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Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 70,410 bioRxiv papers from 307,445 authors.

Most downloaded bioRxiv papers, all time

in category developmental biology

2,070 results found. For more information, click each entry to expand.

121: Multiscale quantification of tissue behavior during amniote embryo axis elongation
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Posted to bioRxiv 13 May 2016

Multiscale quantification of tissue behavior during amniote embryo axis elongation
1,195 downloads developmental biology

Bertrand Bénazéraf, Mathias Beaupeux, Martin Tchernookov, Allison Wallingford, Tasha Salisbury, Amelia Shirtz, Andrew Shirtz, Dave Huss, Olivier Pourquié, Paul François, Rusty Lansford

Embryonic axis extension is a complex multi-tissue morphogenetic process responsible for the formation of the posterior part of the amniote body. Cells located in the caudal part of the embryo divide and rearrange to participate in the elongation of the different embryonic tissues (e.g. neural tube, axial and paraxial mesoderm, lateral plate, ectoderm, endoderm). We previously identified the paraxial mesoderm as a crucial player of axis elongation, but how movements and growth are coordinated between the different posterior tissues to drive morphogenesis remain largely unknown. Here we use the quail embryo as a model system to quantify cell behavior and movements in the various tissues of the elongating embryo. We first quantify the tissue-specific contribution to axis elongation by using 3D volumetric techniques, then quantify tissue-specific parameters such as cell density and proliferation at different embryonic stages. To be able to study cell behavior at a multi-tissue scale we used high-resolution 4D imaging of transgenic quail embryos expressing constitutively expressed fluorescent proteins. We developed specific tracking and image analysis techniques to analyze cell motion and compute tissue deformations in 4D. This analysis reveals extensive sliding between tissues during axis extension. Further quantification of tissue tectonics showed patterns of rotations, contractions and expansions, which are coherent with the multi-tissue behavior observed previously. Our results confirm the central role of the PSM in axis extension; we propose that the PSM specific cell proliferation and migration programs control the coordination of elongation between tissues during axis extension.

122: Motility-gradient induced elongation of the vertebrate embryo
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Posted to bioRxiv 12 Sep 2017

Motility-gradient induced elongation of the vertebrate embryo
1,192 downloads developmental biology

Ido Regev, Karine Guevorkian, Olivier Pourquie, L. Mahadevan

The body of vertebrate embryos forms by posterior elongation from a terminal growth zone called the Tail Bud (TB). The TB produces highly motile cells forming the presomitic mesoderm (PSM), a tissue playing an important role in elongation movements. PSM cells establish an anterior-posterior cell motility gradient which parallels the degradation of a specific cellular signal (Fgf8) known to be implicated in cell motility. Here, we combine electroporation of fluorescent reporters in the PSM to time-lapse imaging in the chicken embryo to quantify cell diffusive movements along the motility gradient. We show that simple microscopic and macroscopic mechano-chemical models for tissue extension that couple Fgf activity, cell motility and tissue rheology at both the cellular and continuum levels suffice to capture the speed and extent of elongation. These observations explain how the continuous addition of cells that exhibit a gradual reduction in motility combined with lateral confinement can be converted into an oriented movement that drives body elongation. The results of the models compare well with our experimental results, with implications for other elongation processes in the embryo.

123: Epigenetic resetting of human pluripotency
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Posted to bioRxiv 06 Jun 2017

Epigenetic resetting of human pluripotency
1,188 downloads developmental biology

Ge Guo, Ferdinand von Meyenn, Maria Rostovskaya, James Clarke, Sabine Dietmann, Duncan Baker, Anna Sahakyan, Samuel Myers, Paul Bertone, Wolf Reik, Kathrin Plath, Austin Smith

Much attention has focussed on conversion of human pluripotent stem cells (PSC) to a more naive developmental status. Here we provide a method for resetting via transient histone deacetylase inhibition. The protocol is effective across multiple PSC lines and can proceed without karyotype change. Reset cells can be expanded without feeders with a doubling time of around 24 hours. Tankyrase inhibition stabilises the resetting process. The transcriptome of reset cells diverges markedly from primed PSC and shares features with human inner cell mass (ICM). Reset cells activate expression of primate-specific transposable elements. DNA methylation is globally reduced to the level in the ICM but is non-random, with gain of methylation at specific loci. Methylation imprints are mostly lost, however. Reset cells can be re-primed to undergo tri-lineage differentiation and germline specification. In female reset cells, appearance of bi-allelic X-linked gene transcription indicates re-activation of the silenced X chromosome. On re-conversion to primed status, XIST-induced silencing restores monoallelic gene expression. The facile and robust conversion routine with accompanying data resources will enable widespread utilisation, interrogation, and refinement of candidate naive cells.

