20.109(S14):Module 1

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20.109(S14): Laboratory Fundamentals of Biological Engineering

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Home        Schedule Spring 2014        Assignments       
Module 1        Module 2        Module 3              

Module 1: DNA Foundations and Diagnostic Engineering

Lecturer: Jonathan Runstadler
Instructors: Shannon Hughes, Aneesh Ramaswamy, and Agi Stachowiak

TA: Chris Bandoro


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 fungus microsporidia. Previous research shows that microsporidia infections are common in several bird populations that have contact with humans – aquatic birds that may visit reservoirs or beaches, pets such as parrots and lovebirds, and pests such as pigeons – and it is speculated that zoonotic transfer may occur. Although most people can rapidly clear such an infection, immunocompromised people such as children, the elderly, and HIV-infected individuals are at risk for serious complications. Improving the sensitivity and/or specificity of microsporidia diagnosis could thus be useful in environmental testing and subsequent health care recommendations.

We thank the Runstadler lab for access to bird samples (pre-screened for flu and everything!), and especially Wendy Puryear for helpful technical discussions as this module was developed. We also thank Professor Karen Snowden at Texas A & M University for access to microsporidia spores and for invaluable advice about imaging methods for identifying microsporidia. Finally, we thank the Broad Institute for generously donating microsporidia DNA.

Module 1 Conceptual Overview. Experimental goals are shown in yellow, related concepts in blue, and related application areas in green. Stars span both experiments, while triangles are associated with a single experiment.

Lab Links

Module 1 Day 1: Microbial DNA extraction
Module 1 Day 2: Diagnostic primer design
Module 1 Day 3: 16S PCR and paper discussion

Note: 1 week between Day 3 and Day 4.

Module 1 Day 4: DNA cloning
Module 1 Day 5: DNA sequencing
Module 1 Day 6: Journal club I
Module 1 Day 7: Phylogenetic and primer analyses
Module 1 Day 8: Journal club II

TA notes, mod 1


Microbiome abstract and summary report

Primer design memo