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

The preprints this month are hosted on bioRxiv and arXiv – use these links below to get to the section you want:

Developmental biology

• Patterning & signalling
• Morphogenesis & mechanics
• Genes & genomes
• Stem cells, regeneration & disease modelling
• Plant development
• Environment, evolution and development

Cell Biology

Modelling

Tools & Resources

Research practice and education

Developmental biology

| Patterning & signalling

Hypomorphic NOTCH1 Expression Alters Cardiomyocyte Cellular Architecture in Hypoplastic Left Heart Syndrome

Jordann Lewis,  Travis B. Lear, Brent Schlegel, Dominic Woods, Krithika Rao, Amy Sentis,  Jay Tan, Rajaganapathi Jagannathan, Zaineb Javed, Aine N. Boudreau,  Timothy Nelson,  Mousumi Moulik,  Nadine Hempel, Bill B. Chen,  Sruti Shiva,  Dhivyaa Rajasundaram, Toren Finkel,  Anita Saraf

Collaborative role of two distinct cilium-specific cytoskeletal systems in driving Hedgehog-responsive transcription factor trafficking

Pei-I Ku,  Jamuna S Sreeja, Abhishek Chadha, David S Williams, Martin F Engelke, Radhika Subramanian

The C. elegans LON-1 protein requires its CAP domain for function in regulating body size and BMP signaling

Maria Victoria Serrano, Stephanie Cottier, Lianzijun Wang, Sergio Moreira-Antepara, Anthony Nzessi, Zhiyu Liu, Byron Williams, Myeongwoo Lee,  Roger Schneiter,  Jun Liu

An evolutionarily conserved role for VEGF signaling in the expansion of non-vascular tissue during regeneration

 Aaron M. Savage, Alexandra C. Wagner,  Ryan T. Kim, Paul Gilbert,  Hani D. Singer,  Erica Chen,  Elane M. Kim,  Noah Lopez,  Kelly E. Dooling,  Julia C. Paoli,  S.Y. Celeste Wu,  Sebastian Bohm,  Rachna Chilambi,  Tim Froitzheim,  Steven J. Blair,  Connor Powell,  Adnan Abouelela, Anna G. Luong,  Kara N. Thornton,  Benjamin Tajer,  Duygu Payzin-Dogru,  Jessica L. Whited

A spatially-resolved blueprint of the developing human lung reveals a WNT-driven niche for basal stem cells

Peggy P. Hsu,  Ansley S. Conchola,  Tristan Frum, Xiangning Dong, Lila Tudrick, Varun Ponnusamy, Michael S. Downey, Manqi Wu, Mengkun Yang, Yusoo Lee, Emma Niestroy, Yu-Hwai Tsai, Angeline Wu, Sha Huang, Ian A. Glass, Sofia D. Merajver,  Jason R. Spence

EPHA2 Regulates SOX2 during Esophageal Development

 Tianxia Li,  Yosuke Mitani,  Ricardo Cruz-Acuña, Tatiana A. Karaksheva,  Varun Sahu, Cecilia Martin,  Hiroshi Nakagawa,  Joel Gabre

BMP signaling modulations control primitive streak patterning

 Gaël Simon, Jean-Louis Plouhinec,  Pascale Gilardi-Hebenstreit,  Benoit Sorre,  Jérôme Collignon

doi: https://doi.org/10.1101/2024.10.01.616050

Single-nucleus transcriptomics of wing sexual dimorphism and scale cell specialization in sulphur butterflies

 Ling S. Loh,  Joseph J. Hanly,  Alexander Carter,  Martik Chatterjee, Martina Tsimba,  Donya N. Shodja,  Luca Livraghi,  Christopher R. Day,  Robert D. Reed,  W. Owen McMillan,  Gregory A. Wray,  Arnaud Martin

WNT-mediating TCF/LEF transcription factor gene expression in early human pluripotency and cell lineages differs from the rodent paradigm

Connor Ross,  Takuya Azami, Marika Salonna, Richard Gyuris,  Jennifer Nichols,  Stefan Hoppler

Cellular signalling protrusions enable dynamic distant contacts in spinal cord neurogenesis

 Joshua Hawley,  Robert Lea,  Veronica Biga,  Nancy Papalopulu,  Cerys Manning

MMP21 behaves as a fluid flow transported morphogen to impart laterality during development

Tim Ott, Amelie Brugger, Emmanuelle Szenker-Ravi, Yvonne Kurrle, Olivia Aberle, Matthias Tisler, Martin Blum, Sandra Whalen, Patrice Bouvagnet, Bruno Reversade, Axel Schweickert

Independent control of neurogenesis and dorsoventral patterning by NKX2-2

Sumin Jang, Elena Abarinov, Julie Dobkin, Hynek Wichterle

CMTM4 is an adhesion modulator that regulates skeletal patterning and primary mesenchyme cell migration in sea urchin embryos

Abigail E. Descoteaux, Marko Radulovic, Dona Alburi,  Cynthia A. Bradham

Evidence for strong cell-scale signalling during planar polarisation in the Drosophila wing

Alexandre Carayon,  David Strutt

Shh signaling directs dorsal ventral patterning in the regenerating X. tropicalis spinal cord

 Avery Angell Swearer, Samuel Perkowski,  Andrea Wills

Cluster Assembly Dynamics Drive Fidelity of Planar Cell Polarity Polarization

 Silas Boye Nissen,  Alexis T. Weiner, Kaye Suyama,  Pablo Sanchez Bosch, Song Song, Yuan Gu,  Alexander R. Dunn,  Jeffrey D. Axelrod

Capicua maintains anterior-posterior axis in Blattella germanica ovaries

 Nashwa Elshaer,  Jorge Escudero,  Maria-Dolors Piulachs

Shc1 cooperates with Frs2 and Shp2 to recruit Grb2 in FGF-induced lens development

Qian Wang, Hongge Li, Yingyu Mao, Ankur Garg, Eun Sil Park, Yihua Wu, Alyssa Chow, John Peregrin,  Xin Zhang

