Journal+Club+Fall+16

__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

- **see the INSERT LINK**
 * For Order of Presenters,**


 * JOURNAL CLUB PRESENTATIONS**
 * On Thursday before 2pm (or Friday), meet with Dr. B to go over initial questions about the paper (read it at least once beforehand)
 * then follow the presentation instructions below.....


 * PRESENTATIONS INSTRUCTIONS (for all: Journal Club, Technical or Research presentations)**
 * Prepare a draft of your slides
 * On Thursday before 2pm (or 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**
 * give it a super awesome VDS style filename so that we can tell what it is.


 * 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?

Tips for making your Research Presentation Slides
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// //In presentations - start out BIG PICTURE --> then drill down to more detailed info.// 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 take image), etc) -If you have a crystal structure of //your protein// - make your own PyMol image and show it. -- What does your protein look like?

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. Sometime this can be a flow chart or a diagram of some sort. (or thumbnail images of each procedures)

Pro Tip: instead of talking about procedures all at once, talk about 1 procedure and then show the results. Then move on to talking about 2nd procedure and its results, and so on and so forth.

RESULTS: Show some data! - everyone likes to see data because it is the most exciting part. - transformation plates, gel images (agarose or SDS-PAGE), Nanodrop spectra, FPLC graphs, Virtual Screening (Score tables & PyMol Images of docked compound), Enzyme assay graphs, DSF binding data, ........

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


 * 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.
 * What is the most significant contribution of the specific work to the field in general?

- 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;">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

- 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

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............ ).

<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.
 * PAST PAPERS:**
 * September 7th, 2016 - Wed -** Aakash, Hailey
 * 1st Paper**


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

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 in Journal Club,**

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 - Wed, Oct. 5th, 2016** - Rachel, Justin
 * 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
 * 3rd Paper - Wed Oct. 19th -no presenters**
 * 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.
 * 4th Paper - Wed Nov 2nd - Kelly, Thomas**
 * Study Q's:** answer these and bring paper copy to class. They can be found in: Google Drive/JournalClub

**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.


 * Guidelines:**
 * <span style="font-family: Arial,Helvetica,sans-serif;">prepare a 10 minute powerpoint slide show
 * <span style="font-family: Arial,Helvetica,sans-serif;">__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**'
 * <span style="font-family: Arial,Helvetica,sans-serif;">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.
 * <span style="font-family: Arial,Helvetica,sans-serif;">Include a picture or image that helps give a visual for the background.
 * <span style="font-family: Arial,Helvetica,sans-serif;">Include any statistics about the disease and its prevalence (this is motivation)
 * <span style="font-family: Arial,Helvetica,sans-serif;">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?
 * <span style="font-family: Arial,Helvetica,sans-serif;">__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. <span style="font-family: Arial,Helvetica,sans-serif;">You can also make your own cartoons and schematic diagrams or show relevant pictures to get across the point.
 * <span style="font-family: Arial,Helvetica,sans-serif;">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__.__?


 * <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


 * 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