Cornelius Bernardus Van Niel
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And the Winner Should Be
EDITORIAL And the winner should be… It is time that the tremendous contribution made by Carl Woese to microbiology, medicine and biology as a whole is rewarded by the Nobel committee. Among microbiologists, Carl Woese’s achievements are isolates can allow rapid disease diagnosis. As culturing is well known. His most lauded accomplishments include the not required, sequence analysis can be used to diagnose recognition of an entirely new domain of organisms, many different infectious diseases and is now common in the Archaea1, and the subsequent introduction of the clinical diagnostic laboratories. In the case of Whipple’s three-domain phylogeny2 that is now widely recognized as disease, it even led to the identification of a previously the most accurate reflection of the relatedness of all organ- unknown bacterium (Tropheryma whipplei) as the cause4. isms. We are so used to using neatly organized taxonomic Second, using 16S rRNA-based phylogeny, it is possible to trees to demonstrate the relationships between different study the human microbiota at a detailed level. In recent microorganisms that it is easy to forget that not so long ago years, we have begun to obtain a comprehensive picture the classification of bacteria was considered hopeless. In of the composition of the human-associated microbiota 1963 Roger Stanier, then one of the foremost researchers in various niches, including the gut, skin and oral cavity. in the field of bacterial classification, proclaimed that “The This has led to the insight that shifts in the gut-associated ultimate scientific goal of biological classification cannot microbiota are associated with diseases such as Crohn’s be achieved in the case of bacteria” (REF. -
Introduction to Bacteriology and Bacterial Structure/Function
INTRODUCTION TO BACTERIOLOGY AND BACTERIAL STRUCTURE/FUNCTION LEARNING OBJECTIVES To describe historical landmarks of medical microbiology To describe Koch’s Postulates To describe the characteristic structures and chemical nature of cellular constituents that distinguish eukaryotic and prokaryotic cells To describe chemical, structural, and functional components of the bacterial cytoplasmic and outer membranes, cell wall and surface appendages To name the general structures, and polymers that make up bacterial cell walls To explain the differences between gram negative and gram positive cells To describe the chemical composition, function and serological classification as H antigen of bacterial flagella and how they differ from flagella of eucaryotic cells To describe the chemical composition and function of pili To explain the unique chemical composition of bacterial spores To list medically relevant bacteria that form spores To explain the function of spores in terms of chemical and heat resistance To describe characteristics of different types of membrane transport To describe the exact cellular location and serological classification as O antigen of Lipopolysaccharide (LPS) To explain how the structure of LPS confers antigenic specificity and toxicity To describe the exact cellular location of Lipid A To explain the term endotoxin in terms of its chemical composition and location in bacterial cells INTRODUCTION TO BACTERIOLOGY 1. Two main threads in the history of bacteriology: 1) the natural history of bacteria and 2) the contagious nature of infectious diseases, were united in the latter half of the 19th century. During that period many of the bacteria that cause human disease were identified and characterized. 2. Individual bacteria were first observed microscopically by Antony van Leeuwenhoek at the end of the 17th century. -
1 Molecular Analysis of Honey Bee Foraging Ecology Dissertation
