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Component Number: 5-12-06-2-00
TEC credits approved: 40 Master Plan Points
3 Graduate Semester Hours
Instructor: Dr. Yu-Wai Peter Lin
Office/Lab: SNHS 330 Phone: (305)899-3226
e-mail: plin@mail.barry.edu
Office Hours: Posted on office door or by appointment
 | Course (Biotechnology) Outline |
| Instructional Method |
| Class Schedule |
| Daily Time Table |
| Links and Assignments |
Permission to use the Copyright DNA image granted by:Paul A. Thiessen http://cherubino.med.jhmi.edu/~paul
| Disability Statement: |
Students with documented special learning needs may want to inform the instructor so that accommodations may be made, or contact the Barry Office of Services for Students with Disabilities 305-899-3489.
| Course Outline: |
The biotechnology laboratory workshop is designed to give students extensive "hands-on" experience with modern laboratory techniques. Students also learn how to use computers to analyze data and find information on current biotechnology research.
| Goals and Objectives: |
Goals -- The major goal of this workshop is to allow the student the opportunity to acquire a "hands-on" experience in modern biotechnology techniques. A secondary aim is to familiarize students with current scientific literature and the use of the vast biomedical resources on the World Wide Web for biotechnology research.
Objectives -- Upon completion of this course the student will be able to:
1. use the scientific method to solve biotechnology problems.
2. keep an industry standard laboratory notebook and use computers to find information and analyze data.
3. work with microorganisms, recombinant DNA, and gene expression system.
4. construct a cDNA library and determine DNA sequences using dideoxy chain-termination method.
5. clone gene and characterize the gene by restriction mapping, polymerase chain reaction (PCR) and SDS-polyacrylamide gel electrophoresis.
6. increase analytical skills by reading, interpreting and discussing current scientific literature in the field of biotechnology research.
Text:
No required textbook. I will give out photocopies of Laboratory Protocols and necessary background information.
| Instructional Methods: |
This course will follow a "hands-on" workshop and journal club format. The lecture portion of the course will consist of oral presentations given by the instructor and supplemented with overhead transparencies and AV slides. Peer review, cooperative learning, and active discussions with the students are encouraged. Critical reading and discussion of recent scientific journal articles will be part of the regular student activities.
Computer assignments (HyperCELL), Internet connection to biology web site on the World Wide Web (The Biology Place), online journals (BioMedNet- http://biomednet.com), CD-ROM (Current Content), Medline Search (Internet Grateful Med- http://igm.nlm.nih.gov), web connection to the National Library of Medicine, National Center for Biotechnology Information (PubMed- www.ncbi.nlm.nih.gov/pubmed) and simulations (PCGene) will be used during the course.
We will also utilize a number of On-line Scientific Journals through the Internet (Current Opinion in Genetics- http://biomednet.com, The Journal of the American Medical Association- http://www.ama-assn.org, Medline- http://igm.nlm.nih.gov, NIH AIDS information resources, www.biology.com etc.)
For references and links to some hot biology sites on the Internet, please visit the School of Natural and Health Science Instructional Web Page on the World Wide Web at http://socrates.barry.edu/SNHS-plin
Back to Table of Contents
Day 1 DNA Extraction
Central Dogma, DNA Structure and Replication
http://www.biology.com
Instructional Web Portal
Day 2 Recombination DNA Technology
Manipulation of DNA and RNA
mRNA isolation
Restriction Enzyme Digestion of DNA
by Peter
Russell, Reed College
© 1997, Peregrine Publishers, Inc., All Rights Reserved
http://www.biology.com/learning/red/introduction.html
Day 3 Restriction Endonucleases
Agarose gel electrophoresis
Restriction mapping of viral DNA
Restriction Enzyme Analysis
Construction of Restriction Map
A Hypothetical (Tutorial) DNA Mapping
Day 4 Polymerase Chain Reaction
Human Alu Insertion Polymorphism
Chromosome 16, PV-92 Locus
Day 5 Plaque Morphology
Bacteriophage
Infective titer, Serial diultion
Host Specificity
Day 6 Colony Transformation
Genetic engeering, Host bacterium,
Plasmid vector
Day 7 Sequencing of Gonadotropic Hormones
Dideoxy (Sanger) DNA Sequencing
Polyacrylamide gel electrophoresis (PAGE)
DNA Sequence Analysis
Day 8 DNA Fingerprinting (DNA Typing)
VNTR (Variable Number of Tandem Repeat)
RFLP (Restriction Fragment Length Polymorphism)
Day 9 Bioinformatics
Fun with GenBank
Entrez Search
Blast, Protein and Nucleotide Sequence Homology
Clustal, Multiple Sequence Alignment
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> DAILY WORKSHOP SCHEDULE
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[Mon Jun24] [Tue Jun25] [Wed Jun26] [Thu Jun27]
BARRY UNIVERSITY
BIOTECHNOLOGY WORKSHOP
BIO 545 (01)
June 17-June 27, 2002
School
of Natural and Health Sciences Building
SNHS
Room 202
DAILY WORKSHOP SCHEDULE
Welcome to the BIO 545 (01) "Biotechnology Workshop". We hope you find each one of the scheduled activities exciting and useful to your teaching or research projects. We ask that you try to observe the times in order to ensure successful completion of daily workshop activities.
