Nick Pullen

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Genomics at William Woods University, Nick Pullen

Course Overview

Biochemistry Lab, Spring 2014

The laboratory component of the CHM440/CHM441 courses (Biochemistry). Participants will gain practical competencies in modern experimental biochemistry dealing with the major classes of biomolecules, with emphasis placed upon proteins. Additionally, substantial, independent immersion in primary literature research is a key feature of this course. Participants will design, execute, and analyze a relevant and novel biochemical experiment producing data that could potentially be published.

Students and instructor typically meet 3-6h/week for the laboratory component.

Any student who has successfully completed genetics (BIO 231/232) and organic chemistry I (CHM 313/314) is eligible for enrollment in this course.

Implementation

Historically, GEP activities have been utilized in another course (BIO 405/406, Advanced Cell & Molecular Biology). Due to overall biology curriculum revisions and an enrollment boon in the program, I have had to cover more biochemistry sections, while another faculty member teaches BIO 405/406. Since my biochemistry lab course currently follows a fairly standard curriculum focusing upon techniques for isolating and detecting the four major classes of biomolecules, I opted to replace other in silico labs at the beginning of the semester and use the following:

GEP Materials Used

-An Introduction to NCBI/BLAST (W. Leung)

-Introduction to BLAST using human Leptin (J.R. DiAngelo)

-A Simple Annotation Exercise

Process

-Between weeks 1 & 2 of the laboratory course students were expected to  (1) make their best efforts to independently follow the Leung tutorial; (2) in the two days leading up to the second lab meeting, during "lecture" meetings, discuss that tutorial and any questions arisen from it.

-During week 2 of lab students were expected to go through, first, the DiAngelo tutorial in pairs and with the asistance of the instructor [me], then move on to the simple annotation exercise.

-In week 5 students were assessed for understanding via a laboratory practical.

Lessons Learned and Future Plans

One of greatest lessons, for the department, was discovering that most of the students had little-to-no prior knowledge of any NCBI-related resources. Approximately 50% more time was spent with the tutorials than initially budgeted, and work on the annotation aspect suffered as a consequence. This was a valuable experience nonetheless, as it helped us identify a major gap in our general curriculum.

-only 33.33% of students succeeded on the simple BLAST assessment given three weeks subsequent to the laboratory activity.


Moving forward, I envision using introductory GEP materials [and other NCBI resources] earlier in the Biology curriculum and across multiple courses, e.g. General Biology and Genetics. Furthermore, the faculty here unanimously decided that it was innapropriate to occupy the entire BIO 406 semester with genomics, because of other content interests - this in combination with our University switching to a Windows-based Virtual Desktop Interface for all student computers, indicates that other annotation and finishing GEP materials are unlikely to be used in the coming year. A genomics or systems biology special topic course (BIO 400) is possible within two years, however, I feel that our current GEP efforts should be focused on first second-year students at WWU.

Syllabus for CHM 441 (Biochemistry Lab, 2014)

TENTATIVE COURSE SCHEDULE

Exam dates will not change.
Topics may change and will be announced in class.

Dates                              Topics

14 Jan                             Introductions, Basic Lab Practices, Project ideas

21 Jan                             The Internet, Genomics, Research Assignments

28 Jan                             Chromatography

4 Feb                              Lipid Isolation

11 Feb                            Lab Practical

18 Feb                            Vitamin C, research consultation

25 Feb                            Enzymes - Michaelis-Menten

4 March                          NO LAB – Biology Major Review

11 March                        Fractionation, research consultation, and supplies Biomolecular fractionation - Trizol

18 March                        Measuring biomolecular concentration, Cell Culture Introduction

24-28 March                   Spring Break

1 April                            Lab Practical

8 April                            Group experiment planning, Cell Culture, treatments

15 April                          Sample Collection/isolation

22 April                          Western Blotting I

29 April                          Western Blotting II, data analysis

6 May                            Results submission
                                         Lab Final Poster