Honors Collegium 70AL: Gene Discovery Laboratory Summer 2014


sponsored by National Science Foundation

Course Information:
  Laboratory: Tuesday & Thursday 1 - 6 PM, Terasaki Life Sciences 4128
  Open Laboratory & Research Consultation: Wednesday & Friday 1 - 6 PM, Terasaki Life Sciences 4128
  Introduction To Laboratory Research: Monday 1 - 3 PM, Terasaki Life Sciences 5100
  Office Hours: Friday 1 - 2 PM, Terasaki Life Sciences 4121
Class Handouts and Powerpoint Presentations:
8-4-14 Syllabus (pdf)
Data Recording & Organization - Introduction to the Webbook and Lab Research Notebook - Kelli Henry & Min Chen (pdf)
Introduction 1: Lab Safety - Kelli Henry & Min Chen
Introduction 2: Proper Micropipetting Techniques - Kelli Henry & Min Chen (pdf)
Articles For Discussion:
  •  Jose M. Alonso & Joseph R. Ecker, Moving Forward in Reverse: Genetic Technologies to enable genomic-wide phenomic screens in Arabidopsis, Nature (2006), 7:524-536 (pdf)
  •  Jose M. Alonso, et al., Genome-Wide Insertional Mutagenesis of Arabidopsis thaliana, Science (2003), 301:653-657 (pdf)
  •  Brandon Le, et al., Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors, Proc. Natl. Acad. Sci. (2010), 170:8063-8070 (pdf)
  •  Takashi Kuromori, et al., Phenome Analysis in Plant Species Using Loss-of-Function and Gain-of-Function Mutants, Plant Cell Physiol. (2009), 50: 1215-1231 (pdf)
  •  Ronan C. O’Malley & Joseph R. Ecker, Linking genotype to phenotype using the Arabidopsis unimutant collection, Plant Journal (2010), 61:928-940 (pdf)
  •  Mark F. Belmonte, et al., Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed, Proceedings of the National Academy of Sciences (2013), 110:E435-E444 (pdf)
  •  On Being a Scientist - A Guide to Responsible Conduct in Research, 3rd Ed., National Academy of Sciences (pdf)
    		•
    8-5-14 Introduction 1: Sizing DNA on Agarose Gels - Mike Lyons (pdf) Introduction 2: Genomic DNA Isolation - Mike Lyons
    8-6-14 Introduction 1: Polymerase Chain Reaction (PCR) - Mike Lyons (pdf)
    Introduction 2: Plant Genotyping - Mike Lyons (pdf)
    8-11-14 Introduction to Seed Development & Research - Professor Bob Goldberg (pdf)
    Introduction to Knockout Screens and Genetics - Professor Bob Goldberg
    Discussion of Data from Experiment One - Professor Bob Goldberg
    8-12-14 Introduction: Review of Plant Genotyping - Mike Lyons
    8-14-14 Introduction: Using Bioinformatics to Analyze DNA Sequences - Kelli Henry(pdf)
    Analysis of Sequenced PCR Product - Kelli Henry
    Handouts:
    Gene Annotation Worksheet (pdf)
    8-19-14 Introduction 1: Observing Plants & Seeds for Mutant Phenotypes
    Introduction 2: Light Microscopy & Chi-Square Analysis - Mike Lyons(pdf)
    Introduction 3: Nomarski Microscopy - Kelli Henry(pdf)

