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Credit:
1 course unit
Elective course
Motivation:
The Bioengineering curricula at Penn and other BE/BME programs require extensive biology. BE students take 3 biology courses, BE121 (+lab), molecular biology, BIOL202, Cell Biology, and BIOL215 Vertebrate Physiology (or an equivalent physiology course). However, our students do not have an opportunity to be exposed to the basic engineering applications and design principles enabled by the biology. This course fills the gap.
Catalog Description:
This course is designed to expose students to the principles underlying engineering microbial systems. The fundamentals of DNA, RNA and proteins will be reviewed. An emphasis will be placed on recombinant DNA technologies, mutagenesis, cloning, gene knockouts, altered gene expression and analysis, with practical real world examples of their application. Throughout this course, we will also focus on case studies and critical literature evaluation.
Objectives:
Provide the scientific tools to design an application based on a microbial engineering platform.
1. Fundamental molecular biology of bacteria
2. Technology for microbial modification, with engineering approach
3. Analysis/evaluation of wild type and modified organisms
4. Identification and evaluation of existing technology/applications (academic, industrial, journal)
Prerequisites:
Biol 121, Biol 202, BE209, BE210 or permission of instructor
Grading:
45% Homework/quizzes
15% Midterm
25% Final Paper: Critically evaluate journal article
15% Final Presentation: Present critical review of journal article
Textbook(s) and/or
other Required Material:
Required:
Molecular Genetics of Bacteria, L. Snyder and W. Champness, ASM Press 2007.
Reference:
Molecular Biotechnology, B. Glick and J. Pasternak, ASM Press 2007.
Tools:
This course is designed around two core libraries: (1) a library of data collected from actual patients and devices, and (2) a library of algorithm routines that the students will use during the course to analyze the data archive. Homework will utilize these tools, and develop increasing proficiency gradually over the semester, culminating in their final projects.
Topics Covered:
Week 1:
Fundamentals of prokaryotes
Microbial Growth and Fermentation: O2, T, pH measurement, control, equations; Bacterial life cycle, stress response, small molecule (antibiotic) production
Week 2:
DNA – structure, function, replication (including errors), genome structure
RNA – structure, function, production, regulation
Week 3:
Protein - structure, function, production, regulation
Case study: Cell free protein synthesis
Week 4:
Recombinant DNA (rDNA) technology: Discovery, Enzymes involved, Fundamental principles, PCR
rDNA for new products – examples: LS9
rDNA for affecting bacterial performance – examples: E. coli used in small molecule production, modified E. coli for laboratory use (removal of transposases etc.), E. coli minimal genome project
Case study: Cohen and Boyer
Week 5:
Cloning and Plasmids – Fundamental Construction, Techniques, Overexpression, Gene expression regulation, Conjugation/transformation, Transduction, Phages, Temperature sensitive plasmids
Guest Speaker: Jonathan Viventi, MSEE, UPenn
Week 6:
Gene knockouts: Fundamentals, Homologous recombination, Cosmid library
examples: Antibiotic production competing pathway removal, Laboratory functionality studies
Week 7:
Mutagenesis: Natural mutations – rate/type, stress response, Site-directed mutagenesis, Error-prone PCR, UV/Chemical, Transposons
Week 8:
Mutagenesis Case Studies: Example: Maxygen genome shuffling
Midterm
Week 9:
Analyses:
Whole cells (microscopy)
Separation (centrifugation, chromatography, electrophoresis)
RNA, DNA, Protein, Arrays (Total NA, Protein), Snp arrays
Specific component detection (Immunodetection…)
Protein sequence/structure determination (edman degradation, mass spec, nmr, x-ray crystallography)
DNA Sequencing
Case Study: Pacific Biosciences
Weeks 11 - 14:
50% Student presentations of literature
50% Technology application case studies
Examples
- Health: Artemisinin Project (Keasling)
- Tools: Pacific Biosciences – Enzyme modification and technology development for DNA sequencing
- Energy: LS9
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