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https://www.readbyqxmd.com/read/28526029/cell-fixation-and-preservation-for-droplet-based-single-cell-transcriptomics
#1
Jonathan Alles, Nikos Karaiskos, Samantha D Praktiknjo, Stefanie Grosswendt, Philipp Wahle, Pierre-Louis Ruffault, Salah Ayoub, Luisa Schreyer, Anastasiya Boltengagen, Carmen Birchmeier, Robert Zinzen, Christine Kocks, Nikolaus Rajewsky
BACKGROUND: Recent developments in droplet-based microfluidics allow the transcriptional profiling of thousands of individual cells in a quantitative, highly parallel and cost-effective way. A critical, often limiting step is the preparation of cells in an unperturbed state, not altered by stress or ageing. Other challenges are rare cells that need to be collected over several days or samples prepared at different times or locations. METHODS: Here, we used chemical fixation to address these problems...
May 19, 2017: BMC Biology
https://www.readbyqxmd.com/read/28515048/essential-function-of-the-serine-hydroxymethyl-transferase-shmt-gene-during-rapid-syncytial-cell-cycles-in-drosophila
#2
Franziska Winkler, Maria Kriebel, Michaela Clever, Stephanie Gröning, Jörg Großhans
Many metabolic enzymes are evolutionary highly conserved and serve a central function for catabolism and anabolism of cells. The serine hydroxymethyl transferase (SHMT) catalysing the conversion of serine and glycine and vice versa feeds into the tetrahydrofolate mediated C1 metabolism. We identified a Drosophila mutation in SHMT (CG3011) in a screen for blastoderm mutants. Embryos from SHMT mutant germline clones specifically arrest the cell cycle in interphase 13 at the time of the mid blastula transition (MBT) and prior to cellularisation...
May 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28506995/apical-constriction-is-driven-by-a-pulsatile-apical-myosin-network-in-delaminating-drosophila-neuroblasts
#3
Yanru An, Guosheng Xue, Yang Shaobo, Deng Mingxi, Xiaowei Zhou, Weichuan Yu, Toyotaka Ishibashi, Lei Zhang, Yan Yan
Cell delamination is a conserved morphogenetic process important for generation of cell diversity and maintenance of tissue homeostasis. Here we used Drosophila embryonic neuroblasts as a model to study the apical constriction process during cell delamination. We observe dynamic myosin signals both around the cell adherens junctions and underneath the cell apical surface in the neuroectoderm. On the cell apical cortex the non-junctional myosin forms flows and pulses, which are termed as medial myosin pulses...
May 15, 2017: Development
https://www.readbyqxmd.com/read/28506986/soxneuro-and-shavenbaby-act-cooperatively-to-shape-denticles-in-the-embryonic-epidermis-of-drosophila
#4
Nicholas P Rizzo, Amy Bejsovec
During development, extracellular signals are integrated by cells to induce the transcriptional circuitry that controls morphogenesis. In the fly epidermis, Wingless (Wg)/Wnt signaling directs cells to produce either a distinctly-shaped denticle or no denticle, resulting in a segmental pattern of denticle belts separated by smooth, or "naked", cuticle. Naked cuticle results from Wg repression of shavenbaby (svb), which encodes a transcription factor required for denticle construction. We have discovered that although the svb promoter responds differentially to altered Wg levels, Svb alone cannot produce the morphological diversity of denticles found in wild-type belts...
May 15, 2017: Development
https://www.readbyqxmd.com/read/28500793/integrating-the-genomic-architecture-of-human-nucleolar-organizer-regions-with-the-biophysical-properties-of-nucleoli
#5
REVIEW
Hazel Mangan, Michael Ó Gailín, Brian McStay
Nucleoli are the sites of ribosome biogenesis and the largest membraneless sub-nuclear structures. They are intimately linked with growth and proliferation control and function as sensors of cellular stress. Nucleoli form around arrays of ribosomal gene (rDNA) repeats also called nucleolar organizer regions (NORs). In humans, NORs are located on the short arms of all five human acrocentric chromosomes. Multiple NORs contribute to the formation of large heterochromatin-surrounded nucleoli observed in most human cells...
