Biophysical Journal Club Web Page - Fall 2008 - Spring 2009

Meetings:  Room 4.238 Welch, Wednesdays, at noon.

Contact:  David Hoffman, email:  dhoffman@mail.utexas.edu 

Link to last year's Biophysical J. Club web page  

****************   Schedule for Fall 2008 - Spring 2009  *******************

Sept 24, 2008 -  Lauren Webb.  "Electrostatic fields near the active site of human
                           aldolase reductase: New inhitors and vibrational Stark effect measurements"
                           Biochem. 47, 1588-1598 (2008)
                            Link to article

Oct 1, 2008 -    Angeline Lyon.  "RNA repair: an antidote to cytotoxic eukaryal RNA damage."
                          Nandakumar, J. et al. Mol Cell (2008) 31(2), 278-286.
                          Link to article    

Oct 8, 2008 -   Adrian Keatinge-Clay will talk about his own research & plans.

Oct 15, 2008 -   Rick Russell.  Two papers will be discussed:
                          Solem et al. A DEAD protein that activates intron self-splicing
                          without unwinding RNA.  Mol. Cell 24 (2006), 611-617.   Link

                          &

                          Del Campo et al. Do DEAD-box proteins promote group II intron
                          splicing without unwinding RNA?  Mol. Cell 28 (2007), 159-166.  Link

Oct 22, 2008 -  Eric Montemayor. "Structural elucidation of a PRP8 core domain from
                         the heart of the spliceosome".  Nature Struct. & Mol. Biol.
                         Published on-line Oct. 2, 2008.    link to article

Nov 5, 2008 -   Jessie Zhang will tell us about her own recent work.

Nov 12, 2008 - Amanda Chadee.  “Structural insights into amino acid binding and gene control
                          by a lysine riboswitch.” – Alexander Serganov, Lili Huang and Dinshaw Patel,
                          Published in Nature Vol 455 pg 1263.  Link to article

Nov 19, 2008 -  Jeff Knight. "The RNA Polymerase Switch Region Is a Target for Inhibitors"
                          This topic is related to the development of novel antibiotics.
                           Link to article

Nov 26, 2008 -   Hey Hae Chang. "Structure of the guide-strand-containing argonaute
                           silencing complex".  Nature Vol 456, pg. 209-214 13 November 2008
                           Link to article
 
Dec 3, 2008 -  Brian Cannon. "Hopping of a processivity factor on DNA revealed by
                        single-molecule assays of diffusion".
                        Proc Natl Acad Sci USA. 2008 Aug 5;105(31):10721-6
                        Komazin-Meredith G, Mirchev R, Golan DE, van Oijen AM, Coen DM
                         Link to article

Jan 21, 2009 -  Tom Linsky.  "Consistent blind protein structure generation from NMR chemical
                         shift data".  by Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, Liu G,
                         Eletsky A, Wu Y, Singarapu KK, Lemak A, Ignatchenko A, Arrowsmith CH,
                         Szyperski T, Montelione GT, Baker D, Bax A.  (2008) PNAS, 105, 4685-4690.
                         Mar 25, 2008.    Link to full article at PNAS.org 

Jan 28, 2009 - Cassidy Terrell. "Internal dynamics control activation and activity of the
                        autoinhibited Vav DH domain". 
                        P. Li, I. Martens, G. Amarasinghe & M.K. Rosen. 
                         Nature Structural Biology, 15, 613-618 (2008).
                         Link to article  

Feb 4, 2009 - Young-Sam Lee.  "Structural Basis for DNA-Hairpin Promoter Recognition
                        by the Bacteriophage N4 Virion RNA Polymerase"
                       Gleghorn ML, Davydova EK, Rothman-Denes LB, Murakami KS.
                       Mol Cell. 2008 Dec 5;32(5):707-17.  Link to article 

Feb 11, 2009 - Yaqi Wan. "Transcription inactivation through local refolding of the RNA
                         polymerase structure".  Georgiy A. Belogurov et. al.
                         Nature 457, 332-335 (15 January 2009)
                         Link to article 

