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1
Fowler, Joe. "Unlabled Level Planarity." Diss., The University of Arizona, 2009. http://hdl.handle.net/10150/195812.
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Consider a graph G with vertex set V in which each of the n vertices is assigned a number from the set {1, ..., k} for some positive integer k. This assignment phi is a labeling if all k numbers are used. If phi does not assign adjacent vertices the same label, then phi partitions V into k levels. In a level drawing, the y-coordinate of each vertex matches its label and the edges are drawn strictly y-monotone. This leads to level drawings in the xy-plane where all vertices with label j lie along the line lj = {(x, j) : x in Reals} and where each edge crosses any of the k horizontal lines lj for j in [1..k] at most once. A graph with such a labeling forms a level graph and is level planar if it has a level drawing without crossings.We first consider the class of level trees that are level planar regardless of their labeling. We call such trees unlabeled level planar (ULP). We describe which trees are ULP and provide linear-time level planar drawing algorithms for any labeling. We characterize ULP trees in terms of two forbidden subdivisions so that any other tree must contain a subtree homeomorphic to one of these. We also provide linear-time recognition algorithms for ULP trees. We then extend this characterization to all ULP graphs with five additional forbidden subdivisions, and provide linear-time recogntion and drawing algorithms for any given labeling.
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Bachmaier, Christian. "Circle planarity of level graphs." [S.l.] : [s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=973953985.
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Hayer, Matthias. "Testing planarity in linear time." Thesis, Georgia Institute of Technology, 1994. http://hdl.handle.net/1853/30483.
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Taylor, Martyn G. "Planarity testing by path addition." Thesis, University of Kent, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.580367.
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The first linear-time planarity testing algorithm was developed in 1974 by Hopcroft and Tarjan (H&T) [32] using a method to split a biconnected graph up into edge disjoint paths and then sequentially embed them to test for planarity (a path addition method). Shortly afterwards Booth and Leuker [5] developed an alternative vertex addition linear-time planarity test, based on the earlier work of Lempel, Evan and Cederbaum [47], using a new PQ-Tree data structure. Since then there have been many developments in PQ- Tree vertex addition (and related PC-Tree edge addition) methods including authors such as: Chiba et al. [14]; Shih & Hsu [35, 69]; Boyer and Myrvold [10, 11]; and Haeupler and Tarjan [29]. In comparison, path addition has changed very little from the original algorithm. In 1984, Williamson [84] showed how H&T's algorithm can be extended to find Kuratowski sub-graphs in the event of a non-planar graph; and, in 1993, Mehlhorn, Mutzel and Naher [53] produced an implementation (in C) of H&T's algorithm and extended it to create a planar embedding of a graph. This has remained the state-of-the-art in path addition algorithms for over a decade. Recently", de Fraysseix formulated an algorithm [15, 17], based on Tremaux Trees and a characterisation of planarity by W. Wu [87]; this may prove to be a highly optimised version of H&T's algorithm but is difficult to definitively prove as only an outline of its planarity testing phase is provided. These authors represent the majority of the work on path addition methods of planarity testing and embedding; indicating that it receives little attention compared to vertex or edge addition methods This thesis attempts to reinvigorate the field of path addition and demonstrates: • How Trernaux Trees, which allow undirected connected graphs to be represented as a simple partial order relationship are fundamentally related to H&T-‘^planarity testing algorithm and includes some related invariant properties of these trees; • That the restriction on H&T's planarity testing algorithm to test undirected biconnected graphs can be relaxed to undirected connected graphs; • How to generate all possible embeddings of a biconnected component and how to extend this to generate all possible embeddings of separable graphs; and • Empirical Testing of various graph types and sizes to validate these results.
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Estrella, Balderrama Alejandro. "Simultaneous Embedding and Level Planarity." Diss., The University of Arizona, 2009. http://hdl.handle.net/10150/195738.
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Graphs are a common model for representing information consisting of a set of objects or entities and a set of connections or relations between them. Graph Drawing is concerned with the automatic visualization of graphs in order to make the information useful. That is, a good drawing should be helpful in the application domain where it is used by capturing the relationships in the underlying data. We consider two important problems in automated graph drawing: simultaneous embedding and level planarity. Simultaneous embedding is the problem of drawing multiple graphs while maintaining the readability of each graph independently and preserving the mental map when going from one graph to another. In this case, each graph has the same vertex set (same entities) but different edge sets (different relationships). Level planarity arises in the layout of graphs that contain hierarchical relationships. When drawing graphs in the plane, this translates to a restricted form of planarity where the vertical order of the entities is pre-determined. We consider the computational complexity of the simultaneous embedding problem. In particular, we show that in its generality the simultaneous embedding problem is NP-hard if the edges are drawn as straight-lines. We present algorithms for drawing graphs on predetermined levels, which allow the simultaneous embedding of restricted types of graphs, such as outerplanar graphs, trees and paths. Finally, our practical contribution is a tool that implements known and novel algorithms related to simultaneous embedding and level planarity and can be used both as a visualization software and as an aid to study theoretical problems.
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Klein, Philip N. (Philip Nathan). "An efficient parallel algorithm for planarity." Thesis, Massachusetts Institute of Technology, 1986. http://hdl.handle.net/1721.1/34303.
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Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1986.MICROFICHE COPY AVAILABLE IN ARCHIVES AND ENGINEERING
Bibliography: leaves 56-57.
by Philip Nathan Klein.
M.S.
7
Heinz, Adrian. "Planarity testing and drawing in Jedit 4.0." Virtual Press, 2001. http://liblink.bsu.edu/uhtbin/catkey/1204201.
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In this project, an enhanced version of Jedit is presented. Jedit is a Graph Editor developed at Ball State University by a group of students under the direction of Dr. Jay Bagga. The following paper describes the new version, named Jedit 4.0.In this version two new algorithms are implemented. These are: Planarity Testing and Planarity Drawing. The first algorithm tests a graph for planarity and the second one makes a planar embedding of the graph in a grid of size (n-2) x (n-2), where n is the order of the graph. Planar graphs have important applications in the fields of computer engineering, architecture, and many others.Jedit 4.0 also includes new features that were not available in earlier versions. The new features include: graph rotation operation, graph complement, drawing of well-known graphs, and credits window. Several modifications and additions to existing features and algorithms have also been carried out.Jedit 4.0 uses swing java technology what provides a more elegant look. Drop down menus have also been added to provide the user an easier way to use Jedit.Department of Computer Science
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Zschalig, Christian. "Characterizations of Planar Lattices by Left-relations." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2009. http://nbn-resolving.de/urn:nbn:de:bsz:14-ds-1240834941828-67021.
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Recently, Formal Concept Analysis has proven to be an efficient method for the analysis and representation of information. However, the possibility to visualize concept hierarchies is being affected by the difficulty of drawing attractive diagrams automatically. Reducing the number of edge crossings seems to increase the readability of those drawings. This dissertation concerns with a mandatory prerequisite of this constraint, namely the characterization and visual representation of planar lattices. The manifold existing approaches and algorithms are thereby considered under a different point of view. It is well known that exactly the planar lattices (or planar posets) possess an additional order ``from left to right''. Our aim in this work is to define left-relations and left-orders more precisely and to describe several aspects of planar lattices with their help. The three approaches employed structure the work in as many parts: Left-relations on lattices allow a more efficient consideration of conjugate orders since they are uniquely determined by the sorting of the meet-irreducibles. Additionally, the restriction on the meet-irreducibles enables us to achieve an intuitive description of standard contexts of planar lattices similar to the consecutive-one property. With the help of left-relations on diagrams, planar lattices can indeed be drawn without edge crossings in the plane. Thereby, lattice-theoretically found left-orders can be detected in the graphical representation again. Furthermore, we modify the left-right-numbering algorithm in order to obtain attribute-additive and plane drawings of planar lattices. Finally, we will consider left-relations on contexts. They turn out to be fairly similar structures to the Ferrers-graphs. Planar lattices can be characterized by a property of these graphs, namely the bipartiteness. We will constructively prove this result. Subsequently, we can design an efficient algorithm that finds all non-similar plane diagrams of a latticeDie Formale Begriffsanalyse hat sich in den letzten Jahren als effizientes Werkzeug zur Datenanalyse und -repräsentation bewährt. Die Möglichkeit der visuellen Darstellung von Begriffshierarchien wird allerdings durch die Schwierigkeit, ansprechende Diagramme automatisch generieren zu können, beeinträchtigt. Offenbar sind Diagramme mit möglichst wenig Kantenkreuzungen für den menschlichen Anwender leichter lesbar. Diese Arbeit beschäftigt sich mit mit einer diesem Kriterium zugrunde liegenden Vorleistung, nämlich der Charakterisierung und Darstellung planarer Verbände. Die schon existierenden vielfältigen Ansätze und Methoden werden dabei unter einem neuen Gesichtspunkt betrachtet. Bekannterweise besitzen genau die planaren Verbände (bzw. planare geordnete Mengen) eine zusätzliche Ordnung "von links nach rechts". Unser Ziel in dieser Arbeit ist es, solche Links-Relationen bzw. Links-Ordnungen genauer zu definieren und verschiedene Aspekte planarer Verbände mit ihrer Hilfe zu beschreiben. Die insgesamt drei auftretenden Sichtweisen gliedern die Arbeit in ebensoviele Teile: Links-Relationen auf Verbänden erlauben eine effizientere Behandlung konjugierter Ordnungen, da sie durch die Anordnung der Schnitt-Irreduziblen schon eindeutig festgelegt sind. Außerdem erlaubt die Beschränkung auf die Schnitt-Irreduziblen eine anschauliche Beschreibung von Standardkontexten planarer Verbände ähnlich der consecutive-one property. Mit Hilfe der Links-Relationen auf Diagrammen können planare Verbände tatsächlich eben gezeichnet werden. Dabei lassen sich verbandstheoretisch ermittelte Links-Ordnungen in der graphischen Darstellung wieder finden. Weiterhin geben wir in eine Modifikation des left-right-numbering an, mit der planare Verbände merkmaladditiv und eben gezeichnet werden können. Schließlich werden wir Links-Relationen auf Kontexten betrachten. Diese stellen sich als sehr ähnlich zu Ferrers-Graphen heraus. Planare Verbände lassen sich durch eine Eigenschaft dieser Graphen, nämlich die Bipartitheit, charakterisieren. Wir werden dieses Ergebnis konstruktiv beweisen und darauf aufbauend einen effizienten Algorithmus angeben, mit dem alle nicht-ähnlichen ebenen Diagramme eines Verbandes bestimmt werden können
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Nowlin, Jeffrey L. "Planarity in ROMDD's of multiple-valued symmetric functions." Thesis, Monterey, Calif. : Springfield, Va. : Naval Postgraduate School ; Available from National Technical Information Service, 1996. http://handle.dtic.mil/100.2/ADA309273.
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Thesis (M.S. in Electrical Engineering) Naval Postgraduate School, March 1996.Thesis advisor(s): Jon T. Butler. "March 1996." Bibliography: p. 51. Also available online. Mode of access: World Wide Web.
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Zeranski, Robert [Verfasser]. "Satisfiability Characterizations of Upward Planarity Problems / Robert Zeranski." München : Verlag Dr. Hut, 2014. http://d-nb.info/105155053X/34.
