Immunology and Microbiology
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DNA: the Timeline and Evidence of Discovery
1/19/2017 DNA: The Timeline and Evidence of Discovery Interactive Click and Learn (Ann Brokaw Rocky River High School) Introduction For almost a century, many scientists paved the way to the ultimate discovery of DNA and its double helix structure. Without the work of these pioneering scientists, Watson and Crick may never have made their ground-breaking double helix model, published in 1953. The knowledge of how genetic material is stored and copied in this molecule gave rise to a new way of looking at and manipulating biological processes, called molecular biology. The breakthrough changed the face of biology and our lives forever. Watch The Double Helix short film (approximately 15 minutes) – hyperlinked here. 1 1/19/2017 1865 The Garden Pea 1865 The Garden Pea In 1865, Gregor Mendel established the foundation of genetics by unraveling the basic principles of heredity, though his work would not be recognized as “revolutionary” until after his death. By studying the common garden pea plant, Mendel demonstrated the inheritance of “discrete units” and introduced the idea that the inheritance of these units from generation to generation follows particular patterns. These patterns are now referred to as the “Laws of Mendelian Inheritance.” 2 1/19/2017 1869 The Isolation of “Nuclein” 1869 Isolated Nuclein Friedrich Miescher, a Swiss researcher, noticed an unknown precipitate in his work with white blood cells. Upon isolating the material, he noted that it resisted protein-digesting enzymes. Why is it important that the material was not digested by the enzymes? Further work led him to the discovery that the substance contained carbon, hydrogen, nitrogen and large amounts of phosphorus with no sulfur. -
Frederick Griffith and Transformation
Balderdash Example Griffith’s Transformation Experiment Ever since Edward Jenner invented the first vaccine in 1796 scientists have been working to vaccinate the world against all known diseases. Frederick Griffith wanted to save the world from pneumonia, a disease that was killing off much of Europe during the 1920’s. He didn’t build the pneumonia vaccine, but he did accidentally discover one of the most important concepts in bacterial survivability: Griffith discovered the principle of bacterial transformation. (In other words, why bacteria can fight off antibiotics) Griffith’s Transformation Experiment In 1928, Frederick Griffith was working with mice and two strains of Streptococcus pneumoniae One strain was “rough” in appearance and non-virulent, meaning that it wasn’t strong enough to hurt it’s host One strain was “smooth” in appearance and virulent. It was deadly to anyone who contracted the strain. The smooth strain looked smooth because it lacked a special protein coat that was rough in appearance and acted as a beacon summoning the mice’s immune systems. When injected with the rough (non-virulent) strain, mice lived When injected with the smooth (virulent) strain, mice died. Both as expected. Griffith’s Transformation Experiment Next, Griffith boiled the deadly, smooth strand of bacteria to kill it. He then injected mice with the deadly but boiled strand. Once again, as expected, the mice still lived. Finally, he injected the mice with BOILED smooth strands and LIVING rough strands The smooth strands are normally deadly, but Griffith had boiled them so they were not dangerous anymore. The rough strands were never deadly even when they were alive. -
Lesson Overview to Answer That Question, the First Thing You Need to 12.1 Identifying the Know Is What Genes Are Made Of