124: Efficient expression of genes in the Drosophila germline using a UAS-promoter free of interference by Hsp70 piRNAs
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Posted to bioRxiv 01 Mar 2018

Efficient expression of genes in the Drosophila germline using a UAS-promoter free of interference by Hsp70 piRNAs
1,180 downloads developmental biology

Steven Z DeLuca, Allan C. Spradling

Controlling the expression of genes using a binary system involving the yeast GAL4 transcription factor has been a mainstay of Drosophila developmental genetics for twenty-five years. However, most existing GAL4 expression constructs only function effectively in somatic cells, but not in germ cells during oogenesis, for unknown reasons. A special UAS promoter, UASp was created that does express during oogenesis, but the need to use different constructs for somatic and female germline cells has remained a significant technical limitation. Here we show that the expression problem of UASt and many other Drosophila molecular tools in germline cells is caused by their core Hsp70 promoter sequences, which are targeted in female germ cells by Hsp70-directed piRNAs generated from endogenous Hsp70 gene sequences. In a genetic background lacking genomic Hsp70 genes and associated piRNAs, UASt-based constructs function effectively during oogenesis. By reducing Hsp70 sequences targeted by piRNAs, we created UASz, which functions better than UASp in the germline and like UASt in somatic cells.

125: Functional regulatory evolution outside of the minimal even-skipped stripe 2 enhancer
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Posted to bioRxiv 18 Jan 2017

Functional regulatory evolution outside of the minimal even-skipped stripe 2 enhancer
1,175 downloads developmental biology

Justin Crocker, David L. Stern

Transcriptional enhancers are regions of DNA that drive gene expression at precise times, levels, and locations. While many studies have elucidated how individual enhancers can evolve, most of this work has focused on what are called "minimal" enhancers, the smallest DNA regions that drive expression that approximates an aspect of native gene expression. Here we explore how the Drosophila erecta even-skipped (eve) locus has evolved by testing its activity in the divergent D. melanogaster genome. We found, as has been reported previously, that the minimal D. erecta eve stripe 2 enhancer (eveS2) fails to drive appreciable expression in D. melanogaster. However, we found that a large transgene carrying the entire D. erecta eve locus drives normal eve expression, including in stripe 2. We performed a functional dissection of the region upstream of the D. erecta eveS2 region and found that regulatory information outside of the minimal D. erecta eveS2 contains multiple Zelda motifs that are required for normal expression. Our results illustrate how sequences outside of minimal enhancer regions can evolve functionally through mechanisms other than changes in transcription factor binding sites that drive patterning.

126: A tensile ring drives tissue flows to shape the gastrulating amniote embryo
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Posted to bioRxiv 10 Sep 2018

A tensile ring drives tissue flows to shape the gastrulating amniote embryo
1,168 downloads developmental biology

Mehdi Saadaoui, Francis Corson, Didier Rocancourt, Julian Roussel, Jerome Gros

Tissue morphogenesis is driven by local cellular deformations, themselves powered by contractile actomyosin networks. While it is well demonstrated that cell-generated forces at the microscopic scale underlie a variety of local morphogenetic processes (e.g. lengthening/narrowing, bending, or folding), how such local forces are transmitted across tissues to shape them at a mesoscopic scale remains largely unknown. Here, by performing a quantitative analysis of gastrulation in entire avian embryos, we show that the formation of the primitive streak and the associated large-scale rotational tissue flows (i.e. "polonaise movements") are integral parts of a global process that is captured by the laws of fluid mechanics. We identify a large-scale supracellular actomyosin ring (2mm in diameter and 250μm thick) that shapes the embryo by exerting a graded tension along the margin between the embryonic and extra-embryonic territories. Tissue-wide flows arise from the transmission of these localized forces across the embryonic disk and are quantitatively recapitulated by a fluid-mechanical model based on the Stokes equations for viscous flow. We further show that cell division, the main driver of cell rearrangements at this stage, is required for fluid-like behavior and for the progress of gastrulation movements. Our results demonstrate the power of a hydrodynamic approach to tissue-wide morphogenetic processes and provide a simple, unified mechanical picture of amniote gastrulation. A tensile embryo margin, in addition to directing tissue motion, could act as an interface between mechanical and molecular cues, and play a central role in embryonic self-organization.

