DOCSLIB.ORG

Standoff Detection and Classification of Bacteria by Multispectral Laser-Induced Fluorescence

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Standoff Detection and Classification of Bacteria by Multispectral Laser-Induced Fluorescence Adv. Opt. Techn. 2017; 6(2): 75–83 Research Article Open Access Frank Duschek*, Lea Fellner, Florian Gebert, Karin Grünewald, Anja Köhntopp, Marian Kraus, Peter Mahnke, Carsten Pargmann, Herbert Tomaso and Arne Walter Standoff detection and classification of bacteria by multispectral laser-induced fluorescence DOI 10.1515/aot-2016-0066 OCIS codes: 160.1435; 280.1415; 300.2530; 280.0280; Received December 2, 2016; accepted February 6, 2017; previously 000.3860. published online March 31, 2017 Abstract: Biological hazardous substances such as cer- tain fungi and bacteria represent a high risk for the broad 1 Introduction public if fallen into wrong hands. Incidents based on Hazardous bacteria represent a major threat to modern bio-agents are commonly considered to have unpredict- societies if released into the environment. Aerosols of bac- able and complex consequences for first responders and teria can occur naturally when infected animals or humans people. The impact of such an event can be minimized spread a pathogen, but they can also be released by acci- by an early and fast detection of hazards. The presented dents and as a terrorist attack. Once people are infected, approach is based on optical standoff detection apply- bacteria may easily spread aided by the fact that their detri- ing laser-induced fluorescence (LIF) on bacteria. The LIF mental effects can occur with a certain time delay. Therefore, bio-detector has been designed for outdoor operation fast and reliable detection and identification of bacteria is at standoff distances from 20 m up to more than 100 m. essential for the containment and the decontamination of The detector acquires LIF spectral data for two different affected areas and people. Commonly used methods for excitation wavelengths (280 and 355 nm) which can be bacterial identification are mass spectrometry, polymerase used to classify suspicious samples. A correlation analy- chain reaction, DNA sequencing and flow cytometry [1], all sis and spectral classification by a decision tree is used to of which are employed in the form of point sensors. These discriminate between the measured samples. In order to methods are highly sensitive and able to identify bacteria demonstrate the capabilities of the system, suspensions of very accurately. At the same time they require direct contact the low-risk and non-pathogenic bacteria Bacillus thuring- with a sample, can only be used to cover small areas, iensis, Bacillus atrophaeus, Bacillus subtilis, Brevibacillus and are not suitable for real-time detection or tracking of brevis, Micrococcus luteus, Oligella urethralis, Paenibacil- moving aerosol sources. Optical, i.e. laser-based methods lus polymyxa and Escherichia coli (K12) have been inves- on the other hand are capable of monitoring large areas in tigated with the system, resulting in a discrimination real time and from a safe distance. Here, additional chal- accuracy of about 90%. lenges lie in compensating the atmospheric interferences, Keywords: bacteria; biological agents; classification; i.e. incident sunlight, light scattering and absorption from laser-induced fluorescence (LIF); standoff detection. air, and airborne particles (pollen, dust, raindrops) and other weather-related phenomena. Furthermore, in inhab- *Corresponding author: Frank Duschek, German Aerospace Center, ited areas the used laser radiation must be eye-safe. Bio- Institute of Technical Physics, Langer Grund, Lampoldshausen, logical samples contain a large number of fluorophores. 74239 Hardthausen, Germany, e-mail: [email protected] Therefore, laser-induced fluorescence (LIF) yields high Lea Fellner, Florian Gebert, Karin Grünewald, Marian Kraus, Carsten Pargmann and Arne Walter: German Aerospace Center, Institute signal intensities at relatively low excitation energies [2, 3]. of Technical Physics, Langer Grund, Lampoldshausen, 74239 As fluorescence spectra usually show very few distinct fea- Hardthausen, Germany tures, the combination with sophisticated data analysis is Anja Köhntopp and Peter Mahnke: German Aerospace Center, necessary to increase specificity and sensitivity. The use of Institute of Technical Physics, 70569 Stuttgart, Germany several excitation wavelengths has been shown to strongly Herbert Tomaso: Friedrich-Loeffler-Institute, Institute of Bacterial enhance the capabilities for identification/classification Infections and Zoonoses, 07743 Jena, Germany [4]. Additionally, the fluorescence lifetime of bacteria has www.degruyter.com/aot been used to characterize a small set of them [5, 6]. © 2017 THOSS Media and De Gruyter ©2017, Frank Duschek et al., published by De Gruyter. