Lab 05 - GAPDH Nested PCR

Arabidopsis thaliana

_______________________________________________

Today we started the exercise in which students will learn the basics of a nested PCR. We will work with the gene that encodes one of the GAPDH isomers, GAPC, in Arabidopsis thaliana, the model organism of plants. Some people call it "the fruit-fly of plants".

GAPDH is an enzyme in charge of catalyzing one of the reactions in glycolysis. There are several nuclear genes that encode GAPDH isomers (proteins with different amino acid sequences but with the same function), and we are targeting the gene GAPC in the A. thaliana genome. We ran a first round of PCR, with our initial primers, and tomorrow, Friday, we will run the second run, with the nested primers.

----------------------

Lecture, Chapter 5 - DNA replication

We continued covering chapter 5, on DNA replication. We finished talking about DNA replication in prokaryotes, topic in which students should have an understanding of the replication fork, including the functioning of all the enzymes involved in the process.

We started talking about DNA replication in eukaryotes, organisms in which some differences are found, mainly because of the linearity of chromosomes. In prokaryotes chromosomes are circular.

----------------------

Lecture, Chapters 4 and 5 - Genes, Genomes, and DNA & DNA Replication

Today we covered the end of chapter 4, focusing mainly on the mechanisms prokaryotes and eukaryotes use to supercoil their DNA.

Then we started with chapter 5, on DNA replication. We introduced the concept of replication fork and went over some of the issues the cell has to solve in order to get supercoiled DNA to replicate.

Reminder: We are in week 3 and students should be meeting with me to decide the topic of the review paper.

----------------------

Lab 04 - Detection of genetic modification in crops

Friday Sep 18 2009

We started the exercise in which we will test corn and soy samples students brought to the lab to see if they have been genetically modified (if they are Genetically Modified Organisms or GMOs).

We extracted DNA from corn and soy leaves, as well as from a certified non-GMO seed provided by Bio-Rad with the kit. We set up PCRs using primers that will amplify de 35S promoter of the cauliflower mosaic virus (CaMV 35S) and the nopaline synthase (NOS) terminator of Agrobacterium tumefaciens, which are present in about 85% of all modified crops in the U.S. As a positive control for the presence of DNA, we also used primers that amplify the photosystem II chloroplast gene, which should be present in all plants, regardless of genetic modification.

Next week we will run an agarose gel electrophoresis to confirm the results.

----------------------

Lab 03 - PV92 PCR (postponed)

Thursday Sep 17 2009

Due to the power outage in Ada and subsequent evacuation of Meyer Hall and the Mathile Center, the lab has been postponed until weeks 09 and 10. That way we will be able to still do the lab without disrupting the flow of the following labs, which sequence is of greater importance than that of the PV92 PCR lab.

----------------------