Browsing by Author "Sharpe, James"

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  • 4D reconstruction of murine developmental trajectories using spherical harmonics
    Dalmasso, Giovanni; Musy, Marco; Niksic, Martina; Robert Moreno, Alexandre; Badía Careaga, Claudio; Sanz-Ezquerro, Juan José; Sharpe, James (Elsevier, 2022)
    Normal organogenesis cannot be recapitulated in vitro for mammalian organs, unlike in species including Drosophila and zebrafish. Available 3D data in the form of ex vivo images only provide discrete snapshots of the ...
  • A computational clonal analysis of the developing mouse limb bud
    Marcon, Luciano, 1983-; Arqués, Carlos G.; Torres, Miguel S.; Sharpe, James (Public Library of Science (PLoS), 2011)
    A comprehensive spatio-temporal description of the tissue movements underlying organogenesis would be an extremely useful resource to developmental biology. Clonal analysis and fate mappings are popular experiments to study ...
  • A dynamic Turing model of digit patterning : a Turing mechanism modulated by positional information underlies digit specification
    Marcon, Luciano, 1983- (Universitat Pompeu Fabra, 2013-11-05)
    The specification of the vertebrate limb skeleton is a classical model to study pattern formation during development. Two different theories have been proposed to explain this process: the Turing mechanism and the Positional ...
  • A shift in anterior–posterior positional information underlies the fin-to-limb evolution
    Onimaru, Koh; Kuraku, Shigehiro; Takagi, Wataru; Hyodo, Susumu; Sharpe, James; Tanaka, Mikiko (eLife, 2015)
    The pectoral fins of ancestral fishes had multiple proximal elements connected to their pectoral girdles. During the fin-to-limb transition, anterior proximal elements were lost and only the most posterior one remained as ...
  • Attenuation artifacts in light sheet fluorescence microscopy corrected by OPTiSPIM
    Mayer, Jürgen, 1977-; Robert Moreno, Alexandre; Sharpe, James; Swoger, Jim (Nature Research, 2018)
    Light sheet fluorescence microscopy (LSFM) is rapidly becoming an essential technology for mesoscopic imaging of samples such as embryos and adult mouse organs. However, LSFM can suffer from optical artifacts for which ...
  • Cellular mechanisms behind vertebrate limp outgrowth
    Lesnicar-Pucko, Gaja, 1981- (Universitat Pompeu Fabra, 2014-12-12)
    In this work we use a novel in vivo imaging technique and cell behaviour analysis to investigate the cellular basis of limb bud elongation. Recently, it has become clear that oriented cell activities must be involved in ...
  • Clonal analysis in mice underlines the importance of rhombomeric boundaries in cell movement restriction during hindbrain segmentation
    Jiménez Guri, Eva; Udina, Frederic; Colas, Jean-François; Sharpe, James; Padrón Barthe, Laura; Torres, Miguel S.; Pujades Corbi, Cristina (Public Library of Science (PLoS), 2010)
    Background: Boundaries that prevent cell movement allow groups of cells to maintain their identity and follow independent developmental trajectories without the need for ongoing instructive signals from surrounding tissues. ...
  • Data-driven modelling of a gene regulatory network for cell fate decisions in the growing limb bud
    Uzkudun, Manu; Marcon, Luciano, 1983-; Sharpe, James (Wiley Blackwell, 2015)
    Parameter optimization coupled with model selection is a convenient approach to infer gene regulatory networks from experimental gene expression data, but so far it has been limited to single cells or static tissues where ...
  • Design principles of stripe-forming motifs: the role of positive feedback
    Munteanu, Andreea; Cotterell, James; Solé Vicente, Ricard, 1962-; Sharpe, James (Nature Publishing Group, 2014)
    Interpreting a morphogen gradient into a single stripe of gene-expression is a fundamental unit of patterning in early embryogenesis. From both experimental data and computational studies the feed-forward motifs stand out ...
  • Dynamical feature extraction at the sensory periphery guides chemotaxis
    Schulze, Aljoscha, 1980-; Gómez Marín, Alex; Rajendran, Vani G.; Lott, Gus; Musy, Marco; Ahammad, Parvez; Deogade, Ajinkya, 1989-; Sharpe, James; Riedl, Julia, 1981-; Jarriault, David; Trautman, Eric T.; Werner, Christopher; Venkadesan, Madhusudhan; Druckmann, Shaul; Jayaraman, Vivek; Louis, Matthieu (eLife, 2015)
    Behavioral strategies employed for chemotaxis have been described across phyla, but the sensorimotor basis of this phenomenon has seldom been studied in naturalistic contexts. Here, we examine how signals experienced during ...
  • Dynamics of gene circuits shapes evolvability
    Jiménez, Alba; Cotterell, James; Munteanu, Andreea; Sharpe, James (Cold Spring Harbor Laboratory Press, 2015)
    To what extent does the dynamical mechanism producing a specific biological phenotype bias the ability to evolve into novel phenotypes? We use the interpretation of a morphogen gradient into a single stripe of gene expression ...
