LEARNING
SYNTHETIC
BIOLOGY
IN
THE
SECOND
LIFE:


SYNTHETIC
BIOLOGY
INTERACTIVE

Mandy
Cheung,
Patrick
King,
Stefan
Marcus,
&
Katie
Ovens


iGEM
2009
 
 Supervisors:

Sonja
Georgijevic,
M.Sc.
 Instructor
 iGEM
Facilitator
 
 Faculty
of
Education

 University
of
Calgary
 1426
Education
Tower,

 2500
University
Dr
NW
 Calgary,
Alberta,
Canada


 T2N
1N4
 
 Email:
sgeorgij@ucalgary.ca
 
 Christian
Jacob,
Ph.D.
 Associate
Professor
 Director
of
Bioinformatics,
Bachelor
of
 Health
Sciences
 
 Dept.
of
Computer
Science
and
 Dept.
of
Biochemistry
&
Molecular
Biology
 University
of
Calgary,

 Calgary,
Alberta,
Canada
 T2N
1N4
 
 Email:
cjacob@ucalgary.ca


Written
By:
Mandy
Cheung
&
Stefan
Marcus

Email:
ahtcheun@ucalgary.ca
&
smarcus@ucalgary.ca


Mandy
Cheung
&
Stefan
Marcus






















































































Synthetic
Biology
Interactive


What
is
Second
Life?
 Second
Life
is
an
application
accessible
through
the
Internet
in
which
users
can
access
a
 virtual
 world.
 They
 can
 then
 create
 an
 online
 representation
 of
 themselves,
 called
 avatars,
 and
 interact
 with
 many
 other
 learners
 from
 around
 the
 world.
 Everything
 in
 Second
 Life
 is
 user‐created,
 meaning
 that
 the
 possibilities
 are
 endless
 in
 what
 can
 be
 thought
 up
 and
 built
 in‐world.
 This
 creativity
 has
 not
 only
 been
 funneled
 into
 the
 entertainment
aspect
but
also
the
educational
aspect
of
Second
Life.
Islands
exist
which
 are
science
related
and
aimed
at
teaching
learners
or
showcasing
advances
in
multiple
 fields.
Many
universities
have
established
virtual
campuses
within
Second
Life
to
teach
 a
 variety
 of
 subjects
 (e.g.
 The
 Harvard
 Law
 School
 holds
 classes
 such
 as
 “Law
 in
 the
 Court
 of
 Public
 Opinion”
 in
 a
 virtual
 Austin
 Hall:
 http://slurl.com/secondlife/Berkman/69/54/24).
In
particular,
the
use
of
Second
Life
 to
teach
scientific
subjects
has
increased,
as
the
creating
tools
allow
for
the
visualization
 of
 things
 that
 cannot
 be
 seen
 with
 the
 naked
 eye.
 A
 notable
 one
 is
 Genome
 Island
 (http://slurl.com/secondlife/Genome/130/130/48),
 built
 by
 Mary
 Anne
 Clark
 (also
 known
 as
 Max
 Chatnoir),
 which
 allows
 visitors
 to
 see
 a
 number
 of
 famous
 biology
 experiments
in
action
and
to
learn
a
bit
about
basic
Mendelian
Genetics.

 It
 is
 important
 to
 note
 the
 two
 facets
 of
 creating
 objects
 in
 Second
 Life,
 scripting
 and
 building,
because
they
are
essential
in
understanding
this
virtual
world.
Objects
can
be
 made
fairly
easily
in
a
spot
that
allows
it
by
clicking
on
the
desired
shape
in
the
build
 menu
 (this
 process
 is
 known
 as
 rezzing).
 Rezzing
 multiple
 objects
 and
 linking
 them
 together
is
the
simplest
and
usually
most
effective
way
to
replicate
anything
that
exists
 in
real
life.
Adding
a
texture
adds
another
dimension
to
the
realism.
Afterwards,
a
script
 can
 be
 added
 to
 make
 an
 object
 dynamic.
 Scripts
 serve
 a
 variety
 of
 functions
 such
 as
 making
something
move,
change
colour,
and
interact
with
other
objects.
Combined
and
 used
 skillfully,
 these
 two
 seemingly
 simple
 components
 can
 make
 your
 Second
 Life
 world
come
alive,
and
our
team
has
worked
tirelessly
to
perfect
our
magic
touch.
 
