Schedule

This schedule is subject to change as the semester progresses. Test dates and Discussion session dates will remain fixed, but topics and especially papers for discussion are very likely to change.

Click on the title of any posted Topic or Module to go to a web page with resources relevant to that material.


Section Topics Modules Date Updated?

Introduction Course Overview Course Overview Jan 08
What is Microbial Diversity?

Context & Historical Baggage

Chapters 1 & 2 of the textbook
The fundamental similarity of all living things Jan 10
The evolution of evolutionary thought
Taxonomy and phylogeny
The false eukaryote/prokaryote dichotomy

Discussion session : The Hot Springs of Yellowstone Jan 12

Martin Luther King Day - NO CLASS Jan 15  

Phylogenetic analysis How to do a phylogenetic analysis

Chapters 3-6 of the textbook

Step 1: Deciding on sequences for analysis Jan 17 ONLINE only (No class due to weather)
Step 2 : Obtaining the sequence data

Discussion session : Pelagibacter ubique (SAR 11) Jan 19

Step 3 : Identifying homologous residues Jan 22
Step 4 : Tree-construction, starting with Neighbor-joining
Alternative treeing algorithms
Alternative substitution models

Alternatives to ssu-rRNA Jan 24
Step 5 : Interpreting phylogenetic trees
Bootstrapping

Discussion session : TBA Jan 26

Example analysis : ES-2 Jan 29
Using the Ribosomal Database Project web site

What does this all mean?

Chapter 7 of the textbook
A review of "The Big Tree" Jan 31
Rooting the Universal Tree  
The caveat - horizontal transfer  

Discussion session : Exam study session Feb 02

Left-overs
in Chapter 6 of the textbook
Other methods for identification Feb 05

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 07
Feb 07/09
 

  Discussion session : TBA Feb 09

The Bacteria Primitive Thermophilic Bacteria

Chapter 8 of the textbook
Phylum Aquificae (Aquifex and relatives) Feb 12
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 14
Phylum Chlorobi (Green sulfur Bacteria)
Phylum Cyanobacteria (Blue-green algae)
Other Green phototrophs
Bacterial photosynthesis
Carbon fixation

  Discussion session : TBA Feb 16

Proteobacteria

Chapter 10 of the textbook
Class α-proteobacteria Feb 19
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 21
Phylum Actinobacteria (high G+C Gram-positive Bacteria)
Bacterial Development
Bacterial Multicellularity

Discussion session : TBA Feb 23

Spirochaetes & Bacteroids

Chapter 12 of the textbook
Phylum Spirochaetes Feb 26
Phylum Bacteroids (Sphingobacteria, or Bacteroides/Flavobacterium/Cytophaga)
Bacterial Motility

Deincocci, Chlamydia & Planctomycetes

Chapter 13 of the textbook
Phylum Deinococci (Deinococcus/Thermus) Feb 28
Phylum Chlamydiae (Chlamydia and relatives)
Phylum Planctomycetes (Planctomyces & relatives)
Reductive evolution in parasites

Discussion session : CANCELED! Mar 02  

Spring Break - No class Mar 05  
Mar 07  
Mar 09  

Bacterial phyla with few or no cultivated species

Chapter 14 of the textbook
Phyla with few cultivated species Mar 12
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 14
Plantae
Chromalveolates
Rhizaria
Excavates

Discussion session : TBA Mar 16

Archaea

Chapter 15 of the textbook
Phylum Euryarchaea Mar 19
Phylum Nanoarchaeum
Phylum Crenarchaea Mar 21
Phylum Korarchaea
Archaea as...

Discussion session : exam study session? Mar 23

Viruses & Prions

Chapter 17 of the textbook
The origin of viruses Mar 26

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 28
Mar 28/30
 

  Spring Holiday - NO CLASS Mar 30  

Microbial Populations

The identifications of uncultivable organisms

Chapter 18 of the textbook

Determining the phylotype of the Octopus Spring pink filaments organism Apr 02
Cultivation and isolation of the pink filaments organism, Thermocrinus ruber

Sequence-based microbial surveys

Chapter 19 of the textbook
Molecular phylogenetic analysis of bacterial symbionts of the deep-sea hydrothermal vent scaly snail Apr 04

  Discussion session : TBA Apr 06

Sequence-based microbial surveys

Chapter 19 of the textbook
Molecular phylogenetic analysis of bacterial symbionts of the deep-sea hydrothermal vent scaly snail Apr 09
The Human Microbiome Apr 11

Discussion session : TBA Apr 13

Molecular fingerprinting of microbial populations

Chapter 21 of the textbook
Denaturing Gradient Gel Electrophoresis Apr 16
tRFLP
Oral microbial profiles

Linking phylotype and phenotype

Chapter 22 of the textbook
Stable Isotope Probing Apr 18
Identification of ciliate grazers of autotrophic Bacteria in ammonia-oxidizing activated sludge by RNA stable isotope probing

Discussion session : TBA Apr 20

Metagenomics Apr 23
Evidence for a new type of phototrophy in the sea

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

Discussion session : exam study session? Apr 27

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 04
May 02/04