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Holovchenko, A. I. "Optimized measurements of planarity of the nanostructure surfaces." Thesis, Видавництво СумДУ, 2012. http://essuir.sumdu.edu.ua/handle/123456789/27596.
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Supervisor: T.J. KippenbergIn micro- nanofabrication planarity of the surfaces is the key of successful process flow. Defects, caused by processes such as etching, inhomogeneity caused either deposition or sputtering can be detected via special metrology techniques and tools. Detection can be done in two ways: by a digital image comparison technique or by laser scanning technology. Noticeable, that both techniques are used in industry and science. Laser scattering tool mostly destined for blank monitor wafers, as image comparison is for patterned wafers. When you are citing the document, use the following link http://essuir.sumdu.edu.ua/handle/123456789/27596
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Borradaile, Glencora. "Exploiting planarity for network flow and connectivity problems." View abstract/electronic edition; access limited to Brown University users, 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3318294.
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Zschalig, Christian. "Characterizations of Planar Lattices by Left-relations." Doctoral thesis, Technische Universität Dresden, 2008. https://tud.qucosa.de/id/qucosa%3A23687.
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Recently, Formal Concept Analysis has proven to be an efficient method for the analysis and representation of information. However, the possibility to visualize concept hierarchies is being affected by the difficulty of drawing attractive diagrams automatically. Reducing the number of edge crossings seems to increase the readability of those drawings. This dissertation concerns with a mandatory prerequisite of this constraint, namely the characterization and visual representation of planar lattices. The manifold existing approaches and algorithms are thereby considered under a different point of view. It is well known that exactly the planar lattices (or planar posets) possess an additional order ``from left to right''. Our aim in this work is to define left-relations and left-orders more precisely and to describe several aspects of planar lattices with their help. The three approaches employed structure the work in as many parts: Left-relations on lattices allow a more efficient consideration of conjugate orders since they are uniquely determined by the sorting of the meet-irreducibles. Additionally, the restriction on the meet-irreducibles enables us to achieve an intuitive description of standard contexts of planar lattices similar to the consecutive-one property. With the help of left-relations on diagrams, planar lattices can indeed be drawn without edge crossings in the plane. Thereby, lattice-theoretically found left-orders can be detected in the graphical representation again. Furthermore, we modify the left-right-numbering algorithm in order to obtain attribute-additive and plane drawings of planar lattices. Finally, we will consider left-relations on contexts. They turn out to be fairly similar structures to the Ferrers-graphs. Planar lattices can be characterized by a property of these graphs, namely the bipartiteness. We will constructively prove this result. Subsequently, we can design an efficient algorithm that finds all non-similar plane diagrams of a lattice.Die Formale Begriffsanalyse hat sich in den letzten Jahren als effizientes Werkzeug zur Datenanalyse und -repräsentation bewährt. Die Möglichkeit der visuellen Darstellung von Begriffshierarchien wird allerdings durch die Schwierigkeit, ansprechende Diagramme automatisch generieren zu können, beeinträchtigt. Offenbar sind Diagramme mit möglichst wenig Kantenkreuzungen für den menschlichen Anwender leichter lesbar. Diese Arbeit beschäftigt sich mit mit einer diesem Kriterium zugrunde liegenden Vorleistung, nämlich der Charakterisierung und Darstellung planarer Verbände. Die schon existierenden vielfältigen Ansätze und Methoden werden dabei unter einem neuen Gesichtspunkt betrachtet. Bekannterweise besitzen genau die planaren Verbände (bzw. planare geordnete Mengen) eine zusätzliche Ordnung "von links nach rechts". Unser Ziel in dieser Arbeit ist es, solche Links-Relationen bzw. Links-Ordnungen genauer zu definieren und verschiedene Aspekte planarer Verbände mit ihrer Hilfe zu beschreiben. Die insgesamt drei auftretenden Sichtweisen gliedern die Arbeit in ebensoviele Teile: Links-Relationen auf Verbänden erlauben eine effizientere Behandlung konjugierter Ordnungen, da sie durch die Anordnung der Schnitt-Irreduziblen schon eindeutig festgelegt sind. Außerdem erlaubt die Beschränkung auf die Schnitt-Irreduziblen eine anschauliche Beschreibung von Standardkontexten planarer Verbände ähnlich der consecutive-one property. Mit Hilfe der Links-Relationen auf Diagrammen können planare Verbände tatsächlich eben gezeichnet werden. Dabei lassen sich verbandstheoretisch ermittelte Links-Ordnungen in der graphischen Darstellung wieder finden. Weiterhin geben wir in eine Modifikation des left-right-numbering an, mit der planare Verbände merkmaladditiv und eben gezeichnet werden können. Schließlich werden wir Links-Relationen auf Kontexten betrachten. Diese stellen sich als sehr ähnlich zu Ferrers-Graphen heraus. Planare Verbände lassen sich durch eine Eigenschaft dieser Graphen, nämlich die Bipartitheit, charakterisieren. Wir werden dieses Ergebnis konstruktiv beweisen und darauf aufbauend einen effizienten Algorithmus angeben, mit dem alle nicht-ähnlichen ebenen Diagramme eines Verbandes bestimmt werden können.
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Chan, Hubert. "A Parameterized Algorithm for Upward Planarity Testing of Biconnected Graphs." Thesis, University of Waterloo, 2003. http://hdl.handle.net/10012/1090.
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We can visualize a graph by producing a geometric representation of the graph in which each node is represented by a single point on the plane, and each edge is represented by a curve that connects its two endpoints.
Directed graphs are often used to model hierarchical structures; in order to visualize the hierarchy represented by such a graph, it is desirable that a drawing of the graph reflects this hierarchy. This can be achieved by drawing all the edges in the graph such that they all point in an upwards direction. A graph that has a drawing in which all edges point in an upwards direction and in which no edges cross is known as an upward planar graph. Unfortunately, testing if a graph is upward planar is NP-complete.
Parameterized complexity is a technique used to find efficient algorithms for hard problems, and in particular, NP-complete problems. The main idea is that the complexity of an algorithm can be constrained, for the most part, to a parameter that describes some aspect of the problem. If the parameter is fixed, the algorithm will run in polynomial time.
In this thesis, we investigate contracting an edge in an upward planar graph that has a specified embedding, and show that we can determine whether or not the resulting embedding is upward planar given the orientation of the clockwise and counterclockwise neighbours of the given edge. Using this result, we then show that under certain conditions, we can join two upward planar graphs at a vertex and obtain a new upward planar graph. These two results expand on work done by Hutton and Lubiw.
Finally, we show that a biconnected graph has at most k!8k-1 planar embeddings, where k is the number of triconnected components. By using an algorithm by Bertolazzi et al. that tests whether a given embedding is upward planar, we obtain a parameterized algorithm, where the parameter is the number of triconnected components, for testing the upward planarity of a biconnected graph. This algorithm runs in O(k!8kn3) time.
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Brückner, Guido [Verfasser], and D. [Akademischer Betreuer] Wagner. "Planarity Variants for Directed Graphs / Guido Brückner ; Betreuer: D. Wagner." Karlsruhe : KIT-Bibliothek, 2021. http://d-nb.info/1238148018/34.
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Noschinski, Lars Verfasser], Tobias [Akademischer Betreuer] [Gutachter] [Nipkow, and Kurt [Gutachter] Mehlhorn. "Formalizing Graph Theory and Planarity Certificates / Lars Noschinski. Betreuer: Tobias Nipkow. Gutachter: Kurt Mehlhorn ; Tobias Nipkow." München : Universitätsbibliothek der TU München, 2016. http://d-nb.info/1104933624/34.
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Bläsius, Thomas [Verfasser], and D. [Akademischer Betreuer] Wagner. "New Approaches to Classic Graph-Embedding Problems - Orthogonal Drawings & Constrained Planarity / Thomas Bläsius. Betreuer: D. Wagner." Karlsruhe : KIT-Bibliothek, 2015. http://d-nb.info/1075809401/34.
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Rutter, Ignaz [Verfasser], and D. [Akademischer Betreuer] Wagner. "The many faces of planarity : matching, augmentation, and embedding algorithms for planar graphs / Ignaz Rutter. Betreuer: D. Wagner." Karlsruhe : KIT-Bibliothek, 2011. http://d-nb.info/1015557848/34.
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Bhandari, Yuba R. "Pressure Induced Structural Changes and Gas Diffusion Pathways in Monomeric Fluorescent Proteins." FIU Digital Commons, 2013. http://digitalcommons.fiu.edu/etd/886.
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Fluorescent proteins (FPs) are extremely valuable biochemical markers which have found a wide range of applications in cellular and molecular biology research. The monomeric variants of red fluorescent proteins (RFPs), known as mFruits, have been especially valuable for in vivo applications in mammalian cell imaging. Fluorescent proteins consist of a chromophore caged in the beta-barrel protein scaffold. The photophysical properties of an FP is determined by its chromophore structure and its interactions with the protein barrel.
Application of hydrostatic pressure on FPs results in the modification of the chromophore environment which allows a systematic study of the role of the protein-chromophore interactions on photophysical properties of FPs. Using Molecular Dynamics (MD) computer simulations, I investigated the pressure induced structural changes in the monomeric variants mCherry, mStrawberry, and Citrine. The results explain the molecular basis for experimentally observed pressure responses among FP variants. It is found that the barrel flexibility, hydrogen bonding interactions and chromophore planarity of the FPs can be correlated to their contrasting photophysical properties at vaious pressures.
I also investigated the oxygen diffusion pathways in mOrange and mOrange2 which exhibit marked differences in oxygen sensitivities as well as photostability. Such computational identifications of structural changes and oxygen diffusion pathways are important in guiding mutagenesis efforts to design fluorescent proteins with improved photophysical properties.
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Singh, Mandeep. "STUDIES ON THE SIZE AND NON-PLANARITY OF AROMATIC STACKING MOIETY ON CONFORMATION SELECTIVITY AND THERMAL STABILIZATION OF G-QUADRUPLEXES." Scholarly Commons, 2020. https://scholarlycommons.pacific.edu/uop_etds/3725.
