Labs and Protocols


DATE TOPIC

Protocol

Monday, 8/4 We will use the PowerBiofilm DNA Isolation Kit to isolate bacterial DNA from samples taken from our mouths. Day 1 protocol
Tuesday, 8/5 We will perform PCR amplification of the 16s rDNA region of the bacterial genomes we isolated on 8/5. We will purify the resulting product and run on a gel to verify that the correct products are present.

Day 2 protocol

Wednesday, 8/6 We will clone the PCR products from 8/6 into a special TOPO vector. Day 3 protocol
Thursday, 8/7 We will perform colony PCR on colonies from yesterday's transformation. We will then purify the PCR products and send for sequencing. Day 4 protocol
Friday, 8/8 We will plate yeast cultures on canavanine-containing plates to explore the statistics of survival mutations.

Short protocol (describes what we will do in lab).

Full protocol (gives background on experiment in addition to experimental protocol).

Monday, 8/11 We will count the number of colonies from the yeast cultures plated on Friday. Time permitting, we will also spend some time analyzing the mutations in the CAN1 found from a previous run of this experiment.

CAN1 wild-type (reference) sequence

CAN1 sequences: CAN1 sequences from Luria-Delbruck experiment to look at in lab.

Tuesday, 8/12 Analysis day. Meet in the classroom. We'll analyze the distribution of mutant colony numbers from yesterday. We'll also spend some time looking at the 16s sequencing results. You should download the following files which we will use in class.

Function that we'll use to make histograms.

Instructions for CAN1 gene analysis.

Wednesday, 8/13 Analysis day. Meet in the classroom. We'll spend some time looking at the 16s sequencing results. You should download the oral microbiome sequences.

 

Oral microbiome sequences