IIT DELHI Eco - 2015.igem.org2015.igem.org/files/presentation/IIT_Delhi.pdf · •PROOF –IGEM IIT...
Transcript of IIT DELHI Eco - 2015.igem.org2015.igem.org/files/presentation/IIT_Delhi.pdf · •PROOF –IGEM IIT...
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IIT DELHI
Eco.coli
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INTRODUCTION
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INTRODUCTIONPollutants Emission Standards Annual Pollution
Emitted
Hydrocarbons 0.95 Kg 35 Kg
Carbon monoxide 43 Kg 261 Kg
NOx 0.64 Kg 17.3 Kg
Carbon-dioxide 0.19 Kg 5,190 Kg
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POLLUTION CRUSADER
PRESENT FUTURE
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PURPOSE OF TEAM ìGEM IIT DELHI
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POLLUTION CRUSADER - SCRDRAWBACKS
• Expensive Pt and Pd metals used.
• Over time performance
deteriorates; entire setup has to be
replaced/replenished.
• Non recyclable; adds to junk on
earth. Non biodegradable.
• Needs high temp to work properly.
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POLLUTION CRUSADER - RSPM
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Eco.coli POLLUTION CRUSADER
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POLLUTION CRUSADER – JOURNEY BEGINS
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INTRODUCTION
Components of motor exhaust
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HEADSTART - IGEM 2014 PARTS SUBMITTED
NITRITE REDUCTASE SULPHIDE QUIONONE REDUCTASE
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CHARATERIZATION
Nessler’s testFAILED
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TROUBLESHOOTING
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PROBLEMS – TURNING POINT
1) NO RBS UDOWNSTREAM OF PROMOTER
2) PERIPLASMIC PROTEIN
3) CYTOCROME C HEMOPROTEIN 4) SOOT / RSPM
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POLLUTION CRUSADER
SOOT / RSPM
• PM10 highly dangerous
• Wears down respiratory
tract, exposing to NOx
and SOx
• 47% in air
• Doctor’s advice – No
workout/exercise
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SOOT / RSPM SOLUTION
MECHANICAL SYSTEM
PROTOTYPE TEAM WAS
FORMED RIGHT AWAY
LOOKING AT
MECHANICAL ASPECT
OF PROJECT.
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POLLUTION CRUSADER – BIOLOGICAL PART
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BIOLOGICAL PART - CLONING
1) NO RBS UDOWNSTREAM OF PROMOTER 2) PERIPLASMIC PROTEIN
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PERIPLASMIC PROBLEM
. Two of our genes (nrfA and nosZ) coded for periplasmic
proteins
Solution- Doing a protein blast on the genes helped us find
that they contain a hydrophobic alpha helix, which will guide
the protein to the periplasmic space
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Methodology
How we cloned, what we cloned!
Part A = Constitutive promoter + Strong RBS
Part B = Pollution Crusader Gene
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Methodology
Nitrite Reductase (nrfA)
Our “Part Bs”
From E.coli
From P.aeruginosa
Sulfite reductase (cysI)
Nitrous oxide reductase (nosZ)
From Synechococcus
Sulfide quinone Reductase (SQR)
NO/NO2- NH3
N2O N2
SO2 H2S
H2S S
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Methodology – CLONING STRATEGY
Cloning Strategy
1. Cloning a strong promoter + Strong RBS upstream
2. Cloning a Yellow Fluorescence Protein downstream
NrfA
SYFP-2
3A assembly compatible
3A assembly compatible
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Methodology
Cloning Strategy
1. Cloning a Yellow Fluorescence Protein downstream
2. Cloning a strong promoter + Strong RBS upstream
NosZ
3A assembly compatible
Not 3A assembly compatible
SYFP-2
SYFP-2
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Methodology – CLONING STRATEGY
NosZ
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Methodology - CLONINGCloning Strategy
SQR
Cloning a strong promoter + Strong RBS upstream
3A assembly compatible
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Results
Pollution Crusader-
Parts Submitted
Bba_K1866000
Bba_K1866004
Bba_K1866003Bba_K1866002
Bba_K1866001
P + RBS + NrfA
NosZ + YFPP + RBS + NosZ
P + RBS + SQRP + RBS + NrfA
+YFP
+YFP
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Characterisation & Results
Clone Confirmation by Double Digestion
• Lane 3- Bba_K1866000• Lane 4- Bba_K1866002• Lane 6- Bba_K1866001• Lane 8- Bba_K1866003
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Characterisation & Results
Clone Confirmation by
Sequencing• Plasmids from our
clones were extracted
and sent to eurofins for
sequencing
• Sequencing revealed that
the cloning that we had
done was correct
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Characterisation & ResultsCharacterisation of Part Bba_K1866000
Promoter + RBS + NrfA
Lane 6- Total protein content for clone containing NrfA
Lanes 3&4- Periplasmic fractionation for clone containing NrfA
Bands are exactly where we want them!
