1 5 1
Final Exam Objectives
Email Kathy

Final Exam Objectives
Tuesday December 11, 2007 6-8 pm

Important Disclaimer 1: These objectives are provided to help you study and to organize your thoughts (and notes!). They are NOT a guarantee of what will - or won't - be on the exam.

Important Disclaimer 2: I will give those who missed a Warm Up ONE last chance to fill in that unpleasant 'empty space' in their gradebook ("THANK YOU, DR. MARRS") Just for fun, there will be ONE 5-point matching question on the exam that will ask you to correctly match the NAMES and BASIC DESCRIPTIONS of the 14 group projects. (*One person from each of the 14 groups*: Please go to the CHAT ROOM option of Oncourse(in the black toolbar on the left of the page) and add the drug NAME and a couple-word description! Remember that the NAME ALONE is often enough to determine the drug's function.... (ie: DenGONE...hmmm wonder what THAT drug does?!?) PS. NO, you can't use this for extra-extra credit, or to replace MORE than one missing Warm Up - this is just a second chance for those who missed one Warm UP along the way = many people had interviews, work complications, or oncourse issues along the way.

 

Important Disclaimer 3: A last Extra Credit assignment for those who did't get a chance to do so yet - I'll send an Oncourse assouncement with the info. Due December 15th.

From Exam 1: (will be ~70 points of final)

Objectives for What is Biotechnology?
August 23, 2007

 

once again, make sure that you, as a Biotech 540 smarty-pants, can NOW answer all the First Night questions!

Objectives for Biotechnology Timeline 2007 and Questions
August 28, 2007

1.Identify Nobel-winning scientists and their research stated above. Why? YOU KNOW WHY!
2.Explain how the Cohen-Boyer partnership resulted in 'the birth of biotech' (aka Cloned beef to cloning), the role of Robert Swanson developing the biotechnology company Genentech

3.Explain the major results of the Cohen-Boyer 1974 PNAS paper. We will go over this paper in class Tuesday evening
4. What were the major recommendations of the 1974 paper "Potential Biohadards of Recombinant DNA molecules? What was the outcome of this manuscript?

5. What were the major conclusions from Asilomar conference and what are their significance in the use of recombinant DNA technology? Be able to discuss the the initial concerns and recommendations that surround this important event.

Objectives for Surfing the First Wave: rDNA drugs and Drug case studies

August 30, 2007 and Sept 4, 2007

1. Know all the "parts" of a eukaryotic gene
2. Describe how restriction enzymes function to create recombinant DNA
3. Describe how bacteria can be used to produce eukaryotic proteins


For each of the companies studied, be able to list:
1. The Protein Product: what human protein is formulated as the drug?
2. Indication: why is the drug prescribed and what it does it do in the body?

1: Epogen /Procrit
2. Aranesp
3: Neupogen
4: Neulasta

5. Activase /CathFlo Activase:
6. TNKase
7. Pulmozyme
8. Nutropin
9. Avonex
10. Amevive
11. Humulin
12. Xigris

13. Forteo
14. Betaseron
15. Proleukin
16. Regranex

 

Objectives for Biotech's Second Wave: mAb Drugs plus MOAs

September 6, 2007

  1. When making monoclonal antibodies, What are myeloma cells and why are they so useful in this technique? What is a hybridoma? How are experimental conditions set up to select for hybridomas?
  2. For each drug listed below, be sure to know:
    (1) The Target: what human protein is recognized by the mAb?
    (2) Indication: why the mAb is prescribed and what it does it do in the body?
Transplantation:
Oncology:
T-cell Autoimmune:
Misc:

Orthoclone OKT3, Simulect , Zenapax
 Rituxan, Zevalin, Bexxar, Herceptin, Avastin, Erbitux, Campath, Mylotarg
Enbrel, Remicade,  Humira, Amevive, Raptiva   
Synagis, ReoPro, Xolair, Lucentis

Objectives for Investing in Biotechnology
September 11, 2007:

  1. You will not be tested on your knowledge of compound interest, stocks, bonds, or other assets! That material is all there to educate you about investing...hopefully you will be motivated to get a jump start on your financial future $$$$$!
  2. The Rule of 72 is a very important concept. Ask Albert Einstein.
  3. Please know the characteristics of companies worth your investment dollar, as provided by The Fool.
  4. Be able to explain what an IPO is and the benefits and costs to a company that goes public.

