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Which of the following is an application involving De Bruijn graphs?

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9.12 Describe the steps you would take to obtain a null allele in your favorite yeast gene (YFG) using homologous recombination if you have available a yeast strain that is sensitive to the antibiotic kanamycin, pBluescript II plasmids (see Chapter 8, p. 176) with the DNA inserts diagrammed in Figure 9.B, and are able to transform yeast with a targeting vector, once you construct it. In Figure 9.B, EcoRI, HaeII, HindIII, and PstI are restriction enzymes (see Chapter 8, p. 174) that cleave these DNAs at the sites shown, and the distances between the sites aregiven in kb. As part of your answer, diagram the targeting vector you would construct and the structure of the chromosomal region once YFG is knocked out using this targeting vector. Also, describe how you would use PCR to confirm that you had obtained a null allele at the gene, and indicate on your diagrams the regions you would use for designing PCR primers. Remember that the absence of a PCR product does not provide strong evidence for a specific DNA arrangement, as a PCR could fail for any number of reasons.

*9.22 A central theme in genetics is that an organism's phenotype results from an interaction between its genotype and the environment. Because some diseases have strong environmental components, researchers have begun to assess how disease phenotypes arise from the interactions of genes with their environments, including the genetic background in which the genes are expressed. (See http://pga.tigr.org/desc.shtml for additional discussion.) How might DNA microarrays be useful in a functional genomic approach to understanding human diseases that have environmental components, such as somecancers?

9.26 Mycobacterium leprae is an intracellular bacterium that is the causative agent of leprosy, a chronic disease that infects the skin, nerves, and mucous membranes. It has not been possible to grow the bacterium in a culture medium, unlike its relative Mycobacterium tuberculosis, the causativeagent of tuberculosis (TB). M. tuberculosis can also grow intracellularly, as in the lungs it is taken up by alveolar macrophages and can multiply unchecked. The following table compares the genomes of these two organisms. M. leprae-M. tuberculosis:*Genome size (Mb): 3.27 -4.41*Percent of genome encodingproteins: 49.5 -90.8*Protein-coding genes (ORFs): - - 1,604- 3,959*Pseudogenes: 1,116- 6*Gene density (bp per gene): - - 2,037- 1,114*Average gene length: - 1,011-1,012a. Pseudogenes are nucleotide sequences that no longer produce functional gene products because they have accumulated inactivating mutations. Why might M. leprae have many more pseudogenes than M. tuberculosis?b. What analyses would you perform to understand how these two bacteria differ in terms of the enzymatic functions they can carry out?c. How might your analyses help you understand how to culture M. leprae?

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