    Articles For Discussion:
  •  William A. Haseltine, Discovering Genes for New Medicine, Scientific American, March 1997, 92-97 (pdf)
    		•
    8-25-14 How To Prepare and Present Research Data - Professor Bob Goldberg (pdf)
    Ethics in Scientific Research - Professor Bob Goldberg (pdf)
    8-26-14 Introduction: Review of Data Organization - Mike Lyons
    Lab Schedule:
    Week One
    Date Topic
    8-4-14 Data Recording & Organization - Introduction to the Webbook and Lab Research Notebook - Kelli Henry & Min Chen
      Introduction 1: Lab Safety - Kelli Henry & Min Chen
    Introduction 2: Proper Micropipetting Techniques - Kelli Henry & Min Chen
    Pipetting Exercise
    Serial Dilution Experiment-Serial Dilution of a DNA Stock & Determination of Pipetting Accuracy Using a Spectrophotometer
    8-5-14 Experiment One - Introduction to General Molecular Biology Techniques
      Introduction 1: Sizing DNA on Aragose Gels - Mike Lyons
    Serial Dilution Experiment: Determination of Pipetting Accuracy by Gel Electrophoresis
    Experiment Two: Screening Salk T-DNA Mutagenesis Lines (Gene One)
    Introduction 2: Genomic DNA Isolation - Mike Lyons
    Isolation of Genomic DNA:
    Tissue Collection from Plants
    Isolating Genomic DNA from Wild-Type and Salk Lines
    Determining DNA Concentration Using Nanodrop Spectrophotometer
    Gel Electrophoresis of Genomic DNA
    8-6-14 Experiment Two - Screening Salk T-DNA Mutagenesis Lines (Gene One)
      Introduction 1: Polymerase Chain Reaction (PCR) - Mike Lyons
    Introduction 2: Plant Genotyping - Mike Lyons
    Determination of Genotype
    Determining Genotype of Salk Plants Using PCR
    Gel Electrophoresis of PCR Product
    Week Two
    Date Topic
    8-11-14 Introduction to Seed Development & Research - Professor Bob Goldberg
    Introduction to Knockout Screens and Genetics - Professor Bob Goldberg
      Discussion of Data from Experiment One - Professor Bob Goldberg
    Experiment One Lab Report Due
    8-12-14 Screening Salk T-DNA Mutagenesis Lines (Gene One)
      Introduction: Review of Plant Genotyping - Mike Lyons
    Determination of Genotype
    Discussion of PCR Results
    label T-DNA-Tagged Plants Gel Electrophoresis of Gene-Specific Products
    Determination of T-DNA Insertion Site
    Purification of PCR Products
    Sequencing PCR Product with T-DNA and Gene-Specific Salk Primer
    8-14-14 Experiment TWO - Screening Salk T-DNA Mutangenesis Line (Gene One ONE)
      Introduction: Using Bioinformatics to Analyze DNA Sequences - Kelli Henry
    Determination of T-DNA Insertion Site
    Analysis of Sequenced PCR Product - Kelli Henry
    Gene Annotation Worksheet for Gene 1
    Week Three
    Date Topic
    8-18-14 Discussion of Data from Experiment Two
      Experiment Two Lab Report Due
     Gene Annotation Worksheet for Gene 1 Due
    8-19-14 Experiment Three - Identifying Features of Mutant Seeds Using Nomarski Microscopy (Gene One)
      Introduction 1:Observing Plants & Seeds for Mutant Phenotypes - Mike Lyons
    Introduction 2: Chi-Square Analysis - Mike Lyons
    Introduction 3: Light Microscopy & Nomarski Microscopy - Kelli Henry
    Observation of Seed Phenotypes by Light Microscopy
    Examine and Compares Wild Type and Mutant Seeds
    Fix Seeds for Nomarski Microscopy
    Make Appointment to Use Nomarski Optics Microscope
    Observation of the Mature Plant Phenotype
    8-21-14 Experiment Three - Identifying Features of Mutant Seeds Using Nomarski Microscopy (Gene One)
      Observation of Seed Phenotypes by Nomarski Microscopy
    Experiment Four - Screening Salk T-DNA Mutagenesis Lines (Gene Two)
    Extraction of Genomic DNA
    Tissue Collection from plants
    Isolating Genomic DNA from Wild-type and Salk Lines
    Determining DNA Concentration Using Nanodrop Spectrophotometer
    Gel Electrophoresis of Genomic DNA
    Week Four
    Date Topic
    8-25-14 How to Prepare and Present Research Data - Professor Bob Goldberg
    Discussion of Data from Experiment Three - Professor Bob Goldberg
      Experiment Three Lab Report Due
    8-26-14 Experiment Four - Screening Salk T-DNA Mutagenesis Lines (Gene Two)
      Introduction: Review of Data Organization - Mike Lyons
    Determination of Genotype
    Determining Genotype of Salk Plants Using PCR
    Gel Electrophoresis of PCR Product
    8-28-14 Experiment Four - Screening Salk T-DNA Mutagenesis Lines (Gene Two)
     

    Determination of Genotype
    Discussion of PCR results
    Label T-DNA-Tagged Plants
    Determination of T-DNA Insertion Site
    Purification of PCR Products
    Sequencing PCR Products with T-DNA and Gene-Specific Salk Primer

    Week Five
    Date Topic
    9-1-14 Labor Day - No Class
    9-2-14 Experiment Four - Screening Salk T-DNA Mutagenesis Lines (Gene Two)
      Determination of T-DNA Insertion Site
    Analysis of Sequenced PCR Product
    Gene Annotation Worksheet for Gene 2
    Experiment Five: Identifying Features of Mutant Seeds Using Nomarski Microscopy (Gene Two) Observation of Seed Phenotypes by Light Microscopy
    Examine and Compare Wild Type and Mutant Seeds
    Fix Seeds for Nomarski Micrscope
    Make Appointment to Use Nomarski Optics Microscope
    Observation of the Mature Plant Phenotype
    9-4-14 Experiment Five - Identifying Features of Mutant Seeds Using Nomarski Microscopy (Gene Two)
      Observation of Seed Phenotypes by Nomarski Microscopy
    Week Six
    Date Topic
    9-8-14 Discussion - What Did I Learn in HC70A and HC70AL? - Professor Bob Goldberg
    Discussion of Data from All Experiments - Professor Bob Goldberg
      Experiments Four & Five Lab Reports Due
    Gene Annotation Worksheet for Gene 2 Due
    9-9-14 General Laboratory
      Finish Experiments, Summarize Data & Prepare Powerpoint Presentation
    Clean-Up Benches, Summarize Data, & Organize Lab Notebook & Webbook
    Organize & Practice Research Talks
    9-11-14 All-Class Research Symposium
      Lab Notebook, Webbook and CD with Digital Data Files Due