 iGEM
and
Synthetic
Biology
Interactive
 iGEM
(International
Genetically
Engineered
Machines)
is
a
competition
founded
in
2004
 that
 gives
 undergraduate
 a
 chance
 to
 work
 in
 a
 team
 in
 order
 to
 design
 a
 biological
 system.
 This
 is
 done
 using
 Biobrick
 parts,
 which
 are
 DNA
 components
 flanked
 by
 Biobrick
sites
that
can
be
incorporated
into
bacteria
such
as
E.
coli.
These
are
restriction
 enzyme
 sites
 that
 allow
 for
 the
 easy
 construction
 of
 genetic
 circuits.
 Through
 this
 method
many
projects
have
been
done
in
previous
years
including
bacteria
that
smell
 like
banana
or
peppermint,
buoyant
bacteria,
and
an
arsenic
biosensor
(Lizarazo,
2009).
 This
year,
the
University
of
Calgary
iGEM
team
has
decided
to
work
on
an
AI‐2
signalling
 system
that
bacteria
can
use
to
combat
the
formation
of
biofilm
using
quorum
sensing.
 In
 addition,
 four
 members
 of
 the
 team
 worked
 in
 Second
 Life
 to
 create
 an
 interactive
 learning
environment
for
synthetic
biology,
laboratory
methods,
Biobrick
parts
and
the
 Registry
of
Standard
Biological
Parts.

 Like
 any
 novel
 discipline,
 synthetic
 biology
 requires
 some
 base
 knowledge
 about
 the
 subject.
 Unfortunately
 since
 it
 is
 a
 relatively
 new
 field,
 limited
 resources
 exist
 on
 the
 subject.
This
is
one
of
the
most
important
reasons
why
part
of
the
University
of
Calgary
 iGEM
 team
 created
 an
 island
 in
 Second
 Life,
 Synthetic
 Biology
 Interactive
 (SBI).
 We
















































University
of
Calgary
iGEM
2009













igem@ucalgary.ca

































2


Mandy
Cheung
&
Stefan
Marcus






















































































Synthetic
Biology
Interactive


believe
 that
 by
 making
 this
 learning
 tool
 available,
 more
 learners
 would
 become
 interested
 and
 be
 willing
 to
 become
 versed
 in
 this
 new
 field,
 thus
 encouraging
 the
 development
of
the
synthetic
biology
all
over
the
world.
Our
island
was
designed
to
be
 all‐inclusive,
 so
 learners
 would
 not
 need
 to
 use
 many
 outside
 resources
 or
 leave
 to
 another
location
in
order
to
learn
or
understand
the
concepts
shown
on
the
island.
The
 three
areas
of
SBI
are
Synthetic
Kingdom,
The
Biobrick
Simulator
and
Virtual
Labs.
Each
 section
 is
 designed
 to
 explore
 the
 various
 facets
 of
 synthetic
 biology
 from
 the
 applications
of
synthetic
biology
to
Biobricks
to
laboratory
techniques.


 


SYNTHETIC
KINGDOM

The
Synthetic
Kingdom
is
the
first
area
that
users
will
encounter.

As
an
introduction
to
 the
 entire
 island,
 we
 wanted
 to
 show
 users
 the
 potential
 applications
 of
 synthetic
 biology.
 Using
 these
 applications,
 a
 general
 idea
 of
 what
 synthetic
 biology
 is
 can
 be
 formed.
 As
 well,
 this
 section
 allows
 for
 the
 learning
 and
 practice
 of
 key
 control
 skills
 that
are
used
in
the
other
two
sections
of
Synthetic
Biology
Interactive.

 Development
of
the
Synthetic
Kingdom
 To
 begin
 the
 development
 of
 the
 Synthetic
 Kingdom,
 we
 built
 many
 different
 types
 of
 bacteria
based
on
the
morphology
of
bacterial
genera
such
as
Sarcina
(spherical
groups
 of
 4
 to
 8)
 and
 Bacillus
 (rod­shaped)
 to
 populate
 this
 area
 (Salton
 &
 Kim,
 1996).
 These
 bacteria
were
scripted
to
float
around,
making
the
Kingdom
a
dynamic
environment.
In
 addition,
a
list
of
potential
and
actual
applications
of
synthetic
biology
was
generated.
 These
 ideas
 included
 the
 use
 of
 bacteria
 for
 bioremediation
 and
 production
 of
 bacteriocins.
 Bacteria
 were
 made
 to
 demonstrate
 these
 applications
 through
 simple
 user
 interaction.
 For
 example,
 clicking
 on
 one
 of
 the
 bacteria
 would
 cause
 it
 to
 create
 vitamins
(represented
by
colourful
shapes).


















































University
of
Calgary
iGEM
2009













igem@ucalgary.ca

































3


Mandy
Cheung
&
Stefan
Marcus






















































































Synthetic
Biology
Interactive



 Figure
1.
The
clickable
bacteria
producing
red,
yellow,
and
blue
vitamins
 
 While
 the
 moving
 bacteria
 made
 the
 Kingdom
 more
 interesting
 to
 look
 at,
 we
 also
 recognized
 that
 without
 organization,
 learners
 might
 become
 lost.
 Also,
 without
 clear
 information
 about
 what
 each
 bacterium
 did
 and
 without
 more
 structure
 in
 the
 environment,
we
could
not
ensure
that
learners
would
learn
about
the
applications
we
 were
 showcasing.
 In
 this
 case,
 the
 bacteria
 would
 be
 just
 for
 show
 and
 not
 useful
 in
 demonstrating
the
uses
of
synthetic
biology.
 In
 order
 to
 highlight
 specific
 applications
 of
 bacteria
 to
 make
 it
 easier
 for
 users
 to
 discover,
 the
 Synthetic
 Kingdom
 was
 organized
 into
 six
 separate
 stations,
 with
 a
 pathway
that
would
guide
the
user
through
each
respective
station
from
an
entrance
to
 the
 exit.
 Each
 station
 shows
 the
 user
 a
 potential
 or
 actual
 application
 of
 synthetic
 biology,
and
a
general
description
of
this
application’s
importance.

