UCSF iGEM Program: Team Based Science Education from the Classroom to the Laboratory - Veronica Zepeda, David Pincus, and Saber Khan - Presented at the International Teacher - Scientist Partnership Conference - February 13, 2013

1. UCSF
iGEM
Program:
Team
Based
Science
Educa9on
from
the
Classroom
to
the
Laboratory
Veronica
Zepeda,
David
Pincus,
and
Saber
Khan
Interna9onal
Teacher-­‐Scien9st
Partnership
Conference
February
13,
2013

2. Why
Synthe9c
Biology?
A
video
by
UCSF,
Abraham
Lincoln
High
School
and
SynBERC
Link:
hTps://vimeo.com/55897123

3. Principles
of
Biotechnology
• Founded
by
George
Cachianes
in
1996
• Second
Year
Course
added
in
2005
• Now
5
sec9ons
~
150
Students
Per
Year
• Over
1,800
students
have
been
through
the
program
• Now
spread
to
7
Other
SFUSD
High
Schools
georgecachianes@gmail.com

4. Principles
of
Biotechnology
• Overlying
Goal:
Students
Will
Choose
A
Career
in
Science
• Prepared,
Aware,
and
Mo9vated
Students
• Address
3
Deficiencies
Of
New
Employees
/
College
Students:
1.
Need
beTer
wri9ng
skills
2.
Need
experience
working
in
teams
3.
Need
to
know
how
to
actually
“do
things”
• Wri9ng:
~150
Pages
Of
Lab
Notebook
In
Legal
Scien9fic
Format
Reading
Of
Primary
Cita9ons
/
Journal
Ar9cles
Poster
In
Professional
Mee9ng
Format
• Team
Work:
A
Year
Long
Project
Focusing
On
Industry
Structure
• Doing:
Applica9ons,
Implica9ons,
and
Limita9ons
Of
Current
Research

5. Biotechnology
at
Abraham
Lincoln
High
• ALHS
Biotechnology
is
a
two
year
pathway
• First
Year:
Introduc9on
to
biotechnology,
DNA
cloning,
and
the
industry
and
career
opportuni9es

6. Biotechnology
at
Abraham
Lincoln
High
• ALHS
Biotechnology
is
a
two
year
pathway
• First
Year:
Introduc9on
to
biotechnology,
DNA
cloning,
and
the
industry
and
career
opportuni9es
• Second
Year:
students
study
and
perform
several
lab
protocols
(running
polyacrylamide
and
agarose
gels,
western
blots,
DNA
minipreps,
column
chromatography).

10. iGEM
at
UCSF
From
the
classroom
to
the
compe99on

13. What
is
iGEM?
• Summer
compe99on
for
undergrads
• Universi9es
worldwide
compete,
with
191
interna9onal
teams
involved
in
2012
– Regional
compe99ons,
followed
by
finals
at
MIT
• Aims
to
expand
the
field
of
synthe9c
biology

14. Synthe9c
Biology
• The
crea9on
of
new
biological
systems
•
The
redesign
of
exis9ng
biological
systems
• Applica9ons
include:
Biofuels,
Pharmaceu9cals,
Materials,
and
many
more...
hTp://www.bifcpresidency.tn.gov.in/artemis.html
Artemisinin

15. Parts
à
Devices
à
Systems
Computer
Chip
à
Motherboard
à
Computer

16.
•
Fun,
engaging,
mo9va9ng
•
Easy
to
understand
goals/applica9ons
•
Simple
goals
let
students
develop
their
own
crea9ve
ideas
and
solu9ons
•
Students
can
see
the
logic
of
how
things
work
•
Allows
students
to
immediately
experience
the
crea9vity
in
the
scien9fic
process
Why
is
synthe9c
biology
so
compelling
for
young
students?

17. Timeline
for
UCSF
iGEM
• March/April:
Classroom
Visits
by
scien9sts
• May:
Ajer
school
visits
with
team
and
project
leaders
• June:
2-­‐week
bootcamp,
research
begins
• July-­‐September:
Research,
build
website,
make
poster
and
presenta9on
• October:
Regional
Champshionship
• November
World
Championship

18. iGEM
Bootcamp
• A
two
week
learning
experience
and
introduc9on
to
the
program
• First
Week:
lectures
about
our
model
organism
and
on
cloning
workflow,
read
and
discuss
ar9cles/reviews
from
scien9fic
journals,
Lab
Safety
Training,
etc
• Second
Week:
summarize
informa9on
learned
in
previous
week,
form/finalize
project
idea
through
"post-­‐it
brainstorming"
with
guidance
from
our
iGEM
mentors

19. The
mentors
help
the
team
brainstorm
ideas
for
their
project

20. Brainstorming
and
Presenta9ons

21. Working
in
the
Lab

22. Poster
presenta9on
at
the
Jamboree
The
team
in
front
of
the
poster
(lej)
and
speaking
to
a
judge
(boTom)

23. Mee9ng
with
other
iGEM
Teams
=
Networking

24. 2012
Americas
West
Group
Photo

28. IISME - Industry Initiatives for
Science and Math Education
Mission
-­‐
IISME
exists
to
address
the
cri9cal
need
for
a
strong,
highly
skilled
workforce
in
math,
science
and
technological
fields.
This
industry-­‐educa9on
partnership
focuses
on
teachers
as
the
primary
agents
for
effec9ng
meaningful
change
in
our
schools.
Eligibility
-­‐
K-­‐16
full-­‐9me
teachers
in
the
Bay
Area.
-­‐
Completed
at
least
two
full
years
of
teaching.
-­‐
CommiTed
to
con9nuing
to
teach
for
the
next
three
years.
-­‐
Available
for
full-­‐9me
summer
work.

