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Lectures

The format of the Monday and Wednesday lectures is traditional. The first part of the semester covers introductory material, then describes molecular phylogenetic analysis in detail, from a problem-solving perspective. After this follows a survey of microbial diversity, approached from the phylogenetic perspective. Most lectures will begin with a discussion of some aspect of microbial diversity or approaches to studying microbial populations, followed by a general description of a phylogenetic group of organisms in the context of a primary scientific paper.

The discussion sessions are Fridays, and are used to review background material, go over problem sets or exams, hash over difficult concepts from different angles, chat about microbiologically-oriented things in the news, interesting scientific papers, etc. The format of these discussion sessions is informal, being student-driven on a daily basis.

This schedule very tentative and is subject to continuous change as the semester progresses; click on the title of any posted lecture to go to that lecture page.

Lectures will be at 11:20am in 220 Dabney Hall.

Date Format Topics
Status
Jan 9 Lecture 1 Welcome to Microbial Diversity | The fundamental similarity of all living things
Done
Jan 11 Discussion 1 Hot Springs of Yellowstone
Done
Jan 14 Lecture 2 Evolutionary Concepts | Taxonomy vs phylogeny | The false eukaryote:prokaryote dichotomy
Done
Jan 16 Lecture 3 Molecular phylogenetic analysis | Why rRNA?| Obtaining sequences | Sequence alignment
Done
Jan 18 Discussion 2 Review of the alignment problem set
How the labs work (Bacillus & Purple non-sulfur Bacteria)
Done
Jan 21 No class Martin Luther King Day
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Jan 23 Lecture 4 Building phylogenetic trees | Interpreting trees
Done
Jan 25 Discussion 3 Review the problem sets
How the labs work (Yeast, chitin degraders, Winogradsky column)
Done
Jan 28 Lecture 5 Other treeing methods; Substitution models, algorithms & bootstrapping
Done
Jan 30 Lecture 6 Example Analysis - ES2 | Other phylogenetic & taxonomic methods
Done
Feb 1 Exam Midterm #1
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Feb 4 Lecture 7 The Big Tree | Rooting a universal tree | The basics of rRNA identification
Done
Feb 6 Lecture 8 Aquifex & relatives | Identification of uncultured organisms | Octopus Spring pink filaments
Done
Feb 8 Discussion 5 How to read a scientific paper
Canine transmissible venereal tumor, a contageous cancer
Done
Feb 11 Lecture 9 Bacteroids & green sulfur Bacteria | rRNA microbial surveys | The human gut flora
Done
Feb 13 Lecture 10 Bacterial groups with few or no cultivated members | How much of the microbial world have we missed?
Done
Feb 15 Discussion 6 Detection of 400-year old Yersinia pestis DNA in human dental pulp
Done
Feb 18 Lecture 11 Green Non-Sulfur Bacteria & relatives | Fluorescent in situ hybridization surveys | Chloroflexi in alkaline hot spring mats
Done
Feb 20 Lecture 12 Thermus & Deinococcus | DGGE microbial surveys | Microbes in various parts of an alkaline hot spring
Done
Feb 22 Discussion 7 ALH 84001: Evidence for past life on Mars?
Done
Feb 25 Lecture 13 Spirochaetes | Terminal RFLP surveys | Surveying human periodontal pathogens
Done
Feb 27 Lecture 14 Delta & Epsilon Proteobacteria | Large-scale rRNA analysis | The deep marine biosphere
Done
Feb 29 No class Discussion session cancelled
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Mar 3 No class Spring Break
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Mar 5 No class Spring Break
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Mar 7 No class Spring Break
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Mar 10 Lecture 15 Gamma Proteobacteria | Linking phylotype & phenotype using genomics | Proteorhodopsin in SAR86
Done
Mar 12 Lecture 16 Beta Proteobacteria | Linking phylotype and phenotype using stable-isotope probing (SIP)
Done
Mar 14 Discussion 8 Exam study session
Done
Mar 17 Exam Midterm #2
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Mar 19 Lecture 17 Thermotoga | Life and high temperatures | The T. maritima genome | Lateral gene transfer
Done
Mar 21 No class Spring Holiday
---
Mar 24 Lecture 18 Chlamydiae | Genomics & comparative genomics | The genome of Parachlamydia amoebophila
Done
Mar 26 Lecture 19 Cyanobacteria | Bacterial photosynthesis | Metagenomics | The Sargasso Sea
Done
Mar 28 Discussion 9 The Term Project
Done
Mar 31 Lecture 20 Firmicutes | Microbe:Eukaryote symbiosis | Arthromitis
Done
Apr 2 Lecture 21 Planctomycetes | Prokaryotic cell biology | Anaerobic ammonia oxidation (anammox)
Done
Apr 4 Discussion 10 CANCELED
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Apr 7 Lecture 22 Alpha Proteobacteria | Bacterial chromosome structure | Do bacteria have mitosis?
Done
Apr 9 Lecture 23 Actinobacteria | Secondary metabolites | Prokaryotic multicellularity | Programmed cell death
Done
Apr 11 Discussion 11 The hydrothermal vent scaly snail
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Apr 14 Lecture 24 Crenarchaea | Microbe:Microbe symbiosis | The smallest organism
Done
Apr 16  Lecture 25 Euryarchaea | Methanogenesis | Transcription & nucleosomes in euryarchaea
Done
Apr 18 Discussion 12 Nanobacteria
Done
Apr 21 Lecture 26 Eukaryotes - mostly microbes
Done
Apr 23 Lecture 27 Viruses | The origins of viruses | Are prions for real? Are you sure?
Done
Apr 25 Discussion 13 Final Exam study session
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May 2 Exam Final exam @ 8:00am
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Last updated April 23, 2008 by James W Brown | Department of Microbiology | College of Ag and Life Sciences | NC State University