DOCSLIB.ORG

Sanguineus Bacterial Communities Rhipicephalus

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Sanguineus Bacterial Communities Rhipicephalus Composition and Seasonal Variation of Rhipicephalus turanicus and Rhipicephalus sanguineus Bacterial Communities Itai Lalzar, Shimon Harrus, Kosta Y. Mumcuoglu and Yuval Gottlieb Appl. Environ. Microbiol. 2012, 78(12):4110. DOI: 10.1128/AEM.00323-12. Published Ahead of Print 30 March 2012. Downloaded from Updated information and services can be found at: http://aem.asm.org/content/78/12/4110 These include: SUPPLEMENTAL MATERIAL Supplemental material http://aem.asm.org/ REFERENCES This article cites 44 articles, 17 of which can be accessed free at: http://aem.asm.org/content/78/12/4110#ref-list-1 CONTENT ALERTS Receive: RSS Feeds, eTOCs, free email alerts (when new articles cite this article), more» on June 10, 2013 by guest Information about commercial reprint orders: http://journals.asm.org/site/misc/reprints.xhtml To subscribe to to another ASM Journal go to: http://journals.asm.org/site/subscriptions/ Composition and Seasonal Variation of Rhipicephalus turanicus and Rhipicephalus sanguineus Bacterial Communities Itai Lalzar,a Shimon Harrus,a Kosta Y. Mumcuoglu,b and Yuval Gottlieba Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel,a and Department of Microbiology and Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, Hadassah Medical School, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israelb A 16S rRNA gene approach, including 454 pyrosequencing and quantitative PCR (qPCR), was used to describe the bacterial com- munity in Rhipicephalus turanicus and to evaluate the dynamics of key bacterial tenants of adult ticks during the active questing season. The bacterial community structure of Rh. turanicus was characterized by high dominance of Coxiella and Rickettsia and extremely low taxonomic diversity. Parallel diagnostic PCR further revealed a novel Coxiella species which was present and nu- Downloaded from Coxiella sp. densities were significantly higher in female versus male .(187 ؍ merically dominant in all individual ticks tested (n ticks and were overall stable throughout the questing season. In addition, we revealed the presence of the novel Coxiella sp. in Rh. sanguineus adult ticks, eggs, and hatched larvae, indicating its vertical transmission. The presence of both spotted fever group Rickettsia spp. (SFGR) and non-SFGR was verified in the various individual ticks. The prevalence and density of Rickettsia spp. were very low compared to those of Coxiella sp. Furthermore, Rickettsia sp. densities were similar in males and females and significantly declined toward the end of the questing season. No correlation was found between Coxiella sp. and Rickettsia sp. densities. These results suggest different control mechanisms in the tick over its different bacterial populations and point to an obligatory and facultative association between the two tick species and Coxiella sp. and Rickettsia spp., respectively. http://aem.asm.org/ any pestiferous arthropods carry obligatory and facultative to develop future strategies for the prevention and control of tick- Mbacterial symbionts, which fundamentally shape their biol- borne diseases. ogy and may determine their efficiency as disease vectors and their In Israel, the brown dog tick, Rhipicephalus sanguineus (Acari: performance as pests (2, 35). Ticks are considered among the most Ixodidae), is most common and is often found with a second important vectors of pathogens of medical and veterinary impor- sympatric species, Rhipicephalus turanicus (16, 30). While Rh. san- tance (10). guineus is the known vector of Rickettsia conorii (9, 22), several Incidences of arthropod-borne epidemics, such as the Crime- other bacterial pathogens, such as Coxiella burnetii, Ehrlichia ca- on June 10, 2013 by guest an-Congo hemorrhagic fever transmitted by ticks (48), are ex- nis, and Anaplasma platys, have also been found in these two tick pected to increase due to global climate changes and other drivers species, making them potential vectors (10, 20). In addition, Rh. associated with modern life (reviewed in references 9, 21, and 28). sanguineus also harbors a Coxiella-like endosymbiont (34). Indeed, the prevalence of tick-borne pathogens such as Borrelia In this study, we adopted a 16S rRNA gene-based approach to burgdorferi and Anaplasma phagocytophilum has been correlated describe the composition and dynamics of the bacterial commu- with seasonal climatic changes (14). Therefore, it is expected that nities in Rh. turanicus and Rh. sanguineus. PCR-DGGE and 454 other microbial tenants within tick hosts are affected in the same pyrosequencing were used to describe the tick bacterial commu- manner. nity, and quantitative PCR (qPCR) assays were used to follow the In studies based on low-throughput techniques such as