127: A damped oscillator imposes temporal order on posterior gap gene expression in Drosophila
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Posted to bioRxiv 05 Aug 2016

A damped oscillator imposes temporal order on posterior gap gene expression in Drosophila
1,165 downloads developmental biology

Berta Verd, Erik Clark, Karl R. Wotton, Hilde Janssens, Eva Jiménez-Guri, Anton Crombach, Johannes Jaeger

Insects determine their body segments in two different ways. Short-germband insects, such as the flour beetle Tribolium castaneum, use a molecular clock to establish segments sequentially. In contrast, long-germband insects, such as the vinegar fly Drosophila melanogaster, determine all segments simultaneously through a hierarchical cascade of gene regulation. Gap genes constitute the first layer of the Drosophila segmentation gene hierarchy, downstream of maternal gradients such as that of Caudal (Cad). We use data-driven mathematical modelling and phase space analysis to show that shifting gap domains in the posterior half of the Drosophila embryo are an emergent property of a robust damped oscillator mechanism, suggesting that the regulatory dynamics underlying long- and short-germband segmentation are much more similar than previously thought. In Tribolium, Cad has been proposed to modulate the frequency of the segmentation oscillator. Surprisingly, our simulations and experiments show that the shift rate of posterior gap domains is independent of maternal Cad levels in Drosophila. Our results suggest a novel evolutionary scenario for the short- to long-germband transition, and help explain why this transition occurred convergently multiple times during the radiation of the holometabolan insects.

128: Pan-embryo cell dynamics of germlayer formation in zebrafish
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Posted to bioRxiv 08 Aug 2017

Pan-embryo cell dynamics of germlayer formation in zebrafish
1,165 downloads developmental biology

Gopi Shah, Konstantin Thierbach, Benjamin Schmid, Anna Reade, Ingo Roeder, Nico Scherf, Jan Huisken

Cell movements are coordinated across spatio-temporal scales to achieve precise positioning of organs during vertebrate gastrulation. In zebrafish, mechanisms governing such morphogenetic movements have so far only been studied within a local region or a single germlayer. Here, we present pan-embryo analyses of fate specification and dynamics of all three germlayers simultaneously within a gastrulating embryo, showing that cell movement characteristics are predominantly determined by its position within the embryo, independent of its germlayer identity. The spatially confined fate specification establishes a distinct distribution of cells in each germlayer during early gastrulation. The differences in the initial distribution are subsequently amplified by a unique global movement, which organizes the organ precursors along the embryonic body axis, giving rise to the blueprint of organ formation.

129: In vivo optochemical control of cell contractility at single cell resolution by Ca2+ induced myosin activation
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Posted to bioRxiv 29 Jan 2018

In vivo optochemical control of cell contractility at single cell resolution by Ca2+ induced myosin activation
1,156 downloads developmental biology

Deqing Kong, Zhiyi Lv, Matthias Häring, Fred Wolf, Joerg Grosshans

The spatial and temporal dynamics of cell contractility plays a key role in tissue morphogenesis, wound healing and cancer invasion. Here we report a simple, single cell resolution, optochemical method to induce minute-scale cell contractions in vivo during morphogenesis. We employed the photolabile Ca2+ chelator o-nitrophenyl EGTA to induce bursts of intracellular free Ca2+ by laser photolysis. Ca2+ bursts appear within seconds and are restricted to individual target cells. Cell contraction reliably followed within a minute, to about half of the cross-sectional area. Increased Ca2+ levels and contraction were reversible and the target cells further participated in tissue morphogenesis. Depending on Rho kinase (Rok) activity but not RhoGEF2, cell contractions are paralleled with non-muscle myosin-II accumulation in the apico-medial cortex, indicating that Ca2+ bursts trigger non-muscle myosin II activation. Our approach can be easily adapted to many experimental systems and species, as no specific genetic elements are required and a widely used reagent is employed.

