Wearestudentsofhighschoolandfirstsemesters ofcollege. - PowerPoint PPT Presentation

• We
are
students
of
high
school
and
first
semesters
 of
college.
 • Under
the
guidance
of
PhD.
Raúl
Cuero,
who
is
our
 mentor.

 • Dr.
Cuero
founded
the
IPOC


Name:
Ruiz
snowcapped
mountain
 Height:
5.389
m
(17,784
@.)
 Extension:
58.300
ha


AtlanZc
 Ocean
 Pacific
 Ocean
 Manizales
 • The
world
is
running
out
of
potable
water.
 • Device
detects
ions
of
sea
water
and
 



separate
them
by
breaking
the
bonds
 



of
the
sea
water
molecules.
 • More
available
potable
water.
 • CONSTRUCTION
OF
NEW
PARTS!

 RNA
switch
/
Cytochrome
C
/
Ion
Channels
/
Proteins


Goals:
 • 

 • Purify
sea
water
 • Use
the
neural
and
E‐nose
algorithms
to
 experimentally
analyze
data
and
to
 further
predict
addiZonal
unknown
 informaZon


DEVICE
 COMPONENTS
 Chassis:

 Geobacillus
stearotermophilus
 • (Thermopile
Bacterium)
 Ion
Channels:

 • E.
Coli
 ‐TonB





‐ExbB 
 Promoters:

 Cytochrome
C:

 • T7
Promoter
 • Iron
(Fe
Cuero)
 Proteins:

 Reporter:
 ‐Chloride



‐Sodium
 • Cyan
Reporter
 RNA
Switch:
 ON
 RBS:
 Stop:
 OFF
 ON OFF

¿How
does
our
 device
works?


Control


Cytochrome
 Electrons
 NADH

 C
 Ubiquinone
 dehydrogenase
 OXIDATION
 Ubiquinone
 NADH
 NADH

dehydrogenase
 Electrons
 Cl
molecule
 Na
molecule
 Cytochrome
C


P P P Hydrogenions
 A Ubiquinone
 ATP
 NADH
 synthase

 dehydrogenase
 P P P P P A e A P NADH
 P P A

Devices
 • Basic
device
 • Secondary
device


ConstrucZng
the
device
 Amp
 Amp
 PBSK
II

 PBSK
II

 Cyan
Reporter
 Chloride
 Cl
Channel
 Amp
 RBS
 PBSK
II

 Reporter
 Sodium
 Na
Channel
 Stop


ConstrucZng
the
device
 Amp
 Amp
 Cl
Channel
 PBSK
II

 PBSK
II

 Cyan
Reporter
 Chloride
 Na
Channel
 Amp
 RBS
 PBSK
II

 Reporter
 Sodium
 Stop


ConstrucZng
the
device
 Na
Channel
 Amp
 PBSK
II

 Cyan
Reporter
 RBS
 Reporter
 Cl
Channel
 T7
 Stop


RNA
SWITCH
ON
 O N ParZal
 RNA
Switch
 Molecule
 ON
 Expression
 O OFF N RNA
Switch
 RNA
Switch
 ON
 OFF
 Complete
 Molecule
 Expression


Results
 DNA
ConcentraFons:
 DNA
ConcentraFon
(ng/ Devices
 µl)
 Device
1
(Final
LigaZon)
 1107
 Control
Device
 917
 Devices
 OpFcal
Density
 Device
1
(Final
LigaZon)
 0,4
 Control
Device
 0,4


Gel
from
PCR
 LigaZon
of
NaCl
with
 desinged
primers


Bioassays
 100%
=

 24
g
of
NaCl

 +

 5
g
of
MgCl 2 
 0%
 100%
 200%
 ConcentraZon
of
NaCl
and
MgCl
 on
the
Culture
medium


Parameters
to
measure
device
 efficiency
 • 
Salt
concentraZon
in
the
medium
 • DNA
concentraZon
 • Bacterial
growth
 • ATP
producZon
 • Fluorescence
intensity
 • RNA
concentraZon


