November in preprints
Posted by the Node, on 15 December 2022
Welcome to our monthly trawl for preprints in developmental and stem cell biology (and related topics).
The preprints this month are hosted on bioRxiv – use these links to get to the section you want.
- Patterning & signalling
- Morphogenesis & mechanics
- Genes & genomes
- Stem cells, regeneration & disease modelling
- Plant development
- Evo-devo
Developmental biology
| Patterning & signalling
The Alternate Ligand Jagged Enhances the Robustness of Notch Signaling Patterns
Mrinmoy Mukherjee, Herbert Levine
GDF3 simultaneously antagonizes BMP signaling and activates TGFβ receptor signaling
Deepti Ramachandran, Nagasuryaprasad Kotikalapudi, David E. Maridas, Anton Gulko, Linus T. Tsai, Vicki Rosen, Alexander S. Banks
A macrophage subpopulation promotes airineme-mediated intercellular communication in a Matrix Metalloproteinase-9 dependent manner
Raquel Lynn Bowman, Daoqin Wang, Dae Seok Eom
Voltage-gated sodium channel activity mediates sea urchin larval skeletal patterning through spatial regulation of Wnt5 expression
Christopher F. Thomas, Dakota Y. Hawkins, Viktoriya Skidanova, Simone R. Marrujo, Janay Gibson, Ziqing Ye, Cynthia A. Bradham
Evolutionarily conserved waves of tooth replacement in the gecko are dependent on local signaling
Kirstin S. Brink, Eric Cytrynbaum, Theresa M. Grieco, Joaquin I. Henriquez, Anna Zhitnitsky, Joy M. Richman
Target of Rapamycin Complex 2 modulates development through Hedgehog/Patched signaling in C. elegans
Sinclair W. Emans, Armen Yerevanian, Fasih M. Ahsan, Yifei Zhou, Lucydalila Cedillo, Alexander A. Soukas
How enhancers regulate wavelike gene expression patterns: Novel enhancer prediction and live reporter systems identify an enhancer associated with the arrest of pair-rule waves in the short-germ beetle Tribolium
Christine Mau, Heike Rudolf, Frederic Strobl, Benjamin Schmid, Timo Regensburger, Ralf Palmisano, Ernst Stelzer, Leila Taher, Ezzat El-Sherif
Fendrr synergizes with Wnt signalling to regulate fibrosis related genes during lung development via its RNA:dsDNA Triplex Element
Tamer Ali, Sandra Rogala, Nina M. Krause, Jasleen Kaur Bains, Maria-Theodora Melissari, Sandra Währisch, Harald Schwalbe, Bernhard G Herrmann, Phillip Grote
Integrated multi-omics reveals minor spliceosome inhibition causes molecular stalling and developmental delay of the mouse forelimb
Kyle D. Drake, Saren M. Springer, Kevon O. Afriyie, Tomas D. Lopes, Kaitlin N. Girardini, Rahul N. Kanadia
Combinatorial interpretation of BMP and WNT allows BMP to act as a morphogen in time but not in concentration
Elena Camacho-Aguilar, Sumin Yoon, Miguel A. Ortiz-Salazar, Aryeh Warmflash
Characterisation of the role and regulation of Ultrabithorax in sculpting fine-scale leg morphology
Alexandra D. Buffry, Sebastian Kittelmann, Alistair P. McGregor
The Arabidopsis ARID-HMG protein AtHMGB15 modulates JA signalling by regulating MYC2 during pollen development
Sonal Sachdev, Ruby Biswas, Adrita Roy, Shubho Chaudhuri
cdon and boc affect trunk neural crest cell migration non-cell autonomously through a reduction of hedgehog signaling in zebrafish slow-twitch muscle
Ezra Lencer, Rytis Prekeris, Kristin Artinger
Awakening adult neural stem cells: NOX signalling as a positive regulator of quiescence to proliferation transition in the Xenopus retina
A. Donval, CV Hernandez Puente, A. Lainé, D. Roman, R. Vessely, J. Leclercq, M. Perron, M. Locker
Patterning precision under non-linear morphogen decay and molecular noise
Jan A. Adelmann, Roman Vetter, Dagmar Iber
| Morphogenesis & mechanics
Neuregulin1 regulates cardiomyocyte dynamics, proliferation, and maturation during ventricular chamber morphogenesis
Joaquim Grego-Bessa, Paula Gómez-Apiñaniz, Belén Prados, Manuel José Gómez, Donal MacGrogan, José Luis de la Pompa
A Dystroglycan–Laminin–Integrin axis controls cell basal geometry remodeling in the developing Drosophila retina
Rhian F. Walther, Courtney Lancaster, Jemima J. Burden, Franck Pichaud
Shear and hydrostatic stress regulate fetal heart valve remodeling through YAP-mediated mechanotransduction
Mingkun Wang, Belle Yanyu Lin, Shuofei Sun, Charles Dai, FeiFei Long, Jonathan T. Butcher
CITED2 is a Conserved Regulator of the Uterine-Placental Interface
Marija Kuna, Pramod Dhakal, Khursheed Iqbal, Esteban M. Dominguez, Lindsey N. Kent, Masanaga Muto, Ayelen Moreno-Irusta, Keisuke Kozai, Kaela M. Varberg, Hiroaki Okae, Takahiro Arima, Henry M. Sucov, Michael J. Soares
AKT1-FOXO4 AXIS RECIPROACLLY REGULATES HEMOCHORIAL PLACENTATION
Keisuke Kozai, Ayelen Moreno-Irusta, Khursheed Iqbal, Mae-Lan Winchester, Regan L. Scott, Mikaela E. Simon, Masanaga Muto, Marc R. Parrish, Michael J. Soares
Homeotic compartment curvature and tension control spatiotemporal folding dynamics
