Microbiology for dummies

pt. I. Getting started with microbiology 1. Microbiology and you Why microbiology? Introducing microorganisms Deconstructing microbiology 2. Microbiology : the young science Before microbiology : misconceptions and superstitions Discovering microorganisms Debunking the myth of spontaneous generation Improving medicine, from surgery to antibiotics and more Looking at microbiology outside the human body The future of microbiology Frontiers Challenges 3. Microbes : they're everywhere and the can do everything Habitat diversity Metabolic diversity Getting energy Capturing carbon Making enzymes Secondary metabolism The intersection of microbes and everyone else

pt. II. Balancing the dynamics of microbial life Seeing the shapes of cells Life on a minute scale : considering the size of prokaryotes The cell : an overview Scaling the outer membrane and cell walls Examining the outer membrane Exploring the cell wall Other important cell structures Divining cell division Tackling transport systems Passive transport Active transport Keeping things clean with efflux pumps Getting around with locomotion 5. Making sense of metabolism Converting with enzymes In charge of energy : oxidation and reduction Donating and accepting electrons Bargaining with energy-rich compounds Storing energy for later Breaking down catabolism Digesting glycolysis Stepping along with respiration and electron carriers Moving with the proton motive force Turning the citric acid cycle Stacking up with anabolism Creating amino acids and nucleic acids Making sugars and polysaccharides Putting together fatty acids and lipids 6. Getting the gist of microbial genetics Organizing genetic material DNA : the recipe for life Perfect plasmids DNA replication Assembling the cellular machinery Making messenger RNA Other types of RNA synthesizing protein DNA regulation Regulating protein function Changing the genetic code Slight adjustments Major rearrangements 7. Measuring microbial growth Getting growth requirements right Physical requirements Chemical requirements Culturing microbes in the lab Observing microbes Counting small things Seeing morphology Calculating cell division and population growth dividing cells Following growth phases Inhibiting microbial growth Physical methods Disinfectants

pt. III. Sorting out microbial diversity 8. Appreciating microbial ancestry Where did microbes come from? Tracing the origins of life Diversifying early prokaryotes The impact of prokaryotes on the early earth Hitching a ride : endosymbiosis Understanding evolution Studying evolution Choosing marker genes Seeing the direction of gene transfer in prokaryotes Classifying and naming microbes Climbing the tree of life 9. Harnessing energy, fixing carbon Forging ahead with autotrophic processes Fixing carbon Using the energy in light Harvesting light : chlorophylls and bacteriochlorophylls Helping photosynthesis out : carotenoids and phycobilins Generating oxygen (or not) : oxygenic and anoxygenic photosynthesis Getting energy from the elements : chemolithotrophy Harnessing hydrogen Securing electrons from sulfur Pumping iron Oxidizing nitrate and ammonia 10. comparing respiration and fermentation Lifestyles of the rich and facultative Digging into respiration Spinning the citric acid cycle Stepping down the electron transport chain Respiring anaerobically Figuring out fermentation 11. Uncovering a variety of habitats Defining a habitat Understanding nutrient cycles Carbon cycling Nitrogen cycling Sulfur cycling Phosphorous cycles in the ocean Microbes socializing in communities Using quorum sensing to communication Living in biofilms Exploring microbial mats Discovering microbes in aquatic and terrestrial habitats Thriving in water Swarming soils Getting along with plants and animals Living with plants Living with animals Living with insects Living with ocean creatures Tolerating extreme locations Detecting microbes in unexpected places

pt. IV. Meeting the microbes 12. Meet the prokaryotes Getting to know the bacteria The gram-negative bacteria : proteobacteria More gram-negative bacteria The gram-positive bacteria Acquainting yourself with the archaea Scalding : extreme thermophiles Acidic : extreme acidophiles Salty : extreme halophiles Not terribly extreme archaea 13. Say hello to eukaryotes Fun with fungi Figuring out fungal physiology Itemizing fungal diversity Interacting with plant roots Ascomycetes MUshrooms : basidiomycetes Perusing the protists Making us sick : apicoplexans Making plants sick : oomycetes chasing amoeba and ciliates Encountering the algae 14. Examining the vastness of viruses Hijacking cells Frugal viral structure Simplifying viral function Making heads or tails of bacteriophage Lytic phage Temperate phage Transposable phage Discussing viruses of eukaryotes Infecting animal cells Following plant viruses How host cells fight back Restriction enzymes CRISPR Interfering with RNA viruses : RNAi

pt. V. Seeing the impact of microbes 15. Understanding microbes in human health and disease Clarifying the host immune response Putting up barriers to infection Inflammation Innate immunity Adaptive immunity Antibodies Relying on antimicrobials for treating disease Fundamental features of antibiotics Targets of destruction Unraveling microbial drug resistance Discovering new antibiotics Searching out superbugs Vancomycin-resistant enterococci Methicillin-resistant staphylococcus aureus Clostridium difficile Extended-spectrum beta-lactamases Prebiotics and probiotics Antiviral drugs 16. Putting microbes to work : biotechnology Using recombinant DNA technology Making the insert Employing plasmids Restriction enzymes Getting microbes to take up DNA Using promoters to drive expression Expression vectors Folding proteins Metabolic load Long, multigene constructs Providing therapies Improving antibiotics Developing vaccines Using microbes industrially Protecting plants wit microbial insecticides Making biofuels Bioleaching metals Cleaning up with microbes 17. Fighting microbial diseases Protecting public health : epidemiology Tracking diseases Investigating outbreaks Identifying a microbial pathogen characterizing morphology Using biochemical tests Typing strains with phage Using serology Testing antibiotic susceptibility Understanding vaccines How vaccines work Ranking the types of vaccines

pt. VI. New frontiers in microbiology 18. Teasing apart communities Studying microbial communities Borrowing from ecology Seeing what sets microbial communities apart from plants and animals Observing communities : microbial ecology methods Selecting something special with enrichment Seeing cells through lenses Measuring microbial activity Identifying species using marker genes Getting the hang of microbial genetics and systematics Sequencing whole genomes Using metagenomics to study microbial communities Reading microbial transcriptomics Figuring out proteomics and metabolomics Looking for microbial dark matter 19. Synthesizing life Regulating genes : the lac operon Using a good natural system Improving a good system Designing genetic networks Switching from one state to another Oscillating between states Keeping signals short The synthetic biologist's toolbox Making it modular Participating in iGEM competition

pt. VII. The part of tens

20. Ten (or so) diseases caused by microbes

Ebola

Anthrax

Influenza

Tuberculosis

HIV

Cholera

Smallpox

Primary amoebic menigoencephalitis

The unknown

21. Ten great uses for microbes

Making delicious foods

Growing legumes

Brewing beer, liquor, and wine

Killing insect pests

Treating sewage

Contributing to medicine

Setting up your aquarium

Making and breaking down biodegradable plastics

Turning over compostable waste

Maintaining a balance

22. Ten great uses for microbiology

Medical care

Dental care

Veterinary care

Monitoring the environment

Making plants happy

Keeping fish swimming strong

Producing food, wine, and beer

Science hacking

Looking for microbes in clean rooms

Producing pharmaceuticals.