29. Three Fellowships
2008
-­‐
Setup
the
High
School
Biotech
Training
Program
at
the
Joint
BioEnergy
Ins9tute.
Took
a
group
of
underserved
high
school
students
through
an
inves9ga9on
to
iden9fy
cellulose-­‐
degrading
bacteria.
The
program
is
now
gepng
ready
for
it
sixth
summer
program.
2009
-­‐
Joined
the
UCSF
iGEM
team
as
a
teacher
intern.
Par9cipated
in
research
to
help
engineer
mo9le
cellular
robots.
Developed
curriculum
to
teach
the
concepts
of
synthe9c
biology
using
Lego
Robo9cs.
It
is
taught
as
a
part
of
the
7th
grade
Life
Science
curriculum
at
the
San
Francisco
Friends
School.
2012
-­‐
Worked
at
the
Fletcher
Lab
at
UC
Berkeley
to
develop
the
CellScope,
a
portable
digital
microscope,
for
educa9on.

30. Cells as Bots: Synthetic Bio
Link:
hTps://vimeo.com/6773532

31. Unit Plan: CellBots
Connection between Biology and Engineering:
Part 1: Cells as Machines – One class session
Part 2: What synthetic biologist go - Half class session
Part 3: Synthetic Biology - The Micro-oxen project - Half class session
Bots as Cell Curriculum:
Introduction - Cells as Robot – One class session
Pre-challenge – Building and programming the Ball Hunter - One or
more class session
Part A – Inputs (Receptors and Sensors) – One class session
Challenge 1 – Modifying the Input – One or two sessions
Presentation of Results – Two sessions

32. Student work: Abstract
In science, we have been working with Lego NXT robots to
simulate a cell. We are testing the bot, modifying it to perform
better, and finally, adding to the bot to help it carry out a more
specific, important task. Using a scoring system that measures
time and success, we put the robot through trials in different
environments, while observing it to connect and contrast it to
a cell. The main robot we tested on, the Ball Hunter, is a robot
that has to find a red ball in the midst of blue balls. This could
simulate a cell ignoring certain surroundings, and instead
targeting a virus, or something similar. After we modified our
bot, it improved the completion percentage by a lot. For our
addition, we were going to create a mix between a NXT
Forklift, a NXT Ball Hunter, and a NXT Ball Sorter. It would
get a ball, pick it up, make the ball move up, see the ball, and
drop the ball into one of two buckets according to the color.
Unfortunately, we did not have enough time to finish the
addition.

33. Modifying the BallHunter

34. Results: Before/After Modifications

35. Averages: Before/After

36. Findings/Observations/Interpretation
-Our ball hunter needed more weight on back — the back pivot wheel wouldn’t
touch the ground, making the needed rotations spun off. To fix this we added a
second NXT Brick to the back.
-Back wheel couldn’t roll on tile. We added treads and made it wider.
-Our BH would over-rotate which increased the time it took the BH to complete
all steps and made the completion percentage lower.
-After grabbing the blue ball, our BH would back up too far (to the starting
position) and would knock the red ball away. We fixed that by lowering the power the
motors would run on to back up.
This project helped us in a lot of ways and will continue to help us in the future.
First of all we had to put ourselves if the place of the robot while using our own
opinion. Our job is to see what we can change in the program but in order to do this
we have to see what the robot does and how it “thinks” so we can use human to use
trial and error to bring the accuracy level of the bots performance higher. Another
way the BH project has benefited us is that it is a good analogy for other things that
are being created or trying to be created like a cell that finds only cancer cells and
destroys them. Although engineering cells and tweaking the BHs ability are very
different it gives you a general idea so we can understand what and how they are
doing this.

37. Poster Session

38. Feedback: Challenges/Favorite

39. Feedback: Improvements/Scientist

40. The Research: Micro-Oxen Project
Link:
hTps://vimeo.com/6826871

41. iGEM:
High
School
Division
• 3rd
year
of
division,
grown
from
4
to
26
teams
• Jamboree
in
Indianapolis,
June
2012
• Teams
receive
kit
of
gene9c
“parts”
• Cloning
tools
donated
by
NEB
• Teams
form
in
the
Fall,
research
completed
in
Spring
• In
class
exercise
or
extra-­‐curricular

42. BioBuilder.org

43. Acknowledgements
• Prof.
Wendell
Lim
(UCSF)
and
George
Cachianes
(Lincoln
High-­‐SF)
• Kate
Spohr
(SynBERC-­‐Berkeley)
and
Natalie
Kuldell
(SynBERC-­‐MIT)
• Connie
Lee
(Center
for
Systems
and
Synthe9c
Biology-­‐UCSF)