Through the microscope: A look at all things small

Dedication

• Chapter 1 The Relevance and History of Microbiology
  • 1-1 Introduction
  • 1-2 Microbes have a large impact on human health
  • 1-3 Microbes are often helpful, not harmful
  • 1-4 Microbes have profound effects on the environment
  • 1-5 Studying microbes helps us to understand the world around us
  • 1-6 The history of microbiology is a web of discoveries
  • 1-7 Microscopes allowed the discovery of microbes
  • 1-8 Robert Koch developed many microbiological techniques
  • 1-9 Spontaneous generation was an attractive theory to many people, but was ultimately disproven.
  • 1-10 Microbes are discovered to cause disease
  • 1-11 Viruses are shown to parasitize organisms
  • 1-12 The power of vaccination is discovered
  • 1-13 Antimicrobial compounds are developed to kill microorganisms
  • 1-14 Beijerinck and Winogradsky initiate the field of environmental microbiology
  • 1-15 Studying microbes provides insight into life at the molecular level
  • 1-16 Work on microbes paves the way to taking control of the genome
  • 1-17 Summary
• Chapter 2 Cell structure and organization
  • 2-1 Introduction
  • 2-2 Sugars are common in the cell
  • 2-3 Nucleic acids store information and process it
  • 2-4 Proteins are made of amino acids
  • 2-5 The primary structure of proteins is the amino acid sequence
  • 2-6 Secondary structure is the local geometry of the protein
  • 2-7 Tertiary structure is the 3D structure of individual polypeptides
  • 2-8 Quaternary structure is the total complex of a functional protein
  • 2-9 Lipids are the building blocks of membranes
  • 2-10 Small molecules are also important in the cell
  • 2-11 The cell is organized into functional units
  • 2-12 Membranes surround the cell and hold it in
  • 2-13 Membranes are a selective barrier
  • 2-14 Membranes can help generate energy
  • 2-15 Membranes are also important in their own synthesis and can fold inward for specialized functions
  • 2-16 The cytoplasm is the area inside the membrane
  • 2-17 Enzymes serve as catalysts in the cytoplasm
  • 2-18 The cell DNA is organized into a nucleoid
  • 2-19 Transcription and translation occur on the surface of the nucleoid
  • 2-20 Translation involves messenger RNA
  • 2-21 Ribosomes are composed of RNA and protein
  • 2-22 Transfer RNA is the ferry for amino acids
  • 2-23 Inclusions and other internal structures are found in many prokaryotic cells
  • 2-24 The periplasm is between the cytoplasmic and outer membranes in gram-negative bacteria
  • 2-25 The cell wall surrounds and holds in the microbe
  • 2-26 Some bacteria lack cell walls
  • 2-27 The cell surface extends into the environment
  • 2-28 Flagella are one type of structure used for motility
  • 2-29 Advantages of motility
  • 2-30 Some bacteria move by gliding motility
  • 2-31 Pili and fimbriae are involved in adhesion, motility and DNA exchange
  • 2-32 Bacterial cells are often covered in glycocalyx
  • 2-33 Bacteria can exist in different cell states
  • 2-34 Endospores are very resistant structures
  • 2-35 Some microbes make other types of spores
  • 2-36 Heterocysts are differentiated cells that specialize in nitrogen fixation
  • 2-37 Archaea, a different type of microbe
  • 2-38 The major differences between Archaea and other domains of life
  • 2-39 Eukaryotic cells have much in common with prokaryotic cells
  • 2-40 Things that are different between eukaryotes and prokaryotes
  • 2-41 Unique structures in eukaryotes
  • 2-42 Eukaryotic cells absorb things by endocytosis
  • 2-43 The nucleus holds the cells genetic material in eukaryotes
  • 2-44 Mitochondria and plastids are organelles of energy generation in eukaryotic cells
  • 2-45 The implications of eukaryotic structures on their growth
  • 2-46 Summary
• Chapter 3 Viral Structure and function
  • 3-1 Introduction
  • 3-2 Viruses face several common obstacles that they must overcome to successfully replicate
  • 3-3 Viruses often have common structures
  • 3-4 The genome of viruses can be DNA or RNA
  • 3-5 Viruses are classified by the nature of their viral nucleic acid
  • 3-6 The life cycle of a virus is divided into several phases
  • 3-7 To infect cells, viruses first need to attach to them.
  • 3-8 Bacterial viruses almost always enter cells by injecting their nucleic acid.
  • 3-9 Entry of eukaryotic viruses can involve penetration at the membrane or use of natural uptake pathways.
  • 3-10 Viruses are lytic or lysogenic
  • 3-11 The lytic cycle requires copying of the nucleic acid genome.
  • 3-12 Viruses regulate viral protein production in a manner consistent with their host
  • 3-13 After the parts of the virus are synthesized, they assemble into complete virions.
  • 3-14 The lytic cycle ends with release of the finished virions from the cell.