 To
 increase
 the
 interaction
 of
 participants
 in
 the
 Synthetic
 Kingdom
 beyond
 reading
 about
 and
 looking
 at
 the
 showcase
 applications,
 activities
 were
 designed
 for
 each
 station.
These
activities
give
a
visual
demonstration
of
applications
while
allowing
users
 to
directly
control
the
outcome.
For
example,
the
station
that
showcases
bioremediation
 allows
 the
 user
 to
 pick
 up
 bacteria
 that
 can
 clean
 up
 the
 waste
 from
 an
 oil
 spill.
 By
 controlling
 the
 bacteria
 to
 ‘eat
 up’
 the
 waste,
 the
 user
 creates
 an
 ‘enactment’
 of
 how
 bioremediation
functions.

 In
 addition
 to
 utilizing
 hands‐on
 activities
 to
 teach
 users
 about
 synthetic
 biology,
 multiple
stations
also
require
advanced
Second
Life
controls
which
are
required
in
the
 Biobrick
Simulator
and
Virtual
Lab
parts
of
the
Island.
For
example,
the
ability
to
move
















































University
of
Calgary
iGEM
2009













igem@ucalgary.ca

































4


Mandy
Cheung
&
Stefan
Marcus






















































































Synthetic
Biology
Interactive


an
 object
 from
 an
 avatar’s
 inventory
 to
 an
 object’s
 is
 used
 to
 show
 the
 isolation
 of
 a
 coding
 sequence
 and
 its
 insertion
 into
 another
 organism.
 This
 procedure
 is
 also
 required
to
operate
the
lab
equipment
in
the
Virtual
Labs.
 To
guide
users
around
these
various
interactive
stations,
markers
were
set
up
at
each
 station
so
that
the
ground
lights
up,
letting
users
know
they
have
reached
a
new
station.
 Signs
point
users
along
a
pathway
towards
the
next
station.




 Figure
 2.
 A
 red
 arrow
 sign
 points
 the
 user
 along
 the
 path
 from
 their
 current
 station
(marked
by
the
glowing
platform).
The
station
also
has
a
Squid
Buddy
who
 provides
activity
instructions.
 As
well,
each
station
has
a
‘Squid
Buddy’,
who
provides
notecards
with
descriptions
of
 the
showcased
application
and
gives
helpful
instructions
for
the
activities.
These
squid
 buddies
are
crucial
in
giving
the
users
direction,
and
are
also
a
nod
to
our
iGEM
team’s
 current
 project.
 They
 are
 modeled
 after
 Hawaiian
 Bobtail
 Squid
 that
 have
 a
 symbiotic
 with
Vibrio
Fischeri,
that
use
quorum
sensing
to
light
up
the
squid’s
underbelly
in
order
 to
 camouflage
 its
 shadow
 from
 predators.
 In
 return
 the
 bacteria
 feed
 on
 sugars
 and
 amino
acids
solutions
made
by
the
squid
(Young
&
Roper,
1976).


 The
 structure
 of
 the
 Synthetic
 Kingdom
 allows
 for
 intuitive
 navigation
 throughout
 the
 area,
exploring
the
current
and
potential
applications
of
Synthetic
Kingdom
to
form
an
 illustration
of
the
field
of
synthetic
biology.
While
the
users
explore
the
many
activities
 to
learn
about
these
applications
and
to
practice
controls
in
Second
Life,
other
colourful
 models
 of
 bacteria
 float
 and
 move
 above
 them
 in
 this
 underwater
 space,
 keeping
 the
 environment
dynamic
and
interesting.
 

















































University
of
Calgary
iGEM
2009













igem@ucalgary.ca

































5


Mandy
Cheung
&
Stefan
Marcus






















































































Synthetic
Biology
Interactive


BIOBRICK
SIMULATOR


 After
an
introduction
to
what
the
field
of
synthetic
biology
can
do,
learners
can
move
on
 to
the
next
region:
The
Biobrick
Simulator.
Here,
learners
explore
how
genetic
circuits
 are
constructed
using
Biobricks.

 



 Figure
3.
The
Biobrick
Simulator
Helix,
with
some
assembled
DNA
genetic
circuits
 on
one
of
the
levels.
 
