Journal Club Presentations/Discussions

Presentation Order:
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
6th Week - SKIP - Dr. B out of town
7th Week - Candida -JC5 Edd, Kahn
8th week - HIV - JC6 Marcus, Allison

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.
HerschhornHIVreversetranscriptaseVirtualScreenJMedChem2008.pdf




Reading Strategies for Journal Articles

First pass - Skim Abstract, Conclusions, Figures
Second pass - Read Introduction, Methods, Results
---- 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
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
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.
VDS_UBL3_bioorgmedchem2007.pdf






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.
SinghVirtualTGFbetaBioorgMedChemLett2003.pdf



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.
HenrikksonMtDXR_JBiolChem2007.pdf


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.
TomlinsonWatowichDengueVirusInfectiousDisordersDrugTargets2009.pdf


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.
SacchettiniTuberculosis_DrugsVsBugsNatRevMicrobiol2008.pdf


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.
MochalkinVirtualScreeningBiotinCarboxylaseFASII_ACSCHemBiol2009.pdf


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.
BaiRicinVirtualScreenToxicon2010.pdf



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.
Zolli_JuranDHFRbacteriaHTSBioorgMedChemLett2003.pdf


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.
ParkHsp90drugVirtualScreenBioorgMedChemLett2007.pdf

Week 3

3rd Paper
Zhang, Y.; White, S.; Rock, C., Inhibiting bacterial fatty acid synthesis. J Biol Chem 2006, 281 (26), 17541-4.
FASII_review_jbc2006.pdf


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.
PrasannanPriya_MetSynthaseKinetic_RobertusBiochemBiophysResComm2009.pdf