Aurélien Villedieu, Lale Alpar, Isabelle Gaugue, Amina Joudat, François Graner, Floris Bosveld, Yohanns Bellaïche
Relationship between thyroid hormones, their associated metabolites, and gene expression bioindicators in the serum of Rana [Lithobates] catesbeiana tadpoles and frogs during metamorphosis
Rikke Poulsen, Shireen H. Jackman, Martin Hansen, Caren C. Helbing
The RNF220 domain nuclear factor Teyrha-Meyrha (Tey) regulates the migration and differentiation of specific visceral and somatic muscles in Drosophila
Manfred Frasch, Afshan Ismat, Ingolf Reim, Jasmin Raufer
Rab11 is essential to pancreas morphogenesis, lumen formation and endocrine mass
Haley R. Barlow, Yadanar Htike, Luke Fassetta, Neha Ahuja, Tyler Bierschenk, D. Berfin Azizoglu, Juan Flores, Nan Gao, Denise Marciano, Ondine Cleaver
Branched germline cysts and female-specific cyst fragmentation facilitate oocyte determination in mice
Kanako Ikami, Suzanne Shoffner, Malgorzata Gosia Tyczynska Weh, Santiago Schnell, Jingqun Ma, Shosei Yoshida, Edgar Diaz Miranda, Sooah Ko, Lei Lei
Heterogeneous migration of neuronal progenitors to the insula shapes the human brain
Arka N. Mallela, Hansen Deng, Ali Gholipour, Simon K Warfield, Ezequiel Goldschmidt
Planar polarized force propagation integrates cell behavior and tissue morphogenesis during convergent extension
Shinuo Weng, Robert J. Huebner, Caitlin C. Devitt, Bill M. Nyaoga, José R. Alvarado, John B. Wallingford
A compound PCP scheme underlies sequential rosettes-based cell intercalation
Yichi Xu, Yunsheng Cheng, Allison T. Chen, Zhirong Bao
Rap1 promotes epithelial integrity and cell viability in a growing tissue
C. Luke Messer, Jocelyn A. McDonald
Mechanisms of vascular maturation and maintenance captured by longitudinal imaging of live mouse skin
Chen Yuan Kam, Ishani D. Singh, Catherine Matte-Martone, David G. Gonzalez, Paloma Solá, Guiomar Solanas, Júlia Bonjoch, Edward D. Marsh, Karen K. Hirschi, Valentina Greco
SRGP-1/srGAP and AFD-1/Afadin stabilize HMP-1/α-Catenin at rosettes to seal internalization sites following gastrulation in C. elegans
Joel M. Serre, Mark M. Slabodnick, Bob Goldstein, Jeff Hardin
Systematic analysis of cell morphodynamics in C. elegans early embryogenesis
Yusuke Azuma, Hatsumi Okada, Shuichi Onami
Cut homeodomain transcription factor is a novel regulator of cortical glia morphogenesis and niche maintenance around neural stem cells
Vaishali Yadav, Papri Das, Ramkrishna Mishra, Richa Arya
The mesodermal source of fibronectin is required for heart morphogenesis and cardiac outflow tract elongation by regulating cell shape, polarity, and mechanotransduction in the second heart field
Cecilia Arriagada, Sophie Astrof
| Genes & genomes
Unique functions of two overlapping PAX6 retinal enhancers
Kirsty Uttley, Andrew S. Papanastasiou, Manuela Lahne, Jennifer M. Brisbane, Ryan B. MacDonald, Wendy A. Bickmore, Shipra Bhatia
Optogenetic dissection of transcriptional repression in a multicellular organism
Jiaxi Zhao, Nicholas C. Lammers, Simon Alamos, Yang Joon Kim, Gabriella Martini, Hernan G. Garcia
Histone exchange sensors reveal variant specific dynamics in mouse embryonic stem cells
Marko Dunjić, Felix Jonas, Gilad Yaakov, Roye More, Yoav Mayshar, Yoach Rais, Naama Barkai, Yonatan Stelzer
Systematic investigation of imprinted gene expression and enrichment in the mouse brain explored at single-cell resolution
M. J. Higgs, M. J. Hill, R. M. John, A. R. Isles
Higher-order epistasis shapes natural variation in germ stem cell niche activity
Sarah R Fausett, Asma Sandjak, Bénédicte Billard, Christian Braendle
Regulation of human trophoblast gene expression by endogenous retroviruses
Jennifer M. Frost, Samuele M. Amante, Hiroaki Okae, Eleri M. Jones, Brogan Ashley, Rohan M. Lewis, Jane K. Cleal, Matthew P. Caley, Takahiro Arima, Tania Maffucci, Miguel R. Branco
Spatially resolved single-cell multiomics map of human trophoblast differentiation in early pregnancy
Anna Arutyunyan, Kenny Roberts, Megan A Sheridan, Ilia Kats, Luz Garcia-Alonso, Britta Velten, Regina Hoo, Kevin Troulé Lozano, Louis-Francois Handfield, Luca Marconato, Elizabeth Tuck, Lucy Gardner, Cecilia Icoresi Mazzeo, Iva Kelava, Elena Prigmore, Sarah A Teichmann, Omer Ali Bayraktar, Ashley Moffett, Oliver Stegle, Margherita Y Turco, Roser Vento-Tormo
Generation of a new Adar1p150-/- mouse demonstrates isoform-specific roles in embryonic development and adult homeostasis
Zhen Liang, Carl R Walkley, Jacki E Heraud-Farlow
Identifying cross-lineage dependencies of cell-type specific regulators in gastruloids
Luca Braccioli, Teun van den Brand, Noemi Alonso Saiz, Charis Fountas, Patrick H. N. Celie, Justina Kazokaitė-Adomaitienė, Elzo de Wit
Transposable element competition shapes the deer mouse genome