Characterization of Hippo Signaling Components in the Early Dorsal Pancreatic Bud

 Neha Ahuja,  Caitlin Maynard, Tyler Bierschenck,  Ondine Cleaver

Irx3/5 define the cochlear sensory domain and regulate vestibular and cochlear sensory patterning in the mammalian inner ear

Yuchen Liu,  Tianli Qin,  Xin Weng, Bernice Leung, Karl Kam Hei So, Boshi Wang, Wanying Feng, Alexander Marsolais, Sheena Josselyn,  Pingbo Huang, Bernd Fritzsch, Chi-Chung Hui,  Mai Har Sham

Differential Sensitivity of Midline Patterning to Mitosis during and after Primitive Streak Extension

 Zhiling Zhao,  Rieko Asai,  Takashi Mikawa

Notch, β-catenin and MAPK signaling segregate endoderm and mesoderm in the diploblast Nematostella vectensis

Emmanuel Haillot, Tatiana Lebedeva, Julia Steger,  Grigory Genikhovich, Juan D. Montenegro,  Alison G. Cole,  Ulrich Technau

| Morphogenesis & mechanics

Morphomechanic tuning of ERK by actin-TFII-IΔ regulates cell identity

 Qiao Wu,  Jian Zhang, Bing Long, Xiao Hu, Bruna Mafra de Faria, Stephen Maxwell Scalf, Kutay Karatepe, Wenxiang Cao, Nikolaos Tsopoulidis, Andres Binkercosen, Masaki Yagi, Aaron Weiner, Mary Kaileh, Enrique M. De La Cruz,  Ananda L Roy,  Konrad Hochedlinger,  Shangqin Guo

Anisotropic stretch biases the self-organization of actin fibers in multicellular Hydra aggregates

 Anaïs Bailles, Giulia Serafini, Heino Andreas,  Christoph Zechner,  Carl Modes,  Pavel Tomancak

Melanocyte differentiation and mechanosensation are differentially modulated by distinct extracellular matrix proteins

 Carole Luthold,  Marie Didion,  Emilio Benedum,  Ann-Kathrin Burkhart,  Nina Demmerle,  Gubesh Gunaratnam,  Vanessa Samira Rácz,  Markus Bischoff,  Annika Ridzal,  Sandra Iden

Rho/Rok-dependent regulation of actomyosin contractility at tricellular junctions controls epithelial permeability in Drosophila

 Thea Jacobs,  Jone Isasti Sanchez, Steven Reger,  Stefan Luschnig

Three-dimensional quantitative micro-elastography reveals alterations in spatial elasticity patterns of follicles and corpora lutea in murine ovaries during ageing

Anna Jaeschke, Matt S. Hepburn, Alireza Mowla, Brendan F. Kennedy,  Chii Jou Chan

Mechanical properties are tuned during development with the fibrous network nature of the Arabidopsis cell wall

Si Chen, Isabella Burda, Purvil Jani, Bex Pendrak, Meredith N. Silberstein, Adrienne H.K. Roeder

Mechanical control of germ cell specification in Arabidopsis anthers

Chan Liu, Hui Shi, Yuting Han, Pan Wang, Kexin Li, Zhishuai Zhang, Jiazheng Liu, Yafeng Zheng, Linlin Li, Limei Lin, Chen Liang, Binjun Qin, Hua Han, Shunong Bai, Xiao Liu, Wenqian Chen, Feng Zhao

Spatiotemporal dynamics of primary and motile cilia throughout lung development

 Stephen Spurgin, Ange Michelle Nguimtsop,  Fatima N. Chaudhry,  Sylvia N. Michki,  Jocelynda Salvador,  M. Luisa Iruela-Arispe,  Jarod A. Zepp,  Saikat Mukhopadhyay,  Ondine Cleaver

IGF2 mediates Hippo signaling to control liver size

 Zhenxing Zhong, Ruxin Jin, Yiting Zhong, Li Zhang, Deqian Chen, Zhihan Jiao, Fanhui Zhou, Rui Zhu, Jian Wu, Rui Dong, Kuiran Dong, Fei Lan, Yu Wang, Kun-Liang Guan,  Fa-Xing Yu

Mechanical regulation of tissue flatness in Marchantia

 Jordan Ferria, Carla J.A. Fournié, Magdalena H. Jankowska, Doron Grossman,  Adrienne H.K. Roeder,  Stéphanie Drevensek,  Arezki Boudaoud

A mitochondrial redox switch licenses the onset of morphogenesis in animals

Updip Kahlon, Francesco Dalla Ricca, Saraswathi J. Pillai,  Marine Olivetta,  Kevin M. Tharp,  Li-En Jao,  Omaya Dudin, Kent McDonald,  Mustafa G. Aydogan

Mechanochemical Patterning Localizes the Organizer of a Luminal Epithelium

Sera Lotte Weevers, Alistair D. Falconer, Moritz Mercker, Hajar Sadeghi, Jaroslav Ferenc, Albrecht Ott, Dietmar B. Oelz, Anna Marciniak-Czochra, Charisios D. Tsiairis

Tissue-Like Multicellular Development Triggered by Mechanical Compression in Archaea

Theopi Rados, Olivia S. Leland, Pedro Escudeiro, John Mallon, Katherine Andre, Ido Caspy, Andriko von Kügelgen, Elad Stolovicki, Sinead Nguyen, Inés Lucía Patop, Thiberio Rangel, Sebastian Kadener, Lars D. Renner, Vera Thiel, Yoav Soen,  Tanmay A.M. Bharat, Vikram Alva,  Alex Bisson

| Genes & genomes

Early zygotic engineering promotes targeted large transgene integration and direct production of fully transgenic animals

 Khusali Gupta, Ping Xu, Judith Gallant, Yeonsoo Yoon, Jaime A. Rivera-Pérez,  Jeanne B. Lawrence

doi: https://doi.org/10.1101/2024.09.29.615605

Epigenome profiling identifies H3K27me3 regulation of extra-cellular matrix composition in human corticogenesis

