Syllabus & Schedule

ChE 130, Biomolecular Engineering Laboratory, Spring 2015
Course Syllabus
Course Description
This laboratory focuses on the design, construction, and characterization of engineered biological systems and is
comprised of: (i) open-ended research projects emphasizing experimental techniques in biomolecular
engineering, (ii) oral presentations, and (iii) written reports of scientific results. The course has two phases – a
tutorial phase and a project phase. During the tutorial phase, all students complete the same lab exercises.
During the project phase, students work on different research problems in the general areas of biomolecular
engineering and synthetic biology. Emphasis is on projects that apply rational design strategies, subject to
constraints, toward engineering biological systems that exhibit programmed behavior.
Instructors
Professor David A. Tirrell
office: 225 Spalding
phone: x3140
e-mail: [email protected]
admin. assistant: Anne Hormann, 221 Spalding
Dr. Mike Vicic
117 Spalding
x4613
[email protected]
Head Teaching Assistant
The head teaching assistant leads the tutorial at the beginning of the course and provides support as a technical
consultant and expert during the project phase of the course. The head teaching assistant is NOT the primary
contact for help, advice or questions during the project phase of the course.
Michael Srienc ([email protected])
Project Teaching Assistants
Project teaching assistants are your primary contacts during the project phase of the course, and you’ll get to
know them during the tutorial phase of the course.
Bradley Silverman ([email protected])
Yong Wu ([email protected])
Emily Wyatt ([email protected])
Reference Materials
Course website: http://che130.che.caltech.edu/
Laboratory handouts: Protocols will be distributed as .pdf files via email and the course website.
Textbook (recommended): Gene Cloning and DNA Analysis – An Introduction, Sixth edition, T. A. Brown, Blackwell
Publishing, 2010.
Available in the Laboratory: Molecular cloning: A laboratory manual, 3rd edition, J. Sambook and D.W. Russell,
Cold Spring Harbor Laboratory Press, 2001.
Available in Millikan Library: Molecular Biology of the Cell, 4th edition, B. Alberts, et. al., Garland Science, 2002.
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ChE 130, Biomolecular Engineering Laboratory, Spring 2015
Course Meeting Times
Course Syllabus
Lecture: During the tutorial phase, one lecture will highlight background information, current technologies and
experimental techniques to support the tutorials and project execution. Plus, project options will be discussed.
All Students: 4/1 (Wednesday) 3-4pm in 102 Spalding
Project Pre-Proposal: Midway through the tutorial phase, each student will meet with Prof. Tirrell (and maybe
others) to verbally discuss their proposed project. Each student will spend 5-10 minutes discussing and providing
their rationale for their design strategy, their set of constructs, and their objectives. You don’t need slides, but
you should come with a list of constructs (e.g., how many different promoters or ribosome binding sites and the
characteristics of the promoter or RBS sequences). Meetings will be scheduled during the following times:
All Students: 4/8 (Wednesday) 1-5:30pm in 225 Spalding
Project Updates: During the project phase, each student will twice meet with Prof. Tirrell and Dr. Vicic to receive
individualized feedback and guidance to achieve project success. Each meeting will be 5-10 minutes in duration,
and will tentatively be scheduled during the following times:
Seniors: 5/6 (Wednesday) 2-4:30pm & 5/20 (Wednesday) 1-3:30pm in 225 Spalding
Juniors: 5/13 (Wednesday) 3-4:30pm & 5/21 (Thursday) 3-4:30pm in 225 Spalding
Laboratory: During the tutorial and project phases, students and TAs will be in lab during the scheduled lab
times. Two sections are scheduled:
Section #1: Mon/Fri, 1-4pm, 16 & 17 Braun
Section #2: Tue/Thu, 1-4pm, 16 & 17 Braun
Students are only allowed in the laboratory when at least one graduate teaching assistant, staff member or
faculty member is present. Because of this restriction, we are currently working through scheduling and resource
issues to provide as much lab time as possible during the project phase, but available lab time will be a significant
constraint on your design options. As soon as we finalize these additional times – likely 11pm – 1am multiple
nights per week – we will announce them, but project lab times will definitely include the lab times shown above.
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ChE 130, Biomolecular Engineering Laboratory, Spring 2015
Course Syllabus
Course Outline
Weeks 1-3: General Laboratory Training (with recommended reading)
You should read and understand the protocols before the lab session and you may want to read the
recommended text if you want to learn additional background material.
Laboratory:
First Meeting (one hour): safety training.
Reading: None
Tutorial, Day 1 (three hours): growing bacteria on solid media; growing bacteria in liquid
culture; isolating plasmid DNA.
Reading: Protocols 1, 2, 3 & 4; Brown, Chapters 1, 2 & 3
Tutorial, Day 2 (three hours): amplifying DNA segments through PCR; digesting DNA; analysis of
DNA by gel electrophoresis.
Reading: Protocols 5, 6 & 7; Brown, Chapters 4 & 9
Tutorial, Day 3 (three hours): ligating DNA; transforming cells.
Reading: Protocols 8 & 9; Brown, Chapters 5 & 6
Tutorial, Day 4 (three hours): colony PRC; measuring optical density and fluorescence (time
course); sequencing.