THINK ABOUT IT How do genes work? Lesson Overview To answer that question, the first thing you need to 12.1 Identifying the know is what genes are made of. Substance of Genes How would you go about figuring out what molecule or molecules go into making a gene? Griffith’s Experiments Bacterial Transformation Griffith isolated two different strains of the same bacterial The discovery of the chemical nature of the gene began in 1928 species. with British scientist Frederick Griffith, who was trying to figure Both strains grew very well in culture plates in Griffith’s lab, but out how certain types of bacteria produce pneumonia. only one of the strains caused pneumonia. The disease-causing bacteria (S strain) grew into smooth colonies on culture plates, whereas the harmless bacteria (R strain) produced colonies with rough edges. Griffith’s Experiments Griffith’s Experiments When Griffith injected mice with disease-causing bacteria, First, Griffith took a culture of the S strain, heated the cells the mice developed pneumonia and died. to kill them, and then injected the heat-killed bacteria into When he injected mice with harmless bacteria, the mice laboratory mice. stayed healthy. The mice survived, suggesting that the cause of pneumonia Perhaps the S-strain bacteria produced a toxin that made was not a toxin from these disease-causing bacteria. the mice sick? To find out, Griffith ran a series of experiments. Griffith’s Experiments Griffith’s Experiments In Griffith’s next experiment, he mixed the heat-killed, The lungs of these mice were filled with the disease-causing S-strain bacteria with live, harmless bacteria from the R bacteria. -
Ureaplasma Urealyticum and Ureaplasma Parvum
The Journal of Molecular Diagnostics, Vol. 13, No. 2, March 2011 Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved. DOI: 10.1016/j.jmoldx.2010.10.007 Modified Real-Time PCR for Detecting, Differentiating, and Quantifying Ureaplasma urealyticum and Ureaplasma parvum Ellen Vancutsem,* Oriane Soetens,* microbiological methods and are, therefore, usually re- Maria Breugelmans,† Walter Foulon,† ferred to as Ureaplasma species. They are found in the and Anne Naessens* lower genital tract of nearly 50% of pregnant women as part of the normal vaginal flora. However, in some cases, From the Departments of Microbiology and Infection Control* Ureaplasma species have interfered with normal fetal de- and Obstetrics,† Universitair Ziekenhuis Brussel, Brussels, velopment by causing an ascending infection.2–7 The Belgium reason for this infection is not fully understood but may be associated with the virulence of the microorganism, the host immune system, or local factors present in the lower We evaluated a previously described quantitative real- genital tract. Species differentiation might be important time PCR (qPCR) for quantifying and differentiating because previous studies2,8,9 suggest that nongonococ- Ureaplasma parvum and U. urealyticum. Because of cal urethritis and an adverse pregnancy outcome with nonspecific reactions with Staphylococcus aureus respect to birth weight, gestational age, and preterm DNA in the U. parvum PCR, we developed a modified delivery are implicated with the presence of U. urealyti- qPCR and designed new primers. These oligonucleo- cum and not with U. parvum. tides eradicated cross-reactions, indicating higher Because strains can only be differentiated with la- specificity. -
Mycoplasma Pirum Sp. Nov. a Terminal Structured Mollicute from Cell Cultures
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1985, p. 285-291 Vol. 35, No. 3 0020-7713/85/030285-07$02.00/0 Copyright 0 1985, International Union of Microbiological Societies Mycoplasma pirum sp. nov. a Terminal Structured Mollicute from Cell Cultures RICHARD A. DEL GIUDICE,'" JOSEPH G. TULLY,* DAVID L. ROSE,2 AND ROGER M. COLE3? Diagnostic Microbiology Laboratory, National Cancer Institute-Frederick Cancer Research Facility,' and Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases,2 Frederick, Maryland 21 701 and Laboratory of Streptococcal Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 202053 More than 200 mycoplasma isolates recovered from a variety of contaminated cell cultures from 1968 to the present were found to belong to a distinct serological group (serogroup 38). An analysis of representative strains of this collection showed that they possessed all of the characteristics of organisms belonging to the genus Mycoplasma. These organisms were capable of fermenting glucose and of hydrolyzing arginine, and they required cholesterol or serum for growth. These organisms were unusual in that they possessed an organized terminal structure or tip, a morphological structure which has been found in at least six other species in the genus Mycoplasma. These organisms were also serologically distinct from all previously established species in the genus Mycoplasma and the genus Acholeplasma. On the basis of these findings and other morphological, biological, and serological characteristics of the strains recovered, we propose that mycoplasmas with these properties belong to a new species, Mycoplasma pirum sp. nov. Strain HRC 70-159 (= ATCC 25960) is the type strain of this species. -
