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Arxiv:2105.11503V2 [Physics.Bio-Ph] 26 May 2021 3.1 Geometry and Swimming Speeds of the Cells
The Bank Of Swimming Organisms at the Micron Scale (BOSO-Micro) Marcos F. Velho Rodrigues1, Maciej Lisicki2, Eric Lauga1,* 1 Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0WA, United Kingdom. 2 Faculty of Physics, University of Warsaw, Warsaw, Poland. *Email: [email protected] Abstract Unicellular microscopic organisms living in aqueous environments outnumber all other creatures on Earth. A large proportion of them are able to self-propel in fluids with a vast diversity of swimming gaits and motility patterns. In this paper we present a biophysical survey of the available experimental data produced to date on the characteristics of motile behaviour in unicellular microswimmers. We assemble from the available literature empirical data on the motility of four broad categories of organisms: bacteria (and archaea), flagellated eukaryotes, spermatozoa and ciliates. Whenever possible, we gather the following biological, morphological, kinematic and dynamical parameters: species, geometry and size of the organisms, swimming speeds, actuation frequencies, actuation amplitudes, number of flagella and properties of the surrounding fluid. We then organise the data using the established fluid mechanics principles for propulsion at low Reynolds number. Specifically, we use theoretical biophysical models for the locomotion of cells within the same taxonomic groups of organisms as a means of rationalising the raw material we have assembled, while demonstrating the variability for organisms of different species within the same group. The material gathered in our work is an attempt to summarise the available experimental data in the field, providing a convenient and practical reference point for future studies. Contents 1 Introduction 2 2 Methods 4 2.1 Propulsion at low Reynolds number . -
Anaerobic Bacteria Confirmed Plenary Speakers
OFFICIALOFFICIAL JOURNALJOURNAL OFOF THETHE AUSTRALIAN SOCIETY FOR MICROBIOLOGY INC.INC. VolumeVolume 3636 NumberNumber 33 SeptemberSeptember 20152015 Anaerobic bacteria Confirmed Plenary speakers Professor Peter Professor Dan Assoc Prof Susan Lynch Dr Brian Conlon Professor Anna Hawkey Andersson University of California Northeastern Durbin University of Upsalla University San Francisco University, Boston Johns Hopkins Birmingham Environmental pollution Colitis, Crohn's Disease Drug discovery in Dengue and vaccines Nosocomial by antibiotics and its and Microbiome soil bacteria infection control and role in the evolution of Research antibiotic resistance resistance As with previous years, ASM 2016 will be co-run with NOW CONFIRMED! EduCon 2016: Microbiology Educators’ Conference 2016 Rubbo Oration Watch this space for more details on the scientific and Professor Anne Kelso social program, speakers, ASM Public Lecture, workshops, CEO NHMRC ASM awards, student events, travel awards, abstract deadlines and much more.. Perth, WA A vibrant and beautiful city located on the banks of the majestic Swan river. Come stay with us in WA and experience our world class wineries and restaurants, stunning national parks, beaches and much more.. www.theasm.org.au www.westernaustralia.theasm.org.au Annual Scientific Meeting and Trade Exhibition The Australian Society for Microbiology Inc. OFFICIAL JOURNAL OF THE AUSTRALIAN SOCIETY FOR MICROBIOLOGY INC. 9/397 Smith Street Fitzroy, Vic. 3065 Tel: 1300 656 423 Volume 36 Number 3 September 2015 Fax: 03 9329 1777 Email: [email protected] www.theasm.org.au Contents ABN 24 065 463 274 Vertical For Microbiology Australia Transmission 102 correspondence, see address below. Jonathan Iredell Editorial team Guest Prof. Ian Macreadie, Mrs Jo Macreadie Editorial 103 and Mrs Hayley Macreadie Anaerobic bacteria 103 Editorial Board Dena Lyras and Julian I Rood Dr Chris Burke (Chair) Dr Gary Lum Under the Prof. -
Proteome Characterization of Brachyspira Strains
