Iowa Biotechnology/Bioprocessing Workforce Development Model Project
Biotech Industry Survey and Proteomics Curriculum Development
Funded by the U.S. Department of Labor
Proteomics Industry Survey Results
Des Moines Area Community College contacted thirty companies asking them to complete a proteomics workforce survey. 30% of the companies completed the survey. The results are as follows:
1a. Does your company conduct proteomics research? 2 Yes 7 No (22% / 78%)
1b. If yes, what is the focus of the research?
1 - Human and veterinary diagnostics
1 - Targeted protein identification, quantification, and interactions
2a. Would it be beneficial to your firm if employees received training in one or more areas of proteomics? 1 Yes 8 No (11% / 89%)
2b. If yes, proteomics training in what areas?
2D SDS Page, Mass Spec, Data analysis software
2c. How many employees would you send to training? 5
3a. Our organization would benefit by being able to hire technicians trained in proteomics.
1 Yes 9 No (11% / 89%)
3b. Skill sets/competencies you would expect from a Proteomics Technician:
Respondent 1 - 2D SDS Page, Mass Spec, Data analysis software
Respondent 2 – Gel electrophoresis and staining, high performance liquid chromatography, high computer skills
4a. Our organization would hire technicians that graduated from a two-year program that included proteomics along with nucleic acid techniques. 1 Yes 8 No (11% / 89%)
4b. If yes, how many technicians would you employ? 2
5a. Over the next five years, does your organization expect to increase staff working with proteomics? 1 Yes 8 No (11% / 89%)
5b. If yes, how many employees do you expect to hire? 2
6a. Does your organization expect to increase spending for proteomics equipment/research over the next five years? 1 Yes 8 No (11% / 89%)
6b. If yes, how much of a spending increase is expected?
Affirmative respondent reports a $10,000 increase.
7a. What is your company's product or service?
2 – Feed additives (22%)
1 – Human and Veterinary Diagnostics (11%)
1 – Plant Made Pharmaceuticals (11%)
1 – Plant genetics (seeds) (11%)
1 – Diagnostic tests (11%)
1 – 1 Germplasm (11%)
1 – Microbiological cultures (11%)
1 – Biotechnology Manufacturing (11%)
7b. How many employees work at your company?
125
45
1
> 5,000
2
20
125
20
83
Total = > 5,421
8a. Name the areas your firm is presently engaged in.
5 – Protein Purification/Separation
5 – Ultrafiltration
5 – PAGE/SDS PAGE
3 – Isoelectric Focusing
4 – 2-D Electrophoresis
4 – Gel Imaging/Analysis
5 – Mass Spectrometry
4 – Liquid Chromotography
3 – Western Blotting
5 – Enzyme Assays
2 – Protein Digestion
2 – Protein Identification
3 – Protein Characterization
1 – Protein Informatics
3 – ELISA
1 – Capillary Electrophoresis
8b. What areas do you plan to add in the next five years?
2 – Protein Purification/Separation
1 – Ultrafiltration
1 – Gel Imaging/Analysis
1 – Mass Spectrometry
1 – Protein Informatics
2 – ELISA
2 – Capillary Electrophoresis
1 – Enzyme Kinetics
1 – Protein Arrays
8c. Other areas present or planned.
1 – Microbiology
1 – General Nutrition
1 – General Aquaculture
2 – Fermentation
1 – Cheese Ripening
1 – Animal performance studies
Academic Training Components Developed With D.O.L Funding
I. Non-Credit Proteomics Curriculum (Workshops)
II. Credit Curriculum Incorporating Proteomics
III. Proteins Lab Overview
IV. Biotech Academy with Des Moines Independent School District
I. Non-Credit Proteomics Curriculum (42 Hours)
Title of Course/Workshop Series: Proteins and Proteomics Technical Training
Description: The success of the human genome project and advances in DNA technology have generated new interest in protein science. This workshop series includes the study of protein structure, protein separation techniques, immunoproteins and proteomics. Each workshop will include practical information for working with proteins and hands-on laboratory experiences. Participants will work with basic to more advanced instrumentation used in the study of proteins. The series is designed for individuals with a background in biology and/or chemistry who want to update or add to their laboratory skills. Enrollment in each workshop is limited.