Invivogen Insight Newsletter: Mycoplasma
November/December 2005 An Insightful Look At InvivoGen’s Innovative Products Mycoplasma contamination remains a significant problem to Mycoplasma: The Insidious Invader of Cell Cultures the culture of mammalian cells. Mycoplasmas are the smallest and simplest and enzymatic procedures. However, none of these self-replicating organisms. Due to their seriously methods is 100% reliable. Direct growth methods are The detection of mycoplasma degraded genome they cannot perform many relatively sensitive to most species but the overall contamination is an important metabolic functions, such as cell wall production or procedure is lengthy (3 weeks), costly and less synthesis of nucleotides and amino acids. sensitive to noncultivable species. The PCR method, part of mycoplasma control and Mycoplasmas are strictly parasites. They parasitize a although rather fast and inexpensive, is limited by its should be an established wide range of organisms including humans, animals, sensitivity and the risk of positive and false negative method in every cell culture insects, and plants. results. Mycoplasma and Acholeplasma are Mollicutes, that InvivoGen has developed a new mycoplasma detection laboratory. InvivoGen is pleased comprise together more than 100 recognized species. method that promises to resolve these issues. This to introduce PlasmoTest™, a Among them, about 20 species have been described as method is based on the detection of mycoplasmas by contaminants of eukaryotic cell cultures. However engineered cells that express Toll-like receptor 2, a Mycoplasma detection kit based 5 species (Mycoplasma (M.) arginini, M. fermentans, pathogen recognition receptor that detects mycoplasmas. on a brand new technology. M. orale, M. hyorhinis and Acholeplasma laidlawii) PlasmoTest™, InvivoGen’s new mycoplasma detection are isolated in 90-95% of contaminated cell cultures1. -
Managing Science: Methodology and Organization of Research
Innovation, Technology, and Knowledge Management Series Editor Elias G. Carayannis, George Washington University, Washington D.C., USA For other titles published in this series, go to www.springer.com/series/8124 wwwwwwwww Frederick Betz Managing Science Methodology and Organization of Research Frederick Betz Department of Engineering and Technology Portland State University Portland, OR USA [email protected] ISBN 978-1-4419-7487-7 e-ISBN 978-1-4419-7488-4 DOI 10.1007/978-1-4419-7488-4 Springer New York Dordrecht Heidelberg London © Springer Science+Business Media, LLC 2011 All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com) For Nancy, my dear wife who has been with me on this journey through life, while also being a marvelously insightful editor. wwwwwwwww Series Foreword The Springer Book Series on Innovation, Technology, and Knowledge Management was launched in March 2008 as a forum and intellectual, scholarly “podium” for global/local (gloCal), transdisciplinary, trans-sectoral, public–private, leading/“bleeding”-edge ideas, theories, and perspectives on these topics. -
Discovery of the Secrets of Life Timeline
