Assignment task:
Problem 1. You have been chosen to design a plasmid containing the red fluorescent protein (RFP) gene that future BIOL& 211 classes will use instead of the current pGLO plasmid that contains the GFP gene. Instead of the much more expensive arabinose, your plasmid will use lactose to induce gene expression of RFP, saving the Biology Department precious funding! Describe clearly, demonstrating your understanding of plasmids, gene expression, and the lac operon, how you would design your plasmid in order to accomplish this. You should include a carefully labelled sketch of your plasmid showing genes and regulatory components. Once transformed, E. coli should 1) only survive on a plate containing ampicillin if they have the plasmid and 2) express RFP only in the presence of lactose.
Problem 2. An extensive and comprehensive research project is conducted in which a single species of bacteria is grown in two different steady state chemostats under completely different growth conditions with the goal of understanding how the species differs under these two forms of growth conditions. The two cultures are grown, and then mRNA, proteins, and DNA are all extracted and quantified as follows:
1) microarray analysis
2) proteomics - proteins present quantified via GC-mass spectrometry (gas chromatography-mass spectrometry, a technique that allows quantification of all the proteins present in a sample, e.g. MALDI-TOF or related)
3) complete sequencing of all the mRNA present
4) complete sequencing of all the DNA present
For each of these, briefly explain what each approach would yield, i.e., what would it tell us about the species of bacteria grown under the two different conditions? Please explain briefly but clearly for each of the four approaches.
Microarray analysis
Proteomics
mRNA sequencing
DNA sequencing
Of these four approaches, which two do you think would yield the closest set of information? Explain.