DOCSLIB.ORG

Comparative Genomics of Microbial Chemoreceptor Sequence, Structure, and Function

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Comparative Genomics of Microbial Chemoreceptor Sequence, Structure, and Function University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 12-2014 Comparative Genomics of Microbial Chemoreceptor Sequence, Structure, and Function Aaron Daniel Fleetwood University of Tennessee - Knoxville, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Part of the Bacteriology Commons, Biochemistry Commons, Bioinformatics Commons, Computational Biology Commons, Environmental Microbiology and Microbial Ecology Commons, Genomics Commons, Microbial Physiology Commons, Molecular Biology Commons, Organismal Biological Physiology Commons, Other Biochemistry, Biophysics, and Structural Biology Commons, Pathogenic Microbiology Commons, Structural Biology Commons, and the Systems Biology Commons Recommended Citation Fleetwood, Aaron Daniel, "Comparative Genomics of Microbial Chemoreceptor Sequence, Structure, and Function. " PhD diss., University of Tennessee, 2014. https://trace.tennessee.edu/utk_graddiss/3125 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Aaron Daniel Fleetwood entitled "Comparative Genomics of Microbial Chemoreceptor Sequence, Structure, and Function." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Life Sciences. Igor B. Jouline, Major Professor We have read this dissertation and recommend its acceptance: Robert Hettich, Elias Fernandez, Elizabeth Howell Accepted for the Council: Carolyn R. Hodges Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Comparative Genomics of Microbial Chemoreceptor Sequence, Structure, and Function A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Aaron Daniel Fleetwood December 2014 Copyright © by Aaron Daniel Fleetwood All rights reserved. ii Dedication To my Wife, Dr. Ellen Ann Fleetwood To my Family, Dan, Betsy, Zach, and Nathan To The Messengers, Mark, Theresa, and Paul And To Friends Cougar, Ketra, Nash, Ginger, and Piece iii Acknowledgments I would like to express sincere and profound appreciation to my mentor, Dr. Igor B. Zhulin, who has been an unwavering source of support and guidance in addition to expanding and sharpening my scientific worldview. I would also like to thank the Genome Science and Technology Program for taking a chance on what on paper might have appeared to be an economist and linguist, not a biologist. In particular, Dr. Albrecht von Arnim has been a tremendous resource and advisor over the years. I am ever grateful to my committee members, Dr. Robert Hettich, Dr. Elias Fernandez, and Dr. Elizabeth Howell. They, along with Dr. Zhulin, are responsible for fostering and nurturing my passion for genome and protein science, as well as shaping my scientific philosophy at every stage and level of my graduate experience. Additionally, many outstanding faculty, including Dr. Jerome Baudry and Dr. Tim Sparer, were instrumental in both my academic education and my growth as a scientist and professional. Thank you also to my lab mates Amit Uphadyay, Ogun Adebali, Dr. Kirill Borziak, and Dr. Davi Ortega for wonderful meetings, discussions, and camaraderie. I also owe a debt of gratitude to past members of the Zhulin Lab whose past and current work have served as a foundation and inspiration for my research (Drs. Kristen Wuichet, Luke Ulrich, Roger Alexander, and Brian Cantwell). Finally, thank you to our experimental collaborators and advisors (Drs. Brian Crane, Victoria Korolik, Caroline Harwood, and Harry Mobley) for bringing our ideas to vivo. I would not be here today without tremendous support and funding from the Genome Science and Technology Program, the J. Wallace and Katie Dean Multi-Year Graduate Fellowship, the UTK Graduate School, the Microbiology Department, Oak Ridge National Laboratory and the National Institutes of Health. iv Abstract Microbial chemotaxis receptors (chemoreceptors) are complex proteins that sense the external environment and signal for flagella-mediated motility, serving as the GPS of the cell. In order to sense a myriad of physicochemical signals and adapt to diverse environmental niches, sensory regions of chemoreceptors are frenetically duplicated, mutated, or lost. Conversely, the chemoreceptor signaling region is a highly conserved protein domain. Extreme conservation of this domain is necessary because it determines very specific helical secondary, tertiary, and quaternary structures of the protein while simultaneously choreographing a network of interactions with the adaptor protein CheW and the histidine kinase CheA. This dichotomous nature has split the chemoreceptor community into two major camps, studying either an organism’s sensory capabilities and physiology or the molecular signal transduction mechanism. Fortunately, the current vast wealth of sequencing data has enabled comparative study of chemoreceptors. Comparative genomics can serve as a bridge between these communities, connecting sequence, structure, and function through comprehensive studies on scales ranging from minute and molecular to global and ecological. Herein are four works in which comparative genomics illuminates unanswered questions across the broad chemoreceptor landscape. First, we used evolutionary histories to refine chemoreceptor interactions in Thermotoga maritima, pairing phylogenetics with x-ray crystallography. Next, we uncovered the origin of a unique