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Targeting DNA has the advantage over proteins for cancer remediation because of the fewer copies of the ligands required for the desired therapeutic effect. Traditionally, covalent DNA binders like alkylating agents have been used to induce genetic instability through the formation of DNA lesions and strand breaks, leading to cellular apoptosis. The primary drawback of this treatment is the non-specific binding that affects both cancerous and non-cancerous cells. G-quadruplexes are the DNA secondary structures that are present in abundance near the promoter regions of the oncogenes and are involved in the regulation of their activities. A ligand-mediated stabilization of G-quadruplexes in the promoter regions and down-regulation of the associated oncogenes have been validated. In contrast to alkylating agents, G-quadruplex ligands induce genetic stabilization through non-covalent interactions. They can be designed to interact specifically with G-quadruplex DNA over duplex DNA, which reduce side effects arising from the off-targeting. G-quadruplex ligands invariably have the large planar aromatic moiety to interact with G-quadruplexes through π- π stacking interactions. For determining the size effect of the aromatic moiety on stabilization of G-quadruplexes, a series of ligands were synthesized by conjugating nucleobases or 1,10-phenanthroline with an aminoglycoside, neomycin. The resulting conjugates increased the binding affinity synergistically and enabled us to study the effect of the stacking moiety required for G-quadruplex stabilization. Nucleobase-neomycin conjugates did not show stabilization stabilize of human telomeric G-quadruplex. 1,10-Phenanthroline-neomycin conjugate (7b) on the other hand binds to human telomeric G-quadruplex with a Ka of (8.92.4)×108 M-1 and inhibits telomerase activity at 1.56 µM probably through G-quadruplex stabilization. Moving forward, we further enlarged the aromatic moiety by tethering two 1,10-phenantholine molecules together through a five-atom linker. The resulting molecule (2-Clip-phen) was conjugated with various amino-containing side chains. 2-Clip-phen derivatives showed at least 30 times weaker binding to duplex DNA over G-quadruplex DNA. In addition, compounds showed a preference for the antiparallel G-quadruplex conformation over parallel and hybrid G-quadruplex conformations, as shown in the CD spectroscopy studies. Ligands 11 and 13 induced the formation of an antiparallel G-quadruplex from random coils and stabilize it to 60 oC (Tm) in a salt-free condition. Mass spectrometry study showed the formation of a two-tetrad G-quadruplex with the 2-Clip-phen ligand. Docking study showed that the ligand interacts most favorably with antiparallel G-quadruplex conformation, which is supported further by the larger thermal stabilization effect on antiparallel G-quadruplex compared with other G-quadruplex conformations. Our study suggests that 2-Clip-phen can be used as a scaffold for designing G-quadruplex binding ligands that preferentially bind to antiparallel G-quadruplexes, which has never been reported before.
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Coelho, Vinícius de Sousa. "Um estudo aplicado de paralelismo para o problema do subgrafo planar de peso máximo." Universidade Federal de Goiás, 2018. http://repositorio.bc.ufg.br/tede/handle/tede/8503.
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The Maximum Weight Planar Subgraph Problem (MWPSP) consists of identifying a planar subgraph of maximum weight of a given edge-weighted graph. This work proposes new heuristic solutions, mainly using Graphic Processing Units, based on local transformations on the graph topology, consisting of vertex and edge insertion/relocation moves. Sequential and parallel implementations were built and applied to various numerical instances with promising results. One of the approaches requires only 25 seconds of execution, being more than 200 times faster than its corresponding sequential version, for a 100-vertex instance. In terms of quality, the proposed solutions obtained better results than state of the art proposals.
O problema do subgrafo planar de peso máximo (MWPSP) consiste em extrair um subgrafo planar maximal, a partir de um grafo completo com pesos atribuídos às arestas, cuja soma dos pesos das arestas seja máxima. Este trabalho propõe soluções heurísticas, construídas por meio de Unidades de Processamento Gráfico (GPUs), baseadas em transformações locais na topologia do grafo através da inserção/realocação de vértices e arestas. Implementações sequencias e paralelas foram propostas, apresentando resultados satisfatórios. Em uma das propostas, a versão paralela requer cerca de 25 segundos de execução em uma instância de 100 vértices, sendo cerca de 200 vezes mais rápida que a versão sequencial correspondente. Em termos de qualidade da solução, as propostas superaram os resultados obtidos por algoritmos no estado da arte.
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Streib, Noah Sametz. "Planar and hamiltonian cover graphs." Diss., Georgia Institute of Technology, 2011. http://hdl.handle.net/1853/43744.
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This dissertation has two principal components: the dimension of posets with planar cover graphs, and the cartesian product of posets whose cover graphs have hamiltonian cycles that parse into symmetric chains. Posets of height two can have arbitrarily large dimension. In 1981, Kelly provided an infinite sequence of planar posets that shows that the dimension of planar posets can also be arbitrarily large. However, the height of the posets in this sequence increases with the dimension. In 2009, Felsner, Li, and Trotter conjectured that for each integer h at least 2, there exists a least positive integer c(h) so that if P is a poset with a planar cover graph (the class of posets with planar cover graphs includes the class of planar posets) and the height of P is h, then the dimension of P is at most c(h). In the first principal component of this dissertation we prove this conjecture. We also give the best known lower bound for c(h), noting that this lower bound is far from the upper bound. In the second principal component, we consider posets with the Hamiltonian Cycle--Symmetric Chain Partition (HC-SCP) property. A poset of width w has this property if its cover graph has a hamiltonian cycle which parses into w symmetric chains. This definition is motivated by a proof of Sperner's theorem that uses symmetric chains, and was intended as a possible method of attack on the Middle Two Levels Conjecture. We show that the subset lattices have the HC-SCP property by showing that the class of posets with the strong HC-SCP property, a slight strengthening of the HC-SCP property, is closed under cartesian product with a two-element chain. Furthermore, we show that the cartesian product of any two posets from this strong class has the (weak) HC-SCP property.
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Dehdari, Jonathan M. "Crossing Dependencies in Persian." Diss., CLICK HERE for online access, 2006. http://contentdm.lib.byu.edu/ETD/image/etd1441.pdf.
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Rasmussen, Danne Rene, and danne@optusnet com au. "A Theoretical Approach to Molecular Design: Planar-Tetracoordinate Carbon." The Australian National University. Research School of Chemistry, 2000. http://thesis.anu.edu.au./public/adt-ANU20010702.115616.
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A number of novel hydrocarbon cage systems have been designed and characterized using ab initio molecular orbital calculations at the MP2 and B3-LYP levels. In particular,equilibrium structures for five families of molecules, hemialkaplanes, hemispiroalkaplanes, alkaplanes, spiroalkaplanes and dimethanospiroalkaplanes, have been examined in detail with the aim of designing a saturated hydrocarbon with a planar-tetracoordinate carbon atom and with a view to identifying appropriate synthetic targets.
¶
The hemialkaplanes and hemispiroalkaplanes are constructed from a spiropentane or neopentane subunit, respectively, which is capped by a cyclic hydrocarbon. The hemispiroalkaplanes are predicted to contain a pyramidal-tetracoordinate carbon atom possessing a lone pair of electrons. Protonation at this apical carbon atom is found to be highly favorable, resulting in a remarkably high basicity for a saturated hydrocarbon. The proton affinities of the hemispiroalkaplanes are calculated to be more than 1170 kJ mol[superscript -1] , even greater than those for the diamine "proton sponges".
¶
The alkaplanes and the spiroalkaplanes, which are constructed by bicapping a neopentane or spiropentane subunit, respectively, with a pair of cyclic hydrocarbons, show unprecedented flattening of a tetracoordinate carbon atom. Linking the spiroalkaplane caps with methano bridges gives the dimethanospiroalkaplanes, two of which, dimethanospirooctaplane and dimethanospirobinonaplane, achieve exact planarity at the central carbon atom. They are the first neutral saturated hydrocarbons predicted to contain an exactly planartetracoordinate carbon atom. This has been achieved through structural constraints alone. The electronic structure at the central carbon atom results in a highest occupied molecular orbital corresponding to a p-type lone pair. Consequently, the adiabatic ionization energies for octaplane, spirooctaplane and dimethanospirooctaplane (approximately 5 eV) are predicted to be similar to those of lithium and sodium - incredibly low for a saturated hydrocarbon.
¶
Some consideration has been given to likely pathways for unimolecular decomposition for all species. Predicted structures, heats of formation and strain energies for all the novel hydrocarbons are also detailed. Tetramethylhemispirooctaplane and dimethanospirobinonaplane are identified as the preferred synthetic targets.
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Luo, Ying. "SLURRY CHEMISTRY EFFECTS ON COPPER CHEMICAL MECHANICAL PLANARIZATION." Master's thesis, University of Central Florida, 2004. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/4470.
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Chemical-mechanical Planarization (CMP) has emerged as one of the fastest-growing processes in the semiconductor manufacturing industry, and it is expected to show equally explosive growth in the future (Braun, 2001). The development of CMP has been fueled by the introduction of copper interconnects in microelectronic devices. Other novel applications of CMP include the fabrications of microelectromechanical systems (MEMS), advanced displays, three dimensional systems, and so on (Evans, 2002). CMP is expected to play a key role in the next-generation micro- and nanofabrication technologies (Singh, et al., 2002). Despite the rapid increase in CMP applications, the fundamental understanding of the CMP process has been lacking, particularly the understanding of the wafer-slurry-pad interactions that occur during the CMP process. Novel applications of CMP are expected to expand to materials that are complex chemically and fragile mechanically. Thus, fundamental understanding and improvement of slurry design for CMP is the key to the development of sophisticated next-generation CMP processes. Slurry performance for CMP can be determined by several output parameters including removal rate, global planarity, surface topography, and surface defectivity. To achieve global planarity, it is essential to form a very thin passivating surface layer (<2 nm) that is subsequently removed by the mechanical component of the slurry (Kaufman et al., 1991) or by combined chemo-mechanical effects (Tamboli, 2000). Chemical additives like hydrogen peroxide (H?O?), potassium ferricyanide, and ferric chloride are added to slurries as oxidizers in order to form a desirable surface layer. Other chemical additives such as inhibitors (e.g. benzotriazole) and complexing agents (e.g. ammonia) are added to the copper slurry in order to modify the oxide layer. That the removal rate of the thin surface layer is greater at the highest regions of the wafer surface than at the lowest regions leads to surface planarity. In this study, various complexing agents and inhibitors are combined to form slurry chemistry for copper CMP processing in H?O? based slurries at pH values ranging from 2 to 10. Two complexing agents (glycine and Ethylenediamine) and one inhibitor (3-amino-1, 2, 4-triazole) were selected as slurry constituents for detailed chemical synergistic effect study because they showed good materials removal and surface planarity performances. To understand the fundamental mechanisms involved in copper CMP process with the afore-mentioned slurry chemical formations, various techniques, such as electrochemical testing techniques (including potentiodynamic polarization and electrochemical impedance spectroscopy), x-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), and scanning electron microscopy (SEM), were applied. As a result, guidelines for optimized slurry chemical formulation were arrived at and the possible mechanisms of surface-chemical-abrasive interactions were determined. From applications point of view, this study serves as a guide for further investigations in pursuing highly effective slurry formulations for copper/low-k interconnect applications.M.S.
Department of Mechanical, Materials and Aerospace Engineering;
Engineering and Computer Science
Mechanical, Materials and Aerospace Engineering;
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Tassion, Vincent. "Planarité et Localité en Percolation." Phd thesis, Ecole normale supérieure de lyon - ENS LYON, 2014. http://tel.archives-ouvertes.fr/tel-01061007.
