Molecular Biology 480/580
Laboratory Schedule*
-Spring 2012-
*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: 208 Burruss
Phone Number: 568-3343
Email: rifetk@jmu.edu
Office Hours: T 9:30 a.m. - 11: 30 a.m., W 1- 3 p.m. and F 10 - 11 a.m. by appointment
Dr. Liz Doyle
Office Number: 107 Burruss
Phone Number: 568-5523
Email: doyleea@jmu.edu
Office Hours: W 10:00 a.m. - 12:00 p.m. , Th 1:00 - 2:00 p.m., F 10:00 a.m. - 12:00 p.m. and by appointment.

Laboratory:  Burruss 328 - BIO480 Section 1 (#12411): Monday - 1:25-5:15 p.m., BIO 480 Section 2 (#15439): 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 - 50 % of Class Grade

TR>

Graded Item

Due Dates

Points

Midterm Lab Report

Friday, March 23

120

Lab Exam
(Take-Home- made available on April 9)

Monday, April 16

120

Assignments (Lab)

Throughout Semester (See Lab Schedule Below)

140

Final Lab Report

Friday, April 27

120

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Lab Schedule and Protocol Links


Week of:
Scheduled
Activities
Procedures and
Resources
January 9

Introduction

Completion of GCAT Assessment by Friday (10 pts)

GCAT Assessment (use Rife as instructor name for the purposes of filling out this survey)

Dr. Temple's Assessment

Instructions for Array Web Poster

January 16

LABS WILL NOT MEET = MLK DAY

 

January 23

RNA Isolation

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

RNA Isolation and Analysis (Updated on Jan. 13)

RNA Quality Guide


January 30

Making cDNA

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

February 6

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

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

February 13

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

Microarray Analysis I - Gridding and Segmenting

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

Journal Club Presentations (20 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 20

Microarray Analysis II-

Statistical Analysis and Begining Array Interpretation

Excel Spread Sheet for R program prepared (10 pts)

Proposal for Project II (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.

Useful Links for Class:

Stats Analysis Prepared by Alexa Romasco

Stats Analysis Prepared by Charlie Cuccherini

February 27

Array Analyisis III -

Intermediate Array Analysis and Individual Work

Introduction to Project II

Excel Spread Sheet Annotated (10 pts)

*Final Array Report Due March 19 (120 pts)

 

 

March 5

 

NO CLASS = Spring Break

 

March 12

Protein Extraction and Quantification

 

 

March 19

 

Western Blot

- plan on 1 hour of work outside of the lab the day after your lab

Proposal for Project 2 Revisions Due (10 pts)

Western Blot Protocol  

March 26

 

Antibody Detection

Grading of Array Posters Due

 

Antibody Detection

April 2

DNA Extraction

Note: This lab tends to run overtime.

Web Poster 2 Began (10 pts)

DNA Extraction

 

April 9

 

Real Time PCR

Lab Exam Due April 16 (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 16

Interpretation of Real Time Results

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

 

Agarose Gel of Real time

April 23

Lab Wrap Up

Final GCAT Assessment (10 pts)

Final Rubisco Report Due April 27 (120 pts)

 


January 2012 - copyright- T. Rife