ADVERTIMENT. Lʼaccés als continguts dʼaquesta tesi queda condicionat a lʼacceptació de les condicions dʼús establertes per la següent llicència Creative Commons: http://cat.creativecommons.org/?page_id=184 ADVERTENCIA. El acceso a los contenidos de esta tesis queda condicionado a la aceptación de las condiciones de uso establecidas por la siguiente licencia Creative Commons: http://es.creativecommons.org/blog/licencias/ WARNING. The access to the contents of this doctoral thesis it is limited to the acceptance of the use conditions set by the following Creative Commons license: https://creativecommons.org/licenses/?lang=en Department of Cellular Biology, Physiology and Immunology Doctoral Program in Immunology Proteome characterization of Brachyspira strains. Identification of bacterial antigens. Doctoral Thesis Mª Vanessa Casas López Bellaterra, July 2017 Department of Cellular Biology, Physiology and Immunology Doctoral Program in Immunology Proteome characterization of Brachyspira strains. Identification of bacterial antigens. Doctoral thesis presented by Mª Vanessa Casas López To obtain the Ph.D. in Immunology This work has been carried out in the Proteomics Laboratory CSIC/UAB under the supervision of Dr. Joaquin Abián and Dra. Montserrat Carrascal. Ph.D. Candidate Ph.D. Supervisor Mª Vanessa Casas López Dr. Joaquin Abián Moñux CSIC Research Scientist Department Tutor Ph.D. Supervisor Dra. Dolores Jaraquemada Pérez de Dra. Montserrat Carrascal Pérez Guzmán CSIC Tenured Scientist UAB Immunology Professor Bellaterra, July 2017 “At My Most Beautiful” R.E.M. from the album “Up” (1998) “And after all, you’re my wonderwall” Oasis from the album “(What´s the Story?) Morning Glory” (1995) Agradecimientos A mis directores de tesis, por su tiempo, sus ideas y consejos. -
The Exposed Proteomes of Brachyspira Hyodysenteriae and B. Pilosicoli
ORIGINAL RESEARCH published: 21 July 2016 doi: 10.3389/fmicb.2016.01103 The Exposed Proteomes of Brachyspira hyodysenteriae and B. pilosicoli Vanessa Casas 1, Santiago Vadillo 2, Carlos San Juan 2, Montserrat Carrascal 1 and Joaquin Abian 1* 1 Consejo Superior de Investigaciones Científicas/UAB Proteomics Laboratory, Instituto de Investigaciones Biomedicas de Barcelona–Consejo Superior de Investigaciones Científicas, Institut d’investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain, 2 Departamento Sanidad Animal, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain Brachyspira hyodysenteriae and Brachyspira pilosicoli are well-known intestinal pathogens in pigs. B. hyodysenteriae is the causative agent of swine dysentery, a disease with an important impact on pig production while B. pilosicoli is responsible of a milder diarrheal disease in these animals, porcine intestinal spirochetosis. Recent sequencing projects have provided information for the genome of these species facilitating the search of vaccine candidates using reverse vaccinology approaches. However, practically no experimental evidence exists of the actual gene products being expressed and of those proteins exposed on the cell surface or released to the cell media. Using a Edited by: cell-shaving strategy and a shotgun proteomic approach we carried out a large-scale Alexandre Morrot, Federal University of Rio de Janeiro, characterization of the exposed proteins on the bacterial surface in these species as well Brazil as of peptides and proteins in the extracellular medium. The study included three strains Reviewed by: of B. hyodysenteriae and two strains of B. pilosicoli and involved 148 LC-MS/MS runs on Ana Varela Coelho, Instituto de Tecnologia Química e a high resolution Orbitrap instrument. -
Spirochete Flagella and Motility
biomolecules Review Spirochete Flagella and Motility Shuichi Nakamura Department of Applied Physics, Graduate School of Engineering, Tohoku University, 6-6-05 Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan; [email protected]; Tel.: +81-22-795-5849 Received: 11 March 2020; Accepted: 3 April 2020; Published: 4 April 2020 Abstract: Spirochetes can be distinguished from other flagellated bacteria by their long, thin, spiral (or wavy) cell bodies and endoflagella that reside within the periplasmic space, designated as periplasmic flagella (PFs). Some members of the spirochetes are pathogenic, including the causative agents of syphilis, Lyme disease, swine dysentery, and leptospirosis. Furthermore, their unique morphologies have attracted attention of structural biologists; however, the underlying physics of viscoelasticity-dependent spirochetal motility is a longstanding mystery. Elucidating the molecular basis of spirochetal invasion and interaction with hosts, resulting in the appearance of symptoms or the generation of asymptomatic reservoirs, will lead to a deeper understanding of host–pathogen relationships and the development of antimicrobials. Moreover, the mechanism of propulsion in fluids or on surfaces by the rotation of PFs within the narrow periplasmic space could be a designing base for an autonomously driving micro-robot with high efficiency. This review describes diverse morphology and motility observed among the spirochetes and further summarizes the current knowledge on their mechanisms and relations to pathogenicity, mainly from the standpoint of experimental biophysics. Keywords: spirochetes; periplasmic flagella; motility; chemotaxis; molecular motor 1. Introduction Motility systems of living organisms are currently classified into 18 types [1]. Even when focusing on bacteria only, the motility is diverse when bacterial species are concerned [2]. -