 This
 second
 section
 of
 SBI
 is
 also
 the
 most
 hands‐on.
 The
 Biobrick
 Simulator
 takes
 molecules
in
the
cell
like
DNA
and
proteins,
represents
them
in
Second
Life
as
objects
 and
 then
 simulates
 some
 of
 their
 behaviour.
 In
 particular,
 the
 process
 of
 gene
 expression
through
production
of
protein
coded
from
DNA.
 
 

















































University
of
Calgary
iGEM
2009













igem@ucalgary.ca

































6


Mandy
Cheung
&
Stefan
Marcus






















































































Synthetic
Biology
Interactive


Figure
 4.
 The
 RNA
 polymerase
 can
 bind
 to
 the
 DNA
 (shown
 by
 a
 series
 of
 connecting
 cylinders),
 and
 proteins
 can
 be
 produced,
 which
 are
 shown
 as
 geometric
 shapes.
 Some
 proteins
 can
 interact
 with
 the
 DNA
 by
 binding
 (such
 as
 the
orange
half­sphere
that
represents
CII
Lambda)
 
 It
 allows
 users
 (such
 as
 future
 iGEM
 learners)
 to
 build
 their
 own
 Biobrick
 circuits
 through
 a
 helpful
 level
 based
 system
 in
 order
 to
 teach
 learners
 how
 genetic
 circuits

 work
before
they
explore
circuit
construction
in
real
life.
Apart
from
the
design
of
their
 own
circuits,
learners
can
explore
different
circuit
types
that
are
used
by
many
teams.
 One
such
circuit
is
one
controlled
by
an
activator.
In
this
system,
an
activating
protein
 must
first
be
made
so
that
it
can
bind
to
the
promoter,
allowing
for
the
expression
of
the
 gene
 behind
 it.
 Without
 the
 production
 of
 the
 activating
 protein,
 the
 RNA
 polymerase
 will
 not
 bind.
 Circuits
 that
 depend
 on
 other
 molecules
 in
 this
 way
 can
 be
 utilized
 in
 systems
 such
 as
 those
 involving
 sensors.
 It
 can
 be
 also
 fully
 self‐directed,
 letting
 learners
choose
what
pieces
to
rez
through
a
Head‐Up
Display
(HUD).
 
 
 
 Development
of
the
Biobrick
Simulator
 
 In
the
beginning
plans
were
made
for
an
interactive
learning
tool
that
could
help
teach
 new
 learners
 about
 Biobrick
 parts.
 First,
 research
 was
 conducted
 on
 the
 ability
 of
 the
 Second
Life
engine
to
handle
the
complexity
of
what
we
were
trying
to
achieve.
Once
it
 was
 deemed
 plausible,
 we
 moved
 forth
 in
 choosing
 how
 the
 parts
 are
 going
 to
 be
 put
 together.

 

















































University
of
Calgary
iGEM
2009













igem@ucalgary.ca

































7


Mandy
Cheung
&
Stefan
Marcus






















































































Synthetic
Biology
Interactive


Parts
 have
 names
 floating
 overhead,
 and
 are
 represented
 by
 coloured
 shapes
 such
 as
 spheres
 and
 cylinders.
 These
 shapes
 allow
 for
 clear
 recognition
 of
 each
 part,
 as
 the
 colours
used
match
those
in
the
Parts
Registry.
For
example,
terminator
sequences
are
 always
 red,
 and
 promoter
 sequences
 are
 always
 green.
 By
 matching
 these
 colouring
 conventions,
learners
are
reminded
that
each
part
can
actually
be
found
in
the
Registry.
 In
 addition,
 other
 colouring
 conventions
 were
 added
 for
 organizational
 purposes:
 custom
parts
made
by
users
are
coloured
navy
blue,
and
fluorescent
proteins
appear
to
 glow.
 As
 well,
 the
 design
 of
 each
 coding
 region
 part
 matches
 its
 protein.
 This
 organization
 is
 helpful
 for
 the
 learner
 to
 keep
 track
 of
 their
 parts,
 especially
 when
 dealing
with
complicated
systems
that
involve
several
parts.

 



 Figure
5.
Each
part
has
a
label
that
is
easily
seen.
Terminators
are
red,
and
both
 promoters
 and
 RNA
 polymerase
 are
 green.
 The
 CII
 Lambda
 coding
 sequence
 is
 coloured
orange
just
like
its
protein;
and
the
CFP
is
a
glowing
cyan
colour.
 
