Host Cell Wall Damage During Pathogen Infection: Mechanisms of Perception and Role in Plant-Pathogen Interactions
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A Hybrid Computational Model for Collective Cell Durotaxis
Biomechanics and Modeling in Mechanobiology https://doi.org/10.1007/s10237-018-1010-2 ORIGINAL PAPER A hybrid computational model for collective cell durotaxis Jorge Escribano1 · Raimon Sunyer2,5 · María Teresa Sánchez3 · Xavier Trepat2,4,5,6 · Pere Roca-Cusachs2,4 · José Manuel García-Aznar1 Received: 13 September 2017 / Accepted: 17 February 2018 © Springer-Verlag GmbH Germany, part of Springer Nature 2018 Abstract Collective cell migration is regulated by a complex set of mechanical interactions and cellular mechanisms. Collective migration emerges from mechanisms occurring at single cell level, involving processes like contraction, polymerization and depolymerization, of cell–cell interactions and of cell–substrate adhesion. Here, we present a computational framework which simulates the dynamics of this emergent behavior conditioned by substrates with stiffness gradients. The computational model reproduces the cell’s ability to move toward the stiffer part of the substrate, process known as durotaxis. It combines the continuous formulation of truss elements and a particle-based approach to simulate the dynamics of cell–matrix adhesions and cell–cell interactions. Using this hybrid approach, researchers can quickly create a quantitative model to understand the regulatory role of different mechanical conditions on the dynamics of collective cell migration. Our model shows that durotaxis occurs due to the ability of cells to deform the substrate more in the part of lower stiffness than in the stiffer part. This effect explains why cell collective movement is more effective than single cell movement in stiffness gradient conditions. In addition, we numerically evaluate how gradient stiffness properties, cell monolayer size and force transmission between cells and extracellular matrix are crucial in regulating durotaxis. -
Mathematical Modelling and Analysis of Aspects of Planktonic Bacterial Motility
Mathematical modelling and analysis of aspects of planktonic bacterial motility Gabriel Aaron Rosser St Anne's College University of Oxford A thesis submitted for the degree of Doctor of Philosophy Michaelmas 2012 Contents 1 The biology of bacterial motility and taxis 8 1.1 Bacterial motility and taxis . .8 1.2 Experimental methods used to probe bacterial motility . 14 1.3 Tracking . 20 1.4 Conclusion and outlook . 21 2 Mathematical methods and models of bacterial motility and taxis 23 2.1 Modelling bacterial motility and taxis: a multiscale problem . 24 2.2 The velocity jump process . 34 2.3 Spatial moments of the general velocity jump process . 46 2.4 Circular statistics . 49 2.5 Stochastic simulation algorithm . 52 2.6 Conclusion and outlook . 54 3 Analysis methods for inferring stopping phases in tracking data 55 3.1 Analysis methods . 58 3.2 Simulation study comparison of the analysis methods . 76 3.3 Results . 80 3.4 Discussion and conclusions . 86 4 Analysis of experimental data 92 4.1 Methods . 92 i 4.2 Results . 109 4.3 Discussion and conclusions . 124 5 The effect of sampling frequency 132 5.1 Background and methods . 133 5.2 Stationary distributions . 136 5.3 Simulation study of dynamic distributions . 140 5.4 Analytic study of dynamic distributions . 149 5.5 Discussion and conclusions . 159 6 Modelling the effect of Brownian buffeting on motile bacteria 162 6.1 Background . 163 6.2 Mathematical methods . 166 6.3 A model of rotational diffusion in bacterial motility . 173 6.4 Results . 183 6.5 Discussion and conclusion . -
Thermotaxis Is a Robust Mechanism for Thermoregulation in Caenorhabditis Elegans Nematodes
12546 • The Journal of Neuroscience, November 19, 2008 • 28(47):12546–12557 Behavioral/Systems/Cognitive Thermotaxis is a Robust Mechanism for Thermoregulation in Caenorhabditis elegans Nematodes Daniel Ramot,1* Bronwyn L. MacInnis,2* Hau-Chen Lee,2 and Miriam B. Goodman1,2 1Program in Neuroscience and 2Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305 Many biochemical networks are robust to variations in network or stimulus parameters. Although robustness is considered an important design principle of such networks, it is not known whether this principle also applies to higher-level biological processes such as animal behavior. In thermal gradients, Caenorhabditis elegans uses thermotaxis to bias its movement along the direction of the gradient. Here we develop a detailed, quantitative map of C. elegans thermotaxis and use these data to derive a computational model of thermotaxis in the soil, a natural environment of C. elegans. This computational analysis indicates that thermotaxis enables animals to avoid temperatures at which they cannot reproduce, to limit excursions from their adapted temperature, and to remain relatively close to the surface of the soil, where oxygen is abundant. Furthermore, our analysis reveals that this mechanism is robust to large variations in the parameters governing both worm locomotion and temperature fluctuations in the soil. We suggest that, similar to biochemical networks, animals evolve behavioral strategies that are robust, rather than strategies that rely on fine tuning of specific behavioral parameters. Key words: behavior; C. elegans; temperature; neuroethology; computational models; robustness Introduction model to investigate the ability of thermotaxis to regulate Tb and its robustness to genetic and environmental perturbation. -
