Announcements

1. 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)

2. Announcements (cont.) • In lab this week: • 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

3. 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

4. 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

5. Conference AbstractGeneral Comments

6. 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 trouble-shooting?

7. 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

8. 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

9. RT-PCR Analysis

10. What can you conclude? +RT 100bp -RT H2O 1 2 3 4 5 6 7 8 500bp UBQ 400bp

11. What can you conclude? +RT 100bp -RT H2O 1 2 3 4 5 6 7 8 500bp UBQ 400bp

12. How could you interpret this gel ? 22°C 30 min 37°C WT WT WT WT WT WT 100bp RT- H2O 1 2 3 4 5 6 Hsp70 500bp UBQ 400bp

13. Phases of a PCR Reaction Plateau phase (saturated) log [DNA Product] Linear phase Cycle # Exponential phase How could you determine whether your products were generated in exponential/linear phase and not during the plateau phase?

14. EXPERIMENTS FLOW CHART OF CLASS ACTIVITIES WRITING 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 Perform Environmental Stress Experiment Methods Paragraph Draft Measure Differences in Gene Expression and Phenotype Peer-Review Abstract Draft Final Conference Abstract

15. 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!