TECBio 2013 Journal Club Intro

1. TECBio 2013 Journal Club Intro With help from… Chakra Chennubhotla Jason Castro Alpay Temiz Armaghan Naik Gustavo Rohde Ivet Bahar Grant Schauer Judith Klein-Seetharaman Andrej Savol May 2013

2. Outline What is Journal Club? Paper Selection and Comprehension Making good slides Presentation skills Example Presentation: Worobey 2010 1 2 3

3. Outline What is Journal Club? Paper Selection and Comprehension Making good slides Presentation skills Example Presentation: Worobey 2010 1 2 3

4. What is Journal Club? Learning the current state of knowledge in a given field.

5. All human knowledge Learning the current state of knowledge in a given field. http://matt.might.net/articles/phd-school-in-pictures/

6. Learning the current state of knowledge in a given field. http://matt.might.net/articles/phd-school-in-pictures/

7. The outside perspective… Learning the current state of knowledge in a given field. http://matt.might.net/articles/phd-school-in-pictures/

8. The inside perspective Learning the current state of knowledge in a given field. http://matt.might.net/articles/phd-school-in-pictures/

9. If you want to push the boundary, you need to know the territory! Learning the current state of knowledge in a given field. http://matt.might.net/articles/phd-school-in-pictures/

10. Journal Club Assignment 1) Select recent paper from high impact journal (Science, Nature, Cell, PNAS) 2) Understand the paper 3) Prepare slides 4) Review with mentor 5) Give 15 minute presentation (5 min. qns)

11. But first, how does a scientific paper get published? http://moviesoddity.com/the-best-10-movies-that-didnt-win-an-oscar/

12. Paper Selection and Comprehension Paper Selection Resources http://f1000.com/

13. Understand the paper Read Be a critical reader: “On first reading, believe everything, on the second, believe nothing” –Donald S. Coffey

14. Understand the paper Read Read through first time then answer following questions What is the main message? (perhaps not title) Ex. Protein A is NOT required for Protein B function. What questionis being answered? Ex. How are proteins A and B related? What are the methodsof study? Ex: Microscopy, Computer Simulation, Literature Search How was the data analyzed?

15. Understand the paper Read Read through second time and answer following questions Why was an experiment/analysis performed? What is the purpose of every figure? Do claims in text follow from data? (i.e. good interpretation)

16. Evaluate the paper Read Some useful criteria… Good Data? Yes No Yes Good Interpretation? No

17. Evaluate the paer Read Some useful criteria… Good Data? Yes No Yes Good Interpretation? No [i.e., particles traveling faster than light]

18. Evaluate the paper Read Some useful criteria… Good Data? Yes No Yes Good Interpretation? No [i.e., particles traveling faster than light]

19. Paper Selection and Comprehension Read Some useful criteria… Good Data? Yes No Yes Good Interpretation? No [i.e., bacteria with arsenic replaced DNA backbones]

20. Evaluate the paper Read Some useful criteria… Good Data? Yes No Yes Good Interpretation? No [i.e., bacteria with arsenic replaced DNA backbones]

21. Evaluate the paper Read Some useful criteria… Good Data? Yes No Yes Good Interpretation? No [i.e., special relativity]

22. Evaluate the paper Read Some useful criteria… Good Data? Yes No Yes Good Interpretation? No [i.e., special relativity]

23. Evaluate the paper Read Have the author’s confused correlation/causation?

24. Evaluate the paper (example) Read # Dr. Pieter Tans, NOAA/ESRL (www.esrl.noaa.gov/gmd/ccgg/trends/) and Dr. Ralph Keeling, Scripps Institution of Oceanography (scrippsco2.ucsd.edu/) Pieter Tans, NOAA/ESRL (www.esrl.noaa.gov/gmd/ccgg/trends/) and Ralph Keeling, Scripps Institution of Oceanography (scrippsco2.ucsd.edu/)

25. Null Hypothesis Coin flip example.. Criminal example…

26. Null Hypothsis Coin flip example.. Criminal example… murder abuse I. Good, “When batterer becomes murderer,” nature.com, Jan. 1996.

