Groups
January 6: All first years together. Room B1-072/074
January 13
Group 1 (room B1-072):
Abeyta, Adey, Arellano-Santoyo, Beltejar, Berg, Boissel,
Davey, Correa, Gamble, Gwiazda, Higdon, Lancaster
Group 2 (room B1-074):
Le, Lee, LeRoux, Levy, Mitchell, Moody, Osman, Tan, Thayer,
Tidwell, Wilken
January 20
Group 1 (room B1-072):
Adey, Beltejar,
Boissel, Correa, Gwiazda, Lancaster , Lee, Levy, Moody, Tan, Tidwell, Wilken
Group 2 (room B1-074):
Abeyta, Arellano-Santoyo, Berg, Davey, Gamble, Higdon, Le,
LeRoux, Mitchell, Osman, Thayer
January 27
Group 1 (room B1-072):
Abeyta, Adey, Arellano-Santoyo, Beltejar, Davey, Gamble
,Gwiazda ,Higdon ,Lee, LeRoux, Moody, Wilken
Group 2 (room B1-074):
Berg, Boissel, Correa, Lancaster,
Le, Levy, Mitchell, Osman, Tan, Thayer, Tidwell
February 3
Group 1 (room B1-072):
Abeyta, Arellano-Santoyo, Berg, Correa , Davey, Gwiazda, Le,
Lee, Mitchell, Moody, Tan, Tidwell
Group 2 (room B1-074):
Adey, Beltejar, Boissel, Gamble
,Higdon , Lancaster, Levy, LeRoux,
Osman, Thayer, Wilken
February 10: All first years together. Room B1-072/074
Schedule Summary
All sessions on Wednesdays 4PM to 5PM at FHCRC
Wed,
Jan 07, 2009: Lit Review Orientation
Michael Emerman
Room B1-072/074
Wed,
Jan 13, 2009: Faculty-led Discussion
Group 1: Muneesh Tewari
Group 2: Susan Parkhurst
Wed,
Jan 20, 2009: Faculty-led Discussion
Group 1: Wenying Shou
Group 2: Beatrice Knudsen
Wed,
Jan 27, 2009: Faculty-led Discussion
Group 1: Toshi Taniguchi
Group 2: Jason Bielas
Wed,
Feb 10, 2009: Faculty-led Discussion
Michael Emerman
Room B1-072/074
note
The papers below are from last years' class. I'll post the new ones by January
January 14
Group 1: Chris Kemp
Science 308 (5727):1466-1469
Questions: 1. Do you believe these results?, If no, why not, if yes, what are the possible mechanisms?
2. If you were a starting graduate student in the Anway lab, and you want to graduate in 4 years, what experiments would you propose?
3. Assuming this phenomenon is more general (e.g. non-genetic transgen. inheritance) how would you approach it experimentally (i.e. using any model system you like)?
2. If you were a starting graduate student in the Anway lab, and you want to graduate in 4 years, what experiments would you propose?
3. Assuming this phenomenon is more general (e.g. non-genetic transgen. inheritance) how would you approach it experimentally (i.e. using any model system you like)?
Group 2: Roland Strong
Science. 2008 Sep 5;321(5894):1315-22.
Questions:
1) What does this structure tell us about the evolution of this multienzyme complex? What evolutionary constraints are imposed by this structural arrangement?
2) What are the advantages and disadvantages of this design?
3) Why is mFAS a homodimer?
2) What are the advantages and disadvantages of this design?
3) Why is mFAS a homodimer?
Group 3: Patrick Paddison
Cell, 126, Issue 4, 663-676, 25 August 2006
Questions: What is an induced pluripotent stem cell (iPSC)? Did the authors demonstrate that iPSCs and ESCs are interchangeable? Is the method of iPSC generation presented in this paper "ideal" for creating human iPSCs? If not, can you think of an alternative one?
