Journal+Club+Fall15

Print out the article, read a few times, answer Study Q's Bring the printed article and your completed Study Q's to class.
 * For Everyone,**

- use PubMed to download the PDF If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network 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.
 * 5th Paper**
 * Study Q's:** answer these and bring paper copy to class. They can be found in: Google Drive/JournalClub

- **see the Schedule Fall15**
 * For Order of Presenters,**


 * TECHNICAL PRESENTATIONS INSTRUCTIONS**
 * Prepare a draft of your slides
 * On Friday, meet with a mentor or Dr. B to go over your slides and discuss
 * On Monday (or maybe Tuesday), meet with Dr. B to go over the final version of your slides in preparation for presenting in class
 * Upload your final presentation at least 1 hour __before__ class to the **GroupMeetingSlides/GroupMeetingSlides/StudentPresentations** folder on **Google Docs**


 * RESEARCH PRESENTATIONS INSTRUCTIONS (see tips below)**
 * Prepare a draft of your slides
 * On Friday, meet with a mentor or Dr. B to go over your slides and discuss
 * On Monday (or maybe Tuesday), meet with Dr. B to go over the final version of your slides in preparation for presenting in class
 * Upload your final presentation at least 1 hour __before__ class to the **GroupMeetingSlides/GroupMeetingSlides/StudentPresentations** folder on **Google Docs**


 * JOURNAL CLUB PRESENTATIONS INSTRUCTIONS (see tips below)**
 * On Friday, meet with Dr. B to go over initial questions about the paper (read it at least once beforehand)
 * Prepare a draft of your slides
 * On Monday - meet with Dr. B to go over your slides and discuss in person
 * Tuesday (maybe meet again to go over final version)
 * Upload your final presentation at least 1 hour __before__ class to the **GroupMeetingSlides/GroupMeetingSlides/StudentPresentations** folder on **Google Docs**


 * Guidelines (for all presentations):**
 * prepare a 10 minute powerpoint slide show
 * __Start__ out with a title slide that has:
 * 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**' or **'VDS Technical Presentation'** or the a **title for your research** if doing a Research Presentation
 * for Journal Club presentations, include the: __Journal Article name__, __Journal Name__ and __Authors__ on it.
 * Display your enthusiasm 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
 * 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?


 * Guidelines (for all Journal Club presentations specifically):**
 * 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.
 * <span style="font-family: Arial,Helvetica,sans-serif;">What is the most significant contribution of the specific work to the field in general?

Tips for making your Research Presentations
use colors with good contrast (i.e. not light blue on lighter blue!) put date of presentation on Title slide number the slides (use the Insert >> Slide Number in powerpoint) Italicize organism name and lower case the species name. e.g.: //Rickettsia prowazekii// Start out with Motivation slides Introduction to disease and/or special techniques Intro about protein target -(include EC number, reaction diagram from Brenda (use Snipping tool to image), etc) -If you have a crystal structure of //your protein// - make your own PyMol image and show it.

Slide on Objective - what are you setting out to do in THIS project Overview of procedures (e.g. explain cloning procedure in general, or protein expression, purification,characterization) -- want this to be a broad view of the procedures.

FOR CLONING SLIDES: Include the length of your gene (the CDS) and include the %GC content. - that helps to tell if your target is 'easy' Include the diagram from the Overlap OCR protocol that shows the schematic of how it works. and Include an image of pNIC-Bsa4 (from the PDF online) when you talk about expression vectors and cloning into it. Label your gel lanes and marker with Text Boxes & Arrows (not just a legen on the side that is hard to read) Show a Nanodrop images of your PCR cleanup or MidiPrep yields of quantity

Save file with the __target name__ and your __initials__ and __date__ in the filename. upload final version to GDocs/GroupMeetingSlides/StudentPresentations

Reading Strategies for Journal Articles
- Skim Abstract, Conclusions, Figures - 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
 * First pass**
 * Second pass**

- Coffee break !
 * Take a break** (couple of hours - to a day or so)

- Read for comprehension
 * Third pass**

- use PubMed to download the PDF If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network 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.
 * 6th Paper**
 * Study Q's:** answer these and bring paper copy to class. They can be found in: Google Drive/JournalClub

Hu, X.; Vujanac, M.; Southall, N.; Stebbins, C. E., Inhibitors of the Yersinia protein tyrosine phosphatase through high throughput and virtual screening approaches. //Bioorg Med Chem Lett// **2013**, 23 (4), 1056-62.
 * 7th Paper**

Supplement:


 * Study Q's:** answer these and bring paper copy to class. They can be found in: Google Drive/JournalClub

1st Paper <span style="font-family: 'Times New Roman','serif';">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 2015**


 * Study Q's:** answer these and bring paper copy to class. They can be found in: Google Drive/JournalClub

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. - use PubMed to download the PDF If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network
 * 2nd Paper**
 * Study Q's:** answer these and bring paper copy to class. They can be found in: Google Drive/JournalClub

- use PubMed to download the PDF If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network <span style="font-family: 'Calibri','sans-serif'; font-size: 14.6667px;">Bai, Y.; Watt, B.; Wahome, P.; Mantis, N.; Robertus, J., Identification of new classes of ricin toxin inhibitors by virtual screening. //Toxicon// **2010,** //56// (4), 526-34.
 * 3rd Paper**
 * Study Q's:** answer these and bring paper copy to class. They can be found in: Google Drive/JournalClub

- use PubMed to download the PDF If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network 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
 * 4th Paper**
 * Study Q's:** answer these and bring paper copy to class. They can be found in: Google Drive/JournalClub

Hey VDSers, Here is a link to a VDS class Mendeley account. This website will enable students to access the papers and create bibliographies. You have the option of downloading a desktop version or using the website for journal article access.

@http://www.mendeley.com/

The username is vdsclass@gmail.com and the password is the same as usual (not the GDocs one - but the one to get on to the laptops in the lab. p............ ).

**Potential Papers:**
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.

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.

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.