HC70AL Spring 2008 Syllabus

Honors Collegium 70AL: Gene Discovery Laboratory Spring 2008

sponsored by National Science Foundation

Week One
Date	Topic
3/31/08	Introduction to Seed Development & Research - Professor Bob Goldberg
4/01/08	Data Recording & Organization - Introduction to the Webbook and Lab Blue Books - Brandon Le Experiment ONE - Introduction to General Molecular Biology Techniques
	Intro: Introduction to Proper Micropipetting Techniques - Anhthu Bui
	A. Proper Micropipetting Techniques Accuracy/Precision Experiments Gel Electrophoresis of Plasmid DNA
4/03/08	Experiment ONE - Introduction to General Molecular Biology Techniques
	Intro: Introduction to Polymerase Chain Reaction (PCR) Intro: Introduction to DNA Sequencing Intro: Introduction to Sizing DNA on Agarose Gel
	B. Polymerase Chain Reaction (PCR) & Sequencing Setting up a Gene-Specific Polymerase Chain Reaction Gel Electrophoresis of Gene-Specific PCR Products Determining DNA Concentration Using Fluorometer Sequencing of Gene-Specific Products
Week Two
Date	Topic
4/07/08	Introduction to Knockout Screens and Genetics - Professor Bob Goldberg Introduction to Bioinformatics - How to Analyze DNA Sequences - Brandon Le
4/08/08	Experiment TWO - Screening SALK T-DNA Mutagenesis Lines (GENE ONE)
	Intro: Introduction to Genomic DNA Extraction - Anhthu Bui
	A. Extraction of Genomic DNA Set I Leaf Collection from Wild Type and SALK Plants Isolating Genomic DNA from Wild Type and SALK Leaves Gel Electrophoresis of Isolated Genomic DNA Determining DNA Concentration Using a Fluorometer Diluting Genomic DNA Sowing Seeds
4/10/08	Experiment TWO - Screening SALK T-DNA Mutagenesis Lines (GENE ONE)
	Intro: Review of Genetics and Genotyping - Bekah Charney & Daisy Robinton
	B. Determination of Genotype Set I Determining Genotype of SALK Plants Using PCR
	C. Extraction of Genomic DNA Set II Leaf Collection from Wild Type and SALK Plants Isolating Genomic DNA from Wild Type and SALK Leaves Gel Electrophoresis of Genomic DNA Determining DNA Concentration Using a Fluorometer Diluting Genomic DNA
Week Three
Date	Topic
4/14/08	Introduction to Bioinformatics - Annotating Genes - Brandon Le Review of Webbook and Data Organization - Brandon Le
4/15/08	Experiment TWO - Screening SALK T-DNA Mutagenesis Lines (Gene ONE)
	Intro: Review of DNA Sequencing -- Bekah Charney & Daisy Robinton
	B. Determination of Genotype Set I Gel Electrophoresis of PCR Product (Section B on 4/10/08)
	D. Determination of T-DNA Insertion Site Set I Discussion of PCR Results Purification of PCR Products Determining DNA Concentration Using Nanodrop Spectrophotometer Sequencing PCR Product with T-DNA and Gene-Specific Primer
	E. Determination of Genotype Set II Determining Genotype of SALK Plants Using PCR
4/17/08	Experiment TWO - Screening SALK T-DNA Mutagenesis Lines (GENE ONE)
	Intro: Introduction to ESTDB and DNA Sequence Analysis -- Brandon Le & Anhthu Bui
	D. Determination of T-DNA Insertion Site - Set I Computer Analysis of Sequenced PCR Product from SALK Line Screening
	E. Determination of Genotype - Set II Gel Electrophoresis of SALK Line PCR Product (From Part E on 4/15/08)
Week Four
Date	Topic
4/21/08	Introduction to Gene Expression - RT-PCR and Microarrays -- Prof. Bob Goldberg Discussion of Data from Experiments ONE & TWO
4/22/08	Experiment THREE - RNA Isolation and RT-PCR Analysis of GENE ONE
	Intro: Introduction to RNA Isolation and Analysis of RNA -- Anhthu Bui
	A. RNA Isolation Preparation & Decontamination of Equipment for RNA Work Isolating Total RNA from Wild type Seeds and Leaves Removal of Genomic DNA from Isolated Total RNA with DNase I Determining RNA Concentration Using UV Spectrophotometer Gel Electrophoresis of Total RNA (Before and After DNase I Treatment)
4/24/08	Experiment THREE - RNA Isolation and RT-PCR Analysis of GENE ONE
	Intro: Discussion of Total RNA Quality - Anhthu Bui Intro: Introduction to cDNA Synthesis & RT-PCR - Anuthu Bui
	B. cDNA Synthesis Synthesizing cDNAs from Isolated Total RNA
	C. RT-PCR Amplification of cDNA by PCR Gel Electrophoresis of RT-PCR Products and Analysis of "Expression" Data
Week Five
Date	Topic
4/28/08	How to Clone an Upstream DNA Sequence & Promoter - Kelli Henry Discussion of Data from Experiment THREE
4/29/08	Experiment FOUR - Amplification & Cloning of the Upstream Region
	Intro: Introduction to Amplification & Cloning of the Upstream Regions - Anhthu Bui
	A. Amplification of an Upstream Region Amplification of a Upstream Region Using PCR Gel Electrophoresis of PCR Product Ligating PCR Product into a Plasmid Vector pENTR/D-TOPO