clone seasonal changes in bacterial populations. libraries and denaturing gradient gel electrophoresis (DGGE), the MATERIALS AND METHODS bacterial communities of several ixodid tick species, among them Amblyomma americanum, Ixodes scapularis, and Ixodes ricinus, Tick collection and rearing. Questing ticks were collected by dragging a 1-m2 white cotton cloth over the vegetation in two consecutive years. In were found to be dominated by a single bacterial genus along with 2009, ticks were collected in March and April from the outskirts of Kib- other less dominant but diverse bacterial species, such as Arseno- butz Hulda, Israel (31° 49= 56.28Љ N, 34° 53= 0.24Љ E) and in May from the phonus sp., Serratia grimesii, and Klebsiella oxytoca. While each sand dunes in Caesarea (32° 30= 0Љ N, 34° 54= 0Љ E). In 2010, ticks were individual tick usually showed relatively few bacteria, a higher collected weekly between March and July from the outskirts of Kibbutz diversity of bacterial taxa was found at the tick population level (4, Hulda. Collected ticks were immediately preserved in 100% ethanol and 8, 23, 31, 39, 44). More recent studies based on high-throughput kept at Ϫ20°C until further use. techniques have revealed higher bacterial diversity of individual ticks. However, to the best of our knowledge, a combined quanti- tative and qualitative assessment of tick bacterial communities has Received 2 February 2012 Accepted 26 March 2012 not been performed to date. Such a dual analysis might be impor- Published ahead of print 30 March 2012 tant for the evaluation of dynamic interactions within bacterial Address correspondence to Yuval Gottlieb, [email protected]. populations (27, 50). Determining seasonal effects on an entire Supplemental material for this article may be found at http://aem.asm.org/. bacterial community within a tick vector might result in better Copyright © 2012, American Society for Microbiology. All Rights Reserved. resolution of host-bacterium interactions and of bacterium-bac- doi:10.1128/AEM.00323-12 terium interactions within the host. This approach could be used 4110 aem.asm.org Applied and Environmental Microbiology p. 4110–4116 June 2012 Volume 78 Number 12 Tick-Associated Bacterial Communities In addition, several fully engorged female ticks were collected in 2010 Mass sequencing of 16S rRNA gene fragments. To characterize the from dogs located in a dog kennel (Rehovot, Israel [31° 53= 38.03Љ N, 34° Rh. turanicus bacterial community, 36 representative samples, 17 male 48= 59.04Љ E]). They were kept in a moistened plastic tube at 25°C until and 19 female ticks collected from Hulda in 2010, were sent to the Re- eggs were laid. A batch from each tick clutch was then surface sterilized in search and Testing Laboratory (Lubbock, TX) for mass-sequencing anal- soapy water and 70% ethanol and preserved in 100% ethanol for DNA ysis. 16S rRNA bacterial tag-encoded FLX amplicon pyrosequencing was extraction. Most of the eggs were incubated until the larvae hatched. The performed using the Roche 454 sequencing system as previously described newly hatched larvae were preserved in 100% ethanol for DNA extraction (12). Amplicons originating from the 530F–1100R (V4–V6) region, num- as described further on. bered in relation to the E. coli 16S rRNA gene, were sequenced. Retrieved Tick species classification. Ticks were first classified as Rh. sanguineus sequences were analyzed using MOTHUR (40). Sequences shorter than or Rh. turanicus according to their morphological characteristics based on 200 bp, as well as those of low quality, were omitted. Sequences were then the work of Walker et al. (45). aligned using the Silva-compatible alignment database, and a distance To ascertain the identity of the collected ticks used in this study, a matrix was calculated (36). Sequences were grouped into operational taxo- specific gene-based assay was developed. Partial fragments of the 12S mi- nomic units (OTUs) at a 97% sequence similarity threshold (i.e., se- tochondrial rRNA gene were sequenced from 10 randomly selected ticks quences that differ by Յ3% are clustered in the same OTU). Representa- as previously described (3). Phylogenetic analysis (detailed below) tives of each OTU were classified with the MOTHUR classify.seqs module, showed that some of the ticks were closely related to Rh. turanicus and and affiliation, down to the genus level, was verified by the ARB program others to Rh. sanguineus (see Fig. S1 in the supplemental material). Based package (25), the Ribosomal Database Project (http://rdp.cme.msu.edu/) Downloaded from on the aligned sequences, a new primer specific to Rh. sanguineus ticks (46),
Load more

Recommended publications
  • Characterization of the Interaction Between R. Conorii and Human
    Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 4-5-2018 Characterization of the Interaction Between R. Conorii and Human Host Vitronectin in Rickettsial Pathogenesis Abigail Inez Fish Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Part of the Bacteria Commons, Bacteriology Commons, Biology Commons, Immunology of Infectious Disease Commons, and the Pathogenic Microbiology Commons Recommended Citation Fish, Abigail Inez, "Characterization of the Interaction Between R. Conorii and Human Host Vitronectin in Rickettsial Pathogenesis" (2018). LSU Doctoral Dissertations. 4566. https://digitalcommons.lsu.edu/gradschool_dissertations/4566 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. CHARACTERIZATION OF THE INTERACTION BETWEEN R. CONORII AND HUMAN HOST VITRONECTIN IN RICKETTSIAL PATHOGENESIS A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Interdepartmental Program in Biomedical and Veterinary Medical Sciences Through the Department of Pathobiological Sciences by Abigail Inez
    [Show full text]
  • Genome Project Reveals a Putative Rickettsial Endosymbiont
    GBE Bacterial DNA Sifted from the Trichoplax adhaerens (Animalia: Placozoa) Genome Project Reveals a Putative Rickettsial Endosymbiont Timothy Driscoll1,y, Joseph J. Gillespie1,2,*,y, Eric K. Nordberg1,AbduF.Azad2, and Bruno W. Sobral1,3 1Virginia Bioinformatics Institute at Virginia Polytechnic Institute and State University 2Department of Microbiology and Immunology, University of Maryland School of Medicine 3Present address: Nestle´ Institute of Health Sciences SA, Campus EPFL, Quartier de L’innovation, Lausanne, Switzerland *Corresponding author: E-mail: [email protected]. yThese authors contributed equally to this work. Accepted: March 1, 2013 Abstract Eukaryotic genome sequencing projects often yield bacterial DNA sequences, data typically considered as microbial contamination. However, these sequences may also indicate either symbiont genes or lateral gene transfer (LGT) to host genomes. These bacterial sequences can provide clues about eukaryote–microbe interactions. Here, we used the genome of the primitive animal Trichoplax adhaerens (Metazoa: Placozoa), which is known to harbor an uncharacterized Gram-negative endosymbiont, to search for the presence of bacterial DNA sequences. Bioinformatic and phylogenomic analyses of extracted data from the genome assembly (181 bacterial coding sequences [CDS]) and trace read archive (16S rDNA) revealed a dominant proteobacterial profile strongly skewed to Rickettsiales (Alphaproteobacteria) genomes. By way of phylogenetic analysis of 16S rDNA and 113 proteins conserved across proteobacterial genomes, as well as identification of 27 rickettsial signature genes, we propose a Rickettsiales endosymbiont of T. adhaerens (RETA). The majority (93%) of the identified bacterial CDS belongs to small scaffolds containing prokaryotic-like genes; however, 12 CDS were identified on large scaffolds comprised of eukaryotic-like genes, suggesting that T.
    [Show full text]
  • Paradoxical Evolution of Rickettsial Genomes
    Ticks and Tick-borne Diseases 10 (2019) 462–469 Contents lists available at ScienceDirect Ticks and Tick-borne Diseases journal homepage: www.elsevier.com/locate/ttbdis Paradoxical evolution of rickettsial genomes T ⁎ Awa Diopa, Didier Raoultb, Pierre-Edouard Fourniera, a UMR VITROME, Aix-Marseille University, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Uuniversitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France b UMR MEPHI, Aix-Marseille University, IRD, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Uuniversitaire Méditerranée Infection, Marseille, France ARTICLE INFO ABSTRACT Keywords: Rickettsia species are strictly intracellular bacteria that evolved approximately 150 million years ago from a Rickettsia presumably free-living common ancestor from the order Rickettsiales that followed a transition to an obligate Genomics intracellular lifestyle. Rickettsiae are best known as human pathogens vectored by various arthropods causing a Evolution range of mild to severe human diseases. As part of their obligate intracellular lifestyle, rickettsial genomes have Virulence undergone a convergent evolution that includes a strong genomic reduction resulting from progressive gene Genome rearrangement degradation, genomic rearrangements as well as a paradoxical expansion of various genetic elements, notably Non-coding DNA Gene loss small RNAs and short palindromic elements whose role remains unknown. This reductive evolutionary process is DNA repeats not unique to members of the Rickettsia genus but is common to several human pathogenic bacteria. Gene loss, gene duplication, DNA repeat duplication and horizontal gene transfer all have shaped rickettsial genome evolution. Gene loss mostly involved amino-acid, ATP, LPS and cell wall component biosynthesis and tran- scriptional regulators, but with a high preservation of toxin-antitoxin (TA) modules, recombination and DNA repair proteins.
