Introduction to Science and Infectious Diseases LECTURE NOTES PDF

INTRODUCTION TO SCIENCE AND INFECTIOUS DISEASES Chapters 1.3 and 2.3 - Types of microorganisms and Instruments of Microscopy LEARNING OBJECTIVES 1. Describe and discuss the characteristics of science including the scientific method (including a clear definition of the terms, hypot...

INTRODUCTION TO SCIENCE AND INFECTIOUS DISEASES Chapters 1.3 and 2.3 - Types of microorganisms and Instruments of Microscopy LEARNING OBJECTIVES 1. Describe and discuss the characteristics of science including the scientific method (including a clear definition of the terms, hypothesis, testing and theory) the requirement to publish, the material, quantitative, probabilistic and tentative nature of scientific knowledge and the use of modeling. 2. Use examples to distinguish between science and other ways of knowing 3. Describe the characteristics that distinguish the 6 kingdoms of life 4. Provide an overview of the field of microbiology 5. List the various types of microorganisms and describe their defining characteristics 6. Give examples of different types of cellular and viral microorganisms and infectious agents 7. Describe the distinguishing features and typical uses for various types of light microscopes, electron microscopes, and scanning probe microscopes  What is Science? Why should we trust science? https://slideplayer.com/slide/7570 434/ THE 6 KINGDOMS OF LIFE - TAXONOMY Current phylogenetic analyses include information from a range of sources, including morphological, genetic, and biochemical data* https://smartclass4kids.com/6-kingdoms-of-life/ CHARACTERISTICS OF EACH KINGDOM Biology 11, McGrawHill Ryerson TAXONOMY https://examples.yourdictionary.com/classification-of-living-things-basic-taxonomy-explained.html MICROBIOLOGY, A FIELD OF STUDY ▪ Microbiology : the study of all different types of microorganisms. ▪ Subfields: ▪ bacteriology is the study of bacteria; ▪ mycology is the study of fungi; ▪ protozoology is the study of protozoa; ▪ parasitology is the study of helminths and other parasites; ▪ virology is the study of viruses. ▪ Immunology, the study of the immune system, is often included in the study of microbiology because host–pathogen interactions are central to our understanding of infectious disease processes.  THE RELATIVE SIZES OF VARIOUS OBJECTS The relative sizes of various microscopic and nonmicroscopic objects. Note that a typical virus measures about 100 nm, 10 times smaller than a typical bacterium (~1 μm), which is at least 10 times smaller than a typical plant or animal cell (~10–100 μm). An object must measure about 100 μm to be visible without a microscope. PROKARYOTIC MICROORGANISMS: BACTERIA Bacteria are found in nearly every habitat on earth, including within and on humans. Most bacteria are harmless or helpful, but some are pathogens, causing disease in humans and other animals. Bacteria have a wide range of metabolic capabilities and can grow in a variety of environments, using different combinations of nutrients. Bacteria are often described in terms of their general shape. Common shapes include spherical (coccus), rod-shaped (bacillus), or curved (spirillum, spirochete, or vibrio): Common bacterial shapes. Note how coccobacillus is a combination of spherical (coccus) and rod-shaped (bacillus). (credit “Coccus”: modification of work by Janice Haney Carr, Centers for Disease Control and Prevention; credit “Coccobacillus”: modification of work by Janice Carr, Centers for Disease Control and Prevention; credit “Spirochete”: Centers for Disease Control and Prevention) PROKARYOTIC MICROORGANISMS: ARCHAEA Archaea are also unicellular prokaryotic organisms. Archaea and bacteria have different evolutionary histories, as well as significant differences in genetics, metabolic pathways, and the composition of their cell walls and membranes. They mainly differ by the cell wall composition. Like bacteria, archaea are found in nearly every habitat on earth, even extreme environments that are very cold, very hot, very basic, or very acidic. Some archaea live in the human body, but none have been shown to be human pathogens. EUKARYOTIC MICROORGANISM: PROTISTS Protists are an informal grouping of eukaryotes that are not plants, animals, or fungi. Algae and protozoa are examples of protists. Assorted diatoms, a kind of algae, live in annual sea ice in McMurdo Sound, Antarctica. Diatoms range in size from 2 μm to 200 μm and are visualized here using light microscopy. (credit: modification of work by National Oceanic and Atmospheric Administration) EUKARYOTIC MICROORGANISM: ALGAE Algae (singular: alga) are protists that can be either unicellular or multicellular and vary widely in size, appearance, and habitat. Their cells are surrounded by cell walls made of cellulose. Algae are photosynthetic organisms Many consumer products contain ingredients derived from algae, such as carrageenan or alginic acid, which are found in some brands of ice cream, salad dressing, beverages, lipstick, and toothpaste. Agar, a gel derived from algae plays a prominent role in the microbiology