Landen Gozashti, Cedric Feschotte, Hopi E. Hoekstra
HAND1 knockdown disrupts trophoblast global gene expression
Robert Fresch, Jennifer Courtney, Heather Brockway, Rebecca L. Wilson, Helen Jones
Eight principal chromatin states functionally segregate the fly genome into developmental and housekeeping roles
Caroline Delandre, John P. D. McMullen, Jonas Paulsen, Philippe Collas, Owen J. Marshall
Bidirectional epigenetic editing reveals hierarchies in gene regulation
Naomi M. Pacalin, Quanming Shi, Kevin R. Parker, Howard Y. Chang
Localization of the pioneer factor GAF to subnuclear foci is driven by DNA binding and required to silence satellite repeat expression
Marissa. M. Gaskill, Isabella V. Soluri, Annemarie E. Branks, Alan P. Boka, Michael R. Stadler, Katherine Vietor, Hao-Yu S. Huang, Tyler J. Gibson, Mustafa Mir, Shelby A. Blythe, Melissa M. Harrison
NR5A2 connects genome activation to the first lineage segregation in early mouse development
Fangnong Lai, Lijia Li, Xiaoyu Hu, Bofeng Liu, Ziqi Zhu, Ling Liu, Qiang Fan, Huabin Tian, Kai Xu, Xukun Lu, Qing Li, Feng Kong, Lijuan Wang, Zili Lin, Hongyu Deng, Jinsong Li, Wei Xie
Transcription factor TFAP2C affects porcine early embryo development via regulating epigenetic modification
Daoyu Zhang, Di Wu, Sheng Zhang, Meng Zhang, Yongfeng Zhou, Xinglan An, Qi Li, Ziyi Li
Transcriptional programs controlling lineages specification of mandibular epithelium during tooth initiation
Fan Shao, An-Vi Phan, Eric Van Otterloo, Huojun Cao
MOF-mediated Histone H4 Lysine 16 Acetylation Governs Mitochondrial and Ciliary Functions By Controlling Gene Promoters
Dongmei Wang, Haimin Li, Navdeep S Chandel, Yali Dou, Rui Yi
Integrated transcriptome and proteome analysis in human brain organoids reveals posttranscriptional regulation of ribosomal genes
Jaydeep Sidhaye, Philipp Trepte, Natalie Sepke, Maria Novatchkova, Michael Schutzbier, Gerhard Dürnberger, Karl Mechtler, Jürgen A. Knoblich
Ratiometric sensing of Pnt and Yan transcription factor levels confers ultrasensitivity to photoreceptor fate transitions in Drosophila
Sebastian M. Bernasek, Suzy SJ Hur, Nicolás Peláez-Restrepo, Jean-François Boisclair Lachance, Rachael Bakker, Heliodoro Tejedor Navarro, Nicelio Sanchez-Luege, Luís A. N. Amaral, Neda Bagheri, Ilaria Rebay, Richard W. Carthew
Low-level repressive histone marks fine-tune stemness gene transcription in neural stem cells
Arjun Rajan, Lucas Anhezini, Noemi Rives-Quinto, Megan C. Neville, Elizabeth D. Larson, Stephen F. Goodwin, Melissa M. Harrison, Cheng-Yu Lee
Sex-determining 3D regulatory hubs revealed by genome spatial auto-correlation analysis
Irene Mota-Gómez, Juan Antonio Rodríguez, Shannon Dupont, Oscar Lao, Johanna Jedamzick, Ralf Kuhn, Scott Lacadie, Sara Alexandra García-Moreno, Alicia Hurtado, Rafael D. Acemel, Blanche Capel, Marc A. Marti-Renom, Darío G. Lupiáñez
Repurposing of the multiciliation gene regulatory network in fate specification of Cajal-Retzius neurons
Matthieu X Moreau, Yoann Saillour, Vicente Elorriaga, Benoît Bouloudi, Elodie Delberghe, Tanya Deutsch Guerrero, Amaia Ochandorena-Saa, Laura Maeso-Alonso, Margarita M Marques, Maria C Marin, Nathalie Spassky, Alessandra Pierani, Frédéric Causeret
Cellular Maturation of Oligodendrocytes is Governed by Transient Gene Melting
Kevin C. Allan, Tyler E. Miller, Andrew R. Morton, Marissa A. Scavuzzo, Matthew S. Elitt, Benjamin L.L. Clayton, Lucille R. Hu, Jost K. Vrabic, Hannah E. Olsen, Daniel C. Factor, Jonathan E. Henninger, Richard A. Young, Charles Y. Lin, Peter C. Scacheri, Paul J. Tesar
doi: https://doi.org/10.1101/2022.11.17.516981
Antagonistic role of the BTB-zinc finger transcription factors Chinmo and Broad-Complex in the juvenile/pupal transition and in growth control
Sílvia Chafino, Panagiotis Giannios, Jordi Casanova, David Martín, Xavier Franch-Marro
ETV2 upregulation marks the specification of early cardiomyocytes and endothelial cells during co-differentiation
Xu Cao, Maria Mircea, Gopala Krishna Yakala, Francijna E. van den Hil, Marcella Brescia, Hailiang Mei, Christine L. Mummery, Stefan Semrau, Valeria V. Orlova
Maternal body condition and season influence RNA deposition in the oocytes of alfalfa leafcutting bees (Megachile rotundata)
Mallory A. Hagadorn, Frances K. Hunter, Tim DeLory, Makenna M. Johnson, Theresa L. Pitts-Singer, Karen M. Kapheim
NuRD independent Mi-2 activity represses ectopic gene expression during neuronal maturation
Gabriel N Aughey, Elhana Forsberg, Krista Grimes, Shen Zhang, Tony D Southall
Decoding gene regulation in the mouse embryo using single-cell multi-omics
Ricard Argelaguet, Tim Lohoff, Jingyu Gavin Li, Asif Nakhuda, Deborah Drage, Felix Krueger, Lars Velten, Stephen J. Clark, Wolf Reik
