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. Whitetravis.white@utexas.eduPAI 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?