 Nora Ditzer, Ezgi Senoglu,  Theresa M. Schütze, Aikaterina Nikolaidi,  Annika Kolodziejczyk,  Katrin Sameith, Sevina Dietz,  Razvan P. Derihaci, Cahit Birdir,  Anne Eugster,  Mike O. Karl,  Andreas Dahl, Pauline Wimberger, Franziska Baenke,  Claudia Peitzsch,  Mareike Albert

Single-cell RNA-seq Reveals Early Transcriptional Programs of the Maternal to Zygote Transition in Mice and Rats

Yangqi Su, Evguenia Kouranova, Jonathan Shea, Xiaoxia Cui,  Zhengchang Su

Tissue-specific transcriptomics uncovers novel craniofacial genes underlying jaw divergence in specialist pupfishes

 M. Fernanda Palominos, Vanessa Muhl,  Christopher H. Martin

Catalytic-dependent and independent functions of the histone acetyltransferase CBP promote pioneer factor-mediated zygotic genome activation

 Audrey J. Marsh,  Sergei Pirogov, Abby J. Ruffridge, Suresh Sajwan, Tyler J. Gibson, George Hunt, Yadwinder Kaur,  Melissa M. Harrison,  Mattias Mannervik

Distinct proliferative and neuronal programmes of chromatin binding and gene activation by ASCL1 are cell cycle stage-specific

 William F Beckman, Lydia M Parkinson, Lewis Chaytor,  Anna Philpott

A piRNA regulating oogenesis and embryo development in cockroaches

 Judit Gonzalvo,  Nuria Farrus,  Jorge Escudero,  David Pujal,  Josep Bau,  Maria-Dolors Piulachs

Deciphering gene regulatory programs in mouse embryonic skin through single-cell multiomics analysis

Qiuting Deng, Pengfei Cai, Yingjie Luo, Zhongjin Zhang, Wen Ma, Zijie Huang, Xiaoya Chen, Shijie Hao, Weiguang Ma, Jiangshan Xu, Mengnan Cheng, Xiumei Lin, Ru Zhou, Shanshan Duan, Junjie Chen, Ronghai Li, Xuyang Shi, Chang Liu, Peng Gao, Jianting Li, Jun Xie, Longqi Liu, Yue Yuan, Chuanyu Liu

Optical Genome Mapping of the human reference iPSC line KOLF2.1J reveals new smaller structural variants in neurodevelopmental genes

 Madison James Yang,  Kamilla Sedov,  Max Y. Chen,  Faria Zafar,  Birgitt Schüle

Setdb1 regulates proper differentiation of adult intestinal stem cells via restraining permissive chromatin structure and transcriptional variability

Dimitris Botskaris, Ioannis K. Deligiannis, Ioanna Peraki, Haroula Kontaki, Marianna Stagaki, Matthieu D. Lavigne,  Celia P. Martinez-Jimenez,  Iannis Talianidis

Loss of Bicra/Gltscr1 leads to a defect in fetal liver macrophages responsible for erythrocyte maturation in mice

Surbhi Sood, Aktan Alpsoy, Guanming Jiao, Alisha Dhiman, Charles Samuel King, Gabriella Grace Conjelko, Judy E. Hallett, Sagar M Utturkar, Jill E Hutchcroft,  Emily C Dykhuizen

Rewired gene interactions during development of serially homologous appendages in male and female Drosophila

Amber M. Ridgway, Javier Figueras Jimenez, Maria D. S. Nunes,  Alistair P. McGregor

Contextualising transcription factor binding during embryogenesis using natural sequence variation

 Olga M. Sigalova,  Mattia Forneris,  Frosina Stojanovska,  Bingqing Zhao,  Rebecca R. Viales, Adam Rabinowitz, Fayrouz Hamal,  Benoît Ballester,  Judith B Zaugg,  Eileen E.M. Furlong

PWWP-ADD and N-terminal domains of DNMT3B1 confer specificity for developmentally regulated CpG island methylation

 Komal Yasmin,  Tatyana B Nesterova,  Neil Brockdorff

Drosophila Trus, the orthologue of mammalian PDCD2L, is required for proper cell proliferation, larval developmental timing, and oogenesis

Saeko Takada, Bonnie J. Bolkan, MaryJane O’Connor, Michael Goldberg,  Michael B. O’Connor

Single-nucleus transcriptional and chromatin accessibility analyses of maturing mouse Achilles tendon uncover the molecular landscape of tendon stem/progenitor cells

Hiroki Tsutsumi,  Tomoki Chiba, Yuta Fujii, Takahide Matsushima, Tsuyoshi Kimura, Akinori Kanai, Akio Kishida, Yutaka Suzuki,  Hiroshi Asahara

Foxn3 is part of a transcriptional network that regulates cilia genes in the developing mouse retina

 Huanqing Zhang,  Fan Meng,  David L. Turner

Spatiotemporal dynamics and selectivity of mRNA translation during mouse pre-implantation development

Hao Ming, Rajan Iyyappan, Kianoush Kakavand, Michal Dvoran, Andrej Susor,  Zongliang Jiang

| Stem cells, regeneration & disease modelling

Axolotl epigenetic clocks offer insights into the nature of negligible senescence

Yuliia Haluza,  Joseph A. Zoller, Ake T. Lu, Hannah E. Walters, Martina Lachnit, Robert Lowe, Amin Haghani, Robert T. Brooke, Naomi Park,  Maximina H. Yun,  Steve Horvath

Lgl resets Par complex membrane loading at mitotic exit to polarize neural stem cells

Bryce LaFoya, Sarah E. Welch,  Kenneth E. Prehoda

RO8191, a new compound for initiating embryo implantation in mice

Junlan Shu, Jumpei Terakawa, Satoko Osuka, Ayako Muraoka, Jiali Ruan, Junya Ito, Atsuo Iida,  Eiichi Hondo

Liver Sinusoidal Endothelial Cells and Laminin dictate cholangiocytes’ fate in chronic liver disease