 We
 wanted
 a
 freedom
 of
 choice
 type
 of
 system
 but
 realized
 that
 learners
 will
 retain
 information
 better
 and
 have
 more
 incentive
 if
 it
 is
 level
 based;
 a
 concept
 more
 appealing
than
chapters
in
textbooks
used
in
traditional
teaching
methods.
Each
level
is
 a
 self‐contained
 set
 of
 parts,
 with
 the
 goal
 of
 introducing
 one
 or
 two
 features
 of
 the
 Biobrick
Simulator
and
molecular
biology.
The
levels
themselves
progress
in
difficulty
 starting
 with
 the
 most
 basic
 of
 circuits
 and
 gradually
 including
 concepts
 like
 external
 repressors,
or
gates,
negative
autoregulation
and
bi‐stable
toggle
switches.
As
learners
 proceed
 through
 the
 multiple
 levels;
 the
 complexity
 of
 systems
 and
 number
 of
 parts
 involved
 increases.
 In
 level
 1,
 translation
 is
 started
 by
 simply
 moving
 the
 RNA
 polymerase
towards
the
promoter
and
bumping
into
it.
Later
levels
are
similar
in
this
 way
but
will
require
many
extra
steps
before
getting
to
this
point.
As
mentioned
before,
 circuits
that
require
activation
would
need
the
binding
of
an
activator
protein
in
order

















































University
of
Calgary
iGEM
2009













igem@ucalgary.ca

































8


Mandy
Cheung
&
Stefan
Marcus






















































































Synthetic
Biology
Interactive


for
 RNA
 polymerase
 to
 bind.
 This
 activator
 may
 also
 need
 to
 be
 produced
 using
 a
 genetic
 circuit.
 As
 another
 example,
 other
 systems
 may
 require
 the
 removal
 of
 a
 repressor
 protein.
 The
 RNA
 polymerase
 glides
 along
 the
 circuit
 and
 the
 gene
 is
 expressed
 as
 a
 floating
 green
 pyramid
 that
 appears
 (in
 this
 case
 it
 represents
 Green
 Fluorescent
Protein).

 



 Figure
 6.
 After
 the
 RNA
 polymerase
 binds
 to
 the
 promoter,
 it
 runs
 along
 the
 circuit
and
GFP
is
produced
 
 Through
 the
 visualization
 of
 protein
 production,
 learners
 can
 see
 the
 outcome
 (or
 product)
 of
 the
 circuit
 they
 have
 built.
 This
 interactivity
 and
 the
 visual
 aspect
 helps
 learners
 understand
 the
 concepts
 better
 and
 get
 a
 feel
 for
 what
 is
 happening
 at
 the
 molecular
 level.
 Of
 course,
 without
 knowing
 some
 basics
 about
 DNA
 interactions,
 the
 Biobrick
Simulator
seems
abstract‐
in
this
simulator,
the
movement
of
RNA
polymerase
 leads
 to
 the
 production
 of
 protein,
 and
 not
 mRNA
 as
 one
 would
 expect.
 The
 mRNA
 production
 step
 was
 omitted
 in
 order
 to
 give
 direct
 production
 of
 a
 final
 product‐
 for
 clarity.
 While
 mRNA
 modification
 is
 something
 we
 are
 considering
 showing
 in
 the
 future,
it
would
add
an
additional
level
of
complexity
to
the
actions
learners
would
have
 to
perform
to
produce
their
protein
product.

 
 The
‘outcome’
(gene
expression
achieved)
through
each
circuit
is
shown
through
direct
 production
of
protein,
but
we
also
want
to
ensure
that
the
genetic
dogma
is
clear
to
the
 learner.
 In
 order
 to
 help
 flesh
 out
 learners’
 understanding
 of
 how
 genetic
 expression
 works,
we
also
made
an
area
at
the
bottom
of
the
helix
that
houses
the
level
platforms.
 There,
 we
 are
 building
 interactive
 demonstrations
 of
 important
 processes:
 The
 transcription
of
DNA
to
RNA
and
then
translation
into
proteins.
 

















































University
of
Calgary
iGEM
2009













igem@ucalgary.ca

































9


Mandy
Cheung
&
Stefan
Marcus






















































































Synthetic
Biology
Interactive



 Figure
 7.
 This
 display
 demonstrates
 DNA
 replication.
 Components
 such
 as
 the
 RNA
 polymerase
 (shown
 as
 a
 complex
 yellow
 and
 blue
 shape)
 and
 Rho
 protein
 (yellow
cone)
can
be
clicked
to
observe
what
they
do.
 
 
A
 Biobrick
 Creator
 Heads
 Up
 Display
 (HUD)
 was
 created
 to
 keep
 parts
 and
 levels
 organized,
 while
 also
 providing
 important
 instructions
 in
 the
 assembly
 of
 genetic
 circuits
and
explanations
regarding
the
systems
explored
in
each
level.

The
HUD
is
in
 the
form
of
a
controller
that
remains
in
the
upper
corner
of
the
learners
screen
when
 manually
attached.
There
are
buttons
allowing
for
the
selection
of
levels,
a
help
button
 that
 provides
 notecards
 with
 instructions,
 and
 buttons
 that
 open
 ‘categories’
 of
 parts,
 which
can
then
be
rezzed.

