MB451 Lectures

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
---

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
---

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
---

Mar 3 No class Spring Break
---

Mar 5 No class Spring Break
---

Mar 7 No class Spring Break
---

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
---

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
---

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
---

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
---

May 2 Exam Final exam @ 8:00am
---

Last updated April 23, 2008 by James W Brown | Department of Microbiology | College of Ag and Life Sciences | NC State University

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	---
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	---
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	---
Mar 3	No class	Spring Break	---
Mar 5	No class	Spring Break	---
Mar 7	No class	Spring Break	---
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	---
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	---
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	---
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	---
May 2	Exam	Final exam @ 8:00am	---