Brachyspira (Serpulina) Pilosicoli and Intestinal Spirochetosis: How DIAGNOSTIC NOTES Much Do We Know? Swine Health Prod
Stevenson GW. Brachyspira (Serpulina) pilosicoli and intestinal spirochetosis: How DIAGNOSTIC NOTES much do we know? Swine Health Prod. 1999;7(6):287–291. Brachyspira (Serpulina) pilosicoli and intestinal spirochetosis: How much do we know? Gregory W. Stevenson, DVM, PhD, Diplomate ACVP here are at least five distinct species of Brachyspira nus name based on historic precedent. The genus Brachyspira was es- (Serpulina) known to infect the large intestine of swine.1–3 tablished when Brachyspira aalborgi was first described,7 which oc- Two species are pathogenic: curred prior to the establishment of the genus Serpulina.5 Unfortu- nately, Serpulina intermedia and murdochii were not included in the • Brachyspira hyodysenteriae (formerly Serpulina or Treponema comparative study. For now, they remain in the genus Serpulina. hyodysenteriae), which causes swine dysentery; and • Brachyspira pilosicoli (formerly Serpulina pilosicoli or Brachyspira pilosicoli Anguillina coli), which causes intestinal spirochetosis. Brachyspira pilosicoli can be presumptively differentiated from other Three additional species are nonpathogenic: Brachyspira (Serpulina) spp. by culture (weak β-hemolysis) and biochemical testing. Brachyspira pilosicoli is indole negative and hip- • Brachyspira innocens, formerly Serpulina or Treponema purate-hydrolysis positive, and lack β-glucosidase activity in the API- innocens ZYM profile.11,12 Definitive identification of B. pilosicoli requires PCR • Serpulina intermedia testing.12,13–15 The medium that is most commonly used to culture B. • Serpulina murdochii hyodysenteriae in diagnostic laboratories, BJ medium,16 is slightly in- Selected characteristics of each species are summarized in Table 1. hibitory when used to isolate B. pilosicoli, due to the moderate sensi- tivity of B. pilosicoli to two of the included antibiotics, rifampicin, and At a light microscopic level, all five of these organisms are morphologi- spiramycin.17 Culture of B. -
Methods for Improving Diagnostic Techniques Used for the Identification and Isolation of Brachyspira Species from Swine Hallie Warneke Iowa State University
Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2017 Methods for improving diagnostic techniques used for the identification and isolation of Brachyspira species from swine Hallie Warneke Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Animal Diseases Commons Recommended Citation Warneke, Hallie, "Methods for improving diagnostic techniques used for the identification and isolation of Brachyspira species from swine" (2017). Graduate Theses and Dissertations. 15453. https://lib.dr.iastate.edu/etd/15453 This Thesis is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Methods for improving diagnostic techniques used for the identification and isolation of Brachyspira species from swine by Hallie L Warneke A thesis submitted to the graduate faculty in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Major: Veterinary Preventive Medicine Program of Study Committee: Eric R Burrough, Major Professor Timothy S Frana Annette M O’Connor The student author and the program of study committee are solely responsible for the content of this thesis. The Graduate College will ensure this thesis is globally accessible and will not permit alterations after a degree is conferred. Iowa State University Ames, Iowa 2017 Copyright © Hallie L Warneke, 2017. All rights reserved. ii TABLE OF CONTENTS Page LIST OF FIGURES ................................................................................................... iii LIST OF TABLES .................................................................................................... -
Isolates from Colonic Spirochaetosis in Humans Show High Genomic