Feb 18, 2009 -  Nandini Chari. "Molecular mechanisms of HipA-mediated multidrug tolerance
                          and its neutralization by HipB." Schumacher MA, Piro KM, Xu W, Hansen S,
                          Lewis K, Brennan RG.  Science, vol. 323, 16 Jan 2009, pages 396-401.
                          Link to article   

Feb 25, 2009 -  Mitra Rana. "Artificial nanopores that mimic the transport selectivity of the
                          nuclear pore complex"
                         Tijana Jovanovic-Talisman et al. (2009) Nature 457; 1023-1027.  Link to article   

Mar 4, 2009 -   Biochemistry qualifying exams.  Jeff Potratz and Stephanie Taylor.
                          Welch Convocation center at 1 pm.

Mar 11, 2009 -  Biochemistry qualifying exams.  
                          Welch Convocation center at 1:30 pm.

Mar 18, 2009 -   spring break

Mar 25, 2009 -  Biochemistry qualifying exam. 

April 1, 2009 -   open date

April 8, 2009 -  Art Monzingo. "Gibberellin-induced DELLA recognition by the gibberellin
                           receptor GID1"
                           Murase et al., Nature 456, 459-463 (2008).  Link to article  

                           "Structural basis for gibberellin recognition by its receptor GID1"
                           Shimada et al., Nature 456, 520-523 (2008).  Link to article  

April 15, 2009 -  David Hoffman. "A hierarchical model for the evolution of  23S ribosomal RNA". 
                             K. Bokov and S.V. Steinberg.  Nature, 457, 977-980 (2009).
                             Link to article

April 22, 2009 -  open date


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Suggestions for Journal Club presentations:

1) Create an introduction that provides a broad perspective for the specific work being presented.  For example, if you are presenting a paper on a new reverse transcriptase (RT) structure, you should provide some background on RTs in general.  Don't assume that everyone in your audience knows the background.  Provide historical perspective, such as when was the first RT discovered?  When was the first structure of a member of the RT family solved?  Why do we care about RT?  This will provide a context for introducing what is special about the paper you are presenting.  Also, explain enough about the work that came immediately before your paper (often from the same research group) so that your audience understands the starting point for the paper you are presenting.

2) Explain why you chose the paper you did.  What do you find most interesting about it?  Why is it important? Also, why is the topic interesting and important?

3) Instead of simply describing the methods used, look at the methods critically, with an eye for anything interesting or unusual.  Point out anything that might be generally useful.  For example, did the authors use any unusual purification or expression tricks?  The people in your audience, many of whom are struggling with purification and expression, may find this helpful.

4) What is the most significant contribution of the specific work to the field in general?

5) As much as possible, make your own cartoons and schematic diagrams  - don't copy these from the paper.  When you make your own figure, you can be sure that it makes exactly the points you want, no more and no less.

6) Do the results suggest any additional experiments to answer any new questions raised by the work?  Hint for 2nd year grad students:  These presentations can be a good source of ideas for qualifying exam topics.

7) Clearly explain the significance of the results.  Results by themselves are dull, unless they have significance.  The significance may not be obvious to the audience, so point it out specifically.  Also, try to think critically about the author's work.  For example, are there any possible alternative interpretations of the results? 

8) Try to appear truly interested (even excited!) about the work you are presenting.  Enthusiasm is contagious, and keeps your audience interested.  Can you think of anything to make your presentation unique?  An unusual prop or visual aid?  Make your presentation "professional".  That means, stand up in front, look directly at your audience, and don't "read" your slides.

9) Arrive at the conference room early.  Make sure you can get into the room (Natalie Potts on the 5th floor in Robertus' and Hackert's office has a key, as do some of the nearby labs).  Make sure you can make the projector work, and make sure you have everything you need for your presentation, such as a pointer. 

10) Practice your talk!