  • 3-15 Summary
• Chapter 4 The Central Dogma
  • 4-1 Introduction
  • 4-2 The DNA sequence directs the synthesis of proteins
  • 4-3 DNA Replication uses a collection of proteins called a replication complex
  • 4-4 After replication, the two copies of the chromosome move to opposite ends of the microbe
  • 4-5 Not all DNA in the prokaryotic cell is chromosomal: the specific case of plasmids
  • 4-6 Plasmids can vary in size and number
  • 4-7 Errors can occur in DNA replication that create potential mutations
  • 4-8 Errors in DNA can also occur outside of replication
  • 4-9 SOS repair can fix serious errors in the DNA, but is error prone
  • 4-10 Recombination repair can accurately fix large errors in the DNA
  • 4-11 There are more complicated mutations: deletions, duplications, and amplifications
  • 4-12 Mobile genetic elements can also cause mutations in the chromosome
  • 4-13 Genetic changes do not become fixed in the DNA until they are copied
  • 4-14 Transcription involves the copying of DNA into RNA
  • 4-15 The level of mRNA is a common regulatory point in prokaryotes
  • 4-16 Prokaryotic mRNAs are typically more than one gene long
  • 4-17 Differential transcription and stability of mRNA can also be used as points of regulation
  • 4-18 Translation is the conversion of mRNA into protein at the ribosome
  • 4-19 Translation is initiated at the Shine-Dalgarno sequence and involves formyl methionine (fMet)
  • 4-20 Some interesting facts about translation
  • 4-21 Chapter summary
• Chapter 5 Microbial Nutrition
  • 5-1 Introduction
  • 5-2 The cell is made up of a few common elements
  • 5-3 Microbes can be classified based upon their nutritional requirements
  • 5-4 Examples of Nutritional Classifications
  • 5-5 Culture Media
  • 5-6 Media can come in both liquid and solid form.
  • 5-7 Culture media is as varied as the microorganisms that grow in it.
  • 5-8 Media can be classified into several different categories
  • 5-9 Sterilization of media
  • 5-10 Chapter Summary
• Chapter 6 Microbial Growth
  • 6-1 Introduction
  • 6-2 Growth for microorganisms is defined as an increase in numbers
  • 6-3 Unicellular microbes grow by cell division
  • 6-4 Cell division is a complex process
  • 6-5 Measurement of cell growth can be accomplished in a number of ways
  • 6-6 Growth in batch culture has four separate phases
  • 6-7 Lag phase is the time before cell growth begins
  • 6-8 In exponential phase, cells begin to divide
  • 6-9 The growth rate in exponential phase can be modeled mathematically
  • 6-10 Cells stop increasing in number during stationary phase
  • 6-11 Cells at some point can no longer sustain themselves and death phase begins
  • 6-12 Continuous culture is an open system where microbes can be maintained in exponential phase
  • 6-13 The environment greatly affects the growth of microbes
  • 6-14 Temperature affects the rate of growth.
  • 6-15 Microbes respond differently to the presence of oxygen.
  • 6-16 The hydrogen ion concentration (pH) affects growth of microbes
  • 6-17 The availability of water or concentration of solutes influences the ability of microbes to grow
  • 6-18 Summary
• Chapter 7 Control of Microbes
  • 7-1 Introduction
  • 7-2 Temperature is a common physical method for controlling microbes
  • 7-3 Empirical data can be used to predict the success of a heat treatment
  • 7-4 Some historical methods of heat treatment are still useful in certain situations
  • 7-5 Autoclaving, dry heat and pasteurization are common methods of heat treatment
  • 7-6 Low temperature slows or stops the growth of microbes
  • 7-7 Irradiation damages critical cellular processes, killing microbes
  • 7-8 Filtration physically removes microbes from a solution
  • 7-9 Reducing the water activity of a sample can prevent the growth of microbes
  • 7-10 Chemical treatments act on microbes to prevent their growth
  • 7-11 Antiseptics and disinfectants control microbes on surfaces
  • 7-12 Preservatives control the growth of microbes in foods
  • 7-13 Antibiotics and chemotherapeutic agents help to control pathogenic microbes in the body
  • 7-14 Antimicrobial activity is measured using standard tests
  • 7-15 Summary
• Chapter 8 Metabolism
  • 8-1 Introduction
  • 8-2 As are all things, microbes are subject to the laws of thermodynamics
  • 8-3 Free Energy (ΔG) is what cells are after
  • 8-4 Cells often perform useful work through oxidation-reduction reactions (redox reactions)
  • 8-5 Energy in the cell is carried by special molecules
  • 8-6 Enzymes are biological catalysts
  • 8-7 Enzymes are often organized in the cell into functional units
  • 8-8 Bacterial diversity is mainly manifested as catabolic diversity
  • 8-9 Fermentations in microbes share some common properties
  • 8-10 The Embden-Meyerhof-Parnas pathway (EMP) is a very common glycolytic pathway
  • 8-11 For anaerobes, the EMP pathway results in an excess of NADH, which is dealt with by reducing pyruvate to fermentation end products.
