Lab 3 - PCI DNA extraction from human blood
Yesterday students finished the PCI DNA extraction from their own blood. The steps that were left included adding the PCI, doing some pellet washes with cold ethanol and eluting the DNA in TE buffer. Samples were incubated overnight at 55ºC.
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Lab 4 - PCR of the PV92 Alu insertion locus
The goal of this lab was to introduce students to the Polymerase Chain Reaction (PCR), the most popular in vitro technique to make copies of (amplify) target DNA fragments. We extracted DNA from our cheek cells and used it to set up 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:
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 insertions, lane 2 to an individual with insertions in both chromosomes, and lane 3 to an individual with an insertion in one chromosome.
What is your genotype like?
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