Molecular analysis of honey bee foraging ecology Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Rodney Trey Richardson Graduate Program in Entomology The Ohio State University 2018 Dissertation Committee Professor Reed Johnson, Advisor Professor Mary Gardiner Professor John Christman Professor Roman Lanno 1 Copyrighted by Rodney Trey Richardson 2018 2 Abstract While numerous factors currently impact the health of honey bees and other pollinating Hymenoptera, poor floral resource availability due to habitat loss and land conversion is thought to be important. This issue is particularly salient in the upper Midwest, a location which harbors approximately 60 percent of the US honey bee colonies each summer for honey production. This region has experienced a dramatic expansion in the area devoted to crop production over the past decade. Consequently, understanding how changes to landscape composition affect the diversity, quality and quantity of available floral resources has become an important research goal. Here, I developed molecular methods for the identification of bee-collected pollen by adapting and improving upon the existing amplicon sequencing infrastructure used for microbial community ecology. In thoroughly benchmarking our procedures, I show that a simple and cost-effective three-step PCR-based library preparation protocol in combination with Metaxa2-based hierarchical classification yields an accurate and highly quantitative pollen metabarcoding approach when applied across multiple plant markers. In Chapter 1, I conducted one of the first ever proof-of-concept studies applying amplicon sequencing, or metabarcoding, to the identification of bee-collected pollen. -
The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment
life Article The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment Sierra R. Athen, Shivangi Dubey and John A. Kyndt * College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA; [email protected] (S.R.A.); [email protected] (S.D.) * Correspondence: [email protected] Abstract: The Eastern Nebraska Salt Marshes contain a unique, alkaline, and saline wetland area that is a remnant of prehistoric oceans that once covered this area. The microbial composition of these salt marshes, identified by metagenomic sequencing, appears to be different from well-studied coastal salt marshes as it contains bacterial genera that have only been found in cold-adapted, alkaline, saline environments. For example, Rubribacterium was only isolated before from an Eastern Siberian soda lake, but appears to be one of the most abundant bacteria present at the time of sampling of the Eastern Nebraska Salt Marshes. Further enrichment, followed by genome sequencing and metagenomic binning, revealed the presence of several halophilic, alkalophilic bacteria that play important roles in sulfur and carbon cycling, as well as in nitrogen fixation within this ecosystem. Photosynthetic sulfur bacteria, belonging to Prosthecochloris and Marichromatium, and chemotrophic sulfur bacteria of the genera Sulfurimonas, Arcobacter, and Thiomicrospira produce valuable oxidized sulfur compounds for algal and plant growth, while alkaliphilic, sulfur-reducing bacteria belonging to Sulfurospirillum help balance the sulfur cycle. This metagenome-based study provides a baseline to understand the complex, but balanced, syntrophic microbial interactions that occur in this unique Citation: Athen, S.R.; Dubey, S.; inland salt marsh environment. -
Open Thweattetd1.Pdf
The Pennsylvania State University The Graduate School CHARACTERIZATION OF PIGMENT BIOSYNTHESIS AND LIGHT-HARVESTING COMPLEXES OF SELECTED ANOXYGENIC PHOTOTROPHIC BACTERIA A Dissertation in Biochemistry, Microbiology, and Molecular Biology and Astrobiology by Jennifer L. Thweatt 2019 Jennifer L. Thweatt Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy December 2019 ii The dissertation of Jennifer L. Thweatt was reviewed and approved* by the following: Donald A. Bryant Ernest C. Pollard Professor in Biotechnology and Professor of Biochemistry and Molecular Biology Dissertation Advisor Chair of Committee Squire J. Booker Howard Hughes Medical Investigator Professor of Chemistry and Professor of Biochemistry and Molecular Biology Eberly Distinguished Chair in Science John H. Golbeck Professor of Biochemistry and Biophysics Professor of Chemistry Jennifer L. Macalady Associate Professor of Geosciences Timothy I. Miyashiro Assistant Professor of Biochemistry and Molecular Biology Wendy Hanna-Rose Professor of Biochemistry and Molecular Biology Department Head, Biochemistry and Molecular Biology *Signatures are on file in the Graduate School iii ABSTRACT This dissertation describes work on pigment biosynthesis and the light-harvesting apparatus of two classes of anoxygenic phototrophic bacteria, namely the green bacteria and a newly isolated purple sulfur bacterium. Green bacteria are introduced in Chapter 1 and include chlorophototrophic members of the phyla Chlorobi, Chloroflexi, and Acidobacteria. The green bacteria are defined by their use of chlorosomes for light harvesting. Chlorosomes contain thousands of unique chlorin molecules, known as bacteriochlorophyll (BChl) c, d, e, or f, which are arranged in supramolecular aggregates. Additionally, all green bacteria can synthesize BChl a, the and green members of the phyla Chlorobi and Acidobacteria can synthesize chlorophyll (Chl) a. -