bioRxiv preprint doi: https://doi.org/10.1101/544502; this version posted February 8, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Isolates from colonic spirochaetosis in humans show high genomic divergence and carry 2 potential pathogenic features but are not detected by 16S amplicon sequencing using 3 standard primers for the human microbiota 4 5 Kaisa Thorell a, b, Linn Inganäs a, c, Annette Backhans d, Lars Agréus c, Åke Öst e, Marjorie 6 Walker f, Nicholas J Talley f, Lars Kjellström g, Anna Andreasson c, h, Lars Engstrand a, i 7 8 a Center for Translational Microbiome Research, Department of Microbiology, Cell and 9 Tumor biology, Karolinska Institutet, Stockholm, Sweden 10 b Department for Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, 11 Gothenburg, Sweden 12 c Division for Family Medicine and General Practice, Department for Neurobiology, Care 13 Sciences and Society, Karolinska Institutet, Huddinge, Sweden 14 d Department of Clinical Sciences, Swedish University of Agriculture, Uppsala, Sweden 15 e Pathology, Aleris Medilab, Taby, Sweden. 16 f University of Newcastle, New South Wales, Australia 17 g Gastromottagningen City, Stockholm, Sweden 18 h Stress Research Institute, Stockholm University, Stockholm, Sweden 19 i Clinical Genomics, Science for Life Laboratory, Stockholm, Sweden 20 Corresponding authors: [email protected], [email protected] 21 bioRxiv preprint doi: https://doi.org/10.1101/544502; this version posted February 8, 2019. -
Intestinal Spirochetosis: an Interesting Cause of Chronic Diarrhea
Case Report Annals of Infectious Disease and Epidemiology Published: 22 Feb, 2021 Intestinal Spirochetosis: An Interesting Cause of Chronic Diarrhea Harshad Joshi* Department of Pathology, Sir H. N. Reliance Foundation Hospital and Research Centre, India Abstract Forty-six-year male from India presented with 2-year history of small volume non bloody diarrhea with mild abdominal pain. He had no history of fever or constitutional symptoms and only minimal weight loss. His blood evaluation showed mild iron deficiency anemia with normal serum albumin and renal profile. Routine stool examination showed no blood, pus cells, ova or parasites. Celiac serology was negative. Contrast enhanced CT (Computed Tomography) abdomen showed subcentimetric mesenteric lymph nodes, bowel was normal in size and thickness. Upper GI endoscopy was normal with normal duodenal biopsy; Ileocolonoscopy showed few aphthous ulcers in terminal ileum with mild nodularity. Ileal biopsies showed bluish filamentous structure on surface epithelium forming a thick false brush border appearance, suggestive of intestinal spirochetosis. Rest of ileal architecture was well preserved. Patient was commenced on cyclical antibiotics including Nitazoxanide, Metronidazole, doxycycline and Rifaximin. Patient on follow up showed improvement in symptoms and weight gain. Intestinal spirochetosis is commonly transmitted to human from infected animals. Our patient was butcher by occupation. Our case is an interesting presentation of Intestinal Spirochetosis in form of chronic diarrhea. Keywords: Spirochetosis; Chronic diarrhea; False brush border Introduction OPEN ACCESS Spirochete induced diarrhea is common in veterinary medicine, which is observed in swine, *Correspondence: poultry, dogs, cats and non-human primates [1]. Humans are usually affected due to close proximity Harshad Joshi, Department of and is common in animal handlers like poultry workers, butchers, etc. -
Brachyspira Murdochii Type Strain (56-150)
Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of Brachyspira murdochii type strain (56-150). Permalink https://escholarship.org/uc/item/2x39941n Journal Standards in genomic sciences, 2(3) ISSN 1944-3277 Authors Pati, Amrita Sikorski, Johannes Gronow, Sabine et al. Publication Date 2010-06-15 DOI 10.4056/sigs.831993 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2010) 2:260-269 DOI:10.4056/sigs.831993 Complete genome sequence of Brachyspira murdochii type strain (56-150T) Amrita Pati1, Johannes Sikorski2, Sabine Gronow2, Christine Munk3, Alla Lapidus1, Alex Copeland1, Tijana Glavina Del Tio1, Matt Nolan1, Susan Lucas1, Feng Chen1, Hope Tice1, Jan-Fang Cheng1, Cliff Han1,3, John C. Detter1,3, David Bruce1,3, Roxanne Tapia3, Lynne Goodwin1,3, Sam Pitluck1, Konstantinos Liolios1, Natalia Ivanova1, Konstantinos Mavromatis1, Natalia Mikhailova1, Amy Chen4, Krishna Palaniappan4, Miriam Land1,5, Loren Hauser1,5, Yun-Juan Chang1,5, Cynthia D. Jeffries1,5, Stefan Spring2, Manfred Rohde6, Markus Göker2, James Bristow1, Jonathan A. Eisen1,7, Victor Markowitz4, Philip Hugenholtz1, Nikos C. Kyrpides1, and Hans-Peter Klenk2* 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 DSMZ – German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 6 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Hans-Peter Klenk Keywords: host-associated, non-pathogenic, motile, anaerobic, Gram-negative, Brachyspira- ceae, Spirochaetes, GEBA Brachyspira murdochii Stanton et al. -