 

















































University
of
Calgary
iGEM
2009













igem@ucalgary.ca

































10


Mandy
Cheung
&
Stefan
Marcus






















































































Synthetic
Biology
Interactive



 Figure
 8.
 The
 HUD
 in
 the
 corner
 provides
 level
 and
 part
 selection,
 along
 with
 instructions
and
explanations
 
 This
HUD
was
necessary
to
give
learners
full
control
over
which
parts
they
want
to
rez
 should
they
so
choose.
Still,
a
level
selector
exists,
allowing
learners
to
have
the
choice
 of
 trying
 the
 variety
 of
 levels
 in
 any
 order
 they
 wish,
 with
 the
 parts
 necessary
 being
 automatically
created
when
the
level
is
selected.
In
addition
to
the
levels,
learners
can
 also
choose
from
a
large
number
of
available
parts
to
build
their
own
genetic
circuits.
As
 well,
 custom
 parts
 with
 distinct
 functions
 can
 be
 produced
 using
 the
 HUD.
 Using
 both
 these
 tools,
 learners
 can
 take
 what
 they’ve
 learned
 about
 different
 systems
 and
 apply
 them
 in
 the
 design
 of
 their
 own
 circuits.
 Thus,
 both
 freedom
 of
 exploration
 and
 structured
learning
are
offered
in
this
section.


 
 

















































University
of
Calgary
iGEM
2009













igem@ucalgary.ca

































11


Mandy
Cheung
&
Stefan
Marcus






















































































Synthetic
Biology
Interactive


VIRTUAL
LABS


 The
Virtual
Labs
are
currently
the
last
stop
in
the
exploration
of
our
island.
There
are
 two
 identical
 labs
 that
 can
 facilitate
 multiple
 avatars.
 These
 labs
 were
 built
 to
 mirror
 the
techniques
we
are
using
for
constructing
biological
circuits
and
transforming
them
 into
bacteria
in
the
wetlab
portion
of
our
iGEM
project
as
well
as
reinforcing
concepts
 and
 general
 techniques
 learned
 in
 molecular
 biology.
 Laboratory
 equipment
 and
 procedures
are
interactive
and
user
friendly,
providing
an
accurate
and
realistic
virtual
 lab
experience
without
using
expensive
reagents.

 
 
 
 Development
of
the
Virtual
Labs
 
 While
 it
 is
 the
 final
 region,
 we
 developed
 ideas
 for
 the
 Virtual
 Labs
 early
 on
 in
 the
 development
 of
 SBI,
 as
 lab
 work
 was
 chosen
 as
 an
 integral
 part
 of
 our
 learning
 environment.
 One
 of
 our
 fundamental
 goals
 was
 to
 teach
 laboratory
 techniques
 to
 learners
 before
 they
 started
 actually
 working
 in
 the
 lab
 during
 iGEM.
 Before
 actually
 using
 reagents
 and
 equipment,
 learners
 can
 figure
 out
 the
 basics
 of
 laboratory
 techniques,
and
why/how
each
technique
is
performed.
.

 
 As
soon
as
we
could
build
well
enough,
the
objects
in
the
lab
were
built
to
be
as
close
to
 their
real
life
counterparts
in
our
lab
as
possible.
The
scripting
did
not
come
until
later
 because
it
was
harder
to
learn
and
script
proficiently.
What
we
wanted
to
do
is
have
all
 of
the
procedures
in
the
virtual
lab
be
as
close
to
the
real
thing
as
possible
because
the
 Virtual
Labs
would
be
useless
if
learners
used
equipment
in
the
real
lab
and
it
behaved
 differently
than
they
expected.
While
the
actual
pipetting,
transferring
bacteria,
making
 gels,
 and
 handling
 general
 materials
 in
 the
 lab
 is
 difficult
 to
 recreate
 due
 to
 the
 limitations
 of
 Second
 Life,
 the
 procedures
 could
 be
 scripted
 and
 thus
 the
 Virtual
 Labs
 started
taking
shape.

 
 Situated
 around
 different
 lab
 benches
 and
 equipment,
 we
 have
 created
 introductions
 and
 activities
 for
 the
 following
 lab
 techniques:
 bacterial
 transformation,
 DNA
 sequencing,
polymerase
chain
reaction,
gel
electrophoresis,
DNA
extraction,
restriction
 digest
 of
 DNA,
 &
 biobrick
 construction
 of
 genetic
 circuits.
 Most
 of
 these
 activities
 involve
 the
 collection
 of
 reagents
 and
 components
 from
 around
 the
 lab,
 and
 then
 placing
these
in
equipment
(by
dropping
the
objects
in
equipment
inventory).

