Through the Microscope: Adventures in Microbiology

1 - The Relevance and History of Microbiology

2 - Fundamental concepts for understanding microbiology

3 - Cell Structure and Organization

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 The moving polymerase problem

4 - 9 Summary

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

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

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

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

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

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

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 <i>lac</i> 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 <i>Bacillus subtilis</i> is directed by sigma factors and turned on by a phosphorelay system

11 - 7 <i>Vibrio fischeri</i> 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

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

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 Q&beta; is a small, single-stranded RNA virus

13 - 10 M13 has a genome composed of a single-stranded, circular DNA molecule

13 - 11 Summary

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 Some examples of host-microbe interactions

14 - 6 Microbes that live in close association with plants

14 - 7 Insects associate with microbes for nutrition and protection

14 - 8 The human microbiome

14 - 9 Summary

15 - Immunity - Introduction and Innate Immunity

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

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

18 - Introduction to Pathogens and Airborne and Contact Transmission

18 - 1 Introduction

18 - 2 Introduction to pathogenesis

18 - 3 <i>Bacillus anthracis</i> is an endospore forming microbe that can causes a lethal toxic infection called anthrax

18 - 4 <i>Bordetella pertussis</i> causes whooping cough and was a major killer of children

18 - 5 Streptococcal diseases are major causes of infectious disease

18 - 6 <i>Staphylococcus aureus</i> 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 <i>Corynebacterium diphtheriae</i> is the cause of diphtheria

18 - 10 Fungal infections

18 - 11 Cold and flu viruses

18 - 12 Summary

19 - Fecal to Oral Transmission

19 - 1 Introduction

19 - 2 <i>Helicobacter pylori</i> Is the Cause of Many Ulcers

19 - 3 Some <i>Escherichia coli</i> Strains Cause Diarrheal Diseases by Colonizing the Intestine, while Others Are Capable of Extraintestinal Infections.

19 - 4 <i>Salmonella enterica</i> Causes a Common Form of Gastroenteritis

19 - 5 <i>Vibrio cholerae</i> Is the Cause of Cholera

19 - 6 Infections with protozoa

19 - 7 Infections with Helminths

19 - 8 The hepatitis viruses

19 - 9 Summary

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 <i>Treponema pallidum</i> is the cause of syphilis

20 - 4 <i>Neisseria gonorrhoeae</i> 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

21 - Vector Borne and Other Diseases

21 - 1 Introuction

21 - 2 <i>Yersinia pestis</i> is the causative agent of plague

21 - 3 <i>Borrelia burgdorferi</i> causes the tick-borne Lyme disease

21 - 4 <i>Plasmodium</i> 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

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

23 - Microbial Ecology

23 - 1 Introduction

23 - 2 Our view of the environment clarifies

23 - 3 Modern molecular methods of microbial census

23 - 4 The environment influences microbial activity

23 - 5 Why are the majority of the world's microbes unculturable?

23 - 6 Culturing the unculturable

23 - 7 Microbial Communities in the Acid Mine

23 - 8 Summary

24 - Terrestrial Micorbiology

24 - 1 Introduction

24 - 2 Physical Characteristics of Soil

24 - 3 Soil community structure and degradation patterns

24 - 4 Nutrient flow in the soil

24 - 5 Microbes in soil

24 - 6 Subsurface environments are hot, high-pressure environments

24 - 7 Summary

25 - Aquatic Microbiology

25 - 1 Introduction

25 - 2 Aquatic environments are the largest surface environments on earth

25 - 3 Microbiology of rivers

25 - 4 Microbiology of lakes

25 - 5 The open ocean

25 - 6 Microbial life below the surface of the ocean has fewer nutrients, except at deep sea ocean vents.

25 - 7 Microorganisms participate in the cycling of elements

25 - 8 Summary

26 - Applied Microbiology

26 - 1 Introduction

26 - 2 Useful metabolites from microbes

26 - 3 Growth of microbes in industry

26 - 4 Water treatment is essential to public health

26 - 5 Health and Food microbiology are important industries

26 - 6 Fermentations of milk

26 - 7 Yeast fermentations and food spoilage

26 - 8 Bread, sauerkraut and food spoilage

26 - 9 Enzymes from microorganisms are used in a wide variety of products

26 - 10 Industrial microbiology is also important in agriculture

26 - 11 Summary

27 - Eukaryotic Microbial Diversity

27 - 1 Introduction

27 - 2 Examples of protozoa and macroorganism relatives

27 - 3 More protists

27 - 4 Fungi

27 - 5 More Fungi - Dikaryomycota, rusts, smuts and yeast

27 - 6 Slime molds are unusual organisms that share both protozoan and fungal properties

27 - 7 Summary

28 - Bacterial Diversity

28 - 1 Introduction

28 - 2 &alpha; Proteobacteria, Part 1

28 - 3 &alpha; Proteobacteria, Part 2

28 - 4 &beta; Proteobacteria

28 - 5 &gamma; Protoebacteria - Part 1

28 - 6 &gamma; Protoebacteria, Part 2

28 - 7 &delta; Proteobacteria

28 - 8 &epsilon; Proteobacteria

28 - 9 Acinetobacteria - High GC microbes

28 - 10 Firmicutes, Part 1

28 - 11 Firmicutes, Part 2

28 - 12 Other photosynthetic divisions, Cyannobacteria, Chlorobi and Chloroflexi

28 - 13 Spirochaetes, Planctomycetes and Deinococcus

28 - 14 Bacteroidetes and Thermotogae

28 - 15 Summary

29 - Archaeal Diversity

29 - 1 Introduction

29 - 2 <i>Euryarchaeota</i> - Methanogens

29 - 3 <i>Euryarchaeota</i> - Extreme halophiles

29 - 4 <i>Euryarchaeota</i> - Thermoacidophilic bacteria and extreme thermophiles

29 - 5 Crenarchaeota

29 - 6 <i>Korarchaeota</i> and <i>Nanoarchaeota</i>

29 - 7 Summary

30 - Microbial Methods