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Enhancing genetically engineered Escherichia coli bioreporters forthe detection of buried TNT-based landmines
Eden AmielSupervised by: Dr. Sharon Yagur-Kroll & Prof. Shimshon BelkinThe Department of Plant and Environmental SciencesThe Institute of Life Sciences
This Lecture:• 1. Introduction • Project overview and objectives• Landmines- background• Implications of landmines• Explosives trace signatures and detection techniques• Biosensors • Remote detection of buried landmines
• 2. Methods• Directed Evolution• Random Mutagenesis• Cloning + Ligation• Transformation• Screening + Isolation
• 3. Results• 4. Conclusions• 5. Further Research
Project Overview • Interdisciplinary R&D of a highly sensitive detection system
capable of covering large areas of land for the remote detection of buried TNT-based landmines.
• ‘munitions placed under, or near the ground or other surface area and designed to be exploded by the presence, or proximity of a person or vehicle'.
Landmines - background
AT’s: pressure > 150kg
AP’s: pressure > 5kg
2,4,6-Trinitrotoluene (TNT)
- International Committee of the Red Cross, 1996
Implications of landmines• Impacts on civilians safety:
1. Landmines remain dangerous after the conflict in which they were deployed has ended, killing and injuring civilians
2. 20,000 injuries/deaths worldwide each year3. Over half a million victims suffering from injuries caused by mines
• Impacts on the whole ecological system:1. Access denial2. Loss of biodiversity3. Chemical contamination4. Loss of productivity in arable lands
These make landmines a global problem; but despite efforts towards
landmine eradication, mines clearance remains a challenge.
1 Mine = 3$-30$ to produce, 300$-1000$ to find and clear
Explosives trace signatures • Approximately 80% of all landmines are TNT-based• These contain manufacturing impurities and degradation products• Leakage occurs through cracks in the mine casing and vapors
diffuse through the plastic housing of the mine.• The 3 most important vapors include: (1) 2,4,6-TNT (2) 2,4-DNT (3) 1,3-DNB
TNT-based landmine
TNT2,4 DNT1,3 DNB
Surface
Gas phase
Solid phase
Underground water
Liquid phase
Why 2,4-DNT sensor?1. Present in the vapor phase2. Environmentally more stable 3. Easier to work with
The main detection techniques
1. Metal detector 2. Chemical detection 3. Biological detection
• Dogs • Rats• Bees• Plants• Bacteria
Escherichia coli bioreporters
DNT-sensing element GFP-reporting elementyqjF gene promoter
Landmines and explosives biosensors
Optical system + detector
Immobilized sensor bacteria on soil
Telescope
Beam expander
Chopper
ShutterLaser
Mobile optical system detector
330
mW
laser beam at λ=445nm
Remote detection of landminesOptical systemdetector
Detection limits
Improvement of the sensitivity is required in order to consider this method as applicable
היום גילוי טווח
רצוי גילוי טווח
How do we do it ??
Directed evolution• Based on Darwinian evolution – in Nature: the survival of the fittest.
• In the lab: we generate genetic diversity in the gene of interest and perform a powerful screening or selection assay to isolate improved protein variants.
• Insertion of random mutations along the gene of interest (yqjF) using non optimal PCR conditions (Error prone PCR)
• No prior knowledge of structure or function is required.
How do we generate genetic diversity?