DNA Extraction
Instructional Web Portal
8:00 AM Welcome and Introduction
8:15 AM DNA Extraction
DNA
Structure and Replication
by Peter
Russell, Reed College
© 1998, Peregrine Publishers, Inc. All Rights Reserved.
Development
Team
http://www.biology.com/learning/dnarep/intro.html
9:45-10:00 AM Coffee Break
10:00 AM Leading and Lagging Strand
http://www.biology.com/kimball/D/DNAReplication.html
Messelson and Stahl's Experiment
11:00 AM Rehydrate DNA Samples (for Tuesday Gel electrophoresis)
12:00-1:00 PM Lunch
1:00 PM Pour Agarose Gel (for Tuesday electrophoresis)
2:00 PM The Biology Place
Central Dogma, DNA Structure and Replication
2:30-2:45 PM Break
2:45-4:00 PM Instructional WebPages Construction
Microsoft FrontPage (R)
DNA Gel Electrophoresis
8:00 AM Load Restriction Enzyme-Digested DNA sample, Run Agarose Gel electrophoresis
| Restriction Endonuclease- DNA Electrophoresis; |
9:45-10:00 AM Coffee Break
10:00 AM Ethidium Bromide Staining of DNA
10:30 AM Photodocumentation of DNA Fragments
12:00-1:00 PM Lunch
1:00 PM Standard Curve Construction
http://www.biology.com/learning/molecular/standcur.html
2:00 PM Restriction Enzyme Analysis
2:30-2:45 PM Break
2:45-4:00 PM Partial and Complete Enzyme Digestion
Restriction Enzyme Analysis
8:00 AM A Hypothetical (Tutorial) DNA Mapping
9:45-10:00 AM Coffee Break
10:00 AM Practice Problems, Restriction Map
12:00-1:00 PM Lunch
1:00 PM Restriction Mapping continue
2:00 PM Polymerase Chain Reaction (Pre-Lab preparation)
http://www.dnalc.org/Shockwave/pcranwhole.html
2:30-2:45 PM Break
2:45-4:00 PM Teaching Molecular Biology using the Internet
Laboratory-based Activities
Inquiry-based Curricula
Tutorial on DNA Replication
http://www.biology.com/news/cells/replicat.html
Polymerase Chain Reaction (PCR)
http://www.dnalc.org/Shockwave/pcranwhole.html
PV-92 Locus Amplification
8:00 AM DNA Template Preparation
Cheek Cells Isolation
Prepare Genomic DNA from Cheek Cell Samples
9:00 AM Hair Root Cell Preparation
9:45-10:00 AM Coffee Break
10:00 AM PCR Amplification
Set up and Perform PCR Reactions
12:00-1:00 PM Lunch
1:00 PM Pour Agarose Gel
2:30-2:45 PM Break
2:45-4:00
PM Hardy-Weinberg
Equilibrium
Allele Frequency, Genotype Distribution
Human Alu Insertion
Polymorphism
8:00 AM Load and Electrophorese PCR products
9:45-10:00 AM Coffee Break
10:00 AM Ethidium Bromide Staining
11:00 AM Photodocumentation
12:00-1:00 PM Lunch
1:00 PM Analysis and Interpretation of PCR Results
PCR Primer Construction
2:00 PM Prepare LB and LB+Ampicillin Plates (for Tuesday Colony Transformation)
2:30-2:45 PM Break
2:45-4:00 PM Plaque Morphology Pre-Lab
Plaque Morphology, Bacteriophages
| The Hershey-Chase Experiment |
8:00 AM Ready Soft Agar and Agar Plate for Inoculation
9:00 AM Inoculate Soft Agar with Bacteria
9:45-10:00 AM Coffee Break
10:00 AM Serial Dilution
11:00 AM Host Specificity
12:00-1:00 PM Lunch
