Schedule

This schedule is subject to change as the semester progresses; click on the title of any posted Topic or Module to go to that web page.


Section Topics Modules Date

Introduction Course Overview
Chapter 1 of the textbook
Course Overview Jan 06

Context & Historical Baggage

Chapter 2 of the textbook
What is Microbial Diversity?
The fundamental similarity of all living things

The evolution of evolutionary thought Jan 08
Taxonomy and phylogeny
The false eukaryote/prokaryote dichotomy

Phylogenetic analysis How to do a phylogenetic analysis

Chapters 3 and 4 of the textbook
Step 1: Deciding on sequences for analysis Jan 11
Step 2 : Obtaining the sequence data
Step 3 : Identifying homologous residues
Alignment problem set

Step 4 : Tree-construction
Tree construction problem set
Jan 15
Step 5 : Interpreting the phylogenetic tree
Tree interpretation problem set
Example analysis : ES-2

Discussion session : A second transmissible cancer in Tasmanian Devils Jan 15

MLK Day - No class Jan 18

Complications

Chapters 5 and 6 of the textbook
Alternative substitution models Jan 20
Alternative treeing algorithms
Bootstrapping

Discussion session : Phylogenetic Analysis problems sets Jan 22

Alternatives to ssu-rRNA Jan 25
Other methods for identification

What does this all mean?

Chapter 7 of the textbook
A review of "The Big Tree" Jan 27
Rooting the Universal Tree
The caveat - horizontal transfer

Discussion session : The Hot Spring of Yellowstone
The Hot Springs of Yellowstone slideshow
Jan 29

Midterm Exam #1 Feb 01

The Bacteria Primitive Thermophilic Bacteria

Chapter 8 of the textbook
Phylum Aquificae (Aquifex and relatives) Feb 03
Phylum Thermotogae (Thermotoga and relatives)
Other primitive thermophiles
Thermophilic ancestry of Bacteria
Life at high temperatures

Discussion session : The Great Tree of Life Feb 05

Green Phototrophic Bacteria

Chapter 9 of the textbook
Phylum Chloroflexi (Green non-sulfur Bacteria) Feb 08
Phylum Chlorobi (Green sulfur Bacteria)
Phylum Cyanobacteria (Blue-green algae)
Other Green phototrophs
Bacterial photosynthesis
Carbon fixation

Proteobacteria

Chapter 10 of the textbook
Class α-proteobacteria Feb 10
Class β-proteobacteria
Class γ-proteobacteria
Class δ-proteobacteria
Class ε-proteobacteria
The concept of Proteobacteria

Discussion session : Can cyanobacteria see? Feb 12

Gram-positive Bacteria

Chapter 11 of the textbook
Phylum Firmicutes (Low G+C Gram-positive Bacteria) Feb 15
Phylum Actinobacteria (high G+C Gram-positive Bacteria)
Bacterial Development
Bacterial Multicellularity

Spirochaetes & Bacteroids

Chapter 12 of the textbook
Phylum Spirochaetes Feb 17
Phylum Bacteroids (Sphingobacteria, or Bacteroides/Flavobacterium/Cytophaga)
Bacterial Motility

Discussion session : Plagues aren't what they used to be Feb 19

Deincocci, Chlamydia & Planctomycetes

Chapter 13 of the textbook
Phylum Deinococci (Deinococcus/Thermus) Feb 22
Phylum Chlamydiae (Chlamydia and relatives)
Phylum Planctomycetes (Planctomyces & relatives)
Reductive evolution in parasites

Bacterial phyla with few or no cultivated species

Chapter 14 of the textbook
Phyla with few cultivated species Feb 24
Phyla with no cultivated species
Phylogenetic groups at all levels are dominated by uncultivated sequences
How much of the microbial world do we know about?

Discussion session : Nanobacteria, Fact or Fiction? Feb 26

Eukaryotes

Chapter 16 of the textbook
Unikonts Feb 29
Plantae
Chromalveolates
Rhizaria
Excavates

Viruses & Prions

Chapter 17 of the textbook
The origin of viruses Mar 02

Discussion Session canceled - No class Mar 04

Spring Break - No class Mar 07
Mar 09
Mar 11

Archaea

Chapter 15 of the textbook
Phylum Euryarchaea Mar 14
Phylum Nanoarchaeum

Phylum Crenarchaea Mar 16
Phylum Korarchaea
Archaea as...

Discussion session : Pelagibacter ubique : NOTE : Dr. Brown will be out of town Mar 18

Midterm Exam #2 Mar 21

Microbial Populations The identifications of uncultivable organisms

Chapter 18 of the textbook
Determining the phylotype of the Octopus Spring pink filaments organism Mar 23
Cultivation and isolation of the pink filaments organism, Thermocrinus ruber

Spring Holiday - No class Mar 25

Sequence-based microbial surveys
(including 454 sequencing)

Chapter 19 of the textbook
Molecular phylogenetic analysis of bacterial symbionts of the deep-sea hydrothermal vent scaly snail Mar 28

The Human Microbiome Mar 30

Discussion session : The human microbial hand-ome Apr 01

CLASS CANCELLED Apr 04

Molecular fingerprinting of microbial populations

Chapter 21 of the textbook
Denaturing Gradient Gel Electrophoresis Apr 06
Different bacteria in different temperature zones of a Tibetan hot spring.
Terminal Restriction Fragment Length Polymorphism
Realtime PCR
Changes in oral microflora after treatment for peridontal disease

Discussion session : Class microbiome project Apr 08

Linking phylotype and phenotype

Chapter 22 of the textbook
Stable Isotope Probing Apr 11
Identification of ciliate grazers of autotrophic Bacteria in ammonia-oxidizing activated sludge by RNA stable isotope probing

Metagenomics Apr 13
Evidence for a new type of phototrophy in the sea

Discussion session : RDP workshop Apr 15

Genomics

Chapter 23 of the textbook
How to sequence a genome Thermotoga maritima and evidence for lateral gene transfer Apr 18

Metagenomics The metagenome of the Sargasso Sea Apr 20

Discussion session : New tree of life? Apr 22

Origins

Chapter 24 of the textbook
The time scale A 3.2 billion year old fossilized ecoystem Apr 25
The Last Common Ancestor
The RNA World
The emergence of Life

Final Exam at 8:00AM! Apr 27