laboratory. can be mixed with various nutrients and used to grow microorganisms in a Petri dish. Algae are also being developed as a possible source for biofuels. EUKARYOTIC MICROORGANISMS: PROTOZOANS Protozoa (singular: protozoan) are protists that make up the backbone of many food webs by providing nutrients for other organisms. Protozoa are very diverse. Some protozoa are photosynthetic; others feed on organic material. Some are free-living, whereas others are Giardia lamblia, an intestinal protozoan parasite that infects parasitic, only able to survive by humans and other mammals, extracting nutrients from a host causing severe diarrhea. (credit: modification of work by Centers organism. for Disease Control and Prevention) Most protozoa are harmless, but some are pathogens that can cause disease in animals or humans. EUKARYOTIC MICROORGANISMS: FUNGI Fungi (singular: fungus) are also eukaryotes. Some multicellular fungi, such as mushrooms, resemble plants, but they are actually quite different. Fungi are not photosynthetic. EUKARYOTIC MICROORGANISMS: FUNGI Unicellular fungi—yeasts—are included within the study of microbiology. Some yeasts have beneficial uses, such as causing bread to rise and beverages to ferment; but yeasts can also cause food to spoil. Some even cause diseases, such as vaginal yeast infections and oral thrush. Candida albicans is a unicellular fungus, or yeast. It is the causative agent of vaginal yeast infections as well as oral thrush, a yeast infection of the mouth that commonly afflicts infants. C. albicans has a morphology similar to that of coccus bacteria; however, yeast is a eukaryotic organism (note the nuclei) and is much larger. (credit: modification of work by Centers for Disease Control and Prevention) EUKARYOTIC MICROORGANISMS: FUNGI Molds are multicellular organisms made up of long filaments (Hyphae) that form visible colonies. Molds are found in many different environments, from soil to rotting food to dank bathroom corners. Large colonies of microscopic fungi can often be observed with the naked eye, as seen on the surface of these moldy oranges. Molds play a critical role in the decomposition of dead plants and animals. Some molds can cause allergies, and others produce disease-causing metabolites called mycotoxins. Molds have been used to make pharmaceuticals, including penicillin, which is one of the most commonly prescribed antibiotics, and cyclosporine, used to prevent organ rejection following a transplant. EUKARYOTIC MICROORGANISMS: HELMINTHS Multicellular parasitic worms called helminths are not technically microorganisms, as most are large enough to see without a microscope. However, these worms fall within the field of microbiology because diseases caused by helminths involve microscopic eggs and larvae. Dracunculus medinensis, causes dizziness, vomiting, diarrhea, and painful ulcers on the legs and feet when the worm works its way out of the skin. (a) The beef tapeworm, Taenia saginata, infects both cattle and humans. T. saginata eggs are Infection typically occurs after a microscopic (around 50 μm), but adult worms like the one shown here can reach 4–10 m, taking up person drinks water containing residence in the digestive system. water fleas infected by guinea- (b) An adult guinea worm, Dracunculus medinensis, is removed through a lesion in the patient’s skin by worm larvae. winding it around a matchstick. (credit a, b: modification of work by Centers for Disease Control and Prevention) ACELLULAR MICROORGANISMS: VIRUSES Viruses are acellular microorganisms, which means they are not composed of cells. Essentially, a virus consists of proteins and genetic material— either DNA or RNA, but never both— that are inert outside of a host organism. However, by incorporating themselves into a host cell, viruses are able to co-opt the host’s cellular mechanisms to multiply and infect (a) Members of the Coronavirus family can cause other hosts. respiratory infections like the common cold, severe acute respiratory syndrome (SARS), and Middle East Viruses can infect all types of cells, respiratory syndrome (MERS). Here they are viewed from human cells to the cells of other under a transmission electron microscope (TEM). microorganisms. (b) Ebolavirus, a member of the Filovirus family, as In humans, viruses are responsible visualized using a TEM. (credit a: modification of work by Centers for Disease Control and Prevention; credit for numerous diseases, from the b: modification of work by Thomas W. Geisbert) common cold to deadly Ebola. However, many viruses do not cause disease. INSTRUMENTS OF MICROBIOLOGY In this section, we will survey the broad range of modern microscopic technology and common applications for each type of microscope: Light Microscopes: use lenses to focus light on a specimen to produce an image. Commonly Electron Microscopes: focus electrons on the specimen using magnets, producing much greater magnification than light microscopy. LIGHT MICROSCOPES The brightfield microscope, perhaps the most commonly used type of microscope, is a compound microscope with two or more lenses that