BIOTECHNOLOGY LABORATORY (BIO-390/590)
SPRING 2006
Place and time:
Tuesdays 1:50 – 5:50.
Discussion and organizational meetings: Tu, 1:50 for ~ 30-50 minutes, HS
202 (We may hold a second, follow-up meeting Th. 1:50 if schedules allow).
Otherwise most of the work will be done in the HS 240 Biotechnology Lab &
the HS 163/145 Bioseparations-Proteomics Labs. Students will have
access at all times via keypads.
Instructor:
Dr. Toivo Kallas
Office:
Halsey 245 (phone 424-7084; e-mail: kallas@uwosh.edu)
webpage (in progress): http://www.uwosh.edu/faculty_staff/kallas
Office hours:
MW 11:30 – 12:30, 1:50 – 2:50. Other times by appointment. Anytime by
phone or e-mail. If I am not in, please leave a message or check one of the
lab rooms (HS 238, 240, or 163/145 Bioseparations-Proteomics Labs).
Lab manual:
Kallas, T. 2006 (under revision). Experiments in Biotechnology.
UW
Oshkosh. Pending completion of the lab manual, we will use the 2003 Lab
Manual (provided in PDF format) and handouts as needed.
Other materials:
Lab notebook and USB memory stick for saving computer data.
Locks & pipetors:
A set of 3-4 micro-pipetors will be checked out to each lab group. Each group
is responsible for returning their pipetors in good condition at the end of the
semester. Students will have to pay for repairs or replacement of damaged or
lost pipetors. Typical replacement cost is $200 - $250. A drawer and lock will
be issued to each lab group. The final grade will depend on return of all locks
and pipetors.
Some useful Biotechnology laboratory references:
Note that many useful references for current protocols are available via web sites.
Copeland, R. A. 1994. Methods for Protein Analysis. Chapman & Hall, New York.
Erlich, H. A. 1989. PCR Technology, Principles and Applications for DNA Amplification. Stockton
Press, New York.
Griffin, H. G. 1994. PCR Technology, Current Innovations. CRC Press, Boca Raton.
Primrose, S. B., Twyman, R. M. and Old, R. W. 2001. Principles of Gene Manipulation. Blackwell,
Oxford.
rd
Sambrook, J and Russell, D. (2000) Molecular Cloning: A Laboratory Manual 3 ed., Cold Spring
Harbor Laboratory.
Instructions for accessing the D2L (Desire2Learn) site: Go to the UW Oshkosh home page, > then
“Resources for: Current Students,” > then “Technology, Desire2Learn.” On the D2L login page, use the
username and password that you use for UW Oshkosh e-mail. Once in D2L, go to the Biotechnology lecture or
lab courses to access the lab manual, presentations, PDF files of articles, and other materials.
Some BIOTECHNOLOGY resources on the internet:
1.
2.
3.
4.
Class Web-site (in progress).
American Society for Microbiology (ASM) home page: http://www.asmusa.org
BioWeb http://bioweb.uwlax.edu/index.htm. (A nice collection of data and tools for genetics and biology.
DOE Joint Genomics Institute, Microbial Genome Projects:
http://www.jgi.doe.gov/JGI_microbial/html/index.html
5. ExPASy Molecuar Biology Server: http://www.expasy.ch/. (A very useful site for molecular biology,
genomics, and proteomics included predicted peptide mass fingerprints.)
6. VIRTUAL GENOME CENTER: http://alces.med.umn.edu/VGC.html.
7. ***THE NATIONAL CENTER FOR BIOTECHNOLOGY INFORMATION: http://www.ncbi.nlm.nih.gov/. (This
site includes the GenBank and other DNA, protein, and genomic databases and extremely useful search
programs such as “BLAST.” Includes the PubMed, MEDLINE literature database.)
8. TIGR (The Institute for Genomic Research): http://www.tigr.org.
9. Kazusa Genome Research Institute: http://www.kazusa.or.jp. (Includes the database for the genome
sequence of the cyanobacterium Synechocystis PCC 6803.)
10. E. coli Genetics Stock Center: http://cgsc.biology.yale.edu/. (a useful site for gene names, maps, etc.)
11. E. coli Genome Center: http://www.genetics.wisc.edu:80/index.html
12. The Chlamydomonas Genetics Center: http://www.biology.duke.edu/chlamy/
13. The Human Genome Research Institute: http://www.genome.gov/
14. The RCSB Protein DATA Bank: http://www.rcsb.org/pdb/. (Site from which to download “.pdb” files of
coordinates for viewing and manipulating protein 3D structures).