chemoreceptor, isolated only from hypervirulent strains of Campylobacter jejuni, by comparing chemoreceptor signaling and sensory regions from Campylobacter and Helicobacter. We then selected the opportunistic human pathogen Pseudomonas aeruginosa to address the question of assigning multiple chemoreceptors to multiple chemotaxis pathways within the same organism. We assigned all P. aeruginosa receptors to pathways using a novel in silico approach by incorporating sequence information spanning the entire taxonomic order Pseudomonadales and beyond. Finally, we surveyed the chemotaxis systems of all environmental, commensal, v laboratory, and pathogenic strains of the ubiquitous Escherichia coli, where we discovered an ancestral chemoreceptor gene loss event that may have predisposed a well-studied subpopulation to adopt extra-intestinal pathogenic lifestyles. Overall, comparative genomics is a cutting edge method for comprehensive chemoreceptor study that is poised to promote synergy within and expand the significance of the chemoreceptor field. vi Preface In the following dissertation, comparative genomics methods were used to study microbial chemoreceptor sequences, structures, and functions. Microbial in this case refers primarily to Bacteria, though chemoreceptors are found in Archaea as well (hence the broader term in the title). The first chapter will be an introduction, in which I provide a brief overview of the motivations behind this work before diving into the scientific discipline (computational biology), methods (comparative genomics), and tools (bioinformatics) that are utilized throughout. This section covers aspects ranging from the basic (core tenets of biology) to the technical (pitfalls and nuances of comparative work). I will then introduce the field of chemotaxis with a special emphasis on chemoreceptors. This introductory “review” will be further subdivided into two major sections corresponding to the two major communities that study chemoreceptors: structure-focused signal transduction work and microbiology-based behavioral/physiological studies. The motivations of these two fields are quite different, with the former pursuing more fundamental and mechanistic understanding and the latter seeking applied connections, such as links to pathogenicity. After the introductory chapter, the main body of the dissertation is divided into four additional chapters which correspond to full peer-reviewed publications, manuscripts submitted for review, or featured aspects of manuscripts in preparation, all of which have been produced during my graduate work. Biology today (especially computational work) is a collaborative and highly interdisciplinary endeavor, so for each chapter I provide the contributions of myself and the other authors, as well as contributions outside of authorship but still deserving of mention. Each chapter will consist of an abstract, introduction, results, and discussion section, and any materials and methods specific to that paper or published in the manuscript will accompany these chapters as well. Chapter 3 (Assigning Chemoreceptors to Pathways in Pseudomonas aeruginosa) represents my most significant independent effort as a graduate student. Beginning vii with the first chapter, the studies increase in organizational complexity from studying a handful of proteins in a limited set of organisms to comparing entire sets of chemotaxis systems across broad taxonomic divisions. This serves to illustrate the power of comparative genomics to adapt to the scale of the biological problem, and for proteins like chemoreceptors,
Load more

Recommended publications
  • Decoupling Hamp from Tm2 in the Eschericha Coli
    DECOUPLING HAMP FROM TM2 IN THE ESCHERICHA COLI ASPARTATE CHEMORECEPTOR A Senior Scholars Thesis by RACHEL LEANN CROWDER Submitted to the Office of Undergraduate Research Texas A&M University in partial fulfillment of the requirements for the designation as UNDERGRADUATE RESEARCH SCHOLAR April 2009 Major: Biology DECOUPLING HAMP FROM TM2 IN THE ESCHERICHA COLI ASPARTATE CHEMORECEPTOR A Senior Scholars Thesis by RACHEL LEANN CROWDER Submitted to the Office of Undergraduate Research Texas A&M University in partial fulfillment of the requirements for the designation as UNDERGRADUATE RESEARCH SCHOLAR Approved by: Research Advisor: Michael D. Manson Associate Dean for Undergraduate Research: Robert C. Webb April 2009 Major: Biology iii ABSTRACT Decoupling HAMP from TM2 in the Escherichia coli Aspartate Chemoreceptor. (April 2009) Rachel Leann Crowder Department of Biology Texas A&M University Research Advisor: Dr. Michael D. Manson Department of Biology The HAMP (often found in Histidine kinases, Adenylate cyclases, Methyl-accepting chemotaxis proteins, and Phosphatases) domain is a widely conserved motif often found in transmembrane signaling proteins in many prokaryotes and lower eukaryotes. It consists of a pair of two amphipathic helices connected by a flexible linker. Recently, the solution structure of the Archeoglobus fulgidis Af1503 HAMP domain was isolated and resolved using NMR. The Af1503 HAMP domain forms a stable four helix bundle with parallel helices that pack into a non-canonical knob-on-knob conformation. Several models have been proposed in methyl-accepting chemotaxis proteins (MCPs) to explain how the four-helix bundle transmits the downward piston movement of transmembrane 2 (TM2) into the signaling domain, inhibiting kinase activity.
