Top 8 Biorxiv Papers Today in Developmental Biology


2.022 Mikeys
#1. Emergence of neuronal diversity during vertebrate brain development
Bushra Raj, Jeffrey A Farrell, Aaron McKenna, Jessica L Leslie, Alexander F Schier
Neurogenesis in the vertebrate brain comprises many steps ranging from the proliferation of progenitors to the differentiation and maturation of neurons. Although these processes are highly regulated, the landscape of transcriptional changes and progenitor identities underlying brain development are poorly characterized. Here, we describe the first developmental single-cell RNA-seq catalog of more than 200,000 zebrafish brain cells encompassing 12 stages from 12 hours post-fertilization to 15 days post-fertilization. We characterize known and novel gene markers for more than 800 clusters across these timepoints. Our results capture the temporal dynamics of multiple neurogenic waves from embryo to larva that expand neuronal diversity from ~20 cell types at 12 hpf to ~100 cell types at 15 dpf. We find that most embryonic neural progenitor states are transient and transcriptionally distinct from long-lasting neural progenitors of post-embryonic stages. Furthermore, we reconstruct cell specification trajectories for the retina and...
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Erky321: Single cell “catalog of >200,000 zebrafish brain 🧠 cells encompassing 12 stages...(reveal) neurogenic waves from embryo to larva that expand neuronal diversity from ~20 cell types at 12 hpf to ~100 cell types at 15 dpf” @schierlab https://t.co/CV4Egn7ru6 https://t.co/zYfUXcWzh0
PromPreprint: Emergence of neuronal diversity during vertebrate brain development https://t.co/oDw1AwTUpP
1stDarwin: RT @biorxivpreprint: Emergence of neuronal diversity during vertebrate brain development https://t.co/2JWIxArTCH #bioRxiv
sourish_m: RT @biorxivpreprint: Emergence of neuronal diversity during vertebrate brain development https://t.co/2JWIxArTCH #bioRxiv
embryologistics: RT @biorxivpreprint: Emergence of neuronal diversity during vertebrate brain development https://t.co/2JWIxArTCH #bioRxiv
IchiroNakanoNS: RT @biorxivpreprint: Emergence of neuronal diversity during vertebrate brain development https://t.co/2JWIxArTCH #bioRxiv
Github

GESTALT processing pipeline for barcodes captured with single-cell RNA sequencing

Repository: SC_GESTALT
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Language: Scala
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Authors: 5
Total Words: 11248
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2.006 Mikeys
#2. Spatiotemporal Control of CRISPR/Cas9 Function in Cells and Zebrafish using Light-Activated Guide RNA
Wenyuan Zhou, Wes Brown, Anirban Bardhan, Michael Delaney, Amber S Ilk, Randy R Rauen, Shoeb I Kahn, Michael Tsang, Alexander Deiters
We developed a new method for conditional regulation of CRISPR/Cas9 activity in mammalian cells and zebrafish embryos via photochemically activated, caged guide RNAs. Caged gRNAs are generated by substituting four nucleobases evenly distributed throughout the 5'-protospacer region with caged nucleobases during synthesis. Caging confers complete suppression of gRNA:target dsDNA hybridization and rapid restoration of CRISPR/Cas9 function upon optical activation. This tool offers simplicity and complete programmability in design, high spatiotemporal specificity in cells and zebrafish embryos, excellent off to on switching, and stability by preserving the ability to form Cas9:gRNA ribonucleoprotein complexes. caged gRNAs are novel tools for conditional control of gene editing thereby enabling the investigation of spatiotemporally complex physiological events by obtaining a better understanding of dynamic gene regulation.
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biorxivpreprint: Spatiotemporal Control of CRISPR/Cas9 Function in Cells and Zebrafish using Light-Activated Guide RNA https://t.co/gIf2398NXk #bioRxiv
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1.997 Mikeys
#3. Regulation of nerve growth and patterning by cell surface protein disulphide isomerase
Geoffrey M.W. Cook, Catia Sousa, Julia Schaeffer, Katherine Wiles, Prem Jareonsettasin, Asanish Kalyanasundaram, Eleanor Walder, Catharina Casper, Serena Patel, Pei Wei Chua, Gioia Riboni-Verri, Mansoor Raza, Nol Swaddiwudhipong, Andrew Hui, Ameer Abdullah, Saj Wajed, Roger Keynes
Contact repulsion of growing axons is an essential mechanism for spinal nerve patterning. In birds and mammals the embryonic somites generate a linear series of impenetrable barriers, forcing axon growth cones to traverse one half of each somite as they extend towards their body targets. This study shows that protein disulphide isomerase provides a key component of these barriers, mediating contact repulsion at the cell surface in half-somites. Repulsion is reduced both in vivo and in vitro by a range of methods that inhibit enzyme activity. The activity is critical in initiating a nitric oxide/S-nitrosylation-dependent signal transduction pathway that regulates the growth cone cytoskeleton. Rat forebrain grey matter extracts contain a similar activity, and the enzyme is expressed at the surface of cultured human astrocytic cells and rat cortical astrocytes. We suggest this system is co-opted in the brain to counteract and regulate aberrant nerve terminal growth.
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Authors: 17
Total Words: 17591
Unqiue Words: 6000

