Courses:

Laboratory Fundamentals in Biological Engineering >> Content Detail



Syllabus



Syllabus

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.



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:


MODULE #TOPICSMAJOR ASSIGNMENTS
1Genome engineeringPortfolio
2Expression engineeringWritten report
3Biomaterials engineeringOral 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.



Grading



ACTIVITIESPERCENTAGES
Genome engineering assignment25%
Expression engineering assignment25%
Biomaterial engineering assignment20%
Journal club oral presentation10%
Daily lab quizzes5%
Homework10%
Laboratory notebooks5%



Recommended Citation


For any use or distribution of these materials, please cite as follows:

Angela Belcher, Drew Endy, Natalie Kuldell and Agi Stachowiak. Course materials for 20.109 Laboratory Fundamentals in Biological Engineering, Fall 2007. MIT OpenCourseWare (http://ocw.mit.edu), Massachusetts Institute of Technology. Downloaded on [DD Month YYYY].



Calendar


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


SES #MODULE DAYTOPICSKEY DATES
1Orientation
Module 1: Genome engineering
21Start-up genome engineering
32Agarose gel electrophoresis
43DNA ligation and bacterial transformation
54Examine candidate clones
65

M13.1

Lecture on oral presentations

76Western analysis
87

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
98Oral presentationsFirst draft of genome engineering portfolio part 3 only is due before you arrive in lab
Module 2: Expression engineering
101siRNA design and start-up in cell culture
112Transfection
123Luciferase assays and RNA prep
134

Journal article discussion

Lecture on written reports and scientific writing

145cDNA synthesis and microarray
156Microarray data analysis
167Lecture on high throughput technologies; no labFirst draft of expression engineering report is due by 5 PM on the day you meet for lab
178Oral presentations
Module 3: Biomaterials engineering
181Growth of phage materials
192Phage nanowires
203TEM
214Phage by design, part 1
225Phage by design, part 2
236ECD assembly
247Oral presentations
258End of term celebration

 








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