Functional Genomics Research Stream

Research Meeting: January 25, 2011Research Progress Reports: The Plan for the Semester

Maslow’s Hierarchy of Needs

How does this apply to research?

Research Progress Reports

Research Progress Reports

• RPR I: Pre-Training - Complete

• RPR II: Cellular Training

• RPR III: Molecular Training

• RPR IV: Research Proposal

distributed today!

Due Date for RPR II & III: March 8, 3:30pmDue Date for RPR IV: Multiple Dates, Details Inside

This means I should panic and drop this class pronto?

=

right?

+

No. Not at all. Everyone smile.

Least amount of training ever for this research group.

Goals In Mind:

• Self-pace.

• See the big picture & understand the semester.

• Asynchronous work.

• Superstars unfettered.

• Redo assays if difficulty the first time.

• Teaching you the first lesson about authentic research:

Responsibility for timing and completeness in your hands.

The Semester

spring break spring break

RPR I

RPR IIRPR III

RPR IV

through rest of semester ...

II&III due

spring break

I due

Research Progress Report II

• Aseptic Technique

• Spectrophotometry

• Growth Characterization

• Growth Media & Culturing

• Growth Profiling (Solid & Liquid Media)

• ..... everything needed to work with cells .....

Research Progress Reports• Section I:

Research Fundamentalsread first, follow instructions at end** before doing section III - check for section II assessments

• Section II:Research Practical Skill Assessment competency checks before you get started

• Section III:Research Progress & Productivitylaboratory work and deliverables

Evaluation GuidelinesEvaluation GuidelinesEvaluation Guidelines

Section Possible Earned

II.B Aseptic Technique Assessment 25

II.D - Saccharomyces cerevisiae Growth Assessment 25

II.G - Micropipette Accuracy & Precision Assessment 25

III.A - Safety & Media Production Training 25

III.C - Laboratory Notebook Preparation 25

III.D - Saccharomyces cerevisiae Growth 25

III.F - Essential Mathematics 25

III.G - Micropipette Accuracy & Precision 25

III.H - Differential Growth Characterization 50

III.I - Results Central Progress Report (for III.D) 50

III.I - Results Central Progress Report (for III.G) 50

III.I - Results Central Progress Report (for III.H) 50

Late Penalty -

Final Grade 400

Table of Contents

• Sections ....

• Subsections ....

• Hopefully helps with the “staple situation” ....

Research Progress Reports• Section I:

Research Fundamentalsread first, follow instructions at end** before doing section III - check for section II assessments

• Section II:Research Practical Skill Assessment competency checks before you get started

• Section III:Research Progress & Productivitylaboratory work and deliverables

Reading Section I.A

• Starting on page 8 of RPR II ....

• Read ....

• Read ....

• Complete Section III.A

• Check Table of Contents .... page 25 .....

This Week: Required Training• See Course Calendar and Results Central:

Times & Dates

• Safety Issues & Equipment

• Basic Aseptic Technique

• Media Preparation:Liquid & Solid, Pouring Plates

• Sterilization by Autoclave:Media, Equipment, Glassware, Liquids

Reading Section I.B

• Starting on page 9 of RPR II ....

• Read ....

• Read ....

• Complete Section II.B

• Check Table of Contents .... page 22 .....

... and onward ...

Always feel free to ask me or any member of the research staff questions about the completion of any of the Research Progress Reports.

RPR II Goal: Grow cell cultures in clean and defined ways. This is the base prerequisite for any molecular experiment that you will perform in the name of your research proposal and agenda.

Research Progress Report III• Reagent Production

• Buffers & pH

• Controlled Cellular Growth & Sample Prep

• Nucleic Acid Preparation (DNA, RNA)

• Quantity & Quality Evaluation

• Gel Electrophoresis

• Enzymatic Reactions (PCR)

• .... blowing cells apart, working with insides ....

Evaluation GuidelinesEvaluation GuidelinesEvaluation Guidelines

Section Possible Earned

I.D - Nucleic Acid Preparation 25

II.G - Polymerase Chain Reaction (PCR) Assessment 25

III.A - Reagent Production 50

III.B - Buffers & pH 50

III.C - Controlled Cellular Growth & Sample Preparation 50

III.D - Nucleic Acid Preparation 75

III.E - Nucleic Acid Quantity & Quality Evaluation 25

III.F - Gel Electrophoresis 50

III.G - Polymerase Chain Reaction (PCR) 50

III.H - Results Central Progress Reports 100(20 points each x 5)

Late Penalty -

Final Grade 500

... and onward ...

RPR III Goal:

It is assumed you can work with and grow cells.

Now you will blow them apart with reagents you synthesize and own in the lab, harvest DNA and RNA and perform enzymatic reactions to ask biological questions.

You will use gel electrophoresis to analyze results.

The Semester

spring break spring break

RPR I

RPR IIRPR III

RPR IV

through rest of semester ...

II&III due

spring break

I due

Research Progress Report IV• March 8 through Rest of Semester ....

• Research!

• Research Proposal

• Gene Deletion & Verification by PCR

• RNA-seq Experimentation & Library Preparation

• Progress Will Be Variable ....

• Productivity Reported Online ....

• Good Representation of the Fall Semester ....

• More Discussion Later in Semester ....

The Whole Plan for the Semester is Now Clear!

=+Maslow’s Hierarchy of Needs

Safety and Basic Operations

Aseptic Cell Culture

Molecular Preparations

Enzymatic Assays

GenomicsResearchAgenda

I

II

III

III

IV

Safety and Basic Operations

Aseptic Cell Culture

Molecular Preparations

Enzymatic Assays

GenomicsResearchAgenda

~ 50% Spring Semester

~ 50% Spring Semester

Safety and Basic Operations

Aseptic Cell Culture

Molecular Preparations

Enzymatic Assays

GenomicsResearchAgenda

100% Fall Semester

Laboratory Issues

Remember: Check the calendar for training sessions!

Course Textbook

Laboratory Notebook

National Brand Computation Notebook (43-648)75 sheets, 11-3/4 x 9-1/4 inches, quad-ruled (no carbon)

Laboratory Log