Molecular Biology 480/580
Laboratory Information*
-Spring 2014-
*Note see: http://csmbio. for the complete course expectations.



Dr. Terrie Rife
Office Number:3028D Biosciences
Phone Number:568-3343
Office Hours:  T 1:00-2:00 p.m., W 2:00- 3:00 p.m., F 10:00 a.m. to 11 a.m. and by appointment


Attendance - Reminder that Attendance in Lab is Mandatory- a 10% reduction in grade will be given for each lab day missed unless prior permisson from the instructor is obtained or documentation of an illness or family emergency is turned in within a timely fashion. Prompt arrival will also be expected from students. Failure to arrive to class on time may also result in a grade reduction of up to 5% of the lab grade.

Time Expectations for Lab Work Outside of the Class - Molecular biological experiments often involve doing something quickly, and then waiting, and then do something else, thus, time will be required outside of the normal class time to finish several of the experiments. As often as possibe you wil be informed in advance of the expectations outside of class for a given weeks experiments.

Lab Safety - Students are required to wear close-toed shoes at all times in the lab and safety glasses when working on the bench with chemicals. Students should not work alone in the laboratory. Students must fill out a lab safety sheet which indicates their understanding of these and other JMU safety regulations.

Class Preperation - Starting the second week of lab, students are required to familiarize themselves with the protocols ahead of the lab period and to bring a copy of the protcol to lab. During two lab periods of the semester, quizes will be given (worth 10 lab assignment points each) to insure students are prepared to participate in the day's lab activities, ie have looked over the days protocol before class.

Lab Notebook - While lab notebooks will not be graded, maintainence of a quility lab notebook is strongly suggested as lab notebook information will be needed for both the lab take-home exam and lab reports. Suggestions for keeping a quality lab notebook can be found at

Learning Goals (Based on JMU Biology Learning Goals)

1. Formulate a hypothesis and identify relevant variables necessary to test that hypothesis.
2. Design and execute experiments to test hypothesis.
3. Obtain and organize Molecular data.
4. Analyze and interpret Molecular data.
5. Use effective professional communication in posters.
6. Use effective professional communication in oral reports.
7. Use mathematics to understand and analyze biological phenomena
8. Synthesize information and concepts, and apply that knowledge to new situations.
9. Experience working “at the bench” in a controlled environment.
10. Be able to perform several molecular techniques including microarray analysis, real time PCR, Western Blotting, protein, RNA and DNA isolation.



Graded Item

Due Dates


Microarray Lab Report

Friday, March 28


Lab Exam
(Take-Home- made available on April 12)

Friday, April 4-14


Assignments (Lab)

Throughout Semester (See Lab Schedule for due dates)

Quiz (10 pts)
The Microarray Lab Report (10 pts.)
Attendance at Alzheimer's Disease Lecture (10pts)
Alzheimer's Journal Club (20 pts)
Attendance at Statistic's Lecture (10 pts)
Exel Spread Sheet for R prepared (10 pts.)
Google Doc on Gene Identification Completed (10 pts.)
Microarray Project Report (10pts.)
Microarray Hypothesis and Primer Design (10pts)
Rubisco Hypothesis (10 pts)
Rubisco Hypothesis Revised (10 pts)


Rubisco Report

Monday, April 21


Microarray Report Final

Monday, April 30



Lab Schedule and Protocol Links

Week of:
Procedures and
January 13


Lab Safety Form Link

January 20

NO Lab MLK Day


January 27


RNA Isolation

Quiz (10 pts)


The Basic Math of Solution Preparation

RNA Isolation and Analysis

RNA Quality Guide

February 3

RNA Quality Analysis

Microarray Lab Report Initiated (10 pts)

February 10

Making cDNA

Alzheimer's Lecture (10 pts)

Febrary 17

* Labs Require Time Outside of Lab


Alzheimer's Journal Club (20 pts)


February 24

Microarray Analysis I - Gridding and Segmenting

Statistic's Lecture (10 pts)

Please Print out copies of: Scanalyze Guide

From Scanalzye to R (Updated Feb. 20, 2014)

and before class please watch a video of how to use Scanalyze and a video of how to move your data from Scanalyze to Excel . These videos were put together by a now graduated class member, Lisa Brown for a microarray workshop held for faculty at JMU. Note that the second video refers specifically to arrays used at that workshop so the protocol is slightly different for your data but you will get a good idea of the basic steps that will be required of you this week from watching this video.

Useful Links for Class:

GCAT Information
Analyzing your Array Picture
Magic Tool Information

March 3

Microarray Analysis II-

Statistical Analysis and Begining Array Interpretation

Rubisco Hypothesis (10 pts)

Excel Spread Sheet for R (10 pts)

Please Print a copy of the:

R Protocol by now graduated classmate Dallas Joder who put this program together for his Honors Thesis

March 10


Spring Break




March 17

Microarray Analyisis III -

Intermediate Array Analysis

Array Project Report Due ( 10 pts)

Google Docs Due (10pts)



March 24


Protein Isolation

Rubisco Hypothesis Revised (10 pts)

Protein Isolation Protocol

March 31

Western Blot


Western Blot Protocol

April 7

Antibody Detection

Microarray Hypotheis and Primer Design Due (10 pts)

April 14

Real Time PCR

LAB EXAM (120 pts)

Real Time PCR Protocol

Standard Curve for Realtime.doc (once you have set up your samples, we will work together as a class to set up a standard curve)

April 21

Interpretation of Real Time Results


Agarose Gel of Real time

April 28

Lab Wrap-UP


January 2014- copyright (c)- T. Rife