    [Show full text]
  • Bimodal Rheotactic Behavior Reflects Flagellar Beat Asymmetry in Human Sperm Cells
    Bimodal rheotactic behavior reflects flagellar beat asymmetry in human sperm cells Anton Bukatina,b,1, Igor Kukhtevichb,c,1, Norbert Stoopd,1, Jörn Dunkeld,2, and Vasily Kantslere aSt. Petersburg Academic University, St. Petersburg 194021, Russia; bInstitute for Analytical Instrumentation of the Russian Academy of Sciences, St. Petersburg 198095, Russia; cITMO University, St. Petersburg 197101, Russia; dDepartment of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139-4307; and eDepartment of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom Edited by Charles S. Peskin, New York University, New York, NY, and approved November 9, 2015 (received for review July 30, 2015) Rheotaxis, the directed response to fluid velocity gradients, has whether this effect is of mechanical (20) or hydrodynamic (21, been shown to facilitate stable upstream swimming of mamma- 22) origin. Experiments (23) show that the alga’s reorientation lian sperm cells along solid surfaces, suggesting a robust physical dynamics can lead to localization in shear flow (24, 25), with mechanism for long-distance navigation during fertilization. How- potentially profound implications in marine ecology. In contrast ever, the dynamics by which a human sperm orients itself relative to taxis in multiflagellate organisms (2, 5, 18, 26, 27), the navi- to an ambient flow is poorly understood. Here, we combine micro- gation strategies of uniflagellate cells are less well understood. fluidic experiments with mathematical modeling and 3D flagellar beat For instance, it was discovered only recently that uniflagellate reconstruction to quantify the response of individual sperm cells in marine bacteria, such as Vibrio alginolyticus and Pseudoalteromonas time-varying flow fields. Single-cell tracking reveals two kinematically haloplanktis, use a buckling instability in their lone flagellum to distinct swimming states that entail opposite turning behaviors under change their swimming direction (28).
    [Show full text]
  • Structural Basis for C-Di-GMP-Mediated Inside- out Signaling Controlling Periplasmic Proteolysis
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Biblioteca Digital da Produção Intelectual da Universidade de São Paulo (BDPI/USP) Universidade de São Paulo Biblioteca Digital da Produção Intelectual - BDPI Departamento de Física e Ciência Interdisciplinar - IFSC/FCI Artigos e Materiais de Revistas Científicas - IFSC/FCI 2011-02 Structural basis for c-di-GMP-mediated inside- out signaling controlling periplasmic proteolysis PLoS Biology, San Francisco : Public Library Science, v. 9, n. 2, p. e1000588-1-e1000588-21, Feb. 2011 http://www.producao.usp.br/handle/BDPI/50077 Downloaded from: Biblioteca Digital da Produção Intelectual - BDPI, Universidade de São Paulo Structural Basis for c-di-GMP-Mediated Inside-Out Signaling Controlling Periplasmic Proteolysis Marcos V. A. S. Navarro1.¤, Peter D. Newell2., Petya V. Krasteva1., Debashree Chatterjee1., Dean R. Madden3, George A. O’Toole2, Holger Sondermann1* 1 Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America, 2 Department of Microbiology and Immunology, Dartmouth Medical School, Hanover, New Hampshire, United States of America, 3 Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire, United States of America Abstract The bacterial second messenger bis-(39–59) cyclic dimeric guanosine monophosphate (c-di-GMP) has emerged as a central regulator for biofilm formation. Increased cellular c-di-GMP levels lead to stable cell attachment, which in Pseudomonas fluorescens requires the transmembrane receptor LapD. LapD exhibits a conserved and widely used modular architecture containing a HAMP domain and degenerate diguanylate cyclase and phosphodiesterase domains. c-di-GMP binding to the LapD degenerate phosphodiesterase domain is communicated via the HAMP relay to the periplasmic domain, triggering sequestration of the protease LapG, thus preventing cleavage of the surface adhesin LapA.