Cell Wall Chemistry Roger M
3 Cell Wall Chemistry Roger M. Rowell1,3, Roger Pettersen1, James S. Han1, Jeffrey S. Rowell2, and Mandla A. Tshabalala 1USDA, Forest Service, Forest Products Laboratory, Madison, WI 2Department of Forest Ecology and Management, University of Wisconsin, Madison, WI 3Department of Biological Systems Engineering, University of Wisconsin, Madison, WI CONTENTS 3.1 Carbohydrate Polymers ..........................................................................................................37 3.1.1 Holocellulose ..............................................................................................................37 3.1.2 Cellulose .....................................................................................................................37 3.1.3 Hemicelluloses............................................................................................................39 3.1.3.1 Hardwood Hemicelluloses ..........................................................................41 3.1.3.2 Softwood Hemicelluloses............................................................................42 3.1.4 Other Minor Polysaccharides .....................................................................................43 3.2 Lignin......................................................................................................................................43 3.3 Extractives ..............................................................................................................................45 3.4 Bark.........................................................................................................................................46 -
The Origin of Alternation of Generations in Land Plants
Theoriginof alternation of generations inlandplants: afocuson matrotrophy andhexose transport Linda K.E.Graham and LeeW .Wilcox Department of Botany,University of Wisconsin, 430Lincoln Drive, Madison,WI 53706, USA (lkgraham@facsta¡.wisc .edu ) Alifehistory involving alternation of two developmentally associated, multicellular generations (sporophyteand gametophyte) is anautapomorphy of embryophytes (bryophytes + vascularplants) . Microfossil dataindicate that Mid ^Late Ordovicianland plants possessed such alifecycle, and that the originof alternationof generationspreceded this date.Molecular phylogenetic data unambiguously relate charophyceangreen algae to the ancestryof monophyletic embryophytes, and identify bryophytes as early-divergentland plants. Comparison of reproduction in charophyceans and bryophytes suggests that the followingstages occurredduring evolutionary origin of embryophytic alternation of generations: (i) originof oogamy;(ii) retention ofeggsand zygotes on the parentalthallus; (iii) originof matrotrophy (regulatedtransfer ofnutritional and morphogenetic solutes fromparental cells tothe nextgeneration); (iv)origin of a multicellularsporophyte generation ;and(v) origin of non-£ agellate, walled spores. Oogamy,egg/zygoteretention andmatrotrophy characterize at least some moderncharophyceans, and arepostulated to represent pre-adaptativefeatures inherited byembryophytes from ancestral charophyceans.Matrotrophy is hypothesizedto have preceded originof the multicellularsporophytes of plants,and to represent acritical innovation.Molecular -
Cell Wall Ribosomes Nucleus Chloroplast Cytoplasm
Cell Wall Ribosomes Nucleus Nickname: Protector Nickname: Protein Maker Nickname: Brain The cell wall is the outer covering of a Plant cell. It is Ribosomes read the recipe from the The nucleus is the largest organelle in a cell. The a strong and stiff and made of DNA and use this recipe to make nucleus directs all activity in the cell. It also controls cellulose. It supports and protects the plant cell by proteins. The nucleus tells the the growth and reproduction of the cell. holding it upright. It ribosomes which proteins to make. In humans, the nucleus contains 46 chromosomes allows water, oxygen and carbon dioxide to pass in out They are found in both plant and which are the instructions for all the activities in your of plant cell. animal cells. In a cell they can be found cell and body. floating around in the cytoplasm or attached to the endoplasmic reticulum. Chloroplast Cytoplasm Endoplasmic Reticulum Nickname: Oven Nickname: Gel Nickname: Highway Chloroplasts are oval structures that that contain a green Cytoplasm is the gel like fluid inside a The endoplasmic reticulum (ER) is the transportation pigment called chlorophyll. This allows plants to make cell. The organelles are floating around in center for the cell. The ER is like the conveyor belt, you their own food through the process of photosynthesis. this fluid. would see at a supermarket, except instead of moving your groceries it moves proteins from one part of the cell Chloroplasts are necessary for photosynthesis, the food to another. The Endoplasmic Reticulum looks like a making process, to occur. -
The Structure, Function, and Biosynthesis of Plant Cell Wall Pectic Polysaccharides