  • 8-12 The Entner-Doudoroff pathway is a third common pathway for the catabolism of glucose
  • 8-13 Respiration involves donation of electrons to an inorganic terminal electron acceptor
  • 8-14 Catabolism of sugar (glucose) through respiration involves the tricarboxylic acid cycle
  • 8-15 Catabolism of fats (lipids) uses β-oxidation
  • 8-16 High-energy electrons are converted into ATP using a membrane
  • 8-17 Protons move across the membrane during ETS
  • 8-18 ATP synthesis involves protons moving through ATP synthase
  • 8-19 Many microbes are capable of anaerobic respiration
  • 8-20 Nitrate reduction can generate energy, but not as much as aerobic respiration
  • 8-21 Sulfate reduction is common in anaerobic environments
  • 8-22 Carbonate can also serve as a terminal electron acceptor
  • 8-23 Some microbes can grow completely on inorganic sources of carbon, energy and electrons
  • 8-24 Nitrifying bacteria are chemoautotrophic lithotrophs that use ammonia as a source of energy and electrons.
  • 8-25 Chapter Summary
• Chapter 9 Photosynthesis
  • 9-1 Introduction
  • 9-2 Photosynthetic microbes have several common characteristics
  • 9-3 Light is collected by protein complexes containing photopigments
  • 9-4 Chlorophyll is the molecule that collects light and energizes an electron, while carotenoid protects the cell from the damaging effects of light
  • 9-5 The placement of the photopigments is important in the performance of their function
  • 9-6 Light energy is focused at the reaction center
  • 9-7 Photosynthetic microorganisms are classified as oxygenic and anoxygenic
  • 9-8 Purple bacteria are anoxygenic photosynthetics that are metabolically versatile
  • 9-9 Purple bacteria house their photosynthetic apparatus in intracytoplasmic membranes
  • 9-10 The reaction center of purple bacteria is made of three polypeptides and contains many photopigments
  • 9-11 Three systems regulate photosynthesis in the purple bacteria
  • 9-12 The green bacteria are anoxygenic photosynthetics that form a chlorosome
  • 9-13 The reaction center in green bacteria contains an iron-sulfur center
  • 9-14 The cyanobacteria perform oxygenic photosynthesis
  • 9-15 Cyanobacteria contain two reaction centers
  • 9-16 Photosynthesis in cyanobacteria is constitutively expressed
  • 9-17 The energy generated by photosynthesis is used to drive the dark reactions
  • 9-18 Summary
• Chapter 10 Anabolism
  • 10-1 Introduction
  • 10-2 Microbes must first find and transport the elements that they need
  • 10-3 Carbon can be assimilated from organic source or synthesized from CO₂
  • 10-4 Nitrogen assimilation can involve the uptake of reduced nitrogen compounds or nitrogen fixation
  • 10-5 Sulfur can come from organic or inorganic sources
  • 10-6 Phosphate enters metabolism by ATP synthesis and substrate-level phosphorylation.
  • 10-7 Metal ions, important components of many enzymes, must be taken up from the environment
  • 10-8 The environment influences the ability of a microbe to make monomers
  • 10-9 Amino acids that are simple in structure have simple biosynthetic pathways
  • 10-10 The synthesis of some amino acids share common steps
  • 10-11 Amino acids with more complex structures have longer biosynthesis pathways
  • 10-12 Nucleotide synthesis is complex and expensive
  • 10-13 Lipid synthesis involves a carrier protein
  • 10-14 Monomers are assembled to form polymers
  • 10-15 Peptidoglycan begins in the cytoplasm and ends in the periplasm
  • 10-16 Synthesized polymers combine in orderly fashion to make cellular stuctures.
  • 10-17 Summary
• Chapter 11 Regulation of Metabolism
  • 11-1 Introduction
  • 11-2 Regulation is a way to respond to a changing environment
  • 11-3 There are common steps in regulation
  • 11-4 Allosteric proteins sense small molecules and change their activity because of them
  • 11-5 Regulation occurs at many different points during gene expression
  • 11-6 Positive and negative regulation involves proteins that bind to DNA
  • 11-7 Attenuation is regulatory mechanism in which translation affects transcription
  • 11-8 Protein activity in prokaryotes is also regulated at the post-transcriptional and translational level
  • 11-9 Expression of the lac operon requires the presence of lactose and the absence of glucose
  • 11-10 The tryptophan operon is controlled by repression, attenuation and feedback inhibition
  • 11-11 Sporulation in Bacillus subtilis is directed by sigma factors and turned on by a phosphorelay system
  • 11-12 Vibrio fischerii senses cell density using a small diffusible molecule that binds to an activator
  • 11-13 Heat-shock gene expression is controlled by σ factors, mRNA secondary structure, and protein stability
  • 11-14 Nitrogen fixation can be controlled by a positive activator, mRNA stability, and enzyme modification
  • 11-15 Summary
• Chapter 12 Genomics and genetics
  • 12-1 Introduction
  • 12-2 Sequence information is obtained by performing enzymatic reactions on small amounts of pure DNA
  • 12-3 What does sequence information look like?
