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 09

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 11
Taxonomy and phylogeny
The false eukaryote/prokaryote dichotomy

    Discussion session : A second Tasmanian Devil transmissible cancer Jan 13
   
    Martin Luther King Day - NO CLASS Jan 16

Phylogenetic analysis How to do a phylogenetic analysis

Chapters 3 and 4 of the textbook
Step 1: Deciding on sequences for analysis Jan 18
  Step 2 : Obtaining the sequence data
  Step 3 : Identifying homologous residues
Alignment problem set
 
  Discussion session : Rob Knight - How our microbiomes make us what we are Jan 20
 
  Step 4 : Tree-construction
Tree construction problem set
Jan 23
  Step 5 : Interpreting the phylogenetic tree
Tree interpretation problem set
 
  Complications

Chapters 5 and 6 of the textbook
Alternative substitution models Jan 25
  Alternative treeing algorithms
  Bootstrapping
 
  Discussion session : Measles vaccine mystery solved? Jan 27
 
  Alternatives to ssu-rRNA Jan 30
  Other methods for identification
  Example analysis : ES-2
   
  What does this all mean?

Chapter 7 of the textbook
A review of "The Big Tree" Feb 01
    Rooting the Universal Tree  
    The caveat - horizontal transfer  
   
    Discussion session : Phylogenetic Analysis problems sets Feb 03
 
Reprise What is Microbial Diversity? Feb 06
The fundamental similarity of all living things

Midterm Exam #1 Traditional students (section 001) - take the exam at the usual class time and place
DE/online students (section 601) - take the exam in the DELTA Testing Center
Feb 08
Feb 08/10

    Discussion session : The Hot Springs of Yellowstone National Park Feb 10

The Bacteria Primitive Thermophilic Bacteria

Chapter 8 of the textbook
Phylum Aquificae (Aquifex and relatives) Feb 13
Phylum Thermotogae (Thermotoga and relatives)
Other primitive thermophiles
Thermophilic ancestry of Bacteria
Life at high temperatures

Green Phototrophic Bacteria

Chapter 9 of the textbook
Phylum Chloroflexi (Green non-sulfur Bacteria) Feb 15
Phylum Chlorobi (Green sulfur Bacteria)
Phylum Cyanobacteria (Blue-green algae)
Other Green phototrophs
Bacterial photosynthesis
Carbon fixation

  Discussion session : Pelagibacter ubique Feb 17

Proteobacteria

Chapter 10 of the textbook
Class α-proteobacteria Feb 20
Class β-proteobacteria
Class γ-proteobacteria
Class δ-proteobacteria
Class ε-proteobacteria
The concept of Proteobacteria

Gram-positive Bacteria

Chapter 11 of the textbook
Phylum Firmicutes (Low G+C Gram-positive Bacteria) Feb 22
Phylum Actinobacteria (high G+C Gram-positive Bacteria)
Bacterial Development
Bacterial Multicellularity

Discussion session : Nanobacteria, Fact or Fiction? Feb 24

Spirochaetes & Bacteroids

Chapter 12 of the textbook
Phylum Spirochaetes Feb 27
Phylum Bacteroids (Sphingobacteria, or Bacteroides/Flavobacterium/Cytophaga)
Bacterial Motility

Deincocci, Chlamydia & Planctomycetes

Chapter 13 of the textbook
Phylum Deinococci (Deinococcus/Thermus) Mar 01
Phylum Chlamydiae (Chlamydia and relatives)
Phylum Planctomycetes (Planctomyces & relatives)
Reductive evolution in parasites

Discussion session : CANCELED! Mar 03

Spring Break - No class Mar 06
Mar 08
Mar 10

Bacterial phyla with few or no cultivated species

Chapter 14 of the textbook
Phyla with few cultivated species Mar 13
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?

Eukaryotes

Chapter 16 of the textbook
Unikonts Mar 15
Plantae
Chromalveolates
Rhizaria
Excavates

Discussion session : Vision in cyanobacteria Mar 17

Archaea

Chapter 15 of the textbook
Phylum Euryarchaea Mar 20
Phylum Nanoarchaeum

Phylum Crenarchaea Mar 22
Phylum Korarchaea
Archaea as...

Discussion session : Black widow venom gene in a bacteriophage Mar 24

Viruses & Prions

Chapter 17 of the textbook
The origin of viruses Mar 27

Midterm Exam #2 Traditional students (section 001) - take the exam at the usual class time and place
DE/online students (section 601) - take the exam in the DELTA Testing Center
Mar 29
Mar 29/31

    Discussion session : Plagues aren't hat they used to be Mar 31

Microbial Populations The identifications of uncultivable organisms

Chapter 18 of the textbook
Determining the phylotype of the Octopus Spring pink filaments organism Apr 03
    Cultivation and isolation of the pink filaments organism, Thermocrinus ruber
   
  Fluorescent in-situ hybridization (FISH) Paper - TBA Apr 05
   
    Discussion session : The new tree of life? Apr 07
 
  Sequence-based microbial surveys

Chapter 19 of the textbook
Molecular phylogenetic analysis of bacterial symbionts of the deep-sea hydrothermal vent scaly snail Apr 10
    The Human Microbiome Apr 12
   
    Spring Holiday - NO CLASS Apr 14
 
  Molecular fingerprinting of microbial populations

Chapter 21 of the textbook
Denaturing Gradient Gel Electrophoresis Apr 17
    Paper - TBA  
 
  Linking phylotype and phenotype

Chapter 22 of the textbook
Stable Isotope Probing Apr 19
    Identification of ciliate grazers of autotrophic Bacteria in ammonia-oxidizing activated sludge by RNA stable isotope probing
   
    Discussion session : The Human Microbial Hand-ome Apr 21
   
    Metagenomics Apr 24
    Evidence for a new type of phototrophy in the sea

Genomics

Chapter 23 of the textbook
Comparative gemonics Paper - TBA Apr 26
   
    Discussion session : Microbiome Class Project Apr 28

Final Exam Traditional students (section 001) - take the exam at 8:00AM-11:00AM
DE/online students (section 601) - take the exam in the DELTA Testing Center
May 05
May 01/05