130: Turing patterns are common but not robust
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Posted to bioRxiv 20 Jun 2018

Turing patterns are common but not robust
1,156 downloads developmental biology

Natalie S. Scholes, David Schnoerr, Mark Isalan, Michael Stumpf

Turing patterns (TPs) underlie many fundamental developmental processes, but they operate over narrow parameter ranges, raising the conundrum of how evolution can ever discover them. Here we explore TP design space to address this question and to distill design rules. We exhaustively analyze 2- and 3-node biological candidate Turing systems: crucially, network structure alone neither determines nor guarantees emergent TPs. A surprisingly large fraction (>60%) of network design space can produce TPs, but these are sensitive to even subtle changes in parameters, network structure and regulatory mechanisms. This implies that TP networks are more common than previously thought, and evolution might regularly encounter prototypic solutions. Importantly, we deduce compositional rules for TP systems that are almost necessary and sufficient (≈96% of TP networks contain them, and ≈95% of networks implementing them produce TPs). This comprehensive network atlas provides the blueprints for identifying natural TPs, and for engineering synthetic systems.

131: Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos
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Posted to bioRxiv 26 Jul 2018

Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos
1,152 downloads developmental biology

Mustafa Mir, Michael R Stadler, Stephan A Ortiz, Melissa M. Harrison, Xavier Darzacq, Michael B. Eisen

The regulation of transcription requires the coordination of numerous activities on DNA, yet it remains poorly understood how transcription factors facilitate these multiple functions. Here we use lattice light-sheet microscopy to integrate single-molecule and high-speed 4D imaging in developing Drosophila embryos to study the nuclear organization and interactions of the key patterning factors Zelda and Bicoid. In contrast to previous studies suggesting stable, cooperative binding, we show that both factors interact with DNA with surprisingly high off-rates. We find that both factors form dynamic subnuclear hubs, and that Bicoid binding is enriched within Zelda hubs. Remarkably, these hubs are both short lived and interact only transiently with sites of active Bicoid dependent transcription. Based on our observations we hypothesize that, beyond simply forming bridges between DNA and the transcription machinery, transcription factors can organize other proteins into hubs that transiently drive multiple activities at their gene targets.

132: Stem cells in Nanomia bijuga (Siphonophora), a colonial animal with localized growth zones
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Posted to bioRxiv 06 Jan 2014

Stem cells in Nanomia bijuga (Siphonophora), a colonial animal with localized growth zones
1,148 downloads developmental biology

Stefan Siebert, Freya E. Goetz, Samuel H Church, Pathikrit Bhattacharyya, Felipe Zapata, Steven H.D. Haddock, Casey W. Dunn

Background: Siphonophores (Hydrozoa) have unparalleled colony-level complexity, precision of colony organization, and functional specialization between zooids (i.e., the units that make up colonies). Previous work has shown that, unlike other colonial animals, most growth in siphonophores is restricted to one or two well-defined growth zones that are the sites of both elongation and zooid budding. It remained unknown, however, how this unique colony growth and development is realized at the cellular level. Results: To understand the colony-level growth and development of siphonophores at the cellular level, we characterize the distribution of proliferating cells and interstitial stem cells (i-cells) in the siphonophore Nanomia bijuga. Within the colony we find that i-cells are present at the tip of the horn, the structure within the growth zone that gives rise to new zooids. They persist in the youngest zooid buds, but as each zooid matures i-cells become progressively restricted to specific regions within the zooids until they are mostly absent from the oldest zooids. I-cell marker-gene expression remained in gametogenic regions. I-cells are not found in the stem between maturing zooids. Domains of high cell proliferation include regions where i-cells can be found, but also include some areas without i-cells such as the stem within the growth zones. Cell proliferation in regions devoid of marker gene expression indicates the presence of mitotically active epithelial cell lineages and, potentially, progenitor cell populations. Conclusions: Restriction of stem cells to particular regions in the colony may play a major role in facilitating the precision of siphonophore growth, and also lead to a reduced developmental plasticity in other, typically older, parts of the colony. This helps explain why siphonophore colonies have such precise colony-level organization.