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License. 76 F. Duschek et al.: Biohazard detection by LIF While spectroscopy on chemical solutions is rather In cooperation with LDI Innovations (Estonia), straightforward due to well-defined structures of chemical we presented a setup for dual-excitation wavelength agents, bacteria represent a more complex problem. They (280 nm, 355 nm) LIF detection and classification of dif- greatly differ in size and shape, and sometimes they form ferent bioorganic substances [20, 21]. The online classi- clusters, films or chains. Depending on the environmental fier used therein relies on spectral feature extraction and conditions bacteria can exist in different states, i.e. vegeta- selection and has been trained with a basic set of experi- tive cells, endospores or dead. As their chemical composi- mental spectra by bootstrap aggregation and a decision tion is very complex, a number of fluorophores contribute tree classification. The results showed the discrimination to the observed overall fluorescence. For Escherichia coli of a variety of bioorganic substances into four classes: 15 different fluorophores have been identified [7]. After plants, oils, chemicals and bacteria [3, 22]. excitation in the UV (280 nm) the observed fluorescence The next step is to investigate the ability to discrimi- is dominated by the amino acid tryptophan and shows nate different bacterial species with optical methods. smaller contribution from tyrosine, while at an excitation Here, we present the experimental results for a small set of wavelength of 355 nm, nicotinamide adenine dinucleotide eight different low-risk bacteria. Multispectral LIF spectra (NADH) and flavins are the main contributors. were recorded at a standoff distance of 22 m at excitation The discrimination of different bacteria by their intrin- wavelengths of 280 and 355 nm. Within this predeter- sic fluorescence has been demonstrated under laboratory mined group of bacteria, we demonstrate the discrimi- conditions [8, 9]. Furthermore, several approaches towards nation of samples containing different genera as well as a standoff detection system based on multiple-wavelength closely related bacteria by their LIF signature. LIF have been presented. Pan et al. [10, 11] developed an instrument that detects LIF from excitation wavelengths of 263 and 351 nm and scattering of single aerosol parti- 2 Experimental section cles. The instrument is capable of classifying airborne pollen and fungal particles. The US Naval Research Lab- 2.1 Experimental setup oratory presented a similar approach, in which the dual excitation wavelength fluorescence of single aerosol par- The standoff LIF detection system used in this study is operated on ticles is recorded in four different wavelength channels an outdoor optical test range at the German Aerospace Center, Lam- [12]. Under laboratory conditions, the discrimination of poldshausen. The laser and detection system is operated indoors, whereas the target is positioned outdoors. Experiments can be car- different biological and non-biological aerosol particles ried out with both generated aerosols and liquids in a cuvette. All by LIF techniques was successfully demonstrated [13]. data shown here were measured for suspensions at a distance of 22 m The Swedish Defence Research Agency (FOI) developed at both excitation wavelengths of 280 and 355 nm. a light detection and ranging (LIDAR) UV-LIF system for The experimental setup was designed as a generic system to be standoff aerosol detection, which has been field-tested used not only for LIF but also for Raman and laser-induced break- for the classification of different biological particles and down spectroscopy, which require higher spectral resolutions. As described in Section 4, a more dedicated LIF detection system with interferants [14]. The LIDAR technique has also been used compact detection optics and lower spectral resolution will be pre- by others, for example, research groups from Italy [15], sented in future work. India [16] and Canada [17, 18]. The Canadian SINBAHD system has gone through several field tests concerning 2.1.1 Optics: The schematic setup of the detection system is shown the recording of spectral signatures of different bacteria, in Figure 1. A frequency tripled Nd:YAG laser Spitlight 600-10 (InnoLas toxins and virus simulants under cross-wind conditions GmbH, Krailing, Germany) supplies pulses of 7 ns pulse length at at standoff distances up to the kilometer range. Recently, 355 nm with a repetition rate of 10 Hz. Each second pulse is frequency a scanning IR-LIDAR has been developed that monitors converted to 280 nm, resulting in an effective repetition rate of 5 Hz with pulse energies of about 10 mJ for each wavelength. For the the surroundings for aerosol clouds and triggers a staring generation of the