Workshop I Working With Proteins – The Basics
Six-Hour Training Schedule: M (9/11) 4:30 – 7:30 and W (9/13) 4:30 – 7:30
Description: Participants will explore the structure of proteins starting with amino acids and peptide bonds and advance into the dynamics of protein folding. The composition and properties of solutions useful for working with and storing proteins will be discussed. The lab component of the course will include instructions in the use of micropipettes and the spectrophotometer. Participants will analyze a protein solution for its concentration based on a colorimetric assay.
Competencies:
- Demonstrate an understanding of amino acid chemistry.
1.1 Memorize the general structure of an amino acid.
1.2 Categorize the amino acids according to the properties of the side chains.
- Give a detailed explanation of protein structure
2.1 Draw and list the properties of the peptide bond
2.2 Describe the four structural levels of proteins
2.3 List and describe the forces involved in protein folding and conformation
- Discuss proper handling of proteins.
3.1 List the properties of a solution that is appropriate for protein solutions.
3.2 Describe working and storage conditions that maintain protein integrity.
- Demonstrate the proper use of basic lab equipment
4.1 Accurately pipette a sample using a micropipette.
4.2 Draw a simple sketch of the components of a spectrophotometer.
4.3 Explain the purpose of each component of the spectrophotometer.
4.4 Measure absorbance of samples using a spectrophotometer
- Determine the concentration of an unknown protein solution.
5.1 Prepare a series of standard dilutions for measurement on a spectrophotometer.
5.2 Use spectrophotometer software to generate a standard curve from solutions of known concentration.
5.3 Read a standard curve and calculate the concentration of the unknown sample.
Workshop II Separation Techniques for Proteins
Twelve-Hour Training Schedule: M (9/25), W (9/27), M(10/2), W (10/4) 4:30 – 7:30
Description: Participants will review the structure of proteins and how differences in structures can be used to separate proteins from complex mixtures. A variety of separation techniques will be discussed and students will get hands-on lab experience by purifying a protein starting with a tissue sample from beef heart. Lab work will include liquid chromatography, SDS-PAGE and gel imaging.
Competencies:
- Describe the structure of a protein
1.1 Describe the four structural levels of a protein.
1.2 Explain the dynamics driving protein folding.
1.3 Discuss how protein folding creates important surface and internal protein characteristics.
- Discuss how a single protein can be separated from a complex biological sample.
2.1 List methods used in fractionating cellular samples.
2.2 Describe common methods used in protein purification.
2.3 Explain the underlying mechanism for separation techniques.
- Purify a protein from a biological sample.
3.1 Process a sample to allow cell lysis and the release of soluble proteins.
3.2 Perform centrifugation steps for initial separation of soluble proteins from membrane components of the cell.
3.3 Use liquid chromatography for final protein separation.
- Verify success of a protein purification process.
4.1 Perform SDS-PAGE on samples from purification process.
4.2 Calculate total protein yield.
4.3 Document gel analysis using gel imaging.
Workshop III Immunoproteins – Using Proteins to Study Proteins
Twelve-Hour Training Schedule: M (10/16), W (10/18), M (10/23), W (10/25) 4:30 – 7:30
Description: An overview of the human immune system, antibody structure and antibody-antigen interactions will be discussed. The use of immunoproteins for identification and quantification will be the main focus of the workshop. In the lab, participants will perform an ELISA and a Western blot analysis.
Competencies:
- Discuss the roles of immunoproteins.
1.1 Explain how antibodies are made in vivo.
1.2 Draw and label a generalized model of an antibody.
1.3 Describe the mechanism of action of antibodies.
1.4 Give examples of antigens and the properties of antigens.
- Discuss the importance of antibodies in biotechnology applications.
2.1 Contrast monoclonal versus polyclonal antibodies.
2.2 Draw models demonstrating an enzyme-linked immunosorbent assay (ELISA).
2.3 Explain the importance of each component of the ELISA.
2.4 Draw a flow chart for preparing a Western blot.
2.5 Explain the importance of each step and component of the Western blot.
- Perform an ELISA.
3.1 Wash test plates using an automatic plate washer.
3.2 Load test plates using an automatic plate dispenser.
3.3 Collect data from the test plates using a plate reader.
3.4 Analyze data from an ELISA
- Perform a Western blot.
