Journal+Club+Fall+12

=**Journal Club Discussions**=

Every other week we will have a Journal Club wherein we discuss a paper in **small group format**s.

There will also be a sheet of **Study Questions** posted on Wikispaces - that you are to __complete before class__ and turn in.

You are required to __PRINT OUT__ the __paper__ and the __Study Q's__ and __BRING them to class with you!__ (bringing it on your laptop or phone does not count!)
 * bringing the paper with you is part of your grade
 * you are welcome to print these papers in the Painter Lab (please do 2 pages per sheet to conserve paper)
 * Also, while you are at it - be sure to ask a friend if they need a copy printed too!

During the class small group discussion in class, there will be a __Question sheet that each group will work on collectively__ - but each person will turn theirs in __for a grade__.

1st Week: none 2nd Week: Sept. 5th - none 3rd Week: Sept.12th - **1st Journal Club** 4th Week: Sept. 19th - none 5th Week: Sept. 26th - **2nd Journal Club** 6th Week: Oct. 3rd - none 7th Week: Oct 10th - **3rd Journal Club** 8th Week : Oct. 17th - **4th Journal Club** 9th Week: Oct. 24th - NONE - FRI Open House 10th Week: Oct. 31st - **5th Journal Club** 11th Week: Nov. 7th - none 12th Week: Nov. 14th - **6th Journal Club** 13th Week: Nov 21st - none 14th Week: Nov 28th - **7th Journal Club** ?? 15th Week: Dec 5th (Last Class)
 * Journal Club Schedule (updated 090512)**

Paper: Identification of novel bacterial histidine biosynthesis inhibitors using docking, ensemble rescoring, and whole-cell assays. Henriksen ST, Liu J, Estiu G, Oltvai ZN, Wiest O. //Bioorg Med Chem//. **2010** Jul 15;18(14):5148-56. Study Q's: These are not 'take home' questions - we will do these in class as 2 separate teams. But you may want to look over them to see if you are able to answer them in class.
 * 6th Journal Club - Nov 14th**

Some good extra reading for the Springers & Sidestreamers: Paper: >
 * 1) Park, H.; Kim, Y. J.; Hahn, J. S., A novel class of Hsp90 inhibitors isolated by structure-based virtual screening. //Bioorganic & Medicinal Chemistry Letters// **2007,** //17// (22), 6345-6349.
 * Park Hsp90 paper
 * 1) Alanis, A. J., Resistance to antibiotics: are we in the post-antibiotic era? //Arch Med Res// **2005,** //36// (6), 697-705.
 * Alanis paper
 * 1) Zolli-Juran, M.; Cechetto, J. D.; Hartlen, R.; Daigle, D. M.; Brown, E. D., High throughput screening identifies novel inhibitors of Escherichia coli dihydrofolate reductase that are competitive with dihydrofolate. //Bioorganic & Medicinal Chemistry Letters// **2003**, 13 (15), 2493-2496.

Paper: Kovac, A.; Konc, J.; Vehar, B.; Bostock, J.; Chopra, I.; Janezic, D.; Gobec, S., Discovery of new inhibitors of D-alanine:D-alanine ligase by structure-based virtual screening. //J Med Chem// **2008,** //51// (23), 7442-8.
 * 1st Journal Club Fall 2012**


 * Study Q's:** answer these and bring paper copy to class JournalClubQuestions091212_DalaDalaLigase_StudyQs.doc

Paper: Tomlinson, S.; Malmstrom, R.; Watowich, S., New approaches to structure-based discovery of dengue protease inhibitors. //Infect Disord Drug Targets// **2009,** //9// (3), 327-43.
 * 2nd Journal Club**



Paper:  Bai, Y.; Monzingo, A.; Robertus, J., The X-ray structure of ricin A chain with a novel inhibitor. //Arch Biochem Biophys// **2009,** //483// (1), 23-8.
 * 3rd Journal Club - Oct. 10th**

Study Q's:

Paper: Ruda, G.; Campbell, G.; Alibu, V.; Barrett, M.; Brenk, R.; Gilbert, I., Virtual fragment screening for novel inhibitors of 6-phosphogluconate dehydrogenase. //Bioorg Med Chem// **2010,** //18// (14), 5056-62.
 * 4th Journal Club - Oct. 17th**

Study Q's:

Paper: A Novel Small-Molecule Inhibitor of the Avian Influenza H5N1 Virus Determined through Computational Screening against the Neuraminidase. Jianghong An, Davy C. W. Lee, Anna H.Y. Law, Cindy L.H. Yang, Leo L.M. Poon, Allan S.Y. Lau, and Steven J.M. Jones //J. Med. Chem.// **2009,** //52,// 2667–2672
 * 5th Journal Club - Oct 31st**

Study Q's:

Henriksson, L. M.; Unge, T.; Carlsson, J.; Aqvist, J.; Mowbray, S. L.; Jones, T. A., Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis. //J Biol Chem// **2007,** //282// (27), 19905-16.
 * LEFTOVER FROM SUMMER:**

GAPDH paper - ?? for Fall

6th Papers:

Hirayama, K.; Aoki, S.; Nishikawa, K.; Matsumoto, T.; Wada, K., Identification of novel chemical inhibitors for ubiquitin C-terminal hydrolase-L3 by virtual screening. **Bioorg Med Chem** 2007, 15 (21),  6810-8.

Sacchettini, J.; Rubin, E.; Freundlich, J., Drugs versus bugs: in pursuit of the persistent predator Mycobacterium tuberculosis. //Nat Rev Microbiol// **2008**, 6 (1), 41-52.

5th Papers

Singh, J.; Chuaqui, C.; Boriack-Sjodin, P.; Lee, W.; Pontz, T.; Corbley, M.; Cheung, H.; Arduini, R.; Mead, J.; Newman, M.; Papadatos, J.; Bowes, S.; Josiah, S.; Ling, L., Successful shape-based virtual screening: the discovery of a potent inhibitor of the type I TGFbeta receptor kinase (TbetaRI). **Bioorg Med Chem Lett** 2003, 13 (24), 4355-9.

4th Papers

Mochalkin, I.; Miller, J.; Narasimhan, L.; Thanabal, V.; Erdman, P.; Cox, P.; Prasad, J.; Lightle, S.; Huband, M.; Stover, C., Discovery of antibacterial biotin carboxylase inhibitors by virtual screening and fragment-based approaches. ACS Chem Biol 2009, 4 (6), 473-83.

OLD:


 * Journal Club Presentations**


 * Guidelines:**
 * prepare a 10 minute powerpoint slide show
 * __#|Start__ out with a title slide that has the Journal Article name and Authors on it.
 * Put YOUR name on title slide also since you are presenting.
 * Put the date of the presentation on their as well - and something like '**VDS Summer Journal Club**'
 * 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 protein, you should provide some background on the protein family and what it does. Don't assume that everyone in your audience knows the background. You can use your own content if you like - along with that given by the authors.
 * Include a picture or image that helps give a visual for the background.
 * Include any statistics about the disease and its prevalence (this is motivation)
 * 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 techniques that we are currently using in our lab?
 * __Include graphs and figures from the paper__. You can also make your own cartoons and schematic diagrams or show relevant pictures to get across the point.
 * Make an effort to explain what is going on in the figures (try to include all of them - but you can leave out some if they do not contribute to a 10 minute presentation)
 * <span style="font-family: Arial,Helvetica,sans-serif;">Be sure to actually show the images and figures from the paper when talking about them (include some type of caption)
 * <span style="font-family: Arial,Helvetica,sans-serif;"> Do the results suggest any additional experiments that would be the next __#|step__?


 * <span style="font-family: Arial,Helvetica,sans-serif;">Feel __#|free__ to interject your own viewpoint of the research (is it valuable, did they do anything you liked or disliked?)
 * <span style="font-family: Arial,Helvetica,sans-serif;"> 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.
 * <span style="font-family: Arial,Helvetica,sans-serif;">What is the most significant contribution of the specific __#|work__ to the field in general?
 * <span style="font-family: Arial,Helvetica,sans-serif;"> 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.
 * <span style="font-family: Arial,Helvetica,sans-serif;"> Go through your talk at least once as a practice run

Run a **draft** of your presentation by **Dr. B** a few days before you present it. Upload your presentation __before__ class to the **GroupMeetingSlides/Journal Club** folder on **Google Docs**
 * TIPS:
 * for __#|best__ contrast and readability - use black text on white background.
 * Put date on the title slide
 * When you get to a figure, explain what is on the X axis and what is on the Y-axis. This helps them understand the graph and also gives a little time for them to view the graph and digest what is being shown.
 * For graphs and tables - be sure to explicitly state what the 'take home message' of that figure is. What does the graph tell the reader?