HC70AL Spring 2009 Syllabus

Honors Collegium 70AL: Gene Discovery Laboratory Spring 2009

sponsored by National Science Foundation

Course Information:

Laboratory:

Tuesday & Thursday 2 - 6 PM, Life Sciences 2822

Open Laboratory:

Wednesday & Friday 2 - 6 PM, Life Sciences 2822

Discussions:

Monday 6 - 8 PM, Life Sciences 2805

Office Hours:

Wednesday & Friday 2 - 6 PM, Life Sciences 2822

Class Handouts and Powerpoint Presentations:

3-30-09	Syllabus (pdf) Introduction to Plant & Seed Development - Dr. Goldberg (ppt)
3-31-09	Data Recording & Organization - Introduction to Webbook and Lab Blue Books - Anhthu Bui (ppt)
4-02-09	Introduction to DNA Sequencing - Dr. Goldberg (ppt) Introduction to Polymerase Chain Reaction (PCR) - Daisy Robinton (ppt) Introduction to Sizing DNA on Agarose Gel - Kristin Gill (ppt)
4-06-09	How To Sequence a New Plant Genome? & Knocking-Out Seed Transcription Factor Genes - Dr. Goldberg (ppt) On Being A Scientist - National Academy of Sciences (pdf)
4-07-09	Using The Computer to Analyze DNA Sequences - Brandon Le & Min Chen (ppt) Isolation of Genomic DNA from Scarlet Runner Bean Leaves Using DNeasy Plant Mini Kit - Anhthu Bui (ppt)
4-09-09	Isolation of Genomic DNA from Arabidopsis Leaves in Screening for T-DNA Knockout Plants - Anhthu Bui (ppt) Introduction of Plant Genotyping - Kristin Gill & Daisy Robinton (ppt)
4-13-09	Introduction of 454 Genome Sequence Assembly and Analysis - Brandon Le (ppt)
4-20-09	RNA and Tools For Studying Differential Gene Expression During Seed Development - Dr. Goldberg (ppt)
4-21-09	SRB Genome Assembly and Analysis From 454 Sequences - Brandon Le & Min Chen (ppt) Gene Prediction Decision Tree for SRB Genome Sequences (pdf)
4-23-09	Introduction to RNA Isolation and Analysis of RNA - Chen Cheng (ppt)
4-27-09	Introduction to Cloning of Promoters - Kelli Henry (ppt) Strategy for Determining the Activity of a Gene's Promoter (pdf)
5-4-09	Research Paper Discussion - Dr. Goldberg (ppt) The Manipulation of Genes (pdf)
5-5-09	HC70AL Project Timeline (ppt)
5-18-09	How To Give A Research Talk - Dr. Goldberg (ppt)
5-28-09	Exit Questionnaire (word) Exit Interview Schedule (word)
6-4-09	Final Symposium Schedule (word)

Lab Schedule:

Week One
Date	Topic
3/30/09	Introduction to Plant & Seed Development - Professor Bob Goldberg
	What Will You Do This Quarter? - Professor Bob Goldberg
3/31/09	Experiment ONE - Introduction to General Molecular Biology Techniques
	Intro: Lab Orientation & Tour - Anhthu Bui Intro: Data Recording & Organization - Introduction to the Webbook and Lab Blue Books - Anhthu Bui Intro: Introduction to Proper Micropipetting Techniques - Anhthu Bui
	A. Proper Micropipetting Techniques Accuracy/Precision Experiments Gel Electrophoresis of Plasmid DNA Sowing Seeds from Wild Type (Ecotype Col-0) and SALK Lines
4/02/09	Experiment ONE Continumed - Introduction to General Molecular Biology Techniques
	Intro: Introduction to DNA Sequencing - Professor Bob Goldberg Intro: Introduction to Polymerase Chain Reaction (PCR) - Daisy Robinton Intro: Introduction to Sizing DNA on Agarose Gel - Kristin Gill
	B. Polymerase Chain Reaction (PCR) & DNA Sequencing Setting up a Gene-Specific Polymerase Chain Reaction Gel Electrophoresis of Gene-Specific PCR Products Purification of PCR Products Determining DNA Concentration Using a UV Spectrophotometer Sequencing of Gene-Specific Products
Week Two
Date	Topic
4/06/09	Sequencing the Scarlet Runner Bean Genome - Professor Bob Goldberg
	Introduction to Arabidopsis Knockout Screens and Genetics - Professor Bob Goldberg
4/07/09	Experiment ONE Continued- Introduction to General Molecular Biology Techniques
	Intro: Using the Computer to Analyze DNA Sequences - Brandon Le & Min Chen
	C. Characterization of a Gene Being Studied Processing a DNA Sequence from UCLA Sequencing Facility Server Charactering Gene Corresponding to the DNA Sequence
	Experiment TWO - Shotgun Sequencing of Scarlet Runner Bean Genome
	Intro: Introduction to Genomic DNA Isolation: Part One - Anhthu Bui
	Isolating Genomic DNA from Scarlet Runner Bean Leaves Gel Electrophoresis of Isolated Genomic DNA
4/09/09	Experiment THREE- Screening SALK T-DNA Mutagenesis Lines (GENE ONE)
	Intro: Introduction to Genomic DNA Extraction: Part Two - Anhthu Bui Intro: Introduction to Plant Genotyping - Kristin Gill & Daisy Robinton
	A. Extraction of Genomic DNA Leaf Collection from Wild Type and SALK Plants Isolating Genomic DNA from Leaves of Wild Type and SALK Plants Determining DNA Concentration Using a Fluorometer Gel Electrophoresis of Isolated Genomic DNA
Week Three
Date	Topic
4/13/09	Introduction to Bioinformatics - Annotating DNA Scaffolds - Brandon Le & Min Chen
	Discussion of Data From Experiment ONE Experiment ONE Lab Report Due
4/14/09	Experiment TWO Continued- Shotgun Sequencing of Scarlet Runner Bean Genome
	Intro: Annotation of DNA Sequences: Part One - Brandon Le & Min Chen
	Annotating a Scarlet Runner Bean DNA Scaffold
	Experiment Three Continued - Screening SALK T-DNA Mutagenesis Lines (GENE ONE)
	B. Determining Genotypes of Segregating Plant Population Determining Genotypes of SALK Plants Using PCR
4/16/09	Experiment THREE Continued - Screening SALK T-DNA Mutagenesis Lines (GENE ONE)
	C. Gel Electrophoresis of SALK Line PCR Products Discussion of PCR Results Purification of PCR Products Determining DNA Concentration Using a UV Spectrophotometer Sequencing PCR Products with a T-DNA Primer and a Gene-Specific Primer
Week Four
Date	Topic
4/20/09	Introduction to Gene Expression - RT-PCR and Microarray - Professor Bob Goldberg
	Discussion of Data From Experiment TWO - Professor Bob Goldberg & Brandon Le
4/21/09	Experiment TWO Continued- Shotgun Sequencing of Scarlet Runner Bean Genome
	Intro: Annotation of DNA Sequences: Part Two - Brandon Le & Min Chen
	Annotating a Scarlet Runner Bean DNA Scaffold (in class)
	Experiment THREE Continued - Screening SALK T-DNA Mutagenesis Lines (GENE ONE)
	Intro: Review of Genetics and Genotyping - Kristin Gill & Daisy Robinton
	D. Determination of T-DNA Insertion Site Analysis of Sequenced PCR Products from SALK Line Screening (in class)
4/23/09	Experiment FOUR - RNA Isolation and RT-PCR Analysis
	Intro: Introduction to RNA Isolation and Analysis of RNA - Chen Cheng
	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 a UV Spectrophotometer Gel Electrophoresis of Total RNA (Before and After DNase I Treatment)