4.1 Prepare an SDS-gel with a sample for analysis.
4.2 Use electroblotting equipment for protein transfer.
4.3 Analyze for the presence of a protein using immunodetection
Workshop IV Proteomics – Advances in Protein Science
Twelve-Hour Training Schedule: M (11/6), W (11/8), M (11/13), W (11/15) 4:30 – 7:30
Description: Participants will learn about the field of proteomics and why it is important. Various methods for studying the proteome of cells and tissues will be discussed beginning with sample preparation and ending with protein identification through mass spectrophotometry and MALDI-TOF analysis. Participants will prepare a two dimensional gel in the laboratory using isoelectric focusing and SDS-PAGE.
Competencies:
- Discuss the field of proteomics
1.1 Review progress in genomics in recent history.
1.2 List the limitations of genomics in understanding cell function.
1.3 Explain the relationship between the genome and the proteome.
1.4 Discuss the importance of studying the cell proteome.
- Provide an explanation for differential protein expression with cells.
2.1 List stimuli that may alter the protein content of cells.
2.2 Relate differential protein expression to cell specialization.
2.3 Discuss how the protein content of a diseased cell might compare to a healthy cell.
- Discuss various methods in studying the proteome
3.1 List methods employed to fractionate proteins.
3.2 Describe how mass spectrometry can be used to identify fractionated proteins.
3.3 Draw a simple schematic for MALDI-TOF and MALDI-OTOF
3.4 Explain the MALDI-TOF and MALDI-OTOF processes.
- Perform two dimensional gel electrophoresis
4.1 Prepare a sample for isoelectric focusing (IEF).
4.2 Separate proteins in a sample using IEF.
4.3 Prepare IEF sample for SDS-PAGE
4.4 Separate proteins in the IEF sample by molecular weight using SDS-PAGE
4.5 Analyze 2-D images using appropriate imaging software.
- Perform a simulated analysis of MALDI-TOF data
5.1 Describe the meaning of MALDI-TOF data.
5.2 Compare peak data to banding patterns in a gel.
5.3 Discuss data bases available for analyzing MALDI-TOF data.
Course/Workshop(s) Syllabi
Unit I/Workshop 1 – Protein Chemistry Basics
Theory –
1. Protein structure (amino acids, peptide bonds, folding and side chain
interactions)
2. Proteins solutions and storage (pH, ionic strength, temperature,
protease inhibitors)
Laboratory –
1. Micropipettes
2. UV/Vis spectrometry
3. Total protein analysis (UV and colorimetric)
Unit II/Workshop II – Separation Techniques
Theory –
1. Protein structure review
2. Properties of proteins
3. Separation techniques
Laboratory –
1. Protein purification (cytochrome c from beef heart)
2. Analysis of purified protein
a. SDS-PAGE
b. Gel imaging
Unit III/Workshop III – Immunoproteins
Theory –
1. Immune system overview
2. Antibody structure
3. Antigen/antibody interactions
Laboratory –
1. Western blotting
2. ELISA
Unit IV/Workship IV – Proteomics
Theory –
1. Proteomics – definition and usefulness
2. Methods
a. 2-D gels
b. Liquid chromatography
c. Mass spectrophotometry
d. Tandem Mass Spectrophotometry
e. MALDI
f. SELDI
g. Multidimensional fractionation
3. Challenges in proteomics
a. Sample processing
b. Data analysis
Laboratory –
1. Sample preparation
2. Isoelectric focusing
3. SDS-PAGE
4. Gel Imaging and data analysis
5. Tutorial on MALDI-TOF
II. Credit Curriculum Incorporating Proteomics
Note: The following course, developed as part of a federal government project has received state-sanctioned commission approval for credit. The assessment instrument recommended for use prior to enrollment is COMPASS.