  • 12-4 What conclusions can you draw about the function of the protein product of your new ORF?
  • 12-5 What are the applications of the information gained through genomics?
  • 12-6 In addition to insights about gene products, what else can be learned from studying genomes?
  • 12-7 An introduction to genetics and genetic engineering
  • 12-8 How to find a needle in a hay stack
  • 12-9 Generation of random mutations
  • 12-10 Effects of mutations
  • 12-11 Engineering specific mutations in the lab
  • 12-12 Gene Transfer Systems
  • 12-13 Genetic Mapping
  • 12-14 Complementation Analyses
  • 12-15 There can be complications in complementation analysis
  • 12-16 Gene fusions can be used to make large quantities of a protein or to monitor the regulation of a gene
  • 12-17 Suppressors are second-site mutations that change the phenotype of a mutant to be more like that of the wild type
  • 12-18 Summary
• Chapter 13 Bacterial Viruses
  • 13-1 We can monitor bacterial viruses with the naked eye by seeing their effects on the bacterial hosts.
  • 13-2 Lambda phage is a lysogenic virus with double-stranded DNA.
  • 13-3 DNA damage causes lambda to enter the lytic cycle.
  • 13-4 T4 is a large, lytic phage with a large double-stranded DNA genome
  • 13-5 Restriction-modification systems limit the host range of T4.
  • 13-6 Viruses need to pack virions with complete genomes and also provide energy for entry into a new host
  • 13-7 P22 is a lysogenic, double-stranded DNA phage that was important in the development of bacterial genetics.
  • 13-8 P1 is a double-stranded DNA phage with an unusual ability to infect different hosts
  • 13-9 P1 replicates its DNA independently of the host chromosome when in a lysogenic state.
  • 13-10 Qβ is a small, single-stranded RNA virus.
  • 13-11 As an RNA virus, Qβ has special problems to overcome.
  • 13-12 Qβ packs a great deal of information into its small RNA genome.
  • 13-13 M13 has a genome composed of a single-stranded, circular DNA molecule.
  • 13-14 M13 expresses all of its genes at the same time and produces progeny without killing the host cell.
  • 13-15 Some phage lysogens cause their hosts to become pathogenic.
  • 13-16 Summary
• Chapter 14 Host-Microbe Interactions
  • 14-1 Introduction
  • 14-2 Microbes that interact with eukaryotes face some common challenges and utilize similar strategies
  • 14-3 Types of host-microbe interactions
  • 14-4 Microbes face many challenges when associating with a host
  • 14-5 Once a microbe detects a host, it then attaches to it
  • 14-6 Microbes may invade deeper into host tissues once attached
  • 14-7 Mutualistic outcomes
  • 14-8 Pathogenic outcomes
  • 14-9 Direct damage to host
  • 14-10 The nature and role of Exotoxins
  • 14-11 The nature and action of endotoxins
  • 14-12 Indirect damage to host
  • 14-13 Three examples of host-microbe interactions
  • 14-14 Vibrio fischeri and squid form a mutualistic relationship under the sea
  • 14-15 Quorum sensing and autoinduction
  • 14-16 The process of autoinduction
  • 14-17 Biochemistry of bioluminescence
  • 14-18 Euprymna scolopes selects for V. fischeri
  • 14-19 Microbes that live in close association with plants
  • 14-20 How plants recognize the proper rhizobia
  • 14-21 Not all associations between plants and nitrogen-fixing bacteria is as involved as the rhizobial system
  • 14-22 The normal flora of humans
  • 14-23 The skin and eyes as habitats
  • 14-24 The microbial population in the mouth
  • 14-25 The respiratory tract has mostly harmless bacteria, but can contain pathogens.
  • 14-26 The gastrointestinal tract has the largest number and greatest diversity of microbes in our body.