Reading: Protocols 5, 6, 11 & 12
Lectures:
Week 1: Overview, background and description of available projects. General design strategies that can
be used for any project in biomolecular engineering, focusing on those applicable to this year’s projects.
Weeks 2-10: Laboratory Design Project (Approximate)
Week 2, 3 & 4: Design engineered system; order primers; list materials & supplies.
Weeks 4, 5 &6: Construction of system.
Weeks 7 & 8: Initial system characterization and analysis.
Weeks 9 & 10: Additional construction, final system characterization and analysis.
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ChE 130, Biomolecular Engineering Laboratory, Spring 2015
Course Syllabus
Grading Scheme
Time Management, Preparedness & Results
Project Proposal
Tutorial Data Summary
Project Updates (2)
Project Report
Project Presentation
20%
7.5%
7.5%
15%
25%
25%
Submitting Work
Proposals, Plans and Reports: Before 4pm PDT on the due date, send an email to [email protected]
with a .pdf of your written work (e.g., proposal; project plans; data summary; project report). Your work will
automatically be distributed to both instructors and all of the TAs.
Presentations: At least 15 minutes before the start of the presentation period, send an email to
[email protected] with a .pdf and a .ppt of your presentation. Your work will automatically be
distributed to both instructors and all of the TAs. We will then download all presentations on a single computer
so that the presentation periods will proceed quickly.
Project Updates: At the beginning of each meeting, or shortly after, you should distribute a handout or submit an
electronic file. If you bring a handout, bring two copies – one for each. If you submit an electronic version,
email the file to [email protected].
Policy for Late Work
•
•
•
There will be a cumulative 10% deduction for every hour an assignment is late. If the assignment is more
than nine (9) hours late, the student gets no credit. If an assignment is due at 4:00PM, it is considered:
o one hour late (10% deduction) if submitted between 4:01-5:00PM;
o two hours late (20% deduction) if submitted between 5:01-6:00PM;
o and so on.
We will provide extensions for health reasons and family emergencies at any time before the assignment
is due. Send an email to Mike Vicic.
Extensions for non-emergency reasons (e.g., interviews, athletic trips, etc.) are handled on a case-by-case
basis as long as the request is made at least 24 hours in advance of the time the assignment is due. Send
an email to Mike Vicic.
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ChE 130, Biomolecular Engineering Laboratory, Spring 2015
Course Syllabus
Week 1
SCHEDULE: DAYS, TIMES & DETAILS SUBJECT TO CHANGE (LAST UPDATE 4/1/2015)
Monday
Tuesday
Wednesday
Thursday
Friday
Mar 30
31
2
3
Lab Intro &
Safety Training
Lab Intro &
Safety
Training
7
Apr 1
Lecture: Design
Strategies & Projects
3-4 PM (102 Spldg)
Tutorial, Day 1
Tutorial, Day 1
8
9
10
Pre-Proposal
Individual Mtgs. (All)
1-5:30 PM (225 Spldg)
15 NO MEETING
Tutorial, Day 3
(w/ Primer Design
Tutorial)
16 LAB CLOSED
Tutorial, Day 3
(w/ Primer Design
Tutorial)
17 LAB CLOSED
Week 3
Week 2
6
Tutorial, Day 2
Project Selection
Completed (All)
13
Tutorial, Day 2
Tutorial, Day 4
Tutorial, Day 4
OPTIONAL OFFICE
HOURS WITH TAS
3-4PM (make appt)
21
22 NO MEETING
Project Plan, Pt 1
(Design; Primer Seq.;
Construction Plan)
(Model-Based Proj)
Due: 4PM PDT
29 NO MEETING
Project Plan, Pt 2
(Characterization Plan)
(Model-Based Proj)
Due: 4PM PDT
6
Project Update #1
(Seniors)
2-4:30PM (225 Spldg)
13
Project Update #1
(Juniors)
3-4:30PM (225 Spldg)
20
Project Update #2
(Seniors)
1-3:30PM (225 Spldg)
14
One Page Proposal
(All Students)
Due: 4PM PDT
Week 4
20
23
24
30
Project Plan, Pt 2
(Characterization Plan)
(Library-Based Proj)
Due: 4PM PDT
May 1
7
8
14
15
21
Proj. Update #2
(Juniors)
3-4:30PM (225 Spldg)
22
27
28
4
Tutorial Data
Summary (All)
Due: 4PM PDT
11
5
18
19
25 LAB CLOSED
Memorial Day
(Institute Holiday)
26
27 NO MEETING
28
29
Jun 1
2
3
Proj. Presentations
(Seniors)
1-6PM (102 Spldg)
4
5 LAST LAB DAY
Project Report
(Seniors)
Due: 4PM PDT
8
9
10
Proj. Presentations
Page 5
(Juniors)
3:30-6:30PM (102
Spldg)
11
12
Project Report
(Juniors)
Due: 4PM PDT
Week 5
Week 6
Week 7
Week 8
Week 9
Week 10
Finals
Project Plan, Pt 1
(Design; Primer Seq.;
Construction Plan)
(Library-Based Proj)
Due: 4PM PDT
12