Molecular Biology 480/580
Laboratory Schedule*
-Spring 2013-
*Note see: http://csm.jmu.edu/biology/courses/bio480_580/Syllabus/sylFall2011.html for the complete course expectations.

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Instructors:

Dr. Terrie Rife
Office Number:3028D Biosciences
Phone Number:568-3343
Email: rifetk@jmu.edu
Office Hours: M 10:30 - 11:30 a.m., T 10 a.m. - 12 p.m., W 1- 3 p.m. and by appointment
Dr. Liz Doyle
Office Number:3028C Biosciences
Phone Number:568-5523
Email: doyleea@jmu.edu
Office Hours: Monday 12:00 – 1:00, Tuesday 9:00 – 11:00, Thursday 1:30 – 3:30, and by appointment.

Laboratory: Biosciences 3033

Section 1( #12191- Dr. Rife): Monday - 1:25-5:15 p.m.

Section 2 (#13809- Dr. Doyle): Tuesday- 12:30 p.m.- 4:20 p.m.

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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, pop-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 http://homegrownscientists.org/note-taking/keeping-a-good-lab-notebook.html.

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.

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Grading

Graded Item

Due Dates

Points

Midterm Lab Report

Friday, March 22

120

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

Friday, April 12- 19

100

Assignments (Lab)

Throughout Semester (See Lab Schedule for due dates)

Pop Quizzes x 2 (10 pts each= 20 pts.)
Webposter 1- Title page (10 pts.)
Rife Lecture (10 pts.)

Jahan Lecture (10 pts.)
Journal Club Presentation (20pts.)
Gridding Completed (10pts)
GoogleDoc Completed (10 pts)
Proposal for Project 2 (20 pts.)
Webposter 2-Title Page+ (10 pts)
Webposter 2 Draft (10 pts)

 

130

Final Lab Report

Friday, April 26

120

 

Lab Schedule and Protocol Links


Week of:
Scheduled
Activities
Procedures and
Resources
January 9

Introduction

Lab Safety Form

Instructions for Array Web Poster

January 14

RNA Isolation

Reminder: Pop Quizzes on the lab protocol will be given twice during the semester (10 pts each)

RNA Isolation and Analysis

RNA Quality Guide

January 21

MLK DAY = NO LAB


January 28

Making cDNA

Web Poster 1 Begun ( Working Link to be sent to Dr. Rife by end of the week) (10 pts)

February 4

Note: Labs require time outside of class for completion.

Microarray Hybridization and Washing(Note: some of this will take place outside of the regular class times)

Journal Club Presentations Assigned (20 pts)

 

February 11

Note: Tuesday Labs will meet after completion of biology/biotechnology assessment (1pm)

Microarray Analysis I - Gridding and Segmenting

 

Attendance at Dr. Rife's Talk ( Feb 10 in lecture) - 10 pts

Attendance at Dr. Jahan's Talk (Feb. 15 in lecture- 10 pts)

 


Please Print out copies of: Scanalyze Guide

Getting your data ready for R (Updated Feb. 3, 2012)

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

Intro to Project 2

February 18

Microarray Analysis II-

Statistical Analysis and Begining Array Interpretation

Excel Spread Sheet for R program prepared (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.

 

 

February 25

Microarrray Analyisis III -

Intermediate Array Analysis and Individual Work

Introduction to Project II

Excel Spread Sheet Annotated (10 pts)

Proposal for Project II (10 pts)

*Final Array Report Due March 22 (120 pts)

 

 

 

March 4

 

NO CLASS = Spring Break

 

March 11

Protein Extraction and Quantification

Web Poster 2 Began (10 pts)

 

 

March 18

 

Western Blot

Midterm Lab Report Due

Western Blot Protocol  

March 25

Antibody Detection

Grading of Array Posters Due

Antibody Detection

April 1

DNA Extraction

Proposal for Project 2 Revisions Due (10 pts)

DNA Extraction

 

April 8

Real Time PCR

Lab Exam Given April 12 (100 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 15

Interpretation of Real Time Results

Web Poster 2 (Should have Intro/ Methods/ Results from Western Completed) (10 pts)

Agarose Gel of Real time

April 22

Lab Wrap Up

Final Rubisco Report

Due April 26 (120 pts)

 


January 2013 - copyright (c)- T. Rife