May 13, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28495673/parallel-imaging-of-drosophila-embryos-for-quantitative-analysis-of-genetic-perturbations-of-the-ras-pathway
#6
Yogesh Goyal, Thomas J Levario, Henry H Mattingly, Susan Holmes, Stanislav Y Shvartsman, Hang Lu
The Ras pathway patterns the poles of the Drosophila embryo by downregulating the levels and activity of a DNA-binding transcriptional repressor Capicua (Cic). We demonstrate that the spatiotemporal pattern of Cic during this signaling event can be harnessed for functional studies of the Ras-pathway mutations from human diseases. Our approach relies on a new microfluidic device that enables parallel imaging of Cic dynamics in dozens of live embryos. We found that although the pattern of Cic in early embryos is complex, it can be accurately approximated by a product of one spatial profile and one time-dependent amplitude...
May 11, 2017: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/28477406/metaphase-chromosome-structure-is-dynamically-maintained-by-condensin-i-directed-dna-de-catenation
#7
Ewa Piskadlo, Alexandra Tavares, Raquel A Oliveira
Mitotic chromosome assembly remains a big mystery in biology. Condensin complexes are pivotal for chromosome architecture yet how they shape mitotic chromatin remains unknown. Using acute inactivation approaches and live-cell imaging in Drosophila embryos, we dissect the role of condensin I in the maintenance of mitotic chromosome structure with unprecedented temporal resolution. Removal of condensin I from pre-established chromosomes results in rapid disassembly of centromeric regions while most chromatin mass undergoes hyper-compaction...
May 6, 2017: ELife
https://www.readbyqxmd.com/read/28476946/in-vivo-calcium-signaling-during-synaptic-refinement-at-the-drosophila-neuromuscular-junction
#8
Fernando Vonhoff, Haig Keshishian
Neural activity plays a key role in pruning aberrant synapses in various neural systems, including the mammalian cortex, where low frequency (0.01 Hz) calcium oscillations refine topographic maps. However, the activity-dependent molecular mechanisms remain incompletely understood. Activity-dependent pruning also occurs at embryonic Drosophila neuromuscular junctions (NMJs), where low frequency Ca(2+) oscillations are required for synaptic refinement and the response to the muscle-derived chemorepellant Sema2a...
May 5, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28476861/the-centrioles-centrosomes-basal-bodies-and-cilia-of-drosophila-melanogaster
#9
Ramona Lattao, Levente Kovács, David M Glover
Centrioles play a key role in the development of the fly. They are needed for the correct formation of centrosomes, the organelles at the poles of the spindle that can persist as microtubule organizing centers (MTOCs) into interphase. The ability to nucleate cytoplasmic microtubules (MTs) is a property of the surrounding pericentriolar material (PCM). The centriole has a dual life, existing not only as the core of the centrosome but also as the basal body, the structure that templates the formation of cilia and flagellae...
May 2017: Genetics
https://www.readbyqxmd.com/read/28468905/pervasive-behavioural-effects-of-microrna-regulation-in-drosophila
#10
Joao Picao-Osorio, Ines Lago-Baldaia, Pedro Patraquim, Claudio R Alonso
The effects of microRNA (miRNA) regulation on the genetic programs underlying behaviour remain largely unexplored. Despite this, recent work in Drosophila shows that mutation of a single miRNA locus (miR-iab4/iab8) affects the capacity of the larva to correct its orientation if turned upside-down (self-righting, SR) suggesting that other miRNAs might also be involved in behavioural control. Here we explore this possibility studying early larval SR behaviour in a collection of eighty-one Drosophila miRNA mutants covering almost the entire miRNA complement of the late embryo...