 Rita Manco, Camilla Moliterni, Gauthier Neirynck, Maxime De Rudder, Corinne Picalausa, Leana Ducor, Montserrat Fraga, Frédéric Lemaigre, Christine Sempoux, Alexandra Dili, Isabelle A. Leclercq

Branched actin polymerization drives invasive protrusion formation to promote myoblast fusion during skeletal muscle regeneration

Yue Lu, Tezin Walji, Pratima Pandey, Chuanli Zhou, Christa Whelan Habela, Scott Snapper, Rong Li,  Elizabeth Chen

The Xenopus respiratory system reveals common tetrapod mechanisms for growth, regeneration and healing

Shiri Kult Perry, Nikko-Ideen Shaidani,  Marko E Horb,  Neil Shubin

Injury-induced transcription in the planarian outer epithelium is critical for tissue regeneration

Pallob Barai, Mariya S. Kibtiya, Nathan G. Maggard, Shishir Biswas,  Elizabeth M. Duncan

Coordinate post-transcriptional regulation by microRNAs and RNA binding proteins is critical for early embryonic cell fate decisions

 Carolyn Sangokoya,  Robert Blelloch

Female-germline specific protein Sakura interacts with Otu and is crucial for germline stem cell renewal and differentiation and oogenesis

Azali Azlan, Li Zhu,  Ryuya Fukunaga

A post-mitotic in vitro murine as a model of muscle damage and repair

Angelo Galluccio, Samantha Maurotti, Francesca Rita Noto, Francesca Scionti, Carmelo Pujia, Elisa Mazza, Yvelise Ferro,  Rosario Mare, Nadia Geirola,  Bernadette Scopacasa,  Patrizio Candeloro,  Luca Tirinato, Angela Sciacqua, Arturo Pujia,  Stefano Romeo, Tiziana Montalcini

Loss of 18q alters TGFβ signalling affecting anteroposterior neuroectodermal fate in human embryonic stem cells

Yingnan Lei, Mai Chi Duong,  Nuša Krivec,  Charlotte Janssens,  Marius Regin,  Anfien Huyghebaert,  Edouard Couvreu de Deckersberg,  Karen Sermon, Diana Al Delbany,  Claudia Spits

Dissecting compounded hepatocyte injury in a model of MASLD progression from human induced pluripotent stem cells

Julian Weihs, Fatima Baldo, Alessandra Cardinali, Gehad Youssef, Katarzyna Ludwik, Harald Stachelscheid, Nils Haep, Peter Tang, Igor Sauer, Pavitra Kumar, Cornelius Engelmann, Susanna Quach, Philip Bufler, Namshik Han, Milad Rezvani

Nicotine enhances the stemness and tumorigenicity in intestinal stem cells via Hippo-YAP/TAZ and Notch signal pathway

Ryosuke Isotani,  Masaki Igarashi, Masaomi Miura, Kyoko Naruse, Satoshi Kuranami, Manami Katoh, Seitaro Nomura, Toshimasa Yamauchi

Fetal Liver-like Organoids Recapitulate Blood-Liver Niche Development and Multipotent Hematopoiesis from Human Pluripotent Stem Cells

Milad Rezvani, Kyle Lewis, Susanna Quach, Kentaro Iwasawa, Julian Weihs, Hasan Al Reza, Yuqi Cai, Masaki Kimura, RanRan Zhang, Yuka Milton, Praneet Chaturvedi, Konrad Thorner, Ramesh C. Nayak, Jorge Munera, Phillip Kramer, Brian R. Davis, Appakalai N. Balamurugan, Yeni Ait Ahmed, Marcel Finke, Rose Yinghan Behncke, Adrien Guillot, René Hägerling, Julia K. Polansky, Philip Bufler, Jose A Cancelas, James M. Wells, Momoko Yoshimoto,  Takanori Takebe

STAT3 signalling enhances tissue expansion during postimplantation mouse development

Takuya Azami, Bart Theeuwes, Mai-Linh N Ton, William Mansfield, Luke Harland, Masaki Kinoshita,  Berthold Gottgens,  Jennifer Nichols

Single-cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches

 Léa Torcq, Catherine Vivier, Sandrine Schmutz,  Yann Loe-Mie,  Anne A. Schmidt

A limbal stem cell deficiency murine model with residual limbal stem cells

Hideaki Someya,  Shintaro Shirahama, Margarete M. Karg, Meredith S. Gregory-Ksander, Reza Dana,  Bruce R. Ksander

Functional differentiation of Human Dental Pulp Stem Cells into neuron-like cells exhibiting electrophysiological activity

 B. Pardo-Rodríguez,  A.M. Baraibar,  I. Manero-Roig,  J. Luzuriaga,  J. Salvador-Moya,  Y. Polo,  R. Basanta-Torres,  F. Unda,  S. Mato,  G. Ibarretxe,  J.R. Pineda

Actomyosin Contractility is a Potent Suppressor of Mesoderm Induction by Human Pluripotent Stem Cells

 Loic Fort, Wenjun Wang,  Ian Macara

map3k1 suppresses terminal differentiation of migratory eye progenitors in planarian regeneration

 Katherine C. Lo,  Christian P. Petersen

Local control of cellular proliferation underlies neuromast regeneration in zebrafish

 Natalia G. Lavalle,  Jerónimo Miranda-Rodríguez,  Emanuel Cura Costa,  Augusto Borges,  Oriol Viader-Llargués, Hernán López-Schier,  Osvaldo Chara

Integrated local and systemic communication factors regulate nascent hematopoietic progenitor escape during developmental hematopoiesis

Carson Shalaby, James Garifallou,  Christopher S Thom

The PUF RNA-binding protein, FBF-2, maintains stem cells without binding to RNA

 Brian H. Carrick,  Sarah L. Crittenden,  MaryGrace Linsley,  Stephany J. Costa Dos Santos,  Marvin Wickens,  Judith Kimble

The E3 Ubiquitin Ligase Trip12 attenuates Wnt9a/Fzd9b signaling during hematopoietic stem cell development