Load more

Recommended publications
  • Kaistella Soli Sp. Nov., Isolated from Oil-Contaminated Soil
    A001 Kaistella soli sp. nov., Isolated from Oil-contaminated Soil Dhiraj Kumar Chaudhary1, Ram Hari Dahal2, Dong-Uk Kim3, and Yongseok Hong1* 1Department of Environmental Engineering, Korea University Sejong Campus, 2Department of Microbiology, School of Medicine, Kyungpook National University, 3Department of Biological Science, College of Science and Engineering, Sangji University A light yellow-colored, rod-shaped bacterial strain DKR-2T was isolated from oil-contaminated experimental soil. The strain was Gram-stain-negative, catalase and oxidase positive, and grew at temperature 10–35°C, at pH 6.0– 9.0, and at 0–1.5% (w/v) NaCl concentration. The phylogenetic analysis and 16S rRNA gene sequence analysis suggested that the strain DKR-2T was affiliated to the genus Kaistella, with the closest species being Kaistella haifensis H38T (97.6% sequence similarity). The chemotaxonomic profiles revealed the presence of phosphatidylethanolamine as the principal polar lipids;iso-C15:0, antiso-C15:0, and summed feature 9 (iso-C17:1 9c and/or C16:0 10-methyl) as the main fatty acids; and menaquinone-6 as a major menaquinone. The DNA G + C content was 39.5%. In addition, the average nucleotide identity (ANIu) and in silico DNA–DNA hybridization (dDDH) relatedness values between strain DKR-2T and phylogenically closest members were below the threshold values for species delineation. The polyphasic taxonomic features illustrated in this study clearly implied that strain DKR-2T represents a novel species in the genus Kaistella, for which the name Kaistella soli sp. nov. is proposed with the type strain DKR-2T (= KACC 22070T = NBRC 114725T). [This study was supported by Creative Challenge Research Foundation Support Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF- 2020R1I1A1A01071920).] A002 Chitinibacter bivalviorum sp.
    [Show full text]
  • Laboratory Exercises in Microbiology: Discovering the Unseen World Through Hands-On Investigation
    City University of New York (CUNY) CUNY Academic Works Open Educational Resources Queensborough Community College 2016 Laboratory Exercises in Microbiology: Discovering the Unseen World Through Hands-On Investigation Joan Petersen CUNY Queensborough Community College Susan McLaughlin CUNY Queensborough Community College How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/qb_oers/16 Discover additional works at: https://academicworks.cuny.edu This work is made publicly available by the City University of New York (CUNY). Contact: [email protected] Laboratory Exercises in Microbiology: Discovering the Unseen World through Hands-On Investigation By Dr. Susan McLaughlin & Dr. Joan Petersen Queensborough Community College Laboratory Exercises in Microbiology: Discovering the Unseen World through Hands-On Investigation Table of Contents Preface………………………………………………………………………………………i Acknowledgments…………………………………………………………………………..ii Microbiology Lab Safety Instructions…………………………………………………...... iii Lab 1. Introduction to Microscopy and Diversity of Cell Types……………………......... 1 Lab 2. Introduction to Aseptic Techniques and Growth Media………………………...... 19 Lab 3. Preparation of Bacterial Smears and Introduction to Staining…………………...... 37 Lab 4. Acid fast and Endospore Staining……………………………………………......... 49 Lab 5. Metabolic Activities of Bacteria…………………………………………….…....... 59 Lab 6. Dichotomous Keys……………………………………………………………......... 77 Lab 7. The Effect of Physical Factors on Microbial Growth……………………………... 85 Lab 8. Chemical Control of Microbial Growth—Disinfectants and Antibiotics…………. 99 Lab 9. The Microbiology of Milk and Food………………………………………………. 111 Lab 10. The Eukaryotes………………………………………………………………........ 123 Lab 11. Clinical Microbiology I; Anaerobic pathogens; Vectors of Infectious Disease….. 141 Lab 12. Clinical Microbiology II—Immunology and the Biolog System………………… 153 Lab 13. Putting it all Together: Case Studies in Microbiology…………………………… 163 Appendix I.
