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| Honors Introduction to Molecular Biology & Biochemistry Research 694:215 |
Lecture: T3
Tues 12:00-1:20
Waksman, Rm 1001
(Directions)
Lab:
Tues 1:40-5:00
Waksman, Room 19 |
Fall 2008 Introduction • Independent Undergraduate Research • Fellowships
• Sequences • DNA Sequence Analysis Program |
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Announcements: Contact Dr. Vershon for additional information about this course
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Week |
Date |
Topic |
Notes (pdf) |
Figs. (pdf) |
Podcasts
(Bad
Audio) |
Podcasts
(Better
Audio) |
1 |
9/2 |
Introduction, Project |
Course Intro |
Intro
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Intro. |
Intro. |
1 |
9/2 |
The Basics |
Ch0 Basics |
Ch0.pdf |
Basics |
Basics
Basics-06 |
2 |
9/9 |
Cloning Vectors |
Ch1 Vectors |
Ch1.pdf |
Ch1 |
Ch1 |
3 |
9/16 |
DNA libraries Why study other organisms, Human Genome |
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Ch1b |
Ch1b |
4 |
9/23 |
Analyzing DNA - Restriction enzymes & PCR, Advanced Mapping
Animations: Restriction Digests, PCR, ELectrophoresis |
Ch2 RE/PCR |
Ch2.pdf |
Ch2A
Ch2B |
Ch2A
Ch2B |
5 |
9/30 |
Bioinformatics Analysis Part I: Sequencing DNA, Crop and edit DNA sequences
DNA Sequencing: Bench to bedside and beyond
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Ch3 Sequencing
Ch4 Cropping
Ch5 Editing
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Ch3.pdf
Ch4.pdf
Ch5.pdf
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Ch3
Ch4
Ch5
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6 |
10/7 |
Bioinformatics Analysis Part II: Crop XP sequence, determine if the SP and XP Overlap, construct a contig |
Ch 6 XP anal.
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Ch6.pdf |
Ch6 |
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7 |
10/14 |
Bioinformatics Analysis Part III: BLASTN, BLASTX, |
Ch7 BLASTN
Ch8 BLASTX
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Ch7.pdf
Ch8.pdf |
Ch7
Ch8
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8 |
10/21 |
In Class Exam (Analysis of Clones PC1-3 to BLASTX step due 12:00 noon) |
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9 |
10/28 |
Bioinformatics Analysis Part III:ORF, BLASTP,
Benefits of sequencing multiple organisms |
Ch9 ORF Analysis
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Ch9.pdf
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Ch9
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10 |
11/4 |
Bioinformatics Analysis Part IV: Lit search, Clustal and Structure
Span the sequence gap |
Ch10 Literature
Ch11 Clustal
Ch12 Span gap |
Ch10.pdf
Ch11.pdf
Ch12.pdf
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Ch 10-11
Ch12 |
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11 |
11/11 |
Tools of Molecular Biology
Giving Presentations
Due: Indicate topic of your presentation
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Ch13 Mol. Bio.
Ch14 Presentations
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Ch13.pdf
Ch14.pdf |
Ch13
Ch14 |
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12 |
11/18 |
Finding a Lab
Careers in Biomedical Sciences
Due: Outline of research presentation and abstract of an original research article |
Ch15 Lab & Careers |
Ch15.pdf
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Ch15
Careers |
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13 |
11/25 |
No Class - Designated as a Thursday Schedule |
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14 |
12/2 |
Presentations: DUE: Powerpoint files and Abstracts are due for all students by 10:00 AM |
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15 |
12/9 |
Presentations |
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12/18 |
Exam 12:00 noon - 3:00 PM |
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Week |
Date |
Topic |
Lab Notes (.pdf) |
1 |
9/2 |
Lab Introduction and Rules, Pipeting, Plating Library |
Lab 0, Lab 1, Lab 2 |
2 |
9/9 |
Basic Techniques: Dilutions, DNA concentration, Set up ONs |
Lab 3, Lab 4 |
3 |
9/16 |
Plasmid DNA Minipreps |
Lab 5 |
4 |
9/23 |
Restriction Digests & PCR |
Lab 6 |
5 |
9/30 |
Gel ELectrophoresis |
Lab 7, Lab 4 |
6 |
10/7 |
DNA Sequencing (round 1), Minipreps, PCR Due: Analysis of gels |
Lab 8, Lab 5, Lab 6 |
7 |
10/14 |
Restriction Digests & Gel Electrophoresis, Sequence Analysis |
Lab 6, Lab 7 |
8 |
10/21 |
DNA Sequencing (round 2), Sequence Analysis
Plasmid sublconing: Digest, ligation & transformation |
Lab 8, Lab 9A-C |
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10/22 or 10/23 |
Examine transformation plates and Set up ON cultures for minipreps.
The lab will be open from 7:00 AM to 5:00 PM on both days |
Lab 9D |
9 |
10/28 |
DNA minipreps of subclone colonies, set up digests and PCR, Sequence Analysis, |
Lab 9E |
10 |
11/4 |
Run agarose gel on subclone digests. Sequence Analysis,
DUE: Notebook & Clone Management Sheet |
Lab 9E
Clone Management Sheet |
11 |
11/11 |
Sequence Analysis,
DUE: Gene of Interest Summary |
Analysis review |
12 |
11/18 |
Sequence Analysis,
DUE: Outline of Presentation and Abstract of a Primary Article |
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13 |
11/25 |
No Class - Designated as a Thursday Schedule
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14 |
12/2 |
Presentations
DUE: Powerpoint files and Abstracts are due for all students by 10:00 AM
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15 |
12/9 |
Presentations
Due: Completion of the analysis of all practice and real clones |
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