April 28, 2010- Lecture on Antifungal Drug Resistance and Pma1p
1. What type of compound is ergosterol? Why do yeast cells need it?
2. What is the problem associated with amphotericin B?
3. Which enzyme is blocked by azoles such as fluconazole? Is this enzyme one which can mutate and confer drug resistance upon fungal cells?
4. Why is upregulation of Mdr1p a causative factor of fluconazole-resistance?
5. What is the plasma membrane H+-ATPase in yeast? Why is it important?
6. Design an experiment in which you want to use an inhibitor to block this pump. What would your endpoint measurement be? What would the graph look like?
See you at the final!
Remember: 6:10 PM- 7:00 PM, ORAL EXAM
Remember: 7:00 PM -8:00 PM, WRITTEN EXAM
April 21, 2010: Lecture on Transgenic Mice, Knockout Mice, and Genetically-Modified Foods
After this lecture, you should be able to answer the following:
1. What is the difference between a transgenic mouse and a knockout mouse? How can such tools be used to answer experimental questions relating to human disease states?
2. You have generated a chimeric knockout mouse using embryonic stem cells. Describe how you did it. What were some of the features of the vector that you used? You thought that knocking out this gene would produce an embryonic lethal phenotype, but it did not. To your surprise, the mouse survived and did not appear to have any phenotypic abnormalities. What do you conclude?
3. How could you make a transgenic mouse which will express the transgene in a tissue-specific manner, such as in the prostate, rather than throughout the body?
HINT: This web-site has some helpful information:
http://www.biochem.arizona.edu/classes/bioc471/pages/Lecture19/Lecture19.html4. What kinds of crops have been genetically modified using biotechnologies? What percentage of the biotech food market is accounted for by the USA and Canada? By China? What percentage of the soy beans sold in the USA are genetically-modified?
5. What are some of the advantages and disadvantages of genetically-modified foods?
Lecture on Stem Cells
After this lecture, you should be able to answer the following:
1. What are stem cells? What kinds of cells can they give rise to? What are some sources of stem cells?
2. Why do people care about stem cells? What is an embryonic stem cell and where does it come from? What is an adult stem cell and where does it come from?
3. What is the difference among totipotent, pluripotent, and multipotent stem cells?
4. What kinds of medical advances might be achieved by using stem cells?
5. What does the U.S. President’s Executive Order signed in August, 2001, say about stem cells? What did the 2009 Executive order achieve?
6. What is therapeutic cloning and how is it related to stem cells? What is reproductive cloning? What was the name of the first animal that was ‘reproductively’ cloned?
7. What is the purpose of feeder layers in the culturing of embryonic stem cells?
8. Briefly explain the 2006 experiment by Takahashi and Yamanaka in which they generated iPSC cells. Which genes were used to produce the iPSC cells? What are iPSC cells? Why might these types of cells be useful? How do these iPSC cells differ from adult stem cells or embryonic stem cells? (HINT: see BBRC paper)
9. What is a teratoma and how is it related to stem cells?
10. How is a stem cell line prepared? How does one determine whether or not an embryonic cell line derived from the inner mass of the blastocyst can be characterized as an embryonic stem cell line?
11. What types of bone marrow derived stem cells have been identified? What kinds of tissues will such cells give rise to? What types of neural cells can be made from stem cells found in the brain? What types of gastrointestinal cells can be made from stem cells found in the gut? What types of skin cells can be made from stem cells found in the skin? Where in the skin do the stem cells usually reside?
12. What cellular functions are normally regulated by Oct 3/4? by Sox-2? By Klf4? By Lin28? c-Myc? (HINT: see BBRC manuscript).
GRANT PROPOSAL-RELATED:
1. What are keloids? What are they composed of? What might happen to to keloids if AP-1 activity within the lesion is suppressed?
April 7, 2010: Cancer Risk and BRCA1 Missense Variants
After this lecture, you should be able to answer the following:
1. Why is BRCA1 an important protein to humans?
2. Are all mutations of BRCA1 associated with an increased risk of breast or ovarian cancer? If not, which kind of mutations increase risk of disease?
3. Describe the role of the BRCT domains in the risk of BRCA1-associated breast cancer.
4. What are the strengths and limitations of using clinical data to predict cancer breast cancer risk?
5. What are the strengths and limitations of using structural analysis to predict the effect of BRCA1 mutations?
6. How can the conclusions of structural analysis of rare BRCA1 variants be validated?
7. [See Article by Carvalho et. al, 2009]. What are the goals and objectives of the study? How were these goals and objectives achieved by the authors? What was the major outcome of the study? What is the significance of their observations?
GRANT PROPOSAL RELATED:
1. Why might non-viral liposome-mediated gene therapy vectors be useful in the treatment of X-SCID?
2. What is TRPV2 and why might it be a relevant target in the treatment of multiple sclerosis?
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?