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Cette thèse s'inscrit dans l'étude mathématique de la percolation, qui regroupe une famille de modèles présentant une transition de phase. Des avancées majeures au cours des quinze dernières années, notamment l'invention du SLE et la preuve de l'invariance conforme de la percolation de Bernoulli critique, nous permettent aujourd'hui d'avoir une image très complète de la percolation de Bernoulli sur le réseau triangulaire. Cependant, de nombreuses questions demeurent ouvertes, et ont motivé notre travail.La première d'entre elle est l'universalité de la percolation plane, qui affirme que les propriétés macroscopiques de la percolation plane critique ne devraient pas dépendre du réseau sous-jacent à sa définition. Nous montrons, dans le cadre de la percolation Divide and Color, un résultat qui va dans le sens de cette universalité et identifions, dans ce contexte, des phénomènes macroscopiques indépendants du réseau microscopique. Une version plus faible d'universalité est donnée par la théorie de Russo-Seymour-Welsh (RSW), et sa validité est connue pour la percolation de Bernoulli (sans dépendance) sur les réseaux plans suffisamment symétriques. Nous étudions de nouveaux arguments de type RSW pour des modèles de percolation avec dépendance. La deuxième question que nous avons abordée est celle de l'absence d'une composante connexe ouverte infinie au point critique, une question importante du point de vue physique, puisqu'elle traduit la continuité de la transition de phase. Dans deux travaux en collaboration avec Hugo Duminil-Copin et Vladas Sidoravicius, nous montrons que la transition de phase est continue pour la percolation de Bernoulli sur le graphe Z^2x{0,...,k}, et pour la percolation FK sur le réseau carré avec paramètre q inférieur ou égal à 4. Enfin, la dernière question qui nous a guidés est la localité du point critique : la donnée des boules de grands rayons d'un graphe suffit-elle à identifier avec une bonne précision la valeur du point critique? Dans un travail en collaboration avec Sébastien Martineau, nous répondons de manière affirmative à cette question dans le cadre des graphes de Cayley de groupes abéliens.
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Belhedi, Amira. "Modélisation du bruit et étalonnage de la mesure de profondeur des caméras Temps-de-Vol." Thesis, Clermont-Ferrand 1, 2013. http://www.theses.fr/2013CLF1MM08/document.
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Avec l'apparition récente des caméras 3D, des perspectives nouvelles pour différentes applications de l'interprétation de scène se sont ouvertes. Cependant, ces caméras ont des limites qui affectent la précision de leurs mesures. En particulier pour les caméras Temps-de-Vol, deux types d'erreur peuvent être distingués : le bruit statistique de la caméra et la distorsion de la mesure de profondeur. Dans les travaux de la littérature des caméras Temps-de-Vol, le bruit est peu étudié et les modèles de distorsion de la mesure de profondeur sont généralement difficiles à mettre en œuvre et ne garantissent pas la précision requise pour certaines applications. L'objectif de cette thèse est donc d'étudier, modéliser et proposer un étalonnage précis et facile à mettre en œuvre de ces 2 types d'erreur des caméras Temps-de-Vol. Pour la modélisation du bruit comme pour la distorsion de la mesure de profondeur, deux solutions sont proposées présentant chacune une solution à un problème différent. La première vise à fournir un modèle précis alors que le second favorise la simplicité de la mise en œuvre. Ainsi, pour le bruit, alors que la majorité des modèles reposent uniquement sur l'information d'amplitude, nous proposons un premier modèle qui intègre aussi la position du pixel dans l'image. Pour encore une meilleure précision, nous proposons un modèle où l'amplitude est remplacée par la profondeur de l'objet et le temps d'intégration. S'agissant de la distorsion de la mesure de profondeur, nous proposons une première solution basée sur un modèle non-paramétrique garantissant une meilleure précision. Ensuite, pour fournir une solution plus facile à mettre en œuvre que la précédente et que celles de l'état de l'art, nous nous basons sur la connaissance à priori de la géométrie planaire de la scène observée3D cameras open new possibilities in different fields such as 3D reconstruction, Augmented Reality and video-surveillance since they provide depth information at high frame-rates. However, they have limitations that affect the accuracy of their measures. In particular for TOF cameras, two types of error can be distinguished : the stochastic camera noise and the depth distortion. In state of the art of TOF cameras, the noise is not well studied and the depth distortion models are difficult to use and don't guarantee the accuracy required for some applications. The objective of this thesis is to study, to model and to propose a calibration method of these two errors of TOF cameras which is accurate and easy to set up. Both for the noise and for the depth distortion, two solutions are proposed. Each of them gives a solution for a different problem. The former aims to obtain an accurate model. The latter, promotes the simplicity of the set up. Thereby, for the noise, while the majority of the proposed models are only based on the amplitude information, we propose a first model which integrate also the pixel position in the image. For a better accuracy, we propose a second model where we replace the amplitude by the depth and the integration time. Regarding the depth distortion, we propose a first solution based on a non-parametric model which guarantee a better accuracy. Then, we use the prior knowledge of the planar geometry of the observed scene to provide a solution which is easier to use compared to the previous one and to those of the litterature
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Assunção, Guilherme Puglia. "Representações retangulares de grafos planares." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/45/45134/tde-07052012-164622/.
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Uma representação retangular de um grafo plano G é uma representação de G, onde cada vértice é desenhado como um retângulo de modo que dois retângulos devem compartilhar algum segmento de seus lados se e somente se existe uma aresta em G entre os vértices correspondentes aos retângulos. Ainda, a representação de G deve formar um retângulo e não deve existir buracos, ou seja, toda região interna deve corresponder a algum vértice de G. Um desenho retangular de um grafo plano H é um desenho de H, onde todas as arestas são desenhadas como segmentos horizontais ou verticais. Ainda, todas as faces internas são retângulos e as arestas que incidem na face externa também formam um retângulo. Nesta dissertação, apresentamos os principais trabalhos existentes na literatura para problemas associados à representação retangular. Também apresentamos resultados para problemas associados ao desenho retangular. Por fim, apresentamos o algoritmo que desenvolvemos para determinar as coordenadas dos vértices de um desenho retangular quando a orientação das arestas já foram determinadas.A rectangular representation of a plane graph G is a representation of G, where each vertex is drawn as a rectangle, such as two rectangles have to share some boundary if and only if exist an edge in G between the corresponding vertices. Also, the representation of G must form a rectangle and does not contain any holes, in other words, every point inside the formed rectangle must correspond to some vertex of G. A rectangular drawing of a plane graph H is a drawing of H, where all edges are drawn either in vertical or in horizontal. Also, every internal face is a rectangle and the edges which are incident in the external face define a rectangle. In this dissertation, we present the main studies in the literature for problems associated with the rectangular representation. We also present results for problems associated with rectangular drawing. Finally, we present the algorithm we developed to determine the coordinates of the vertices of a rectangular drawing when the orientation of the edges have been determined.
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Rojo, Laguna José Ignacio. "Proliferative and positional instructions underliying planarian regeneration and tissue renewal = Instrucciones proliferativas y posicionales subyacentes a la regeneración y el recambio tisular en planaria." Doctoral thesis, Universitat de Barcelona, 2017. http://hdl.handle.net/10803/406952.
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Some animals have incredible regenerative abilities which kept researchers fascinating during decades. How these animals are able to regenerate missing parts and restore damaged tissues can give researchers insights in the regenerative medicine field. Here, we use the planarian Schmidtea mediterranea, specie which is able to fully regenerate every missing part, to deeper understand the regeneration and the tissue renewal processes. Both processes share several mechanisms which are essentials for their correct development. In this Thesis, we described some aspect of the balance between proliferation and apoptosis, the stem cell differentiation and the positional instructions required all of them to properly regenerate any structure and produce the tissue turn over required during the normal homeostasis of the animals.
To study the balance between proliferation and apoptosis, we were focused in the description of Krüppel-like factor 10/11, which in other organisms is also involved in these mechanisms. Here we show that klf10/11 is required for the proper regulation of proliferation and apoptosis in regeneration and that they are essential for the correct remodelling of the organism structures, probably downstream c-Jun N-terminal kinase.
On the other hand, we have been focused on the study of the transcriptional complex Nuclear Factor Y in order to understand its role during differentiation events in planarian. We have shown that planarian NF-Y is essential for regeneration and homeostasis and that its inhibition generates neoblast accumulation and absence of epidermal progenitors which demonstrates that NF-Y is involved in the early differentiation of epidermal lineage progenitors.
Finally, the positional instructions which are essential for the correct positioning of cells and organs during regeneration and homeostasis have been studied. Here, we have been focused in the control of the medio-lateral organization of the central nervous system in planarian, where Wnt5 and Slit play an essential role. Wnt5, Slit and their receptors create a self-regulatory system to establish the medio-lateral pattern in planarians which guide the CNS to be positioned in this axisAlgunos animales tienen habilidades regenerativas increíbles, las cuales han mantenido a los investigadores fascinados durante décadas. Cómo estos animales son capaces de regenerar partes perdidas y recuperar los tejidos dañados podría dar a los investigadores claves en el campo de la medicina regenerativa. Aquí, nosotros usamos la planaria Schmidtea mediterránea, una especie que es capaz de regenerar completamente cada parte perdida, para entender más profundamente el proceso de regeneración y recambio tisular. Ambos procesos comparten varios mecanismos los cuales son esenciales para su correcto desarrollo. En esta Tesis, describimos algunos aspectos del balance entre la proliferación y la apoptosis, la diferenciación de células madre y las instrucciones posicionales, requeridas todos ellos para regenerar cualquier estructura y producir el recambio tisular requerido durante la homeostasis normal de los animales. Para estudiar el balance entre la proliferación y la apoptosis, nos hemos centrado en la descripción del factor Krüppel-like 10/11, el cual se ha relacionado con estos procesos en otros organismos. Aquí hemos visto que, klf10/11 se requiere durante la regeneración para la correcta regulación de la proliferación y de la apoptosis y que es necesario para el correcto remodelaje de las estructuras del organismo, probablemente aguas abajo de la kinasa c-Jun N-terminal. Por otra parte, nos hemos centrado en el estudio del complejo transcripcional Nuclear Factor Y para así comprender su papel durante los eventos de diferenciación en la planaria. Hemos visto que el NF-Y presente en planaria es esencial para la regeneración y homeostasis y que su inhibición produce la acumulación de neoblastos y la pérdida de progenitores epidérmicos, lo cual demuestra que NF-Y está involucrado en la diferenciación temprana de los progenitores tempranos epidérmicos. Finalmente, se han estudiado las instrucciones posicionales, las cuales son esenciales para el correcto posicionamiento de las células y órganos durante la regeneración y homeostasis. Aquí, nos hemos centrado en el control de la organización medio-lateral del sistema nervioso central en la planaria, donde Wnt5 y Slit juegan un papel esencial. Wnt5, Slit y sus receptores crean un sistema auto-regulativo para establecer el patrón medio-lateral en las planarias, el cual guía al SNC para ser posicionado en este eje.
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Mori, Ricardo de Almeida. "Grafos : planaridade e projeto de ensino." reponame:Repositório Institucional da UFABC, 2015.
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Orientador: Prof. Dr. Rafael de Mattos GrisiDissertação (mestrado) - Universidade Federal do ABC, Programa de Pós-Graduação em Mestrado Profissional em Matemática em Rede Nacional, 2015.
Este trabalho apresenta uma introdução ao estudo da Teoria dos Grafos, com um dicionário visual e um histórico detalhado das origens deste ramo da matemática. Será dada uma ênfase especial ao estudo de grafos planares e na imersão de grafos em outras superfícies. Por fim, é apresentado um plano de aula para o professor interessado em introduzir o ensino de grafos a alunos do ensino fundamental e médio.
This paper presents an introduction to the study of Graph Theory, with a visual dictionary and a detailed history of the origins of this branch of mathematics. It will be given a special emphasis on the study of planar graphs and also in immersion graphs in other surfaces. Finally, we present a lesson plan for teacher interested in introducing the teaching of graphs to students of primary and secondary education.
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Ribeiro, Alyson Rogério 1986. "Potencial do uso de planárias na avaliação de contaminantes ambientais=Potential use of planarians for environmental contaminants evaluation." [s.n.], 2012. http://repositorio.unicamp.br/jspui/handle/REPOSIP/267776.
