Service-Learning Designation Application
Course: Advance Biochemistry Lab (CH432)
Instructor: Ken Cornell, Ph.D.
Date: Spring 2008
Syllabus:
Course Title: Biochemistry Lab / CH 432 / 2 credits
Instructor:
Office Hours:
Ken Cornell, Ph.D., office SN 320, lab SN 410, ext 5429, email: kencornell@boisestate.edu
M, T 10:30 – 11:30 pm, room SN 320 (other times possible by appointment)
Class Schedule: T 12:40 pm– 6:10 pm, room SN 305 and Chemistry Conference rm.
Weekly attendance is required. You must be present when experiments are performed.
Textbook:
None, however Handouts detailing the experiments to be performed will be distributed in class and posted
on blackboard. A lab notebook for recording experimental details is required (I recommend the gray spiral bound National
Brand laboratory notebook, 4x4 quadrille ruled 43-647 white numbered pages with yellow duplicates [carbons]). Other
notebook types are also acceptable as long as you have copies to attach to reports when requested, and the pages are
numbered.
Laboratory Description: Approximately the first six weeks of the semester will be devoted to developing biochemical
skills involved in protein / enzyme characterization. The main protein we will focus on is the E. coli MTA/SAH nucleosidase
(E.C. 3.2.2.9) an enzyme found in the methionine / purine salvage pathway of microbes and plants. This protein will serve as
a model for the biochemical and biophysical experiments that will be used as skill building exercises for later experiments
involved in the service learning project.
There will be a strong service learning portion to the course. Service learning involves integrating coursework with exercises
designed to investigate community probles (for sample definitions see:
http://servicelearning.boisestate.edu/index.cfm?fuseaction=content.view&section=9&page=24) This year, the topic will be
the identification of West Nile Virus (WNV) in mosquito samples collected in Ada, Gem, and Canyon counties. This project
will relate to the course by focusing on training in analytical / biochemical skills that are used to solve real-life problems
facing our community. As part of the service learning project, students will be expected to do the following:
a.
Perform literature surveys to identify the problem faced with WNV, both internationally, nationally, and locally.
b.
Develop analytical procedures based on literature descriptions and technical bulletins supplied by the Idaho Bureau
of Labs and local mosquito abatement districts.
c.
Collect data, perform analysis, and summarize project findings in a short written technical report form for
presentation to the Idaho Bureau of Labs and local mosquito abatement districts (community partners).
d.
Design new detection schemes for WNV based on literature review procedures and bioinformatics exercises.
e.
Validate new detection schemes by comparison to results previously obtained from standardized commercial tests.
f.
Prepare and deliver oral and poster presentations of the topic to high school students (another community partner)
and university / scientific community during local science meetings.
g.
Write up the project and results in a scientific journal article format that is suitable for publication in the Journal of
the Idaho Academy of Sciences or other journal.
Where possible, data from the experiments performed in this class will be compared to previously published results.
Particularly at the beginning of the course, we will initiate are studies by examining the scientific literature on the topic and
performing bioinformatic studies to examine the predicted biochemical properties of the protein / DNA sequences.
Subsequent studies will involve a variety of molecular and biochemical techniques used to amplify genes of interest, subclone
them into prokaryotic expression vectors, produce and purify recombinant proteins, and characterize enzyme properties and
catalytic activity. These studies are meant to introduce some of the research processes used in a scientific investigation. In
the latter part of the course, the learned techniques will be applied to the comparative study detection schemes for WNV.
Homework, Examination Schedule & Grading Policy: The course will be graded based on lab notebooks, research reports, homework
problems assigned in class, poster and oral presentations of the project, and a final exam. While you will work in groups to
collect data, many aspects of the course (analysis, writeups, reports. tests, etc.) are to be performed individually. You will be
directed on this during the course of the laboratory. Direct copying of another lab members work or cutting and pasting
information from other sources (Internet, scientific articles, etc.) without appropriate citation represents plagiarism and
constitutes cheating, and is a punishable crime (zero on assignment, plus other institutional ramifications).
