Functional Genomics Research Stream
Research Meeting: August 30, 2011Introduction to Fall Research
Philosophy forFall Semester
• Opportunity
• Ownership
• Growth
• Low Stress
• Exposure
• Understanding
• Accomplishment
• Pride
Weekly Schedule
Tuesdays 3:30 PM to 4:30 PM PAI 4.28
Research Meetings
Office Hours
Mondays
Thursdays
1:30 PM to 3:30 PM PAI 3.04N
2:30 PM to 4:30 PM PAI 3.04N
Laboratory Open Hours
Daily 7:00 AM to 10:00 PM PAI 2.46
Freshman Research Initiative Functional Genomics Research Stream
Course(s): BIO 377 (50255), CH 369K (51835), CS 378 (52526)
Semester: Fall 2011
Instructor: Dr. Travis B. [email protected] 3.04N, (512) 232-8349
Undergraduate Mentors: Michael Luo, Najwa Majida & Hilary Rabago
Course Website URL: http://fg.cns.utexas.edu/
Course Lecture: Tuesdays, 3:30 to 4:30 PM, PAI 4.28
Laboratory Location: PAI 2.46
Online Course Materials1. Course Website
• Course Calendar
• Research Resource Calendars★ username and password available on Blackboard-linked syllabus
• Results Central
2. Blackboardexceptions for critical announcements
• Emailexceptions for private communications
Course Website
• Research Meeting Agendas
• Research Progress Reports Requirements
• Course Calendars
• Research Protocols
• Research Literature
Course Calendar
Resource Calendars
Results Central
Results Central
• Up to the minute research results
• General research progress discussions
• Tips and improvements on research methods (including computation)
• Research Progress Reports
Student Evaluation
Grade Allocation
Research Meeting Preparations 30%
Laboratory Hours 40%
Research Progress Reports 30%
Evaluation Standard
What You Earn
What I Assign
University Credit
What You Earn
What I Assign
University Credit
> 93.33 A 4.0 > 70 C- 1.67> 90 A- 3.67 > 66.66 D+ 1.33> 86.66 B+ 3.33 > 63.33 D 1.0> 83.33 B 3.0 >= 60 D- 0.67> 80 B- 2.67 < 60 F 0.0> 76.66 C+ 2.33> 73.33 C 2.0
Research Meetings
• Research meeting attendance will not be counted toward your grade.
• This is an upper-division course and as such I will trust in your responsibility to attend.
Research Meeting Preparations
• Research Meeting Preparations will be counted for 30% of your total grade.
• Preparatory reports will be in the form of a standard set of questions we will ask for each paper that we analyze in some of our research meetings.
• These questions will be posted in the Fall 2011 section of the course website as well as the PDFs for our journal club sessions.
Preparations (continued)• Check website (Fall 2011) for dates ....
• Typed and printed ....
• Essential for our discussions ....
• Laboratory time is allowed ....
• Collaboration is allowed and encouraged ....
• Effort judged, not accuracy ....
• Due at the end of Research Meetings in which we discuss a paper ....
Preparation Questions1. What specific question(s) was this paper addressing?
2. How does this research paper relate to its field? Is it big picture, focused, a major technical step forward, a major step forward in biological understanding?
3. What are the main technologies employed?
4. Provide an example of a conclusion that derives clearly from the data presented in the paper.
5. Are any of the conclusions possibly speculative or off-target?If yes, provide an example.
6. Provide an an example of an interesting observation or discussion assertion.
7. What are the strengths of this paper? What are the weaknesses?
8. What next-step questions and/or experiments could result from this paper?
Laboratory Hours• Laboratory hours will be counted for 40% of
your total grade.
• This calculation will simply be (number of hours logged divided by number of laboratory hours required).
It is currently estimated that total laboratory access for the semester will be 12 weeks (I am being generous and rounding down significantly). When multiplied by 10 hours per week the estimated number of laboratory hours required is 120.