Carbohydrate Research 344 (2009) 1879–1900 Contents lists available at ScienceDirect Carbohydrate Research journal homepage: www.elsevier.com/locate/carres The structure, function, and biosynthesis of plant cell wall pectic polysaccharides Kerry Hosmer Caffall a, Debra Mohnen a,b,* a University of Georgia, Department of Biochemistry and Molecular Biology and Complex Carbohydrate Research Center, 315 Riverbend Road Athens, GA 30602, United States b DOE BioEnergy Science Center (BESC), 315 Riverbend Road Athens, GA 30602, United States article info abstract Article history: Plant cell walls consist of carbohydrate, protein, and aromatic compounds and are essential to the proper Received 18 November 2008 growth and development of plants. The carbohydrate components make up 90% of the primary wall, Received in revised form 4 May 2009 and are critical to wall function. There is a diversity of polysaccharides that make up the wall and that Accepted 6 May 2009 are classified as one of three types: cellulose, hemicellulose, or pectin. The pectins, which are most abun- Available online 2 June 2009 dant in the plant primary cell walls and the middle lamellae, are a class of molecules defined by the pres- ence of galacturonic acid. The pectic polysaccharides include the galacturonans (homogalacturonan, Keywords: substituted galacturonans, and RG-II) and rhamnogalacturonan-I. Galacturonans have a backbone that Cell wall polysaccharides consists of -1,4-linked galacturonic acid. The identification of glycosyltransferases involved in pectin Galacturonan a Glycosyltransferases synthesis is essential to the study of cell wall function in plant growth and development and for maxi- Homogalacturonan mizing the value and use of plant polysaccharides in industry and human health. -
The Behavior of Fishes by Antonios Pappantoniou
The Behavior of Fishes by Antonios Pappantoniou I. A GENERAL OVERVIEW OF FISH BEHAVIOR This article is the first in a series of articles on the behavior of North American freshwater fishes. Althou~h this first ~rticle will not stress any species in particular, each !~ture article will focus on the behavior of a single species or group of closely related fishes. It is the intent of the articles to supply the readers with a knowledge of fish behavior so that they may better understand and enjoy their aquarium fishes. The articles will draw on information from the scien tific literat~re and the authors' own observations. The behavior of fishes is very much dictated by their environment. Two factors, temperature and light, are probably the most critical environmental factors control ling fish behavior. Fish are classed as ectothermic animals. Ectothermic means they must rely on outside sources of he~r. to maintain their body temperature. Temperature governs biochemical and physiological activities which in turn control fish behavior. The preferred te~perature of fish varies with the species. Fish species adapted to swift-flowing streams prefer cooler temperatures than those species adapted to life in a small pond. Temperatures may fluctuate on a daily or seasonal basis. Daily fluctuations, especially in the s~~er months, can cause onshore - offshore movements in species of lake fish. Seasonal changes in temperature are partly responsible for initiati~g physiological changes which lead to reproductive activity in fish. Light is the other critical environmental factor controlling fish behavior. 1 fish may be diurnal. Such a fish would be active during the day. -
IAWA Bulletin N.S., Vol. 3 (1),1982 3 ANTONI V an LEEUWENHOEK
IAWA Bulletin n.s., Vol. 3 (1),1982 3 ANTONI VAN LEEUWENHOEK AND HIS OBSERVATION ON THE STRUCTURE OF THE WOODY CELL WALL by Pieter Baas Rijksherbarium, Leiden, The Netherlands Summary Following general remarks on the life of Van be traced back to negative but ill-informed Leeuwenhoek and his role in wood anatomy, judgements in some authoritative 19th and his account of the structure of a torn vessel 20th century publications (Baas, 1982a, b). wall of nutmeg rootwood is discussed in detail. Van Leeuwenhoek should be credited with The cross-wise orientation of minute 'vessels or many detailed and original wood and bark ana fibres' as observed and interpreted by Van tomical observations, but his work is not easily Leeuwenhoek can be considered to be the first accessible, being scattered in numerous letters, (unintentional) correct record of the fibrillar most of them also dealing with other microsco nature of the woody cell wall. pic subjects. Although most of these letters were published in various instalments and sev Introduction eral languages during Van Leeuwenhoek's life Antoni van Leeuwenhoek was born in 1632, time, this presentation cannot compete with 350 years ago, in Delft (the Netherlands) as the the balanced treatises by Grew and Malpighi, son of a basket maker. Apprenticed to a cloth who each published books solely dealing with merchant, Van Leeuwenhoek's career started as plant structure and function. a shopkeeper. Later he would serve as usher to Interest in Van Leeuwenhoek's plant anato the aldermen, chief warden and wine-gauger of mical work has recently also been revived by the City of Delft, and surveyor to the Court of the rediscovery of some of his sections among Holland. -
Primary and Secondary Plant Cell Walls: a Comparative Overview*