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Orientador: Gisela de Aragão UmbuzeiroDissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Tecnologia
Made available in DSpace on 2018-08-21T02:00:16Z (GMT). No. of bitstreams: 1 Ribeiro_AlysonRogerio_M.pdf: 3701819 bytes, checksum: b2f0a69f435398e5de38f031d75649e3 (MD5) Previous issue date: 2012
Resumo: As planarias de água doce possuem vasta distribuição geográfica, plasticidade biologica, facilidade de cultivo em laboratório, sensibilidade a contaminantes diversos e capacidade regenerativa, por isso vem sendo utilizadas como organismos-teste em ensaios ecotoxicologicos. Porem, ainda não ha normatização internacional ou nacional que padronize esses ensaios. O objetivo deste trabalho foi verificar o potencial do uso de planarias de agua doce (Girardia tigrina) na avaliação de alguns contaminantes e amostras ambientais utilizando protocolos padronizados avaliando-se mortalidade e atraso na regeneração encefálica. Foram empregados 15 organismos por concentração-teste nos ensaios de mortalidade de filhotes (96h) e 20 planarias adultas regenerantes por concentração-teste nos ensaios de regeneração encefálica (120h). Avaliou-se cromo e zinco como substancias de referencia e empregou-se cobre, azo corante têxtil Disperse Red 1, herbicida atrazina, nanotubos de carbono de parede múltipla, alem de amostras da ETE Carioba e do Ribeirão dos Cristais. Carta controle com substancia de referencia foi realizada, sendo estabelecido um protocolo para o monitoramento da sensibilidade das culturas de G. trigrina. O zinco foi a substancia mais apropriada que o cromo, com a vantagem do ensaio de sensibilidade poder ser finalizado em 24h. Os métodos utilizados para realização do ensaio de regeneração encefálica e de mortalidade de filhotes foram eficazes para a observação de efeitos adversos das substancias analisadas. Todas as amostras testadas apresentaram toxicidade as planarias, exceto os nanotubos de carbono. Atraso na regeneração encefálica foi o endpoint mais sensível para os contaminantes avaliados. Os protocolos utilizados neste estudo podem ser utilizados como subsídios na elaboração futura de normas técnicas de testes ecotoxicologicos com planarias de agua doce
Abstract: Freshwater planarians are worldwide distributed, have biological plasticity and a unique body regenerative capacity. They are easily maintained under laboratorial conditions and are sensitive for several compounds. For these reasons they have been used in ecotoxicological testing although the lack of national or international guidelines. This research aimed to verify the potential use of freshwater planarians (Girardia tigrina) in mortality and regeneration delay endpoints to assess the toxicity of environmental contaminants using standardized protocols. The culture sensitivity of G. tigrina was monitored with zinc, which was the most suitable substance for this purpose, providing responses in only 24h. The adopted protocols for regeneration and mortality tests were efficient to assess the adverse effects of the chemical agents (copper, an azo textile dye, atrazine), carbon nanotubes and wastewater and water samples from Carioba WWTP and Cristais River. The regeneration test was the most sensitive endpoint and all analyzed substances showed toxicity for planarians, except carbon nanotubes. The methods adopted in this research can be used as basis for the development of a testing guideline using freshwater planarians
Mestrado
Tecnologia e Inovação
Mestre em Tecnologia
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Lewallen, Melissa A. "The Metabolic Physiology of Planarian Flatworms." Thesis, University of North Texas, 2019. https://digital.library.unt.edu/ark:/67531/metadc1538679/.
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Using a high throughput closed respirometry method to measure oxygen consumption, I determined metabolic rates in asexual and sexual Schmidtea mediterranea and Girardia dorotocephala, as a function of temperature, taxon, stressors, reproductive mode, age, regeneration, and specific dynamic action. This study has shown that oxygen consumption can reliably be measured in planaria using optode closed respirometry, and also provided a reliable method for measuring wet mass in planaria, which has been a challenge to researchers in the past. This research revealed that oxygen consumption in S. mediterranea is 1.5-2.1X greater in the sexual strain over the asexual strain at 13-18°C. Within the sexual strain, oxygen consumption is 1.5 -2.2X greater in sexually mature adults over the sexually immature groups (hatchlings, juveniles, and regenerating sexuals). Furthermore, I was able to quantify differences in sexual morphology between these groups exhibiting significant differences in oxygen consumption. The results of this research supports a theory of higher metabolic costs with sexual maturity in S. mediterranea. Therefore, this study has established sexual and asexual S. mediterranea as simple, yet attractive models for investigating energetic costs between sexual and asexual phenotypes. This research also provided quantitative values for specific dynamic action in planaria, with a maximum increase in oxygen consumption of 160% induced by feeding, as well as metabolic relationships in planaria involving temperature, age, and regeneration. These values establish planaria as one of the simplest animal models in which common metabolic patterns, such as SDA and poikilothermic temperature sensitivity, have been demonstrated. Therefore, this research has contributed to the overall knowledge of the basic physiology in this animal, providing the framework for future metabolic studies in planaria involving environmental factors, reproduction, regeneration, development, and aging. Information from this study may supplement interpretation and understanding of modern cellular, molecular, and genomic studies in planaria.
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Mustonen, Katie Lynn. "Endocannabinoid System in a Planarian Model." Thesis, University of North Texas, 2010. https://digital.library.unt.edu/ark:/67531/metadc33188/.
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In this study, the presence and possible function of endocannabinoid ligands in the planarian is investigated. The endocannabinoids ananadamide (AEA) and 2-arachidonoylglycerol (2-AG) and entourage NAE compounds palmitoylethanolamide (PEA), stearoylethanolamide (SEA) and oleoylethanolamide (OEA) were found in Dugesia dorotocephala. Changes in SEA, PEA, and AEA levels were observed over the initial twelve hours of active regeneration. Exogenously applied AEA, 2-AG and their catabolic inhibition effected biphasic changes in locomotor velocity, analogous to those observed in murines. The genome of a close relative, Schmidtea mediterranea, courtesy of the University of Utah S. med genome database, was explored for cannabinoid receptors, none were found. A putative fatty acid amide hydrolase (FAAH) homolog was found in Schmidtea mediterranea.
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An, Yang. "Genome analysis of the planarian Dugesia japonica." 京都大学 (Kyoto University), 2015. http://hdl.handle.net/2433/199140.
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Tan, Thomas Ching-Jen. "Telomere biology in the freshwater planarian Schmidtea mediterranea." Thesis, University of Nottingham, 2011. http://eprints.nottingham.ac.uk/12308/.
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Freshwater planarian Schmidtea mediterranea is an emerging model for studying in vivo gene functions and regulation in native cell niches. The obligate asexual strain of this species reproduces by fission, in which succession of soma occurs without passing through the germline. To achieve this somatic immortality the somatic stem cells need to overcome the end replication problem. Therefore it can be hypothesised that somatic telomere maintenance in asexual S. mediterranea must possess a germ-like property, with which age-related erosions can be adequately repaired. In this PhD project, the telomere repeat unit in S. mediterranea was confirmed to be the vertebrate-like TTAGGG. Attrition of whole body telomere length was found in ageing sexual worms and also in asexual worms which had not gone through recent fission events. Opposite telomere length dynamics were observed in regenerated samples of the two strains, with erosion in the sexuals and reset in the asexuals. The telomere maintenance was found to increase during regeneration in both strains, with a higher level of increase in asexual worms. A homolog of the telomerase reverse transcriptase subunit, Smed_Tert, was identified and characterised in this organism. High level of Smed_Tert expression was seen in germ cells in mature sexual worms and adult stem cells in asexual worms. Knockdown of Smed_Tert expression by RNA interference caused progressive telomere erosion, however effects on cell proliferation and viability have not been observed in knockdown samples. Four alternate splice isoforms of Smed_Tert were identified. The enhanced telomerase activity during regeneration correlates with a proportional increase in the full-length isoform and a decrease in isoforms with a truncated TRBD domain, suggesting a dominant negative regulation of telomerase by alternative splicing. Significant increase in the expression of the full-length isoform was seen in regenerating asexual samples but not in sexual strains, which correlates with their telomere length dynamics. It is hoped that the comparative studies between the sexual and asexual strains can improve our understanding of how soma can evolve to become an effective inheritable unit.
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Shen, Yun, and 沈筠. "The role of extracellular matrix in planarian regeneration." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2014. http://hdl.handle.net/10722/206722.
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Lapan, Sylvain William. "Regeneration and maintenance of the planarian nervous system." Thesis, Massachusetts Institute of Technology, 2012. http://hdl.handle.net/1721.1/87912.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2012.Cataloged from PDF version of thesis.
Includes bibliographical references
Planarians can regenerate all tissues, including the central nervous system and the eyes. This process depends on a population of cells in the adult, the neoblasts, that includes pluripotent stem cells. Whether the neoblast population also includes progenitors specialized for forming specific lineages has not been demonstrated. This thesis describes the identification of progenitors that contribute to eyes during regeneration. Expression and functional analyses identified the genes eyes absent, six- 1/2 and ovo as critical for the formation of all cells of the eye. otxA and soxB were specifically required for photoreceptor regeneration, and sp6-9 and dlx were required for regeneration of the optic pigment cup. Expression analysis of these transcription factors in situ revealed that eye progenitors were distributed in mesenchymal trails extending posteriorly from the regenerating eye. These progenitors originate in the neoblasts, and promixity to the eye primordium correlates with increased differentiation. The spatial and genetic identification of a progenitor population in planarians elucidates migratory and morphogenetic mechanisms underlying organ regeneration in these animals. RNA sequencing of eye tissue also identified hundreds of genes with highly enriched expression in the eye, including numerous orthologs of eye pathology-related gene as well as likely components of key visual processes such as phototransduction and optic pigment cell function. The planarian brain is composed of dozens of cell types with regionalized distribution. The function of the planarian hedgehog gene in the patterning of CNS regions was investigated. hedgehog was expressed in the medial planarian brain, flanked by nkx2 and nkx6, then pax6b, and finally dlx-1 and msx at the most distal positions. This organization is similar to the expression domains of orthologous transcription factors in the vertebrate neural tube. However, in contrast to vertebrates, the expression of nkx2, nkx6, and pax6b in planarians was not affected by loss of hedgehog expression. RNA sequencing analysis identified a strong effect of Hedgehog signaling genes on a medially positioned cell with glia-like features. Therefore, Hedgehog signaling affects formation of at least one cell type in the planarian brain, but does not broadly regulate transcription factor expression domains and cell type identity.
by Sylvain William Lapan.
Ph. D.
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Barbanchon, Régis. "Réductions fines entre problèmes NP-complets : linéarité, planarité, parcimonie, et minimalité logique." Caen, 2003. http://www.theses.fr/2003CAEN2066.