5/01/08	Experiment FOUR - Amplification & Cloning an Upstream Region
	Intro: Introduction to Transformation & Bacterial Techniques - Anhthu Bui
	B. Transformation of E. coli Cells Transformation of E. coli Competent Cells with Ligation Mixtures Growing Transformed E. coli Cells in SOC Medium Spreading Transformed E. coli Cells on LB + Antibiotic Plates Incubating Cells Overnight at 37oC Counting Bacterial Colonies
Week Six
Date	Topic
5/05/08	Ethics in Research: Case Studies (Part One) - Anhthu Bui Discussion of Data from Experiment FOUR
	Note: Inoculation of LB Broth + Antibiotics with Selected Bacterial Colonies
5/06/08	Experiment FOUR - Amplification & Cloning a Promoter Region
	Intro: Introduction to Plasmid DNA Preparation - Anhthu Bui
	C. Isolation & Verification of Recombinant Plasmid DNA Isolating Plasmid DNA from Four Colonies Determining Plasmid DNA Concentration Verification of Recombinant Plasmid via Restriction Enzyme Analysis Gel Electrophoresis of Restriction Digested Plasmid DNA
5/08/08	Experiment FIVE - Observation & Characterization of Known & Unknown Mutants
	Intro: Strategy to Dissect Siliques and Seeds - Anhthu Bui
	A. Observation of Plant & Seed Phenotypes Examine and Compare Wild Type and Mutant Plants If Mutant Plant is Homozyogus, Then Open Silique & Observe Seeds If Mutant Plant is Heterozygous, Then Open Silique & Count White/Green Seeds
	B. Characterization of Mutant Seeds Using Microscopy Fix Wild Type and Mutant Seeds in Fixative for Nomarski Optics Microscopy Make Appointment to Use Nomarski Optics Microscope (Appointments should be made from 5-12-08 to 5-30-08)
Week Seven
Date	Topic
5/12/08	Ethics in Research: Case Studies (Part Two) - Professor Goldberg
5/13/08	Experiment FOUR - Amplification & Cloning a Gene Promoter Region
	C. Isolation & Verification of Recombinant Plasmid DNA Sequencing of Recombinant Plasmid DNA
	Experiment SIX - Screening SALK T-DNA Mutagenesis Lines (GENE TWO)
	Intro: Bekah Charney & Daisy Robinton
	A. Extraction of Genomic DNA Tissue Collection from Plants Isolating Genomic DNA from Wild Type and SALK Lines Gel Electrophoresis of Genomic DNA
5/15/08	Experiment FOUR - Amplification & Cloning a Gene Promoter Region
	Intro: Analyzing and Verifying Cloned Upstream Region DNA Sequence - Anhthu Bui
	Experiment SIX - Screening SALK T-DNA Mutagenesis Lines (GENE TWO)
	A. Extraction of Genomic DNA Determining DNA Concentration Using Fluorometer Diluting Genomic DNA
	B. Determination of Genotype Determining Genotype of SALK Plants Using PCR
Week Eight
Date	Topic
5/19/08	How to Prepare For & Give a Research Talk -- Professor Goldberg Discussion of Data from Experiment FIVE
5/20/08	Experiment SIX - Screening SALK T-DNA Mutagenesis Lines (GENE TWO)
	B. Determination of Genotype Con't Gel Electrophoresis of PCR Product (From Part B on 5/15/08)
	Experiment SEVEN - RT-PCR Analysis of GENE TWO
	Amplification of cDNA (Generated in Week 4) Using PCR Gel Electrophoresis of RT-PCR Products and Analysis of "Expression" Data
5/22/08	Experiment EIGHT - Observation & Characterization of Known & Unknown Mutants (GENE TWO)
	Intro: Visualiztion and Genetics of Mutant Seeds - Anhthu Bui
	A. Observation of Plant & Seed Phenotypes Examine and Compare Wild Type and Mutant Plants If Mutant Plant is Homozyogus, Then Open Silique & Observe Seeds If Mutant Plant is Heterozygous, Then Open Silique & Count White/Green Seeds
	B. Characterization of Mutant Seeds Using Microscopy Fix Wild Type and Mutant Seeds in Fixative for Nomarski Optics Microscopy Make Appointment to Use Nomarski Optics Microscope (Appointments should be made from 5-27-08 to 5-30-08)
Week Nine
Date	Topic
5/26/08	Memorial Holiday -- No Class
5/27/08	Experiment EIGHT - Experiment EIGHT - Observation & Characterization of Known & Unknown Mutants (GENE TWO)
	B. Characterization of Mutant Seeds Using Microscopy Con't Nomarski Optics Microscopy of Mutant Seeds
	General Laboratory
	Summarize Data, Prepare PowerPoint Presentation, & Finish Experiments
5/29/08	General Laboratory
	Summarize Data, Prepare PowerPoint Presentation, & Finish Experiments
Week Ten
Date	Topic
6/02/08	Discussion of Data From Experiment EIGHT - Bekah Charney & Daisy Robinton
6/03/08	Clean-up Benches, Summarize Data, & Organize Lab Notebook & Webbook Organize & Practice Group Research Talks
6/05/08	All-Class Research Symposium and Oral Presentations of Research Results
6/06/08	Exit Interview With Professor Goldberg
Week Eleven
6/09/08	Exit Interview With Professor Goldberg
6/10/08	Exit Interview With Professor Goldberg