Things to remember in the lab
Lab notebooks- same attention to detail practiced in the previous semester
Log your hours in the lab
Wear close-toed shoes and pants at all times (keep a set in the lab if you have to!)Wear lab coats and glasses when working with hazardous materials
Research Progress Reports
• These reports will be counted for 30% of your total course grade.
• Posted to Results Central.
• At this time it is expected there will be three total Research Progress Reports - I, II, III.
It should be noted that each of these reports will individually be worth 10% of final course grade.
• See Fall 2011 Sample Research Progress Report in the Must Read! section of Results Central.
• Not cumulative - approximately one month of research, laboratory work.
• Give complete introduction/ rationale for experimental process.
• Not all work needed; filter appropriately. Tell an interesting story regarding your work ....
• Scientific voice, good organization, labeling and interpretation of results is expected.
• Remember: You cannot possibly do a month’s worth of productive work in one or two weeks.
Research Report Dates
• All dates posted on Course Calendar
• Research Progress Report IMonday October 3, 11 PM
• Research Progress Report IIMonday November 7, 11 PM
• Research Progress Report IIIMonday December 12, 11 PM
Lab Hours Breakdown• Week 1: 5 hours
• Week 2: 10 hours
• Week 3: 10 hours
• Week 4: 10 hours
• Week 5: 10 hours
• Week 6: 10 hours
• Week 7: 10 hours
• Week 8: 10 hours
• Week 9: 10 hours
• Week 10: 10 hours
• Week 11: 10 hours
• Week 12: 10 hours
• Week 13: 5 hours
Total = 120 hours
Sep 5
Dec 5
Safety Courses• OH 101, 102, 201, 202, 207, CW 512, FF 205
• See Results Central must read post for links on how to fulfill classes. OH 102 is on-site training done in the lab and FF 205 is a fire safety training class.
• I need your printed and up-to-date training history handed in at our next Research Meeting (September 6). This needs to show either completion or registration for the above courses.
Fire Safety Training• FF 205 classes are offered Thurs. Sep. 22
9am-10, 11am-12. Wed. Oct. 19 11am-12, 1pm-2. Thurs. Nov. 17 11am-12, 1pm-2
• See Results Central must read post for links for registering.
• You get to spray a fire extinguisher at a fire!
Getting Started• Get the safety courses done ....
• Choose an area of yeast expression analysis that interests you ....
• Refer to the Gasch et al. 2000 paper to study an identical stimulus in our four yeast species
• Come up with a stimulus not described in the Gasch paper and give a rationale/foundation for the study in our four yeast species
• Do computational analysis on our ever-expanding yeast transcriptome data sets
Summer ProjectsExperiment Team
Heat Stress Michael Luo
DNA Damage Katie, Allison
Cold Stress David
H2O2 Michael Z’s
Hyper-osmotic Stress Najwa
Hypo-osmotic Stress Hilary
Amino Acid Starvation Neha, Elise
Nitrogen Starvation Mary Alice
Research PlanS. cerevisiaeS. byanus S. mikatae S. paradoxus
Plating assay:Control vs.Stress Condition
Growth in culture:Control vs.Stress Condition
Whole RNA extraction from Control vs.Stress Condition cells
RNA-SeqCompare Control and Stress Condition expressionCompare across species
RT-PCR of S. cerevisiae sample- ACT1 gene (normalization) and gene known to respond to stress
Examples:YPD Plates 30ºC vs. 37CºYPD vs. YPD + MMS
Heat-Shock Example:Grow to early log phaseSplit in two, spin cells downResuspend in 30ºC vs. 39Cº YPD
Split RNA
Examples:30ºC vs. 37Cº gene- HSP70YPD vs. YPD + MMS gene- MET18
Once RT-PCR established
move to RNA-seq
Start from master plates in 4Cº cooler
Fairchild, 2011
Initial heat-shock dataS. cerevisiae
Seq-CHIPfrom Gasch et al. 2000
RNA-seq
Next Week!
• Turn in safety course printout ....
• Research update & discussion ....
• Stresses ....
• RT-PCR ....
• RNA library construction for SOLiD sequencing ....
• Chromatin immunoprecipitation (ChIP) overview
Questions?