    [Show full text]
  • 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.
    [Show full text]
  • Proquest Dissertations
    INFORMATION TO USERS This manuscript has been reproduced from the microfihn master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type of computer printer. The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand comer and continuing from left to right in equal sections with small overlaps. Each original is also photographed in one exposure and is included in reduced form at the back of the book. Photographs included in the original manuscript have been reproduced xerographically in this copy. Higher quality 6” x 9” black and white photographic prints are available for any photographs or illustrations appearing in this copy for an additional charge. Contact UMI directly to order. UMI A Bell & Howell Information Company 300 North Zeeb Road, Ann Arbor MI 48106-1346 USA 313/761-4700 800/521-0600 STARVATION-INDUCED CHANGES IN MOTILITY AND SPONTANEOUS SWITCHING TO FASTER SWARMING BEHAVIOR OF SINORHIZOBIUM MELILOTI DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in the Graduate School at The Ohio State University By Xueming Wei.
    [Show full text]
  • PDF- Software
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Structure Article Structure and Proposed Mechanism for the pH-Sensing Helicobacter pylori Chemoreceptor TlpB Emily Goers Sweeney,1 J. Nathan Henderson,1,5 John Goers,4 Christopher Wreden,1 Kevin G. Hicks,1,6 Jeneva K. Foster,1 Raghuveer Parthasarathy,1,2,3 S. James Remington,1,3 and Karen Guillemin1,* 1Institute of Molecular Biology 2Materials Science Institute 3Department of Physics University of Oregon, Eugene, OR 97403, USA 4Department of Chemistry, California Polytechnic State University, San Luis Obispo, CA 93407, USA 5Present address: Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA 6Present address: Department of Microbiology, University of Washington, Seattle, WA 98195, USA *Correspondence: [email protected] DOI 10.1016/j.str.2012.04.021 SUMMARY Candidate molecular moieties for pH sensing by a protein receptor include titratable side chains such as aspartate, gluta- pH sensing is crucial for survival of most organisms, mate, and histidine that have pKa values near neutrality. The yet the molecular basis of such sensing is poorly pKa for a sensor can be tuned over a wide range by the imme- understood. Here, we present an atomic resolution diate environment of the protonatable residue. Protonation of structure of the periplasmic portion of the acid- critical residues is generally thought to lead to conformational sensing chemoreceptor, TlpB, from the gastric path- changes that confer signaling states. Examples of bacterial pH ogen Helicobacter pylori. The structure reveals sensors relevant to our studies include the histidine kinase HP165 (ArsS) of H.
    [Show full text]
  • Thermotaxis Ofdictyostelium Discoideum Amoebae and Its Possible Role in Pseudoplasmodial Thermotaxis
    Proc. Natl. Acad. Sci. USA Vol. 80, pp. 5646-5649, September 1983 Developmental Biology Thermotaxis of Dictyostelium discoideum amoebae and its possible role in pseudoplasmodial thermotaxis (temperature/sensory transduction/slime mold) CHOO B. HONG*, DONNA R. FONTANAt, AND KENNETH L. POFFt Michigan State University-Department of Energy, Plant Research Laboratory, -Michigan State University, East Lansing, Michigan 48824 Communicated byJ. T. Bonner, June 6, 1983 ABSTRACT Thermotaxis by individual amoebae of Dictyo- bae. For example, the amoebae respond to cyclic AMP and fo- stelium discoideum on a temperature gradient is described. These late, whereas the multicellular pseudoplasmodia do not, and amoebae showpositive thermotaxis attemperatures between 14°C the action spectra for phototaxis by the amoebae substantially and 28WC shortly (3 hr) after food depletion. Increasing time on the differ from those for phototaxis by the pseudoplasmodia, sug- gradient reduces the positive thermotactic response at the lower gesting different photoreceptor pigments regulating the re- temperature gradients (midpoint temperatures of 14, 16, and 18°C), sponses to light. and amoebae show an apparent negative thermotactic response Thermotaxis by the pseudoplasmodia has been knownfor many after 12 hr on the gradient. The thermotaxis response curve for years (8). The characteristics of this response include (i) a very "wild-type" amoebae after 16 hr on the gradient is similar to that high sensitivity (response to less than 0.0005'C across an in- shown for the pseudoplasmodia. Growth of the amoebae at a dif- and a relatively narrow temper- ferent temperature causes a shift in the thermotaxis response curve dividual pseudoplasmodium) for the amoebae. This adaptation is similar to that shown for the ature range across which the response is given, (ii) negative pseudoplasmodia.
