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MICRB320 Lecture Notes - Lecture 10: Relative Change And Difference, Proteorhodopsin, Haloarcula

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orangecheetah563
22 Oct 2015
School
University of Alberta
Department
Microbiology (Biological Sciences)
Course
MICRB320
Professor
Rebecca Case

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Document Summary

Micrb320 lec10 midterm only up to molecular methods why,how would you do it with molecular methods. Not that focused on the examples and stuffs. Shorter reads - costs less per base pair. High throughput sequencing and diversity: move from 10s, 100s, 1000s to 100 000s 16s rrna gene sequences, able to move to high numbers of sequences due to new sequencing technology, reads much shorter and unpaired (go from. 1500 bp (800 bp unpaired) to 150 bp: poor identification due to only sequencing 2-3 variable regions of 16s rrna gene, but able to detect a lot of new diversity. Rarefaction analysis for one sample based on pairwise distance. Take sample > sequence pyro > 16s > built a rarefaction curve. Figure: rarefaction analysis for sample fs396 based on pairwise distance. Rarefaction is shown for otus that contain unique sequences and otus with differences that do not exceed 1%, 2%, 3%, 5%, or 10%.

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Related Questions

In the October 2011 issue of PLoS Genetics, Pierson et al. used whole-exome sequencing to identify the mutations responsible for a rare spastic ataxia-neuropathy syndrome. The paper and supporting information can be found at http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002325, and you will need to access the paper to answer these questions. The paper is focused primarily on the phenotype and the particular gene, but our attention will be primarily on the methods used for the exome-sequencing approach, which is found in the Methods and in the Supporting Information.

a. Figure 1A shows a pedigree of the family with two affected sons, who are not identical twins.


i. Recalling pedigree analysis from your introductory genetics course, what is the most likely mode of inheritance for this syndrome?

ii. What is the probability that the next child born to this couple will be disease-free?

b. Summarize the experimental strategy that yielded the results shown in Supplemental Table S2, as found under Supporting Information. Your summary should define the abbreviations used in the column headings and what the numbers mean. You should also include an explanation of why the numbers decrease as one reads from left to right from columns 2 through 6 (not including Total Protein Coding Exons Sequenced). c. The numbers of candidate genes in Supplemental Table S3 are 71 and 7, but these numbers do not appear anywhere in Supplemental Table S2. What inference from the data was made that allowed the investigators to arrive at the numbers in Table S3 based on the numbers in Table S2?

d. What further inferences led the investigators to conclude that AFG3L2 is the gene most likely responsible for this syndrome?

e. In the analysis of Miller Syndrome described in the chapter, the affected children did not have the same mutation on each homologous chromosome, and were in fact heteroallelic for the mutations. In this example, the children have the same mutation on each homologous chromosome. Why did the authors expect that the affected children would be homozygous for the same mutation?

f. What is the postulated mechanism by which this mutation results in this phenotype?

g. In this chapter, genes can be cloned and identified based on the following five properties: map position, mutations and allelic differences, expression patterns, complementation testing, and homology with genes in other organisms. Using a flow chart, diagram how these five properties led to the identification of the gene for this syndrome.