May 3, 2017: Genetics
https://www.readbyqxmd.com/read/28465336/segga-a-toolset-for-rapid-automated-analysis-of-epithelial-cell-polarity-and-dynamics
#11
Dene L Farrell, Ori Weitz, Marcelo O Magnasco, Jennifer A Zallen
Epithelial remodeling determines the structure of many organs in the body through changes in cell shape, polarity and behavior and is a major area of study in developmental biology. Accurate and high-throughput methods are necessary to systematically analyze epithelial organization and dynamics at single-cell resolution. We developed SEGGA, an easy-to-use software for automated image segmentation, cell tracking and quantitative analysis of cell shape, polarity and behavior in epithelial tissues. SEGGA is free, open source, and provides a full suite of tools that allow users with no prior computational expertise to independently perform all steps of automated image segmentation, semi-automated user-guided error correction, and data analysis...
May 1, 2017: Development
https://www.readbyqxmd.com/read/28461810/ancient-role-of-ten-m-odz-in-segmentation-and-the-transition-from-sequential-to-syncytial-segmentation
#12
Axel Hunding, Stefan Baumgartner
BACKGROUND: Until recently, mechanisms of segmentation established for Drosophila served as a paradigm for arthropod segmentation. However, with the discovery of gene expression waves in vertebrate segmentation, another paradigm based on oscillations linked to axial growth was established. The Notch pathway and hairy delay oscillator are basic components of this mechanism, as is the wnt pathway. With the establishment of oscillations during segmentation of the beetle Tribolium, a common segmentation mechanism may have been present in the last common ancestor of vertebrates and arthropods...
2017: Hereditas
https://www.readbyqxmd.com/read/28459456/dux-family-transcription-factors-regulate-zygotic-genome-activation-in-placental-mammals
#13
Alberto De Iaco, Evarist Planet, Andrea Coluccio, Sonia Verp, Julien Duc, Didier Trono
In animal embryos, transcription is mostly silent for several cell divisions, until the release of the first major wave of embryonic transcripts through so-called zygotic genome activation (ZGA). Maternally provided ZGA-triggering factors have been identified in Drosophila melanogaster and Danio rerio, but their mammalian homologs are still undefined. Here, we provide evidence that the DUX family of transcription factors is essential to this process in mice and potentially in humans. First, human DUX4 and mouse Dux are both expressed before ZGA in their respective species...
May 1, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28457868/cell-cycle-coupled-oscillations-in-apical-polarity-and-intercellular-contact-maintain-order-in-embryonic-epithelia
#14
Katerina Ragkousi, Kendra Marr, Sean McKinney, Lacey Ellington, Matthew C Gibson
Throughout animals, embryonic cells must ultimately organize into polarized epithelial layers that provide the structural basis for gastrulation or subsequent developmental events [1]. Precisely how this primary epithelium maintains continuous integrity during rapid and repeated cell divisions has never been directly addressed, particularly in cases where early cleavages are driven in synchrony. Representing the early-branching non-bilaterian phylum Cnidaria, embryos of the sea anemone Nematostella vectensis undergo rapid synchronous cell divisions and ultimately give rise to a diploblastic epithelial body plan after gastrulation [2, 3]...
May 8, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28457866/rapid-rates-of-pol-ii-elongation-in-the-drosophila-embryo
#15
Takashi Fukaya, Bomyi Lim, Michael Levine
Elongation of RNA polymerase II (Pol II) is thought to be an important mechanism for regulating gene expression [1]. We measured the first wave of de novo transcription in living Drosophila embryos using dual-fluorescence detection of nascent transcripts containing 5' MS2 and 3' PP7 RNA stem loops. Pol II elongation rates of 2.4-3.0 kb/min were observed, approximately twice as fast as earlier estimates [2-6]. The revised rates permit substantial levels of zygotic gene activity prior to the mid-blastula transition...
