Jim Youngblom - California State Univeristy, Stanislaus

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Course Overview-

At CSU Stanislaus all juniors take general genetics and all seniors take an advanced genetics course. Genetic Biotechnology (BIOL 4870) is a lecture/lab course for seniors majoring in biology. This class meets on Mondays and Wednesdays for lecture and on Fridays for a 2 hour computer lab activity. The lectures discuss recombinant DNA techniques from PCR to next-generation sequencing. The lab exercises all revolve around various types of DNA sequence analysis software.  Each pair of students annotate one fosmid in conjunction with the Genomics Education Partnership.

Implementation of Drosophila annotation-

Students annotated D. erecta fosmids in Fall 2007 and have annotated D. erecta or D. ananassae fosmids every year since. The class size was 12 in 2007 and has progressively increased in size.  Spring 2012 was the largest class to date- 26 students.   I have taught the class in a similar manner the last couple of years.  The first four labs introduce the students to a number of tools and websites including BLASTn, BLASTp, BLASTx, the Gene Record Finder, and the UCSC genome browser.  Each pair of students recieves a folder (from the GEP website) in the fifth week.  The folder contains information about their fosmid.  The studnents have 6-8 weeks to annotate their fosmid.  In Fall 2007 the annotation projects were not initiated until mid-semester and the UCSC genome browser was not introduced until later. My students (working in pairs), with one exception, did not finish their annotation projects.  Every time since, nearly all of my pairs of students successfuly annotated a fosmid.  This term I am anticipating that the annotation projects will be completed soon enough for my students to spend 3 weeks learning how to use new DNA analysis tools-  tools that allow them to learn about molecular phylogeny.

SYLLABUS-  Genetic Biotechnology - Biology 4840 - Spring 2013 

BIOL 4840 provides CSU Stanislaus undergraduates the opportunity to contribute to original research involving a large-scale DNA sequencing projects from Washington University St. Louis Genome Sequencing Center. Students will analyze portions of chromosome 3 of Drosophila ananassae and compare the data with to chromosome 3 of D. melanogaster to determine genome organization.

Instructor- Dr. James J. Youngblom
Email- jyoungblom@csustan.edu
Office- N264 (667-3950)

Required Materials- From Genes to Genomes: Concepts and Applications of DNA Technology by Jeremy W. Dale, Malcolm von Schantz and Nicholas Plant, 3rd edition.  

“The Genome War” by James Shreeve- Ballantine Books, 2005


Lab Reports (weeks 1-4) 30 pts. possible
EXAM 1-Wed. Feb. 27- 60 pts.
Quiz #1- Friday, Mar. 8, 8 pts (The Genome War)
Quiz #2- Friday, Mar. 15, 8 pts (The Genome War)
Quiz #3- Friday, Mar. 22, 8 pts (The Genome War)
EXAM 2- Wed. Apr. 10- 60 pts.
Journal Article Quiz- Friday Apr.19, 26 pts.

Final Annotation reports, Friday, Apr.26, 50 points

Oral Presentation, Friday May 15 or 17, 20 points

FINAL EXAM- Monday, May 20 11:15- 120 pts.

The labs:

In the lab periods students will have an opportunity to conduct original research in genomics. The lab tools will be various examples of DNA sequence analysis software. Each pair of students will be assigned a 35-45 kb fosmid of unanalyzed Drosophila ananassae DNA. Students will annotate or genetically analyze this segment of DNA.

• During the first four Fridays of the semester, the class will work together to explore several DNA analysis software tools. During this time, students will learn how to analyze genomic data.
• At the fifth meeting of the semester each pair of students will be assigned a 35-45 kb segment of DNA from D. ananassae.
• Independent project work will happen in class and outside of class, with final reports due on Apr. 26

Week 1- Basic BLAST Exercise (from Genomics Education Partnership)

Week 2- Reveiw BLAST, Introduction to UCSC Genome Browser

Week 3- A Simple Annotation Problem (from Genomics Education Partnership)

Week 4- Review Annotation, Introduce the Gene Record Finder, the Gene Model Checker

Week 5- 12- Finish Annotation Projects and Reports

Week 13-15- Molecular Phylogeny

The lectures:

The lectures in this course analyze molecular biotechnology. All course materials relate to the recombinant DNA revolution of the past 35 years. We will discuss the tools and materials necessary for gene cloning and analysis. In this course I will attempt to introduce you to thinking on a genomic scale. In particular we will discuss how our ability to sequence genomes gave rise to genomics, proteomics, transcriptomics, etc.

Lecture topics:
1. Review Molecular Genetics
2. Restriction Enzymes
3. Cloning Vectors
4. Gel Electrophoresis, PCR
5. Genetic Libraries
6. Advanced Cloning Vectors
7. Screening a Genetic Library
8. Chemical Synthesis of DNA
9. DNA sequencing Methods
10. DNA sequencing Methods II
11. DNA sequencing Strategies
12. High-throughput Sequencing
13. Creation of Genetic Maps
14. SNPs vs. STRs
15. ESTs, RNAi
16. Mass Protein Production
17. Biotech Industry, Drug approval
18. Gene Therapy
19. Transgenics, Biotech crops
20. Transcriptomics
21. DNA Microarrays
22. Proteomics
23. Protein structure Determination

Class information:

The website http://blackboard.csustan.edu will have a link for this class. On Blackboard, I will post journal articles pertaining to this class . The lectures for this class will be presented in PowerPoint. The PowerPoint lectures will also be available on-line at http://blackboard.csustan.edu.

The exam questions are taken from the lectures, handouts, assigned readings, & assigned chapters in "From Genes to Genomes".   The exams are a combination of matching, true or false, multiple choice, short essay, and problem solving. The first 2 exams are not comprehensive. Most of the final exam is also noncomprehensive. However, I reserve the option of incorporating some important topics from the early part of the semester into final exam. Students are expected to demonstrate their knowledge of the gene annotation process on the final exam. No leaving the classroom during exams.

Grading: I will grade on a curve using the +/- grading system. Students at or above 90% will be guaranteed an A- or higher, students at or above 80% will be guaranteed a B-or higher, students at or above 70% will be guaranteed a C- or higher, students at or above 60% will be guaranteed a D- or higher.

How to do well in this class-

1. COME TO CLASS- take good notes, ask questions
2. Read the chapters accompanying each lecture
3. Reread the chapters if necessary
4. Study the new terms- use the internet for extra help (there is unlimited amounts of information related to course topics online)
5. If material is unclear, see me during my office hours
6. Start early and work diligently on your lab projects. Keep good lab notes.