University of Wisconsin–Madison

Team Research Projects in Biochemical Engineering

Professor John Yin, Chemical and Biological Engineering 560

Team Project 1: Engineering Beyond Natural Boundaries

The chemicals of life include lipids, sugars, nucleic acids, and proteins, as you have encountered in your biology and biochemistry coursework and reading.  Today an active and growing area of research is to biochemically expand the repertoire of biological products and processes by use of non-natural building blocks.  For example, one may incorporate non-natural amino acids into proteins, non-natural bases into nucleic acids, or non-natural sugars into polysaccharides.  These examples will serve as topic areas for your group assignment.

Review the recent literature in your topic and prepare a group presentation on the topic**.  Address the following:

  1. Why would anyone want to use non-natural building blocks in the synthesis of proteins, nucleic acids or polysaccharides? Give technological motivations. 
  2. What challenges does one encounter when using non-natural building blocks? Provide at least one specific example to show how this challenge has been overcome.
  3. Describe how a specific non-natural product has been characterized and how its offer new properties or activities. What opportunities are opened?
  4. Discuss the broader technological (engineering) challenges to making and applying such non-natural products.

**In-class group-work on Thursday, 4 Feb 2016

Deliverables due on Thursday, Feb 11, during class:

  • Title and Abstract, 300-500 words
  • Group presentation to the class (10-12 min) + Q&A (3 min)
  • Annotated bibliography of references used in the assignment. Annotations should be 1-2 sentence descriptions of how the specific reference was useful to you.  For examples of brief annotations, see cited reference lists in articles in Current Opinion in Biotechnology.

Team Project 2: Research Proposal

A broad goal of biochemical engineering is to apply chemical and biological engineering approaches to define and solve problems that impact human health, energy, agriculture, the environment and food. An aim of this course is to provide an opportunity for you to gain research experience as a member of a team.  Each team will:

  • identify a societal need/problem, determine its magnitude, and quantify specifications for a solution to the problem.
  • supply evidence that demonstrates the feasibility of the proposed solution. Evidence may be drawn from the literature, or theoretical or computational studies.  In addition, teams should propose relevant experimental or theoretical/simulation studies to demonstrate the feasibility of their idea.
  • learn to work effectively as a member of a team and communicate your idea to your peers and to Prof. Yin

Each team will prepare a 10-12min presentation (plus 3 min questions), and a 12 page double-spaced proposal that describes a novel approach to address an important societal need. The project should be completely new, not based on previous project(s) you may have proposed for other classes or related to research being actively pursued anywhere, as detected by a keyword websearch. The 12 pages includes at 3500-word maximum that include all tables and figures.  The bibliography does not fall within the length limits. Each team will meet with Prof. Yin: 15 min team meeting to present and briefly discuss preliminary ideas (aim to meet before Spring recess).

Presentations & Written Proposals due on Tuesday, 3 May 2016

Project Summary (1 page max)

The proposal must contain a summary of the proposed activity suitable for publication, not more than one page in length. It should not be an abstract of the proposal, but rather a self-contained description of the activity that would result if the proposal were funded. The summary should be written in the third person and include a statement of objectives and methods to be employed. It should be informative to other persons working in the same or related fields and, insofar as possible, understandable to a scientifically or technically literate lay reader.

Project Description

The Project Description should provide a clear statement of the work to be undertaken and must include: objectives for the period of the proposed work and expected significance; and relation to the present state of knowledge in the field. The Project Description should include: Specific aims (2 or 3, one page max), Research Strategy, Significance (background), Innovation (1 page max), Research Plan (addressing how each specific aim will be carried out).