Course: BIOEN 498/599 – Biofilm Engineering

Instructor: James Bryers

UW General Catalog Course Description: Develop a quantitative understanding of the complex biological systems known as biofilms. Advanced concepts of microbiology, biochemistry, and immunology will be integrated with principles of stoichiometry, kinetics, and transport phenomena in order to critically analyze, interpret, design, and control biofilm processes.

Prerequisites: recommended MATH 307 or AMATH 351, BIOEN 335, BIOL 220

Overview: This course combines the fundamentals of microbiology, immunology, molecular genetics coupled with molecular diffusion, reaction kinetics, and convective transport to analyze and control bacterial biofilms. Through a diet of published literature and lectures, the student will be exposed to the breadth and depth of bacterial biofilms as they impact engineered and medical systems.

Textbook: None required.
Recommended readings for references/amplification:
Bryers, J. D., (Editor) Biofilms, Second Edition, J. Wiley Interscience, New York, NY (2000).
Biofilms: The Hypertext Book. http://www.hypertextbookshop.com/biofilmbook/v004/r003/ Gavin Lear and Gillian D. Lewis (Editors).
Microbial Biofilms: Current Research and Applications, Caister Academic Press, Norfolk, UK (2012).
Plus any number of a hundred books on special topics with biofilms; Google “Biofilms Books”.

Learning Objectives: Students will demonstrate the ability to analyze and design complex biological systems that comprise bacteria interacting with mammalian cells, within engineered systems and medical environments.

Course Grading:
Undergraduate students:
Consists of 2 exams (100 points each) and 4-5 homework assignments (total 100 points) [maximum course points = 200; Grade based on % acquired course points].

Graduate students:
Consists of 2 exams (100 points each), 4-5 homework assignments (total 100 points), and a term paper for the graduate (100 points) [maximum course points = 300; Grade based on % acquired course points].

Computer Use: Requires word-processing software and PDF conversion software for preparing homework assignments; Internet deposit of homework assignments. Use of Matlab, Mathematica, or Comsol for biofilm system mathematical modeling exercises.

Course Topics:
Week Lecture Topics
1 Intro: The Good, the Bad, and the Ugly of microbial biofilms
2 The Microbiology of Biofilms
3 Processes that Govern the Formation and Persistence of Biofilms
4 Processes that Govern the Formation and Persistence of Biofilms
5 Processes that Govern the Formation and Persistence of Biofilms
6 The Engineering of Biofilm Reactors (how to make Lot$$ of money!!)
7 Diagnostics Techniques for Analyzing Biofilms
8 Controlling (non-medical) Biofilms
9 Medical Biofilms; Interactions of bacteria and the host immune system
10 Medical Biofilms; Exogenous approaches to Controlling Biofilms

Outcomes Addressed By This Course:
A. An ability to apply knowledge of mathematics, science and engineering.

Portions of this course will use applied mathematics directed toward developing students’ ability to describe complex biological processes that combine fluid movement and biological reaction. Homework exercises and examinations will be used to assess student competency in this outcome.

L. An understanding of biology and physiology.

A major portion of this course will discuss the basic microbiology and immunology of medical biofilms; their formation, persistence and virulence.  Certain homework exercises will be used to assess student competency in this outcome.

M. The capability to apply advanced mathematics (including differential equations and statistics), science, and engineering to solve the problems at the interface of engineering and biology.

This entire course uses applied mathematics directed toward developing students’ ability to  describe complex biological processes that combine fluid movement and biological reaction.  All  homework exercises and examinations will be used to assess student competency in this outcome.

Relationship of course to departmental objectives:
The goal of our BIOEN program is to prepare our graduates for industry, graduate programs, and medicine. BIOEN 499/599 contributes to the department’s Program Educational Objectives as follows:

  1. Pursue educational opportunities and/or employment in bioengineering-related fields, such as medicine, device development, or biotechnology.
    Earn advanced degrees and/or obtain employment in bioengineering-related fields such as medicine, device development, and biotechnology.
  2. Advance their careers by obtaining appropriate educational and professional qualifications. The course is almost entirely journal article and literature research driven providing an excellent experience in professional growth.
  3. Serve their profession and community. The course does not directly address this objective.
  4. Contribute to responsible development of new technical knowledge. The course is almost entirely journal article and literature research driven providing an excellent experience in developing new technical skills and knowledge.
  5. Take leadership roles in addressing domestic or global bioengineering-related issues. The course does not directly address this objective.

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