Bee Pollen Diet Alters the Bacterial Flora and Antimicrobial Peptides in the Oral Cavities of Mice
foods Article Bee Pollen Diet Alters the Bacterial Flora and Antimicrobial Peptides in the Oral Cavities of Mice Ariuntsetseg Khurelchuluun 1,2,† , Osamu Uehara 3,† , Durga Paudel 1 , Tetsuro Morikawa 1, Yutaka Kawano 4 , Mashu Sakata 5, Hiroshi Shibata 5, Koki Yoshida 1 , Jun Sato 1, Hiroko Miura 3, Hiroki Nagayasu 2 and Yoshihiro Abiko 1,* 1 Division of Oral Medicine and Pathology, Department of Human Biology and Pathophysiology, School of Dentistry, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293, Japan; [email protected] (A.K.); [email protected] (D.P.); [email protected] (T.M.); [email protected] (K.Y.); [email protected] (J.S.) 2 Division of Oral and Maxillofacial Surgery, Department of Human Biology and Pathophysiology, School of Dentistry, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293, Japan; [email protected] 3 Division of Disease Control and Molecular Epidemiology, Department of Oral Growth and Development, School of Dentistry, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293, Japan; [email protected] (O.U.); [email protected] (H.M.) 4 Institute of Preventive Medical Science, Health Sciences University of Hokkaido, Ainosato 2-5, Kita-ku, Sapporo, Hokkaido 002-8072, Japan; [email protected] 5 Belle Coeur Institute, Utsukushigaoka 5-9-10-30, Kiyota-ku, Sapporo, Hokkaido 004-0851, Japan; [email protected] (M.S.); [email protected] (H.S.) * Correspondence: [email protected]; Tel.: +81-133-23-1390 † Both authors contributed equally to this work. -
History of the Department of Microbiology 1868 – 2009
June 2015 HISTORY OF THE DEPARTMENT OF MICROBIOLOGY 1868 – 2009 University of Illinois at Urbana-Champaign 1 A HISTORY OF THE DEPARTMENT OF MICROBIOLOGY 1868 – 2009 This 141 year history of the Department of Microbiology includes an article (Chapter 1), written and published in 1959 by the Department, which covers the period 1868 to 1959. I joined the Department in 1953, and my recounting of the Department’s history includes personal observations as well as anecdotes told to me by H. O. Halvorson and others. Later I realized what a unique experience it had been to join a first-class department, and I resolved to play a role in maintaining its research stature. Ralph Wolfe 2 Department of Microbiology History of the Headship: 1950 – 1959 Halvor Halvorson 1960 – 1963 Kim Atwood 1963 – 1972 Leon Campbell 1972 – 1982 Ralph DeMoss 1982 – 1987 Samuel Kaplan 1987 – 1990 Jordan Konisky 1990 – 1991 Ralph Wolfe (Acting Head) 1991 – 1997 Charles Miller 1997 – 2002 John Cronan 2003 – 2004 Jeffrey Gardner (Acting Head) 2005 – Present John Cronan 3 Organization of the History of the Department In Chapters 2 to 6 the data are divided into Academic Decades, each containing the following sections: Section I, an overview of the decade; Section II, some events for each year of the decade; Section III, a summary of the research interests, honors received, publications, and invited off-campus lectures or seminars for each faculty member. These data have been obtained from the annual reports of the faculty submitted to the departmental secretary. 4 CHAPTER 1 1868 – 1959 During this time period the name of the Department was Department of Bacteriology (Anecdotes by Ralph Wolfe) A SHORT HISTORY OF THE DEPARTMENT OF BACTERIOLOGY H. -
Effects of Shade Stress on Morphophysiology and Rhizosphere Soil Bacterial Communities of Two Contrasting Shade-Tolerant Turfgrasses