Full textAbstract:
Nous étudions les problèmes combinatoires NP-complets autour de la Satisfaisabilité (SAT) : 3-Colorabilité (3COL), Hamiltonicité (HAM), etc. , et les réductions fines entre ces problèmes et leurs versions planaires. Nous cherchons à préserver la structure des solutions (parcimonie), la complexité des problèmes (linéarité), et la géométrie des instances (planarité). Nous exhibons une réduction quadratique et parcimonieuse de 3COL à PLAN-3COL et une réduction linéaire, planaire, et parcimonieuse de SAT à 3COL, unifiant et rafinant les preuves de NP-complétude et de \#P-complétude pour 3COL, PLAN-3COL, \#3COL et \#PLAN-3COL, et montrant la DP-complétude de UNIQUE-3COL et UNIQUE-PLAN-3COL. Nous établissons l'équivalence linéaire et parcimonieuse de PLAN-SAT et de PLAN-HAM, un lien peu probable entre SAT et HAM. Nous exhibons enfin une formule Existentielle Monadique du Second Ordre prouvée minimale et unique, définissant un problème NP-complet sur structures bijectives.
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Kravarik, Kellie M. (Kellie Marie). "Neoblast specialization during regeneration of the planarian S. mediterranea." Thesis, Massachusetts Institute of Technology, 2018. http://hdl.handle.net/1721.1/115681.
Full textAbstract:
Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2018.Cataloged from PDF version of thesis. "Due to the condition of the original material, there are unavoidable flaws in this reproduction. Table 3.1 is missing from page 167"-- Disclaimer Notice page.
Includes bibliographical references (pages 175-186).
Planarians are well known for their ability to regenerate an entire animal from small tissue fragments. Planarian regeneration requires a population of dividing cells called neoblasts that are distributed throughout the body. Historically, neoblasts have been considered a homogeneous population of stem cells capable of differentiating into all cell types. Most studies, however, analyze neoblasts at the population rather than the single cell level, making it difficult to determine how heterogeneous the neoblast population is. A bulk RNA sequencing approach with expression screening identified 33 new transcription factors transcribed in specific differentiated cells that were also expressed in small fractions of neoblasts during regeneration. Transcription factors of distinct differentiated tissues were expressed in different subsets of neoblasts, whereas transcription factors expressed in the same differentiated tissues were expressed in the same neoblasts. These results suggest roles for neoblast-expressed transcription factors in the specification of distinct tissues. Furthermore, the transcription factors klf, Pax3/7, and FoxA were required for the differentiation of cintillo-expressing sensory neurons, dopamine- beta-hydroxylase-expressing neurons, and the pharynx, respectively. The planarian nervous system is comprised of numerous different cell types, providing an opportunity to study how neoblasts acquire the diverse cell fates that comprise a particular tissue. We used single-cell sequencing to identify the transcriptomes of hundreds of planarian neurons and neoblasts. Using computational analysis of these data we identified the transcriptomes of several specific types of planarian neuronal cells, including cholinergic, dopaminergic, and serotonergic neurons, as well as glial cell types. In neoblasts, we identified a population of cells that expressed both markers of differentiated neurons and transcription factors expressed in various neural cell types, which we hypothesize to be neural specialized neoblasts. We found a number of unique populations of neural neoblasts that correspond with specific neural sub-types. Interestingly, however, these neural specialized neoblasts do not express a detectable unified gene regulatory network. These results are consistent with direct specification of neural sub-types in neoblasts and suggest that neoblasts do not differentiate down a highly hierarchical lineage path as has been described for many developmental lineages.
by Kellie M. Kravarik.
Ph. D.
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Abnave, Prasad. "Exploring mammalian immunity against intracellular bacteria through planarian flatworms." Thesis, Aix-Marseille, 2014. http://www.theses.fr/2014AIXM5049.
Full textAbstract:
Les interactions hôte-pathogène sont un jeu vaste et complexe entre agent pathogène et hôtepour la victoire de la bataille de la pathogenèse. Plusieurs organismes modèles sont étudiéspour illustrer les mécanismes impliqués dans ces interactions. Dans ma thèse, j'ai utilisé lesplanaires comme un organisme modèle pour explorer les interactions hôte-pathogène. Comme les différents organismes modèles peuvent mettre enévidence les différentes caractéristiques de l'immunité, j'ai décidé de tirer avantage del'absence de connaissances sur l'immunité des planaires en explorant l'inexplorée. Dans monprojet, j'ai infecté les planaires avec 16 bactéries pathogènes : les planaires y sont très résistantes. Pour en explorer lemécanisme j'ai effectué un profilage du transcriptome à partir deplanaires infectées, suivie par un criblage par ARN interférence des gènes up-régulés. J'aidécouvert les gènes qui régissent la résistance antibactérienne dans les planaires, et de façonintéressante, le criblage a permis de mettre en évidence un gène, MORN2, dont la fonctionimmunologique était complètement inconnue. L'induction et l'extinction de l'expression de MORN2dans les macrophages ont révélé que MORN2 contrôle l'internalisation, la réplication et letrafic des bactéries à l'intérieur de la cellule. Dans mon étude, j'ai démontré que MORN2 estun composant de la phagocytose associée à LC3 et qu'il peut surmonter le blocage de lafusion phagolysosomale imposée par les bactéries pathogènes. Ainsi ma thèse met en avantl'importance d'utiliser des organismes modèles inhabituels afin de dévoiler des mécanismesinexplorées et des molécules impliquées dans les interactions hôte-pathogèneHost-pathogen interaction is a vast and complex interplay between pathogen and hostto conquer the battle of pathogenesis. Several model organisms are being studied to illustratethe mechanisms involved in these interactions. In my thesis I have used planarians as a modelorganism to explore host-pathogen interactions. As different model organismscan highlight different features of immunity I decided to take advantage of lack of knowledgeabout planarian immunity and get benefits from exploring unexplored. In my project I haveinfected planarians with 16 pathogenic bacteria and I found that in contrary to othercommonly used model organisms such as Drosophila, C. elegans and zebrafish the planariansare highly resistant to bacterial infections. To explore the mechanism behind this resistance Iperformed infection induced transcriptome profiling followed by RNA interference screeningof up-regulated gens. I discovered genes governing antibacterial resistance in planarians andinterestingly the screening highlighted a gene MORN2 of which the immunological functionwas completely unknown. The human ortholog of MORN2 is then further assessed for itsantimicrobial function. Induced expression and down regulation of MORN2 in macrophagesrevealed that MORN2 controls uptake, replication and trafficking of bacteria inside the cell.In my study I demonstrated that MORN2 is a component of LC3-associated phagocytosis andit can overcome phagosome maturation blockage imposed by pathogenic bacteria. Thus mythesis propounds the importance of using unusual model organisms to unveil unexploredmechanisms and molecules involved in host-pathogen interactions
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Cote, Lauren E. (Lauren Esther). "The instructive roles of muscle cells in planarian regeneration." Thesis, Massachusetts Institute of Technology, 2019. https://hdl.handle.net/1721.1/122066.
Full textAbstract:
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2019
Cataloged from student-submitted PDF version of thesis. Vita.
Includes bibliographical references.
Regeneration requires both new cell production and patterning information to correctly place new tissue. Planarians are flatworms with remarkable capacity to regenerate after nearly any injury and to indefinitely maintain tissue homeostasis. Dividing cells, neoblasts, are the source of all new tissue, whereas positional information is hypothesized to be harbored by post-mitotic muscle, including the subepidermal body wall musculature. Single-muscle-cell mRNA sequencing along the anterior-posterior axis revealed regional gene expression within muscle cells. The resulting axial gene expression map included FGF receptor-like (FGFRL) homologs and genes encoding components of Wnt signaling. Two distinct FGFRL-Wnt circuits, involving juxtaposed anterior FGFRL and posterior Wnt expression domains, controlled head and trunk patterning.
Inhibition of FGFRL-Wnt circuit components led to the formation of ectopic posterior eyes or secondary pharynges, indicating their importance in maintaining the anterior-posterior axis. Inhibition of different myogenic transcription factors specifically ablated orthogonal subsets of the body wall musculature. Longitudinal fibers, oriented along the anterior-posterior axis, are required for regeneration initiation. Circular fibers maintained medial-lateral patterning during head regeneration. During early regeneration, transcriptional changes in muscle cells comprised part of a generic wound response displayed by all injuries, from incisions to decapitations. The sole exception to this generic response was the expression in body-wall muscle of the Wnt inhibitor notum, which occurs preferentially at anterior-facing wounds in longitudinal muscle fibers. Therefore, anterior-posterior polarity, the choice of head or tail regeneration, involves longitudinal body wall muscle fibers.
Planarian muscle were found to be highly secretory. Combining an in silico definition of the planarian matrisome and recent whole animal single-cell transcriptome data revealed that muscle is a major source of extracellular matrix (ECM). Inhibition of hemicentin-1 (hmcn-1), which encodes a highly conserved ECM glycoprotein expressed in body wall muscle, resulted in ectopic localization of internal cells, including neoblasts, outside of the muscle fiber layer. ECM secretion and maintenance of tissue separation indicated that muscle functions as planarian connective tissue. Whereas muscle is often viewed as a strictly contractile tissue, these findings reveal that planarian muscle has specific regulatory roles in axial patterning, wound signaling, and tissue architecture to enable correct regeneration.
by Lauren E. Cote.
Ph. D.
Ph.D. Massachusetts Institute of Technology, Department of Biology
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Baptista, Vanessa dos Anjos. "Estrutura e composição de comunidades de tricladidos terrestres (Platyhelminthes: Tricladida: Terricola) em áreas de floresta estacional decidual do sul do Brasil." Universidade do Vale do Rio do Sinos, 2007. http://www.repositorio.jesuita.org.br/handle/UNISINOS/2302.
Full textAbstract:
Made available in DSpace on 2015-03-05T16:19:36Z (GMT). No. of bitstreams: 0
Previous issue date: 30Bolsa para curso e programa de Pós Graduação
As planárias terrestres formam um grupo relativamente numeroso em espécies (cerca de 800 espécies) com distribuição mundial, principalmente pan-tropical. Muitas espécies de planárias terrestres são especialistas de hábitat e, em geral, apresentam capacidade de locomoção reduzida, havendo assim, muitas espécies endêmicas. Sua utilização em estudos de diversidade, visando determinar áreas prioritárias para conservação, é indicada por serem predadores de topo de cadeia alimentar no seu microhábitat. No Brasil, um grande número de espécies de planárias terrestres foi registrado em áreas originalmente cobertas por floresta ombrófila densa localizadas nos estados de Santa Catarina, São Paulo e Rio de Janeiro. Estudos recentes da composição e da estrutura de comunidades de Terricola, realizados no Rio Grande do Sul, têm se concentrado na região do Planalto das Araucárias, no nordeste do estado, em áreas de floresta ombrófila, registrando um elevado número de espécies de planárias terrestres em diferentes localidades
Land flatworms constitute a relatively species rich zoological group, being distributed world wide, but mainly pan-tropical. They show very strict habitat requirements and a reduced locomotion capacity, so that there are many endemic species. Their use as indicator-taxa in conservation and biodiversity studies is recomended because land planarians are top-predatores within their soil ecosystem. In Brazil, the diversity of land planarians is better known in areas that were originally covered by the southeastern dense ombrophilous forest, located in the states of São Paulo, Rio de Janeiro e Santa Catarina. Recent studies on the composition and structure of land planarian communities, mainly done in the region of the Planalto das Araucárias, located at the northeast of Rio Grande do Sul state, in areas of mixed and dense ombrophilous forest, have registered high species richness in various localities, many of the species being new taxa and/or endemic for each type of forest. The caducifolious forest is one of th
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Felix, Daniel André. "PBC and MEIS class genes in the planarian Schmidtea mediterranea." Thesis, University of Nottingham, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.575479.