WORK NEEDS TO BE TURNED IN ON TIME!
The approximate points assigned for different activities are as follows:
Grades will be based on the
% points achieved during
the whole course.
90% +
A
80-89 %
B
Item
Points
Lab reports/ notebook pages
100 points
Technical report IBL(groups)
40 points
Presentations(High School/ Sci mtg)
40 points
Discussion/ Reflection activities 20 points
Scientific paper/HW assignments
50 points
Final exam
50 points
Total
300 points
Formal Lab Reports: 2-3 formal lab reports will be required during the course of the term. These must be individually written and will
consist of 5-10 page typewritten reports. Copies of laboratory notebook pages must accompany each report. Laboratory
notebook pages and calculations may be handwritten, but must be legible. If I cannot easily read what you did in your
notebook, I cannot assign value to the work. All reports must be completed in order to pass the course. Laboratory reports
will be organized in a research paper format and are due two weeks following the completion of the experiments. Examples
of formal laboratory report formats will be provided. If you have questions regarding the report you generate, by all means
contact me well before the due date so that we may discuss them. Nothing in this course is meant to be purposefully tricky,
although you are meant to spend time developing your scientific judgment and ability to discuss results.
Technical Report: A short (3-5 pages) technical report will be prepared for submission to the Idaho Bureau of Laboratories and the local
mosquito abatement districts. The format will be based on templates commonly used by IBL.
Presentations: Each lab group will be expected to present their results in poster format one time during the semester. Targeted meetings
include the Annual Undergraduate Research Conference (BSU SUB, April 14th), The Service Learning Conference (BSU
ILC, May 5-9), the Annual Idaho Academy of Science Research Conference (CWI, March 28th). Students will also engage in
outreach activities by presenting the project and its findings to science classes at Skyview High School, as well as
demonstrate techniques used in mosquito collection and WNV detection. The high school students will subsequently be
enlisted to collect additional mosquito samples from their campus, which will be tested by the BSU students as part of the
overall study. These activities are planned for March 18th and April 1st.
Lab Behavior: It is expected that all the individuals involved in this course will behave in a cooperative and respectful manner (to each
other and ESPECIALLY TO ME). Be safe at all times. Safety glasses / goggles are required. Lab jackets are
recommended. Due to equipment limitations, we will frequently be sharing instruments and every effort should be made to
treat them with the utmost care so that they are available to the next lab group. Also, much of the equipment that we will be
using is located within the research labs of BSU investigators. When in these research labs, every effort should be made to
minimize your impact and avoid disrupting the daily operation of that lab. This may require that alternate times be scheduled
to perform the necessary work.
There will be time during classes to work on presentations and write-ups, so work diligently and use your time wisely. On
group projects, tasks should be assigned within the group so that the work proceeds efficiently.
APPROPRIATE ATTIRE IS REQUIRED: No shorts, No sandals / open-toed shoes, No exposed body parts except from the
elbow to the finger tip, and the neck up to the top of the head.
CH 432 Biochemistry II Lab Schedule Spring 2008 Approximate Schedule
One
Week/Date
1/22
Two
1/29
State Lab
Tour
Lab
1
Topics
Course Intro: outline assignment expectations, grading policies, Lab safety, etc.
Bioinformatics exercise: intro to GenBank / ExPasy / PubMed / proteomics applet
Assignment #1: problem set on calculations, dilutions, conversions, etc. (due 1/27)
Assignment #2: Look up protocols for WNV detection, cloning and expression, primer design, etc.
Service Learning Activity: Review Goals, perform initial reflection (turn in at end of class)
2
Operation of lab equipment: pipettes, spectrophotometers, pH meters, electrophoresis.
Experiment #1a: Protein Characterization.
