BIO 480 Syllabus - Spring 2012


Course Home Page | Laboratory Schedule

Grading| Attendance and Exam Policies |Honor Code | Learning Objectives

Course Home Page: http://csm.jmu.edu/biology/courses/bio480_580/home.html

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.

Course Information:

Course Description: Cellular constitutes and genetics are emphasized at the molecular level. This course builds upon basic molecular knowledge previously learned in BIO 214 and BIO 224.
Prerequisites: Students enrolled in this course should have satisfactorily completed Organic Chemistry (Chem 241 or 342) and Genetics and Development (BIO 224). Students who have not completed these courses should understand that the instructor will assume that all students have such a background.
Credit Hours: 4
Lecture:
.
 MWF 9:05- 9:55 a.m. in Burruss 0032.
Lecture Text:  Lodish et al. 2007.  Molecular Cell Biology, 6th ed.  Freeman
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.
Lab Materials:  All written materials needed for the laboaratory are available online, http://csm.jmu.edu/biology/courses/bio480_580/mblab/schedule.htm. Prior to each laboratory meeting, starting the second week of classes, each student is responsible for reading and printing out a copies of all laboratory procedures that will be conducted during the week.   Students are required to bring safety glasses to class and wear closed toed shoes at all times in the lab.


Learning Objectives/Goals:

I. Learning Goals for the Lecture (More detailed objectives for LECTURE EXAMS and QUIZZES can be found at: http://csm.jmu.edu/biology/courses/bio480_580/Objectives/objectives.html):

A. Knowledge Objectives

1. The Basics of Molecular Biology (Lodish Chapters 2-5)

2. The Molecular Processes: Transcription, Translation and Replication (Lodish Chapters 4,7-8, 20,21,22)

3. Molecular Biology at the Genomic Level (Chapter 6 and 24)

B. Skills Objectives

4. Applying The Science of Molecular Biology

II. Learning Goals for the Laboratory:

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.


Link to Specific Biology Department Objectives Met by BIO 480


Grading (1000 points total):
Item Date Scheduled Points

Assignments (Lecture)

Daily Questions (40pts) and BLAST Assignment (15 pts)

55

Lecture Exam 1

Friday, January 27

80

Lecture Exam 2

Friday, February 24

100

Lecture Exam 3

Friday, March 30

100

Final Exam

Monday, April 30 , 8 a.m. - 10 a.m.

120

Quizzes (Lecture)

January 23 , Feb. 20, March 26, April 23
(15 pts each, 3/4 will count toward the final grade)

45

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)

140

Final Lab Report

Friday, April 27

120


% Earned
Grade
93 +
A
90-92
A-
87-89
B+
83-86
B
80-82
B-
77-79
C+
73-76
C
70-72
C-
60-69
D

Grading Policies:

Lecture
Attendance will be taken only on specified lecture days where class participation is required. Students will be informed of these days in advance. Attendance and participation in these class periods will count toward laboratory assignment grade. Students who miss the mandatory class days may write three- to five- page papers on the subjects missed to make up the points missed.   Note that students who attend lecture regularly do much better than students who miss several lectures.

Note: Students and instructor together will choose five lecture classes to skip to make up for the extra-long lab times. These five lecture days will also be used in leui of making up missed lectures for adverse weather conditions.

Examinations, Quizzes and Assignment Points
Students are required to take examinations at scheduled times. Only under extenuating circumstances such as a severe illness or family emergency will a student be permitted to make up an examination. Such instances must be documented and the instructor should be contacted as soon as possible after a missed exam. Exceptions may only be made with prior instructor permission, see the general policies section below.
Quizzes cannot be made up although the lowest quiz grade for each student will be dropped. Daily Assignment Points cannot be made up. These points can be earned by correctly answering daily questions in lecture, presenting on timely journal or news article to the class with prior permission from the instructor, or participating in a designated lecture or lab activity. Students will be given at least 50 points worth of daily questions throughout the semester so students attending regularly will have ample opportunity to earn the required 40 points even if they miss a day or two of lecture or a question or two. Students may earn more than 40 points.