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Characterisation & ResultsCharacterisation of Part Bba_K1866000
Promoter + RBS + NrfA
Functional assay of Protein
Minimal Media
Nitrate Fumarate Luria Broth(5%)
Minimal Media Clone containing nrfA
Nitrite (NO2-)
FAILED
No growth
Minimal Media Growth
Reference- Clarke, TA., Mills, PC. et al (2008). Escherichia coli cytochrome c nitrite reductase NItalic textrfA.. Methods in Enzymology
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Characterisation & ResultsCharacterisation of Part Bba_K1866000
Promoter + RBS + NrfA
Functional assay of Protein
• Neither the control (DH5 alpha), nor our clones showed growth on minimal media after 18 hours.
• A white pellet was obtained, but later we realized that the pellet was of ampicillin, which had formed a white precipitate with formate
Minimal Media Growth
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Characterisation & ResultsCharacterisation of Part Bba_K1866000
Promoter + RBS + NrfA
Functional assay of Protein
Luria Broth Clone containing nrfA
Nitrite (NO2-)
Growth
After 16 hours, for different nitrite conc.,
Monitor pHSUCCESSFUL
pH Monitoring
Reference- Evaluation of pH indicator-based colorimetric films for ammonia detection using optical waveguides-J. Courbata, D. Brianda, J. Damon-Lacostea, J. Wöllensteinb, N.F. de Rooij
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Characterisation & ResultsCharacterisation of Part Bba_K1866000
Promoter + RBS + NrfA
Functional assay of Protein
• The experiment showed results as expected, with the pH of our clones being higher than the control, which can be attributed to the presence of excess ammonia in the solution.
• We also saw that at concentrations of Nitrite greater than 2mM, the pH showed a sharp decline. This could be due to the fact that high concentrations of nitrite (NO2
-) become toxic for the cells, due to which cell death occurs.
DH5 alpha (control) NrfA Clone
pH Monitoring
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Characterisation & ResultsCharacterisation of Part Bba_K1866000
Promoter + RBS + NrfA
Functional assay of Protein
• Cultures of our clones were grown anaerobically in 5ml Luria broth, along with standard DH5α cells, used as control. These were then subcultured into 50 ml LB containing tubes, also grown anaerobically, with different concentrations of Sodium Nitrite.
• To a 1ml aliquot, 40µl phenol, 40µl sodium nitroprusside and 100µl of oxidising reagent (tri- sodium citrate + sodium hypochlorite) was added, giving an orange-yellow colour
• The absorbance of this was measured at a wavelength of 540nm
The Indophenol Test
Reference-Koroleff, F. 1976. Determination of ammonia. In Methods of Seawater Analysis (K. Grasshoft, ed.). Verlag Chemie
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Characterisation & ResultsCharacterisation of Part Bba_K1866000
Promoter + RBS + NrfA
Functional assay of Protein
Nitrite (NO2-)
Growth
Luria Broth Clone containing nrfA
After different time intervals, for Nitrite concentration = 1mM,
1ml culture aliquot
Indophenol test
Check OD 540SUCCESSFUL
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Characterisation & ResultsCharacterisation of Part Bba_K1866000
Promoter + RBS + NrfA
Functional assay of Protein
The experiment showed results as expected, with the absorbance value of our clones being higher than the control, which can be attributed to the presence of excess ammonia in the solution.