The process
yqjF cloned up-streamto the luxCDABE genes
1. Construct a library of variants by error-prone PCR
2. Insert fragments into an expression vector
3. Transform into bacteria host
4. Screen colonies with 2,4-DNT
5. Isolate improved performances
yqjF promoter
yqjF geneKpnI SacI
KpnI SacI לעמידות גןלאנטיביוטי
קה
הכנסת KpnIפרומוטר
SacI
2
3
4
5
X4DH5α E.coli
Screen colonies with 2,4-DNT
- DNT + DNT
Divide culture into 2 plates
Grow bacteria over-night
Incubation, 37°C
OD & RLU measures every 20 min
Isolate improved promoters• An algorithm was developed in order to find and isolate the best variants
האלגוריתם:הלומיניסציה 1. ערכי את שולף
(RLU( )העכירות מתוך( O.Dוערכי. הגולמיות התוצאות קבצי
.2- ה מערכי בלאנק .O.Dמחסר
.3- ה ערכי של נרמול על RLUמבצע- ה בערכי חלוקה .O.Dידי
על 4. התוצאות של אנליזה מבצע: והפרש יחס ערכי חישוב ידי
אחד 5. לכל קינטיקה גרף בונה , עבור אלו מחושבים ערכים משני , . עבור מחשב כן כמו ווריאנט כל
. , מתאים לינארי קו גרף כל
Time
Ratio
Time
Delta
הלינארית. 6 המשוואה מתוך , את שולף לקו המתאימה
השיפוע.השיפועים. 7 ערכי את מסדר
. לקטן מהגדולהווריאנטים. 8 את כפלט מציג
הגדולים השיפועים ערכי עם . כן כמו המדדים בשני ביותר
חמשת את גם מציגשיפוע להם הווריאנטים
אשר deltaה- ביותר הגדול הינושני בחיתוך מופיעים לא
המדדים.
𝑹𝑳𝑼 (𝑫𝑵𝑻 )<𝑹𝑳𝑼 (𝒄𝒐𝒏𝒕𝒓𝒐𝒍 )?
Time
Delta
A10 + C5
Dose-dependent screening
Choosing colonieswith the best results
No DNT + DNT
1 2 3 4 5 6 7 8 9 10 11 12A 100 50 25 0 100 50 25 0 100 50 25 0BCDEFGH
Picking the colonies that showed best results
Performing a dose dependent experiment to a select few
Results
0 50 100 150 200 2500
500,000
1,000,000
1,500,000
2,000,000
2,500,000
3,000,000
100ppm
Fwt1st2nd3rd4th-A104th-C5
Time (min)
Lum
ines
cenc
e (R
LU)
Delta RLU = Ratio RLU =RLU (DNT )RLU (control )
RLU (DNT )− RLU (control )
0 50 100 150 200 2500
10,000
20,000
30,000
40,000
50,000
60,000
70,000
80,000
90,000
Fwt1st
Time (min)
Lum
ines
cenc
e (R
LU)
0 50 100 150 200 2500
100,000
200,000
300,000
400,000
500,000
600,000
Fwt1st2nd
Time (min)
Lum
ines
cenc
e (R
LU)
0 50 100 150 200 2500
500,000
1,000,000
1,500,000
2,000,000
2,500,000
Fwt1st2nd3rd
Time (min)
Lum
ines
cenc
e (R
LU)
אינפורמטיביים RLUערכי לא
0 20 40 60 80 100 120 140 160 180 2000
1,0002,0003,0004,0005,0006,0007,000
Fwt::lux
+DNT"-DNT"
Time (min)
Lum
ines
cenc
e (R
LU)
50pp
m
0 20 40 60 80 100 120 140 160 180 2000
5,000
10,000
15,000
20,000
FB1::lux - 1st
Time (min)
0 20 40 60 80 100 120 140 160 180 2000
100,000200,000300,000400,000500,000600,000
FB2A1:lux - 2nd
Time (min) 0 20 40 60 80 100 120 140 160 180 2000
500,000
1,000,000
1,500,000
2,000,000
2,500,000
FB2A1#14::lux - 3rd
Time (min)
0 20 40 60 80 100 120 140 160 180 2000
200,000400,000600,000800,000
1,000,0001,200,0001,400,000
F-A10::lux - 4th
Time (min)
0 20 40 60 80 100 120 140 160 180 2000
500,0001,000,0001,500,0002,000,000
F-C5::lux - 4th
Time (min)
0 20 40 60 80 100 120 140 160 180 2000
5,000
10,000
15,000
20,000
25,000
30,000
35,000
40,000
45,000
50,000
FB2A1#14::lux - 3rd
Time (min)
Lum
ines
cenc
e (R
LU)
50pp
m
ΔRLU
0 10 20 30 40 50 60 70 80 90 1000
100
200
300
400
500
600
700
800