Development of a Real-Time PCR for Identification of Brachyspira Species in Human Colonic Biopsies
Development of a Real-Time PCR for Identification of Brachyspira Species in Human Colonic Biopsies Laurens J. Westerman1, Herbert V. Stel2, Marguerite E. I. Schipper3, Leendert J. Bakker4, Eskelina A. Neefjes-Borst5, Jan H. M. van den Brande6, Edwin C. H. Boel1, Kees A. Seldenrijk7, Peter D. Siersema8, Marc J. M. Bonten1, Johannes G. Kusters1* 1 Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands, 2 Department of Pathology, Tergooiziekenhuizen, Hilversum, The Netherlands, 3 Department of Pathology, University Medical Centre Utrecht, Utrecht, The Netherlands, 4 Central Laboratory for Bacteriology and Serology, Tergooiziekenhuizen, Hilversum, The Netherlands, 5 Department of Pathology, VU Medical Centre, Amsterdam, The Netherlands, 6 Department of Internal Medicine, Tergooiziekenhuizen, Hilversum, The Netherlands, 7 Department of Pathology, St. Antonius Hospital, Nieuwegein, Nieuwegein, The Netherlands, 8 Department of Gastroenterology and Hepatology, University Medical Centre Utrecht, Utrecht, The Netherlands Abstract Background: Brachyspira species are fastidious anaerobic microorganisms, that infect the colon of various animals. The genus contains both important pathogens of livestock as well as commensals. Two species are known to infect humans: B. aalborgi and B. pilosicoli. There is some evidence suggesting that the veterinary pathogenic B. pilosicoli is a potential zoonotic agent, however, since diagnosis in humans is based on histopathology of colon biopsies, species identification is not routinely performed in human materials. Methods: The study population comprised 57 patients with microscopic evidence of Brachyspira infection and 26 patients with no histopathological evidence of Brachyspira infection. Concomitant faecal samples were available from three infected patients. Based on publically available 16S rDNA gene sequences of all Brachyspira species, species-specific primer sets were designed. -
Comparative Genomics to Investigate Genome Function and Adaptations in the Newly Sequenced Brachyspira Hyodysenteriae and Brachyspira Pilosicoli
Comparative genomics to investigate genome function and adaptations in the newly sequenced Brachyspira hyodysenteriae and Brachyspira pilosicoli Phatthanaphong Wanchanthuek A Thesis presented for the degree of Doctor of Philosophy Murdoch University Australia March 2009 Dedication I would like to dedicate this dissertation to my family and my fiancée Ratchaneekorn. i Comparative genomics to investigate genome function and adaptations in the newly sequenced Brachyspira hyodysenteriae and Brachyspira pilosicoli Phatthanaphong Wanchanthuek Submitted for the degree of Doctor of Philosophy March 2009 ii ABSTRACT Brachyspira hyodysenteriae and Brachyspira pilosicoli are anaerobic intestinal spirochaetes that are the aetiological agents of swine dysentery and intestinal spirochaetosis, respectively. As part of this PhD study the genome sequence of B. hyodysenteriae strain WA1 and a near complete sequence of B. pilosicoli strain 95/1000 were obtained, and subjected to comparative genomic analysis. The B. hyodysenteriae genome consisted of a circular 3.0 Mb chromosome, and a 35,940 bp circular plasmid that has not previously been described. The incomplete genome of B. pilosicoli contained 4 scaffolds. There were 2,652 and 2,297 predicted ORFs in the B. hyodysenteriae and B. pilosicoli strains, respectively. Of the predicted ORFs, more had similarities to proteins of the enteric Clostridium species than they did to proteins of other spirochaetes. Many of these genes were associated with transport and metabolism, and they may have been gradually acquired through horizontal gene transfer in the environment of the large intestine. A construction of central metabolic pathways of the Brachyspira species identified a complete set of coding sequences for glycolysis, gluconeogenesis, a non‐oxidative pentose phosphate pathway, nucleotide metabolism and a respiratory electron transport chain.