Objectives for Clinical Trials - TWO lectures:
September 18 (Dr. Michael Turik) and Sept 20, 2007 (kmarrs)

  1. Describe the acronym ADME/Tox
  2. Explain the purpose of an IND and what pre-clinical data must be presented to the FDA to justify the testing of the drug in humans (look in both our web notes and Dr. Turek's slides, especially slides 25-27, 39). When must the FDA make their deteminiation after the IND is submitted, and what are two alternate outcomes of the FDA decision?
  3. Compare and contrast Phase I, II, III, and IV clinical trials (look in both our web notes and Dr. Turek's slides, especially slides 28-32). For each stage, be sure to have a rough idea of how many years, how much $$, and how many patients (where applicable) would be involved at each stage.
  4. Distinguish between inclusion and exclusion criteria for a clinical trial.
  5. Compare the 3 main routes to get a drug into the bloodstream (parenteral, enteral, and pulmonary) - advantages and disadvantages.
  6. Explain the 6 'way cool' drug delivery options manufactured by Alza: OROS (ex: Concerta), D-trans (ex: Nicoderm, Estroderm, Fentanyl), Stealth Lisposimes (ex: Doxil), DUROS (ex: Viadur), E-Trans (ex: E-Trans Fentanyl), Macroflux (no products yet!)
  7. Important: Compare and contrast the three process that can speed up NDA consideration and FDA approval: Fast Track P- (priority) Designation (PDUFA Date) and Accelerated Approval (surrogate vs. primary endpoint, continuation of clinical trials).
  8. Describe the Orphan Drug Act, and Compassionate access.

From Exam 2: (will be ~70 points of final)

The Cloning of Dolly and other Mammals
September 27, 2007 Objectives:

  1. Please be able to state 'who' these cloned animals are and why we are discussing them: Dolly, Polly, Cumulina, Noah, Cc, Idaho Gem, Ralph, Kaguya, Prometea, and Snuppy.
  2. Define cloning and the 'ingredients' needed to make a cloned mammal = What is the purpose of the diploid nucleus, the recipient enucleated egg , the electric shock?
  3. What is quiescence and why does it appear to be crucial to cloning mammals?
  4. List three reasons scientists are interested in cloning livestock animals or research animals like mice, and specific examples like DKO pigs and TC calves.
  5. List two reasons scientists are interested in cloning animals like guars, cats and dogs.
  6. Explain several reasons why it is NOT a good idea to clone humans (Be sure to re-read “Don't Clone Humans!” by Rudolf Jaenisch and Ian Wilmut Science 30 March 2001

Human Embryonic Stem Cells
October 2, 2007 Objectives:

  1. What were the major findings and conclusions from Thompson's 1998 paper? What are teratomas and their significance in “stem cell-ness”?
  2. What are the 4 characteristics of hES cells that make them a unique / useful human tissue?
  3. Explain the role of GERON in the development of hES cells, and their major patents.
  4. List the 3 main uses of hES cells in medicine and science. Give examples of tissue types.
  5. Explain the difference between totipotent and pleuripotent regarding hES cells.
  6. Summarize the importance of Doug Melton - Boston IVF, HHMI, and the HSCI.

Gene Therapy - Ken Cornetta MD [web], Chair, Department of Medical and Molecular Genetics, IUSM; Director, Indiana University Gene Vector Facility
(Powerpoint was distributed in class – focus on slides 1-21 only)

  1. Define gene therapy and contrast germline vs. somatic gene therapy
  2. Describe 4 types of non-viral gene therapy and the pros and cons of this approach
  3. Describe how viruses can be used as vectors for gene delivery
    • Specific example: Modification of MLV as a gene therapy vector
  4. Discuss the pros and cons of viral gene therapy and the 5 types of viral vectors”
    • Retrovirus – Stable integration, but insertional mutagenesis; dividing cells only
    • Adenovirus – Works with non-dividing cells, but non-integrating and antigenic
    • AAV – Non-toxic, but non-integrating
    • Herpes – Large genome (insert size), but non-integrating
    • Lentivirus – Stable integration and works with non-dividing cells, but HIV risk
  5. Describe the 3 main applications / indication of gene therapy:
  6. Gene replacement, drug delivery, cell engineering
  7. Describe the “suicide gene therapy” / selective killing approach using the herpes simplex virus HSV-TK / gancyclovir method (this is a very nice approach to killing cancer cells)

Adult and Pleuripotent Stem Cells - Merv Yoder, MD, Department of Pediatrics, IUSM; Biochemistry and Molecular Biology.