produce a dark image on a bright background. Components of a typical brightfield microscope. Total magnification = ocular x objective if a 40⨯ objective lens is selected and the ocular lens is 10⨯, the total magnification would be (40×)(10×)=400× At very high magnifications, resolution may be compromised. To solve this problem, a drop of oil can be used to fill the space between the specimen and an oil immersion lens, a special lens designed to be used with immersion oils. DARKFIELD MICROSCOPE Use of a darkfield microscope allows us to view living, unstained samples of the spirochete Treponema pallidum. Similar to a photographic negative, the spirochetes appear bright against a dark background. (credit: Centers for Disease Control and Prevention) PHASE-CONTRAST MICROSCOPE This figure compares a brightfield image (left) with a phase-contrast image (right) of the same unstained simple squamous epithelial cells. The cells are in the center and bottom right of each photograph (the irregular item above the cells is acellular debris). Notice that the unstained cells in the brightfield image are almost invisible against the background, whereas the cells in the phase-contrast image appear to glow against the background, revealing far more detail. DIFFERENTIAL INTERFERENCE CONTRAST MICROSCOPE A DIC image of Fonsecaea pedrosoi grown on modified Leonian’s agar. This fungus causes chromoblastomycosis, a chronic skin infection common in tropical and subtropical climates. FLUORESCENCE MICROSCOPES (a)A direct immunofluorescent stain is used to visualize Neisseria gonorrhoeae, the bacterium that causes gonorrhea. (b)An indirect immunofluorescent stain is used to visualize larvae of Schistosoma mansoni, a parasitic worm that causes schistosomiasis, an intestinal disease common in the tropics. In direct immunofluorescence, the stain is absorbed by a primary antibody, which binds to the antigen. (c)In indirect immunofluorescence, the stain is absorbed by a secondary antibody, which binds to a primary antibody, which, in turn, binds to the antigen. (credit a: modification of work by Centers for Disease Control and Prevention; credit b: modification of work by Centers for Disease Control and Prevention) CONFOCAL MICROSCOPE Confocal microscopy can be used to visualize structures such as this roof-dwelling cyanobacterium biofilm. (credit: modification of work by American Society for Microbiology)  FIGURE 2.28 (credit “Brightfield”: modification of work by American Society for Microbiology; credit “Darkfield”: modification of work by American Society for Microbiology; credit “Phase contrast”: modification of work by American Society for Microbiology; credit “DIC”: modification of work by American Society for Microbiology; credit “Fluorescence”: modification of work by American Society for Microbiology; credit “Confocal”: modification of work by American Society for Microbiology; credit “Two-photon”: modification of work by Alberto Diaspro, Paolo Bianchini, Giuseppe Vicidomini, Mario Faretta, Paola Ramoino, Cesare Usai) ELECTRON MICROSCOPES The magnifying power of an electron microscope (EM) is very high, as it uses short-wavelength electron beams rather than light to increase magnification and resolution. Electrons, like electromagnetic radiation, can behave as waves, they can produce much better resolution than visible light. An EM can produce a sharp image that is magnified up to 100,000⨯. Thus, EMs can resolve subcellular structures as well as some molecular structures (e.g., single strands of DNA); however, electron microscopy cannot be used on living material because of the methods needed to prepare the specimens. ELECTRON MICROSCOPES (credit “TEM”: modification of work by American Society for Microbiology; credit “SEM”: modification of work by American Society for Microbiology) A TRANSMISSION ELECTRON MICROSCOPE (TEM). FIGURE 2.24 (a) This TEM image of cells in a biofilm shows well-defined internal structures of the cells because of varying levels of opacity in the specimen. (b) This color-enhanced SEM image of the bacterium Staphylococcus aureus illustrates the ability of scanning electron microscopy to render three-dimensional images of the surface structure of cells. (credit a: modification of work by American Society for Microbiology; credit b: modification of work by Centers for Disease Control and Prevention) FIGURE 2.26 In this image, multiple species of bacteria grow in a biofilm on stainless steel (stained with DAPI for epifluorescence miscroscopy). (credit: Ricardo Murga, Rodney Donlan) FIGURE 2.27 STMs and AFMs allow us to view images at the atomic level. (a) This STM image of a pure gold surface shows individual atoms of gold arranged in columns. (b) This AFM image shows long, strand-like molecules of nanocellulose, a laboratory-created substance derived from plant fibers. (credit a: modification of work by “Erwinrossen”/Wikimedia Commons) This OpenStax ancillary resource is © Rice University under a CC-BY 4.0 International license; it may be reproduced or modified but must be attributed to OpenStax, Rice University and any changes must be noted.