Laboratory
Attendance in laboratory is mandatory. Failure to attend a laboratory session or extreme tardiness without a documented excuse for an illness or family emergency presented to the instructor will result in a 10% reduction of the lab portion of the grade for each lab day missed.
In the case of an illness, acceptable documentation is limited to a signed note from a doctor indicating that the student was too ill to sit the exam or a verifiable record of visit to the JMU Health Center on the day of the exam. In the case of family emergency, acceptable documentation is limited to a signed note from a parent or guardian stating that a family emergency prevented the student from sitting the exam. It is not necessary that the instructor be told the nature of the illness or family emergency which prevented the student from sitting the exam. Exceptions may only be made with prior instructor permission, see the general policies section below.

Molecular experiments often require time outside of the scheduled lab. As often as possible students will be informed in advance of expectations outside of class for a given weeks experiment.

All lab assignments and the take-home examination will be docked 10% for every day late.

General Policies
If a student wishes to appeal an exam or report grade, they must present their case to the instructor within one week of receiving the graded exam. After one week, no appeals will be accepted, regardless of their merit.

Exceptions to scheduling of exams or a request to miss a mandatory lab must be made before the add/drop deadline for the class. Requests should be made in person and must be reasonable. Reasonable requests include missing because of a verifiable reason such as a religious observance, school sponsored outing, or giving a presentation at a scientific conference.


Other Applicable JMU Policies:

Adverse Weather Event- In the case of an adverse weather event that causes a cancellation of a a lab, students will be required to make up the lab on the University scheduled make-up day.

Disability Accommodations- Students with disabilities who require reasonable accommodations to fully participate in course activities and/or meet course requirements must register with the Office of Disability Services (ODS) and contact me to discuss access issues. ODS will provide you with an Access Plan Letter that will verify your need for services and make recommendations for accommodations to be used in my classroom.  ODS is located in the Wilson Learning Center, Room 107; Phone: 568-6705

Academic Honesty- Students are referred to the current student handbook for a description of the university honor system. All provisions of the honor system are applicable in this course, including the violations listed in the handbook. The collaborative nature of the laboratory encourages students to work together, however, and collaborative work such as preparation of the posters and planning and execution of laboratory experiments are not considered violations of the honor code.

Making references to the work of others strengthens your own work by granting you greater authority and by showing that you are part of a discussion located within an intellectual community. When you make references to the ideas of others, it is essential to provide proper attribution and citation. Failing to do so is considered academically dishonest, as is copying or paraphrasing someone else’s work. The consequences of such behavior will lead to consequences ranging from failure on an assignment to failure in the course to dismissal from the university. Because collaborative work is valued, you will be encouraged to share ideas and to include the ideas of others in papers, but please ask if you are in doubt about the use of a citation. Honest mistakes can be prevented.

Course Registration Information Students are responsible for registering for classes and for verifying their class schedules on e-campus. The deadline for adding a Spring Semester class without instructor and academic unit head signatures is January 17. Between Tuesday, January 17, 2012 and Thursday, January 26, instructor and academic unit head signatures are required to add a class for Spring Semester 2012. No student will be allowed to register for a Spring Semester class after Thursday, January 26, 2012. No exceptions will be made to these deadlines.

Religious Observations- All faculty are required to give reasonable and appropriate accommodations to students requesting them on grounds of religious observation. The faculty member determines what accommodations are appropriate for his/her course. Students should notify the faculty by no later than the end of the Drop-Add period the first week of the semester of potential scheduled absences and determine with the instructor if mutually acceptable alternative methods exist for completing the missed classroom time, lab or activity.


Tenative Lab Schedule and Protocol Links


Week of:
Scheduled
Activities
Procedures and
Resources
January 9

Introduction

Completion of GCAT Assessment (10 pts)

GCAT 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

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. Monroe's Talk (TBD) - 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 (TBD - 10 pts)

Journal Club Presentations (20 pts)


Please Print out copies of: Scanalyze Guide

Getting your data ready for statistical analysis: From Scanalyze to Excel

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)

 


Course Home Page
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Revised December 2011
Copyright (C) 2011, Terrie Rife. All rights reserved.