1:00 PM Streak Starter Plate (for Tuesday Transformation Experiment), Incubate at 37 degree C overnight
2:30-2:45 PM Break
2:45-4:00 PM Colony Transformation Pre-Lab Preparation
Colony Transformation
Bacterial Transformation
http://www.biology.com/learning/molecular/concept1.html
© 1998, Peregrine Publishers, Inc., All Rights Reserved
Cloning into a Plasmid
http://www.accessexcellence.org/AB/GG/plasmid.html
8:00 AM Insertion of Foreign Gene into E. coli
9:45-10:00 AM Coffee Break
10:00 AM Genetic Engineering, host bacterium,
Plasmid Vector
12:00-1:00 PM Lunch
1:00 PM Analysis of Plaque Morphology Results
2:30-2:45 PM Break
2:45-4:00 PM DNA Sequencing Pre-Lab
DNA Sequencing
© 1998 Cold
Spring Harbor Laboratory
How DNA is sequenced : Sanger Chain Termination Sequencing
http://vector.cshl.org/dnaftb/23/animation/
 |
DNA Sequencing |
Look up DNA Sequencing in the NHGRI Talking Glossary
![[-- DNA sequencing --]](../cell-biology/DNA_sequencing.gif){kind=small}
| defined: | Determining the exact order of the
base pairs in a segment of DNA. |
|
| explained: |
Listen to a detailed explanation. Dr. Eric Green, of the National Human Genome Research Institute's Genome Technology Branch, defines DNA sequencing. |
___________________________________
http://vector.cshl.org/Shockwave/cycseq.html
|
|
© 1998 Cold Spring Harbor Laboratory
Polyacrylamide Gel
Electrophoresis (PAGE)
| Proc Natl Acad Sci U S A 2002 Mar 19;99(6):3712-6 | Related Articles, Books, LinkOut |
| Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4143-4. |
| Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4145-6. |
On the sequencing of the human genome.
http://www.pnas.org/cgi/content/full/99/6/3712
Waterston RH, Lander ES, Sulston JE.
Genome Sequencing Center, Washington University, Saint Louis, MO 63108, USA.
bwaterst@watson.wustl.edu
8:00 AM DNA Sequencing
Dideoxy Chain Termination Reaction
9:45-10:00 AM Coffee Break
10:00 AM Polyacryamide Gel Casting
11:00 AM Analysis of Autoradiogram
DNA sequencing gel
12:00-1:00 PM Lunch
1:00 PM Analysis of Colony Transformation Results
Sense and AntiSense Strand
2:30-2:45 PM Break
2:45-4:00 PM Reading Frames Exercise
 |
Bioinformatics Frequently Asked Questions (FAQ, Bioinformatics.org) |
GenBank (NCBI)
 |
National Center for Biotechnology Information (NCBI) (Tutorials) |
|
|
DNA Data Mining Tools: VacScreen, Blast, Complementary & Sequence Translation, Entrez, Multiple Sequence Aligment (Clustal), Primer Design (GeneFisher), Primers Synthesis (BioSource International), GenBank (Bankit Submission) |
8:00 AM Fun with GenBank
Tutorial on GenBank at the National Center for Biotechnology Information
9:00 AM Entrez Search
9:45-10:00 AM Coffee Break
10:00 AM Protein
and Nucleotide Sequence Search
12:00-1:00 PM Lunch
1:00 PM Basic Local Alignment Search Tools (BLAST)
2:30-2:45 PM Break
3:00 PM Clustal, Multiple Sequence Alignment
4:00 PM Workshop Conclusion and Evaluation
| Dr. Lin's Biology Links (unframed) |
Cycle