lifetime
Kim Hoa Ho, Valentina Scarpetta, Chiara Salio, Elisa D’Este, Martin Meschkat, Christian A. Wurm, Matthias Kneussel, Carsten Janke, Maria M. Magiera, Marco Sassoè-Pognetto, Monika S. Brill, Annarita Patrizi

Modelling

Unbalanced response to growth variations reshapes the cell fate decision landscape
Jingwen Zhu, Pan Chu, Xiongfei Fu

Artificial intelligence supports automated characterization of differentiated human pluripotent stem cells
Katarzyna Marzec-Schmidt, Nidal Ghosheh, Sören Richard Stahlschmidt, Barbara Küppers-Munther, Jane Synnergren, Benjamin Ulfenborg

CoVar: A generalizable machine learning approach to identify the coordinated regulators driving variational gene expression
Satyaki Roy, Shehzad Z. Sheikh, Terrence S. Furey

A Clock and Wavefront Self-Organizing model explains somitogenesis in vivo and in vitro
Julie Klepstad, Luciano Marcon

Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics
Iris. A. Unterweger, Julie Klepstad, Edouard Hannezo, Pia R. Lundegaard, Ala Trusina, Elke A. Ober

Machine-guided cell-fate engineering
Evan Appleton, Jenhan Tao, Greg Fonseca, Songlei Liu, Christopher Glass, George Church

Flow similarity model predicts the allometry and allometric covariation of petiole dimensions
Charles A. Price

Tools & Resources

hiPSC and cardiomyocyte co-cultures from Dvinskikh, et al.

Remote-refocusing light-sheet fluorescence microscopy enables 3D imaging of electromechanical coupling of hiPSC-derived and adult cardiomyocytes in co-culture
L Dvinskikh, H Sparks, L Brito, K MacLeod, SE Harding, C Dunsby

Utilization of an Artery-on-a-chip to unravel novel regulators and therapeutic targets in vascular diseases
Valentina Paloschi, Jessica Pauli, Greg Winski, Zhiyuan Wu, Zhaolong Li, Nadiya Glukha, Nora Hummel, Felix Rogowitz, Sandro Meucci, Lorenzo Botti, Albert Busch, Ekaterina Chernogubova, Hong Jin, Nadja Sachs, Hans-Henning Eckstein, Anne Dueck, Reinier A. Boon, Andreas R. Bausch, Lars Maegdefessel

Hep3D: A 3D single-cell digital atlas of the liver to study spatio-temporal tissue architecture
Dilan Martínez, Valentina Maldonado, Cristian Pérez, Rodrigo Yañez, Valeria Candia, Yannis Kalaidzidis, Marino Zerial, Hernán Morales-Navarrete, Fabián Segovia-Miranda

Generation of human alveolar epithelial type I cells from pluripotent stem cells
Claire L Burgess, Jessie Huang, Pushpinder Bawa, Konstantinos-Dionysios Alysandratos, Kasey Minakin, Michael P Morley, Apoorva Babu, Carlos Villacorta-Martin, Anne Hinds, Bibek R Thapa, Feiya Wang, Adeline M Matschulat, Edward E Morrisey, Xaralabos Varelas, Darrell N Kotton

A 3-dimensional molecular cartography of human cerebral organoids revealed by double-barcoded spatial transcriptomics
Gwendoline Lozachmeur, Aude Bramoulle, Antoine Aubert, François Stüder, Julien Moehlin, Lucie Madrange, Frank Yates, Jean-Philippe Deslys, Marco Antonio Mendoza-Parra

Trophoblast organoids with physiological polarity model placental structure and function
Liheng Yang, Pengfei Liang, Huanghe Yang, Carolyn B. Coyne

Targeted gene deletion with SpCas9 and multiple guide RNAs in Arabidopsis thaliana: four are better than two
Jana Ordon, Niklas Kiel, Dieter Becker, Carola Kretschmer, Paul Schulze-Lefert, Johannes Stuttmann

Ultrasensitive Proteomics Depicted an In-depth Landscape for Mouse Embryo
Lei Gu, Xumiao Li, Wencheng Zhu, Yi Shen, Qinqin Wang, Huiping Zhang, Jingquan Li, Ziyi Li, Zhen Liu, Chen Li, Hui Wang

CRaTER enrichment for on-target gene-editing enables generation of variant libraries in hiPSCs
Clayton E. Friedman, Shawn Fayer, Sriram Pendyala, Wei-Ming Chien, Linda Tran, Leslie Chao, Ashley Mckinstry, Elaheh Karbassi, Aidan M. Fenix, Alexander Loiben, Charles E. Murry, Lea M. Starita, Douglas M. Fowler, Kai-Chun Yang

