1/53 andrej savol may 2013 tecbio 2013 journal club intro with help from… chakra chennubhotla...

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Andrej Savol May 2013

TECBio 2013 Journal Club Intro

With help from…

Chakra ChennubhotlaJason CastroAlpay TemizArmaghan NaikGustavo RohdeIvet BaharGrant SchauerJudith Klein-Seetharaman

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Outline

What is Journal Club?

Paper Selection and Comprehension

Making good slides

Presentation skills

Example Presentation: Worobey 2010

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Outline



Making good slides

Presentation skills


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3

2

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Learning the current state of knowledge in a given field.

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http://matt.might.net/articles/phd-school-in-pictures/

All human knowledge

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The outside perspective…

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The inside perspective

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If you want to push the boundary, you need to know the territory!

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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)

Journal Club Assignment

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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 Resources

http://f1000.com/


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Read

Be a critical reader:

“On first reading, believe everything, on the second, believe nothing” –Donald S. Coffey

Understand the paper

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Read

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?

Read through first time then answer following questions


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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)


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ReadSome useful criteria…

Evaluate the paper

Good Data?

Goo

d In

terp

reta

tion?

Yes

Yes

No

No

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Evaluate the paer

Good Data?

Goo

d In

terp

reta

tion?

Yes

Yes

No

No

[i.e., particles traveling faster than light]

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Evaluate the paper

Good Data?

Goo

d In

terp

reta

tion?

Yes

Yes

No

No

[i.e., particles traveling faster than light]

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Good Data?

Goo

d In

terp

reta

tion?

Yes

Yes

No

No

[i.e., bacteria with arsenic replaced DNA backbones]

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Evaluate the paper

Good Data?

Goo

d In

terp

reta

tion?

Yes

Yes

No

No

[i.e., bacteria with arsenic replaced DNA backbones]

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Evaluate the paper

Good Data?

Goo

d In

terp

reta

tion?

Yes

Yes

No

No

[i.e., special relativity]

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Evaluate the paper

Good Data?

Goo

d In

terp

reta

tion?

Yes

Yes

No

No

[i.e., special relativity]

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Read

Have the author’s confused correlation/causation?

Evaluate the paper

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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/)

Evaluate the paper (example)

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Coin flip example..

Criminal example…

Null Hypothesis

26/53I. Good, “When batterer becomes murderer,” nature.com, Jan. 1996.

abuse

murder

Null Hypothsis

Coin flip example..

Criminal example…


Null Hypothsis

abuse

murder

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Section Summary:

Read until you can confidently argue

for and against results in the paper! 1

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Outline



Making good slides

Presentation skills


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• 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

Make Slides

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slide title slide title slide title

Making Slides – Layering Content

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Practice your talk at least twice

Then…

…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 slidefigures 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-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

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• 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

What is known about Hsp27

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wild-typeGMR-rpr/+ ; TM6B/+

mal

es

fem

ales

GMR-rpr/+ ; Hsp27F6/+

eyes

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wild-type reaper expression

mal

esfe

mal

es

Reaper expression minus Hsp27

Hsp27 mutant suppresses reaper eye phenotype

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Results

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• Sequence• Ramachandran• Solvent access• Cryo-EM• Homology modeling

What we have shown

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Section Summary:

Practice your presentation and review

slides with mentor/lab/etc.

Engage audience!2

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Outline



Making good slides

Presentation skills


1

3

2

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How old is simian immunodeficiency virus?

or

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Backgroundclosely 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


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Background


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MethodsCompared gene sequence of SIV pol from positive animals

http://www.hiv.lanl.gov/content/sequence/HIV/MAP/landmark.html

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MethodsCompared gene sequence of SIV pol from positive animals


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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


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Criticisms

Only one ORF sequenced in tissue samples

Monkeys could have been reintroduced by humans from mainland


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Section Summary:

Get big points across!3

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Thanks!

[email protected]

1/53 andrej savol may 2013 tecbio 2013 journal club intro with help from… chakra chennubhotla...

Documents

paper slide

comprehension slide

paper good data

light slide

oscar slide

good interpretation

human knowledge slide

comprehension good data