The value increased with increase in time, before finally saturating after ~16 hours
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Characterisation & ResultsCharacterisation of Part Bba_K1866000
Promoter + RBS + NrfA
Functional assay of Protein
Nitrite (NO2-)
Growth
Luria Broth Clone containing nrfA
1ml culture aliquot
Indophenol test
Check OD 540
SUCCESSFUL
After 16 hours, for different nitrite conc.,
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Characterisation & ResultsCharacterisation of Part Bba_K1866000
Promoter + RBS + NrfA
Functional assay of Protein
• This experiment was also successful. The graph showed an increase in OD Values with increasing nitrite concentrations.
• At high values of nitrite (>2mM), the graph shows a sharp decline, which can once again be attributed to Nitrite toxicity.
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Characterisation & ResultsCharacterisation of Part Bba_K1866000
Promoter + RBS + NrfA
Functional assay of Protein
The Nessler’s test
• On addition of Nessler’s reagent to a solution containing ammonia, a reddish brown precipitate is formed
• This precipitate can be centrifuged and weighed after pouring out the solution. The weight of the precipitate gives an estimate of the relative amount of ammonia present in the solution.
Reference- Mackie and MacCartney,1989,Practical Medical Microbiology, Collee J.G.,Duguid J.p.,Fraser A.G.and Marmion B.p. (Eds.),13th ed., Churchill Livingstone, edinburgh.
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Characterisation & ResultsCharacterisation of Part Bba_K1866000
Promoter + RBS + NrfA
Functional assay of Protein
Luria Broth Clone containing nrfA
Nitrite (NO2-)
Growth
After 16 hours, for different nitrite conc.,
1ml culture aliquot
Nessler’s reagent test CentrifugePour out media and weigh
SUCCESSFUL
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Characterisation & ResultsCharacterisation of Part Bba_K1866000
Promoter + RBS + NrfA
Functional assay of Protein
This experiment was also successful, showing trends as expected. At high nitrite concentrations, the pellet size reduced drastically (the reason being toxicity at high nitrite concentration).
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HEME PROBLEM – PREVIOUS WORK
IGEM BIELEFELD GERMANYIGEM TEAM MACQUARIE
Many teams working on human
hemoglobin
iGEM14 TU Delft-Leiden
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HEME PROBLEM – WHAT EXACTLY IS THE PROBLEM?
3) TRANSPORTAION OF HEME TO
PERIPLAMIC SPACE
1)HEME PATHWAY IS HIGHYLY
REGULATED
4) MATURATION OF HEME BY
CcmAH COMPLEX IS DONE.
2) Fe+2 INCORPORATION
REQUIRED
5) DOCKING OF ENZYME WITH
HEME.
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HEME – MODELLING IN COPASI
COPASI
• PARAMETERS WERE
TAKEN FROM –
BRENDA,KEGG,
ECOCYC
• LITERATURE
SCANVING OF HEME
PATHWAYS
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Methodology
COPASI
PROBLEM MIGHT THEIR
AT THE DOWNSTREAM
OF TRANSPORTAION
PROCESS
- AT HEME
MATURATION.
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OVEREXPRESSING CcmAH COMPLES
• RATE LIMITING STEP IN
DOCKING
• COMPLEX CASSETE IS VERY
LARGE
• YAC / BAC SHOULD BE USED
TO CLONE THE CASSETE.
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SOLUTIONS TO HEME PROBLEM
EXTRACELLULAR
1) Incorporation of ChuA
receptor.
2)Provide ALA Extracellularly.
INTRACELLAR
1) Clone ALA synthase of rat to avoid
feedback inhibition by heme.
2)Overexpression of CcmAH
complex.
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POLLUTION CRUSADER – MECHANICAL PART
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POLLUTION CRUSADER-prototype
Exhaust from engine De-sooter tank removes Hydrocarbons
Blower pushes gases through silica gel where NOx gets converted to NO
NO rich gases passed through culture containing Eco.coli
Complete assembly
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POLLUTION CRUSADER-prototype components
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Frugal diesel burner to compensate for unavailability of engine
Tube containing silica gel
POLLUTION CRUSADER- working prototype
Ice-cold water for heat exchanger
De-sooter tankSuction pump
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POLLUTION CRUSADER – RESULTS
The pollution crusader prototype showed a positive result, with the desooter tank working even better than expected.
Heat exchanger was efficient in reducing the temperature substantially, which was monitored by a gas thermometer.