Targeted Screening and Identification of Chlorhexidine as a Pro-myogenic Circadian Clock Activator
Tali Kiperman, Weini Li, Xuekai Xiong, Hongzhi Li, David Horne, Ke Ma

Automated staging of zebrafish embryos with KimmelNet
David J. Barry, Rebecca A. Jones, Matthew J. Renshaw

spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content
Joachim De Jonghe, Tomasz S. Kaminski, David B. Morse, Marcin Tabaka, Anna L. Ellermann, Timo N. Kohler, Gianluca Amadei, Charlotte Handford, Gregory M. Findlay, Magdalena Zernicka-Goetz, Sarah A. Teichmann, Florian Hollfelder

Epithelioids from Herms, et al.

Epithelioids: Self-sustaining 3D epithelial cultures to study long-term processes
Albert Herms, David Fernandez-Antoran, Maria P. Alcolea, Argyro Kalogeropoulou, Ujjwal Banerjee, Gabriel Piedrafita, Emilie Abby, Jose Antonio Valverde-Lopez, Inês S. Ferreira, Stefan C. Dentro, Swee Hoe Ong, Bartomeu Colom, Kasumi Murai, Charlotte King, Krishnaa Mahbubani, Kourosh Saeb-Parsy, Alan R Lowe, Moritz Gerstung, Philip H Jones

Emergent dynamics of adult stem cell lineages from single nucleus and single cell RNA-Seq of Drosophila testes
Amelie A. Raz, Gabriela S. Vida, Sarah R. Stern, Sharvani Mahadevaraju, Jaclyn M. Fingerhut, Jennifer M. Viveiros, Soumitra Pal, Jasmine R. Grey, Mara R. Grace, Cameron W. Berry, Hongjie Li, Jasper Janssens, Wouter Saelens, Zhantao Shao, Chun Hu, Yukiko M. Yamashita, Teresa M. Przytycka, Brian Oliver, Julie A. Brill, Henry M. Krause, Erika L. Matunis, Helen White-Cooper, Stephen DiNardo, Margaret T. Fuller

Inducible in vivo genome editing in the sea star Patiria miniata
Olga Zueva, Veronica F. Hinman

Development of Encarsia tabacivora (Viggiani) (Hymenoptera: Aphelinidae) in nymphs of Bemisia tabaci (Gennadius) MEAN 1 (Hemiptera: Aleyrodidae)
Heidy Gamarra, Marc Sporleder, Luz Supanta, Alexander Rodríguez, Jürgen Kroschel, Jan Kreuze

CartoCell, a high-throughput pipeline for accurate 3D image analysis, unveils cell morphology patterns in epithelial cysts
Jesús A. Andrés-San Román, Carmen Gordillo-Vázquez, Daniel Franco-Barranco, Laura Morato, Antonio Tagua, Pablo Vicente-Munuera, Ana M. Palacios, María P. Gavilán, Valentina Annese, Pedro Gómez-Gálvez, Ignacio Arganda-Carreras, Luis M. Escudero

A single-cell, time-resolved profiling of Xenopus mucociliary epithelium reveals non-hierarchical model of development
Julie Lee, Andreas Fønss Møller, Shinhyeok Chae, Alexandra Bussek, Tae Joo Park, Youni Kim, Hyun-Shik Lee, Tune H. Pers, Taejoon Kwon, Jakub Sedzinski, Kedar Nath Natarajan

The Embryonic Origin of Primordial Germ Cells in the Tardigrade Hypsibius exemplaris
Kira L. Heikes, Mandy Game, Frank W. Smith, Bob Goldstein

LoxCode in vivo clonal barcoding resolves mammalian epiblast contribution to fetal organs
Tom S. Weber, Christine Biben, Denise C. Miles, Stephen Zhang, Patrick Tam, Samir Taoudi, Shalin H. Naik

Research practice & education

Talk To A Scientist: A Framework for a Webinar-Based Science Outreach Platform for Children
Shreeya Mhade, Snehal Kadam, Karishma Kaushik

Scientific civility and academic performance
Emma Camacho, Quigly Dragotakes, Isabella Hartshorn, Arturo Casadevall, Daniel L Buccino

Improving Interdisciplinary Teaching through a Complexity Lens
Sarah Neitzel, Yuhao Zhao, Carrie Diaz Eaton

