Chapter 1 The Relevance and History of Microbiology

Chapter 2 Fundamental concepts that are important for understanding microbiology

Chapter 3 Cell Structure and Organization

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

Chapter 16 Immunity - Adaptive Immunity and Errors of the Immune System

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

Chapter 28 Appendix A: Microbial Methods

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