Discovery of the Secrets of Life Timeline: A Chronological Selection of Discoveries, Publications and Historical Notes Pertaining to the Development of Molecular Biology. Copyright 2010 Jeremy M. Norman. Date Discovery or Publication References Crystals of plant and animal products do not typically occur naturally. F. Lesk, Protein L. Hünefeld accidentally observes the first protein crystals— those of Structure, 36;Tanford 1840 hemoglobin—in a sample of dried menstrual blood pressed between glass & Reynolds, Nature’s plates. Hunefeld, Der Chemismus in der thierischen Organisation, Robots, 22.; Judson, Leipzig: Brockhaus, 1840, 158-63. 489 In his dissertation Louis Pasteur begins a series of “investigations into the relation between optical activity, crystalline structure, and chemical composition in organic compounds, particularly tartaric and paratartaric acids. This work focused attention on the relationship between optical activity and life, and provided much inspiration and several of the most 1847 HFN 1652; Lesk 36 important techniques for an entirely new approach to the study of chemical structure and composition. In essence, Pasteur opened the way to a consideration of the disposition of atoms in space.” (DSB) Pasteur, Thèses de Physique et de Chimie, Presentées à la Faculté des Sciences de Paris. Paris: Bachelier, 1847. Otto Funcke (1828-1879) publishes illustrations of crystalline 1853 hemoglobin of horse, humans and other species in his Atlas der G-M 684 physiologischen Chemie, Leizpig: W. Englemann, 1853. Charles Darwin and Alfred Russel Wallace publish the first exposition of the theory of natural selection. Darwin and Wallace, “On the Tendency of 1858 Species to Form Varieties, and on the Perpetuation of Varieties and G-M 219 Species by Natural Means of Selection,” J. -
NOTES: 12-1 DNA (History, Identifying the Substance of Genes)
NOTES: 12-1 DNA (History, Identifying the Substance of Genes) What we’ve learned so far… ● Cells make ● Genetic information is passed on through chromosomes ● = ● Genetic information is stored in the ● Genetic information is essential; each cell must receive all info. (ensured by ) Identifying the Substance of Genes: To truly understand genetics, biologists first had to discover the chemical nature of the gene. How do genes control what you look like? Vocabulary: Key Concepts: ● Transformation ● What did scientists discover about the relationship between genes and DNA? ● Bacteriophage ● What is the role of DNA in heredity? DNA’s “Experiment” History ● For thousands of years, humans have noticed that parents pass on traits to their offspring… ● What is the process and/or molecule that makes this possible…?? ● Frederick Griffith: How do certain types of bacteria cause pneumonia? -The experiment that tested this question led to new knowledge. -Genetic information could be ________________________ (passed) from one bacterium to another. TRANSFORMATION ● Heat killed pathogenic bacteria had passed their disease-causing ability to the harmless strain ● Griffith called this -One strain of bacteria (harmless) had changed into the other (harmful, or disease-causing) ● Some was transferred from the heat killed cells to the live cells -This factor might contain a with information that could change harmless bacteria into disease- causing ones! Avery & DNA ● Oswald Avery’s group of scientists decided to repeat Griffith’s experiment to determine which -
APUTS) Reporting Terminology and Codes Microbiology (V1.0
AUSTRALIAN PATHOLOGY UNITS AND TERMINOLOGY (APUTS) Reporting Terminology and Codes Microbiology (v1.0) 1 12/02/2013 APUTS Report Information Model - Urine Microbiology Page 1 of 1 Specimen Type Specimen Macro Time Glucose Bilirubin Ketones Specific Gravity pH Chemistry Protein Urobilinogen Nitrites Haemoglobin Leucocyte Esterases White blood cell count Red blood cells Cells Epithelial cells Bacteria Microscopy Parasites Microorganisms Yeasts Casts Crystals Other elements Antibacterial Activity No growth Mixed growth Urine MCS No significant growth Klebsiella sp. Bacteria ESBL Klebsiella pneumoniae Identification Virus Fungi Growth of >10^8 org/L 10^7 to 10^8 organism/L of mixed Range or number Colony Count growth of 3 organisms 19090-0 Culture Organism 1 630-4 LOINC >10^8 organisms/L LOINC Significant growth e.g. Ampicillin 18864-9 LOINC Antibiotics Susceptibility Method Released/suppressed None Organism 2 Organism 3 Organism 4 None Consistent with UTI Probable contamination Growth unlikely to be significant Comment Please submit a repeat specimen for testing if clinically indicated Catheter comments Sterile pyuria Notification to infection control and public health departments PUTS Urine Microbiology Information Model v1.mmap - 12/02/2013 - Mindjet 12/02/2013 APUTS Report Terminology and Codes - Microbiology - Urine Page 1 of 3 RCPA Pathology Units and Terminology Standardisation Project - Terminology for Reporting Pathology: Microbiology : Urine Microbiology Report v1 LOINC LOINC LOINC LOINC LOINC LOINC LOINC Urine Microbiology Report -