15. WEBCUTTER (a nice site for on-line restriction site analysis): http://firstmarket.com/cutter/cut2.html.
16. NET PRIMER (a site that allows downloaded or on-line design of PCR primers. They also carry “Plasmid
Premier” a program for plasmid design): http://www.premierbiosoft.com/netprimer.html
17. SWISS-PROT, University of Geneva, Switzerland: http://expasy.hcuge.ch/sprot/sp-docu.html (Site from
which to download the Swiss-PDB viewer program for protein 3D structures).
18. RASMOL home page: http://www.umass.edu/microbiol/rasmol/ (Site from which to download the RASMOL
and PROTEIN EXPLORER programs for protein structure viewing & manipulation).
19. Frontdoor to PROTEIN EXPLORER: http://molvis.sdsc.edu/protexpl/frntdoor.htm (Site for online use of the
PROTEIN EXPLORER program for protein structure viewing & manipulation).
20. PyMOL: http://pymol.sourceforge.net/ (Site for downloading the PyMOL program for very nice viewing and
manipulation of protein and molecular 3D structures on Mac and Windows platforms.)
21. SINCRIS information server for crystallography: http://www.lcmp.jussieu.fr/sincris-top/ (A nice site for
information and access to programs and databases for viewing and manipulating biomolecules).
22. Nature Biotechnology: http://www.nature.com/nbt/, (available on-line via Polk Library)
23. Trends in Biotechnology: http://www.trends.com/tibtech/default.htm
24. New England Biolabs, Restriction Enzyme Database (NEB-REB): http://rebase.neb.com.
25. Promega Corporation (Madison, WI): http://www.promega.com/.
26. UW-O (Polk) Library: http://www.uwosh.edu/departments/llr/home.html. (Polk Library provides access to
a variety of useful literature databases such as Medline and Web of Science and carries on-line, full-text
subscriptions to several relevant journals including Science, the Nature Journals (including Nature and
Nature Biotechnology, and the American Chemical Society (ACS) Journals. Follow on-screen instructions.
See the Polk Reference Desk or me for help.)
COURSE OBJECTIVES:
1) To provide practical, "hands-on" experience in some of the techniques of cell culture, product
recovery, in vitro manipulation of genes, and data analysis that are fundamental to many areas of
biotechnology,
2) to gain experience in designing strategies and experiments to solve
biotechnological problems. To emphasize the interdependence of basic techniques, and to simulate
conditions found in actual research laboratories, exercises will often be set up sequentially; for
example, DNA introduction into host cell, culture of host cells, gene expression, protein isolation and
purification. Topics to be covered include: analysis of DNA sequence databases, DNA amplification
by polymerase chain reaction (PCR), gene cloning and expression techniques, cell culture, protein
overproduction and purification, DNA and protein gel electrophoresis, protein identification by peptidemass-fingerprinting and MALDI (matrix assisted laser desorption ionization) or ESI (electrospray
ionization) mass spectrometry, and possible DNA sequencing and site-directed mutagenesis.
Students, will have the option to pursue selected or independent topics in greater depth.
2
Experiments & projects: We will begin the semester with an experiment to introduce a plasmid
(pOSH37/GFP, which encodes an engineered “fusion” protein containing parts of the proteins thioredoxin, the
jellyfish Green Fluorescent Protein, and an iron-sulfur protein), into a bacterial expression strain (E. coli
AD494(DE3)) for “overproduction” of the “fusion” protein. We will subsequently purify and analyze this protein,
by protein gel electrophoresis (SDS-PAGE) and MALDI mass spectrometry. The GFP tag provides a very nice
visual (fluorescent!) marker for tracking the protein. Subsequently, students will work on one or both (if time
allows, or parts of both) of the following projects or a project of their own design.
I. Genome analysis/gene-construction/expression project:
Objective: To express a “gene of interest” from a genome sequence database (for example the cyanobacterial
(e.g. Synechocystis) or E. coli databases). Students will choose a gene for a soluble protein of their choice,
design PCR primers for amplification of these genes, order the primers, use these primers to amplify the gene,
clone the PCR product into a plasmid vector (pET32a, Novagen, Madison, WI), and express the cloned gene to
produce the desired protein. If the cloned gene has been translationally fused to the thioredoxin (TRX) gene on
plasmid pET32a, metal-chelating affinity chromatography may be used to purify the fusion protein, and the
protease thrombin may be used to separate the protein of interest from the thioredoxin affinity tag. We will
attempt to characterize the recombinant plasmids by sequencing and by analysis of the protein product. All
students are expected to complete the computer/database/bioinformatics segment of this project.