Effects of shade stress on morphophysiology and rhizosphere soil bacterial communities of two contrasting shade-tolerant turfgrasses Juanjuan Fu ( [email protected] ) Northwest Agriculture and Forestry University https://orcid.org/0000-0001-8178-6698 Yilan Luo Northwest A&F University Pengyue Sun Northwest A&F University Jinzhu Gao Northwest A&F University Donghao Zhao Northwest A&F University Peizhi Yang Northwest A&F University Tianming Hu Northwest A&F University Research article Keywords: Community structure and diversity, Rhizosphere bacteria, Shade stress, Shade tolerance, 16S rRNA gene sequencing Posted Date: June 13th, 2019 DOI: https://doi.org/10.21203/rs.2.10288/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/14 Abstract Background: Perturbations in the abiotic stress directly or indirectly affect plants and root-associated microbial communities. Shade stress presents one of the major abiotic limitations for turfgrass growth, as light availability is severely reduced under a leaf canopy. Studies have shown that shade stress inuences plant growth and alters plant metabolism, yet little is known about how it affects the structure of rhizosphere soil bacterial communities. In this study, a glasshouse experiment was conducted to examine the impact of shade stress on the physiology of two contrasting shade-tolerant turfgrasses and their rhizosphere soil microbes. Shade-tolerant dwarf lilyturf (Ophiopogon japonicus, OJ) and shade- intolerant perennial turf-type ryegrasss (Lolium perenne, LP) were used. Bacterial community composition was assayed using high-throughput sequencing. Results: Our physiochemical data showed that under shade stress, OJ maintained higher photosynthetic capacity and root growth, thus OJ was found to be more shade-tolerant than LP. -
Lecture 6 Gram Posi/Ve & Nega/Ve Bacteria
هذا العمل ل يغني عن الرجع الساسي للمذاكرة Lecture 6 Gram Posi0ve & Negave Bacteria • Important • Term • Extra explanaon • Addi0onal notes Objectives • Know the general basic characteristics of bacteria. • Differentiate between gram positive and gram negative bacteria characteristics. • Know the classes and groups of gram positive bacteria and gram negative, cocci and bacilli (rods). • Know the common identification characteristic of these groups. • Know the common infections and diseases caused by these organisms and the antibiotics used for their treatment. Gram Stain • Developed in 1884 by the Danish physician Hans Christian Gram • An important tool in bacterial taxonomy (the branch of science concerned with classification), distinguishing so-called Gram-positive bacteria, which remain colored after the staining procedure, from Gram- negative bacteria, which do not retain dye and need to be counter- stained. • Can be applied to pure cultures of bacteria or to clinical specimens. Type Gram positive cell wall Gram negative cell wall • Thick, homogenous sheath of • Outer membrane containing peptidoglycan 20-80 nm thick lipopolysaccharide (LPS) • Tightly bound acidic • Thin shell of peptidoglycan Consist of polysaccharides, including • Periplasmic space (between the teichoic acid and lipoteichoic cell wall & plasma membrane) acid • Inner membrane • Cell membrane Retain crystal violet and stain Lose crystal violet and stain PINK stain PURPLE or BLUE or RED from safranin counterstain counterstain Safraninٍ تتفظ هذه البكتيريا بلونها بعد أن حتى ل تنسى تذكر أن: تصبغت بصبغة جرام مهما تعرضت الزعفران لونه أحمر و نوع هذه لي مادة كيميائية، فهي كالكرستال البكتيريا تتصبغ باللون الحمر قوية وصلبة Gram Stain لحظ كيف اختفى اللون البنفسجي وأصبحت بل لون (Decolorization) Or acetone Gram Stain Gram Negative Baciili(rods) E.Coli ( Pure culture ) Gram Negative Cocci With Pus Cells Neisseria gonorrhoeae (Smear of urethral pus) - Clinical specimen Gram Positive Bacteria Occurring optionally in response to circumstances rather than by nature. -
Veterinary Parasitology
Andrei Daniel MIHALCA Textbook of Veterinary Parasitology Introduction to parasitology. Protozoology. AcademicPres Andrei D. MIHALCA TEXTBOOK OF VETERINARY PARASITOLOGY Introduction to parasitology Protozoology AcademicPres Cluj-Napoca, 2013 © Copyright 2013 Toate drepturile rezervate. Nici o parte din această lucrare nu poate fi reprodusă sub nici o formă, prin nici un mijloc mecanic sau electronic, sau stocată într-o bază de date, fără acordul prealabil, în scris, al editurii. Descrierea CIP a Bibliotecii Naţionale a României Mihalca Andrei Daniel Textbook of Veterinary Parasitology: Introduction to parasitology; Protozoology / Andrei Daniel Mihalca. Cluj-Napoca: AcademicPres, 2013 Bibliogr. Index ISBN 978-973-744-312-0 339.138 Director editură – Prof. dr. Carmen SOCACIU Referenţi ştiinţifici: Prof. Dr. Vasile COZMA Conf. Dr. Călin GHERMAN Editura AcademicPres Universitatea de Ştiinţe Agricole şi Medicină Veterinară Cluj-Napoca Calea Mănăştur, nr. 3-5, 400372 Cluj-Napoca Tel. 0264-596384 Fax. 0264-593792 E-mail: [email protected] Table of contents 1 INTRODUCTION TO PARASITOLOGY ..................................................................................... 