133: Profiling cellular diversity in sponges informs animal cell type and nervous system evolution
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Posted to bioRxiv 05 Sep 2019

Profiling cellular diversity in sponges informs animal cell type and nervous system evolution
1,147 downloads developmental biology

Jacob M. Musser, Klaske J. Schippers, Michael Nickel, Giulia Mizzon, Andrea B Kohn, Constantin Pape, Jörg U. Hammel, Florian Wolf, Cong Liang, Ana Hernández-Plaza, Kaia Achim, Nicole L. Schieber, Warren R. Francis, Sergio Vargas, Svenja Kling, Maike Renkert, Roberto Feuda, Imre Gaspar, Pawel Burkhardt, P Bork, Martin Beck, Anna Kreshuk, Gert Wörheide, Jaime Huerta-Cepas, Yannick Schwab, Leonid L. Moroz, Detlev Arendt

The evolutionary origin of metazoan cell types such as neurons, muscles, digestive, and immune cells, remains unsolved. Using whole-body single-cell RNA sequencing in a sponge, an animal without nervous system and musculature, we identify 18 distinct cell types comprising four major families. This includes nitric-oxide sensitive contractile cells, digestive cells active in macropinocytosis, and a family of amoeboid-neuroid cells involved in innate immunity. We uncover presynaptic genes in an amoeboid-neuroid cell type, and postsynaptic genes in digestive choanocytes, suggesting asymmetric and targeted communication. Corroborating this, long neurite-like extensions from neuroid cells directly contact and enwrap choanocyte microvillar collars. Our data indicate a link between neuroid and immune functions in sponges, and suggest that a primordial neuro-immune system cleared intruders and controlled ciliary beating for feeding.

134: GDF15 Concentrations in Maternal Serum Associated with Vomiting in Pregnancy: the Cambridge Baby Growth Study
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Posted to bioRxiv 17 Nov 2017

GDF15 Concentrations in Maternal Serum Associated with Vomiting in Pregnancy: the Cambridge Baby Growth Study
1,146 downloads developmental biology

Clive J. Petry, Ken K. Ong, Keith A Burling, Peter Barker, John RB Perry, Carlo L. Acerini, Ieuan A. Hughes, David B. Dunger, Stephen O’Rahilly

Nausea and vomiting in pregnancy (NVP) affects 70-90% of all pregnant women but its pathogenesis is unknown. Growth and Differentiation Factor 15 (GDF15), secreted from the trophoblast and decidual stromal cells, is present at high levels in the blood of pregnant women. The receptor for GDF15 has recently been identified and is specifically expressed in the hindbrain where it transmits aversive signals including nausea and conditioned taste aversion. We explored the relationship between GDF15 concentrations in maternal serum during pregnancy and self-reported NVP. In a study of 791 women from the Cambridge Baby Growth Study maternal GDF15 concentrations were higher in women who reported vomiting in the 2nd trimester (geometric mean: 11,670 pg/mL; 95% confidence interval: 11,056-12,318) and were even higher in the eleven women who reported taking anti-emetics during pregnancy (13,376 (10,821-16,535) compared to those who reported no nausea or vomiting during pregnancy (10,657 (10,121-11,222); P=0.02 and P=0.04, respectively, adjusted for gestational age at sampling and maternal BMI). In conclusion serum GDF15 concentrations early in the second trimester of pregnancy are significantly and positively associated with second trimester vomiting and with maternal anti-emetic use. In the context of the recently revealed biology of GDF15 this data suggests that antagonism of GDF15 may have some potential for therapeutic benefit in NVP.

135: Gain-of-function Shh mutants activate Smo in cis independent of Ptch1/2 function
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Posted to bioRxiv 04 Aug 2017

Gain-of-function Shh mutants activate Smo in cis independent of Ptch1/2 function
1,145 downloads developmental biology

Catalina Casillas, Henk Roelink

Sonic Hedgehog (Shh) signaling is characterized by strict non-cell autonomy; cells expressing Shh do not respond to their ligand. Here, we identify several Shh mutations that gain the ability to activate the Hedgehog (Hh) pathway in cis. This activation requires the extracellular cysteine rich domain of Smoothened, but is otherwise independent of Ptch1/2. Many of the identified mutations disrupt either a highly conserved catalytic motif found in peptidases or an alpha-helix domain frequently mutated in holoprosencephaly-causing SHH alleles. The expression of gain-of-function mutants often results in the accumulation of unprocessed Shh pro-peptide, a form of Shh we demonstrate is sufficient to activate the Hh response cell-autonomously. Our results demonstrate that Shh is capable of activating the Hh pathway via Smo independently of Ptch1/2, and that it harbors an intrinsic mechanism that prevents cell-autonomous activation of the pathway to favor non-cell autonomous signaling.