Mediator 1 ablation induces enamel-to-hair lineage conversion through enhancer dynamics
Roman Thaler, Keigo Yoshizaki, Thai Nguyen, Satoshi Fukumoto, Pamela Den Besten, Daniel D. Bikle, Yuko Oda
Expression bias in retinoic acid responsive genes defines variations in neural differentiation of human pluripotent stem cells
Suel-Kee Kim, Seungmae Seo, Genevieve Stein-O’Brien, Amritha Jaishankar, Kazuya Ogawa, Nicola Micali, Victor Luria, Amir Karger, Yanhong Wang, Thomas M. Hyde, Joel E. Kleinman, Ty Voss, Elana J. Fertig, Joo-Heon Shin, Roland Bürli, Alan J. Cross, Nicholas J. Brandon, Daniel R. Weinberger, Joshua G. Chenoweth, Daniel J. Hoeppner, Nenad Sestan, Carlo Colantuoni, Ronald D. McKay
Diversity within olfactory sensory derivatives revealed by the contribution of Dbx1 lineages
Frédéric Causeret, Maxime Fayon, Matthieu X. Moreau, Enrico Ne, Roberto Oleari, Carlos Parras, Anna Cariboni, Alessandra Pierani
Cell autonomous requirement of imprinted XCI in extra-embryonic polar trophoblast cells
Feng Wang, Ashmita Chander, Yeonsoo Yoon, Mary C. Wallingford, Carmen Espejo-Serrano, Francisco Bustos, Greg M. Findlay, Jesse Mager, Ingolf Bach
Foxp1 acts upstream of Vegfa, suppresses cortical angiogenesis, and promotes hypoxia in radial glia
Caroline A. Pearson, Jessie E. Buth, Michael R.M. Harrison, M. Elizabeth Ross, Bennett G. Novitch
Transcriptomic landscape of early hair follicle and epidermal development
Ana-Marija Sulic, Rishi Das Roy, Verdiana Papagno, Qiang Lan, Riikka Saikkonen, Jukka Jernvall, Irma Thesleff, Marja L Mikkola
A Sox17 downstream gene Rasip1 is involved in the hematopoietic activity of intra-aortic hematopoietic clusters in the midgestation mouse embryo
Gerel Melig, Ikuo Nobuhisa, Kiyoka Saito, Ryota Tsukahara, Ayumi Itabashi, Yoshiakira Kanai, Masami Kanai-Azuma, Mitsujiro Osawa, Motohiko Oshima, Atsushi Iwama, Tetsuya Taga
Single-cell multi-omics decodes regulatory programs during development of mouse secondary palate
Fangfang Yan, Akiko Suzuki, Chihiro Iwaya, Guangsheng Pei, Xian Chen, Hiroki Yoshioka, Meifang Yu, Lukas M. Simon, Junichi Iwata, Zhongming Zhao
Transcriptome profiling of histone writers/erasers enzymes across spermatogenesis, mature sperm and pre-cleavage embryo: Implications in paternal epigenome transitions and inheritance mechanisms
Gastón Barbero, Maximiliano de Sousa Serro, Camila Perez Lujan, Alfredo D. Vitullo, Candela R. González, Betina González
Imprinted Dlk1 dosage as a size determinant of the mammalian pituitary gland
Valeria Scagliotti, Maria Lillina Vignola, Thea Willis, Mark Howard, Eugenia Marinelli, Carles Gaston-Massuet, Cynthia Andoniadou, Marika Charalambous
The binding sites of E2F transcription factor in Drosophila metabolic genes are functionally distinct
Maria Paula Zappia, Yong-Jae Kwon, Anton Westacott, Isabel Liseth, Hyun Min Lee, Abul B.M.M.K. Islam, Jiyeon Kim, Maxim V. Frolov
| Stem cells, regeneration & disease modelling
Adaptation to ex vivo culture drives human haematopoietic stem cell loss of repopulation capacity in a cell cycle independent manner
Carys S. Johnson, Kendig Sham, Serena Belluschi, Xiaonan Wang, Winnie Lau, Kerstin B. Kaufmann, Gabriela Krivdova, Emily F. Calderbank, Nicole Mende, Jessica McLeod, Giovanna Mantica, Matthew J. Williams, Charlotte Grey-Wilson, Michael Drakopoulos, Shubhankar Sinha, Evangelia Diamanti, Christina Basford, Anthony R. Green, Nicola K. Wilson, Steven J. Howe, John E. Dick, Bertie Göttgens, Natalie Francis, Elisa Laurenti
A miRNA screen identifies a transcriptional program controlling adult stem cell maintenance in mammary organoids
F Delom, E Vlachavas, G Lemaître, J Robert, A Chatziioannou, M Puceat, D Fessart
Spatiotemporal coordination of stem cell behavior following alveolar injury
Maurizio Chioccioli, Sumner Magruder, John E. McDonough, Jessica Nouws, Tao Yang, David Gonzalez, Lucia Borriello, Brian Traub, Xianjun Ye, Caroline E. Hendry, David Entenberg, Smita Krishnaswamy, Naftali Kaminski, Maor Sauler
Spatial cell fate manipulation of human pluripotent stem cells by controlling the microenvironment using photocurable hydrogel
Zhe Wang, Akira Numada, Fumi Wagai, Yusuke Oda, Mototsugu Eiraku
SOX9 elongates cell cycle phases and biases fate decisions in human intestinal stem cells
Joseph Burclaff, R. Jarrett Bliton, Keith A Breau, Michael J Cotton, Caroline M Hinesley, Meryem T Ok, Caden W Sweet, Anna Zheng, Eric D Bankaitis, Pablo Ariel, Scott T Magness
Atg1 modulates mitochondrial dynamics to promote germline stem cell maintenance in Drosophila
Minal S. Ayachit, Bhupendra V. Shravage
Hippo signaling impairs alveolar epithelial regeneration in pulmonary fibrosis
Rachel Warren, Handeng Lyu, Shan Gao, Kylie Klinkhammer, Stijn P. De Langhe
LSR Targets YAP to Modulate Intestinal Paneth Cell Differentiation