  • 14-27 The urogenital tract
  • 14-28 Benefits of the normal flora
  • 14-29 Summary
• Chapter 15 Animal defenses against microbes
  • 15-1 Introduction
  • 15-2 Important introductory concepts of the immune system
  • 15-3 Susceptibility to a pathogen varies between and even within species
  • 15-4 The immune system is a complex collection of organs and tissues
  • 15-5 The circulatory system transports the components of the immune system
  • 15-6 Bone marrow is the origin of all immune cells
  • 15-7 Lymphoid tissue is a separate vascular system through which lymph and immune cells move
  • 15-8 The MALT and spleen are collections of immune cells that work to fight infection
  • 15-9 Animal defenses can be classified into innate and adaptive immune systems
  • 15-10 Complement is a set of proteins that detect and kill microbes
  • 15-11 Inflammation is a response to tissue damage that can activate the immune system
  • 15-12 Phagocytes engulf and kill foreign cells
  • 15-13 Phagocytes can detect pathogens and move toward them
  • 15-14 After attaching to a microbe, phagocytes ingest them
  • 15-15 Natural killer cells attack pathogens, but are not inducible
  • 15-16 The adaptive immune system increases its response to a pathogen after initial exposure
  • 15-17 Lymphocytes make antibodies and regulate the immune system
  • 15-18 Antibodies come in five different classes
  • 15-19 Important properties of antibodies
  • 15-20 T lymphocytes regulate the immune system and fight intracellular infections, viral infection and cancer
  • 15-21 Major histocompatibility complex (MHC) molecules are the signal beacons of the immune system
  • 15-22 There are several types of T cells, but all mature in the thymus
  • 15-23 T cell activation occurs when an antigen is presented to a T cell and reacts with its T cell receptor
  • 15-24 Natural killer cell activation involves interferon or IL-2, and IgG
  • 15-25 Putting it all together - examples of responses of the immune system to different types of pathogens
  • 15-26 Host response to viral pathogens relies heavily on T cells
  • 15-27 The immune system is not perfect - Allergies
  • 15-28 Autoimmune diseases involve the host immune system attacking host proteins
  • 15-29 Summary
• Chapter 16 Treatment and prevention of disease
  • 16-1 Introduction
  • 16-2 As disease became more common, efforts were made to combat them
  • 16-3 Quarantine can be an effective method of limiting the spread of disease
  • 16-4 Good water sanitation can prevent the spread of many gastrointestinal diseases
  • 16-5 Control of insects can prevent the spread of some diseases
  • 16-6 Vaccines train the immune system to fight disease
  • 16-7 Many of the recommended vaccines are live attenuated viruses
  • 16-8 Another common vaccine type are component vaccines
  • 16-9 Some groups are wrongly advocating stopping vaccination
  • 16-10 Antimicrobial compounds directly inhibit or kill pathogens, thus curing infectious diseases
  • 16-11 Bacterial cell wall synthesis enzymes are a common target for antibiotics
  • 16-12 A second class targets the cell membrane, but they are often toxic to humans
  • 16-13 A third class of antibiotics target the 70S ribosome
  • 16-14 A fourth class targets nucleic acid metabolism
  • 16-15 A fifth class of antimicrobials are competitive inhibitors of metabolism
  • 16-16 Resistance to antibiotics has diminished the effectiveness of antibiotics
  • 16-17 The overuse of antibiotics is one reason that drug resistance has developed
  • 16-18 Summary
• Chapter 17 Bacterial Pathogens
  • 17-1 Introduction
  • 17-2 A microbe must first find a host
  • 17-3 Once a host is found, a pathogen must colonize (possibly invade) and cause damage
  • 17-4 Pathogens have a collection of properties that are major determinants in pathogenesis
  • 17-5 Bacillus anthracis is an endospore forming microbe that can causes a lethal toxic infection called anthrax
  • 17-6 Anthrax toxin and the polypeptide capsule are key aspects of pathogenesis
  • 17-7 Yersinia pestis is the causative agent of plague
  • 17-8 Y. pestis delivers toxic substances to the host using a type III secretion apparatus and defends itself using LPS
  • 17-9 Bordetella pertussis causes whooping cough and was a major killer of children
  • 17-10 Adhesins and toxins are important in the virulence of Bordetella pertussis
  • 17-11 Streptococcal diseases are major causes of infectious disease
  • 17-12 The pathogenesis of S. pyogenes is understood, while that of S. pnemoniae is less clear.
  • 17-13 Staphylococcus aureus causes a large number of human infections
  • 17-14 S. aureus produces a deadly cocktail of enzymes, polysaccharides, and toxins
  • 17-15 The microbes of the tuberculosis complex are slow-growing pathogens that gradually destroy the host
  • 17-16 Virulence factors of M. tuberculosis allow it to survive the host's defenses
  • 17-17 Tetanus and botulism are intoxications caused by clostridia
  • 17-18 The major virulence factors for botulism and tetanus are the toxins produced
  • 17-19 Helicobacter pylori is the cause of many ulcers
  • 17-20 H. pylori creates a collection of enzymes that allow it to colonize the stomach
  • 17-21 Some Escherichia coli strains cause diarrheal diseases by colonizing the intestine, while others are capable of extraintestinal infections.
