20.109 | Fall 2007 | Undergraduate

Laboratory Fundamentals in Biological Engineering


For many of you this will be the first time in a research lab and for others it will not, but it is our goal to make this class a useful and fun introduction to experiments and techniques in biological engineering. There is not time enough to show you everything you’ll need to know if you go on to do research, but after taking this class you should feel confident and familiar with some fundamental experimental approaches and lab protocols. You will develop good habits at the bench, ones that will increase the likelihood of success in your work and ensure the health and safety of you and those around you. By the end of the semester, you should also be aware of good scientific practice, having had some experience with report writing, notebook keeping and publicly presenting your data. All of us involved in teaching 20.109 hope you will find it a satisfying challenge and an exciting experience that has lasting value.

Course Meeting Times

Lectures: 2 sessions / week, 1 hour / session

Labs: 2 sessions / week, 4 hours / session

How 20.109 Varies from Term to Term

20.109 is offered twice per year in the fall and spring semesters, with rotating instructor responsibilities. Reflecting the instructors’ specific expertise and the evolving biological engineering field, the topics covered will change over time. The fall term focus, led by Natalie Kuldell, reflects her molecular genetics, microbiology, and synthetic biology expertise. The spring term focus reflects Agi Stachowiak’s biomaterial and tissue engineering background.

Layout of the Class: Labs and Assignments

You will perform three series of experiments (called ‘modules’) over the course of the semester. The modules differ in length and in the ways you will be assessed. The experiments and major assignments are:

1 Genome engineering Portfolio
2 Expression engineering Written report
3 Biomaterials engineering Oral presentation plus written text

You will be working as pairs throughout the semester, but you will submit individual lab reports and give individual oral presentations.

In addition to the module assignments listed above, there are several other forms of required coursework.

Journal Club

Each student will give an oral presentation on a paper associated with either Module 1 or Module 2.

Daily Lab Quizzes

These are intended to refresh your memory about the experiment you are performing. They will not be hard and should take no more than 5 minutes at the beginning of lab. [These quizzes are not provided in this OCW site .]

Homework Assignments

These will vary considerably in content and points associated with each assignment. You may be asked to perform a calculation, draw a conclusion, and/or make a figure using the data you have collected. The homeworks can be found in the “for next time” section of each lab day. You can work with your lab partner, friends and teaching assistants on these assignments but you will hand in individual assignments.

Laboratory Notebooks

You will record your data on the white pages of a bound notebook. The yellow, duplicate pages will be collected and evaluated by the teaching assistants. Be sure you follow the guidelines for lab notebooks. Late work will be penalized 1/3 of a letter grade for each day late and will not be accepted after a week.

OpenWetWare Wiki

Since 20.109 is a lab class, we think the students, TAs and instructors would benefit from having a shared space in which to discuss experimental protocols and results. By putting all course materials on the 20.109 (Fall 2007) OpenWetWare Wiki , they can be updated and improved instantly by everyone (not just the instructors).

More about OpenWetWare use in 20.109

Lab Attendance

Lab attendance is mandatory and there are no make-up labs. A family crisis or severe illness requiring attention from the infirmary and prohibiting you from all your coursework are acceptable reasons for missing lab and every effort will be made to accommodate you in these exceptional circumstances.


Genome engineering assignment 25%
Expression engineering assignment 25%
Biomaterial engineering assignment 20%
Journal club oral presentation 10%
Daily lab quizzes 5%
Homework 10%
Laboratory notebooks 5%


Each class session in the following calendar actually consists of a 1 hour lecture and a 4 hour lab.

1   Orientation  
Module 1: Genome engineering
2 1 Start-up genome engineering  
3 2 Agarose gel electrophoresis  
4 3 DNA ligation and bacterial transformation  
5 4 Examine candidate clones  
6 5


Lecture on oral presentations

7 6 Western analysis  
8 7

Probe western

Lecture on environmental health and safety

First draft of genome engineering portfolio parts 1, 2, and 4 only is due before you arrive in lab
9 8 Oral presentations First draft of genome engineering portfolio part 3 only is due before you arrive in lab
Module 2: Expression engineering
10 1 siRNA design and start-up in cell culture  
11 2 Transfection  
12 3 Luciferase assays and RNA prep  
13 4

Journal article discussion

Lecture on written reports and scientific writing

14 5 cDNA synthesis and microarray  
15 6 Microarray data analysis  
16 7 Lecture on high throughput technologies; no lab First draft of expression engineering report is due by 5 PM on the day you meet for lab
17 8 Oral presentations  
Module 3: Biomaterials engineering
18 1 Growth of phage materials  
19 2 Phage nanowires  
20 3 TEM  
21 4 Phage by design, part 1  
22 5 Phage by design, part 2  
23 6 ECD assembly  
24 7 Oral presentations  
25 8 End of term celebration  
Learning Resource Types
Lecture Notes
Presentation Assignments
Written Assignments with Examples