Lecture, chapter 4 - Genes, genomes, and DNA

Today we finished chapter 4, on genes, genomes and DNA.

We discussed the ways in which DNA is supercoiled, both in prokaryotes and eukaryotes, similarities and differences between both, and the implications for the functioning of the cell (in terms of replication and gene expression).

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Module 1, Lab 04 - Detection of GM in crops

In this lab we will test corn and soy samples students collected in the Fall to see if they have been genetically modified (if they are Genetically Modified Organisms or GMOs). Our tool of choice for this test will be PCR.

We extracted DNA from corn and soy leaves, as well as from a certified non-GMO seed provided by Bio-Rad. 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.

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Module 1, Lab 03 - PCR of the PV92 Alu insertion locus

Wednesday, December 09, 2009

The goal in this lab to introduce students to the Polymerase Chain Reaction (PCR), the most popular in vitro technique to make copies of target DNA fragments. We extracted DNA from our cheek cells and used it to set up basic PCRs.

Our target is the PV92 Alu insertion locus, located on chromosome 16.

Alu elements are a family of short interspersed repetitive elements (SINEs) that have mobilized throughout primate genomes for the last 65 My, by retrotransposition.

There are more than 500,000 Alu elements per haploid genome in humans (about 5% of our genome). Depending on the insertion point they may be associated with some genetic diseases (e.g.some cases of hemophilia, familial hypercholesterolemia, severe combined immune deficiency, or neurofibromatosis type 1). But in most cases it has no effect on the individual's health.

Some Alu insertions are very recent and polymorphic. The most recent are human specific (HS) and such is the case of PV92. Because the PV92 insertion locus is HS, polymorphic, neutral (invisible for natural selection), and easy to detect, it has been widely used in human genetic population studies, and it has been one of the markers used to support the out-of-Africa hypothesis.

In this lab we will test the presence of 0, 1, or 2 PV92 Alu insertions in our genomes.

The following picture illustrates the possible outcomes of our PCRs:

The sample on lane 1 belongs to an individual with no PV92 Alu insertion, lane 2 to an individual with insertion in both chromosomes, and lane 3 to an individual with an insertion in one chromosome.

What is your genotype like?

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Lecture, chapter 4 - Genes, genomes and DNA

Today we started chapter 4, on genes, genomes and DNA, a discussion on how DNA is organized and how such organization, contrasting prokaryotes and eukaryotes, affects DNA function and replication.

We discussed the different kinds of non-coding DNA (e.g. LINEs, SINEs, introns, satellite DNA, VNTRs...) a few reasons that explain its existence, and a few applications by using them as molecular markers.

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Lecture, chapter 3 - DNA, RNA and Proteins

Today we covered most of chapter 3, on the (very) basic structure and function of DNA, RNA, and Proteins.

Me discussed important concepts like the central dogma of molecular biology, some of the properties that make DNA a key molecule for life (antiparallelism, complementarity), and some of the roles that RNA has, beyond the transfer of information from the nucleus to the cytoplasm.

In our next meeting we'll finish chapter 3, with a basic discussion about protein structure and function.

Reminder: We are meeting tomorrow, Tuesday, in Meyer 128, at 8:00 am, to make up for the class that was cancelled on Monday Nov 30th.

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