Full textAbstract:
Planarians have outstanding regenerative capabilities which depend on the presence of a pool of somatic stem cells. In addition planarians keep perfect proportion of the body while degrowing during starvation. While the establishment and maintenance of the anteroposterior (AlP) axis has been shown to depend on Wnt and Hedgehog signalling, not much is known about the subsequent patterning events. PBC and MEIS class genes are evolutionary conserved TALE homeobox genes with important functions in patteming and cell differentiation. They are well known co-factors of the Hox genes however they also have other Hox-independent functions. The aim of this study was to identify the planarian orthologs of the PBC and MEIS class genes and to examine their putative role in anteroposterior patteming. Here one PBC class gene, Smed-pbx, and the three MEIS class genes Smed-meis I , Smed-meis2 and Smed-prep were identified and orthology established through phylogenetic analyses. Smed-prep was found to define the cephalic area in which the anterior structures are formed, most prominently the brain. In anterior regenerating Smed-prep(RNAi) worms a reduction or even complete absence of the brain and anterior markers was observed. Importantly, the differentiation of stem cells into nerve cells was shown not to be dependent on Smed-prep. In step with its function the Smed-prep gene was found to have an anteroposterior bias in expression, being highly expressed in the head. While both Smed-meis genes were found to be important for regeneration and maintenance of the eyes and for the adaptation of the body to the new size of the animal after amputation, Smed-pbx was found to have pleiotropic functions, phenocopying aspects of all three MEIS class genes upon RNAi interference, and also producing additional phenotypes. This study has found that the four planarian orthologs of PBC and MEIS class genes are important players in regeneration. Two genes, Smed-pbx and especially Smed-prep, have been found to be necessary for anteroposterior patterning. This is the first time that a homeobox transcription factor has been directly implicated in anteroposterior patterning in planarians.
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Fincher, Christopher T. (Christopher Terry). "Comprehensive single-cell transcriptional profiling of the regenerative planarian Schmidtea mediterranea." Thesis, Massachusetts Institute of Technology, 2020. https://hdl.handle.net/1721.1/129053.
Full textAbstract:
Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2020Cataloged from student-submitted PDF of thesis.
Includes bibliographical references.
Animals can contain hundreds of cell types, each of which has a distinct morphology and function. The transcriptome of a cell dictates this unique cell biology. Recent approaches for high throughput single-cell RNA sequencing have made it possible to generate transcriptomes easily and affordably for tens of thousands of single cells, raising the possibility that transcriptomes could be generated for all cell types and cell states in a complete animal. Planarians are freshwater flatworms renowned for their capacity for whole-body regeneration. They possess a complex body plan with multiple distinct tissues. They also possess a population of dividing cells, called neoblasts, which contain pluripotent stem cells and are the source of all new tissue, with all cell types being turned over throughout the life of the animal. Planarians also constitutively express an arrangement of regionally expressed genes in their muscle that serve as patterning information for the animal.
As such, at a single time point in the adult, pluripotent stem cells, all differentiated cells, and all associated transition states from stem cell to differentiated cell can be recovered, including patterning information expressed in muscle. This makes planarians ideally suited to generating an atlas of transcriptomes for all cell types and cell states in a whole animal. We used the single- cell RNA sequencing technology Drop-seq to determine the transcriptomes for 66,783 cells from adult planarians. In doing so, we identified a number of known and novel cell populations, including a novel class of phagocytic cells. We also uncovered novel neoblast subpopulations and putative transition state populations between neoblasts and differentiated cells, as well as a number of genes with regional expression in muscle.
Through the identification of known rare cell types in the data, we conclude that we have obtained near-to-complete cell type saturation for all cell types and cell states in the adult planarian. We now have full transcriptomes for each of these cell populations, which can be utilized to assay their roles in planarian biology. This approach can also be applied widely to diverse animal species, including those with limited molecular tools available.
by Christopher T. Fincher.
Ph. D.
Ph.D. Massachusetts Institute of Technology, Department of Biology
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Sheng, Wanhui. "AN EXTENSION OF PLANARIAN BEHAVIORAL MODEL: CANNABINOID PHYSICAL DEPENDENCE AND WITHDRAWAL." Master's thesis, Temple University Libraries, 2016. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/402376.
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Pharmaceutical SciencesM.S.
Background: Planarians have mammalian-like neurotransmitter systems and have been established as a novel in vivo model for neuropharmacology. In previous research, planarians exposed to the cannabinoid receptor (CB-R) agonist WIN 55,212-2 (10 μmol/L) for 1 h displayed a significant (p < 0.05) decrease in spontaneous locomotor velocity (pLMV) when subsequently tested in drug-free, but not in drug-containing, water. This demonstrated abstinence-induced withdrawal from a CB-R agonist as a manifestation of the development of physical dependence. Purpose: The purpose of the present study was to extend previous work and to further establish a cannabinoid behavioral model with planarians. Specifically, the goals included (i) confirm the work with WIN 55,212-2 and extend to a second agonist (ii) interfere with agonist-induced physical dependence using several CB-R antagonists, (ii) demonstrate antagonist-induced precipitated withdrawal behavior, and (iii) try to induce withdrawal behavior from CB-R agonists using UV light. Methods: Two CB agonists (WIN 55,212-2 and JWH251) and four CB antagonists (AM251, AM281, SLV319 and SR144528) were used. Planarians were placed individually in CB-R agonist or agonist + antagonist mixtures for 20 and 30 min of exposure (with or without UV radiation), and withdrawal was quantified by measuring pLMV in drug-free vs drug-containing water (with or without UV light irradiation). Results: (i) Four different CB1-R antagonists (AM251, AM281, SLV319 and SR144528) dose-relatedly blocked development of physical dependence induced by two different CB-R agonists (WIN 55,212-2 and JWH251). (ii) None of the same four antagonists (AM251, AM281, SLV319 and SR144528) precipitated withdrawal. (iii) Short wavelength (254 nm), but not long wavelength (366 nm), UV light attenuated abstinence-induced withdrawal from WIN 55,212-2, while short wavelength UV light induced moderate withdrawal behavior. Conclusions: The results confirm the use of a planarian model as a simple yet robust way to study development of physical dependence to cannabinoid agonists. The model is more rapid and sensitive than the usual rodent models. The effect of UV irradiation adds to the supposition that the results are receptor-related. The results also give rise to the surprising suggestion, within the limitations of the methodology, that development of cannabinoid physical dependence and antagonist-induced precipitated withdrawal might be separable phenomena in planarians.
Temple University--Theses
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Mangione, Federica. "The Dachsous/Fat/Four-jointed Signalling Coordinates the Uniform Orientation of Planar Cell Alignement in the Drosophila Abdominal Epithelium." Doctoral thesis, Universitat de Barcelona, 2016. http://hdl.handle.net/10803/402714.
Full textAbstract:
Within multicellular organism, mature tissues and organs reach high degrees of order in the arrangement of their constituent cells. During morphogenesis the emergence of long-range order is subjected to multiple and multilevel developmental constrains. Complex series of temporal and spatial instructions must be integrated to account for reproducible and stereotyped mature tissue arrangements. A remarkable example is given by mature epithelial monolayers were cells are ringed together in specific morphologies via cell-cell adhesion and show highly organized planar patterns. Cells in epithelial tissues acquire a precise planar geometry that is often, if not always, evenly aligned with the tissue axes.
Little is still known on the cellular mechanisms governing the axial orientation of cell arrangement and planar polarity.
The research presented in this Thesis addressed these issues through the analysis of the developing abdominal epithelium of Drosophila melanogaster.
We found that the abdominal epithelial cells reach their final arrangement within about 2 days of pupation. During this time, the abdominal epithelial tissue undergoes extensive morphogenesis by tissue expansion and cellular remodelling. During expansion, epithelial cells divide randomly relative to the tissue axis while migrating dorsally, while during remodelling cell adjust their final position within the plane of the epithelium while migrating anteriorly. When cell movements arrest, a stable arrangement of the cells within the plane of the segmental field is attained. At this time, epithelial cells are oriented and aligned among each other and throughout the tissues invariably in parallel to the A/P axis. We indicated as uniform orientation of planar cell alignment (PCA). We found that the axis orientation of PCA is evolving in a spatiotemporal precise manner along the A/P axis, and that this dynamic oriented behaviour was progressively modulated through expansion and remodelling. We found that the Dachsous/Fat/Four-jointed planar polarity pathway was specifically involved in the orientation of PCA. The steps followed to reach the axial orientation of PCA over developmental times correlates with the pattern of expression of the Dachsous/Fat/Four- jointed pathway. Such correlation was sustained by genetic interferences with the pathway components.
We found that both the dynamics of the axis orientation of PCA and the attainment of its uniformity along the A/P axis were disrupted rearrangements in dachsous, fat or four-jointed mutants. We further found that loss of the axial uniform orientation of PCA in these mutants is accompanied by an overall reduction in mutual cell alignment and in cell shape elongation. These effects were also sustained through local interference in the activity of the pathway through clonal analyses. Local changes in pathway components induce the mutant clones to minimize cell-cell contacts with surrounding wild-type cells, suggesting differential adhesive properties between dachsous, fat, four-jointed mutant cells and the rest of the tissue. Surprisingly, we found that this effect was also directional and that Dachsous has an instructive role in driving the axis orientation of PCA, possibly by regulating the Fat localization across the cells/tissue.
Therefore, from these findings, we propose that the Dachsous/Fat/Four-jointed pathway guide the orientation of PCA by favouring oriented cell-cell contact adhesiveness between abdominal epithelial cells. In particular, different adhesive properties imposed throughout the cell perimeter by Ds-Ft heterodimeric interaction at opposite edges of the cell might align epithelial cells changing and orienting their shape. Over time this biased interaction responding to the Dachsous gradient would be reinforced in response to the activity of Dachsous and Four-jointed onto Fat.En los organismos multicelulares, tejidos y órganos tienen una disposición altamente organizada de las células que los constituyen. En particular, los tejidos epiteliales están constituidos por células que se disponen de manera ordenada con respecto a los ejes del cuerpo aunque los mecanismos que gobiernan esta disposición ordenada son poco conocidos. En esta tesis nos hemos focalizado en el estudio de los mecanismos que guían la orientación del eje celular en el plano de un epitelio en crecimiento. El epitelio abdominal de Drosophila constituye un sistema modelo para estudiar in vivo las dinámicas celulares que ocurren a lo largo de la morfogénesis tisular. Nuestros resultados demuestran que las células del epitelio abdominal empiezan a orientarse progresivamente llegando a una disposición espacial altamente ordenada. En esta disposición las células demuestran una preferencia en alinearse con el eje anteroposterior del tejido dando lugar a una orientación uniforme del alineamiento celular. Por otro lado, hemos descubierto que la vía de señalización de Dachsous/Fat/Four-jointed está involucrada en guiar el eje de orientación celular con respecto a el eje anteroposterior. Nuestros datos indican que los patrones de expresión de los genes dachsous, fat y four-jointed juegan un papel clave para el correcto alineamiento celular con el eje anteroposterior. De hecho, mutaciones en estos genes alteran el alineamiento espacial y afectan la elongación celular. Además, alteraciones locales en la actividad de cada uno de estos genes indican que están involucrados en la modulación orientada de los contactos adhesivos entre células vecinas. En resumen, estos resultados sugieren que la vía de señalización de Dachsous/Fat/Four- jointed tiene un papel clave en el alcance de una orientación celular uniforme a lo largo del tejido abdominal y, posiblemente, en otros epitelios.