  • 17-22 Five different strains of E. coli cause five different gastointestinal infections
  • 17-23 Other E. coli strains are the major cause of urinary tract infections
  • 17-24 Salmonella enterica causes a common form of gastroenteritis
  • 17-25 S. enterica uses a type III secretion system to deliver a toxic mix of proteins into host cells
  • 17-26 Chlamydia are intracellular pathogens that cause the most common forms of venereal disease
  • 17-27 Chlamydial infection causes a strong immune response that results in tissue damage
  • 17-28 Treponema pallidum is the cause of syphilis
  • 17-29 T. pallidum cannot survive outside the host
  • 17-30 T. pallidum spreads rapidly during infection, but can be cured with antibiotics
  • 17-31 Neisseria gonorrhoeae causes the common sexually transmitted disease gonorrhea
  • 17-32 Pili are the major virulence factor for N. gonorrhoeae
  • 17-33 Borrelia burgdorferi causes the tick-borne Lyme disease
  • 17-34 Little is known about the mechanisms of pathogenesis of B. burgdorferi, but the disease can be sucessfully treated with antibiotics
  • 17-35 Vibrio cholerae is the cause of cholera
  • 17-36 Pili and cholera toxin are major determinants in pathogenesis
  • 17-37 Corynebacterium diphtheriae is the cause of diphtheria
  • 17-38 Diphtheria toxin causes most of the symptoms of diphtheria
  • 17-39 Summary
• Chapter 18 Eukaryotic Pathogens
  • 18-1 Introduction
  • 18-2 Infection by eukaryotic pathogens is importantly different from infection by bacterial pathogens.
  • 18-3 Plasmodium species cause malaria
  • 18-4 Cryptosporidiosis, a gastrointestinal infection, is caused by Cryptosporidium species
  • 18-5 Infection with Giardia intestinalis causes giardiasis
  • 18-6 Toxoplasmosis is caused by Toxoplasma gondii
  • 18-7 Trypanosomes cause two forms of trypanosomiasis
  • 18-8 Superficial fungal infections are bothersome, but normally not serious
  • 18-9 Sporotrichosis is caused by Sporothrix schenckii
  • 18-10 Candidiasis is infection with Candida species, a yeast
  • 18-11 Histoplasmosis is caused by two closely related species of fungi
  • 18-12 Blastomycosis is caused by Blastomyces dermatitidis
  • 18-13 Chapter Summary
• Chapter 19 Viral Pathogens
  • 19-1 Introduction
  • 19-2 Rhinovirus is the most common causes of colds
  • 19-3 Rhinoviruses are single-strand RNA viruses that replicate in the cytoplasm of the host cell.
  • 19-4 Adenoviruses also infect the respiratory tract, but can cause illness elsewhere
  • 19-5 The adenovirus is a double-stranded DNA virus with a complex viral capsid
  • 19-6 Influenza virus causes a lower respiratory viral infection with fever
  • 19-7 The influenza viral genome contains eight single-stranded RNAs, which are replicated in the nucleus.
  • 19-8 Human Immunodeficiency virus z(HIV) causes acute immune deficiency syndrome (AIDS).
  • 19-9 HIV contains two copies of a single-stranded RNA that is copied into DNA as part of its replication
  • 19-10 Hepatitis viruses infect the liver
  • 19-11 HAV and HEV are transmitted by enteric routes
  • 19-12 HBV, HCV and HDV are transmitted by blood and other bodily fluids
  • 19-13 Diagnosis of hepatitis depends on blood tests while treatment varies with the specific virus
  • 19-14 Hepatitus viruses have different replication systems
  • 19-15 Herpes viruses cause cold sores and genital herpes
  • 19-16 HSV is a enveloped virus with a double-stranded DNA genome.
  • 19-17 West Nile Virus causes a viral infection that can result in deadly encephalitis
  • 19-18 West Nile Virus (WNV) has a single-stranded RNA genome that is translated as a large polyprotein.
  • 19-19 Ebola virus causes hemorrhagic disease with a high fatality rate
  • 19-20 Ebola is a filamentous virus with a single-stranded RNA genome.
  • 19-21 Satellite viruses are important in some infections.
  • 19-22 Viroids and prions are infectious agents that are very different from viruses.
  • 19-23 Chapter summary
• Chapter 20 Evolution: Implications for microbiology
  • 20-1 What aspects of evolution are we talking about?
  • 20-2 Organisms are similar because of their common ancestry
  • 20-3 A consequence of common ancestry is residual similarity of species
  • 20-4 Macromolecular sequence data shows how microbes evolve
  • 20-5 Ribosomal RNA genes are useful for determining phylogenetic relationships.
  • 20-6 Sequence analysis supports our view of evolution
  • 20-7 A classification scheme that flows from evolution has many advantages over other methods
  • 20-8 The mechanisms of evolution involve genetic change and natural selection
  • 20-9 Limitations and implications of the classifications of organisms
  • 20-10 The difficulty of classifying microorganisms by their obvious properties
  • 20-11 Molecular phylogeny
  • 20-12 The results of molecular phylogenies - the tree of life
  • 20-13 Mitochondria and chloroplasts originated as bacteria
  • 20-14 Eurakyotes are metabolically similar, but morphologically very different.