MG/Fwt1st2nd3rd4th-A104th-C5
DNT mg/l
Max
Rati
o ov
er 3
00 m
in
Ratio RLU
0 10 20 30 40 50 60 70 80 90 1000
500,000
1,000,000
1,500,000
2,000,000
2,500,000
3,000,000
MG/Fwt1st2nd3rd4th-A104th-C5
DNT mg/l
Max
∆RL
U ov
er 3
00 m
in
ΔRLU and Ratio at 25ppm
0 50 100 150 200 250 300 3500
50
100
150
200
250
300
350
400
Fwt1st2nd3rd4th-A104th-C5
Time (min)
Ratio
25pp
m
0 50 100 150 200 250 300 3500
500,000
1,000,000
1,500,000
2,000,000
2,500,000
Fwt1st2nd3rd4th-A104th-C5
Time (min)
∆RLU
25pp
m
Detection threshold
Fwt 1st 2nd 3rd 4th-A10 4th-C50
2
4
6
8
10
12
14
16
18
20
Sens
itivi
ty m
g/l (
EC20
0)
EC200 = the concentration which induces a response (Ratio = 2)
Transfer to a system suitable for field measuring
• Luminescence: Using luxCDABE genes, stronger responses, simpler to use, less background noise.
• Fluorescence: Using GFP gene, a more specific response suitable for the field detection system
DNT-sensing element GFP-reporting elementluxCDABE-reporting element
0 10 20 30 40 50 60 70 80 90 1000
2,0004,0006,0008,000
10,00012,00014,00016,00018,000
MG/Fwt1st2nd3rd4th-A104th-C5
DNT mg/l
Max
∆RF
U ov
er 3
00 m
in
0 10 20 30 40 50 60 70 80 90 1000
1
2
3
4
5
6
MG/Fwt1st2nd3rd4th-A104th-C5
DNT mg/l
Max
Rati
o ov
er 3
00 m
in
ΔRFU and Ratio RFU
ΔRFU and Ratio at 25ppm
0 50 100 150 200 250 300 3500.0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
Fwt1st2nd3rd4th-A104th-C5
Time
Ratio
25pp
m
0 50 100 150 200 250 300 3500
1000
2000
3000
4000
5000
6000
7000
8000
Fwt1st2nd3rd4th-A104th-C5
Time
ΔRFU
25pp
m
Fwt 1st 2nd 3rd 4th-A10 4th-C50
102030405060708090
100
Sens
itivi
ty m
g/l (
EC20
0)Detection threshold
EC200 = the concentration which induces a response (Ratio = 2)
WT CGGTTTTGGCGTATGGAGCGCCTGGCGTCTGGTTAAAACGACCCTCAAGCAGCAACAGCTTCGCGGTTAA
FB2 ..........................A...........................................
FB2A1 ..........................A...........................................
FB2A1#14 ..........................A...............T..........................G
4th-A10 ..........................A...............T..........................G
4th-C5 ..........................A...............T.................C........G
WT CTTCCCTCTGGCCGGAGCCATTCCGGCCTTATCCCTCAAATTTTTTGAAGATTTTTGACAGTTTTCCTTG
FB2 ............................................................A.........
FB2A1 ....................................................C.......A.........
FB2A1#14 ...............................................G....C....T..A.........
4th-A10 ...............................................G....C....T..A.........
4th-C5 ...............................................G....C....T..A.........
WT CTAACAATCATCATTCACCACGTTTATGATTCTCTCCATCGACAGCAACGACGCTAATACCGCGCCATTG
FB2 ......................................................................
FB2A1 ..................................................................T...
FB2A1#14 ..................................................................T...
4th-A10 ..................................................................TC..
4th-C5 .....................A......................A.........C...........T...