A publishing infrastructure for AI-assisted academic authoring
Milton Pividori, Casey S. Greene

Experiential diversity training and science learning for college students alongside peers with intellectual and developmental disabilities
Kaelin N. Rubenzer, Jonathan T. Pierce

Fly-CURE, a Multi-institutional CURE using Drosophila, Increases Students’ Confidence, Sense of Belonging, and Persistence in Research
Julie A. Merkle, Olivier Devergne, Seth M. Kelly, Paula A. Croonquist, Cory J. Evans, Melanie A. Hwalek, Victoria L. Straub, Danielle R. Hamill, David P. Puthoff, Kenneth J. Saville, Jamie L. Siders, Zully J. Villanueva Gonzalez, Jackie K. Wittke-Thompson, Kayla L. Bieser, Joyce Stamm, Alysia D. Vrailas-Mortimer, Jacob D. Kagey

The Preprint Club – A cross-institutional, community-based approach to peer reviewing
Felix Clemens Richter, Ester Gea-Mallorquí, Nicolas Ruffin, Nicolas Vabret

Innovative Research Experiences for Underrepresented Undergraduates: A Collaborative STEM Research Program as a Pathway to Graduate School
Gokhan Hacisalihoglu

Sustained Selective Attention in Adolescence: Cognitive Development and Predictors of Distractibility at School
Michael H. Hobbiss, Nilli Lavie

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From the Node to FocalPlane – a farewell

Posted by , on 2 February 2023

Dear all,

Yesterday was my last official day as the Community Manager of the Node, and I wanted to take this opportunity to thank all the Node community for being so welcoming over the last 18 months. I’ll still be moonlighting on the Node, alongside preLights Community Manager Reinier Prosée, until we have the new Community Manager in place. If you have any questions, comments and feedback, you can still contact us at thenode@biologists.com. It’s lucky that I get to hang around for a while longer, as we have been working on a couple of new projects that we hope to share with you in the next month. Watch this space!

One of the projects that we are working on is a collaboration between the Node and FocalPlane. FocalPlane will be my new home as I have moved across to join the Journal of Cell Science team as FocalPlane Community Manager. If you use microscopy as part of your work, or would like to get started, I recommend checking out our website! Like the Node, FocalPlane is driven by the community, so if you have any feedback, suggestions or comments please get in touch at focalplane@biologists.com or helen.zenner@biologists.com. If you would like to contribute to the site with a blog post, event listing, or job advert, you can register and request permission to write, and once approved you’ll be ready to go.

Thanks again for all the fun times on the Node. I’ve had the opportunity to interact with some amazing people, not least the wonderful team at Development – Alex, who puts up with all my ‘stupid’ questions (not sure this is going to stop), Seema, who helped me so much when I started, and Katherine, who is the most excellent manager! I’m now excited to try and bring some of ‘the Node spirit’ to FocalPlane and hope to see you there.

Best wishes, Helen

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Categories: News

Stories from Christopher Wright

Posted by , on 1 February 2023

At the Joint Society for Developmental Biology (SDB) – Pan-American Society for Evolutionary Developmental Biology Meeting in 2022, I spoke to Christopher Wright, the winner of the 2022 SDB Victor Hamburger Outstanding Educator Prize. You can read the interview in Development, but Chris shared some stories that we couldn’t squeeze in, so with his permission I have reproduced a couple of examples here. I selected these stories as they show the fun side of doing science and the excitement for biology that Chris expressed throughout our interview.

Science on a whim

“When I was in Eddy de Robertis’ lab for my postdoc, we decided to start probing the organizer region – the Spemann-Mangold organizer – for homeobox genes. We did this on a whim when Eddy went on vacation, and when he came back several people in the lab were running around clearly excited running old-school “high-throughput” DNA sequencing by hand. We told Eddy what we’d done and he was somewhat shocked. But, in the end, organizer molecules were what set his lab moving forward for the next 10 or 15 years. Out of that work came goosecoid. A huge amount of work went on after I had left, but finding goosecoid and naming it, based on part of its homeodomain sequence resembling the fruit fly gene gooseberry and the other part bicoid, was great. We decided that ‘bicberry’ sounded wrong but goosecoid stuck. It felt like we had just joined the Drosophila community and could name things crazily! There was an important lesson in this situation: when working with postdocs, the challenge for the PI is to understand that there are often things that are done outside of the PI’s undoubted own brilliance. Great postdocs should be semi-independent almost straightaway. You want them to cause (almost) paroxysmal change in the lab. I think Eddy learnt that. And Eddy was phenomenal to just talk to about science, he was always asking, “what do you think this means?” I remember looking down the microscope together, at the first Xenopus nuclei ever labelled with antibodies I’d made to the homeodomain proteins. He jerked me up from the microscope and gave me a huge hug!”