II. Overproduction from E. coli and purification of recombinant Thermus aquaticus or
Pyrococcus furiousus thermal-stable DNA polymerases:
Objective: To grow a fermenter culture of one of these genetically-engineered, overproducing bacterial strains,
induce expression of the plasmid-borne polymerase gene, purify by FPLC (Fast Protein Liquid
Chromoatography, a form of HPLC) chromatography, and test the polymerase in a PCR reaction. The protein
might be characterized in a variety of ways including MALDI mass spectrometry.
GRADING AND REQUIREMENTS:
Students will work collaboratively in groups of two or three. Master’s students or advanced
undergraduates may serve as team leaders/mentors for less experienced undergraduates.
Requirements are listed below. Most of the grade will be based on lab reports handed in individually by each
student (including 10% for successful results). The main criteria for grading will be clarity of presentation and
understanding of procedures and concepts. Three small (or one small and one major) lab reports are required.
The first report may be re-submitted for a higher score. Additional reports may be used to replace low scores.
Guidelines for lab reports are included in the lab manual as are questions specific to each experiment.
Students are expected to maintain a detailed laboratory notebook where objectives, results, and
conclusions (successes and failures) of experiments are recorded. Lab notebooks will be reviewed midway
during the semester. 10% of the grade may be based on lab notebooks.
10% of the grade will be based on individual and group effort and maintenance of clean and safe
conditions in the lab. GRADING SCALE: 90-100% =A, 80-90% =B, 70-80% =C, 60-70% =D, less than 60% =F.
Grades of AB, BC, and CD will be used for borderline scores.
Genome analysis/gene expression exercise (same
report may be used in both the lecture & lab classes)
due February 28
50
Report: Exp #1, Transformation of E. coli with plasmid
pOSH37/GFP and restriction analysis
due Feb 21 or Feb 28
100
Two additional small lab reports or one major lab
report on a project
due one week after completion
200
Project presentation
week of May 8th
50
Lab notebook and lab maintenance
50
Total
400
3
GRADUATE STUDENTS will be expected to complete both of the semester projects above (or a
project of their own design), show a somewhat more comprehensive understanding of the material,
and will answer additional questions in lab reports.
ATTENDANCE POLICY: All students are required to attend the weekly meeting. The labs will be
accessible at all times via keypads. Students intending to work evenings or weekends need to obtain
an after-hours pass from the Biology Office.
CHEATING POLICY: Interaction and collaboration among students is encouraged but each student is
responsible for submitting his/her own work. Students should be aware of the principle of "academic integrity"
expected at this and other universities. The UW System guidelines state: "Students are responsible for the
honest completion and representation of their work, for the appropriate citation of sources and for respect of
others' academic endeavors." Cheating or obstruction of the efforts of others will not be tolerated in any form.
Students caught cheating will receive an F grade and may be subject to further disciplinary action.
DEADLINES AND LATE WORK: The first lab report will be due February 21 - 28 and the others
within one week of completion of the exercise. All lab reports are due by the last day of the semester.
Assignments handed in late will be receive less than full credit.
TENTATIVE SCHEDULE: The starting weeks of experiments or "mini-projects" are shown. "Miniprojects" as well as experiments will typically take several weeks to complete and consist of several
sequential components. These experiments do not require constant attention and it may be possible
to perform parts of more than one concurrently with the aid of your lab partners. The actual schedule
will depend on class and individual interest. The listed “mini-projects” represent possible activities.
Week
1
Experiment or Project
Components
Exp #1: Transformation of E. coli with plasmid
pOSH37/GFP and restriction analysis
- Plasmid electrotransIntroduction of plasmid pOSH37/GFP into an E. coli expression
formation of E. coli
host. Selection of transformants by antibiotic resistance and - Plasmid isolation and
green fluorescence.
Confirmation of plasmid identity by
analysis by restriction
plasmid isolation and restriction analysis.
The E. coli
digestion and gel
(pOSH37/GFP) strain produced in this experiment will be used
electrophoresis
to produce the GFP fusion protein to be purified in Exp #2.
2
PROJECT
#1:
Genome
analysis/gene- construction/expression. Analysis of sequence databases via the INTERNET. Selection of an open-reading-frame (gene)
for a protein of interest. Design of PCR primers, amplification,
cloning, and expression of the gene. Analysis of recombinant
plasmids by restriction digestion and DNA sequencing.
Possible analysis of expressed proteins by gel
electrophoresis (SDS-PAGE) and MALDI mass spectrometry.
