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 Abstract General 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? H2OH2OH2OH2O 500bp 400bp 100bp -RT12345678 UBQ +RT

11. What can you conclude? H2OH2OH2OH2O 500bp 400bp 100bp -RT 12345678 UBQ +RT

12. How could you interpret this gel ? H2OH2OH2OH2O 500bp 400bp 100bp RT- 123456 UBQ 22°C 30 min 37°C Hsp70 WT WT WT

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

14. Bioinformatics Workshop Identify Gene of Interest Read Environmental Stress Review Methods Paragraph Draft Peer-Review Abstract Draft Genotype Plants Measure Differences in Gene Expression and Phenotype Analyze Class Data 2006-2012 Design Pilot Study Perform Environmental Stress Experiment WRITING EXPERIMENTS FLOW CHART OF CLASS ACTIVITIES Review the Scientific Literature Develop Hypothesis Read & Interpret a Scientific Article Final Conference Abstract Introduction Paragraph Draft

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!