Week Five
Date	Topic
4/27/09	Introduction to Cloning of Promoters - Kelli Henry
	Discussion of Data From Experiment THREE & FOUR Experiments TWO & THREE Lab Reports Due
4/28/09	Experiment FOUR Continued- RNA Isolation and RT-PCR Analysis
	Intro: Introduction to cDNA Synthesis & RT-PCR - Anhthu Bui
	B. cDNA Synthesis Synthesizing cDNAs from Isolated Total RNA
	C. RT-PCR: Part One Amplification of cDNAs by PCR
4/30/09	Experiment FOUR Continued - RNA Isolation and RT-PCR Analysis
	C. RT-PCR: Part Two Gel Electrophoresis of RT-PCR Products
	Experiment Five - Amplification & Cloning an Upstream Region
	Intro: Introduction to Amplification & Cloning of Upstream Regions - Anhthu Bui
	A. Amplification of an Upstream Region Amplification of an Upstream Region Using PCR Gel Electrophoresis of PCR Product Ligating PCR Product into a Plasmid Vector pENTR/D-TOPO
Week Six
Date	Topic
5/04/09	Research Paper Discussion - Professor Bob Goldberg
	Discussion of Data From Experiment FOUR Experiment FOUR Lab Report Due
5/05/09	Experiment FIVE Continued - Amplification & Cloning an Upstream Region
	Intro: Introduction to Transformation &Bacterial Techniques - Anhthu Bui
	B. Transformation of E. coli Cells Counting Bacterial Colonies
	C. Isolation & Verification of Recombinant Plasmid DNA Inoculating of TB Broth containing Antibiotics with Selected Bacterial Colonies
5/07/09	Experiment FIVE Continued - Amplification & Cloning an Upstream 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
Week Seven
Date	Topic
5/11/09	Ethical Research Case Discussion - Professor Bob Goldberg
5/12/09	Experiment EIGHT - Observation & Characterization of Known & Unknown Mutants (GENE ONE)
	Intro: Obervating Plants & Seeds For Mutants Phenotypes - Anhthu Bui
	A. Observation of Plant & Seed Phenotypes Examine and Compare Wild Type and Mutant Plants Phenotypes 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 5-12-09 to 5-19-09)
	Experiment Five Continued - Amplification & Cloning an Upstream Region
	C. Isolation & Verification of Recombinant Plasmid DNA Sequencing of Recombinant Plasmid DNA
5/14/09	Experiment FIVE Continued - Amplification & Cloning an Upstream Region
	Analyzing & Verifying a DNA Sequence of the Cloned Upstream Region
	Experiment SEVEN - Screening SALK T-DNA Mutagenesis Lines (GENE TWO)
	Intro: Review of Knock-Out Screening - Kristin Gill & 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
	B. Determination of Genotype Determining Genotype of SALK Plants Using PCR
Week Eight
Date	Topic
5/18/09	How to Give a Research Talk -- Professor Bob Goldberg
	Discussion of Data from Experiment FIVE Experiment FIVE Lab Report Due
5/19/09	Experiment SEVEN - Screening SALK T-DNA Mutagenesis Lines (GENE TWO)
	B. Determination of Genotype Gel Electrophoresis of PCR Product From a SALK Line (From Part B on 5/14/09)
	Experiment EIGHT - RT-PCR Analysis of GENE TWO
	Amplification of cDNA (Generated in Week 5) Using PCR Gel Electrophoresis of RT-PCR Products
5/21/09	Experiment NINE - Observation & Characterization of Known & Unknown Mutants (GENE TWO)
	A. Observation of Plant & Seed Phenotypes Examine and Compare Wild Type and Mutant Plants Phenotypes 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 5-26-09 to 5-29-09)
Week Nine
Date	Topic
5/25/09	Memorial Holiday -- No Class
5/26/09	Experiment NINE Continued - Observation & Characterization of Known & Unknown Mutants (GENE TWO)
	Experiments SIX & SEVEN Lab Reports Due
	B. Characterization of Mutant Seeds Using Microscopy Nomarski Optics Microscopy of Mutant Seeds
	General Laboratory
	Summarize Data, Prepare PowerPoint Presentation, & Finish Experiments
5/28/09	General Laboratory
	Summarize Data, Prepare PowerPoint Presentation, & Finish Experiments
Week Ten
Date	Topic
6/01/09	Discussion of Data From All Experiment
	Experiments EIGHT & NINE Lab Reports Due
6/02/09	Clean-up Benches, Summarize Data, & Organize Lab Notebook & Webbook
	Organize & Practice Group Research Talks
6/03/09	Exit Interview With Professor Bob Goldberg
6/04/09	All-Class Research Symposium and Oral Presentations of Research Results
6/05/09	Exit Interview With Professor Bob Goldberg