1. Determination of protein extinction coefficient / Beer’s Law/ (CRC Handbook)
2. Comparison of protein concentration by UV absorbance vs. colorimetric BioRad assay.
3. Make some of the required buffers for the course: Electrophoresis buffer, Tris buffers, etc.
Service learning activity: Meet Dr. Chris Ball from IBL tour state lab, discuss WNV project goals, report format
etc. Review timeline for due dates on service learning project
Due: Assignment #1 Calculations
Three
2/5
3
Experiment #1b: Protein Characterization.
1. Electrophoresis. Use of SDS- PAGE, Native gel electrophoresis for MW, purity ,organization
2. Analysis of Enzyme activity: specific activity measurement
Assignment #3: Read and answer questions on commercial test kits for WNV
Assignment #4: Outline reagents required for PCR detection schemes for WNV
Assignment #5: Write up background statement suitable for technical report and poster; Make 2 slides for
Powerpoint presentation
Service learning activity: Discuss WNV project presentation to High School; examine slide show.
Due: Assignment #2: detection, cloning, pcr schemes for WNV (with references)
Four
2/12
4
Five
2/19
5
Six
2/26
6
Experiment #1b: Protein Characterization. (cont)
1. Electrophor fsesis. Use of SDS- PAGE, Native gel electrophoresis for MW, purity ,organization
2. Analysis of Enzyme activity: specific activity measurement
Assignment #6: Outline Report #1 on Characterization of Recombinant MTN
Assignment #7: Read technical report on WNV by Chris Ball. Outline technical report for this year.
Service learning activity: Discuss WNV project and formulate a presentation plan for HS, IBL, undergrad
research meetings. Complete reflection activity #2: Needs/ project importance statement; go over assignment #5 in
class.
Due: Assignment #3 & 4: Questions on commercial kits and reagent requirements
Assignment #5: Background statements, Powerpoint slides.
Experiment #2a. Protein Characterization. Enzyme kinetics & Inhibitor analysis
1. Km / Vmax study
2. Inhibitor analysis
Assignment #8: Prepare full Report #1 on MTN
Service learning activity: Discuss WNV project and formulate sample collection plan; organize work groups.
Review finalized schemes for WNV detection.
Due: Assignment #6: Outline of Report #1 on MTN
Assignment #7: Technical report outline
Experiment #2a. Protein Characterization. Enzyme kinetics & Inhibitor analysis (con’t)
1. Km / Vmax study
2. Inhibitor analysis
Assignment #9: Analyze kinetic and inhibition data in class / Outline report #2 in class
Assignment #10: Prepare materials / methods section for tech report and poster
Service learning activity: Meet David Robinson, HS science teacher Mt View High School
Discuss presentation schedule
Seven
3/4
7
Eight
3/11
8
Due: Assignment #8: Full Report #1 on MTN DUE
Experiment #3a. WNV analysis.
1. Kit analysis of bird swabs / mosquito samples (archives)
2. PCR tests / gel electrophoresis results of RT PCR
Assignment #11: Prepare full report #2 on MTN
Service learning activity: Discuss WNV project presentation: finalize visits. Plan field collections
Meet Mosquito surveillance coordinator. Go over operation of mosquito traps, and ID
Due: Assignment #9: Outline of Report #2 on MTN
Due: Assignment #10: M&M section of poster & report
Experiment #3a. WNV analysis (con’t)
1. Kit analysis of bird swabs / mosquito samples (archives)
2. PCR tests / gel electrophoresis results of RT PCR
3. Cloning and transformation of PCR products
Assignment #12: Prepare Poster for presentation of results: Figures / Discussion / Conclusion
Service learning activity: Discuss WNV project presentation: finalize visits. Plan field collections
Meet Mosquito surveillance coordinator. Go over operation of mosquito traps, and ID
Due: Assignment #11: Full Report #2 on MTN
Nine
3/18
9
Ten
3/25
Eleven…….4/1
10
11
Twelve……4/8
12
Thirteen…4/15
13
Fourteen…4/22
14
Fifteen…...4/29
15
Sixteen……5/6
16
Experiment #3b. WNV analysis (con’t) Field work
1. Set mosquito traps
2. Collect samples, ID, prep for analysis
Service learning activity: Present WNV project at High School, go over analysis, lead class in demonstrations,
Q&A.