Yanan An, Chao Wang, Baozhen Fan, Ying Li, Feng Kong, Chengjun Zhou, Zhang Cao, Jieying Liu, Mingxia Wang, Hui Sun, Shengtian Zhao, Yongfeng Gong
A human mitofusin 2 mutation causes mitophagic cardiomyopathy
Antonietta Franco, Jiajia Li, Daniel P. Kelly, Ray E. Hershberger, Ali J. Marian, Renate M. Lewis, Moshi Song, Xiawei Dang, Alina D. Schmidt, Mary E. Mathyer, Cristina de Guzman Strong, Gerald W. Dorn II
Comparative single-cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration
Ke-Hsuan Wei, I-Ting Lin, Kaushik Chowdhury, Kuan-Ting Liu, Tai-Ming Ko, Yao-Ming Chang, Kai-Chien Yang, Shih-Lei Lai
Lipid Desaturation Regulates the Balance between Self-renewal and Differentiation in Mouse Blastocyst-derived Stem Cells
Chanchal Thomas Mannully, Reut Bruck-Haimson, Anish Zacharia, Paul Orih, Alaa Shehadeh, Daniel Saidemberg, Natalya M Kogan, Sivan Alfandary, Raphael Serruya, Arie Dagan, Isabelle Petit, Arieh Moussaieff
Nod1-dependent NF-kB activation initiates hematopoietic stem cell specification in response to small Rho GTPases
Xiaoyi Cheng, Radwa Barakat, Abigail Gorden, Elizabeth Snella, Yudi Zhang, Karin Dorman, Antonella Fidanza, Clyde Campbell, Raquel Espin-Palazon
Endocrine disruption of early uterine differentiation causes adenocarcinoma mediated by Wnt/β-catenin- and PI3K/AKT signaling
Elizabeth Padilla-Banks, Wendy N. Jefferson, Brian N. Papas, Alisa A. Suen, Xin Xu, Diana V. Carreon, Cynthia J. Willson, Erin M. Quist, Carmen J. Williams
Steroidogenesis and androgen/estrogen signaling pathways are altered in in vitro matured testicular tissues of prepubertal mice
Laura Moutard, Caroline Goudin, Catherine Jaeger, Céline Duparc, Estelle Louiset, Tony Pereira, François Fraissinet, Marion Delessard, Justine Saulnier, Aurélie Rives-Feraille, Christelle Delalande, Hervé Lefebvre, Nathalie Rives, Ludovic Dumont, Christine Rondanino
Inhibition of Centrosome Clustering Reduces Cystogenesis and Improves Kidney Function in Autosomal Dominant Polycystic Kidney Disease
Tao Cheng, Aruljothi Mariappan, Ewa Langner, Kyuhwan Shim, Jay Gopalakrishnan, Moe R. Mahjoub
De-differentiation and Proliferation of Artery Endothelial Cells Drive Coronary Collateral Development
Gauri Arolkar, Sneha K, Hanjay Wang, Karen M. Gonzalez, Suraj Kumar, Bhavnesh Bishnoi, Pamela E. Rios Coronado, Y. Joseph Woo, Kristy Red-Horse, Soumyashree Das
The lncRNA Sweetheart regulates compensatory cardiac hypertrophy after myocardial injury
Sandra Rogala, Tamer Ali, Maria-Theodora Melissari, Sandra Währisch, Peggy Schuster, Alexandre Sarre, Thomas Boettger, Eva-Maria Rogg, Jaskiran Kaur, Jaya Krishnan, Stefanie Dimmeler, Samir Ounzain, Thierry Pedrazzini, Bernhard G Herrmann, Phillip Grote
Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration
Akane Kawaguchi, Jingkui Wang, Dunja Knapp, Prayag Murawala, Sergej Nowoshilow, Wouter Masselink, Yuka Taniguchi-Sugiura, Jifeng Fei, Elly M. Tanaka
A tracheal aspirate-derived airway basal cell model reveals a proinflammatory epithelial defect in congenital diaphragmatic hernia
Richard Wagner, Gaurang M. Amonkar, Wei Wang, Jessica E. Shui, Kamakshi Bankoti, Wai Hei Tse, Frances A. High, Jill M. Zalieckas, Terry L. Buchmiller, Augusto Zani, Richard Keijzer, Patricia K. Donahoe, Paul H. Lerou, Xingbin Ai
Missense and nonsense mutations of the zebrafish hcfc1a gene result in contrasting mTor and radial glial phenotypes
Victoria L. Castro, David Paz, Valeria Virrueta, Igor L. Estevao, Brian I. Grajeda, Cameron C. Ellis, Anita M. Quintana
Focal adhesion protein vinculin inhibits Mef2c-driven sclerostin expression in osteocytes to promote bone formation in mice
Yishu Wang, Jianmei Huang, Sixiong Lin, Lei Qin, Dingyu Hao, Peijun Zhang, Shaochuan Huo, Xuenong Zou, Di Chen, Guozhi Xiao
Pluripotent, germ cell competent adult stem cells underlie cnidarian plant-like life history
Áine Varley, Helen R Horkan, Emma T McMahon, Gabriel Krasovec, Uri Frank
Pituitary stem cells differ according to their position in the gland and maintenance of their progeny depends on physiological context
Karine Rizzoti, Probir Chakravarty, Daniel Sheridan, Robin Lovell-Badge
Size compensation in Drosophila after generalised cell death
Noelia Pinal, Natalia Azpiazu, Ginés Morata
Chromatin remodeller Chd7 is developmentally regulated in the neural crest by tissue-specific transcription factors
Ruth Williams, Güneş Taylor, Irving T C Ling, Ivan Candido-Ferreira, Sarah Mayes, Yavor K Bozhilov, Richard C V Tyser, Shankar Srinivas, Jim R Hughes, Tatjana Sauka-Spengler
Foxa2 lineage+ mesendoderm forms a competitive pulmonary mesenchyme niche crucial for generating the entire lungs
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
| Plant development
Cell surface auxin signalling directly targets PIN-mediated auxin fluxes for adaptive plant development
