Mar. 31, 2010: Lecture- Introduction to Pharmacogenomics
After this lecture, you should be able to answer the following:
1. What is the difference between pharmacogenetics and pharmacogenomics?
2. Describe the clinical implications for poor metabolizers of substrates for N-acetyltransferase (NAT2). What adverse effect of isoniazid is observed in NAT2 poor metabolizers?
3. With respect to CYP2D6, what types of metabolic phenotypes have been observed? Which ethnicities have high percentages of poor metabolizers? Use the metabolic clearance of nortriptyline as an example of interindividual variability in drug clearance. How many alleles of CYP2D6 have been observed in the population?
4. What is thiopurine methyl transferase (TPMT)? What are the common TPMT alleles in the human genome? Describe the interindividual variability among children taking these drugs for leukemia? How can one assay the function of TPMT activity in vitro? What other type of method can be used to test for polymorphisms? With respect to the dose of thiopurine drug, what should be done in patients that are poor-metabolizers?
5. Why are people with glucose 6-phospho dehydrogenase deficiencies prone to severe hemolysis when exposed to oxidant drugs such as antimalarials such as primaquine or chloroquine? What is malignant hyperthermia? Discuss this disorder from a pharmacogenomic point of view.
6. What are SNPs? Are SNPs common or uncommon?
7. What are ABC transporters?
8. What is the MDR1 transporter? What is its physiological role? Its pathophysiological role?
9. You have identified a new SNP in the CYP3A4 enzyme. Design both in vitro and in vivo experiments to determine whether or not that SNP affects the function of the 3A4 enzyme.
10. How is it possible that a life-threatening opioid intoxication developed in a patient after he was given small doses of codeine for the treatment of a cough associated with bilateral pneumonia? Provide a possible explanation.
11. Describe abacavir hypersensitivity in term of pharmacogenomics. What is abacavir normally used for?
The following web-site contains some more information on pharmacogenomics. It is maintained by the U.S. Department of Energy and also has some interesting links relating to pharmacogenomics:
http://ornl.gov/sci/techresources/human_genome/medicine/pharma.shtmlThe following web-site contains information on toxicogenomics. Toxicogenomics is the science interested in understanding the effects of toxicants on the genome. Type in your favorite toxicant, and see what comes out of the database!!
http://ctd.mdibl.org/The following web-site contains information on SNPs.
http://www.aacr.org/home/public--media/patients--family/fact-sheets/cancer-concepts/snps.aspx/Good Luck!
THERE IS CLASS NEXT WEDNESDAY 3/31/10
Just found out from the Dean's office that the 3 pm closure next Wednesday applies only to staff who are not involved in teaching. Therefore, we will meet next week. I have posted the grants for 3/31 and the grant for 4/7 on the professor's drive.
Grant critiques for 3/31: Hazel, Qian, Ripal, Edison
Grant critiques for 4/7: Tak, Yuliya, Priyanka, Renel
24 March 2010: Lecture: Gene Therapy
After this lecture, you should be able to answer the following:
1. What is the basic rationale underlying gene therapy?
2. What is Leber's congenital amaurosis? How has gene therapy been used to treat the disease in dogs?
3. What are the different ways one can use to introduce DNA into human cells?
4. Describe an example of somatic cell genotype modification by DNA transfer.
5. Why are liposomes used for gene transfer? What are liposomes?
6. Describe the three categories of somatic cell gene therapy and provide at least one example of each.
7. List some of the advantages and disadvantages of using viral vectors to transduce DNA into patients. Are there differences among different viral vectors? How so?
8. Describe the success and the limitations encountered in the gene therapy of X-SCID disease. What kind of disease is this? What gene is affected? Do females get this disease? What seems to be the most significant adverse effect associated with the gene therapy of this disease?
9. Explain why gene therapy in the treatment of glaucoma is an area of intense investigation. Why would the introduction of genes into the eye which code for proteins such as MMPs, Prostagalandin Synthases, and Neuroprotectants make sense to use in the treatment of glaucoma?
Lecture 6: DNA Cloning and Isolating Genes
After reading through this lecture supplement, you should be able to answer the following questions:
1. What are the characteristics of restriction enzymes and how are they useful for DNA cloning?
2. What are cloning vectors? What are the different kinds of cloning vectors? What is the size of DNA insert that can be placed into each of these vectors? How are these vectors used to carry and amplify DNA inserts.
3. What is the basic difference between genomic and cDNA libraries? How are genomic libraries constructed? What is the purpose of having overlapping DNA fragments in genomic libraries? What is 'Reverse Transcriptase?' How is it used to generate cDNA libraries?
4. How might you clone a segment of DNA into a plasmid vector? Use pBR322 as an example of the vector. How would you know that bacteria "took-up" the plasmid construct?
5. How might one isolate a gene for an inherited disorder starting with the protein sequence? What are degenerate primers?
6. What is "reproductive" cloning? What are some of the pitfalls of this method? What is "therapeutic" cloning?
7. How was "Dolly" the sheep cloned? When was she cloned?
8. What is meant by the term, "genetic engineering?"
KIT Corner:
1. What is the underlying theory behind the luciferase reporter assay? Is it a fluorescence assay?
2. What is the underlying theory behing the green fluorescent protein reporter assay? What is the excitation wavelength here? emission wavelength here? why the difference?
3. What is the underlying theory behing the nitric oxide fluorometric assay kit?