  1. What is “a stem cell niche”? Important concept!  (Wiki: http://en.wikipedia.org/wiki/Stem_cell_niche)
  2. Diagram how division of one adult stem cell can divide to result in an outcome of:
    • Stem cell maintenance - Stem Cell reduction - or Stem cell expansion
  3. In your own words, describe why embryonic stem cell derivation is so controversial and the three “camps” or moral viewpoints about embryonic stem cell research
  4. Explain the interesting new developments about hES cells related to the Lanza paper (Blastomeres / PGD)
  5. What are at least 6 characteristics of Adult Stem Cells: (in Notes from Dr. Yoder as well as readings for the night) and which are the only Adult Stem Cells that have been used as human therapeutics?
  6. What are some advantages of using hematopoetic stem cells and what are two sources from which these cells might be obtained: National Bone Marrow Donor Program, Umbilical Cord blood (PS. Merv Yoder – Advisory board for the “Genesis Bank”)
  7. What are 4 distinct advantages of using cord blood for these stem cell (low risk, continual new source of donors, naïve infant cells, immediate availability) and two disadvantages (delayed engraftment of WBC/Platelets. Low sample volume),
  8. What are Induced pleuripotent cells (For more information se Yamamata paper from 2007) and what 4 transcription factors are necessary to obtain these cells?

Human Embryonic Stem Cells - and Politics
October 16, 2007 Objectives

  1. What is human Therapeutic Cloning? Why may this procedure be needed to realize the potential of hES cells? What basic steps would be needed to develop this procedure
  2. Prop 71: What is Prop 71 and what it its significance?
  3. Legislation: Be able to state the major provisions and outcomes of:
    • 1995 Dickey-Wicker Amendment:
    • Aug 9, 2001: First Federal Legislation allowing federal funding of hES cell research (Bush)
    • Weldon-Stupak, Human Cloning Prohibition Act of 2001 2001, 2003 (State of the Union), 2007
    • Senate Cloning Bills – competing
      1. Senator Diane Feinstein (D-CA) introduced the Human Cloning Prohibition Act of 2003 (S.1758), on Dec 2, 2002. [2007: Hatch, Feinstein]
      2. Senator Sam Brownback (R-KS) introduced the Human Cloning Prohibition Act of 2003 (S. 245) on Jan 29, 2003, [2007: Brownback, Landrieu]
  4. First Bush Veto: 19 July 2006
    • May 2005: Stem Cell Research Enhancement Act H.R.810 (2005 - Rep. Michael Castle, D-DE)
    • 19 July 2006: Senate Approves Stem Cell Bill [HR 810]; Veto Is Expected
    • 19 July 2006: First Bush Veto Maintains Limits on Stem Cell Use
  5. Third Bush Veto: 20 June 2007
    • April 11, 2007 Stem Cell Research Enhancement Act of 2007 [S.5]
    • June 8, 2007: House Votes to Expand Stem Cell Research
    • June 20, 2007: Bush Vetoes Measure on Stem Cell Research

The Human Genome Project
October 23, 2007 Objectives: HGP Part 1:

  1. DNA Sequencing: Make sure you know the basics of Sanger dideoxy sequencing
  2. Infrastructure: Describe the two main government organizations that together make up the HGP, and list the 5 major HGP sequencing sites: The "G5"
  3. Explain the Bermuda Principles and their importance
  4. Describe the 7 HGP main goals (overall) AND the 7 major scientific goals that guided the project's first ~10 years
  5. Describe the 5 main phases of the HGP - summarize the major milestones of each phase. Who are: James Watson, Francis Collins, Ari Patrinos, Eric Lander, John Sulston and George Weinstock in terms of the HGP?
  6. What have we learned? Be able to describe major genome features detailed above - and be able to list a few genomes completed, perhaps ones with beautiful cover photos!
  7. Provide examples of what is being done to complete the sequence of the human genome. What is the difference between the February 2001, April 13, 2003 and October 2004 papers in terms of "finishing' the genome
  8. What is GenBank, and how do BLAST and ENTREZ fit into GenBank? Who is Gene Meyers? 

The Human Genome Project II - The Private Effort
October 25, 2007 Objectives: HGP Part 2;

  1. Describe ESTs: what are they, how are they made, what they represent, and why are they useful in genome analysis?
  2. Describe Whole Genome Shotgun Sequencing and 2 advantages and 2 disadvantages over Bac-to-Bac sequencing
  3. Describe the effect the formation of Celera Genomics had on the Human Genome Project.
  4. How to the Bermuda Principles relate to Celera's completion of the Human Genome sequence
  5. Describe some of the Major Milestones at each 'phase' of Venter's career NIH - TIGR/ HGSI, Celera - JCV Institute.
  6. Describe the Sorcerer II Expedition, and its major findings.

Nutrigenomics - Starting a Nutritional Genetic Company: Manuel Sanchez-Feliz,We will not have any exam questions on this presentation!