Due: Assignment #12: Poster due (groups)
SPRING BREAK
(Idaho Academy of Science Mtg)
Experiment #3b. WNV analysis (con’t) Field work
1. Set mosquito traps
2. Collect samples, ID, prep for analysis
Service learning activity: Return to High School, lead class activity, discuss results
Presentation at Undergraduate Research Day
(Undergraduate Research Day)
Experiment #3a/b. WNV analysis continued
1. Finish sample prep
2. Complete sample analysis
Assignment #13: Prepare writeup for experiment 3.
Service learning activity: Reflection activity #3 on presentations: successes/ failure/ future prospects
Experiment #4. WNV analysis of PCR tests
Assignment #14: Prepare report outline for IBL
Service learning activity: Review styles for reports, discuss needs of State of Idaho Labs
Due: Assignment #13 Full report of Experiment #3.
Experiment #4. WNV analysis of PCR tests (con’t)
Assignment #14: Prepare complete report for IBL
Service learning activity: Review styles for reports, discuss needs of State of Idaho Labs
Experiment #4. WNV analysis of PCR tests (con’t)
Assignment #15: Modify IBL report for Idaho Academy of Science
Service learning activity: Review styles for reports, discuss needs of State of Idaho Labs
Due: Assignment #14 IBL report due
Final Exam
Service learning activity: Final in class assessment of service learning
Due: Assignment #15 Idaho Acad Sci paper due
Nine Criteria for Designation of Service-Learning Classes*
*Based on to the "National Principles of Good Practice in Community Service-Learning"
1. What service will students provide to individuals, organizations, schools, or other entities in the community?
Students in Advanced Biochemistry lab (CH 432) typically conduct a variety of experiments to train them in
the molecular, biochemical, and biophysical characterization of proteins. In the spring of 2008, biochemistry
lab students will apply this training toward the identification of West Nile Virus in mosquito pools in
Southwest Idaho under the direction of Drs. Ken Cornell (BSU) and Chris Ball (IBL). West Nile Virus (WNV) is
spread by the bite of infected mosquito species that are prevalent throughout the United States. WNV reached
Idaho three years ago, and last year caused more than 1,000 cases of symptomatic disease in the state,
making it the worst hit in the country. Once the virus enters an ecosystem it persists in mosquito populations
and animal reservoirs. Periodically, outbreaks of disease occur when environmental conditions (mild winters,
wet springs) sponsor high mosquito populations that can transmit the disease from infected birds to humans.
While the disease is not eradicated in a particular locale, its impact can be modulated through monitoring for
its presence in mosquito populations and implementation of education and abatement programs (spraying,
pond drainage, etc.).
In the first year of the WNV project, students will examine archived mosquito samples from 2006 (a high
viral load year) and 2007 (a low viral load year) for WNV using antibody and polymerase chain reaction based
tests. Their activities will confirm prior findings by the Idaho Bureau of Laboratories (IBL) and aid in the
validation testing of new procedures. Students will also collect and analyze mosquito samples through the
spring of 2008 in an attempt to identify locations where the virus has over-wintered; as well as perform
bioinformatic exercises to try and develop their own detection schemes for the virus. From their findings a
technical report will be made to the IBL and the mosquito abatement districts of Ada, Canyon, and Gem
counties. Students will also engage in outreach activities by presenting the project and its findings to science
classes at Skyview High School, as well as demonstrate techniques used in mosquito collection and WNV
detection. The high school students will subsequently be enlisted to collect additional mosquito samples
from their campus, which will be tested by the BSU students as part of the overall study.
In subsequent years (2 and 3), the project will be expanded to look at additional sample sites and involve
additional high schools in SW Idaho. The activities of the high school students will also be increased to
include presentations to grade school classrooms on the importance of WNV and strategies to avoid
contracting the disease by reducing mosquito bites. Additional presentations at local meetings (community
engagement mtg, BSU undergraduate research day, Idaho academy of science, INBRE) and publications
(Journal of the Idaho Academy of Science); resulting from the project are planned.