Main
units
of
our
project
 Device
 E‐nose
 PBSK
II
 NaCl
 Sea‐water
 Neural
Network
 SALT
[
]
 OpFcal
density


ComputaZonal
modeling

 • Is
used
in
the
project
to
complement
the
 laboratory
work.
With
this
tool
we
will
predict
 which
device
is
opZmal.
 • Two
systems
are
used
to
increase
their
 efficiency
and
to
reduce
its
error:
 • E‐nose

 • Neural
model


The
basic
equaFons
for
the
E‐nose
 algorithm: 


I N Size
of
the
sequence
 Type
of
chassis
 T R I LocaFon
 Expression
of
reporter
 N S CombinaFon
 Expression
of
proteins
 I C 
 Distance

 RestricFon
sites
 OpFcal
 density
 Number
of
Parts
 Type
of
primer
 LocaFon
regarding
RBS
 Type
of
enzyme
 BLACK
 BOX
 Type
of
vector
 Salt
 E concentraFon
 X Presence
of
O 2
 Salts
ConcentraFon
 T R I Presence
of
F
 Fluorescence
 N S I Presence
of
Ca

 ATP
 C 
 Presence
of
Zn
 Time
of
exposiFon
 Presence
of
Mg
 [DNA]

ConcentraFon
 Volume
 Device
ConcentraFon


I N Size
of
the
sequence
 Type
of
chassis
 T OPTICAL
 R I LocaFon
 Expression
of
reporter
 N DENSITY
 S CombinaFon
 Expression
of
proteins
 I C 
 Distance

 RestricFon
sites
 Number
of
Parts
 Type
of
primer
 LocaFon
regarding
RBS
 Type
of
enzyme
 E X Presence
of
O 2
 Salts
ConcentraFon
 T R I Presence
of
F
 Fluorescence
 N S I Presence
of
Ca

 ATP
 [
SALT
]
 C 
 Presence
of
Zn
 Time
of
exposiFon
 CONCENTRATION 
 Presence
of
Mg
 [DNA]

ConcentraFon
 Volume
 Device
ConcentraFon


HypotheZcal
Model
PredicZon
To
Determine
The
 Importance
Of
Variables

 1.2
 Ion
channels
 Cytochro Cl
 Na
 RNA
swicth
 SeparaFon

 PredicFon
 me
 1
 0
 0
 0
 0
 0
 0
 0,00
 0.8
 1
 0
 0
 0
 0
 0,05
 0,00
 0.6
 Series1
 0
 1
 1
 1
 1
 0,1
 0,11
 Series2
 0.4
 1
 0
 1
 1
 1
 0,1
 0,13
 0.2
 1
 0
 1
 0
 1
 0,1
 0,07
 0
 1
 2
 3
 4
 5
 6
 7
 8
 9
 10
 11
 12
 13
 1
 1
 0
 1
 0
 0,15
 0,22
 1
 1
 0
 0
 1
 0,2
 0,25
 1
 1
 0
 0
 0
 0,45
 0,42
 Different
possible
model
results
 1
 1
 0
 1
 1
 0,5
 0,48
 based
on
theoricall
data
with
a
 1
 1
 1
 0
 0
 0,75
 0,77
 0.4
standard
deviaZon.
 1
 1
 1
 0
 1
 0,75
 0,75
 1
 1
 1
 1
 0
 0,95
 0,94
 1
 1
 1
 1
 1
 1
 1,00


HypotheZcal
Model
PredicZon
To
Determine
The
 Importance
Of
Variables

 0.42
 0.41
 Part
Removed
 Calculated
error
 RNA
 0,415502626
 0.4
 Ion
Channels
 0,406685639
 Cytochromes
 0,378694109
 0.39
 0.38
 0.37
 0.36
 RNA
 Ion
Channels
 Cytochromes


Conclusions
 • All
the
parts
were
assembled
and
the
device
 was
fully
assembled.
 • Ion
Channels
and
Cytochrome
C
increase
the
 performance
 of
 the
 device
 (enhance
 the



































 redox
potenZal).
 • ComputaZonal
 and
 biological
 work
 complement
each
other.
 • We
are
currently
running
bioassays.