    [Show full text]
  • Detecting Phylogenetic Signals from Deep Roots of the Tree of Life
    UNIVERSITY OF CALIFORNIA,MERCED Detecting Phylogenetic Signals From Deep Roots of the Tree of Life A dissertation submitted in partial fulfillment of the requirements for the degree Doctor of Philosophy in Quantitative and Systems Biology by Katherine Colleen Harris Amrine Committee in charge: Professor Carolin Frank, Chair Professor David Ardell Professor Meng-Lin Tsao Professor Suzanne Sindi August 2013 Copyright Katherine C. Amrine All Rights Reserved UNIVERSITY OF CALIFORNIA,MERCED Graduate Division The Dissertation of Katherine Colleen Harris Amrine is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Faculty Advisor: David H. Ardell Committee Members: Chair: Carolin Frank Meng-Lin Tsao Suzanne Sindi Date iii Contents List of Figures ................................................................. vi List of Tables .................................................................. ix Acknowledgements ............................................................. x Vita ........................................................................... xi Abstract ...................................................................... xii 1 Shifting focus in evolutionary biology – identifying a new signal for phylogenetic tree reconstruction and taxonomic classification 1 1.1 The evolution of bacterial classification and phylogeny . .1 1.2 The historical marker – 16S . .2 1.3 Complications in bacterial classification and phylogeny . .2 1.3.1 Horizontal gene transfer . .2 1.3.2 Does a true tree exist? . .3 1.4 Methods for phylogenetic tree reconstruction . .3 1.4.1 DNA . .3 1.4.2 RNA . .4 1.4.3 Proteins . .4 1.4.4 Data compilation . .5 1.5 Bias in tree-building . .5 1.6 Biological bias in biological data . .6 1.7 The tRNA interaction network . .6 1.8 Information theory . .8 1.9 Machine Learning for bacterial classification . .9 2 tRNA signatures reveal polyphyletic origins of streamlined SAR11 genomes among the Alphaproteobacteria 12 2.1 Abstract .
    [Show full text]
  • Host-Microbe Relations: a Phylogenomics-Driven Bioinformatic Approach to the Characterization of Microbial DNA from Heterogeneous Sequence Data
    Host-Microbe Relations: A Phylogenomics-Driven Bioinformatic Approach to the Characterization of Microbial DNA from Heterogeneous Sequence Data Timothy Patrick Driscoll Dissertation submitted to the faculty of the Virginia Polytechnic Institute and State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Genetics, Bioinformatics, and Computational Biology Joseph J Gillespie David R Bevan Madhav V Marathe T M Murali May 1st, 2013 Blacksburg, Virginia Keywords: phylogenomics, genome-mining, host-microbe interactions, genomics, bioinformatics, symbiosis, bacteria, lateral gene transfer Copyright 2013 Host-Microbe Relations: A Phylogenomics-Driven Bioinformatic Approach to the Characterization of Microbial DNA from Heterogeneous Sequence Data Timothy Patrick Driscoll ABSTRACT Plants and animals are characterized by intimate, enduring, often indispensable, and always complex associations with microbes. Therefore, it should come as no surprise that when the genome of a eukaryote is sequenced, a medley of bacterial sequences are produced as well. These sequences can be highly informative about the interactions between the eukaryote and its bacterial cohorts; unfortunately, they often comprise a vanishingly small constituent within a heterogeneous mixture of microbial and host sequences. Genomic analyses typically avoid the bacterial sequences in order to obtain a genome sequence for the host. Metagenomic analysis typically avoid the host sequences in order to analyze community composition and functional diversity of the bacterial component. This dissertation describes the development of a novel approach at the intersection of genomics and metagenomics, aimed at the extraction and characterization of bacterial sequences from heterogeneous sequence data using phylogenomic and bioinformatic tools. To achieve this objective, three interoperable workflows were constructed as modular computational pipelines, with built-in checkpoints for periodic interpretation and refinement.
