Through the Microscope: Adventures in Microbiology
Chapter 1 The Relevance and History of Microbiology
1-2 Microbes have a large impact on human health
1-3 Microbes have profound effects on the environment
1-5 Spontaneous generation was an attractive theory to many people, but was ultimately disproven.
1-6 Microbes are discovered to cause disease
Chapter 2 Fundamental concepts that are important for understanding microbiology
2-2 Fundamental Properties of Matter
2-3 How we describe simple molecules
2-4 Shorthand for chemical reactions
2-5 Sugars are common components of the cell
2-6 Proteins are made of amino acids
Chapter 3 Cell Structure and Organization
3-2 Important structures in the cytoplasm
3-4 The Bacterial Cytoskeleton
3-6 The cell surface extends into the environment
3-7 Bacteria can exist in different cell states
3-9 Eukaryotic cells have much in common with prokaryotic cells
Chapter 4 DNA: Replication, Mutation, Repair and The Central Dogma
4-1 Introduction
4-2 DNA Structure and Replication
4-3 Errors can occur in DNA replication that create potential mutations
4-4 Errors in DNA can also occur outside of replication
4-5 Transcription involves the copying of DNA into RNA
4-6 The level of mRNA is a common regulatory point in prokaryotes
4-7 Translation is the conversion of mRNA into protein at the ribosome
4-8 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 Culture Media
5-5 Sterilization of media
5-6 Summary
Chapter 6 Microbial Growth
6-1 Introduction
6-2 Describing bacterial growth and quantifying it
6-3 Measuring bacterial growth
6-4 Growth in laboratory culture
6-5 The environment greatly affects the growth of microbes
6-6 Summary
Chapter 7 Control of Microbes
7-1 Introduction
7-2 Temperature is a common physical method for controlling microbes
7-3 Other physical forms of treatment
7-4 Chemical treatments act on microbes to prevent their growth
7-5 Antimicrobial activity is measured using standard tests
7-6 Summary
Chapter 8 Metabolism
8-1 Introduction
8-2 Important foundations in metabolism
8-3 Enzymes are biological catalysts
8-4 Fermentation, energy generation without using a membrane
8-5 Respiration involves donation of electrons to an inorganic terminal electron acceptor
8-6 High-energy electrons are converted into ATP using a membrane
8-7 Many microbes are capable of anaerobic respiration
8-8 Some microbes can grow completely on inorganic sources of carbon, energy and electrons
8-9 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 Purple bacteria, one class of anoxygenic photosynthetic bacteria
9-5 The green bacteria are anoxygenic photosynthetics that form a chlorosome
9-6 The cyanobacteria perform oxygenic photosynthesis
9-7 Summary
Chapter 10 Anabolism
10-1 Introduction
10-2 Assimilation of carbon
10-3 Nitrogen and Sulfur assimilation
10-4 Assimiliation of other elements
10-5 Amino acids and simple synthesis
10-6 The synthesis of some amino acids share common steps
10-7 Nucleotide and lipid biosynthesis involved complex pathways
10-8 Monomers are assembled to form polymers
10-9 Summary
Chapter 11 Regulation of Metabolism
11-1 Introduction
11-2 Regulation is a way to respond to a changing environment
11-3 The different types of regulation
11-4 Expression of the lac operon requires the presence of lactose and the absence of glucose
11-5 The tryptophan operon is controlled by repression, attenuation and feedback inhibition
11-6 Sporulation in Bacillus subtilis is directed by sigma factors and turned on by a phosphorelay system
11-7 Vibrio fischeri senses cell density using a small diffusible molecule that binds to an activator
11-8 Heat-shock gene expression is controlled by sigma factors, mRNA secondary structure, and protein stability
11-9 Nitrogen fixation can be controlled by a positive activator, mRNA stability, and enzyme modification
11-10 Summary
Chapter 12 Genomics and Genetics
12-1 Introduction
12-2 Sequencing and what it tells us
12-3 What are the applications of the information gained through genomics?
12-4 An introduction to genetics and genetic engineering
12-5 How to find a needle in a hay stack
12-6 Generation of random mutations
12-7 Gene Transfer Systems
12-8 Genetic mapping, complementation and gene fusions
12-9 Suppressors are second-site mutations that change the phenotype of a mutant to be more like that of the wild type
12-10 Summary
Chapter 13 Basic Virology and Prokaryotic Viruses
13-1 Introduction
13-2 Viral challenges and structures
13-3 The viral life cycle, early events
13-4 The viral life cycle, late events
13-5 Lambda phage is a lysogenic virus with double-stranded DNA.