    [Show full text]
  • Downloaded Skin Zaka Electronic Gmbh, Cologne, Germany)
    Li et al. Microbiome (2021) 9:47 https://doi.org/10.1186/s40168-020-00995-7 RESEARCH Open Access Characterization of the human skin resistome and identification of two microbiota cutotypes Zhiming Li1,2†, Jingjing Xia3,4,5†, Liuyiqi Jiang3†, Yimei Tan4,6†, Yitai An1,2, Xingyu Zhu4,7, Jie Ruan1,2, Zhihua Chen1,2, Hefu Zhen1,2, Yanyun Ma4,7, Zhuye Jie1,2, Liang Xiao1,2, Huanming Yang1,2, Jian Wang1,2, Karsten Kristiansen1,2,8, Xun Xu1,2,9, Li Jin4,10, Chao Nie1,2*, Jean Krutmann4,5,11*, Xiao Liu1,12,13* and Jiucun Wang3,4,10,14* Abstract Background: The human skin microbiota is considered to be essential for skin homeostasis and barrier function. Comprehensive analyses of its function would substantially benefit from a catalog of reference genes derived from metagenomic sequencing. The existing catalog for the human skin microbiome is based on samples from limited individuals from a single cohort on reference genomes, which limits the coverage of global skin microbiome diversity. Results: In the present study, we have used shotgun metagenomics to newly sequence 822 skin samples from Han Chinese, which were subsequently combined with 538 previously sequenced North American samples to construct an integrated Human Skin Microbial Gene Catalog (iHSMGC). The iHSMGC comprised 10,930,638 genes with the detection of 4,879,024 new genes. Characterization of the human skin resistome based on iHSMGC confirmed that skin commensals, such as Staphylococcus spp, are an important reservoir of antibiotic resistance genes (ARGs). Further analyses of skin microbial ARGs detected microbe-specific and skin site-specific ARG signatures.
    [Show full text]
  • Micrococcus Luteus (Schroeter 1872) Cohn 1872, and Desig- Nation of the Neotype Strain M
    INTERNATIONAL JOURNAL of SYSTEMATIC BACTERIOLOGY Vol. 22, No. 4 October 1972, p. 218-223 Printed in U.S.A. Copyright 0 1972 International Association of Microbiological Societies Taxonomic Status of Micrococcus luteus (Schroeter 1872) Cohn 1872, and Desig- nation of the Neotype Strain M. KOCUR, ZDENA PkCOVA, and T. MARTINEC Czechoslovak Collection of Microorganisms, J. E. PurkynE University, Brno, Czechoslovakia An amended description of Micrococcus luteus (Schroeter 1872) Cohn 1872, at present a broad-based species characterized primarily on negative charact er- istics, is proposed on the basis of a taxonomic analysis of 30 strains. CCM 169 (= ATCC 4698) is designated a's the neotype strain of M. luteus. A large number of species of aerobic, diameter and arranged in tetrads and in catalase-positive, yellow-pigmented micrococci irregular clumps of tetrads. Strains CCM 248, have been described, but their incomplete 337, 1674, and 2494 formed packets and characterization has hindered their classifica- irregular clusters of packets. These strains also tion. Some of them are known as Micrococcus produced the largest cells (1.5 to 1.8 pm) of all luteus, M. flaws, M. lysodeikticus, Sarcina of those studied. None of the strains was motile lutea, and S. flava. At present only two of these or produced spores. are generally accepted: M. luteus and M. varians Cultural characteristics. Colonies of all of the (13, 21). strains were circular, convex, and smooth, with Although M. luteus is the type species of the either a glistening or a dull surface. Tetrad- and genus Micrococcus, it is not sufficiently de- packet-forming strains produced matted colo- fined.
