20.109(S15):Module 1: Difference between revisions
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===Lab Links=== | ===Lab Links=== | ||
[[20.109(S15):Microbial DNA extraction (Day1) | | [[20.109(S15):Microbial DNA extraction (Day1) | Day 1: Microbial DNA extraction]]<br> | ||
[[20.109(S15):Diagnostic primer design (Day2) | | [[20.109(S15):Diagnostic primer design (Day2) | Day 2: Diagnostic primer design]]<br> | ||
[[20.109(S15):16S PCR and paper discussion (Day3)| | [[20.109(S15):16S PCR and paper discussion (Day3)| Day 3: 16S PCR and paper discussion]]<br> | ||
Note: 1 week between Day 3 and Day 4. | Note: 1 week between Day 3 and Day 4. | ||
[[20.109(S15):DNA cloning (Day4)| | [[20.109(S15):DNA cloning (Day4)| Day 4: DNA cloning]]<br> | ||
[[20.109(S15):DNA sequencing (Day5)| | [[20.109(S15):DNA sequencing (Day5)| Day 5: DNA sequencing]]<br> | ||
[[20.109(S15):Journal club I (Day6)| | [[20.109(S15):Journal club I (Day6)| Day 6: Journal club I]]<br> | ||
[[20.109(S15):Phylogenetic analysis (Day7)| | [[20.109(S15):Phylogenetic analysis (Day7)| Day 7: Phylogenetic analyses]]<br> | ||
[[20.109(S15):Diagnostic primer analysis (Day8)| | [[20.109(S15):Diagnostic primer analysis (Day8)| Day 8: Diagnostic primer analysis]]<br> | ||
[[20.109(S15):Journal club II (Day9)| | [[20.109(S15):Journal club II (Day9)| Day 9: Journal club II]]<br> | ||
[[20.109(S15): TA notes for module 1| TA notes, mod 1]] | [[20.109(S15): TA notes for module 1| TA notes, mod 1]] |
Revision as of 13:23, 15 December 2014
Module 1: DNA Foundations and Diagnostic Engineering
Lecturer: Jonathan Runstadler
Instructors: Shannon Hughes, Noreen Lyell, and Leslie
TA: [[User:]]
Overview
In this module, you'll complete two mini-investigations while gaining foundational skills – in laboratory techniques, data analysis, and both written and oral communication – that will serve you well in the remaining two modules. Throughout, host–microbe interactions and their implications for human health will be a unifying theme. You will study two classes of microbes that can be present in the bird gut, whether by ingestion or infection. Some of these microbes are pathogenic (disease-causing), and some may have the potential for zoonotic (inter-species) transfer to humans.
In the primary experiment, you will pool data with your peers to perform a phylogenetic analysis of the bacteria found in two distinct populations of migratory birds. You will look for similarities and differences and speculate about the mechanisms that brought these about. This study has parallels to recent investigations of human microbiome diversity that shed light on variations in metabolism, susceptibility to infection, and other measures of health. More directly, your results may suggest a link between a particular factor in a bird's environment, such as climate or diet, and characteristics of the resulting gut bacterial population, such as the dominant species or degree of variety. And hey, we'll also learn what bacteria you might be exposed to the next time you accidentally encounter bird feces!
In the secondary experiment, you will each design and test primers for diagnosing infection with the avian influenza virus (AIV). Blah...
We thank the Runstadler lab for access to bird samples (pre-screened for flu and everything!), and especially Wendy Puryear for helpful technical support and discussions as this module was developed.
Lab Links
Day 1: Microbial DNA extraction
Day 2: Diagnostic primer design
Day 3: 16S PCR and paper discussion
Note: 1 week between Day 3 and Day 4.
Day 4: DNA cloning
Day 5: DNA sequencing
Day 6: Journal club I
Day 7: Phylogenetic analyses
Day 8: Diagnostic primer analysis
Day 9: Journal club II