Lesia Rodriguez, Lukáš Fiedler, Minxia Zou, Caterina Giannini, Aline Monzer, Zuzana Gelová, Inge Verstraeten, Jakub Hajný, Shutang Tan, Lukas Hoermayer, Lanxin Li, Maria Mar Marques-Bueno, Gergely Molnár, Tongda Xu, Ivan Kulich, Yvon Jaillais, Jiří Friml
Self-regulation of PIN1-driven auxin transport by cell surface-based auxin signaling in Arabidopsis
Jiacheng Wang, Mingzeng Chang, Rongfeng Huang, Michelle Gallei, Jiřn Friml, Yongqiang Yu, Mingzhang Wen, Zhenbiao Yang, Tongda Xu
Cell type-specific attenuation of brassinosteroid signalling drives stomatal asymmetric cell division
Eun-Ji Kim, Cheng Zhang, Boyu Guo, Thomas Eekhout, Anaxi Houbaert, Jos R. Wendrich, Niels Vandamme, Manish Tiwari, Claire Simon–Vezo, Isabelle Vanhoutte, Yvan Saeys, Kun Wang, Yuxian Zhu, Bert De Rybel, Eugenia Russinova
MERISTEM-DEFECTIVE / DEFECTIVELY ORGANIZED TRIBUTARIES2 regulates the balance between stemness and differentiation in the root meristem through RNA splicing control
Helen L. Thompson, Weiran Shen, Rodrigo Matus, Medhavi Kakkar, Carl Jones, David Dolan, Sushma Grellscheid, Xiyan Yang, Na Zhang, Sina Mozaffari-Jovin, Chunli Chen, Xianlong Zhang, Jennifer F. Topping, Keith Lindsey
Defining the Parameters to Improve Plant Regeneration with Developmental Regulators
Ryan Nasti, Jon P. Cody, Matt H. Zinselmeier, Nikil B. Badey, Adhvaith Sridhar, Ambika Sharma, Michael F. Maher, Benjamin K. Blackman, Daniel F. Voytas
A polarized nuclear position is required for correct division plane specification during maize stomatal development
M. Arif Ashraf, Le Liu, Michelle R. Facette
Medicago truncatula ABCG40 is a cytokinin importer negatively regulating lateral root density and nodule number
Tomasz Jamruszka, Joanna Banasiak, Aleksandra Pawela, Karolina Jarzyniak, Jian Xia, Wanda Biała-Leonhard, Lenka Plačková, Francesca Romana Iacobini, Ondřej Novák, Markus Geisler, Michał Jasiński
Systematic mining and genetic characterization of regulatory factors for wheat spike development
Xuelei Lin, Yongxin Xu, Dongzhi Wang, Yiman Yang, Xiaoyu Zhang, Xiaomin Bie, Hongzhe Wang, Jiafu Jiang, Yiliang Ding, Fei Lu, Xueyong Zhang, Xiansheng Zhang, Xiangdong Fu, Jun Xiao
Stomatal density affects rice mesophyll cell size and shape and modulates a conserved pattern of cells through the leaf
Sloan Jen, Im-Chai Saranrat, Qi Yang Ngai, Xiao Yi, Armand Jodie, Matthew J. Wilson, Zhu Xin-Guang, Andrew J. Fleming
The soil microbiome reduces Striga infection of sorghum by modulation of host-derived signaling molecules and root development
Dorota Kawa, Benjamin Thiombiano, Mahdere Shimels, Tamera Taylor, Aimee Walmsley, Hannah E Vahldick, Marcio FA Leite, Zayan Musa, Alexander Bucksch, Francisco Dini-Andreote, Alexander J Chen, Jiregna Daksa, Desalegn Etalo, Taye Tessema, Eiko E Kuramae, Jos M Raaijmakers, Harro Bouwmeester, Siobhan M Brady
Dynamic growth re-orientation orchestrates flatness in the Arabidopsis leaf
Kate Harline, Antoine Fruleux, Brendan Lane, Gabriella Mosca, Soeren Strauss, Nik Tavakolian, James W. Satterlee, Chun-Biu Li, Abhyudai Singh, Richard S. Smith, Arezki Boudaoud, Adrienne H.K. Roeder
Mutations in NAKED-ENDOSPERM IDD genes reveal functional interactions with SCARECROW and a maternal influence on leaf patterning in C4 grasses
Thomas E. Hughes, Olga Sedelnikova, Mimi Thomas, Jane A. Langdale
A new gene encoding a cytosolic glutamine synthetase in pine is linked to developing tissues
José Miguel Valderrama-Martín, Francisco Ortigosa, Juan Carlos Aledo, Concepción Ávila, Francisco M. Cánovas, Rafael A. Cañas
The UBP5 histone H2A deubiquitinase counteracts PRC2-mediated repression to regulate Arabidopsis development and stress responses
James Godwin, Eduardo March, Mohan Govindasamy, Clara Bourbousse, Léa Wolff, Antoine Fort, Michal Krzyszton, Jesús López, Szymon Swiezewski, Fredy Barneche, Daniel Schubert, Sara Farrona
| Evo-devo
Time-Aligned Hourglass Gastrulation Models in Rabbit and Mouse
Y Mayshar, O Raz, S Cheng, R Ben-Yair, R Hadas, N Reines, M Mittnenzweig, O Ben-Kiki, A Lifshitz, A Tanay, Y Stelzer
Bat teeth illuminate the diversification of mammalian tooth classes
Alexa Sadier, Neal Anthwal, Andrew L. Krause, Renaud Dessalles, Michael Lake, Laurent Bentolila, Robert Haase, Natalie Nieves, Sharlene Santana, Karen Sears
Evolution of Secondary Cell Number and Position In the Drosophila Accessory Gland
Yoko A. Takashima, Alex C. Majane, David J. Begun
Sex-biased gene expression at single-cell resolution: Cause and consequence of sexual dimorphism
Iulia Darolti, Judith E. Mank
Differential requirement of nanos homologs in the germline suggests the evolutionary path toward an inheritance mechanism of primordial germ cell formation in the silkmoth Bombyx
Hajime Nakao, Yoko Takasu
Cell Biology