    [Show full text]
  • Why Non-Pathogenic Microorganisms Matter in Tick Biology and Pathogen Transmission
    REVIEW published: 08 June 2017 doi: 10.3389/fcimb.2017.00236 The Tick Microbiome: Why Non-pathogenic Microorganisms Matter in Tick Biology and Pathogen Transmission Sarah I. Bonnet 1*, Florian Binetruy 2, Angelica M. Hernández-Jarguín 3 and Olivier Duron 2 1 UMR BIPAR INRA-ENVA-ANSES, Maisons-Alfort, France, 2 Laboratoire MIVEGEC (Maladies Infectieuses et Vecteurs: Écologie, Génétique, Évolution et Contrôle), Centre National de la Recherche Scientifique (UMR5290), IRD (UMR224), Université de Montpellier, Montpellier, France, 3 SaBio Instituto de Investigación en Recursos Cinegéticos CSIC-UCLM-JCCM, Ciudad Real, Spain Ticks are among the most important vectors of pathogens affecting humans and other animals worldwide. They do not only carry pathogens however, as a diverse group of commensal and symbiotic microorganisms are also present in ticks. Unlike pathogens, their biology and their effect on ticks remain largely unexplored, and are in fact often neglected. Nonetheless, they can confer multiple detrimental, neutral, or beneficial effects to their tick hosts, and can play various roles in fitness, nutritional adaptation, development, reproduction, defense against environmental stress, and immunity. Non-pathogenic microorganisms may also play a role in driving transmission of tick-borne pathogens (TBP), with many potential implications for both human and animal health. In addition, the genetic proximity of some pathogens to mutualistic symbionts hosted by ticks is evident when studying phylogenies of several bacterial Edited by: Lorenza Putignani, genera. The best examples are found within members of the Rickettsia, Francisella, and Bambino Gesù Ospedale Pediatrico Coxiella genera: while in medical and veterinary research these bacteria are traditionally (IRCCS), Italy recognized as highly virulent vertebrate pathogens, it is now clear to evolutionary Reviewed by: ecologists that many (if not most) Coxiella, Francisella, and Rickettsia bacteria are Ulrike G.
    [Show full text]
  • Using Core Genome Alignments to Assign Bacterial Species 2
    bioRxiv preprint doi: https://doi.org/10.1101/328021; this version posted May 22, 2018. 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-ND 4.0 International license. 1 Using Core Genome Alignments to Assign Bacterial Species 2 3 Matthew Chunga,b, James B. Munroa, Julie C. Dunning Hotoppa,b,c,# 4 a Institute for Genome Sciences, University of Maryland Baltimore, Baltimore, MD 21201, USA 5 b Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD 6 21201, USA 7 c Greenebaum Comprehensive Cancer Center, University of Maryland Baltimore, Baltimore, MD 21201, 8 USA 9 10 Running Title: Core Genome Alignments to Assign Bacterial Species 11 12 #Address correspondence to Julie C. Dunning Hotopp, [email protected]. 13 14 Word count Abstract: 371 words 15 Word count Text: 4,833 words 16 1 bioRxiv preprint doi: https://doi.org/10.1101/328021; this version posted May 22, 2018. 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-ND 4.0 International license. 17 ABSTRACT 18 With the exponential increase in the number of bacterial taxa with genome sequence data, a new 19 standardized method is needed to assign bacterial species designations using genomic data that is 20 consistent with the classically-obtained taxonomy.
    [Show full text]
  • Identification and Molecular Characterization of Zoonotic Rickettsiae
    Identification and molecular characterization of zoonotic rickettsiae and other vector-borne pathogens infecting dogs in Mnisi, Bushbuckridge, Mpumalanga Province, South Africa Dr Agatha Onyemowo Kolo A dissertation submitted in partial fulfillment of the requirements for the degree of MAGISTER SCIENTIAE (VETERINARY SCIENCE) In the Department of Veterinary Tropical Diseases Faculty of Veterinary Science University of Pretoria South Africa OCTOBER 2014 DECLARATION I declare that this dissertation, which I hereby submit for the Master of Science degree in the Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, is my original work and has not been submitted by me for a degree to any other university. SIGNED: DATE: 16-02-2015 AGATHA ONYEMOWO KOLO 2 DEDICATION To the Lord Almighty, the Most High God my Help, my Refuge, my Provider, my Maker, my greatest Love, my Redeemer, my ever Faithful God; to you I dedicate this work. 3 ACKNOWLEDGEMENTS I wish to extend my gratitude to my Supervisor Prof Paul Tshepo Matjila for his kindness, generosity and support towards me, his acceptance to be my mentor for this specific project I am indeed grateful for the opportunity given to me. To my Co-Supervisors Dr Kgomotso Sibeko-Matjila who painstakingly went through this work with utmost diligence and thoroughness for its success; for her wisdom, humility and approacheability I am most grateful. Dr K I have learnt so much from you may God reward you abundantly for your kindness and dedication. Prof Darryn Knobel for all the extra resources of literature, materials, support and knowledge that he provided his assistance in helping me to think critically and analytically, Sir I am immensely grateful.