  • 20-15 Archaea are fundamentally different from bacteria and eukaryotes
  • 20-16 Bacteria
  • 20-17 Properties in bacteria and their importance to phylogeny
  • 20-18 Summary
• Chapter 21 Eukaryotic Microbial Diversity
  • 21-1 Introduction
  • 21-2 Dinoflagellates are photosynthetic eukaryotes found in many fresh water and marine habitats
  • 21-3 Ciliates contain hair-like structures on their surface involved in motility.
  • 21-4 Apicomplexa are obligate parasites that infect many animal species
  • 21-5 Stramenopiles are photosynthetic and nonphotosynthetic microbes whose evolutionary relationship has been shown by molecular analysis
  • 21-6 Rhodophyta are a third group of photosynthetic protists that grow in coastal areas
  • 21-7 Some protists are related to green plants
  • 21-8 Fungi are critical heterotrophs in the environment
  • 21-9 Different species of fungi are classified by morphology, nutrition and molecular data
  • 21-10 Chytridiomycota look like protists, but are actually fungi
  • 21-11 Zygomycota can be obligate pathogens or free-living saprophytes that live in moist environments
  • 21-12 Glomeromycota form symbiotic relationships with higher plants.
  • 21-13 Dikaryomycota are species of fungi that can form cells with two separate nuclei.
  • 21-14 Ascomycota create complex networks of fruiting bodies
  • 21-15 Basidiomycota are organized as macrofungi, rusts, and smuts
  • 21-16 Smuts and rusts are important agricultural pathogens
  • 21-17 Yeasts are a morphological stage of some fungi.
  • 21-18 Primitive protists
  • 21-19 Some protozoa are closely related to animals
  • 21-20 Amoeba are unicellular protozoa with a naked outer layer
  • 21-21 Flagellates are motile protozoa with flagella
  • 21-22 Slime molds are unusual organisms that share both protozoan and fungal properties
  • 21-23 Summary
• Chapter 22 Archaeal Diversity
  • 22-1 Introduction
  • 22-2 Methanogens produce methane as an end product and form a deep branch of the Archaea.
  • 22-3 The reactions of methanogenesis utilize unique cofactors
  • 22-4 The genomic comparisons of Methanothermobacter thermautotrophicus and Methanococcus jannaschii are informative.
  • 22-5 Extreme halophiles can generate energy using bacteriorhodopsin
  • 22-6 Extreme halophiles survive high-salt conditions by having enzymes that function at high concentrations of potassium.
  • 22-7 Bacteriorhodopsin pumps protons across the membrane using a conformational shift activated by light
  • 22-8 Thermoacidophilic archaea grow in high-temperature acidic environments
  • 22-9 Extreme thermophiles grow at temperatures above 75°C
  • 22-10 Many cultured Crenarchaeota are hyperthermophilic
  • 22-11 Kornarchaeota and Nanoarchaeota have been defined 16S rRNA sequences
  • 22-12 Chapter Summary
• Chapter 23 Bacterial Diversity
  • 23-1 Introduction
  • 23-2 Proteobacteria
  • 23-3 α subdivision - rhizobia are plant symbionts
  • 23-4 α-subdivision - Caulobacter are dimorphic prosthecate bacteria
  • 23-5 Methanotrophs used methane as their carbon and energy source
  • 23-6 α subdivision - Agrobacterium species often colonize plants, not as symbionts, but as pathogens
  • 23-7 Purple non-sulfur bacteria are facultative phototrophs
  • 23-8 α subdivision - Pelagibacter ubique (SAR11), a previously unculturable microbe is present at high populations in many environments
  • 23-9 Ammonia oxidizers, mostly members of the β subdivision, only grow using inorganic chemicals.
  • 23-10 Thiobacillus are chemoautolithotrophic bacteria that use reduced sulfur compounds as a source of energy
  • 23-11 γ subdivision - enteric bacteria contain species that are important pathogens and are ubiquitous in the environment
  • 23-12 Vibrio and Photobacterium
  • 23-13 γ subdivision - pseudomonads are a large group of commonly found microbes that grow on organic compounds.
  • 23-14 γ subdivision - SAR86 may be a new kind of primary producer
  • 23-15 δ subdivision - sulfate-reducing bacteria use sulfur compounds as their terminal electron acceptor
  • 23-16 δ subdivision - myxobacteria are social microbes capable of forming fruiting bodies
  • 23-17 δ subdivision - bdellovibrio are fast-moving predators of other microbes
  • 23-18 ε subdivision - some Campylobacter strains are intestinal pathogens
  • 23-19 High GC - mycobacteria are slow-growing microbes with unusual cell walls.
  • 23-20 High GC - Streptomycetaceae are spore-forming, filamentous microbes that are a major source of antibiotics
  • 23-21 Low GC - Staphylococci are common parasites of animals
  • 23-22 Low GC - lactic acid bacteria are fermentative microbes important in many food processes
  • 23-23 Low GC - Bacillus species are aerobic microbes that form endospores
  • 23-24 Low GC - clostridia are anaerobic, endospore-forming bacteria.