    [Show full text]
  • Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
    Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341
    [Show full text]
  • Micrococcus Luteus - Survival in Amber C.L
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by DigitalCommons@CalPoly Micrococcus luteus - Survival in Amber C.L. Greenblatt , J. Baum , B.Y. Klein , S. Nachshon , V. Koltunov and R.J. Cano Abstract Introduction A growing body of evidence now supports the isolation of There is an accumulating body of data reporting the microorganisms from ancient materials. However, ques­ persistence of bacteria in what are considered extreme and tions about the stringency of extraction methods and the oligotrophic environments [15, 24, 37]. However, the genetic relatedness of isolated organisms to their closest mechanisms used by these bacteria to survive in such living relatives continue to challenge the authenticity of conditions are poorly understood. One extreme niche that these ancient life forms. Previous studies have success­ has consistently yielded such bacteria is amber, from fully isolated a number of spore-forming bacteria from which single isolates and assemblages of multiple bacterial organic and inorganic deposits of considerable age whose species have been characterized [3, 8, 10, 17]. Amber is the survival is explained by their ability to enter suspended fossilized remains of organic tree resins. As volatile terp­ animation for extended periods of time. However, de­ enoids in these resins evaporate and dissipate under nat­ spite a number of putative reports, the isolation of non­ ural forest conditions they leave the nonvolatile fractions spore-forming bacteria and an explanation for their to become fossilized through progressive oxidation and survival have remained enigmatic. Here we describe the polymerization. During the early stages of solidification isolation of non-spore-forming cocci from a 120-million­ microorganisms, and occasionally larger organisms such year-old block of amber, which by genetic, morphologi­ as insects [3], can become entrapped in the resins [31].
    [Show full text]
  • Evaluation of MALDI Biotyper for Identification of Taylorella Equigenitalis and Taylorella Asinigenitalis Kristina Lantz Iowa State University
    Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2017 Evaluation of MALDI Biotyper for identification of Taylorella equigenitalis and Taylorella asinigenitalis Kristina Lantz Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Microbiology Commons, and the Veterinary Medicine Commons Recommended Citation Lantz, Kristina, "Evaluation of MALDI Biotyper for identification of Taylorella equigenitalis and Taylorella asinigenitalis" (2017). Graduate Theses and Dissertations. 16520. https://lib.dr.iastate.edu/etd/16520 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]. Evaluation of MALDI Biotyper for identification of Taylorella equigenitalis and Taylorella asinigenitalis by Kristina Lantz A thesis submitted to the graduate faculty in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Major: Veterinary Microbiology Program of Study Committee: Ronald Griffith, Major Professor Steve Carlson Matthew Erdman Timothy Frana 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
    [Show full text]
  • Final Screening Assessment of Micrococcus Luteus Strain ATCC 4698
    Final Screening Assessment of Micrococcus luteus strain ATCC 4698 Environment and Climate Change Canada Health Canada February 2018 Cat. No.: En14-313/2018E-PDF ISBN 978-0-660-24725-0 Information contained in this publication or product may be reproduced, in part or in whole, and by any means, for personal or public non-commercial purposes, without charge or further permission, unless otherwise specified. You are asked to: • Exercise due diligence in ensuring the accuracy of the materials reproduced; • Indicate both the complete title of the materials reproduced, as well as the author organization; and • Indicate that the reproduction is a copy of an official work that is published by the Government of Canada and that the reproduction has not been produced in affiliation with or with the endorsement of the Government of Canada. Commercial reproduction and distribution is prohibited except with written permission from the author. For more information, please contact Environment and Climate Change Canada’s Inquiry Centre at 1-800-668-6767 (in Canada only) or 819-997-2800 or email to [email protected]. © Her Majesty the Queen in Right of Canada, represented by the Minister of the Environment and Climate Change, 2016. Aussi disponible en français ii Synopsis Pursuant to paragraph 74(b) of the Canadian Environmental Protection Act, 1999 (CEPA), the Minister of the Environment and the Minister of Health have conducted a screening assessment of Micrococcus luteus (M. luteus) strain ATCC 4698. M. luteus strain ATCC 4698 is a bacterial strain that shares characteristics with other strains of the species. M.