1 1.1 DEFINING PARASITOLOGY. DIVERSITY OF PARASITISM IN NATURE. ................................................. 1 1.2 PARASITISM AS AN INTERSPECIFIC INTERACTION ............................................................................... 2 1.3 AN ECOLOGICAL APPROACH TO PARASITOLOGY ................................................................................... 5 1.4 -
Molecular Systematics of Cyanobacteria
MOLECULAR SYSTEMATICS OF CYANOBACTERIA Submitted by Elvina Lee Mei Hui, BSc (Hons) This thesis is presented for the degree of Doctor of Philosophy of Murdoch University i DECLARATION I declare that this thesis is my own account of my research and contains as its main content work, which has not been previously submitted for a degree at any tertiary education institution. ______________________________ Elvina Lee January 2016 ii ABSTRACT Cyanobacteria constitute a phylum of ubiquitous cosmopolitan bacteria with the ability to perform oxygenic photosynthesis. Their ancient origins, ecological and economic potential, biotechnological applications and impact on water systems have attracted much interest from the academia, industry, health authorities and regulators. Despite this, cyanobacteria classification and nomenclature still remains difficult. One of the aims of this project was to further our understanding of cyanobacteria systematics by (1) testing polyphasic characterization methods and (2) examining the effect of various phylogenetic reconstruction strategies. Additionally, (3) Next Generation Sequencing (NGS) assays using novel cyanobacteria 16S rDNA targeted primers were implemented to provide better taxa resolution than that offered by “universal” 16S rDNA primers. Cyanobacteria strains from various water sources in Australia were isolated, characterised at four loci commonly used for cyanobacteria molecular classification, and tested for the presence of genes implicated in toxin and terpene (odour) production. A total of 55 novel cyanobacterial strains were isolated and maintained in culture, forming the first known collection of cyanobacteria isolates from Western Australia. Comparison of molecular– and morphology– based identifications not only showed the limitations of the current methods (only 45% of the isolates showed agreement) but also provided the opportunity to suggest guidelines and conceive a way forward towards more effective identification approaches. -
Periodontal Disease and the Oral Microbiota in New-Onset Rheumatoid Arthritis
Full Length Arthritis & Rheumatism DOI 10.1002/art.34539 Periodontal Disease and the Oral Microbiota in New-Onset Rheumatoid Arthritis Jose U. Scher,1* Carles Ubeda,2,5* Michele Equinda,2 Raya Khanin,2 Yvonne Buischi,3 Agnes Viale,2 Lauren Lipuma,2 Mukundan Attur,1 Michael H. Pillinger,1 Gerald Weissmann,4 Dan R. Littman,4 Eric G. Pamer,2 Walter A. Bretz,3 and Steven B. Abramson1 1Jose U. Scher, MD, Mukundan Attur, PhD, Michael H. Pillinger, MD, Steven B. Abramson, MD: New York University School of Medicine and NYU Hospital for Joint Diseases, New York, New York; 2Carles Ubeda, PhD, Michele Equinda, BS, Raya Khanin, PhD, MSc, Agnes Viale, PhD, Lauren Lipuma, MS, Eric G. Pamer, MD: Memorial Sloan-Kettering Cancer Center, The Lucille Castori Center for Microbes, Inflammation and Cancer, New York, New York; 3Yvonne Buischi, DDS, PhD, Walter A. Bretz, DDS, DrPH: NYU College of Dentistry, New York, New York; 4Gerald Weissmann, MD, Dan R. Littman, MD, PhD: New York University School of Medicine, New York, New York; 5Carles Ubeda, PhD, current address: Department of Genomics and Health, Center for Advanced Research in Public Health, Valencia, Spain. * Drs. Scher and Ubeda contributed equally to this work. ClinicalTrials.gov identifier: NCT01198509 Supported by Grant No. RC2 AR058986 to Drs. Abramson and Littman from the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) through the American Recovery and Reinvestment Act (ARRA) of 2009. and by a KL2 Program in Translational Research to Dr. Scher, Grant No. 1 UL1 RR029893 from the National Center for Research Resources, NIH.