Moving Beyond Serovars
ABSTRACT Title of Document: MOLECULAR AND BIOINFORMATICS APPROACHES TO REDEFINE OUR UNDERSTANDING OF UREAPLASMAS: MOVING BEYOND SEROVARS Vanya Paralanov, Doctor of Philosophy, 2014 Directed By: Prof. Jonathan Dinman, Cell Biology and Molecular Genetics, University of Maryland College Park Prof. John I. Glass, Synthetic Biology, J. Craig Venter Institute Ureaplasma parvum and Ureaplasma urealyticum are sexually transmitted, opportunistic pathogens of the human urogenital tract. There are 14 known serovars of the two species. For decades, it has been postulated that virulence is related to serotype specificity. Understanding of the role of ureaplasmas in human diseases has been thwarted due to two major barriers: (1) lack of suitable diagnostic tests and (2) lack of genetic manipulation tools for the creation of mutants to study the role of potential pathogenicity factors. To address the first barrier we developed real-time quantitative PCRs (RT-qPCR) for the reliable differentiation of the two species and 14 serovars. We typed 1,061 ureaplasma clinical isolates and observed about 40% of isolates to be genetic mosaics, arising from the recombination of multiple serovars. Furthermore, comparative genome analysis of the 14 serovars and 5 clinical isolates showed that the mba gene, used for serotyping ureaplasmas was part of a large, phase variable gene system, and some serovars shown to express different MBA proteins also encode mba genes associated with other serovars. Together these data suggests that differential pathogenicity and clinical outcome of an ureaplasmal infection is most likely due to the presence or absence of potential pathogenicity factors in individual ureaplasma clinical isolates and/or patient to patient differences in terms of autoimmunity and microbiome. -
Rapid, Sensitive PCR-Based Detection of Mycoplasmas In
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Mar. 1994, p. 953-959 Vol. 60, No. 3 0099-2240/94/$04.00 +0 Copyright © 1994, American Society for Microbiology Rapid, Sensitive PCR-Based Detection of Mycoplasmas in Simulated Samples of Animal Sera OLIVIER DUSSURGET AND DAISY ROULLAND-DUSSOIX* Laboratoire des Mycoplasnes, Institut Pasteur, 75724 Paris Cedex 15, Franice Received 2 August 1993/Accepted 17 December 1993 A fast and simple method to detect mycoplasmal contamination in simulated samples of animal sera by using a PCR was developed. The following five mycoplasma species that are major cell culture contaminants belonging to the class Mollicutes were investigated: Mycoplasma arginini, Acholeplasma laidlawii, Mycoplasma hyorhinis, Mycoplasma orale, and Mycoplasma fermentans. After a concentration step involving seeded sera, genus-specific primers were used to amplify a 717-bp DNA fragment within the 16S rRNA gene of mycoplasmas. In a second step, the universal PCR was followed by amplification of variable regions of the 16S rRNA gene by using species-specific primers, which allowed identification of contaminant mycoplasmas. With this method, 10 fg of purified DNA and 1 to 10 color-changing units of mycoplasmas could be detected. Since the sensitivity of the assay was increased 10-fold when the amplification products were hybridized with an internal mycoplasma-specific 32P-labelled oligonucleotide probe, a detection limit of 1 to 10 genome copies per PCR sample was obtained. This highly sensitive, specific, and simple assay may be a useful alternative to methods currently used to detect mycoplasmas in animal sera. Mycoplasmas (the trivial name for microorganisms belong- Like most cell cultures infected by mycoplasmas, serum infec- ing to the class Molliclutes) are the smallest self-replicating tions are rarely detected by visual inspection or light micros- bacteria.