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Arseni, Varvara. "MicroRNAs and the canonical microRNA biogenesis pathway in the planarian Schmidtea mediterranea." Thesis, University of Nottingham, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.581999.
Full textAbstract:
miRNAs are an important class of small non-protein coding RNAs whose specific functions in animals are rapidly being elucidated. miRNAs regulate the expression of many animal genes by post-transcriptional gene silencing and play vital roles in stem cell maintenance, differentiation and apoptosis. In this study, planarians were used as a model system in order to study whether miRNAs have a regulatory role in their stem cell dynamics. Planarians are well known for their remarkable regenerative ability and their amazing capacity for constant re-patterning owing to a population of somatic pluripotent stem cells known as neoblasts. In particular, the aim of the study was to investigate the regulatory role miRNAs may have in planarian stem cell self renewal, proliferation and differentiation. Recently, the differential spatial patterns of expression of miRNAs in whole and regenerating planarians have been characterized by in situ hybridization to nascent miRNA transcripts. These miRNA expression patterns were the first to be determined for a Lophotrocozoan animal. The expression patterns of 42 miRNAs in adult planarians have been characterized, constituting a complete range of tissue specific expression patterns. The majority of planarian miRNAs were expressed either in areas where stem cells (neoblasts) are located and/or in the nervous system. Some miRNAs were definitively expressed in stem cells and dividing cells and moreover miRNAs were found to be expressed in germ stem cells of the sexual strain. Taken the facts that cellular proliferation and differentiation must be controlled during planarian regeneration and tissue homeostasis as well as that miRNAs have been implicated in the control stem cell functions in other organisms, aim of this study was to disrupt the canonical miRNA biosynthesis pathway. In that way, information about the global impact of miRNA regulation in planarian regeneration and tissue homeostasis would be gained.
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Guo, Longhua. "Establishing the foundations for genetic analysis in the sexual planarian Schmidtea mediterranea." Thesis, The University of Utah, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10159126.
Full textAbstract:
We propose to establish a free-living, fresh water flatworm species from the superphylum Lophotrochozoa, Schmidtea mediterranea, to be a genetic model system. S. mediterranea has been vigorously investigated as a powerful system to study adult stem cells and organ regeneration. Its sexual biotype has also been established as a system to understand the inductive mode of germ cell formation that is broadly shared by a lot of species including mammals. However, little is known about the sexual reproduction and genetics in this organism, which limited the availability of genetic approaches. As the sexual planarian is found scattered but with relative abundance in Sardinia, its natural history also presents us the opportunity to study inbreeding?s effect on genetic variability and species survival. Therefore, to study sexual reproduction and genetic inheritance in S. mediterranea will provide us unique opportunities to understand whole body regeneration, inductive germ cell formation, and inbreeding. In this dissertation, progresses in the establishment of the foundation for genetic analysis in S. mediterranea were presented. Though a simultaneous hermaphrodite, the anatomical and genotyping studies concluded that S. mediterranea cross-fertilize. One worm (line S2) was inbred for 10 generations by taking one progeny from each generation and crossing this individual to its regenerated clones. Whole genome sequencing of four different generations in this inbreeding pedigree revealed ~300Mb of the genome maintained their heterozygosity. Further sequencing analysis of the male and female gametes found these regions had low recombination rates, and maintained as two haplotypes (J-/V- haplotypes). Failure of gametes of the same haplotype to form progeny is unlikely due to embryonic lethality as the arrested embryos were significantly less than hatchlings. Additional analysis of two lines (D5D/D5I) with 90% of these regions homozygous as the J-haplotype suggested failure in fertilization between gametes of the same haplotype. Hence, we propose that haplotype incompatibility is the driving mechanisms to maintain genome heterozygosity in the planarian genome. Understanding of the genetic strategies in S. mediterranea will help the development of genetic approaches to study regeneration and germ cell specification. Our findings also suggest S. mediterranea can be a model system to study the evolution of sex and gamete incompatibility.
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González, Sastre Alejandro. "Regeneració i homeòstasi a les planàries: gens i vies de senyalització implicats en l'organogènesi." Doctoral thesis, Universitat de Barcelona, 2017. http://hdl.handle.net/10803/406131.
Full textAbstract:
En aquesta tesi, titulada “Regeneració i homeòstasi a les planàries: gens i vies de senyalització implicats en l'organogènesi”, s’aprofundeix en l’estudi dels processos responsables de l’organogènesi a la planària d’aigua dolça Schmidtea mediterranea, tant durant la regeneració com durant l’homeòstasi. La planària d’aigua dolça Schmidtea mediterranea presenta una extraordinària capacitat de regeneració, gràcies a la presència d’una elevada quantitat de cèl·lules mare, els neoblasts, que poden donar lloc a qualsevol tipus cel·lular de l’organisme. Gràcies a aquesta capacitat de regeneració, , les planàries són un molt bon model per estudiar l’organogènesi en els adults, que d’altra banda en general és difícil d’estudiar fora del desenvolupament embrionari.
Per estudiar l’organogènesi, s’ha treballat en la caracterització de diferents gens i vies de senyalització, que participen en la formació d'òrgans i estructures diferents:
- En primer lloc s’estudia la funció de la via BMP en la formació i manteniment dels ulls, mitjançant l'estudi dels fenotips resultants de la inhibició del lligand extracel·lular Smed-bmp i de l'inhibidor intracel·lular Smed-smad6/7-2. D’aquest estudi se’n deriva que, als ulls, SMED-SMAD6/7-2 modula la via BMP, que controla la formació i manteniment de la subpoblació anterior de les cèl·lules fotoreceptores de l'ull. Així, elevats nivells de la via bloquegen la formació de la subpoblació anterior de les cèl·lules fotoreceptores, mentre que la inhibició de la via en provoca el sobrecreixement.
- En segon lloc, es caracteritza la funció de Smed-meis-like durant la regeneració de la regió anterior, que es veu bloquejada per la inhibició d’aquest gen, ja que participa en la formació del pol anterior i el restabliment del patró de la regió anterior.
- En tercer lloc, s’estudia la funció dels gens de la família dels gata456, amb especial èmfasi en la formació i manteniment de l’intestí. De l’estudi se’n deriva que, per una banda, que Smed-gata456-1 és necessari per la regeneració i homeòstasi de l’intestí, ja que participa en la diferenciació de noves cèl·lules intestinals i en la supervivència de les cèl·lules ja diferenciades. Aquesta degradació es produeix sense que s’afecti la dinàmica de les cèl·lules mare, de manera que es posa en qüestió la possible funció de l’intestí com nínxol dels neoblasts. A més, la resta de teixits no es veu afectat per la inhibició de Smed-gata456-1, de manera que es pot establir que aquest gen participa exclusivament en la formació i manteniment de l’intestí. Per altra banda, Smed-gata456-2 participa en restabliment del patró mediolateral durant la regeneració anterior.En esta tesis se estudian los procesos responsables de la organogénesis en la planaria de agua dulce Schmidtea mediterranea, durante la regeneración y la homeostasis. Para estudiar la organogénesis, se han caracterizado diferentes genes y vías de señalización, que participan en la formación de diferentes órganos y estructuras: - En primer lugar se estudia la función de la vía BMP en la formación y el mantenimiento de los ojos, mediante el estudio de los fenotipos resultantes de la inhibición del ligando extracelular Smed-bmp i del inhibidor intracelular Smed-smad6/7-2. Del estudio se concluye que SMED-SMAD6/7-2 modula la vía BMP, que controla la formación i el mantenimiento de la subpoblación anterior de las células fotoreceptoras de los ojos. - En segundo lugar, se caracteriza la función de Smed-meis-like durante la regeneración de la región anterior. - En tercer lugar, se estudia la función de los genes de la familia de los gata456, Smed-gata456-1 y Smed-gata456-2. Smed-gata456-1 es necesario para la regeneración y la homeostasis del intestino, ya que participa en la diferenciación de nuevas células intestinales y en la supervivencia de las ya diferenciadasSmed-gata456-2 participa en la formación del patrón mediolateral durante la regeneración anterior.
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Jipoulou, José Horacio Grau. "Relações filogenéticas entre os gêneros de Geoplaninae (Platyhelminthes, Tricladida) inferidas de caracteres morfológicos." Universidade de São Paulo, 2010. http://www.teses.usp.br/teses/disponiveis/41/41133/tde-12052010-103936/.
Full textAbstract:
Este trabalho consiste em uma caracterização morfológica das espécies-tipo da maioria dos gêneros que compõem a subfamília Geoplaninae, e quatro espécies destinadas a servir como grupos externos (Pelmatoplanini, Anzoplanini, Caenoplanini, Bipaliinae). A estudo morfológico das espécies resultou em 69 caracteres morfológicos que foram inseridos em uma matriz de dados e preparados para análise filogenética. Quinze espécies adicionais de outros gêneros de Geoplaninae também foram incluídos na análise. Os resultados corroboram o monofiletismo da subfamília Geoplaninae. De acordo com a hipótese de Meixner, o clado formado pelos gêneros Enterosyringa e Xerapoa, que compartilha características morfológicas com espécies do grupo externo, é o grupo de irmãos de todas as demais espécies de Geoplaninae. Descobrimos que as características anatômicas do aparelho copulador, como a presença e o tipo de papila peniana mostraram possuir muitas reversões e não se mostraram filogeneticamente informativas. Caracteres do sistema muscular podem ser usados de forma mais efetiva para a definição de grupos taxonômicos dentro do Geoplaninae e como indicadores de suas relações evolutivas. Nenhum dos aspectos diagnóstico atuais de da Geoplaninae correspondeu a caracteres autopomórficos em nossa análise. Nossos resultados sugerem que vários gêneros de Geoplaninae representam grupos não naturais, i.e., Geoplana e Notogynaphallia, com alguns caracteres diagnósticos sendo homoplásicos.This work consists of a morphological characterization of the type species of most of the genera that compose Geoplaninae, and four species intended to serve as outgroups (Pelmatoplanini, Anzoplanini, Caenoplanini, Bipaliinae). The morphological study of the species resulted in 69 morphological characters that were entered into a data matrix and prepared for phylogenetic analysis. Fifteen additional species from other Geoplaninae genera were also included in the analysis. The results corroborate the monophyletic status of the subfamily Geoplaninae. According with Meixner\'s hypothesis, the clade formed by Enterosyringa and Xerapoa species, sharing morphological characteristics with outgroup species, is the sister group of all other Geoplaninae species. We found that anatomical features of the copulatory apparatus, such as the presence and type of penis papilla showed many reversions and were not phylogenetically informative. Characters of the muscular system can be used much better for defining taxonomic groups within the Geoplaninae and as indicators of their evolutionary relationships. None of the present diagnostic features of the Geoplaninae formed autapomorphic characters in our analysis. Our results suggest that several genera of Geoplaninae represent unnatural groups, viz., Geoplana and Notogynaphallia, with some diagnostic characters being homoplasic.