Maintaining structural and functional homeostasis of the Drosophila respiratory epithelia requires stress-modulated JAK/STAT activity
Xiao Niu, Christine Fink, Kimberley Kallsen, Leizhi Shi, Viktoria Mincheva, Sören Franzenburg, Ruben Prange, Iris Bruchhaus, Judith Bossen, Holger Heine, Thomas Roeder
Optogenetic control of YAP can enhance the rate of wound healing
Pearlyn Jia Ying Toh, Marius Sudol, Timothy Edward Saunders
A meiotic midbody structure in mouse oocytes acts as a barrier for nascent translation to ensure developmental competence
Gyu Ik Jung, Daniela Londoño-Vásquez, Sungjin Park, Ahna R. Skop, Ahmed Z. Balboula, Karen Schindler
Mother cells control daughter cell proliferation in intestinal organoids to minimize proliferation fluctuations
Guizela Huelsz-Prince, Rutger N.U. Kok, Yvonne J. Goos, Lotte Bruens, Xuan Zheng, Saskia I. Ellenbroek, Jacco van Rheenen, Sander J. Tans, Jeroen S. van Zon
Two RNA binding proteins, ADAD2 and RNF17, interact to form novel meiotic germ cell granules required for male fertility
Lauren G. Chukrallah, Sarah Potgieter, Elizabeth M. Snyder
Kinetochore microtubules flux poleward along fixed centrosome-anchored microtubules during the metaphase of C. elegans one-cell embryo
Nina Soler, Laurent Chesneau, Hélène Bouvrais, Sylvain Pastezeur, Loïc Le Marrec, Jacques Pecreaux
P bodies coat germ granules to promote transgenerational gene silencing in C. elegans
Zhenzhen Du, Kun Shi, Jordan S. Brown, Tao He, Wei-Sheng Wu, Ying Zhang, Heng-Chi Lee, Donglei Zhang
Neuronal IL-17 controls C. elegans developmental diapause through p53/CEP-1
Abhishiktha Godthi, Srijit Das, Johnny Cruz-Corchado, Andrew Deonarine, Kara Misel-Wuchter, Priya D. Issuree, Veena Prahlad
Transcriptional regulation and repressive condensates modulate a proliferative-invasive cellular switch in vivo
Taylor N. Medwig-Kinney, Brian A. Kinney, Michael A. Q. Martinez, Callista Yee, Sydney S. Sirota, Angelina A. Mullarkey, Neha Somineni, Justin Hippler, Wan Zhang, Kang Shen, Christopher M. Hammell, Ariel M. Pani, David Q. Matus
Amino acid intake strategies define pluripotent cell states
Pavlina K. Todorova, Benjamin T. Jackson, Vidur Garg, Katrina I. Paras, Yanyang Chen, Sanjeethan C. Baksh, Jielin Yan, Anna-Katerina Hadjantonakis, Lydia W. S. Finley
TORC1 regulation of dendrite regrowth after pruning is linked to actin and exocytosis
Neeraja Sanal, Lorena Keding, Ulrike Gigengack, Esther Michalke, Sebastian Rumpf
rRNA transcription is integral to liquid-liquid phase separation and maintenance of nucleolar structure
Soma Dash, Maureen C. Lamb, Jeffrey J. Lange, Mary C. McKinney, Dai Tsuchiya, Fengli Guo, Xia Zhao, Timothy J. Corbin, MaryEllen Kirkman, Kym Delventhal, Emma L. Moore, Sean McKinney, Rita Shiang, Paul A. Trainor
CHK1-CDC25A-CDK1 regulate cell cycle progression in early mouse embryos to protect genome integrity
Knoblochova Lucie, Duricek Tomas, Vaskovicova Michaela, Zorzompokou Chrysoula, Rayova Diana, Ferencova Ivana, Baran Vladimir, Richard M. Schultz, Eva R. Hoffmann, Drutovic David
Mapping of the podocin proximity-dependent proteome reveals novels components of the kidney podocyte foot process
Gary F. Gerlach, Zachary H. Imseis, Shamus L. Cooper, Anabella N. Santos, Lori L. O’Brien
The dark kinase STK32A regulates hair cell planar polarity opposite of EMX2 in the developing mouse inner ear
Shihai Jia, Evan M. Ratzan, Ellison J. Goodrich, Raisa Abrar, Luke Heiland, Basile Tarchini, Michael R. Deans
Modelling
On the origin of viscosity saturation at high densities during zebrafish morphogenesis
Rajsekhar Das, Sumit Sinha, Xin Li, T. R. Kirkpatrick, D. Thirumalai
The genetic structure within a single tree is determined by the behavior of the stem cells in the meristem
Yoh Iwasa, Sou Tomimoto, Akiko Satake
A bistable autoregulatory module in the developing embryo commits cells to binary fates
Jiaxi Zhao, Mindy Liu Perkins, Matthew Norstad, Hernan G. Garcia
A mathematical theory for the mechanics of three-dimensional cellular aggregates reveals the mechanical atlas for Ascidian embryogenesis
Siqi Liu, Patrick Lemaire, Edwin Munro, Madhav Mani
Tools & Resources
Image-based quantification of Arabidopsis thaliana stomatal aperture from leaf images
Momoko Takagi, Rikako Hirata, Yusuke Aihara, Yuki Hayashi, Miya Mizutani-Aihara, Eigo Ando, Megumi Yoshimura-Kono, Masakazu Tomiyama, Toshinori Kinoshita, Akira Mine, Yosuke Toda
Deep-learning-assisted Sort-Seq enables high-throughput profiling of gene expression characteristics with high precision
Huibao Feng, Fan Li, Tianmin Wang, Xin-hui Xing, An-ping Zeng, Chong Zhang
DrosOmics: a comparative genomics browser to explore omics data in natural populations of D. melanogaster
Marta Coronado-Zamora, Judit Salces-Ortiz, Josefa González
Aneuploid embryos as a proposal for improving Artificial Intelligence performance