Subsequently, NOx sensors placed after the silica gel pipe showed that the silica gel also worked as expected, reducing NO2 to NO. The NOx sensor showed negligible amounts of NO2 coming out of the pipe.
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POLLUTION CRUSADER – RESULTS
Run number amount of soot collected(gram)
1 23.5
2 34.6
3 26.7
4 19.9
5 24.1
Run number NO2 concentration (standard, ppm) NO2 conc (detected)
1 42 9
2 42 8
3 42 11
4 42 9
5 42 10
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CONCLUSIONS
1) CLONING OF ALL THE PARTS WERE SUCCESSFUL.
2) NRFA IS WORKING AS EXPECTED.
3) NRFA WAS CHARACTERIZED BY FOUR DIFFERENT ASSAYS.
4) 3 SHOWED ENZYME IS WORKING AND 1 ASSAY FAILED
5) PROTOTYPE IS WORKING AS EXPECTED.
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ACHIEVEMENTS
1) 5 BIOBRICKS SUBMITTED.
2) 3 ARE STANDARD BIOBRICKS.
3) A PART HAS BEEN EXTENSIVELY CHARACTERIZED.
4) PROTOTYPE IS WORKING.
5) TWO EXISTING PART HAS BEEN IMPROVED BY PLACING SYFP2 DOWNSTREAM
OF GENE
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HUMAN PRACTICES
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GOVERNMENT – POLICY CHANGES
DELHI CHIEF MINISTER
• CONCERNS OVER
ENVIRONMENTAL EXPOSURE
• CONVINCED
• SUPPORTS, FUND OUR
PROJECT
• PROOF – IGEM IIT DELHI 2016 –
DELHI GOVT SPONSORED
• BEAURACRATIC LEVEL STUCK –
2015
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SOCIOLOGIST RESEARCH
PhD STUDY
• ETHICAL STUDY
• STUDIED - TEAM WORK
• RESEEARCH WILL COME
OUT SOON
• HUMANITARIAN MENTOR
OF THE TEAM
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ORIENTATION – BEST BIOTECHNOLOGY COLLEGES
SYNBIO INITIATION
• 20 COLLEGES
PARTICIPATED
• MORE THAN 1000
STUDENTS
• TWO COLLEGES(NSIT
& DTU) WILL
REGISTER FOR IGEM -
2016
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SOCIAL AWARNESS – GROUND LEVEL WORK
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SOCIAL AWARNESSSOCIAL AWARNESS – GROUND LEVEL WORK
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SOCIAL AWARNESS
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SOCIAL AWARNESS
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SOCIAL AWARNESS
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TRYST – OPEN HOUSE 1)Tryst is India’s biggest annual science and technology festival.
2) iGEM Team IIT Delhi was awarded the 1st runner up prize in the
‘Best stall in Tryst 2015’ category WON $302.
3)Open house is an annual event in IIT Delhi which aims to promote
and increase awareness about new technologies specifically for school
children.
4) iGEM team IIT Delhi put up a stall in this event with the goal to
Motivate and encourage school students to develop a greater interest
in Biology and Biotechnology.
5) We also gave a basic introduction about synthetic biology and iGEM with
the hope that it might motivate some of them to enrol as the first high school
team to participate in iGEM from India.
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OTHER HUMAN PRACTICES WORK
1) COMPILED POLLUTION DOUCMENT. IT IS 179 PAGE BOOK ON
POLLUTION IN INDIA. MOST EXTENSIVE STUDY OF AIR
POLLUTION IN INDIA. (PDF LINK ON WIKI)
2) SUBMITTED THE REPORT TO ENVIORNMRNT AND HEALTH
MINISTRY, GOVT. OF INDIA.
3)HELPED IIT KHARAGPUR, IIT MADRAS.
4)ATTENDED IGEM INDIA MEET AT IISER.
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SURVEY
1) iGEM Team IIT Delhi conducted some surveys to get an
idea of the level of awareness among the citizens of Delhi
2) This was done in Central Park in Connaught Place, New
Delhi and Munerika village.
3) The details of the surveys have been enclosed in a
separate document.
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CROWDFUNDING
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ROCKY ROAD
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OUR SPONSORS