136: Genetic knockdown and knockout approaches in Hydra
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Posted to bioRxiv 07 Dec 2017

Genetic knockdown and knockout approaches in Hydra
1,144 downloads developmental biology

Mark Lommel, Anja Tursch, Laura Rustarazo-Calvo, Benjamin Trageser, Thomas W. Holstein

Hydra is a member of the Cnidaria, an ancient phylum at the base of metazoan evolution and sister group to all bilaterian animals. The regeneration capacity of Hydra, mediated by its stem cell systems, is unparalleled in the animal kingdom. The recent sequencing of the Hydra genome and that of other cnidarians has drawn new attention to this well-known model organism. In spite of this, the establishment of methods to manipulate gene expression in Hydra have remained a major challenge. Here we report a CRISPR-Cas9 based targeted mutation approach as well as an optimized, reproducible strategy for the delivery of siRNAs. Both approaches are based on a refined electroporation protocol for adult Hydra polyps. We demonstrate that these strategies provide reliable genetic interference with target gene expression, facilitating functional studies and genome editing in Hydra.

137: Intercellular calcium signaling is regulated by morphogens during Drosophila wing development
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Posted to bioRxiv 01 Feb 2017

Intercellular calcium signaling is regulated by morphogens during Drosophila wing development
1,135 downloads developmental biology

Pavel A. Brodskiy, Qinfeng Wu, Francisco J. Huizar, Dharsan K. Soundarrajan, Cody Narciso, Megan K. Levis, Ninfamaria Arredondo-Walsh, Jianxu Chen, Peixian Liang, Danny Z. Chen, Jeremiah J. Zartman

Organ development is driven by a set of patterned inductive signals. However, how these signals are integrated to coordinate tissue patterning is still poorly understood. Calcium ions (Ca2+) are critical signaling components involved in signal integration and are regulated by a core Ca2+ signaling toolkit. Ca2+ signaling encodes a significant fraction of information in cells through both amplitude and frequency-dependent regulation of transcription factors and key regulatory enzymes. A range of intercellular Ca2+ transients, including coordinated oscillations, recently have been reported in Drosophila wing discs. In an accompanying paper, we show that impaired Ca2+ signaling impacts the final size and shape of the wing. Here, we discover specific spatiotemporal signatures of Ca2+ transients during wing disc development. To do so, we developed a new neural-network-based approach for registration of oscillatory signals in organs that frequently move during imaging, and a pipeline for spatiotemporal analysis of intercellular Ca2+ oscillations. As a specific test case, we further demonstrated that the morphogen pathway, Hedgehog, controls frequencies of Ca2+ oscillations uniformly in the tissue and is required for spatial patterning of oscillation amplitudes. Thus, the time-averaged dynamics of spontaneous intercellular Ca2+ transients reflect the morphogenetic signaling state of the tissue during development. This suggests a general mechanism of physiological signaling that provides a memory of morphogenetic patterns. Additionally, our study provides a powerful approach for registering and quantifying oscillatory dynamics in developing organs.

138: An engineered CRISPR/Cas9 mouse line for simultaneous readout of lineage histories and gene expression profiles in single cells
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Posted to bioRxiv 17 Oct 2019

An engineered CRISPR/Cas9 mouse line for simultaneous readout of lineage histories and gene expression profiles in single cells
1,127 downloads developmental biology

Sarah Bowling, Duluxan Sritharan, Fernando G. Osorio, Maximilian Nguyen, Priscilla Cheung, Alejo Rodriguez-Fraticelli, Sachin Patel, Yuko Fujiwara, Bin E Li, Stuart H. Orkin, Sahand Hormoz, Fernando D Camargo