Jessica Ensing, Amber D. Ide, Carla Gilliland, Visakuo Tsurho, Isabella Caza,  Amber N. Stratman, Nathan J. Lanning,  Stephanie Grainger

| Plant development

A molecular basis for plant SCAR/WAVE functional divergence

 Sabine Brumm,  Aleksandr Gavrin,  Matthew Macleod,  Guillaume Chesneau, Annika Usländer,  Sebastian Schornack

Proline-2’-deoxymugineic acid (PDMA) increases seed quality and yield by alleviating iron deficiency symptoms in soybean under calcareous-alkaline conditions

 Zahit Kaya,  Amir Maqbool,  Motofumi Suzuki,  Emre Aksoy

Stochastic Gene Expression in Auxin Signaling in the Floral Meristem of Arabidopsis thaliana

 Shuyao Kong,  Mingyuan Zhu,  Adrienne H.K. Roeder

NPF4.1 imports embryo-derived GA4 to the endosperm to promote seed germination

Mathilde Sirlin-Josserand, Lali Sakvarelidze-Achard, David Pflieger, Jean-Michel Davière,  Patrick Achard

Co-cultivating rice plants with Azolla filiculoides modifies root architecture and timing of developmental stages

Sara Cannavò,  Chiara Paleni,  Alma Costarelli,  Maria Cristina Valeri,  Martina Cerri,  Antonietta Saccomanno,  Veronica Gregis,  Graziella Chini Zittelli,  Petre I. Dobrev,  Lara Reale, Martin M. Kater,  Francesco Paolocci

The genetic basis of replicated bullseye pattern reduction across the Trionum Complex

 May T. S. Yeo, Alice L. M. Fairnie, Valentina Travaglia, Joseph F. Walker,  Lucie Riglet, Selin Zeyrek,  Edwige Moyroud

PRC2 facilitates the transition from heterotrophy to photoautotrophy during seedling emergence

 Naseem Samo,  María Guadalupe Trejo-Arellano,  Lenka Gahurová, Alexander Erban,  Alina Ebert,  Quentin Rivière,  Jiří Kubásek,  Fatemeh Aflaki,  Helena Hönig Mondeková,  Armin Schlereth,  Annick Dubois,  Mingxi Zhou,  Ondřej Novák,  Jiří Šantrůček,  Daniel Bouyer,  Franҫois Roudier,  Joachim Kopka,  Iva Mozgová

A brassinosteroid receptor kinase is required for sex determination in the homosporous fern Ceratopteris richardii

 Katelin M. Burow,  Xi Yang,  Yun Zhou,  Brian P. Dilkes,  Jennifer H. Wisecaver

ERECTA family signaling controls cell fate specification during ovule initiation in Arabidopsis

 Alex M. Overholt,  Christina Elaine Pierce, Calen Seth Paleologos,  Elena D. Shpak

Shaping Kale Morphology and Physiology Using Different LED Light Recipes

 Sabine Scandola,  Lauren E. Grubb,  Brigo Castillo,  Lexyn Iliscupidez,  Curtis Kennedy, Nicholas Boyce,  R. Glen Uhrig

Highly expressed cell wall genes contribute to robustness of sepal size

 Diego A. Hartasánchez,  Mathilde Dumond, Nelly Dubrulle,  Françoise Monéger,  Arezki Boudaoud

Differential gene expression analysis identifies a group of defensin like peptides from Solanum chacoense ovules with in vitro pollen tube attraction activity

Yang Liu, Valentin Joly, Mohamed Sabar, Daniel Philippe Matton, David Morse

| Environment, evolution and development

Like mother, like daughter? Phenotypic plasticity, environmental covariation, and heritability of size in a parthenogenetic wasp

Alicia Tovar, Scott Monahan, Trevor Mugoya, Adrian Kristan, Walker Welch, Ryan Dettmers, Camila Arce, Theresa Buck, Michele Ruben, Alexander Rothenberg, Roxane Saisho, Ryan Cartmill, Timothy Skaggs, Robert Reyes, MJ Lee, John Obrycki, William Kristan,  Arun Sethuraman

Methylomes reveal recent evolutionary changes in populations of two plant species

 Kevin Korfmann, Andreas Zauchner,  Aurélien Tellier,  Ramesh Arunkumar

Polar bodies serve as a landmark for anteroposterior axis formation in spiders

Ruixun Wang,  Matthias Pechmann

Evolutionary Insights into Muscle Fiber Distribution in the Twin Tails of Ornamental Goldfish

 Kinya G Ota,  Gembu Abe,  Chen-Yi Wang,  Ing-Jia Li,  Paul Gerald Layague Sanchez,  Tzu-Chin Chi

Maternal high-fat, high-sucrose diet-induced excess adiposity is linked to placental hypoxia and disruption of fetoplacental immune homeostasis in late gestation

 Christian J. Bellissimo, Tatiane A. Ribeiro, Erica Yeo, Patrycja A. Jazwiec, Howard Luo, Jaskiran Bains,  Deborah M. Sloboda

Cenozoic evolutionary history obscures the Mesozoic origins of acanthopterygian fishes

Chase D. Brownstein, Alex Dornburg, Thomas J. Near

Reconstructing the deep phylogeny of the MAPK signaling network: functional specialization via multi-tier coevolutionary expansion

 EJ Huang,  Jeeun Parksong,  Amy F. Peterson,  Fernando Torres,  Sergi Regot,  Gabriel S. Bever

Diversity and evolution of Radiolaria: Beyond the stars of the ocean

 Miguel M. Sandin,  Johan Renaudie, Noritoshi Suzuki,  Fabrice Not

Growth compensation upon changes in tissue size in the Drosophila abdomen

Ana Ferreira, Andrea Cairoli, Federica Mangione, Maxine V. Holder, Anna Ainslie, Birgit L. Aerne,  Guillaume Salbreux,  Nicolas Tapon

Evolution of the non-visual and visual opsin gene repertoire in ray-finned fishes