    [Show full text]
  • Fish Bacterial Flora Identification Via Rapid Cellular Fatty Acid Analysis
    Fish bacterial flora identification via rapid cellular fatty acid analysis Item Type Thesis Authors Morey, Amit Download date 09/10/2021 08:41:29 Link to Item http://hdl.handle.net/11122/4939 FISH BACTERIAL FLORA IDENTIFICATION VIA RAPID CELLULAR FATTY ACID ANALYSIS By Amit Morey /V RECOMMENDED: $ Advisory Committe/ Chair < r Head, Interdisciplinary iProgram in Seafood Science and Nutrition /-■ x ? APPROVED: Dean, SchooLof Fisheries and Ocfcan Sciences de3n of the Graduate School Date FISH BACTERIAL FLORA IDENTIFICATION VIA RAPID CELLULAR FATTY ACID ANALYSIS A THESIS Presented to the Faculty of the University of Alaska Fairbanks in Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE By Amit Morey, M.F.Sc. Fairbanks, Alaska h r A Q t ■ ^% 0 /v AlA s ((0 August 2007 ^>c0^b Abstract Seafood quality can be assessed by determining the bacterial load and flora composition, although classical taxonomic methods are time-consuming and subjective to interpretation bias. A two-prong approach was used to assess a commercially available microbial identification system: confirmation of known cultures and fish spoilage experiments to isolate unknowns for identification. Bacterial isolates from the Fishery Industrial Technology Center Culture Collection (FITCCC) and the American Type Culture Collection (ATCC) were used to test the identification ability of the Sherlock Microbial Identification System (MIS). Twelve ATCC and 21 FITCCC strains were identified to species with the exception of Pseudomonas fluorescens and P. putida which could not be distinguished by cellular fatty acid analysis. The bacterial flora changes that occurred in iced Alaska pink salmon ( Oncorhynchus gorbuscha) were determined by the rapid method.
    [Show full text]
  • Assessing the Temporal Dynamics of the Lower Urinary Tract Microbiota and the Effects of Lifestyle
    Loyola University Chicago Loyola eCommons Dissertations Theses and Dissertations 2019 Assessing the Temporal Dynamics of the Lower Urinary Tract Microbiota and the Effects of Lifestyle Travis Kyle Price Follow this and additional works at: https://ecommons.luc.edu/luc_diss Part of the Microbiology Commons Recommended Citation Price, Travis Kyle, "Assessing the Temporal Dynamics of the Lower Urinary Tract Microbiota and the Effects of Lifestyle" (2019). Dissertations. 3367. https://ecommons.luc.edu/luc_diss/3367 This Dissertation is brought to you for free and open access by the Theses and Dissertations at Loyola eCommons. It has been accepted for inclusion in Dissertations by an authorized administrator of Loyola eCommons. For more information, please contact [email protected]. This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License. Copyright © 2019 Travis Kyle Price LOYOLA UNIVERSITY CHICAGO ASSESSING THE TEMPORAL DYNAMICS OF THE LOWER URINARY TRACT MICROBIOTA AND THE EFFECTS OF LIFESTYLE A DISSERTATION SUBMITTED TO THE FACULTY OF THE GRADUATE SCHOOL IN CANDIDACY FOR THE DEGREE OF DOCTOR OF PHILOSOPHY PROGRAM IN MICROBIOLOGY AND IMMUNOLOGY BY TRAVIS KYLE PRICE CHICAGO, IL MAY 2019 i Copyright by Travis Kyle Price, 2019 All Rights Reserved ii ACKNOWLEDGMENTS I would like to thank everyone that made this thesis possible. First and foremost, I want to thank Dr. Alan Wolfe. I could not have asked for a better mentor. I don’t think there will ever be another period of my life where I grow as a scientist, as a professional, or as a person more than I did under your mentorship.