    [Show full text]
  • Supporting Information
    Supporting Information McLean et al. “Candidate Phylum TM6 Genome Recovered from a Hospital Sink Biofilm Provides the First Genomic Insights into this Uncultivated Phylum “ SI Appendix McLean et al. PNAS Supporting Information a b High Fluor TM6 Background 1 Fig. S1. Biofilm sample biomass and Fluorescence Activated Cell Sorting (FACS) plot of a 2 biofilm sample. a) Sample biomass collected directly into buffer solution and from a biofilm in 3 a sink drain within a restroom adjacent to an emergency waiting room. b) Sorting gates set to 4 sort events after staining with SYBR Green DNA stain. The P1 gate includes high fluorescent 5 SYBR Green stained particles, and the background gate indicates that region in which unstained 6 sample events were located. The low fluorescent P2 region was chosen as a sort gate to target a 7 total of 100 events in each of 32 wells of a 384 well plate. 1 Fig. S2. Custom integrated Agilent Technologies BioCel 1200 liquid handling automated 2 platform for high throughput single cell genomics. The BioCel platform allows processing of 3 more than 5,000 single cells per week through a multi-stage protocol that includes multiple 4 displacement amplification (MDA) of DNA, MDA dilution and 16S PCR, MDA and PCR hit 5 picking, Picogreen (Life Technologies) DNA quantitation, 16S Syto 9 (Life Technologies) melt 6 curve assay, 16S Taqman qPCR, and SAP/Exonuclease I (Affymetrix) PCR treatment. All liquid 7 handling is performed on the BioCel with the BioRAPTR (Beckman Coulter) and Bravo 8 (Agilent) performing non-contact dispensing and liquid transfer steps, respectively.
    [Show full text]
  • Copyrighted Material
    361 Index a – PCR 224 abdominal and intestinal anthrax 14 – – virus culture and antigen testing 224 abscesses 40 – prevention 340–341 acid-fast bacilli (AFB) 151 – protection 338–339 activated partial thromboplastin time (APTT) – treatment 342 219 Argentinian hemorrhagic fever (AHF) 213, Advisory Committee on Immunization 217, 219, 220 Practices (ACIP) 203 ‘‘Army Vaccine’’ 97 African tick bite fever (ATBF) 124, 129, 142 arthropod-borne infections 124, 125, 127, agar gel immunodiffusion (AGID) 181 128, 129, 139, 142 Agrobacterium 20 avian influenza viruses (AIVs) 177, 178 Alphaproteobacteria 124 Amblyomma hebraeum 129 b Amblyomma variegatum 129 bacille Calmette–Guerin´ (BCG) 150, 153, amplified fragment length polymorphism 155 (AFLP) 159 Bacillus anthracis 5, 159 Anaplasmataceae 124, 126 – characteristics 5–6 Andes virus (ANDV) 273, 276, 277 – clinical and pathological findings anthrax. See Bacillus anthracis 13–14 antibiotic resistance 7–8 – – abdominal and intestinal anthrax 14 antigen detection 8 – – inhalation and pulmonary anthrax 14 Antiqua biovar 93 – – oropharyngeal anthrax 14 Arenaviridae 253 – clinical guidelines 297 arenaviruses 211–212 – decontamination 296 – clinical signs – diagnosis – – New World hemorrhagic fevers 214–215 – – antibiotic resistance 7–8 – – Old World hemorrhagic fevers 214 – – antigen detection 8 – decontamination 340 – – chromosome 10–11 – diagnostics COPYRIGHTED– – growth characteristics MATERIAL 6–7 – – serological tests 223 – – MLVA, SNR, and SNP typing 11 – disinfection 339–340 – – molecular identification 8–10 – epidemiology – – phage testing and biochemistry 8 – – New World 213–214 – – phenotypical identification 6 – – Old World 212–213 – – serological investigations 11 – pathogenesis 218–223 – disinfection 295, 296 – pathological signs – epidemiology 15 – – New World hemorrhagic fevers 217–218 – pathogenesis – – Old World hemorrhagic fevers 215–216 – – animals 12 BSL3 and BSL4 Agents: Epidemiology, Microbiology, and Practical Guidelines, First Edition.