 Maxime Policarpo,  Lily G. Fogg,  Fabio Cortesi,  Walter Salzburger

The genetic diversity of the soybean rust pathogen Phakopsora pachyrhizi has been driven by two major evolutionary lineages

Vinicius Delgado da Rocha, Everton Geraldo Capote Ferreira, Fernanda Machado Castanho, Marcia Kamogae Kuwahara, Cláudia Vieira Godoy, Maurício Conrado Meyer, Kerry F. Pedley, Ralf T. Voegele, Anna Lipzen, Kerrie Barry, Igor V. Grigoriev, Marco Loehrer, Ulrich Schaffrath, Catherine Sirven,  Sebastien Duplessis,  Francismar Corrêa Marcelino-Guimarães

Phylogeny-aware simulations suggest a low impact of unsampled lineages in the inference of gene flow during eukaryogenesis

 Moisès Bernabeu,  Saioa Manzano-Morales,  Toni Gabaldón

Evolution of plant cell-type-specific cis-regulatory elements

Haidong Yan, John P. Mendieta, Xuan Zhang, Alexandre P. Marand, Yan Liang, Ziliang Luo, Mark A.A. Minow, Hosung Jang, Xiang Li, Thomas Roulé, Doris Wagner, Xiaoyu Tu, Yonghong Wang, Daiquan Jiang, Silin Zhong,  Linkai Huang, Susan R. Wessler,  Robert J. Schmitz

Germplasm stability in zebrafish requires maternal Tdrd6a and Tdrd6c

 Alessandro Consorte, Yasmin El Sherif,  Fridolin Kielisch,  Nadine Wittkopp,  René F. Ketting

Genetic variation in male mate choice for large females in Drosophila melanogaster

Grace S. Freed, Isabella G. Martinez, Avigayil Lev, Ana-Maria Anthony Cuadrado,  Alison Pischedda

Deep-sea fish reveal alternative pathway for vertebrate visual development

 Lily G. Fogg,  Stamatina Isari, Jonathan E. Barnes,  Jagdish Suresh Patel,  N. Justin Marshall,  Walter Salzburger,  Fabio Cortesi,  Fanny de Busserolles

Comparative analysis of rhesus macaque and human placental organoids highlights evolutionary differences in placentation

 Allyson Caldwell,  Liheng Yang,  Elizabeth A. Scheef,  Amitinder Kaur,  Carolyn B. Coyne

Experimental short-term heatwaves negatively impact body weight gain and survival during larval development in a wild pollinator

Laura Wögler,  Christoph Kurze

Male is the default sex: functional significance of the sex determination cascade in horned dung beetles

London C. Mitchell,  Armin P. Moczek,  Erica M. Nadolski

Identification of a specialized lipid barrier for Drosophila metamorphosis

 Lena Lampe,  Clare L. Newell, Bing-Jun Wang, Rami Makki, Cyrille Alexandre,  Ian S. Gilmore,  Li Zhao,  Alex P. Gould

Comparative single-cell analyses reveal evolutionary repurposing of a conserved gene program in bat wing development

Magdalena Schindler, Christian Feregrino, Silvia Aldrovandi, Bai-Wei Lo, Anna A. Monaco, Alessa R. Ringel, Ariadna Morales,  Tobias Zehnder, Rose Yinghan Behncke, Juliane Glaser, Alexander Barclay, Guillaume Andrey, Bjørt K. Kragesteen, René Hägerling, Stefan Haas, Martin Vingron,  Igor Ulitsky, Marc Marti-Renom,  Julio Hechavarria,  Nicolas Fasel, Michael Hiller, Darío Lupiáñez, Stefan Mundlos,  Francisca M. Real

Shaping tiny worlds: Paternal microbiota manipulation influences offspring microbial colonization and development in a sex role-reversed pipefish

 Kim-Sara Wagner, Frédéric Salasc, Silke-Mareike Marten,  Olivia Roth

Single Cell Sequencing Provides Clues about the Developmental Genetic Basis of Evolutionary Adaptations in Syngnathid Fishes

 Hope M. Healey,  Hayden B. Penn,  Clayton M. Small,  Susan Bassham,  Vithika Goyal,  Micah A. Woods,  William A. Cresko

Oxygen level alters energy metabolism in bovine preimplantation embryos

 N. Boskovic,  M. Ivask,  G. Yazgeldi Gunaydin,  B. Yaşar,  S. Katayama,  A. Salumets,  T. Org,  A. Kurg,  K. Lundin,  T. Tuuri,  C. O. Daub,  J. Kere

Hybrid incompatibility emerges at the one-cell stage in interspecies Caenorhabditis embryos

 Jessica Bloom,  Rebecca Green,  Arshad Desai,  Karen Oegema,  Scott A. Rifkin

Evolution of maternal and early zygotic transcript regulation across Drosophila

Charles S. Omura,  Susan E. Lott

Cellular and molecular mechanisms that shape the development and evolution of tail vertebral proportion in mice and jerboas

 Ceri J. Weber,  Alexander J. Weitzel, Alexander Y. Liu,  Erica G. Gacasan,  Robert L. Sah,  Kimberly L. Cooper

Planarians Develop Radiotolerance to Recurrent Ionizing Radiation Exposure

Paul G. Barghouth, Benjamin Ziman, Eli Isael Maciel, Peter Karabinis, Salvador Rojas, Natasha M. Flores, Edelweiss Pfister, Néstor J. Oviedo

Shifts in embryonic oxygen levels cue heterochrony in limb initiation

 Meng Zhu, Rinaldo Catta-Preta, ChangHee Lee, Clifford Tabin

Brassinosteroids and Flavonols Confer Temperature Stress Tolerance to Pollen Tube Germination and Growth

 Kumi Matsuura-Tokita, Ayaka Sakai,  Takamasa Suzuki,  Akihiko Nakano,  Tetsuya Higashiyama

Cell Biology

The multimodal transcriptional response of denervated skeletal muscle involves alterations in cholesterol homeostasis impacting muscle size

