Honors Biotechnology Research Project
2013-2014
Year: 1 credit
Junior/Senior Honors Level
Sr. Mary Jane Paolella
Prerequisite: 3.67 in Biology and Chemistry
Text: Prepared by the Instructor
Readings from: journal articles and recently published materials
DESCRIPTION: Biotechnology and Ethics explores the science of genetic engineering through a class
research project. With an experimental focus, students receive the molecular background and the
laboratory techniques, culminating in DNA sequencing and analysis. They chose a target organism(s),
target gene(s), design primers, amplify their gene of interest using PCR, and sequence the gene. They
finally prepare and present a poster with their findings to the scientific community and/or offer
workshops for the educational community.
Student Objectives:
-use a constructivist approach utilizing a target organism and genes
-work in conjunction with the university/government partnerships, but independently of them
-employ alternative assessments:, concept and Vee mapping
-integrate bioinformatics as a tool to obtain and analyze data
-publish and present class research results via poster at a scientific meeting
-publish results in GenBank
Grading and Assessment:
Data notebook with folder are required. Lab reports are completed in Vee Map format complete with
concept map and flow chart, typed. All handouts, completed assignments and tests are organized in the
folders.
Grading Policy: tests/concept maps: 40%; labs: 30%; homework:10%; quizzes: 20%
Make-up Work: Students are expected to be prompt and prepared for class. In the event of mssing
homework, the student is expected to email the instructor if work is not available on the website. Should
a student be absent on the day of a test, she is expected to make up that test ON the day of her return,
either during free time or after school. Make up work for an extended illness (more than 2 class days,
will be arranged with the teacher.)
Note: because of the orientation and focus of this class, there are more lab assignments than tests.
COURSE OUTLINE:
Introduction to Biotechnology
Mollusc Target Organism provided by NOAA: National Oceanic and Atmospheric
Administration: the Northeast National Marine Fisheries Laboratory
Choice of Gene of Interest for research and analysis
Background Information:
Bioinformatics Introduction: Research using NCBI and US Government/University websites
Molecular level
Structure and Function of Nucleic Acids: Central Dogma revisited
Post Transcriptional and Post Translational Modification
RNA folding, RNAi, snRNA
Protein structure and function
Comparison of mtDNA to nDNA
Use of NCBI: Structure, Cn3d and OneDViewer
DNA Extractions and Purification
DNA Quantification by UV Spectrophotometry/Biophotometer/Nanodrop
Use of Bioinformatics Tools for data and analysis
NCBI: PubMed, OMIM
ClustalW as an alignment tool
Primer3 and idtDNA
Primer Design and PCR Protocol
Use of NCBI: Taxonomy Browser
Primer math and template calculations
Solution preparations
In vitro DNA Synthesis: PCR of gene of interest
Analysis of PCR Product by Agarose Gel Electrophoresis
Photodocumentation
Purification of PCR Product
Quantitation of DNA Template: PCR Product
Automated DNA Sequencing: ABI Prism 310 Genetic Analyzer
Primer math and template calculations for sequencing
Cycle Sequencing Reactions
Purification of Extension Products
Resuspension, Sequencing and Conversion of Raw Data
Data Analysis by NCBI: BLAST
\
Ensembl
UCSC Genome Browser