 
 
 When
learners
first
come
into
the
lab
we
assume
that
they
have
no
prior
knowledge
of
 any
 techniques
 used
 in
 biology.
 This
 is
 why
 we
 supplied
 notecards
 with
 information
 about
what
the
technique
is,
how
it
works,
and
the
procedure
that
goes
along
with
using
 it.
 The
 notecards
 contain
 information
 regarding
 experimental
 conditions
 (when
 pertinent)
and
reagents
used,
along
with
an
explanation
of
why
these
components
are
 important.
 Using
 the
 information
 given
 in
 the
 notecards,
 learners
 can
 then
 perform
 different
 activities
 for
 each
 lab
 technique.
 For
 example,
 the
 processes
 of
 preparing
 plates
in
bacterial
transformation
could
not
be
animated,
thus
the
bacteria
are
shown
to
 be
spread
on
the
plates
automatically.
While
the
avatar
of
the
learner
is
not
animated,
 the
learner
can
still
see
each
step
in
the
process
of
transforming
plasmids
in
to
bacteria,
 and
 the
 verification
 of
 a
 successful
 transformation.
 The
 learner
 still
 controls
 the
 steps
















































University
of
Calgary
iGEM
2009













igem@ucalgary.ca

































12


Mandy
Cheung
&
Stefan
Marcus






















































































Synthetic
Biology
Interactive


taken,
as
a
quiz
question
must
be
answered
correctly
in
order
to
proceed.
The
answers
 to
the
quiz
can
be
found
in
the
information
given
from
the
notecard.
 
 



 Figure
 9.
 The
 bacterial
 transformation
 station
 has
 easily
 accessible
 instructions.
 As
users
correctly
answer
questions
about
this
technique,
the
test
tubes
shown
in
 the
yellow
holder
will
visibly
fill
with
solution.
 
 In
 another
 example,
 the
 notecard
 detailing
 the
 process
 of
 polymerase
 chain
 reaction
 (PCR)
 gives
 a
 list
 of
 the
 components
 used
 in
 the
 PCR
 reaction
 mixture,
 and
 the
 reasoning
 behind
 why
 each
 component
 is
 needed.
 By
 following
 this
 list,
 learners
 can
 collect
the
reagents
required
to
produce
the
reaction
mixture
from
around
the
lab.


















































University
of
Calgary
iGEM
2009













igem@ucalgary.ca

































13


Mandy
Cheung
&
Stefan
Marcus






















































































Synthetic
Biology
Interactive



 Figure
10.
The
PCR
technique
is
explained
in
the
notecard
set
up
next
to
the
PCR
 Thermocycler
equipment.

 
 We
also
wanted
to
give
the
lab
some
structure
rather
than
have
learners
jump
from
one
 station
to
another
with
no
real
understanding
of
the
big
picture.
We
solved
this
problem
 by
 constructing
 a
 narrative;
 making
 each
 user
 a
 secret
 agent
 on
 a
 mission
 will
 make
 learning
 fun
 and
 having
 prizes
 at
 the
 end
 will
 give
 incentive
 for
 learners
 to
 finish
 the
 missions.
 The
 robots
 at
 the
 entrance
 of
 each
 Virtual
 Lab
 give
 each
 new
 agent
 assignments
that
are
to
be
accomplished.
The
three
missions
are
increasing
in
difficulty
 and
 can
 be
 done
 in
 any
 order,
 helping
 beginners
 train
 and
 letting
 more
 experienced
 learners
 practice
 or
 refresh
 their
 memory.
 By
 stringing
 all
 the
 laboratory
 techniques
 together
through
missions
we
can
help
users
simulate
the
thought
process
in
designing
 experiments
 and
 make
 them
 think
 about
 what
 sort
 of
 outcomes
 to
 expect
 when
 performing
certain
lab
techniques.




 
 
 


THE
FUTURE


 Synthetic
 Biology
 Interactive
 is
 an
 ongoing
 project
 and
 was
 built
 for
 expansion.
 The
 visual
 aspects
 of
 the
 SBI
 Island
 can
 be
 changed
 to
 accommodate
 such
 changes.
 For
 example,
 the
 Synthetic
 Kingdom
 can
 be
 expanded
 to
 accommodate
 more
 stations
 because
the
laboratories
and
the
Biobrick
Simulator
are
floating
in
the
air,
leaving
room
 on
 the
 actual
 island
 to
 be
 incorporated
 into
 the
 kingdom’s
 underwater
 realm.
 These
 new
 stations
 would
 showcase
 additional
 interesting
 applications
 of
 synthetic
 biology.
 The
Biobrick
Simulator
has
an
expandable
script
so
new
parts
can
be
added
at
any
time,
 extending
 the
 possibilities
 of
 what
 can
 be
 done
 with
 the
 Biobricker
 in
 creating
 new
 exciting
circuits.
As
well,
the
helix
can
be
expanded
with
additional
levels
to
showcase

















































University
of
Calgary
iGEM
2009













igem@ucalgary.ca

































14


Mandy
Cheung
&
Stefan
Marcus






















































































Synthetic
Biology
Interactive


other
 systems
 that
 can
 be
 used.
 This
 could
 allow
 for
 learners
 to
 submit
 their
 own
 genetic
circuit
designs
to
be
included
as
a
level.

