Download lecture10Sp2013post

Announcements
• Final Abstract due Mon. 6/10 by 1 PM
– Paper copy w/TA graded drafts and comment
sheets attached due in HCK 347
– Electronic version uploaded to Biol 400 Final
Abstract dropbox on course web page. Follow
naming format in instructions
• Lab notebooks due by 10 AM Friday 6/7 in
HCK 347 (can be picked up in the lab starting
Friday 6/14 after 9 AM)
Announcements (cont.)
• In lab this week:
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Final gels/interpretation
Present your group’s results to the class
Decide on lab notebook to turn in (one per group)
Catalogue your cDNA, RNA, gDNA
Evaluations: Partner and TA
Outline
• Peer review discussion
• General feedback on abstracts
Goals:
Defend your review
Gain perspective on your own writing
Apply general feedback to your own writing
Understand how to use control genes to interpret RT-PCR data
Peer Abstract Review
Find the person whose abstract you peer-reviewed
Decide who will be reviewer #1 and who will be reviewer #2
First 15 min:
Reviewer #1
• discusses his/her comments on partner’s abstract, focusing on 4
major criteria
• gives one copy of peer eval form to abstract writer*
Second 15 min:
Reviewer #2
• discusses his/her comments on partner’s abstract, focusing on 4
major criteria
• gives one copy of peer eval form to abstract writer*
*Turn in 2nd copy of peer eval form to Alison for grading
Conference Abstract
General Comments
Address Major Question: What Did You Learn?
– Are stress response genes behaving as expected for
WT plants? What does this suggest?
– Is HAC1 gene itself affected by stress?
– Is HAC1 expression reduced/knocked-out in hac1?
– Do hac1 plants express different levels of stress
genes compared to WT in non-treated conditions, in
treated conditions?
– Is your control gene (UBQ, actin etc.) consistently
expressed? If not, how can you normalize your other
results to compensate for this?
If you do not have matched samples for comparisons, what
else did you learn from your experiments? Is your
approach feasible? Which steps still require troubleshooting?
Results & Conclusion
• Use (B)QMOC format
• Be specific with your words:
– How can you make this statement more specific?
“A PCR reaction was done on the DNA”
• Interpret your data (avoid lists)
– What information did your controls for the method
give you (e.g.. –RT control, primers amplifying
gDNA template)
– What comparisons can you make between
samples?
• In your model:
– Depict HOW HAC1 is affecting stress-response
genes
Overall Presentation
• Data clearly presented (labeled figs, effective
use of charts/tables)
• References/citations
• Grammar/spelling/sentence structure/concise
wording
• Proper scientific nomenclature (genes, proteins,
genus/species)
• Scientific tone appropriate for a conference
abstract
RT-PCR Analysis
What can you conclude?
1
500bp
400bp
2
3
+RT
4 5
6
7
8
UBQ
What can you conclude?
1
500bp
400bp
2
3
+RT
4 5
6
7
8
UBQ
How could you interpret this gel ?
22°C
30 min 37°C
WT WT WT WT WT WT
1
2
3
4
5
6
Hsp70
500bp
400bp
UBQ
Phases of a PCR Reaction
log [DNA Product]
Plateau
phase
(saturated)
Linear phase
Exponential phase
Cycle #
How could you determine whether your products were
generated in exponential/linear phase and not during the
plateau phase?
FLOW CHART OF CLASS ACTIVITIES
WRITING
EXPERIMENTS
Read & Interpret a Scientific Article
Bioinformatics Workshop
Identify Gene of Interest
Read Environmental Stress Review
Genotype Plants
Review the Scientific Literature
Analyze Class Data
2006-2012
Develop Hypothesis
Design Pilot Study
Introduction Paragraph Draft
Methods Paragraph Draft
Peer-Review Abstract Draft
Final Conference Abstract
Perform Environmental
Stress Experiment
Measure Differences in
Gene Expression and
Phenotype
Finishing Up
• Discuss with your group what if
anything you need to complete this
week
• Determine which data you will include
in your abstract
• Discuss your plan with peer TA/grad
TA/instructor to confirm you are on
the right track!