January 21
Nature 454, 780-783 (7 August 2008)
Questions: Latency in herpesvirus viruses is often divided into three phases: establishment, maintenance and reactivation. At which phase(s) do you think the miRNAs described in this paper might act? Why? How could test your hypothesis? Discuss the limitations of any experiments you propose.
Group 2: Wenying Shou
Questions: 1. What is a chemostat? What are its advantages and disadvantages?
2. What aspects of cell growth can a chemostat control?
2. What aspects of cell growth can a chemostat control?
Bonus Q:
3. Explain why if the growth rate of the mutant is smaller than the
original strain, the concentration of the mutant will eventually
remain constant at a level given by Eq 8.
3. Explain why if the growth rate of the mutant is smaller than the
original strain, the concentration of the mutant will eventually
remain constant at a level given by Eq 8.
Group 3: Matthew Fero
Nature 456, 593-598 (4 December 2008)
Questions: In biology we often employ inductive or reductive logic, meaning that we perform a test and show the results are compatible with our hypothesis and try to minimize the likelihood of alternative explanations. Less often can we use deductive reasoning when, given our observations, there can be no other logical explanations. Does the transplantation of human melanoma cells into NOD/SCIDS mice (Figure 1) support or refute the stem cell hypothesis and does it employ inductive or deductive logic? What about the main findings of the paper?
January 28
Group 1: Shibani Mukherjee
Nature. 2008 Dec 4;456(7222):663-6
Questions: 1. What are the mechanisms of tamoxifen resistance described in this paper? Who are the key players in the molecular "tug of war" that the authors have discovered?
2. What are the possible clinical implications for these findings, especially as they pertain to treatment and prognosis?
2. What are the possible clinical implications for these findings, especially as they pertain to treatment and prognosis?
2: Erica Andersen-Nissen
Science. 2008 Dec 12;322(5908):1705-10.
For commentary on article click here.
Questions: 1. What is the model proposed in this paper and why is it novel?
2. What are new questions raised by this paper and what avenues of research might you pursue to answer one of them?
3. The authors do a nice job of demonstrating the same phenomenon in different ways. What is one way in which they do this and how does it add to the paper?
2. What are new questions raised by this paper and what avenues of research might you pursue to answer one of them?
3. The authors do a nice job of demonstrating the same phenomenon in different ways. What is one way in which they do this and how does it add to the paper?
Group 3: Jennifer Cooper
Nature 451, 1121-1124 (28 February 2008)
Questions: 1) What is apomixis and why is it important?
2) What are the 2 major steps to apomictic development in plants?
3) What is the overall hypothesis behind the work in this paper, and do you think the results support this hypothesis?
2) What are the 2 major steps to apomictic development in plants?
3) What is the overall hypothesis behind the work in this paper, and do you think the results support this hypothesis?
February 4
Group 1: Barb Trask
Science. 2008 Oct 17;322(5900):434-8. Epub 2008 Sep 11.
For commentary on article click here.
Questions: What criteria do the authors use to decide which human and mouse sequences match up (i.e., are orthologous)?
What do they mean by "align with"?
Group 2: Cecliia Moens
Nature 452, 892-895 (17 April 2008)
Questions: 1) What is a topographical map in biology?
2) What model for topographical map formation is ruled out by this paper?
3) Try to think of some alternative models for how a topographical map could be built.
2) What model for topographical map formation is ruled out by this paper?
3) Try to think of some alternative models for how a topographical map could be built.
Group 3: Dusty Miller
Science 318:1920-3, 2007
Questions:
1. How successful was this induced pluripotent stem cell approach for treatment of sickle cell anemia in mice - were the mice completely cured of their disease and what percentage of animals were cured?
2. What are the main hurdles to applying this technology to humans, and what solutions can you envision
1. How successful was this induced pluripotent stem cell approach for treatment of sickle cell anemia in mice - were the mice completely cured of their disease and what percentage of animals were cured?
2. What are the main hurdles to applying this technology to humans, and what solutions can you envision
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