Biology 3594A Lecture Notes - Lecture 20: Woolly Mammoth, Haplotype, Asian Elephant
13 May 2018
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One of the more difficult questions on the exam –pull beyond one slide or one lecture. Need to integrate
Give a specific example and ask this question
What do these reports have to have to be really good?
Slides we have with a big list, question might ask us about list (elements of mutator phenotype, characteristics of cyclophosphamide)
Important considerations in designing an experiment to test mutation induction
Proxy: Carp paper: carp is a good proxy because it’s in the water and already eating it, then work with people later
Mechanism of action affects the design of the test
Agent in the right solution –so it doesn’t precipitate out or get absorbed
Ex. Know that the solution itself is not mutagenic
Doses –how much, how often, how long (regimen)
Route –if about something in the diet then don’t apply to skin
If it requires cell tissue but the tissue isn’t dividng that’s an issue
Manifestation period –good term to know!
Toxicity –could be a confounder, couldn’t measure stuff because all the cells died
How to isolate DNA and the challenges –integral to the course
DNA signature
Essay question: what is CGR, how do you make a plot, can you plot out a short sequence and could you explain how this plot works?
How does that differ from MSA –diagrams and a full sentence text
Chaos –all possible subsequence lengths regardless of where they are in the genome, sequence biases
If every possible subsequence was there in equivalent frequencies to all others of the same length, there wouldn’t be sparse and dense regions, random distribution
Eventually fill it in all in and the plot is entirely black
MSA –putting them together as best as we can and looking nucleotide to nucleotide, can see base substitutions, deletions, insertions
Memorize the terms and a definition for all of them
Argue both sides of an issue given a dilemma
Be able to identify the stakeholders in the issue and where the problems are for each of these and how to try to maintain theautonomy, transparency, etc.
Essay question –all writing, no diagrams needed
Not going to be one right answer, but use all terms, convince that we know what they mean, identify all stakeholders
Driver mutation does not only depend on the type of amino acid
Not every change produced the same level of mutation
Some base substitutions produced a change in the codon that created the hypermutation
When Leucine => isoleucine or proline -> mutator phenotype
Other codons caused diff changes
Not only about that particular amino acid Leucine
What about mitochondrial DNA makes it really good for the study of aDNA
More per cell and per nuclear DNA
Easy to sequence, small
Lots of it available, we know genome sequence and annotation and what is functionally relevant
Take all these features from slide^ and form answer to question: why is it so popular in aDNA studies
Female mediated migration, we know where all the variation is
What is in solution capture of DNA
Solution capture of DNA –take Asian Elephant DNA, close to woolly mammoth DNA. How it works and how it was used for the woolly mammoth
Similarities between solution capture DNA and blocker PCR and mutant enrichment
Working with samples of low abundance of your target, and trying to enrich to find it
Either destroying WT to get the mutant, or trying to find the aDNA in all this other clutter -> specificity and increase sensitivity
Not too many questions like this on the exam, but do you understand how to overcome a problem of needing really high sensitivity and keeping specificity
If you know in solution capture slide and mutant enrichment protocol really well, set up nicely for a compare contrast question and see that they’re kind of doing the
same thing
Pictorial representation of the genotype of a variety of people population
SNP haplotype –many loci that can have 1 or 2 alleles, person we’re studying has one set of SNP genotypes, and we’re comparing to other populations
To study genetic Admiture –when a SNP haplotype moves into pop, interbreeding, new alleles coming in (gene flow)
Start to share colour patterns across here
Lec 20 Review
May 13, 2018
3:01 PM
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