  • 23-25 Low GC - Heliobacteriaceae have the unusual combination of photosynthesis and endospore formation
  • 23-26 Low GC - mycoplasma lack a cell wall and are obligate parasites of eukaryotes.
  • 23-27 Cyanobacteria are microbes that carry out oxygenic photosynthesis
  • 23-28 Spirochetes are one of the few groups whose morphology indicates their phylogeny
  • 23-29 Planctomyces and related species contain cells walls lacking peptidoglycan
  • 23-30 Deinococcaceae are highly resistant to radiation
  • 23-31 Cytophagales are pigmented gliding bacteria
  • 23-32 Chlorobiaceae - green sulfur bacteria
  • 23-33 Chloroflexaceae are gliding photosynthetic microbes
  • 23-34 Thermotogales grow at the highest temperature of any bacteria
  • 23-35 Chapter Summary
• Chapter 24 Microbial Ecology
  • 24-1 Introduction
  • 24-2 Determining what microbes are present in an environment is difficult
  • 24-3 With modern molecular techniques, scientists are able to identify organisms in the environment
  • 24-4 Counting all microbes is becoming possible
  • 24-5 Scientists are just beginning to learn the metabolic activities of microbe in the environment
  • 24-6 The surface soil environment is heterogeneous and contains many biological activities
  • 24-7 Microbes cooperate in the soil to degrade biopolymers
  • 24-8 Subsurface environments are hot, high-pressure environments
  • 24-9 Aquatic environments are the largest surface environments on earth
  • 24-10 Environments with running water often contains biofilms
  • 24-11 Microbial communities in lakes and ponds depend upon nutrients and predation
  • 24-12 Oceans contain photosynthetic microbes and chemoheteroorganotrophs
  • 24-13 Microbial life below the surface of the ocean has fewer nutrients, except at deep sea ocean vents.
  • 24-14 Shore habitats contain higher concentrations of microbes due to warmer temperatures, more light and the nutrient run-off from surrounding land.
  • 24-15 Microbes participate in the cycling of elements
  • 24-16 Carbon cycles between organic compounds and carbon dioxide
  • 24-17 Nitrogen gas is converted into biochemically accessible forms by microbes
  • 24-18 H₂S and SO₄ are important inorganic sources of sulfur
  • 24-19 Chapter summary
• Chapter 25 Applied Microbiology
  • 25-1 Introduction
  • 25-2 The difference between primary and secondary metabolites
  • 25-3 Pharmaceutical microbiology uses microbes for the production of medically important compounds
  • 25-4 Finding new antibiotics can involve several different approaches
  • 25-5 Enzyme screens can find inhibitors of important pathogenic proteins
  • 25-6 Once a strain is found that produces something desirable, its growth conditions need to be optimized
  • 25-7 Culture conditions must be optimized for large scale production.
  • 25-8 Methods have been developed to detect pathogens in food and for diagnosis of disease
  • 25-9 Wastewater treatment prevents contamination of our environment
  • 25-10 Water purification ensures safe drinking water
  • 25-11 Food microbiology increases understanding of food fermentations and works to prevent spoilage
  • 25-12 Yogurt is a fermentation of milk by lactic acid bacteria
  • 25-13 Cheese production involves milk fermentation, pressing and ripening
  • 25-14 Beer brewing involves alcoholic fermentation by yeast in the presence of barley and hops.
  • 25-15 Wine is an alcoholic fermentation of grapes by yeast
  • 25-16 Bread making uses yeast to create CO₂, which causing the dough to rise
  • 25-17 Vinegar is made by the action of microbes on sugar or starchy material to produce acetic acid
  • 25-18 Sauerkraut involves a fermentation of cabbage by lactic acid bacteria
  • 25-19 Food processes can be spoiled by the action of undesirable microbes
  • 25-20 Enzymes from microorganisms are used in a wide variety of products
  • 25-21 Some vitamins are manufactured using microorganisms
  • 25-22 Some amino acids are manufactured using microorganisms
  • 25-23 Bioconversion involves catalyzing one or several steps of the synthesis of a complex molecule using microorganisms
  • 25-24 Industrial microbiology is also important in agriculture
  • 25-25 Summary
• Chapter 26 Microbial Methods
  • 26-2 Culturing Bacteria
  • 26-3 Counting microorganisms
  • 26-4 Visualizing microbes
  • 26-5 Microbial molecular biology
  • 26-6 Gel electrophoresis
  • 26-7 Restriction enzymes
  • 26-8 Plasmids
  • 26-9 Cloning
  • 26-10 Transformation and electroporation
  • 26-11 DNA sequencing
  • 26-12 Genomics
  • 26-13 DNA arrays (hybridization)