    [Show full text]
  • Rickettsial Pathogens and Their Arthropod Vectors
    Perspectives Rickettsial Pathogens and their Arthropod Vectors Abdu F. Azad* and Charles B. Beard† *University of Maryland School of Medicine, Baltimore, Maryland, USA; and †Centers for Disease Control and Prevention, Atlanta, Georgia, USA Rickettsial diseases, important causes of illness and death worldwide, exist primarily in endemic and enzootic foci that occasionally give rise to sporadic or seasonal outbreaks. Rickettsial pathogens are highly specialized for obligate intracellular survival in both the vertebrate host and the invertebrate vector. While studies often focus primarily on the vertebrate host, the arthropod vector is often more important in the natural maintenance of the pathogen. Consequently, coevolution of rickettsiae with arthropods is responsible for many features of the host-pathogen relationship that are unique among arthropod-borne diseases, including efficient pathogen replication, long- term maintenance of infection, and transstadial and transovarial transmission. This article examines the common features of the host-pathogen relationship and of the arthropod vectors of the typhus and spotted fever group rickettsiae. Rickettsial diseases, widely distributed associations with obligate blood-sucking throughout the world in endemic foci with arthropods represent the highly adapted end- sporadic and often seasonal outbreaks, from time product of eons of biologic evolution. The ecologic to time have reemerged in epidemic form in separation and reduced selective pressure due to human populations. Throughout history, epi- these associations may explain rickettsial genetic demics of louse-borne typhus have caused more conservation. Their intimate relationships with deaths than all the wars combined (1). The vector hosts (Table 1) are characterized by ongoing outbreak of this disease in refugee camps efficient multiplication, long-term maintenance, in Burundi involving more than 30,000 human transstadial and transovarial transmission, and cases is a reminder that rickettsial diseases can extensive geographic and ecologic distribution.
    [Show full text]
  • The Evolution of a Gene Cluster Containing a Plant-Like Protein In
    EVOLUTION OF A PLANT-LIKE GENE ANCIENTLY ACQUIRED AS PART OF A GENOMIC ISLAND IN XANTHOMONAS A DISSERTATION SUBMITTED TO THE GRADUATE DIVISION OF THE UNIVERSITY OF HAWAI‘I AT MᾹNOA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN MOLECULAR BIOSCIENCES AND BIOENGINEERING May 2012 BY KEVIN SCHNEIDER DISSERTATION COMMITTEE GERNOT PRESTING, CHAIRPERSON ANNE ALVAREZ YANGRAE CHO GUYLAINE POISSON SEAN CALLAHAN Dedicated to my Parents! i Acknowledgments I want to give my biggest thanks to Dr Gernot Presting for providing me with so many opportunities during my career at UH Manoa. The teaching assistantship I received on an unexpected short notice that began my PhD to working and publishing on exciting and interesting topics from corn centromeres to bacterial genomes. I am forever grateful for the time, patience, and energy he has spent mentoring me. This work would not have been possible without Dr Anne Alvarez. She has provided not only her knowledge of plant pathology, but also her collection of bacterial strains that the majority of my research required. Also, I thank Asoka Da Silva whom has provided his expertise and skills to culture and purify the hundreds of strains used in this study. The analysis in this work would not have begun without the initial phylogenomic analysis of Arabidopsis completed by Aren Ewing. His work laid the foundation to stick with studying bacterial genomic evolution in light of all of the wonderful work to study the genomic evolution of the centromeres of Zea mays in our lab. I also thank all of my lab mates Anupma Sharma, Thomas Wolfgruber, Jamie Allison, Jeffrey Lai, Megan Nakashima, Ronghui Xu, Zidian Xie, Grace Kwan, Margaret Ruzicka, Krystle Salazar and Erin Mitsunaga from the past and the present for their advice, help, discussions and their friendship and casual chit-chat.
    [Show full text]