    [Show full text]
  • Role of HAMP Domains in Chemotaxis Signaling by Bacterial Chemoreceptors
    Role of HAMP domains in chemotaxis signaling by bacterial chemoreceptors Cezar M. Khursigara*†, Xiongwu Wu†‡, Peijun Zhang*†§, Jonathan Lefman*, and Sriram Subramaniam*¶ *Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; and ‡Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892 Edited by David J. DeRosier, Brandeis University, Waltham, MA, and approved September 4, 2008 (received for review July 2, 2008) Bacterial chemoreceptors undergo conformational changes in re- sites for the CheA kinase (11, 14, 15), respectively. The confor- sponse to variations in the concentration of extracellular ligands. mational changes resulting from binding of an attractant result These changes in chemoreceptor structure initiate a series of in decreased kinase activity (7, 9). Chemoreceptor methylation signaling events that ultimately result in regulation of rotation of reverses these conformational changes and results in an increase the flagellar motor. Here we have used cryo-electron tomography in kinase activity (7, 16, 17). combined with 3D averaging to determine the in situ structure of Although atomic structures for several chemoreceptor domain chemoreceptor assemblies in Escherichia coli cells that have been fragments have been determined (8, 10, 11), the molecular engineered to overproduce the serine chemoreceptor Tsr. We architectures of intact chemoreceptor homodimers, or of the demonstrate that chemoreceptors are organized as trimers of functionally relevant trimer-of-dimers configuration (3–6), have receptor dimers and display two distinct conformations that differ remained inaccessible to direct structural approaches. More- principally in arrangement of the HAMP domains within each over, the conformational changes involved in signaling are poorly trimer.
    [Show full text]
  • Phototaxis During the Slug Stage of Dictyostelium Discoideum: a Model Study
    Phototaxis during the slug stage of Dictyostelium discoideum: a model study Athanasius F. M. Mare¨ e*, Alexander V. Pan¢lov and Paulien Hogeweg Theoretical Biology and Bioinformatics, University of Utrecht, Padualaan 8, 3584 CH Utrecht,The Netherlands During the slug stage, the cellular slime mould Dictyostelium discoideum moves towards light sources. We have modelled this phototactic behaviour using a hybrid cellular automata/partial di¡erential equation model. In our model, individual amoebae are not able to measure the direction from which the light comes, and di¡erences in light intensity do not lead to di¡erentiation in motion velocity among the amoebae. Nevertheless, the whole slug orientates itself towards the light. This behaviour is mediated by a modi¢cation of the cyclic AMP (cAMP) waves. As an explanation for phototaxis we propose the following mechanism, which is basically characterized by four processes: (i) light is focused on the distal side of the slug as a result of the so-called `lens-e¡ect'; (ii) di¡erences in luminous intensity cause di¡erences in NH3 concentration; (iii) NH3 alters the excitability of the cell, and thereby the shape of the cAMP wave; and (iv) chemotaxis towards cAMP causes the slug to turn. We show that this mechanism can account for a number of other behaviours that have been observed in experiments, such as bidirec- tional phototaxis and the cancellation of bidirectionality by a decrease in the light intensity or the addition of charcoal to the medium. Keywords: Dictyostelium; phototaxis; biological models; movement; ammonia; cyclic AMP slug (Francis 1964), placing the slug in mineral oil 1.
    [Show full text]
  • Studying Electrotaxis in Microfluidic Devices
    sensors Review Studying Electrotaxis in Microfluidic Devices Yung-Shin Sun ID Department of Physics, Fu-Jen Catholic University, New Taipei City 24205, Taiwan; [email protected]; Tel.: +886-2-2905-2585 Received: 11 August 2017; Accepted: 5 September 2017; Published: 7 September 2017 Abstract: Collective cell migration is important in various physiological processes such as morphogenesis, cancer metastasis and cell regeneration. Such migration can be induced and guided by different chemical and physical cues. Electrotaxis, referring to the directional migration of adherent cells under stimulus of electric fields, is believed to be highly involved in the wound-healing process. Electrotactic experiments are conventionally conducted in Petri dishes or cover glasses wherein cells are cultured and electric fields are applied. However, these devices suffer from evaporation of the culture medium, non-uniformity of electric fields and low throughput. To overcome these drawbacks, micro-fabricated devices composed of micro-channels and fluidic components have lately been applied to electrotactic studies. Microfluidic devices are capable of providing cells with a precise micro-environment including pH, nutrition, temperature and various stimuli. Therefore, with the advantages of reduced cell/reagent consumption, reduced Joule heating and uniform and precise electric fields, microfluidic chips are perfect platforms for observing cell migration under applied electric fields. In this paper, I review recent developments in designing and fabricating microfluidic devices for studying electrotaxis, aiming to provide critical updates in this rapidly-growing, interdisciplinary field. Keywords: electrotaxis; microfluidic chips; cell migration; lab-on-a-chip 1. Introduction Collective cell movement is involved in various physiological activities including angiogenesis [1–3], cancer metastasis [4–6], embryonic development [7–9] and wound healing [10–12].