  • Endogenous CRISPR/Cas9 arrays for scalable whole-organism lineage tracing
    Cotterell, James; Vila-Cejudo, Marta; Batlle Morera, Laura; Sharpe, James (Company of Biologists, 2020)
    The past decade has seen a renewed appreciation of the central importance of cellular lineages to many questions in biology (especially organogenesis, stem cells and tumor biology). This has been driven in part by a ...
  • Engineering ultrasensivity and differential diffusion to build spatial patterns in a 3D mammalian cell culture system
    Senthivel, Vivek Raj, 1983- (Universitat Pompeu Fabra, 2017-07-17)
    Engineering self-organised spatial patterns based on reaction-diffusion models can be the stepping stone for tissue engineering. Previous reports based on both theoretical and experimental studies have implied the importance ...
  • GDF5 point mutation strikes twice--causing BDA1 and SYNS2
    Degenkolbe, Elisa; König, Jana; Zimmer, Julia; Walther, Maria; Reißner, Carsten; Nickel, Joachim; Plöger, Frank; Raspopovic, Jelena, 1984-; Sharpe, James; Dathe, Katarina; Hecht, Jacqueline T.; Mundlos, Stefan; Doelken, Sandra C.; Seemann, Petra (Public Library of Science (PLoS), 2013)
    Growth and Differentiation Factor 5 (GDF5) is a secreted growth factor that belongs to the Bone Morphogenetic Protein (BMP) family and plays a pivotal role during limb development. GDF5 is a susceptibility gene for ...
  • Geometric morphometrics on gene expression patterns within phenotypes: a case example on limb development
    Martínez Abadías, Neus; Mateu-Estivill, Roger; Niksic, Martina; Russo, Lucia; Sharpe, James (Oxford University Press, 2016)
    How the genotype translates into the phenotype through development is critical to fully understand the evolution of phenotypes. We propose a novel approach to directly assess how changes in gene expression patterns are ...
  • Green tea catechins modulate skeletal development with effects dependent on dose, time, and structure in a down syndrome mouse model
    Llambrich, Sergi; González-Colom, Rubèn; Wouters, Jens; Roldán, Jorde; Salassa, Sara; Wouters, Kaat; Van Bulck, Vicky; Sharpe, James; Callaerts-Vegh, Zsuzsanna; Vande Velde, Greetje; Martínez Abadías, Neus (MDPI, 2022)
    Altered skeletal development in Down syndrome (DS) results in a brachycephalic skull, flattened face, shorter mandibular ramus, shorter limbs, and reduced bone mineral density (BMD). Our previous study showed that low doses ...
  • Green tea extracts containing epigallocatechin-3-gallate modulate facial development in Down syndrome
    Starbuck, John M.; Llambrich, Sergi; González, Rubén; Albaigès-Ràfols, Júlia; Sarlé, Anna; Wouters, Jens; González, Alejandro; Sevillano, Xavier; Sharpe, James; Torre Fornell, Rafael de la; Dierssen, Mara; Velde, Greetje Vande; Martínez Abadías, Neus (Nature Research, 2021)
    Trisomy of human chromosome 21 (Down syndrome, DS) alters development of multiple organ systems, including the face and underlying skeleton. Besides causing stigmata, these facial dysmorphologies can impair vital functions ...
  • High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals
    Marcon, Luciano, 1983-; Diego, Xavier; Sharpe, James; Müller, Patrick (eLife, 2016)
    The Turing reaction-diffusion model explains how identical cells can self-organize to form spatial patterns. It has been suggested that extracellular signaling molecules with different diffusion coefficients underlie this ...
  • Image formation by linear and nonlinear digital scanned light-sheet fluorescence microscopy with Gaussian and Bessel beam profiles
    Olarte, Omar E.; Licea-Rodriguez, Jacob; Palero, Jonathan A.; Gualda, Emilio J.; Artigas, David; Mayer, Jürgen, 1977-; Swoger, Jim; Sharpe, James; Rocha-Mendoza, Israel; Rangel-Rojo, Raul; Loza-Alvarez, Pablo (Optical Society of America (OSA), 2012)
    We present the implementation of a combined digital scanned light-sheet microscope (DSLM) able to work in the linear and nonlinear regimes under either Gaussian or Bessel beam excitation schemes. A complete characterization ...
  • Key features of turing systems are determined purely by network topology
    Diego, Xavier; Marcon, Luciano, 1983-; Müller, Patrick; Sharpe, James (American Physical Society, 2018)
    Turing’s theory of pattern formation is a universal model for self-organization, applicable to many systems in physics, chemistry, and biology. Essential properties of a Turing system, such as the conditions for the existence ...