Journal+Club+Summer+17


 * Journal Club Presentations/Discussions**

0th Week: none 1st Week: 2nd Week: DHFR paper -**JC1 - Alexandra, Esther** 3rd Week: Hsp90 - **JC2 - Sung-Hoon, Orlando,** 4th Week: Bacterial FAS - **JC3 Megan, Rosa?** 5th Week **-** HisG - **JC4 - Tiger, Haoyi** 7th Week - Candida -**JC5 Edd, Kahn** 8th week - HIV - **JC6 Marcus, Allison**
 * Presentation Order:**
 * 6th Week - SKIP - Dr. B out of town**

Week 0: June 2nd Week 1: Jun-5 Monday - Jun-11 Sunday Week 2: Jun-12 Monday - Jun-18 Sunday - JC1 Week 3: Jun-19 Monday - Jun-25 Sunday - JC2 Week 4: Jun-26 Monday - Jul-2 Sunday - JC3 Week 5: Jul-3 Monday - Jul-9 Sunday - JC4 Week 6: Jul-10 Monday - Jul-16 Sunday - SKIP Week 7: Jul-17 Monday - Jul-23 Sunday - Week 8: Jul-24 Monday - Jul-30 Sunday

For dates See Main Summer 17 page

Week 8
6th Paper Herschhorn, A.; Hizi, A., Virtual screening, identification, and biochemical characterization of novel inhibitors of the reverse transcriptase of human immunodeficiency virus type-1. //J Med Chem// **2008,** //51// (18), 5702-13.

__Reading Strategies for Journal Articles__
Underline – __only up to 10%,__ Make notes in margin, draw sketches - Look up reaction mechanism of enzyme, Circle unfamiliar words --- Then go back afterwards and look up definitions
 * First pass** - Skim Abstract, Conclusions, Figures
 * Second pass** - Read Introduction, Methods, Results
 * Take a break** (couple of hours - to a day or so) - Coffee break !
 * Third pass** - Read for comprehension

UPCOMING PAPERS


 * We will meet on the week before (or earlier) to discuss initial questions on paper
 * Then, show me a draft of your slides by two days before
 * We will meet again on the day before to review final


 * Upload your presentation __before__ class to the **GroupMeetingSlides/GroupMeetingSlides/StudentPresentations** folder on **Google Docs**
 * give it a super awesome VDS style filename so that we can tell what it is.


 * Guidelines:**
 * prepare a 10 minute powerpoint slide show
 * __Start__ out with a title slide that has the __Journal Article name__, __Journal 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__. Use the **SNIPPING tool** in Windows to get pictures of the graphs, etc. from the paper. However, you will want a few 'original' images of your own. 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)
 * Be sure to actually show the images and figures from the paper when talking about them (include some type of caption)
 * Do the results suggest any additional experiments that would be the next__.__?


 * Feel free to interject your own viewpoint of the research (is it valuable, did they do anything you liked or disliked?)
 * 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.
 * What is the most significant contribution of the specific work to the field in general?
 * 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.
 * Go through your talk at least once as a practice run


 * TIPS:
 * for best contrast and readability - use black text on white background.
 * Put date on the title slide
 * Put authors and journal 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
 * Italicize Genus and species names with species being lower case and genus uppercase. - e.g. //Escherichia coli//
 * Put slide numbers on the slides

See Fall Journal Club Page for more Guidelines about other presentations (e.g. Research or Technical Presentations)

Week 9
7th Paper <span style="font-family: 'Times New Roman',serif; font-size: 13.3333px;">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), <span style="font-family: 'Times New Roman',serif; font-size: 13.3333px;">6810-8.


 * Potential 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.

Li, Z.; Garner, A. L.; Gloeckner, C.; Janda, K. D.; Carlow, C. K., Targeting the Wolbachia cell division protein FtsZ as a new approach for antifilarial therapy. //PLoS Negl Trop Dis// **2011,** //5// (11), e1411.
 * LiWolbachia_ftsz_PLOSNegTropDis2011.pdf**

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.

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.

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.

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.

<span style="font-family: Calibri,sans-serif; font-size: 16px;">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.


 * COMPLETED PAPERS 2017 Summer:**

** Week 1 **
1st Paper 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.

Week 2
2nd Paper 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.

Week 3
3rd Paper Zhang, Y.; White, S.; Rock, C., Inhibiting bacterial fatty acid synthesis. //J Biol Chem// **2006,** //281// (26), 17541-4.

Week 4
4th Paper

Cho, Y.; Ioerger, T.; Sacchettini, J., Discovery of novel nitrobenzothiazole inhibitors for Mycobacterium tuberculosis ATP phosphoribosyl transferase (HisG) through virtual screening. //J Med Chem// **2008,** //51// (19), 5984-92.

[|ChoSacchettiniVirtualScreening_TB_HisG_JMedChem2008.pdf]

Week 7
5th Paper Prasannan, P.; Suliman, H. S.; Robertus, J. D., Kinetic analysis of site-directed mutants of methionine synthase from Candida albicans. //Biochem Biophys Res Commun// **2009,** //382// (4), 730-4.