BIO 251 - Cell and Molecular Biology/Proteins
A. Unit I
Lecture –
1. Amino acid chemistry
2. Protein structure
3. Cellular functions of proteins
Lab –
1. Methods for handling and storing proteins
2. Laboratory solutions for proteins
3. Spectrophotometric assay to determine total cellular protein concentration
Instrumentation –
1. Balance
2. pH meter
3. Shimadzu BioSpec 1601 spectrophotometer
B. Unit II
Lecture –
1. Methods for characterizing proteins and protein solutions
a. Concentration, molecular weight, purity
b. Solubility
c. Density
d. Isoelectric point
e. Sequencing
f. X-ray diffraction and crystallography
2. Protein synthesis within cells
a. Prokaryotes
b. Eukayotes
3. Protein modifications within eukaryotic cells
4. Protein targeting and trafficking within the cell
Lab –
1. Protein purification project
2. Liquid chromatography methods
3. SDS-PAGE
4. Spectrophotometric determination of concentration and purity
Instrumentation –
1. Biologic LP System (Bio-Rad)
2. Protean II Vertical Electrophoresis (Bio-Rad)
3. Shimadzu BioSpec 1601 spectrophotometer + software
C. Unit III
Lecture –
1. Enzyme mechanisms
2. Metabolic pathways
3. Basic enzyme kinetics
4. Regulation of enzyme activity
Lab –
1. Colorimetric determination of enzyme activity
2. Measurement of enzyme rates
3. Effects of enzyme, substrate and effector concentrations on enzyme activity
4. Enzyme kinetic simulation software
Instrumentation –
1. Shimadzu Model 6100 spectrophotometer + software
2. Kinetic educational software (to be determined)
D. Unit IV
Lecture –
1. Immunoproteins
a. Antibody structure
b. Functional roles of antibodies in the cell
2. Monoclonal vs. polyclonal antibodies
3. Immunoassays
Lab –
1. Western blotting
2. ELISA
Instrumentation –
1. Mini Trans-Blot Cell
2. Synergy HT Multi-Detection Microplate Reader (Bio-Tek)
3. mFill Microplate Reagent Dispenser (Bio-Tek)
4. ELx50 Microplate Washer (Bio-Tek)
Unit V
Lecture -
1. Regulation of cellular protein synthesis
2. Mechanisms of cellular response
3. Protein expression during cell specialization
4. Stress responses in cells
Lab –
1. Preparation of total cell protein
2. Isoelectric focusing
3. PAGE
4. 2-D gel analysis
Instrumentation –
1. Protean IEF System (Bio-Rad)
2. Protean II XL System (Bio-Rad)
3. Chemidoc XRS System (Bio-Rad)
Course Competencies for BIO 251 - Cell and Molecular Biology/Proteins
During this course, the student will be expected to:
1. Demonstrate an understanding of amino acid chemistry
1.1 Memorize the structure of the twenty amino acids
1.2 Categorize the amino acids according to the properties of the side chains
1.3 Generally describe amino acid synthesis in the cell
2. Give a detailed explanation of protein structure
2.1 Draw and list the properties of the peptide bond
2.2 Describe the four structural levels of proteins
2.3 List and describe the forces involved in protein folding and conformation
2.4 Explain the differences between a fibrous protein and a globular protein
2.5 Correlate protein folding with protein synthesis
3. Demonstrate a general understanding of protein function within the cell
3.1 List functional roles of proteins in living systems.
3.2 Explain how proteins bind and interact with other molecules
4. Discuss methods used in the characterization and purification of proteins
4.1 Describe common methods used in protein purification including differential
centrifugation, dialysis, salting out, liquid chromatography (size exclusion,
ion-exchange and affinity).