-35
-10 +1
F26 F36
F49
F48F3
F124F128F133F138
F186
F195
F213F230
yqjF promoter
Point Mutations – Individual effects
0 20 40 60 80 100 1200
200400600800
1,0001,2001,4001,6001,8002,000 MG/Fwt::lux
MG/F48::luxMG/F49::luxMG/F36:luxMG/F26::luxMG/F3::luxMG/F124::luxMG/F128:luxMG/F133::luxMG/F138::luxMG/F186::luxMG/F195::luxMG/F213::luxMG/F230::luxMG/F138:lux
2,4-DNT mg/l
Max
Rati
o ov
er 2
40'
Point Mutations – Individual
-35 region of σ70
Fwt::lux F124 F128 F133 F138 F3 F26 F48 F490.0
200.0
400.0
600.0
800.0
1000.0
1200.0
1400.0
1600.0
1800.0
2000.0
115.1
611.9
1612.0
1774.8
14.5 22.9 40.2 49.4100.7
Chart Title
ratio
at 1
00 m
g/l
- ב שנכנסה היחידה A10המוטציהאפקט: לבד אין
נוספות מוטציות עם שיפור: בשילוב יש
Point Mutations – Multiple
0 20 40 60 80 100 1200
500,000
1,000,000
1,500,000
2,000,000
2,500,000
3,000,000
3,500,000
4,000,000
4,500,000 MG/Fwt::luxMG/FB2::luxMG/FB2A1::luxMG/FB2A1::lux#14MG/F124-133:luxMG/F124-138:luxMG/F124,128::luxMG/F124,133::luxMG/F128,133::luxMG/F213::luxMG/F230::luxMG/F138:lux
2,4-DNT mg/l
Max
Del
ta R
LU o
ver 2
40'
0 20 40 60 80 100 1200
500,000
1,000,000
1,500,000
2,000,000
2,500,000
3,000,000
3,500,000
4,000,000
4,500,000MG/Fwt::lux
MG/FB2A1::lux#14
MG/F124-133:lux
MG/F124-138:lux
MG/F213::lux
MG/F138:lux
2,4-DNT mg/l
Max
Del
ta R
LU o
ver 2
40'
0 20 40 60 80 100 1200
5,000
10,000
15,000
20,000
25,000
30,000
MG/Fwt::lux
MG/F213::lux
MG/F138:lux
2,4-DNT mg/l
Max
Del
ta R
LU o
ver 2
40'
= = 1716 Possible combinations
Very low Ratio
Fwt 1st 2nd 3rd F124 F128 F133 F124-133
F137 F138 F145100
1,000
10,000
100,000
1,000,000
504 535
3,103
15,6366,634
3,219 2,054
124,008
770420 528
RLU פי גבוה -250רקע !WTמה
Detection thresholdEC200 = the concentration which induces a response (Ratio = 2)
MG/Fwt::lux
FB2 FB2A1 FB2A1#14 F124-133 F124-1380
2
4
6
8
10
12
Sens
itivi
ty m
g/l (
EC20
0)
הלומינסנציה F138המוטציה פעילות את מורידה אמנםהמערכת של הרגישות סף את מעלה אך
Conclusions
• A10 + C5 have both high Ratio and high Delta whereas FB2A1#14 has high Delta but low Ratio and FB2A1 has high Ratio but low Delta• Some specific mutations lower the performance of
the system but might increase performance when combined with other mutations.
Further Research
• Performing RM to a specific area in the promoter, such as the -35 domain
• Searching for TF binding sites and planning mutations accordingly
• Applying different approaches to further lower the detection threshold
• Using mutant strains of several membrane proteins as hosts for the genetic fusion
• Increasing the influx levels of the substance through the fusion of the membrane protein OmpF porin gene to an IPTG-inducible lacZ gene promoter.
Different approaches to lower the detection threshold
Δ
2,4-DNT
• Increasing the influx levels of the substance through the fusion of the membrane protein OmpF porin gene to an IPTG-inducible lacZ gene promoter.
Different approaches to lower the detection threshold
2,4-DNT
ompF
OmpF porin
Thanks
• Prof. Shimshon Belkin• Dr. Sharon Yagur-Kroll• Lab Team:• Dr. Rachel Rosen• Dr. Tal Elad• Dr. Keren Harel-Dasa• Omri Finkel • Neta Bachar• Bini Shemer• Noa Palevski• Adi Fainshtain• Yaara Moskovitz
Questions