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Viewing: BIT 572/BIO 572/CH 572 : Proteomics

Last approved: Thu, 17 Mar 2016 08:45:39 GMT

Last edit: Thu, 17 Mar 2016 08:45:39 GMT

Change Type
BIT (Biotechnology)
572
031302
Dual-Level Course
No
Cross-listed Course
Yes
Course Prefix:
CH
BIO
Proteomics
Proteomics
College of Agriculture and Life Sciences
Biotechnology (11BIT)
Term Offering
Spring Only
Offered Alternate Years
Fall 2015
Previously taught as Special Topics?
No
 
Course Delivery
Face-to-Face (On Campus)

Grading Method
Graded/Audit
3
8
Contact Hours
(Per Week)
Component TypeContact Hours
Laboratory5.0
Lecture3.0
Course Attribute(s)


If your course includes any of the following competencies, check all that apply.
University Competencies

Course Is Repeatable for Credit
No
 
 
David Muddiman and Michael Bereman
David Muddiman Distinguished Professor Chemistry and Michael Bereman Assistant Professor Biological Sciences
Full

Open when course_delivery = campus OR course_delivery = blended OR course_delivery = flip
Enrollment ComponentPer SemesterPer SectionMultiple Sections?Comments
Lecture and Lab1818Yes6 BIT seats
6 CH seats
6 BIO seats
Open when course_delivery = distance OR course_delivery = online OR course_delivery = remote
Prerequisite: BIT 410 or BIT 510 or BCH 454 (or approval from the instructor)
Is the course required or an elective for a Curriculum?
No
Introduction and history of the field of proteomics followed by the principles and applications of proteomics technology to understand protein expression and protein post-transitional modifications. Laboratory sessions include growing yeast with stable-isotope labeled amino acids, protein purification, Western blots, protein identification and quantification, and protein bioinformatic analysis. This is a half-semester course.

Our only revision proposed here is to add BIO as a prefix to this course 


Justification:


Dr. Bereman is an expert in the field of mass spectrometry based proteomics and would like to have BIT572/CH572 cross-listed with his home Department in Biological Sciences.   As the field of biology continues to advance, the ability to quantitatively measure proteins is essential to unraveling the mechanisms of complex disease as transcript levels often do not correlate with protein abundance. In addition, proteins are regulated post-translationally via enzymatic modifications.  As result, we feel it would be greatly beneficial to students in Biological Sciences to supplement their graduate course work with an opportunity to learn about the emerging field of proteomics.


No

Is this a GEP Course?
GEP Categories

Humanities Open when gep_category = HUM
Each course in the Humanities category of the General Education Program will provide instruction and guidance that help students to:
 
 

 
 

 
 

 
 

 
 

 
 

Mathematical Sciences Open when gep_category = MATH
Each course in the Mathematial Sciences category of the General Education Program will provide instruction and guidance that help students to:
 
 

 
 

 
 

 
 

Natural Sciences Open when gep_category = NATSCI
Each course in the Natural Sciences category of the General Education Program will provide instruction and guidance that help students to:
 
 

 
 

 
 

 
 

Social Sciences Open when gep_category = SOCSCI
Each course in the Social Sciences category of the General Education Program will provide instruction and guidance that help students to:
 
 

 
 

 
 

 
 

 
 

 
 

Interdisciplinary Perspectives Open when gep_category = INTERDISC
Each course in the Interdisciplinary Perspectives category of the General Education Program will provide instruction and guidance that help students to:
 
 

 
 

 
 

 
 

 
 

 
 

 
 

 
 

Visual & Performing Arts Open when gep_category = VPA
Each course in the Visual and Performing Arts category of the General Education Program will provide instruction and guidance that help students to:
 
 

 
 

 
 

 
 

 
 

 
 

Health and Exercise Studies Open when gep_category = HES
Each course in the Health and Exercise Studies category of the General Education Program will provide instruction and guidance that help students to:
 
 

 
 

 
 

 
 

 
&
 

 
 

 
 

 
 

Global Knowledge Open when gep_category = GLOBAL
Each course in the Global Knowledge category of the General Education Program will provide instruction and guidance that help students to achieve objective #1 plus at least one of objectives 2, 3, and 4:
 
 

 
 

 
Please complete at least 1 of the following student objectives.
 

 
 

 
 

 
 

 
 

 
 

US Diversity Open when gep_category = USDIV
Each course in the US Diversity category of the General Education Program will provide instruction and guidance that help students to achieve at least 2 of the following objectives:
Please complete at least 2 of the following student objectives.
 
 

 
 

 
 

 
 

 
 

 
 

 
 

 
 

Requisites and Scheduling
 
a. If seats are restricted, describe the restrictions being applied.
 

 
b. Is this restriction listed in the course catalog description for the course?
 

 
List all course pre-requisites, co-requisites, and restrictive statements (ex: Jr standing; Chemistry majors only). If none, state none.
 

 
List any discipline specific background or skills that a student is expected to have prior to taking this course. If none, state none. (ex: ability to analyze historical text; prepare a lesson plan)
 

Additional Information
Complete the following 3 questions or attach a syllabus that includes this information. If a 400-level or dual level course, a syllabus is required.
 
Title and author of any required text or publications.
 

 
Major topics to be covered and required readings including laboratory and studio topics.
 

 
List any required field trips, out of class activities, and/or guest speakers.
 