Seeing is believing

“It is wonderful to look down the microscope at new findings. One fun time was when Yoshiya Kawaguchi, a terrific Japanese postdoc with me, did an experiment that would be the first time that lineage tracing was combined with a gene knockout in the endoderm. He took the pancreas master transcriptional regulator called Ptf1A and hooked it up to Cre. The Cre replaced the protein, so was essentially a knock-in as a knockout, and we had a ROSA26-lacZ reporter in there too. One day he came bowling into my office and said, “Chris, Chris, Chris, you have to come right now and look at this embryo (which had been stained with X-gal overnight). The mutant is amazing”. And I said, “yep, okay, I’m coming right now. I’m really excited. Let me just tell you what I think you have found, I bet you found that all the cells that were going to become pancreas have now become duodenum”. He was shocked, asking “how can you know that?” I said, “don’t let that disturb you. Let’s go and look together.” As soon as I looked down the microscope, I knew this was an important result and we were so excited. It’s a memory that sticks with me, seeing that result for the first time!

Another result that really stuck with me was when we got involved in cloning Nodal, cobbling it together using various parts of the mouse gene, and isolating the frog orthologs. We injected the mRNA into Xenopus embryos and when we came back the next day, well – they had made notochord everywhere. This started our move away from homeobox genes. Left-Right asymmetry patterns came up from our Nodal work early on. This time I absolutely couldn’t believe the result to start with and I told my postdoc (the wonderful Karuna Sampath) that the pattern must be due to the side the embryos were lying down, having had some horrible glass reaction. She very kindly said “No, no, it’s all on the left-hand side of the embryo irrespective of which side they were lying”. Again, off we charged to look down the microscope straight away!

Overall, I have so many exciting moments in my career, and I feel very privileged and fortunate to have been born at the right time, landed in the right place and then to have done at least some of the right experiments!”

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Categories: Interview, Lab Life, Research

The Node in Numbers

Posted by , on 31 January 2023

Thanks to everyone who interacted with the Node in 2022, it been another fantastic year for the site. We have a few new initiatives that we’ll be announcing soon, but first let us look back on 2022!

What are you looking at…

  • >400,000 total page views
  • 18,483 views of our jobs board
  • 4,992 view of our event calendar

What’s being posted…

  • 226 blog posts, including 7 SciArt profiles, 7 Featured resources, 12 behind the paper stories and 12 preprint lists
  • 260 job adverts
  • 163 events listings

Most popular posts from 2022

  1. Everyone loves a bit of controversy, so it probably won’t come as a surprised that our most read post in 2022 was Peter Lawrence’s open letter to Claudio Stern. And Alfonso Martinez Arias’ response was our most liked comment!
  2. At number two on our list was the livestream from our Development meeting ‘From Stem Cells to Human Development. Setting this up was a little nerve wracking and it was fantastic to see so many people tuning in live and viewing the recording, which featured talks from Sarah Teichmann and Sergiu Pasca and a panel discussion on ‘Technical, ethical and legal challenges of studying early human development’.
  3. The third most read post started on a whim, with Alex Eve converting his popular #wordcountchop tweetorial into a blog post. If you have written a tweetorial on a topic relevant to developmental and stem cell biologists and want to give it a more permanent home, do considering sharing it as a blog post on the Node
  4. Voting for your favourite Development cover comes in as our 4th most read post. Everyone loves a competition, and we had a worthy winner with the Issue 21, the mouse lung lobe from Prashant Chandrasekaran, Nicholas Negretti, Aravind Sivakumar, Jennifer Sucre, David Frank and colleagues. Keep your eyes out for our next competition, which is coming soon!
  5. Joachim Goedhart’s Protocols for data visualization came in at number five. In this post, Joachim shared an update on his book, which brings aims to lower the barrier for using R and the ggplot2 package for data visualization. Joachim’s post on Data Visualization with Flying Colours, published in 2019, was again our most read post with a massive 49,405 views!

We would love to hear feedback and suggestions on how we can make the Node better in 2023. You can contact us using our contact form and at thenode@biologists.com. We are always happy to discuss ideas, comment on drafts, or help with website gremlins. Finally, remember the Node is your site and, once registered, you can post freely.

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Categories: Highlights