13-6 T4 is a large, lytic phage with a large double-stranded DNA genome
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 Qβ is a small, single-stranded RNA virus
13-10 M13 has a genome composed of a single-stranded, circular DNA molecule
13-11 Summary
Chapter 14 Host-Microbe Interactions
14-1 Introduction
14-2 Types of host-microbe interactions
14-3 Microbes face many challenges when associating with a host
14-4 Pathogenic outcomes
14-5 Three examples of host-microbe interactions
14-6 Microbes that live in close association with plants
14-7 The normal flora of humans
14-8 Summary
Chapter 15 Immunity - Introduction and Innate Immunity
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, Tissues, and Cells
Chapter 16 Immunity - Adaptive Immunity and Errors of the Immune System
16-2 Adaptive Immunity - introductory concepts
16-3 B Lymphocytes - Humoral Immunity
Chapter 17 Treatment and Prevention of Disease
17-1 Introduction
17-2 The beginnings of disease and efforts to combat them
17-3 Epidemiology helps to track disease outbreaks and stop them
17-4 Vaccines train the immune system to fight disease
17-5 Antimicrobial compounds directly inhibit or kill pathogens
17-6 Resistance to antibiotics has diminished the effectiveness of antibiotics
17-7 Summary
Chapter 18 Introduction to Pathogens and Airborne and Contact Transmission
18-1 Introduction
18-2 Introduction to pathogenesis
18-3 Bacillus anthracis is an endospore forming microbe that can causes a lethal toxic infection called anthrax
18-4 Bordetella pertussis causes whooping cough and was a major killer of children
18-5 Streptococcal diseases are major causes of infectious disease
18-6 Staphylococcus aureus causes a large number of human infections
18-7 The microbes of the tuberculosis complex are slow-growing pathogens that gradually destroy the host
18-8 Tetanus and botulism are intoxications caused by clostridia
18-9 Corynebacterium diphtheriae is the cause of diphtheria
18-10 Fungal infections
18-11 Cold and flu viruses
18-12 Summary
Chapter 19 Fecal to Oral Transmission
19-1 Introduction
19-2 Helicobacter pylori Is the Cause of Many Ulcers
19-3 Some Escherichia coli Strains Cause Diarrheal Diseases by Colonizing the Intestine, while Others Are Capable of Extraintestinal Infections.
19-4 Salmonella enterica Causes a Common Form of Gastroenteritis
19-5 Vibrio cholerae Is the Cause of Cholera
19-6 Infections with protozoa
19-7 Infections with Helminths
19-8 The hepatitis viruses
19-9 Summary
Chapter 20 Sexually Transmitted Disease and Those Transmitted by Blood and Body Fluids
20-1 Introduction
20-2 Chlamydia are intracellular pathogens that cause the most common forms of venereal disease
20-3 Treponema pallidum is the cause of syphilis
20-4 Neisseria gonorrhoeae causes the common sexually transmitted disease gonorrhea
20-5 Human Immunodeficiency virus (HIV) causes acute immune deficiency syndrome (AIDS)
20-6 Herpes viruses cause cold sores and genital herpes
20-7 Ebola virus causes hemorrhagic disease with a high fatality rate
20-8 Summary
Chapter 21 Vector Borne and Other Diseases
21-1 Introuction
21-2 Yersinia pestis is the causative agent of plague
21-3 Borrelia burgdorferi causes the tick-borne Lyme disease
21-4 Plasmodium species cause malaria
21-5 Trypanosomes cause two forms of trypanosomiasis
21-6 West Nile Virus causes a viral infection that can result in deadly encephalitis
21-7 Viroids and prions are infectious agents that are very different from viruses
21-8 Summary
Chapter 22 Evolution: Implications for Microbiology
22-1 Introduction
22-2 Defining Evolution in a microbial sense
22-3 Macromolecular sequence data shows how microbes evolve
22-4 A classification scheme that flows from evolution has many advantages over other methods
22-5 The results of molecular phylogenies - the tree of life and how it relates to Eukarya
22-6 Archaea are fundamentally different from bacteria and eukaryotes
22-7 Bacteria
22-8 Summary
Chapter 23 Eukaryotic Microbial Diversity
23-1 Introduction
23-2 Examples of protozoa and macroorganism relatives
23-3 More protists
23-4 Fungi
23-5 More Fungi - Dikaryomycota, rusts, smuts and yeast
23-6 Slime molds are unusual organisms that share both protozoan and fungal properties
23-7 Summary
Chapter 24 Archaeal Diversity
24-1 Introduction
24-2 Euryarchaeota - Methanogens
24-3 Euryarchaeota - Extreme halophiles
24-4 Euryarchaeota - Thermoacidophilic bacteria and extreme thermophiles
24-5 Crenarchaeota
24-6 Korarchaeota and Nanoarchaeota
24-7 Summary
Chapter 25 Bacterial Diversity
25-1 Introduction
25-2 α Proteobacteria, Part 1
25-3 α Proteobacteria, Part 2
25-4 β Proteobacteria
25-5 γ Protoebacteria - Part 1
25-6 γ Protoebacteria, Part 2
25-7 δ Proteobacteria
25-8 ε Proteobacteria
25-9 Acinetobacteria - High GC microbes
25-10 Firmicutes, Part 1
25-11 Firmicutes, Part 2
25-12 Other photosynthetic divisions, Cyannobacteria, Chlorobi and Chloroflexi
25-13 Spirochaetes, Planctomycetes and Deinococcus
25-14 Bacteroidetes and Thermotogae
25-15 Summary
Chapter 26 Microbial Ecology
26-1 Introduction
26-2 Our view of the environment clarifies
26-3 The environment influences microbial activity
26-4 Microbial Communities in the Acid Mine
26-5 Terrestrial microbiology is heterogeneous and contains may microbial activities
26-6 Aquatic Environments are the largest surface environments on earth
26-7 Life in the ocean is diverse, but can be dominated by just a few microbial species.
26-8 Microorganisms participate in the cycling of elements
26-9 Summary
Chapter 27 Applied Microbiology
27-1 Introduction
27-2 Useful metabolites from microbes
27-3 Growth of microbes in industry
27-4 Water treatment is essential to public health
27-5 Health and Food microbiology are important industries
27-6 Fermentations of milk
27-7 Yeast fermentations and food spoilage
27-8 Bread, sauerkraut and food spoilage
27-9 Enzymes from microorganisms are used in a wide variety of products
27-10 Industrial microbiology is also important in agriculture
27-11 Summary
