Dennis Revie - California Lutheran University

From GEP Wiki
Jump to: navigation, search

Genomics at California Lutheran University

Course Overview

Implementation

 

In Molecular Biology (Biol 426), we do both finishing and annotation.  For the finishing, we use the introductions to Consed and Unix/Linux.  For the annotation, we use BLAST exercises 1 and 2 and Chimp chunks to get up to speed on how to annotate.  In Genomics (Biol 428), we also analyze the most recent GEP genomics paper.


Lessons Learned and Future Plans

Syllabus for Biology 426

Molecular Biology               Biology 426

Instructor

Dr. Dennis Revie

Office

Science Center 117

Web site

Class Web site

Lecture Hours

MWF 1:30-2:20

Lab Hours

Thursdays 9:00 AM - 12:00 PM

Office Hours

MF 9:00-10:00 AM, W

 9:00-11:00 AM, or by appointment

Text

Watson, Baker, Bell, Gann,

 Levine, and Losick

Molecular Biology of the

 Gene, 6th edition (2008)

Benjamin Cummings/Cold

 Spring Harbor Laboratory Press

Biochemistry focuses on the structure, function, and metabolism of the major types of biomolecules (proteins, carbohydrates, lipids, and vitamins).  Molecular Biology covers the synthesis and metabolism of macromolecules.  We cover the structure, function, and metabolism of DNA, RNA, and protein.  We emphasize methods, experiments, and interpretation of experiments.

Grading





Grades will be determined from the following:

There will be three midterms (100 points each).  The exams will be around the 6th, 10th, and 14th weeks.

There will be lab write-ups.  Each write-up will be worth about 20 points per lab day.  25% of the total grade will come from the labs.  Attendance at all the labs is required, with points deducted for missing them.  The lab write-ups are due on Fridayís, one week after the lab has finished.

There will be a final exam (150 points).

You can attend two seminars from an approved list for extra credit (5 points each).

Lecture Schedule

Condensed list of Lecture topics covered over the 15 week course:

  1. Chemistry and Structure of DNA (2 lectures)
  2. Chromatin (3 lectures)
  3. DNA replication and Repair (4 lectures)
  4. Homologous recombination (2 lectures)
  5. Site-specific recombination (2 lectures)
  6. Mechanisms of transcription (2 lectures)
  7. Processing of RNA (2 lectures)
  8. Translation (2 lectures)
  9. Genetic Code (2 lectures)
  10. Gene regulation in Prokayotes (2 lectures)
  11. Gene regulation in Eukaryotes (4 lectures)
  12. Regulatory RNA's (2 lectures)
  13. Microarrays (1 lecture)
  14. Gene regulation in Development (2 lectures)
  15. Comparative genomics (3 lectures)


Labs

            In the labs, you will perform a research project.  This project is a genomics project in collaboration with Dr. Sarah Elgin of Washington University.  The project consists of two parts: Finishing and Annotation.  Finishing is a process where a complete and high quality sequence has been determined.  If there are gaps in the sequence, they must be closed.  If there are bases that are uncertain, they must be determined unambiguously.  The second part, annotation, is a process where the exact positions of the genes and other important features are determined.  We will move back and forth between the two projects, so every other week will be finishing and the other annotation.

We may spend some lecture time on the project if it looks necessary.  There will be a final presentation on each part of the genomics projects.  You will work in groups of two.

           

            The lab meets on Thursdays, 9 AM to 12 PM.  Attendance is required.  Points are deducted for missing the lab.

Lab Schedule


Week

Dates

Topics

2

1/31

Genomics project

 introduction  and finishing example

3

2/7

Finishing, round 1

4

2/14

Annotation introduction:

 BLAST exercise 1

5

2/21

Finishing, round 2

6

2/28

Annotation introduction:

 BLAST exercise 2

7

3/6

Finishing, round 3

8

3/13

Annotation introduction:

 Chimp/Fly chunks

-

3/20

Spring break!

9

3/27

Finishing, round 4

10

4/3

Annotation: BLAST and other

 programs

11

4/10

Finishing presentations

12

4/17

Annotation: Decisions

13

4/24

Annotation: Synteny and

 repeats

14

5/1

Annotation: Checking your

 annotation and preparing it for submission

15

5/8

Annotation presentations