2. How does the service relate to the subject matter of the course?
Students in Advanced Biochemistry lab typically perform a variety of experiments involved in the molecular
characterization of proteins and DNA. The target protein(s) changes from year to year; but the basic
methodology remains largely the same, involving the following series of experiments:
a. determination of protein / DNA concentration by UV/vis spectrophotometry,
b. polymerase chain reaction to amplify target DNA sequences,
c. detection of DNA sequences by gel electrophoresis,
d. cloning of target genes into plasmid vectors
e. analysis of protein expression and purification by chromatography and gel electrophoresis.
f. Analysis of protein enzymatic activity by Uv/vis spectrophotometry
In the service learning course, five of the six experiments will by conducted during the examination of
mosquito samples for West Nile Virus sequences. At the same time, the techniques the students practice will
have practical applications in identifying target regions that potential sources for West Nile transmission in
the next mosquito season (2008).
3.
What methods will you use to encourage students to think about what they are learning through the service and
how it relates to the subject of the class?
Students will meet weekly at the beginning of the laboratory class for a discussion of the project and how
the experiments demonstrate course goals for proficiency in molecular characterization of DNA and protein
samples. As a prelude to these discussions, students will conduct literature surveys and identify basic
science articles and technical publications that relate to the material. As part of the coursework, students will
design additional test procedures to complement the commercial tests that will be performed as part of the
course.
4.
What reflective strategies will you use to assess the learning derived from the service? (Explain how credit will be
given for the learning and its relation to the course, not for the service alone).
Credit for course activities will be assigned based on a combination of written reports on the experiments
performed, presentation of activities and goals to high school students, poster presentations to local
audiences at BSU, and oral / written exams on the subject material.
5. How will the service recipients (clients or agency)l be involved in the planning and evaluation of the service?
Service recipients will be involved in the service by participating in discussions at the beginning of the
course on coursework goals, evaluation of technical reports later in the course as students write up their
results, and evaluation of student presentations planned toward the end of the course.
6. What methods or resources will you use (links, articles, etc.) to illustrate how the discipline relates to the issue
addressed by the service?
On of the central activities for students in this course will be to examine archived samples for the
presence of West Nile Virus. As such, the students will be validating prior results using methods established
by the Idaho Bureau of Laboratories (IBL) and available as a technical protocol from Dr. Chris Ball (IBL).
Additional technical resources will be identified as the students conduct literature reviews on the topic of
West Nile virus identification, and learn to summarize this material into cognate laboratory protocols.
7. How does the Service-Learning experience foster civic responsibility, which may coincide with career preparation?
As part of identifying West Nile virus in mosquito samples, students will examine the local environment for
manmade hazards that favor the multiplication of the Culicine mosquitos that transmit the virus, as well as
cultural activities that put people at risk of contracting the virus through a mosquito bite. Civic responsibility
at a personal level will be fostered by educating the students on what they can do in their own environments
and by their own actions to reduce WNV exposure. At a public level, civic responsibility will be promoted by
having the students give talks and poster presentations on the topic during local science meeting and as part
of outreach activities to the local high school system.
8. What methods will you use to help students learn from each other (e.g. through reflection sessions), as well as
from the instructor?
Students and the instructor will evaluate the progress of the project, and the results of the experiments
during discussion sections that occur at the beginning of each lab. Laboratory records will be kept on all
experiments, and evaluated periodically by the instructor.
9. What course options will you allow to ensure that no student is required to participate in a service placement that
creates a religious, political and/or moral conflict?
The experiments outlined as part of the service learning component of the course are largely technical
procedures that shouldn’t specifically pose religious, political or moral conflicts any more than the
typical experiments involved in the course in years past. At the beginning of the course, the service
learning project will be outlined to students, and they will be polled as to their interest / potential
conflicts in the project. Students objecting to the project on any of the above grounds, will be directed
along another course of experimentation..