    [Show full text]
  • Two Component Regulatory Systems and Antibiotic Resistance in Gram-Negative Pathogens
    International Journal of Molecular Sciences Review Two Component Regulatory Systems and Antibiotic Resistance in Gram-Negative Pathogens Anjali Y. Bhagirath 1,†, Yanqi Li 1,†, Rakesh Patidar 2 , Katherine Yerex 1, Xiaoxue Ma 1, Ayush Kumar 2,* and Kangmin Duan 1,3,* 1 Department of Oral Biology, Rady Faculty of Health Sciences, University of Manitoba, 780 Bannatyne Ave, Winnipeg, MB R3E 0J9, Canada; [email protected] (A.Y.B.); [email protected] (Y.L.); [email protected] (K.Y.); [email protected] (X.M.) 2 Department of Microbiology, Faculty of Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; [email protected] 3 Department of Medical Microbiology & Infectious Diseases, Rady Faculty of Health Sciences, University of Manitoba, 780 Bannatyne Ave, Winnipeg, MB R3E 0J9, Canada * Correspondence: [email protected] (A.K.); [email protected] (K.D.) † Authors have contributed equally to this work. Received: 18 February 2019; Accepted: 8 April 2019; Published: 10 April 2019 Abstract: Gram-negative pathogens such as Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa are the leading cause of nosocomial infections throughout the world. One commonality shared among these pathogens is their ubiquitous presence, robust host-colonization and most importantly, resistance to antibiotics. A significant number of two-component systems (TCSs) exist in these pathogens, which are involved in regulation of gene expression in response to environmental signals such as antibiotic exposure. While the development of antimicrobial resistance is a complex phenomenon, it has been shown that TCSs are involved in sensing antibiotics and regulating genes associated with antibiotic resistance. In this review, we aim to interpret current knowledge about the signaling mechanisms of TCSs in these three pathogenic bacteria.
    [Show full text]
  • Bacterial Rheotaxis
    Bacterial rheotaxis Marcosa,b, Henry C. Fuc,d, Thomas R. Powersd, and Roman Stockere,1 aSchool of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Singapore; bDepartment of Mechanical Engineering, and eDepartment of Civil and Environmental Engineering, Ralph M. Parsons Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139; cDepartment of Mechanical Engineering, University of Nevada, Reno, NV 89557; and dSchool of Engineering and Department of Physics, Brown University, Providence, RI 02912 Edited by T. C. Lubensky, University of Pennsylvania, Philadelphia, PA, and approved February 17, 2012 (received for review December 21, 2011) The motility of organisms is often directed in response to environ- passive hydrodynamic effect, whereby the combination of a mental stimuli. Rheotaxis is the directed movement resulting from gravitational torque and a shear-induced torque orients the fluid velocity gradients, long studied in fish, aquatic invertebrates, swimming direction preferentially upstream (14–16). Responses and spermatozoa. Using carefully controlled microfluidic flows, we to shear are also observed in copepods and dinoflagellates, which show that rheotaxis also occurs in bacteria. Excellent quantitative rely on shear detection to attack prey or escape predators (5, 17– agreement between experiments with Bacillus subtilis and a math- 19), orient in flow (20), and retain a preferential depth (21). ematical model reveals that bacterial rheotaxis is a purely physical Evidence of shear-driven motility in prokaryotes is limited to the phenomenon, in contrast to fish rheotaxis but in the same way as upstream motion of mycoplasma (22), E. coli (23), and Xylella sperm rheotaxis. This previously unrecognized bacterial taxis results fastidiosa (24), all of which require the presence of a solid sur- from a subtle interplay between velocity gradients and the helical face.
    [Show full text]