1.997 Mikeys
#4. Different roles of eye absent in the basal ovarian follicle and germarium of developing cockroach ovaries
Saray Ramos, Fleur Chelemen, Viviana Pagone, Nashwa Elsaher, Paula Irles, Maria-Dolors Piulachs
Eye absent (Eya) is a protein which has been structurally conserved from hydrozoans to humans which has two functions: it is both a transcription cofactor and a protein tyrosine phosphatase. Eya was first described in the fly Drosophila melanogaster for its role in eye development, and the same functions were also later reported in less derived insects. Studies on the involvement of Eya in insect oogenesis are limited to D. melanogaster, which has meroistic ovaries. In this fly, Eya plays a fundamental role in the first stages of ovarian development because Eya mutations abolish gonad formation. In this present work we studied the function of Eya in the panoistic ovary of the cockroach Blattella germanica. We demonstrated that Eya is essential for correct ovary development also in this ovary type. In B. germanica ovaries, Eya affects both somatic and germinal cells in the germarium and the vitellarium, acting differently in different ovarian regions. Development of the basal ovarian follicles is arrested BgEya-depleted females,...
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1.994 Mikeys
#5. Identification of conserved gene regulatory networks that integrate environmental sensing and growth in the root cambium
Goh Choe, Nam Van Hoang, Yi Zheng, Ana Cecilia Aliaga Fandino, Jaeryung Hur, Inyoung Sung, Hongryul Ahn, Sun Kim, Zhangjun Fei, Ji-Young Lee
Cambium drives lateral growth of stems and roots, contributing to diverse plant growth forms. Root crop is one outstanding example of the cambium-driven growth. To understand its molecular basis, we used radish to generate a compendium of root tissue- and stage-specific transcriptomes from two contrasting inbred lines in root growth. Expression patterns of key cambium regulators and hormone signaling components were validated. Clustering and GO enrichment analyses of radish datasets followed by comparative analysis against the newly established Arabidopsis early cambium data revealed evolutionary conserved stress-response transcription factors that might intimately control the cambium. Indeed, in vivo network made of selected stress-response and cambium regulators indicated ERF-1 as a potential key checkpoint of cambial activities, explaining how the cambium-driven growth is altered in response to environmental changes. Together, this study provides rich information about dynamic gene expression changes along the cambium-driven...
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1.994 Mikeys
#6. Sarcomeres regulate cardiomyocyte maturation through MRTF-SRF signaling
Yuxuan guo, Blake Jardin, Isha Sethi, Qing Ma, Behzad Moghadaszadeh, Emily Troiano, Michael Trembley, Eric Small, Guo-Cheng Yuan, Alan Beggs, William Pu
Cardiomyocyte maturation is essential for robust heart contraction throughout life. The signaling networks governing cardiomyocyte maturation remain poorly defined. Our prior studies established the transcription factor SRF as a key regulator of the assembly of sarcomeres, the contractile unit of cardiomyocytes. Whether sarcomeres regulate other aspects of maturation remains unclear. Here we generated mice with cardiomyocyte specific, mosaic mutation of α-actinin-2 (Actn2), a key organizer of sarcomeres, to study its cell-autonomous role in cardiomyocyte maturation. In addition to the expected structural defects, Actn2 mutation triggered dramatic transcriptional dysregulation, which strongly correlated with transcriptional changes observed in SRF depleted cardiomyocytes. Actn2 mutation increased monomeric actin, which perturbed the nuclear localization of the SRF cofactor MRTFA. Overexpression of a dominantnegative MRTFA mutant was sufficient to recapitulate the transcriptional and morphological defects in Actn2 and Srf mutant...
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Authors: 11
Total Words: 13036
Unqiue Words: 3759

1.986 Mikeys
#7. Epithelial Vegfa specifies a distinct endothelial population in the mouse lung
Lisandra Vila Ellis, Margo P Cain, Vera Hutchison, Per Flodby, Edward D Crandall, Zea Borok, Bin Zhou, Edwin J Ostrin, Joshua D Wythe, Jichao Chen
The lung microvasculature is essential for gas exchange and commonly considered homogeneous. We show that VEGFA from the epithelium is required for a distinct endothelial cell (EC) population in the mouse lung. Vegfa is predominantly expressed by alveolar type 1 (AT1) cells and locally required to specify a subset of ECs. Single cell RNA-seq reveals that ~15% of lung ECs are transcriptionally distinct - marked by Carbonic anhydrase 4 (Car4) - and arise from bulk ECs, as suggested by trajectory analysis. Car4 ECs have extensive cellular projections and are separated from AT1 cells by a limited basement membrane without intervening pericytes. Car4 ECs are specifically lost upon epithelial Vegfa deletion; without Car4 ECs, the alveolar space is aberrantly enlarged despite the normal appearance of myofibroblasts. Lung Car4 ECs and retina tip ECs have common and distinct features. These findings support a signaling role of AT1 cells and shed light on alveologenesis.
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1.985 Mikeys
#8. Trophoblast paracrine signaling regulates placental hematoendothelial niche
Pratik Home, Ananya Ghosh, Ram Kumar Parikshan, Avishek Ganguly, Bhaswati Bhattacharya, Md. Rashedul Islam, Soma Ray, Sumedha Gunewardena, Soumen Paul
The placenta acts as a major organ for hematopoiesis. It is believed that placental hematopoietic stem and progenitor cells (HSPCs) migrate to the fetal liver to ensure optimum hematopoiesis in the developing embryo. The labyrinth vasculature in a mid-gestation mouse placenta provides a niche for the definitive hematopoietic stem cell (HSC) generation and expansion. It has been proposed that these processes are regulated by a host of paracrine factors secreted by trophoblast giant cells (TGCs) at the maternal-fetal interface. However, the molecular mechanism by which the TGCs regulate the hematoendothelial niche in a developing placenta is yet to be defined. Using a TGC-specific Gata2 and Gata3 double knockout mouse model, we show that the loss of GATA2 and GATA3 at the TGC layer leads to fetal growth retardation and embryonic death due to disruptions in the delicate hematopoietic-angiogenic balance in the developing placenta. Using single-cell RNA-Seq analyses, we also show that the loss of GATA factors in the TGCs results in the...
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