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  

What is OpenWetWare?

OpenWetWare is a wiki (an application designed to make it easy to create, edit and organize webpages) for biological science and engineering. It basically provides a common space for people to share information about protocols, materials, research projects, meetings or anything else that might be of interest to users.

Also see OpenWetWare: About.

Why are we using OpenWetWare in 20.109?

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 the course materials on the wiki, they can be updated and improved instantly by everyone (not just the instructors).

For instance, one problem often encountered when teaching people new lab techniques is that the “experts” who are writing up the instructions might forget to include certain steps or neglect to explain certain things because they think they are obvious or just don’t think to include that information. Then often, the person learning a new technique might get tripped up by this lack of detail. We’re hoping that by putting all the 20.109 material online and allowing everyone to edit it, the course material will grow to be more comprehensive and ultimately more useful.

How do I get an account?

Fill out the form at how to join to register for an account on OpenWetWare. You will be sent an email with your account information. Once you have an account, you can login from any webbrowser by clicking the login link at the top right corner of the browser window.

What should I contribute?

Feel free to contribute anything you want to OpenWetWare.

  • Find a typo in one of the protocols? Fix it.
  • Have a suggestion for clarifying a step in a protocol? Post it.
  • Do you hate or love a particular experiment? Explain why on the talk page for that day.
  • Have a question about a homework assignment? Ask it on the talk page for that assignment.
  • Have some data or a gel image that you want to share? Upload it.

Basically use OpenWetWare however it might be useful to you. If you think OpenWetWare is a waste of time, you can write that too. (That’s useful for us to know!)

How do I contribute?

Once you have an account, the best way to learn how to edit the wiki is to look at existing pages. Click the “edit” tab at the top of a page to view the “source code” for the page. If you want to play around to see how things appear, you can do that in the Sandbox or even on your own user page.

If you have a question about how encode something in wiki markup language, try googling. There are lots of reference sources out there since OpenWetWare is based on the same software as Wikipedia. Other reference pages include

Why should I contribute?

There are several reasons

  1. You’ll improve the course for others who come after you.
  2. Editing OpenWetWare is like class participation, it usually can only help you to make a favorable impression on your instructors.
  3. OpenWetWare is fast and easy way to share information, pictures, ideas etc. with others.
Learning Resource Types
Lecture Notes
Presentation Assignments
Written Assignments with Examples