May 8, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28457744/piwi-is-required-during-drosophila-embryogenesis-to-license-dual-strand-pirna-clusters-for-transposon-repression-in-adult-ovaries
#16
Abdou Akkouche, Bruno Mugat, Bridlin Barckmann, Carolina Varela-Chavez, Blaise Li, Raoul Raffel, Alain Pélisson, Séverine Chambeyron
Most piRNAs in the Drosophila female germline are transcribed from heterochromatic regions called dual-strand piRNA clusters. Histone 3 lysine 9 trimethylation (H3K9me3) is required for licensing piRNA production by these clusters. However, it is unclear when and how they acquire this permissive heterochromatic state. Here, we show that transient Piwi depletion in Drosophila embryos results in H3K9me3 decrease at piRNA clusters in ovaries. This is accompanied by impaired biogenesis of ovarian piRNAs, accumulation of transposable element transcripts, and female sterility...
May 4, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28456956/role-of-micrornas-in-zygotic-genome-activation-modulation-of-mrna-during-embryogenesis
#17
Alessandro Rosa, Ali H Brivanlou
A fundamental process occurring during early development is the zygotic genome activation, i.e., the initiation of transcription from the embryonic genome. Before that step, cellular processes in the developing embryo are dictated by transcripts produced by the maternal genome and accumulated in the egg during oogenesis. The maternal-to-zygotic transition (MZT) involves both the clearance of maternal RNAs and the initiation of transcription of the embryonic genome and is a tightly regulated process. In some species, decay of maternal transcripts may be facilitated by the activity of microRNAs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28456955/link-of-zygotic-genome-activation-and-cell-cycle-control
#18
Boyang Liu, Jörg Grosshans
The activation of the zygotic genome and onset of transcription in blastula embryos is linked to changes in cell behavior and remodeling of the cell cycle and constitutes a transition from exclusive maternal to zygotic control of development. This step in development is referred to as mid-blastula transition and has served as a paradigm for the link between developmental program and cell behavior and morphology. Here, we discuss the mechanism and functional relationships between the zygotic genome activation and cell cycle control during mid-blastula transition with a focus on Drosophila embryos...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28448610/characterization-and-expression-analysis-of-galnts-in-developing-strongylocentrotus-purpuratus-embryos
#19
Amber L Famiglietti, Zheng Wei, Thomas M Beres, Adina L Milac, Duy T Tran, Divya Patel, Robert C Angerer, Lynne M Angerer, Lawrence A Tabak
Mucin-type O-glycosylation is a ubiquitous posttranslational modification in which N-Acetylgalactosamine (GalNAc) is added to the hydroxyl group of select serine or threonine residues of a protein by the family of UDP-GalNAc:Polypeptide N-Acetylgalactosaminyltransferases (GalNAc-Ts; EC 2.4.1.41). Previous studies demonstrate that O-glycosylation plays essential roles in protein function, cell-cell interactions, cell polarity and differentiation in developing mouse and Drosophila embryos. Although this type of protein modification is highly conserved among higher eukaryotes, little is known about this family of enzymes in echinoderms, basal deuterostome relatives of the chordates...
2017: PloS One
https://www.readbyqxmd.com/read/28432834/molecular-control-of-gut-formation-in-the-spider-parasteatoda-tepidariorum
#20
Natália Martins Feitosa, Matthias Pechmann, Evelyn E Schwager, Vitória Tobias-Santos, Alistair P McGregor, Wim G M Damen, Rodrigo Nunes da Fonseca
The development of a digestive system is an essential feature of bilaterians. Studies of the molecular control of gut formation in arthropods have been studied in detail in the fruit fly Drosophila melanogaster. However, little is known in other arthropods, especially in noninsect arthropods. To better understand the evolution of arthropod alimentary system, we investigate the molecular control of gut development in the spider Parasteatoda tepidariorum (Pt), the primary chelicerate model species for developmental studies...
May 2017: Genesis: the Journal of Genetics and Development
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