Ag Biotech I: Joe Petolino, PhD (powerpoint) plus Class notes
October 30, 2007

  1. Know the 1999 and most current (2006/07) figures for GM crops in the US (corn, cotton, soybean)
  2. Explain how insect resistance is engineered into plants: (Dipel, Bt, cry gene, effect on Lepidopteran insects)
  3. Explain how herbicide resistance is engineered into plants. (EPSP synthase, RoundUp)
  4. How do GM crops with herbicide resistance benefit the farmer? (how does it benefit Monsanto?!)
  5. What is Golden Rice, and what is its promise for the future? What are some of the concerns? What transgenes do these GM rice strains carry?
AgBiotech 2: Ag Biotech Products: Input vs. Output
November 6, 2007 Objectives
  1. List three factors that led to the rapid adoption of GM crops by US farmers (Article)
  2. Distinguish between "Input" and "Output" traits in GM crops
  3. Identify and discuss the two commercial types of "Input traits" on the market today (Monsanto) - Yield/Boll Gard and RR.
  4. What is the difference between YieldGard® Corn Borer, Yield Gard Rootworm, and Yield Gard PLUS?
  5. Make sure you know what you are eating when you are eating GM food!
  6. Explain why ag-biotech crops make sense in terms of yield, insecticide applications, and production costs
  7. VISTIVE /RR Low-Linolenic Soybeans and the Processor Preferred hybrids
Patents: Genes as Intellectual Property
Nov 6-8, 2007  Notes from Dr. Marrs AND Guest Speaker Lynn Tyler
  1. Define IP and its two main categories
  2. What is a patent? What does a patent allow the patent holder to do?
  3. From Lynn Tyler: Describe the basic parts of a patent:  esp Specifications and the two basic categories of Claims  (compare and contrast these two)  What are the advantages of having both broad and narrow claims in the same patent?
  4. What was Diamond vs. Chakrabarty and why was it a landmark Supreme Court decision?
  5. What is "35 U.S.C. (~) 101" and what does it have to do with Gene Patents? (First reading from Lynn Tyler)
  6. Explain for a gene sequence meets all 3 criteria for patentability.
    • New: What is prior art and what is its role in the “novelty” in the patent process?
    • Useful: What is “utility” as it relates to patenting? How do the new utility requirements make it more difficult to patent gene sequences?
    • Non-obvious Discuss the Supreme Court’s recent decision on “non-obviousness” as it relates to gene sequences (2nd reading - Lynn Tyler)
  7. What is a 'submarine' patent? Name two recent disputes involving submarine patents
  8. About how many gene sequence patents have been issued? Name at least 3 companies in the top 10, and know the basics of the “Biotech Hall of Fame” patents.
  9. Roche v. Bayer  - what medical procedure were they fighting about, and what were three main “fatal flaws” made by Bayer that allowed Roche (ie: Barnes and Thornberg) to dominate
AgBiotech 3: Regulatory Approval of Biotech Crops
November 13, 2007  Objectives
  1. Explain the roles of the USDA (APHIS/BRS), the FDA, and the EPA in regulating GMOs.
  2. Define PIPs!
  3. Explain WHY the FDA approval is NOT required for GM crops!
  4. What is the EU's current position of importation of Bt-corn from the US?
  5. What is the Cartagena Protocol on Biosafety and what are two of its main provisions?

AgBiotech 4: Safety of Biotech Crops
November 15, 2007 Objectives:

  1. Bt and bugs: What is IRM? What is a refuge and why does the EPA require its use with Bt Corn and cotton? Are refuges working in practice?
  2. Bt and Monarchs: What is the effect of Bt crops on Non-target insects? Compare the findings of the Losey et al Nature paper (now retracted) with the EPS's 2000 report and Sears et al. 2001 PNAS paper
  3. Why isn't GM food labeled as such by the FDA? - Explain the reasons!
  4. Explain the major findings of the developing discovery (8/06) of the escape of RoundUp Pro Creeping Bentgrass: “Grass Created in Lab Is Found in the Wild”.   How does this finding relate to the StarLink Taco Shells, and the Prodigene story?

New to Final Exam: (~10 points; 5-6 questions max)

Biotechnology and Global Health
November 27, 2007

1. What is One World Health, and who is Victoria Hale?
2. What are the main criteria for Drug candidates at One World Health (or for many global health vaccines)?
3. Be sure to know the approximate Global Burden of the diseases mentioned
4. Investigate the basics of each of the agents that cause the diseases mentioned .
5. Be able to list at least one approach for treating the diseases mentioned above.

6. Describe some specifics of their new drug (paromomycin), for the disease (Kala Alar).

 

Final Exam Format:
50 ONE-point questions (50 points)
50 TWO-point questions (100 points)
Multiple choice, Scan-tron, bring a pencil and a calculator.