Tracing the lineage history of cells is key to answering diverse and fundamental questions in biology. Particularly in the context of stem cell biology, analysis of single cell lineages in their native state has elucidated novel fates and highlighted heterogeneity of function. Coupling of such ancestry information with other molecular readouts represents an important goal in the field. Here, we describe the CARLIN (for CRISPR Array Repair LINeage tracing) mouse line and corresponding analysis tools that can be used to simultaneously interrogate the lineage and transcriptomic information of single cells in vivo . This model exploits CRISPR technology to generate up to 44,000 transcribed barcodes in an inducible fashion at any point during development or adulthood, is compatible with sequential barcoding, and is fully genetically defined. We have used CARLIN to identify intrinsic biases in the activity of fetal liver hematopoietic stem cell (HSC) clones and to uncover a previously unappreciated clonal bottleneck in the response of HSCs to injury. CARLIN also allows the unbiased identification of transcriptional signatures based on in vivo stem cell function without a need for markers or cell sorting.

139: Single-cell RNA-seq identifies a reversible epithelial-mesenchymal transition in abnormally specified epithelia of p63 EEC syndrome
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Posted to bioRxiv 07 Oct 2018

Single-cell RNA-seq identifies a reversible epithelial-mesenchymal transition in abnormally specified epithelia of p63 EEC syndrome
1,124 downloads developmental biology

Eduardo Soares, Quan Xu, Qingqing Li, Jieqiong Qu, Yuxuan Zheng, Henriette H. M. Raeven, Karina Brandao, Isabelle Petit, Willem M.R. van den Akker, Daniel Aberdam, Fuchou Tang, Huiqing Zhou

Mutations in transcription factor p63 are associated with developmental disorders that manifest defects in stratified epithelia including the epidermis. We established an epidermal commitment model using human induced pluripotent stem cells (iPSCs) and characterized differentiation defects of iPSCs derived from ectrodactyly, ectodermal dysplasia, and cleft lip/palate (EEC) syndrome patients carrying p63 mutations. Transcriptome analyses revealed distinct cell fates during epidermal commitment: multipotent simple epithelial, basal stratified epithelial and mature epidermal fates. Differentiation defects of EEC iPSCs caused by mutant p63 occurred during the specification switch from the simple epithelium to the basal stratified epithelial fate. Single-cell transcriptome and pseudotime analyses identified signatures of embryonic epithelial-mesenchymal transition (EMT) associated with the deviated commitment route of EEC iPSCs. Repressing mesodermal activation reversed the EMT and enhanced epidermal commitment. Our findings demonstrate that p63 is required for specification of stratified epithelia, probably by repressing embryonic EMT during epidermal commitment. This study provides insights into disease mechanisms underlying stratified epithelial defects caused by p63 mutations.

140: Dietary lipids modulate Notch signaling and influence adult intestinal development and metabolism in Drosophila
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Posted to bioRxiv 28 Feb 2018

Dietary lipids modulate Notch signaling and influence adult intestinal development and metabolism in Drosophila
1,115 downloads developmental biology

Rebecca Obniski, Matthew Sieber, Allan C. Spradling

Tissue homeostasis is a complex balance of developmental signals and environmental cues that dictate stem cell function. However, it remains poorly understood how nutrients interface with developmental pathways. Using the Drosophila midgut as a model we found that during the first four days of adult life, dietary lipids including cholesterol, determine how many enteroendocrine (ee) cells differentiate and persist in the posterior midgut where lipids are preferentially absorbed. The nuclear hormone receptor Hr96 which functions to control sterol trafficking, storage, and utilization, is required for sterol-mediated changes in ee number. Dietary cholesterol influences new intestinal epithelial cell differentiation from stem cells by altering the level and persistance of Notch signaling. Exogenous lipids modulate signaling by changing the stability of the Delta ligand and Notch intracellular domain and their trafficking in endosomal vesicles. Lipid-modulated Notch signaling occurs in other nutrient-dependent tissues such as the ovary, suggesting that Delta trafficking in many cells is sensitive to cellular sterol levels. These diet-mediated alterations in ee number in young animals contribute to a metabolic program adapted to the prevailing nutrient environment that persists after the diet changes. A low sterol diet also slows the proliferation of enteroendocrine tumors initiated by disruptions in the Notch pathway. These studies show that a specific dietary nutrient can modify a key intercellular signaling pathway to shift stem cell differentiation and cause lasting changes in tissue structure and physiology.

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