Cristofer Calvo, Casey O. Swoboda, Fabian Montecino Morales, Siddhant Nagar, Michael J. Petrany, Chengyi Sun, Hima Bindu Durumutla,  Mattia Quattrocelli,  Douglas P. Millay

The role of cytochrome c in mitochondrial metabolism of human oocytes

 Jakub Maciej Surmacki,  Halina Abramczyk, Bogna Sobkiewicz,  Renata Walczak-Jędrzejowska,  Jolanta Słowikowska-Hilczer,  Katarzyna Marchlewska

The molecular chronology of mammary epithelial cell fate switching

 Queralt Vallmajo-Martin,  Zhibo Ma, Sumana Srinivasan, Divya Murali, Christopher Dravis,  Kavitha Mukund, Shankar Subramaniam,  Geoffrey M. Wahl,  Nikki K. Lytle

Enhanced RNA-targeting CRISPR-Cas technology in zebrafish

 Ismael Moreno-Sanchez, Luis Hernandez-Huertas, Daniel Nahon-Cano, Carlos Gomez-Marin, Pedro Manuel Martinez-García, Anthony J. Treichel, Laura Tomas-Gallardo, Gabriel da Silva Pescador, Gopal Kushawah, Alejandro Díaz-Moscoso, Alejandra Cano-Ruiz, John A. Walker II, Manuel J. Muñoz, Kevin Holden, Joan Galcerán, María Ángela Nieto, Ariel Bazzini,  Miguel A. Moreno-Mateos

Intra-manchette transport employs both microtubule and actin tracks

Jo H. Judernatz, Laura Pérez Pañeda, Tereza Kadavá,  Albert J. R. Heck,  Tzviya Zeev-Ben-Mordehai

Visualizing developmental dynamics of nuclear morphology and transport machinery in Drosophila

 Yuki Shindo, Shruthi Balachandra,  Amanda A. Amodeo

Mammary Epithelial Migration is EMT-Independent

Jing Chen, Rongze ma, Zhixuan Deng, Yunzhe Lu, Jiecan Zhou, Kun Xia, Ophir D. Klein, Pengfei Lu

An interkinetic envelope surrounds chromosomes between meiosis I and II in C. elegans oocytes

Layla El Mossadeq, Laura Bellutti, Rémi Le Borgne, Julie C. Canman,  Lionel Pintard, Jean-Marc Verbavatz,  Peter Askjaer, Julien Dumont

Depolymerizing F-actin accelerates the exit from pluripotency to enhance stem cell-derived islet differentiation

Nathaniel J. Hogrebe, Mason D. Schmidt, Punn Augsornworawat, Sarah E. Gale, Mira Shunkarova,  Jeffrey R. Millman

Autophagy is dispensable in germline stem cells but is required in the cap cells for their maintenance in the Drosophila ovarian niche

Kiran Suhas Nilangekar,  Bhupendra V. Shravage

Mitochondrial fission controls astrocyte morphogenesis and organization in the cortex

Maria Pia Rodriguez Salazar, Sprihaa Kolanukuduru, Valentina Ramirez, Boyu Lyu, Gabrielle Sejourne, Hiromi Sesaki, Guoqiang Yu,  Cagla Eroglu

Impaired erythroid maturation in murine embryos upon loss of the preeclampsia-associated serine protease prostasin

 Sara Di Carlo, Adrian Salas-Bastos, Mariela Castelblanco Castelblanco, Muriel Auberson, Marie Rumpler, Malaury Tournier, Lukas Sommer, Olaia Naveiras, Edith Hummler

Membrane oscillations driven by Arp2/3 constrict the intercellular bridge during neural stem cell divisions

Bryce LaFoya,  Kenneth E. Prehoda

eIF4ET regulates meiotic proteome levels to enable oocyte formation and storage

Priyankaa Bhatia, Ruchi Amin, Nicole E. Familiari, Kan Yaguchi, Vanna M. Tran, Alec Bond, Orhan Bukulmez, Jeffrey B. Woodruff

Human spermatogenesis leads to a reduced nuclear pore structure and function

Ália dos Santos, Oliver Knowles, Tom Dendooven, Thomas Hale, Alister Burt, Piotr Kolata, Giuseppe Cannone, Dom Bellini,  David Barford, Matteo Allegretti

Modelling

Uniaxial force modifies the length of the mammary ductal network and the orientation of ducts during pubertal development: Findings from computational modeling and laboratory experiments

Daisy Ulloa, Kelsey M. Temple,  Theresa M. Casey, Uduak Z George

Quantitative Resolving Cell Fate in the Early Embryogenesis of Caenorhabditis elegans

 Ruiqi Xiong, Yang Su,  Mengchao Yao, Zefei Liu, Jie Lu, Yong-Cong Chen, Ping Ao

Inner ear morphology in wild versus laboratory house micev

Sabrina Renaud, Léa Amar, Pascale Chevret, Caroline Romestaing, Jean-Pierre Quéré, Corinne Régis, Renaud Lebrun

Optimal network sizes for most robust Turing patterns

Hazlam S. Ahmad Shaberi, Aibek Kappassov, Antonio Matas-Gil, Robert G. Endres

Parsing altered brain connectivity in neurodevelopmental disorders by integrating graph-based normative modeling and deep generative networks

Rui Sherry Shen, Yusuf Osmanlıoğlu, Drew Parker, Darien Aunapu, Benjamin E. Yerys, Birkan Tunç, Ragini Verma

Optimizing Non-Intersecting Synthetic Vascular Trees in Nonconvex Organs

Etienne Jessen, Marc C. Steinbach, Dominik Schillinger

Tools & Resources

Unbiased identification of cell identity in dense mixed neural cultures

 Sarah De Beuckeleer, Tim Van De Looverbosch, Johanna Van Den Daele, Peter Ponsaerts,  Winnok H. De Vos