27. Null Hypothsis murder abuse I. Good, “When batterer becomes murderer,” nature.com, Jan. 1996.

28. Null Hypothsis murder abuse I. Good, “When batterer becomes murderer,” nature.com, Jan. 1996.

29. Section Summary: Read until you can confidently argue for and against results in the paper! 1

30. Outline What is Journal Club? Paper Selection and Comprehension Making good slides Presentation skills Example Presentation: Worobey 2010 1 2 3

31. Make Slides • Every slide has a title • Units and axis labels are clear on figure • 7 and 7 rule (guide) • Use consistent fonts/color scheme • Include references • Insert equations with LaTex(it) (www.latex-project.org) rather than y = x/z

32. Making Slides – Layering Content slide title slide title slide title

33. Then… Practice your talk at least twice …out loud… …without notes… …standing up… …in front of others, if possible.

34. Present No notes! – use your slides as guides Have ~3 points to say on each slide figures and/or text will help guide you Minimize reading lots of text Make eye contact Repeat asked questions Answer honestly - if you don’t know, ok to say so Be careful with the laser-pointer!

35. What’s wrong with the following slides?

36. Expression of Hsp28 is both constitutive and heat-shock- • induced expression with a large maternal load • Hsp27 is found mostly in the cytoplasm but is has also been seen in nucleus and associated with the plasma membrane and the nuclear membranes as well as in the nucleus itself. • Hsp27 exists in various oligomerization and phosphorylation states. It is thought to form higher order structures of very large size – often larger than 700 kDa, though these might be aggregates instead of ordered structures. Phosphorylation plays a role in determining the higher order structure of Hsp27 • Multiple functions have been ascribed to Hsp27 proteins • Hsp27 can act as a chaperone like many other heat shock proteins • Hsp27 can have an effect on Redox homeostasis through the transferrin receptor • Hsp2 7 was thought to be an actin capping protein ,but is not thought to be an actin monomer sequestering protein which has the effect of depolymerizing actin. • Inhibitor of induced cell death in culture • Correlation with survival of tumors

37. What is known about Hsp27 • Expression - constitutive and heat-shock-induced • Localization - cytoplasm, nucleus, membranes • Various oligomerization and phosphorylation states • Multiple functions… • Chaperone • Redox homeostasis • Actin depolymerizing • Inhibitor of cell death in culture

38. eyes wild-type GMR-rpr/+ ; TM6B/+ GMR-rpr/+ ; Hsp27F6/+ males females

39. Hsp27 mutant suppresses reaper eye phenotype Reaper expression minus Hsp27 wild-type reaper expression males females

40. Results

41. What we have shown • Sequence • Ramachandran • Solvent access • Cryo-EM • Homology modeling

42. Section Summary: Practice your presentation and review slides with mentor/lab/etc. Engage audience! 2

43. Outline What is Journal Club? Paper Selection and Comprehension Making good slides Presentation skills Example Presentation: Worobey 2010 1 2 3

44. or How old is simian immunodeficiency virus?

45. Background closely related to HIV molecular clock estimates suggest MRCA of ~100s years SIV is common among nonhuman primates, related viruses are 1000s years old Solution: find isolated population of SIV positive monkeys

46. Background Solution: find isolated population of SIV positive monkeys

47. Background Solution: find isolated population of SIV positive monkeys

48. Methods Compared gene sequence of SIV pol from positive animals http://www.hiv.lanl.gov/content/sequence/HIV/MAP/landmark.html

49. Methods Compared gene sequence of SIV pol from positive animals http://www.hiv.lanl.gov/content/sequence/HIV/MAP/landmark.html

50. Conclusions The genetic diversity observed required at least 10,000-12,000 years By recalibrating molecular clocks, MRCA for ALL SIV is estimated at 32,000 years ago Implies humans have had many incidences of contact over history http://www.hiv.lanl.gov/content/sequence/HIV/MAP/landmark.html