4.2 Discuss methods for characterizing proteins including ultracentrifugation,
polyacrylamide gel electrophoresis (PAGE), SDS-PAGE, isoelectric
focusing, UV absorption spectroscopy, X-ray diffraction and crystallography
4.3 Explain how proteins can be sequenced and digested
5. Provide a detailed description of processes involved in protein synthesis
5.1 Describe the structures of mRNA, rRNA and tRNA and their roles in
translation
5.2 Define degenerate and wobble as they relate to translation
5.3 Describe how proteins are targeted and modified within the cell and explain
the importance of these events
5.4 Discuss how translation can be regulated by the cell
6. Discuss the mechanism and dynamics of catalytic proteins
6.1 Draw and discuss a simple model of an enzyme catalyzed reaction
6.2 Describe how processes are accomplished through metabolic pathways
6.3 Explain how enzyme activity can be regulated by feedback inhibition,
allosteric interaction, covalent modification and proteolytic activation
6.4 List key features of the active site
6.5 Memorize the Michaelis-Menton equation and explain how it relates to a
saturation profile of an enzyme
6.6 Explain the significance of Km and Vmax values
6.7 Compare and contrast competitive, non-competitive and uncompetitive
types of reversible inhibition
6.8 Use a graph to describe the effects of temperature and pH on enzyme activity
6.9 Discuss the importance of enzymes in biotechnology applications
7. Discuss the roles of immunoproteins and how they can be used as tools in the laboratory.
7.1 Explain how antibodies are made in vivo
7.2 Draw and label a generalized model of an antibody
7.3 Describe the mechanism of action of antibodies
7.4 Contrast monoclonal versus polyclonal antibodies
7.5 Discuss the importance of antibodies in biotechnology applications
7.6 Draw models demonstrating enzyme-linked immunosorbent assays
8. Provide an explanation for differential proteins expression within the cell.
8.1 List and discuss cellular stimuli that may alter the protein content of cells
8.2 Relate differential protein expression to cell specialization
8.3 Discuss stress responses of some cell types
9. Purify a protein
9.1 Store and handle enzymes using appropriate methods
9.2 Assay samples for total protein content
9.3 Prepare cell extracts and sub-cellular fractions
9.4 Separate proteins using chromatographic methods such as size exclusion,
ion exchange and affinity liquid chromatography
9.5 Characterize a protein using electrophoretic techniques
10. Characterize enzyme activity
10.1 Calculate enzyme activity units
10.2 Detect activity using a colorimetric enzyme assay
10.3 Manipulate kinetic data using appropriate software
10.4 Describe the differences of various effectors on enzyme rate
11. Perform a variety of immunoassays including:
11.1 PAGE
11.2 SDS-PAGE
11.3 Western blot
11.4 ELISA
12. Perform two dimensional gel electrophoresis
12.1 Prepare a sample for isoelectric focusing
12.2 Separate proteins in a sample using isoelectric focusing
12.3 Prepare a sample for separation in the second dimension.
12.4 Set up and run a gel for separation of proteins by molecular
weight (second dimension)
12.5 Analyze 2-D gel images using appropriate imaging software
Prerequisites for BIO 251 - Cell and Molecular Biology/Proteins
BIO 104 – Introductory Biology w/Lab
Introduction to basic concepts in biology. Topics include biochemistry, cell structure and function, metabolism and energetics, classical and molecular genetics and the diversity of life at the organismal level. Biology, as an experimental science and biotechnology, will be explored through laboratory experience.
BIO 112 – General Biology I
First semester of biology for majors. Topics covered include chemistry of life, cells, bioenergetics, genetics, evolution, viruses, prokaryotes, and protists.
CHM 132 – Intro to Organic/Biochemistry
A continuation of the study of biochemistry. Organic topics include the structure of organic molecules, the nature and reactions of functional groups and stereochemistry. Biochemistry topics include carbohydrates, proteins, lipids, nucleic acids, enzymes, and metabolism.
MAT 157 – Statistics
Tabular and graphical presentation, measures of central tendency and variability, standard elementary procedures involving the binomial, normal, student's t's, chi squares and f distributions, correlation, regression, analysis of variance, and several nonparametric procedures.
III. Proteins Lab Overview
The following lab equipment is required for delivery of the stated Proteomics instruction:
A. Computer hardware and software compatible with course instrumentation.
B. General college biology/chemistry laboratory equipment plus:
C. UV/Vis spectrophotometer with photometric and kinetic capabilities
D. LPLC
E. Vertical gel electrophoresis system
F. Electroblotting system
G. Microplate reader
H. Gel Imaging system (absorbance and fluorescence capability minimum)
I. Isoelectric focusing system
J. Vertical gel system compatible with IEF system
IV. Biotech Academy with Des Moines Independent School District
Des Moines Area Community College is finalizing the establishment of a Biotech Academy with the Des Moines Independent School District. Enrollment in the Academy will enable high school students to acquire up to 27 credits required by the college's biotechnology program. The Academy courses include the following:
Communication - 9 credits
ENG 105 Comp I
ENG 106 Comp II
SPC 101 Fund of Oral Communication
Social and Behavioral Sciences - 9 credits
HIS 150 US History to 1877
HIS 153 US History to present
HIS 112 West Civilization Ancient
HIS 113 West Civilization Early
PSY 111 Psychology
Math and Sciences - 9 credits
BIO 104 Intro to Biology
BIO 112 General Biology
BIO 225 Marine Biology I
BIO 227 Marine Biology II
CHM 165 General Chemistry I
CHM 175 General Chemistry II
MAT 157 Statistics
MAT 211 Calculus
Ankeny