A MOUSE ORGANOID PLATFORM FOR MODELING CEREBRAL CORTEX DEVELOPMENT AND CIS-REGULATORY EVOLUTION IN VITRO

 Daniel Medina-Cano, Mohammed T. Islam, Veronika Petrova, Sanjana Dixit, Zerina Balic, Marty G. Yang, Matthias Stadtfeld,  Emily S. Wong,  Thomas Vierbuchen

A stable Netrin-1 fluorescent reporter chicken reveals cell-specific molecular signatures during optic fissure closure

Brian Ho Ching Chan,  Holly Hardy,  Teresa Requena, Amy Findlay,  Jason Ioannidis, Dominique Meunier,  Maria Toms,  Mariya Moosajee, Anna Raper,  Mike McGrew,  Joe Rainger

A minimally guided organoid model for cross-species comparisons of cerebellar development

 Luca Guglielmi, Daniel Lloyd-Davies-Sánchez,  José González Martínez,  Madeline A. Lancaster

CellStudio: a Modular, Tunable and Accessible Platform for Analysis of Growth Factors Secretions in Cell Cultures

 Enrique Azuaje-Hualde,  Naiara Lartitegui-Meneses,  Juncal Alonso-Cabrera,  Asier Inchaurraga-Llamas,  Yara Alvarez-Braña,  Marian Martínez de Pancorbo,  Fernando Benito-Lopez,  Lourdes Basabe-Desmonts

A Combined Computational Fluid Dynamics Modeling and Geometric Morphometrics Methods Approach to Quantifying Hemodynamic and Anatomical Features of Embryonic Chick Heart Anatomies Reconstructed from Light Sheet Fluorescence Microscopy Imaging

 Kirsten Giesbrecht, Simone Rossi, Sophie Liu, Shourya Mukherjee,  Michael Bressan,  Boyce Griffith

CellMet: Extracting 3D shape metrics from cells and tissues

 Sophie Theis,  Mario A Mendieta-Serrano,  Bernardo Chapa-y-Lazo, Juliet Chen,  Timothy E Saunders

CRISPR/Cas9-based somatic knock-in of reporters in the avian embryo in ovo

Alciades Petit Vargas, Baptiste Mida, Rosette Goïame, Olinda Alegria-Prevot, Bojana Djelic,  Evelyne Fischer,  Samuel Tozer,  Jérôme Gros,  Marie Manceau,  Xavier Morin

From Selfies to Science – Precise 3D Leaf Measurement with iPhone 13 and Its Implications for Plant Development and Transpiration

 Gabriel Bar-Sella,  Matan Gavish,  Menachem Moshelion

Zebrahub-Multiome: Uncovering Gene Regulatory Network Dynamics During Zebrafish Embryogenesis

 Yang Joon Kim,  Shruthi Vijay Kumar,  Benjamin Iovino,  Alejandro Granados,  Sarah Ancheta,  Xiang Zhao,  Kyle Awayan, Amanda Seng,  Michael Borja,  Sheryl Paul,  Honey Mekonen, Ritwicq Arjyal,  Angela Detweiler,  Yasin Şenbabaoğlu,  Rafael Gómez-Sjöberg,  Norma Neff,  Merlin Lange,  Loïc A. Royer

inTRACKtive — A Web-Based Tool for Interactive Cell Tracking Visualization

 Teun A.P.M. Huijben,  Ashley G. Anderson III,  Andrew Sweet, Erin Hoops, Connor Larsen,  Kyle Awayan,  Jordão Bragantini, Chi-Li Chiu,  Loïc A. Royer

Enrichment of spermatogonial stem cells and staging of the testis cycle in a dasyurid marsupial, the fat-tailed dunnart

 Gerard A. Tarulli, Patrick R.S. Tatt, Rhys Howlett, Sara Ord, Beth Shapiro, Stephen R. Frankenberg,  Andrew J. Pask

Defining Cellular Diversity at the Swine Maternal-Fetal Interface Using Spatial Transcriptomics and Organoids

 Cole R. McCutcheon,  Allyson Caldwell,  Liheng (Henry) Yang,  Elisa Crisci,  J. Alex Pasternak,  Carolyn B. Coyne

Generation of human iPSC-derived pancreatic organoids to study pancreas development and disease

Jean-Francois Darrigrand, Abigail Isaacson,  Francesca M. Spagnoli

Spatiotemporal map of the developing human reproductive tract at single-cell resolution

 Valentina Lorenzi, Cecilia Icoresi Mazzeo, Nadav Yayon, Elias R. Ruiz-Morales, Carmen Sancho-Serra, Frederick C.K. Wong, Magda Marečková, Liz Tuck, Kenny Roberts, Tong Li, Marc-Antoine Jacques, Xiaoling He, Roger Barker, Berta Crespo, Batuhan Cakir, Simon Murray, Martin Prete, Yong Gu, Iva Kelava,  Luz Garcia Alonso,  John C Marioni,  Roser Vento Tormo

Research practice & education

Distinct patterns of bioscience doctoral publication disparities by gender and race/ethnicity

Katie Leap, Gregory S. Payne, Janet S. Sinsheimer,  Diana E. Azurdia

Features and signals in precocious citation impact: a meta-research study

 John P.A. Ioannidis

Equity in Action: A Four-Year journey towards Gender Parity and Racial Diversity in Biochemistry Hiring

 Sherri L. Christian,  Valerie Booth,  Scott Harding,  Amy M. Todd,  Mark D. Berry

LeDNA: a cut-and-build toolkit to democratize education on CRISPR gene editing technology

 Guilherme E. Kundlatsch,  Alina S. L. Rodrigues,  Vitória F. B. Zocca,  Laura A. S. Amorim,  Gabriela B. de Paiva,  Almiro P. S. Neto,  Juliana A. D. B. Campos,  Danielle B. Pedrolli

Artificial Intelligence’s Contribution to Biomedical Literature Search: Revolutionizing or Complicating?

 Rui Yip, Young Joo Sun, Alexander G. Bassuk, Vinit B. Mahajan

Quantifying Data Distortion in Bar Graphs in Biological Research

 Teng-Jui Lin,  Markita P. Landry

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