Honors Collegium 70AL: Gene Discovery Laboratory Spring 2004

sponsored by Howard Hughes Medical Institute & National Science Foundation



Week One

4/6/04

Introduction to Research & Goals For Quarter
Introduction to Research Blue Books and Goldberg Lab Webbook
Lab Orientation and Tour
Pipetman Introduction and Accuracy Experiments
Fractionation of Gene-Specific PCR Products by Gel Electrophoresis
Bioinformatics and Gene Annotation – Part I

4/8/04

Introduction to the Polymerase Chain Reaction (PCR)
Setting up a Gene-Specific Polymerase Chain Reaction
Fractionation of Gene-Specific Products by Gel Electrophoresis (Repeat)
Bioinformatics and Gene Annotation – Part II
Using the Goldberg Lab Webbook              

 

Week Two

4/13/04

Introduction to DNA Gel Blots, Probes, and Hybridization -- Concepts
DNA Gel Blot of Madison Round One PCR Products Set #1

4/14/04

Disassemble DNA Blot Apparatus

4/15/04

Introduction to Radiation and Use of Radioisotopes
DNA Gel Blot of Madison Round One PCR Products Set #2
Critical Analysis of Experimental Results

4/16/04 Disassemble DNA Blot Apparatus

 

 

Week Three

4/20/04

Introduction to DNA Gel Blots, Probes, and Hybridization -- Techniques
Pre-hybridization of DNA Blots
Labeling of Gene-Specific Probes
Hybridization of DNA Blots with Gene-Specific Probes  

4/22/04

Washing DNA Blots
Autoradiography          

4/23/04

Developing Autoradiogram

 

 

Week Four

4/27/04

Introduction to Madison and SALK T-DNA lines
How to Analyze DNA Blots & Confirm Results?
PCR Amplification of Positive Gel Blot Bands From Relevant Superpools
Sowing Seeds from Wild-Type (Ecotype Col-0) and SALK Lines

4/29/04

Introduction to Sanger DNA Sequencing & Analyzing Results (ESTDB)
Gel Purification of Amplified DNA Bands
Sequencing DNA Bands

4/30/04 Take sequencing reactions to UCLA Sequencing Facility

 


Week Five

5/04/04

Introduction to RNA Gene Expression, RNA extraction, and RT-PCR
Isolating RNA from Scarlet Runner Bean Embryos and Organs
Gel Electrophoresis of Isolated RNAs
Send Off Results to Wisconsin Knock-Out Facility for Round Two

5/06/04

DNase Treatment of RNA
Determining Concentration of RNA
Gel Electrophoresis of DNase Treated RNA

 

 

Week Six

5/11/04

Introduction to Microarrays, Arabidopsis GeneChip‚, and GeneSpring
cDNA Synthesis and RT-PCR
Review of Goldberg Lab Webbook and Data Entry

5/13/04

Fractionation of RT-PCR Products Using Gel Electrophoresis
Oral Presentation of Results to Date (~15 min/student)


 

Week Seven

5/18/04

Introduction to DNA Isolation and Molecular Genotyping
Isolating Genomic DNA from Wild-Type and SALK Lines -- Part I
Determining DNA Concentration Using a Fluorometer
Gel Electrophoresis of Genomic DNA

5/20/04

Fractionation of Madison Round Two PCR Products
Re-Amplification of Madison Positive Round Two DNA Bands
Identifying SALK Plants Containing T-DNA Insertion Using PCR – Part I


 

Week Eight

5/25/04

How to Determine the Genotype of T-DNA-Tagged SALK Plants Using PCR
Gel-Purification of Madison Positive Round Two DNA Bands
Sequencing Madison Positive Round Two DNA Bands
Genotyping T-DNA-Tagged SALK Plants Using PCR – Part I

5/27/04

Isolating Genomic DNA from Wild-Type and SALK Lines – Part II
Determining DNA Concentration Using Fluorometer
Gel Electrophoresis of Genomic DNA

 


Week Nine

6/01/04

How to Phenotype Arabidopsis Plants and Mutant Seeds
Identifying SALK Plants Containing T-DNA Insertion Using PCR -- Part II
Determining the Phenotype of raspberry3 Mutant Plant Controls

6/03/04

Genotyping T-DNA-Tagged SALK Plants Using PCR – Part II
Determining the Phenotype T-DNA-Tagged SALK Plants



Week Ten

6/08/04

Complete Unfinished Experiments
Summarize Data & Prepare Slides for Oral Presentation
6/10/04 Presentation of Research Results For the Quarter
6/18/04 Research Paper of Results For the Quarter Due


MCDB 19 Fiat Lux Seminar on Gene Discovery
Monday 6-8 PM, Life Sciences 2805

DATE

SPEAKER

TOPIC

4/07/04 (9AM – 12PM)

Ken Kessler

Radiation Training Course

4/12/04

Bob Goldberg

Using Genomics to Dissect Seed Development

4/19/04

Brandon Le

Using Reverse Genetics and Microarrays to
Understand Seed Gene Function

4/26/04

Diane Jofuku

Arabidopsis as a Model Plant

5/3/04

Mai Pham
Erin Marsh
Josh Wol

Chilton T-DNA & Arabidopsis KO Articles  

5/10/04 Bob Goldberg
Discussion of Invisible Frontiers

Mid-Quarter Research Techniques Review

5/17/04 Professor Bernard Phinney

Sixty Years of Exciting Research at UCLA

5/24/04 Mai Pham
Erin Marsh
Josh Wolfe


Research Ethics- Specifiv Case Studies

6/07/04 Bob Goldberg
How to  Give a Research Talk