36 New Zealand Journal of Forestry Science 36(1) PRIMARY AND SECONDARY PLANT CELL WALLS: A COMPARATIVE OVERVIEW* PHILIP J. HARRIS School of Biological Sciences, The University of Auckland Private Bag 92019, Auckland, New Zealand [email protected] (Received for publication 23 November 2005; revision 3 February 2006) ABSTRACT Light and transmission electron microscopy are used in studying wall morphology and histochemical methods, including immunocytochemistry, can be used to locate specific compounds in walls. All plant cell walls contain a fibrillar phase of cellulose microfibrils and a matrix phase which contains a high proportion of non-cellulosic polysaccharides that vary in their chemical structures, depending on wall type and plant taxon. The non-cellulosic polysaccharide compositions of three common wall types — lignified secondary walls, non-lignified secondary walls, and non-lignified primary walls — exemplify this. The principles used in constructing the most recent models of non-lignified primary walls can be used in modelling lignified secondary walls. Keywords: primary cell walls; secondary cell walls; cell-wall models; non- cellulosic polysaccharides; transmission electron microscopy; light microscopy; chemistry; lignified walls; immuno- cytochemistry; histochemistry INTRODUCTION This review provides a brief comparative overview of primary and secondary cell walls of seed plants. A primary wall is defined as a wall that is deposited while the cell is still enlarging, whereas a secondary wall is deposited on the primary wall after cell expansion has stopped, and can be seen in sections as a structurally distinct layer (or layers) that is often very much thicker than the primary wall (Harris 2005a). At maturity, the different cell types can be grouped according to whether they have only a primary wall or both a primary and a secondary wall. -
Cell Structure and Function in the Bacteria and Archaea
4 Chapter Preview and Key Concepts 4.1 1.1 DiversityThe Beginnings among theof Microbiology Bacteria and Archaea 1.1. •The BacteriaThe are discovery classified of microorganismsinto several Cell Structure wasmajor dependent phyla. on observations made with 2. theThe microscope Archaea are currently classified into two 2. •major phyla.The emergence of experimental 4.2 Cellscience Shapes provided and Arrangements a means to test long held and Function beliefs and resolve controversies 3. Many bacterial cells have a rod, spherical, or 3. MicroInquiryspiral shape and1: Experimentation are organized into and a specific Scientificellular c arrangement. Inquiry in the Bacteria 4.31.2 AnMicroorganisms Overview to Bacterialand Disease and Transmission Archaeal 4.Cell • StructureEarly epidemiology studies suggested how diseases could be spread and 4. Bacterial and archaeal cells are organized at be controlled the cellular and molecular levels. 5. • Resistance to a disease can come and Archaea 4.4 External Cell Structures from exposure to and recovery from a mild 5.form Pili allowof (or cells a very to attach similar) to surfacesdisease or other cells. 1.3 The Classical Golden Age of Microbiology 6. Flagella provide motility. Our planet has always been in the “Age of Bacteria,” ever since the first 6. (1854-1914) 7. A glycocalyx protects against desiccation, fossils—bacteria of course—were entombed in rocks more than 3 billion 7. • The germ theory was based on the attaches cells to surfaces, and helps observations that different microorganisms years ago. On any possible, reasonable criterion, bacteria are—and always pathogens evade the immune system. have been—the dominant forms of life on Earth. -
Chapter 51 Animal Behavior
Chapter 51 Animal Behavior Lecture Outline Overview: Shall We Dance? • Red-crowned cranes (Grus japonensis) gather in groups to dance, prance, stretch, bow, and leap. They grab bits of plants, sticks, and feathers with their bills and toss them into the air. • How does a crane decide that it is time to dance? In fact, why does it dance at all? • Animal behavior is based on physiological systems and processes. • An individual behavior is an action carried out by the muscular or hormonal system under the control of the nervous system in response to a stimulus. • Behavior contributes to homeostasis; an animal must acquire nutrients for digestion and find a partner for sexual reproduction. • All of animal physiology contributes to behavior, while animal behavior influences all of physiology. • Being essential for survival and reproduction, animal behavior is subject to substantial selective pressure during evolution. • Behavioral selection also acts on anatomy because body form and appearance contribute directly to the recognition and communication that underlie many behaviors. Concept 51.1: A discrete sensory input is the stimulus for a wide range of animal behaviors. • An animal’s behavior is the sum of its responses to external and internal stimuli. Classical ethology presaged an evolutionary approach to behavioral biology. • In the mid-20th century, pioneering behavioral biologists developed the discipline of ethology, the scientific study of how animals behave in their natural environments. • Niko Tinbergen, of the Netherlands, suggested four questions that must be answered to fully understand any behavior. 1. What stimulus elicits the behavior, and what physiological mechanisms mediate the response? 2.