The professors will be teaching this as part of their teaching semester requirements. The course has an in-lab section which requires use of the professors instrumentation and bioinformatics software. In addition, it will require the purchase of reagents to perform such experiments that are covered by BIT and a dedicated classroom

The goal of this course is for students to gain an understanding of how proteomics can be used to study gene expression at the protein level.  Students will receive hands-on experience with extracting proteins from cells, preparing the sample for analysis, separation science, mass spectrometry, and bioinformatics.


Student Learning Outcomes

Student Learning Outcomes


Upon completion of the course, students will be able to:



  1. Design proteomic experiments to address a specific hypothesis

  2. Generate data and understand the outcome of proteomic experiments.

  3. Read and understand contemporary proteomic literature.

  4. Use bioinformatic software for protein identification and quantification.

  5. Discuss the advantages and disadvantages of different separation science and mass spectrometry strategies for the analysis of proteins.


Evaluation MethodWeighting/Points for EachDetails
Multiple exams35%mini-exams (5 total)
Lab Report10%Lab report progress report 10%

Lab Report: The interim and final lab report must be a typed Word document. The lab report should contain each of the following sections: title, introduction, purpose, materials and methods, results, discussion and references. The report should demonstrate an understanding of the proteomics technologies and data analysis. Please integrate the entire laboratory experience into a logical and thoughtful interpretation of the data. The interim laboratory report will be due February 12, 2014 via email and will be returned with comments via email no later than February 19, 2014. The final laboratory report will be due April 25, 2014 to allow students to have sufficient time to analyze their data using contemporary bioinformatics software and prepare an effective laboratory report. You may discuss results with your classmates, but reports are to be written independently. Further information on lab report guidelines will be provided.
Lab Report25%Final Laboratory report 25%

Lab report: The interim and final lab report must be a typed Word document. The lab report should contain each of the following sections: title, introduction, purpose, materials and methods, results, discussion and references. The report should demonstrate an understanding of the proteomics technologies and data analysis. Please integrate the entire laboratory experience into a logical and thoughtful interpretation of the data. The interim laboratory report will be due February 12, 2014 via email and will be returned with comments via email no later than February 19, 2014. The final laboratory report will be due April 25, 2014 to allow students to have sufficient time to analyze their data using contemporary bioinformatics software and prepare an effective laboratory report. You may discuss results with your classmates, but reports are to be written independently. Further information on lab report guidelines will be provided.
Final Exam25%Cumulative Final Exam
Lab Report5%Laboratory Notebook

Lab notebooks: Prior to coming to lab, you are strongly encouraged to write the purpose of the lab in your notebook. Each lab must be dated and must include a purpose, a reference to the protocol, and annotation of any deviations to the protocol given by the instructor or taken by you, all results and conclusions. Also, include any images (e.g., gel image) with appropriate labels. You must complete your notebook entries before leaving the lab. Your lab notebook will be graded at the end of the course.
TopicTime Devoted to Each TopicActivity
Week 11 weekIntroduction to Course and Laboratory
History: From Genomics to Proteomics
Overview of Proteomics: Bottom-up, Middle- and Top-Down
Note: You must bring a bound laboratory notebook to the first lab session on March 4, 2014
Week 21 weekLab 1: Check-In, Orientation, and Safety Training
Culture, Harvest and Prepare Yeast,1D SDS-PAGE

Mini-Exam 1
Basic Genetics, Characteristics of Amino Acids, Peptides, and Proteins, ExPASy, Basic Mass Spectrometry Definitions
Week 31 weekLab 2: Filter-Aided Sample Preparation - Protein Digestion

Mini-Exam 2
Quantitative Proteomics Overview, Protein and Peptide Fractionation Methods, Reduction, Alkylation, Proteolysis, Enrichment of Phosphorylated Proteins, Separation Science, Electrospray Ionization, Q-Exactive, Data-Dependent Tandem Mass Spectrometry, Data Independent Tandem Mass Spectrometry, Decision Tree Methods
Week 41 weekLab 3: Phosphopeptide Enrichment using Fe-NTA

Mini Exam 3
Relative Protein Quantification: Metabolic Labeling, Chemical Labeling, Enzymatic Labeling, and Label Free (AUC, Spectral Counting)
Week 51 weekLab 4: Linear Quadrupole Orbitrap for Global Protein
Identification


Mini-Exam 4
Absolute Protein Quantification: MRM Based Strategies
Week 61 weekLab 5: Bioinformatic Analysis of Data: X-Caliber, Protein
Databases, File Structure/Information, EXPASY Tools, RAWMEAT, Spectral Counting Approaches, Mascot, ProteoIQ, Analysis Strategies, Dissemination of Spreadsheets to Students

Mini-Exam 5
New Directions in OMICS Research
Sign up for 1 hour time slot for Tuesday’s lab 4/15/2014

Week 71 weekPreliminary Laboratory Report Due
Lab 6: SRM/MRM for Protein Quantification
Meet in Dabney 28 during time slot.
Week 81 weekLab 7: Final Laboratory Report Questions and Review for Final Examination

Final Laboratory Report Due Date
Final Exam Week1 classFinal Examination
The only edit we are making to this course is to cross list the course in Biological Sciences. (adding the BIO prefix)

mlnosbis 10/1/2015: Proposal has been approved by Chemistry DGP, CALS, and COS approvers. Only change is cross-listing with COS. No consult needed.

ghodge 10/1/2015 Only a change in cross listing. Ready for ABGS reviewers.

ABGS Reviewer Comments:
-Very minor action, the course contents have already been approved. No objections.
-Since it is an existing course, a statement of approval/consultation from the department should be provided. Response: See workflow, has been approved by both departments and colleges.
brownjw (Fri, 29 May 2015 19:00:15 GMT): Approved
Key: 6370