Enric Güell Penas, Marina Esquerrà Parés, Andreu Vives Perelló, Mikaela Mladenova Koleva
An improved network alignment algorithm of dynamic protein interaction networks of floral development in Arabidopsis
Jiamin Ji, Kailing Zheng, Miao He
“An optimized pipeline for live imaging whole Arabidopsis leaves at cellular resolution”
Kate Harline, Adrienne Roeder
Primordial germ cells adjust their protrusion type while migrating in different tissue contexts in vivo
Lukasz Truszkowski, Dilek Batur, Hongyan Long, Katsiaryna Tarbashevich, Bart E. Vos, Britta Trappmann, Erez Raz
Genome editing in plants using the compact editor CasΦ
Zheng Li, Zhenhui Zhong, Zhongshou Wu, Patrick Pausch, Basem Al-Shayeb, Jasmine Amerasekera, Jennifer A. Doudna, Steven E. Jacobsen
HeatChips: A versatile, low-cost and microscopy-compatible heating system for microfluidic devices
Théo Aspert, Gilles Charvin
Charting the development of Drosophila leg sensory organs at single-cell resolution
Ben R. Hopkins, Olga Barmina, Artyom Kopp
Three-dimensional molecular architecture of mouse organogenesis
Fangfang Qu, Wenjia Li, Jian Xu, Ruifang Zhang, Jincan Ke, Xiaodie Ren, Xiaogao Meng, Lexin Qin, Jingna Zhang, Fangru Lu, Xin Zhou, Xi Luo, Zhen Zhang, Guangming Wu, Duanqing Pei, Jiekai Chen, Guizhong Cui, Shengbao Suo, Guangdun Peng
GECT – Gene Expression Detection in Developing Tissue Using μCT Imaging
Vilma Väänänen, Mona M. Christensen, Heikki Suhonen, Jukka Jernvall
Effects of lactate, super-GDF9 and low oxygen tension during biphasic in vitro maturation on the bioenergetic profiles of mouse cumulus-oocyte-complex
Nazli Akin, Gamze Ates, Lucia von Mengden, Anamaria-Cristina Herta, Cecilia Meriggioli, Katy Billooye, William A. Stocker, Brecht Ghesquiere, Craig A. Harrison, Fabio Klamt, Ann Massie, Johan Smitz, Ellen Anckaert
Image restoration of degraded time-lapse microscopy data mediated by infrared-imaging
Nicola Gritti, Rory M. Power, Alyssa Graves, Jan Huisken
Mapping human social brain specialisation beyond the neuron using multimodal imaging in human infants
Maheen Siddiqui, Paola Pinti, Sabrina Brigadoi, Sarah Lloyd-Fox, Clare E. Elwell, Mark H. Johnson, Ilias Tachtsidis, Emily J.H. Jones
Using unlabeled information of embryo siblings from the same cohort cycle to enhance in vitro fertilization implantation prediction
Noam Tzukerman, Oded Rotem, Maya Tsarfati Shapiro, Ron Maor, Marcos Meseguer, Daniella Gilboa, Daniel S. Seidman, Assaf Zaritsky
Establishment and characterisation of oviductal organoids from farm and companion animals
Edwina F. Lawson, Arnab Ghosh, Victoria Blanch, Christopher G. Grupen, R John Aitken, Rebecca Lim, Hannah R. Drury, Mark A. Baker, Zamira Gibb, Pradeep S. Tanwar
An improved Erk biosensor reveals oscillatory Erk dynamics driven by mitotic erasure during early development
Scott G. Wilcockson, Luca Guglielmi, Pablo Araguas Rodriguez, Marc Amoyel, Caroline S. Hill
Single-cell assessment of trophoblast stem cell-based organoids as human placenta-modeling platforms
Matthew J. Shannon, Gina L. McNeill, Burak Koksal, Jennet Baltayeva, Jasmin Wächter, Barbara Castellana, Maria S. Peñaherrera, Wendy P. Robinson, Peter C. K. Leung, Alexander G. Beristain
Lipotype acquisition during neural development in vivo is not recapitulated in stem cell-derived neurons
Anusha B. Gopalan, Lisa van Uden, Richard R. Sprenger, Nadine Fernandez-Novel Marx, Helle Bogetofte, Pierre Neveu, Morten Meyer, Kyung-Min Noh, Alba Diz-Muñoz, Christer S. Ejsing
More accurate analysis of maternal effect genes by siRNA electroporation into mouse oocytes
Takuto Yamamoto, Shinnosuke Honda, Issei Ideguchi, Motoki Suematsu, Shuntaro Ikeda, Naojiro Minami
Reconstitution of human adrenocortical specification and steroidogenesis using induced pluripotent stem cells
Yuka Sakata, Keren Cheng, Michinori Mayama, Yasunari Seita, Andrea J. Detlefsen, Clementina A. Mesaros, Trevor M. Penning, Kyosuke Shishikura, Wenli Yang, Richard J. Auchus, Jerome F. Strauss III 3rd, Kotaro Sasaki
Research practice & education
Mapping the content of comments on bioRxiv and medRxiv preprints
Clarissa F. D. Carneiro, Gabriel Costa, Kleber Neves, Mariana B. Abreu, Pedro B. Tan, Danielle Rayêe, Flávia Boos, Roberta Andrejew, Tiago Lubiana, Mario Malički, Olavo B. Amaral
Analysis of science journalism reveals gender and regional disparities in coverage
Natalie R. Davidson, Casey S. Greene
Microplastics are present in follicular fluid and compromise gamete function in vitro: Is the Anthropocene throw-away society throwing away fertility?
Nicole Grechi, Roksan Franko, Roshini Rajaraman, Jan B. Stöckl, Tom Trapphoff, Stefan Dieterle, Thomas Fröhlich, Michael J. Noonan, Marcia de A. M. M. Ferraz
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