 
 In
the
Virtual
Labs
equipment
can
be
improved
by
making
results
even
more
realistic.
 Currently,
 any
 mistakes
 in
 adding
 the
 wrong
 reagent,
 etc.
 are
 immediately
 communicated
 to
 the
 learner
 through
 chat
 functions.
 Unless
 mistakes
 are
 corrected,
 experimental
procedures
will
not
be
allowed
to
continue.
By
allowing
the
procedure
to
 continue
 and
 not
 indicating
 any
 mistakes
 until
 the
 end,
 actual
 lab
 work
 can
 be
 better
 simulated.
For
example,
instead
of
stopping
a
restriction
digest
procedure
because
the
 wrong
enzyme
was
used,
the
learner
could
be
allowed
to
continue
with
the
experiment
 until
they
performed
gel
electrophoresis.
A
gel
with
bands
of
unexpected
sizes
would
be
 delivered,
 thus
 indicating
 a
 mistake
 somewhere
 during
 the
 experimental
 process.
 By
 revealing
 errors
 through
 unexpected
 experimental
 results,
 the
 learner
 would
 be
 prompted
 to
 troubleshoot
 what
 went
 wrong
 and
 at
 what
 step,
 which
 is
 an
 important
 laboratory
skill.

 Beyond
 the
 three
 major
 areas,
 we
 have
 a
 whole
 island
 on
 which
 to
 expand
 on
 for
 additional
components
that
would
be
useful
in
teaching
about
synthetic
biology.
There
 are
 plans
 for
 constructing
 an
 amphitheatre
 that
 can
 house
 a
 number
 of
 Second
 Life
 residents
to
be
used
for
science
talks
and
conferences.
By
providing
this
area,
our
team
 can
promote
discussion
about
ethics
and
education
in
synthetic
biology
by
running
such
 events.
Our
island
also
has
a
meeting
spot
that
can
be
used
for
iGEM
teams
to
meat
one
 another
online,
or
for
students
to
meet
in
a
group
and
discuss
what
they
have
learned.
 As
 Second
 Life
 is
 an
 easily
 accessible
 virtual
 world,
 such
 areas
 provide
 facilities
 for
 individuals
from
all
over
to
meet
and
discuss,
which
would
otherwise
be
a
difficult
task.


 
 Before
 expansion
 can
 begin,
 we
 want
 to
 ensure
 that
 the
 areas
 and
 activities
 we
 have
 already
 built
 are
 operating
 effectively.
 To
 do
 so,
 internal
 testers
 will
 be
 trying
 out
 the
 different
regions
of
the
island,
and
leaving
feedback
notes
for
us.
This
will
allow
us
to
 improve
the
clarity
and
ease
of
operation
of
the
various
components
of
SBI.
After
this,
a
 grand
 opening
 will
 be
 held
 to
 open
 our
 island
 to
 the
 public.
 We
 will
 be
 inviting
 other
 educators
in
Second
Life
to
come
explore
and
comment
on
the
value
of
SBI,
providing
us
 with
further
feedback.
We
hope
that
in
the
future,
iGEM
teams’
students
can
learn
about
 synthetic
 biology,
 genetic
 circuits,
 and
 lab
 techniques
 using
 SBI
 instead
 of
 the
 regular
 classroom
learning
methods..

 

















































University
of
Calgary
iGEM
2009













igem@ucalgary.ca

































15


Mandy
Cheung
&
Stefan
Marcus






















































































Synthetic
Biology
Interactive


References
 
 Everts,
S.
(2007,
June
25).
Second
Life
Science:
Taking
a
scientific
field
trip
to
a
digital
 world.
 Chemical
 &
 Engineering
 News:
 Science/Technology.
 85(26):
 49.
 Retrieved
 from
 http://pubs.acs.org/cen/science/85/8526sci3.html
 
 Lizarazo,
M.
(2009,
January
14).
About
the
International
Genetically
Engineered
Machine
 competition.
Retrieved
from
http://2009.igem.org/About
 
 Orland,
 K.
 (2006,
 September
 12).
 Harvard
 class
 invades
 Second
 Life.
 Retrieved
 from
 http://www.joystiq.com/2006/09/12/harvard‐class‐invades‐second‐life/
 
 Salton,
M.R.J.,
&
Kim,
K.S.
(1996).
Structure.
In:
Baron’s
Medical
Microbiology
(Baron
S
et
 al.,
eds.)
(4th
ed.)
University
of
Texas
Medical
Branch.
 
 Young,
R.E.,
&
Roper,
C.F.
(1976).
Bioluminescent
countershading
in
midwater
animals:
 evidence
from
living
squid.
Science.
191(4231):1046‐8.

















































University
of
Calgary
iGEM
2009













igem@ucalgary.ca

































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