    [Show full text]
  • Unknown Report Brynn Allen Bacteria: Micrococcus Luteus and Enterobacter Aerogenes My Steps: GR+ & GR- One: Gram Stain Both
    Unknown Report Brynn Allen Bacteria: Micrococcus Luteus and Enterobacter Aerogenes My Steps: GR+ & GR- One: Gram stain both bacterias labeled “6” and “F.” Purpose: Observe what they may be under oil immersion lens after gram staining. ​ Observations: Gram positive cocci appear to be tetrads in 6 plate, and Gram negative bacillus ​ with long rods in F plate. GR+ & GR- Two: Inoculate the two fresh bacteria’s given to me from the tubes onto Nutrient Agar plates. Incubate for 24 hours. Purpose: Detect growth from my two plated organisms and see if any colors or distinct colonies ​ have revealed themselves. Observations: 6 Plate with Gram positive bacteria reveals vivid yellow streak isolation on it’s ​ plate. F plate reveals a light pink, almost transparent color with high motility and a filamentous colony appearance. GR+ & GR- Three: Performed catalase test on GR+ bacteria from 6 plate and GR- from F plate. Purpose: To see if the bacteria neutralizes toxic forms of oxygen metabolites (Hydrogen ​ Peroxide h2O2) Observations: Bacteria bubbled once catalase solution was applied to both bacteria’s. This ​ indicates a Catalase positive result. GR+ Four: Performed streak isolation on Gr+ bacteria onto an MSA plate. Incubated for 24-48 hours. Purpose: To see if this bacteria can survive in high salt concentration, if it can — the pH will ​ decrease to 6.8 and will change from red to yellow, therefore indicating it uses mannitol. If the pH goes up to 7.4, it uses amino acids and frees ammonia, it will change from red to pink. Observations: Gr+ bacteria had no change once checked after incubation.
    [Show full text]
  • Processing of Metals and Metalloids by Actinobacteria: Cell Resistance Mechanisms and Synthesis of Metal(Loid)-Based Nanostructures
    microorganisms Review Processing of Metals and Metalloids by Actinobacteria: Cell Resistance Mechanisms and Synthesis of Metal(loid)-Based Nanostructures Alessandro Presentato 1,* , Elena Piacenza 1 , Raymond J. Turner 2 , Davide Zannoni 3 and Martina Cappelletti 3 1 Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy; [email protected] 2 Department of Biological Sciences, Calgary University, Calgary, AB T2N 1N4, Canada; [email protected] 3 Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy; [email protected] (D.Z.); [email protected] (M.C.) * Correspondence: [email protected] Received: 6 December 2020; Accepted: 16 December 2020; Published: 18 December 2020 Abstract: Metal(loid)s have a dual biological role as micronutrients and stress agents. A few geochemical and natural processes can cause their release in the environment, although most metal-contaminated sites derive from anthropogenic activities. Actinobacteria include high GC bacteria that inhabit a wide range of terrestrial and aquatic ecological niches, where they play essential roles in recycling or transforming organic and inorganic substances. The metal(loid) tolerance and/or resistance of several members of this phylum rely on mechanisms such as biosorption and extracellular sequestration by siderophores and extracellular polymeric substances (EPS), bioaccumulation, biotransformation, and metal efflux processes, which overall contribute to maintaining metal homeostasis. Considering the bioprocessing potential of metal(loid)s by Actinobacteria, the development of bioremediation strategies to reclaim metal-contaminated environments has gained scientific and economic interests. Moreover, the ability of Actinobacteria to produce nanoscale materials with intriguing physical-chemical and biological properties emphasizes the technological value of these biotic approaches.
    [Show full text]