Van Andel Educational Institute
High School Journal Club
About Journal Clubs
• Participation and discussion is the key to a good journal club
• Ideally:
• Everyone has read the paper
• Everyone participates in the discussion
Pick the paper: Main considerations
• Does it interest you? • Will it interest others?
Pick the paper: Other considerations
• Is the paper in an area you are already familiar with? • Will the paper allow you to learn something that you
wanted to learn?
• Do you understand the paper well?
• Do you think the paper is well done/written? • Do you agree with the conclusions?
Read the paper
• Read all parts of the paper: methods and materials
**supplementary
• Pay attention to:
What is the main question?
How are they addressing that question? What techniques did they use?
Copy figures
• Decide which panels and which figures are important
• Separate panels unless they NEED to be shown together
P element inserted
white mutant
The title of a slide should always
indicate the conclusion you want your
audience to reach.
Flies with Variegated Eye Phenotypes Are
Recovered after P Element Mobilization
P element inserted white mutant
Flies with Variegated Eye Phenotypes Are
Recovered using P Element Mobilization
P element inserted
white mutant P element mobilized
Structure the presentation
There should be a logical progression from the main question to each sub-question to the
conclusions
For each piece of data, follow QuARC: Question
Approach
Results (show data)
Conclusion (in the title)
• Overview of the approach
• Explain any key techniques that are used
throughout
• Details about model organism
• Details about special experimental
techniques
Add background and conclusions
Once you know the logical progression of the presentation, include relevant background for why the experimental questions are important Background should funnel into research
question
Text in red would not be part of the
presentation
For the title slide, rather than just reading the
title , summarize in lay terms the main
question or finding of the paper
• Follow the title slide with background
• Introduce the disease/process
• What is the gap in knowledge
• Use specific background to set up the
main question
Drosphila melanogaster
Question:
Why are some cells red and others whites in this eye?
Why are some cells red and others whites?
Scientific question:
• One genome – but many cell types
• One genome – health or disease
• Study of mitotically heritable marks that
are not encoded in DNA sequence
• Condensed • Gene-poor • Repeat rich • Late replicating
Heterochromatin is marked by HP1 and HP2
C: chromocenter
Hypothesis:
w+ is packaged differently in facets
RESULTS
Question
Approach
Results
Conclusion
How did they test the hypothesis?
1. See where in the genome w+ variegates 2. Test if changing the “packaging material”
changes variegation
3. Test if changing the “packagables” affects variegation
• Question 1: Does PEV depend on genomic position?
• Approach:
• Jump the transgene into different parts of the genome
• Find where it landed
• Question 1: Does PEV depend on genomic position?
• Approach:
• Jump the transgene into different parts of the genome (transposon mutagenesis)
• Find where it landed (in situ hybridization) • See at which landing site transgene is
variegating (look at eyes of males)
Marker Reporter Test
Marker Reporter Test
Flies with Variegated Eye Phenotypes Are
Recovered after P Element Mobilization
P element inserted
white mutant P element mobilized
Where did the variegating transgenes land?
• Question 2: Does PEV depend on the amount of heterochromatin proteins?
• Approach: Change the level of packaging by
crossing the PEV fly to other fly strains that carry mutation for heterochromatin proteins:
Suppressor of variegation or Su(var) mutants
H4 Acetylation high HP1 low
PEV depends on the amount of heterochromatin proteins
HDAC
Ac
• Question 3: Does PEV depend on the amount of heterochromatin DNA?
Normal Less DNA
More DNA
PEV depends on the amount of heterochromatic DNA
• Question 4: Does the variegating gene packaged more tightly?
• Approach: “Let’s use scissors”
• Treat chromatin with restriction enzyme to test for accessibility
• Treat chromatin with micrococcal nuclease and examine nucleosome array over
transgene.
Variegating transgene is less accessible to
nuclease digestion
restriction enzyme
Summary
What is the molecular mechanism of
variegation?
Conclusion:
Significance
Abstract thinking lead to correct hypothesis “Packaging” of genes is a general theme and is
important in development and disease
Follow-up works discovered the molecular nature of Su(var)s
Criticism
• All of the experiments are done D.melanogaster
models – will these results translate to humans?
• Variegating cell is not compared to expressing cell
• Resolution is still low
Questions for discussion
• Are you convinced of the authors conclusions? • What else would you like to know?
• What are the implications for human health? • What would be the next experiment you would
want to do?
Question: Why are some cells red and others whites?