-
4
INTERNET databases
primer design
Gene Construction Kit
(GCK) software
PCR amplification
Gene cloning
Restriction analysis
Gene expression
SDS-PAGE analysis of
protein production
DNA sequencing
Week
3
Experiment or Project
Components
Exp #2: Expression and affinity purification of a GFP fusion protein from plasmid pOSH37/GFP. Fermenter or flask culture of E. coli (pOSH37/GFP, from exp #1 above), gene expression, production of the fluorescent GFP fusion
protein, affinity purification, thrombin cleavage to separate the
iron-sulfur protein segment, analysis by gel electrophoresis (SDS-PAGE), possible immunnoblotting, and MALDI mass spectrometry.
-
5
PROJECT #2: Overproduction and purification of recombinant, thermal-stable DNA polymerases. Fermenter culture of E. coli expressing Thermus aquaticus or
Pyrococcus furiousus DNA polymerases, enzyme purification by FPLC chromatography, and testing of polymerase activity in
a polymerase chain reaction (PCR). Possible protein analysis by gel electrophoresis (SDS-PAGE) and MALDI mass
spectrometry.
8
Exp #3: Protein 3D structure analysis via Swiss-PDB
Viewer and Protein Explorer. Analysis of potential sites
for directed protein modification.
9-14
-
Fermenter culture
Computer analysis
Induction of gene
expression for protein
overproduction
Cell harvest & breakage
Affinity chromatography
(possibly by FPLC)
Thrombin cleavage
SDS-PAGE (possible
immunoblot)
Peptide mass
fingerprinting by MALDI
mass spectrometry
Fermenter culture
Enzyme purification by
FPLC
Functional (PCR) assay
for polymerase activity
Production of a ton of
valuable Taq DNA
polymerase!
Computer-based analysis
of protein 3D structure.
Swiss PDB-Viewer and
Protein Explorer Programs
completion of work in progress
End of semester celebration at Fratello’s! (May 13)
Some ideas for possible miniprojects are listed on the following page:
5
Possible Optional “Mini” Projects
Components
Exp #4 (an option): Site-directed mutagenesis of plasmid pALTER or another plasmid. Creation of a site-directed mutation for restoration of the wild-type lacZ gene (blue colonies on X-gal) in plasmid pALTERTM (Promega) in E. coli . DNA sequence analysis of the mutated site in pALTER or
cyanobacterial pet genes.
-
Oligonucleotide design )
Site-directed mutagenesis
Transformation of E. coli
Possible DNA sequencing
&
computer analysis of DNA
and protein sequences
*Possible alternative or extended projects: a) mutagenesis of
pet genes in cyanobacteria. b) sequence analysis of pet gene
regions.
Exp #5 (an option): Expression and characterization
of an algal (Chlamydomonas) plastocyanin protein from plasmid pOSH-CRE in E. coli. Expression of the
blue-copper protein plastocyanin from a plasmid similar to pOSH37 above, characterization by SDS-PAGE and MALDI
mass spectrometry, and possible determination of the redox
midpoint potential of the copper center.
-
Exp #6 (an option): Expression and characterization
of a cyanobacterial cytochrome c6 protein from plasmids pUC-PetJ1 or pUC-PetJ2 in E. coli.
Expression of soluble, heme-containing proteins from E. coli
carrying one of the above expression plasmids and a second,
helper plasmid encoding genes for heme biosynthesis.
Characterization
by SDS-PAGE
and
MALDI
mass
spectrometry. Possible determination of the cytochrome redox
midpoint potential.
Student designed projects:
For example, design and
construction of a recombinant plasmid or bacterial strain for
use in an independent research project.
Or, for example, 2D gel electrophoresis of
cyanobacterial protein extracts, spot excision and identification
of selected proteins by peptide mass fingerprinting and MALDI
mass spectrometry.
Or, trypsin digestion of a purified protein, separation of
the tryptic fragments by HPLC and characterization of the
tryptic fragments and possible modifications (e.g. covalently
attached heme groups, phosphorylation, or oxidation) by
coupled ESI-MS/MS (electrospray ionization, tandem mass
spectrometry.
6
-
Fermenter culture
Induction of gene
expression
Protein Affinity
chromatography (by
FPLC)
Thrombin cleavage
SDS-PAGE (possible
immunoblot)
MALDI mass spectrometry
Electrochemical redox
midpoint determination
Fermenter culture
Induction of gene
expression in a semianaerobic culture
Protein purification
SDS-PAGE
MALDI mass spectrometry
Electrochemical redox
midpoint determination