Transcript What is Journal Club?

TECBio 2013 Journal Club Intro
With help from…
Andrej Savol
May 2013
Chakra Chennubhotla
Jason Castro
Alpay Temiz
Armaghan Naik
Gustavo Rohde
Ivet Bahar
Grant Schauer
Judith Klein-Seetharaman
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Outline
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2
3
What is Journal Club?
Paper Selection and Comprehension
Making good slides
Presentation skills
Example Presentation: Worobey 2010
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Outline
1
2
3
What is Journal Club?
Paper Selection and Comprehension
Making good slides
Presentation skills
Example Presentation: Worobey 2010
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What is Journal Club?
Learning the current state of
knowledge in a given field.
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All human knowledge
Learning the current state of
knowledge in a given field.
http://matt.might.net/articles/phd-school-in-pictures/
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Learning the current state of
knowledge in a given field.
http://matt.might.net/articles/phd-school-in-pictures/
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The outside perspective…
Learning the current state of
knowledge in a given field.
http://matt.might.net/articles/phd-school-in-pictures/
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The inside perspective
Learning the current state of
knowledge in a given field.
http://matt.might.net/articles/phd-school-in-pictures/
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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/
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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)
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But first, how does a scientific paper get published?
http://moviesoddity.com/the-best-10-movies-that-didnt-win-an-oscar/
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Paper
Selection
and Comprehension
Paper
Selection
Resources
http://f1000.com/
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Read
Understand
the paper
Be a critical reader:
“On first reading, believe everything, on the second, believe
nothing” –Donald S. Coffey
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Read
Understand
the paper
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 question is being answered?
Ex. How are proteins A and B related?
What are the methods of study?
Ex: Microscopy, Computer Simulation, Literature Search
How was the data analyzed?
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Read
Understand
the paper
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)
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Read
Evaluate
the paper
Some useful criteria…
Good Data?
Yes
No
No
Good Interpretation?
Yes
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Read
Evaluate
the paer
Some useful criteria…
Good Data?
Yes
No
No
Good Interpretation?
Yes
[i.e., particles traveling faster than light]
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Read
Evaluate
the paper
Some useful criteria…
Good Data?
Yes
No
No
Good Interpretation?
Yes
[i.e., particles traveling faster than light]
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Paper SelectionRead
and Comprehension
Some useful criteria…
Good Data?
Yes
No
No
[i.e., bacteria with arsenic replaced DNA
backbones]
Good Interpretation?
Yes
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Read
Evaluate
the paper
Some useful criteria…
Good Data?
Yes
No
No
[i.e., bacteria with arsenic replaced DNA
backbones]
Good Interpretation?
Yes
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Read
Evaluate
the paper
Some useful criteria…
Good Data?
Yes
No
No
Good Interpretation?
Yes
[i.e., special relativity]
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Read
Evaluate
the paper
Some useful criteria…
Good Data?
Yes
No
No
Good Interpretation?
Yes
[i.e., special relativity]
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Read
Evaluate
the paper
Have the author’s confused
correlation/causation?
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Evaluate theRead
paper (example)
# 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/)
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Null Hypothesis
Coin flip example..
Criminal example…
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Null Hypothsis
Coin flip example..
Criminal example…
murder
abuse
I. Good, “When batterer becomes murderer,” nature.com, Jan. 1996 .
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Null Hypothsis
murder
abuse
I. Good, “When batterer becomes murderer,” nature.com, Jan. 1996 .
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Null Hypothsis
murder
abuse
I. Good, “When batterer becomes murderer,” nature.com, Jan. 1996 .
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Section Summary:
1
Read until you can confidently argue
for and against results in the paper!
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Outline
1
2
3
What is Journal Club?
Paper Selection and Comprehension
Making good slides
Presentation skills
Example Presentation: Worobey 2010
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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
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Making Slides – Layering Content
slide title
slide title
slide title
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Then…
Practice your talk at least twice
…out loud…
…without notes…
…standing up…
…in front of others, if possible.
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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!
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What’s wrong with the following slides?
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•
Expression of Hsp28 is both constitutive and heat-shockinduced 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
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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
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eyes
GMR-rpr/+ ; TM6B/+
GMR-rpr/+ ; Hsp27F6/+
females
males
wild-type
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Hsp27 mutant suppresses reaper eye phenotype
reaper expression
females
males
wild-type
Reaper expression
minus Hsp27
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Results
12
10
8
6
4
2
0
1
2
3
4
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What we have shown
• Sequence
• Ramachandran
• Solvent access
• Cryo-EM
• Homology modeling
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Section Summary:
Practice your presentation and review
2
slides with mentor/lab/etc.
Engage audience!
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Outline
1
2
3
What is Journal Club?
Paper Selection and Comprehension
Making good slides
Presentation skills
Example Presentation: Worobey 2010
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or
How old is simian
immunodeficiency virus?
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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
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Background
Solution: find isolated population of SIV positive monkeys
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Background
Solution: find isolated population of SIV positive monkeys
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Methods
Compared gene sequence of SIV pol from positive animals
http://www.hiv.lanl.gov/content/sequence/HIV/MAP/landmark.html
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Methods
Compared gene sequence of SIV pol from positive animals
http://www.hiv.lanl.gov/content/sequence/HIV/MAP/landmark.html
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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
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Criticisms
Only one ORF sequenced in tissue samples
Monkeys could have been reintroduced
by humans from mainland
http://www.hiv.lanl.gov/content/sequence/HIV/MAP/landmark.html
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Section Summary:
3
Get big points across!
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Thanks!
[email protected]
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