igem 2015 - cooper.educooper.edu/sites/default/files/uploads/assets/engineering/files/2016... · 1....
TRANSCRIPT
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iGEM 2015
2015 Cooper Union Summer STEM Program
http://www.cmu.edu/bio/research/undergrad_research/summer/igem/images/igem.png
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BiosensorsAn analytical device that detects a substance, and is made from
biological parts that are based on or derived from living
organisms
https://images.accu-chek.com/images/products/metersystems/advantage/nbg_advantage_mg_l.png
http://www.abpischools.org.uk/res/coResourceImport/modules/infectiousdiseases_immunity/en-
images/Pregnancy-Test-12030274-istock.jpg
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Rainbow Kit
● Using parts and methods from Genomikon and Rainbow
Factory kits
● Collection of Lego-like genetic parts, DNA sequences with
different functions, that simplify and accelerate the creation
of genetic circuits
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Rainbow Kit - Basic Parts
http://2009.igem.org/wiki/images/thumb/7/78/II09_GC_Key.png/425px-II09_GC_Key.png
Promoter = gene switch
RBS = binds the protein-building machine
Protein coding region = codes for actual protein
Terminator = stop sign
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Group A
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Ethylene Gas Biosensor: A Fruit Ripening Detector
Anna McNeil, Orenna Brand, Misha Kotlik, Makda Fekade, Rageeb Mahtab
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Global sustainability: food waste
● Fruits and vegetables are the most wasted foods
● 492,000,000 tons of food waste in high and low-income
countries in 2011
● Negative health, financial, and environmental implications
● $15 billion in financial losses per year
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Food waste data1
1Food and Agriculture Organization of the United Nations
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Solution:
Improved purchase and
consumption planning
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Ethylene and fruit ripening
Ethylene gas (C2H4):
natural plant hormone
A: tomato
B: kiwifruit
Plants in Action, Australian Society of Plant Scientists
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Our fruit ripening detectorOur product: a biosensor-
containing sticker that
producers and consumers can
attach to individual fruits
The modified bacteria in the
sticker will change color in
the presence of C2H4.
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Creating the biosensor
1. Create a novel ethylene responsive system by
fusing proteins from the Arabidopsis thaliana
(mustard) plant and E. coli bacteria
2. Modify the system to produce blue protein in
response to ethylene concentrations
3. Insert system into E. coli
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What we’ve accomplished so far...
● Designed and assembled a plasmid containing
amilCP (blue chromoprotein) gene cassettes
using Rainbow Factory (SynbiotaTM)
● Ran trials on amilCP color expression, and
analyzed color output
● Researched fusion proteins (Levskaya et al.)
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Future plans
● Complete testing of reporter gene
● Design and assemble fusion protein system
● Tune system to increase color expression with
increasing ethylene concentration
● Create marketable sticker product
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Thanks to...
Lipshitz Consulting Group
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Group C
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Vitamin B12 Riboswitch
Gina Kim, Jee Hae Han, Ariella Himelstein, Sonal Kumar
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Vitamin B12
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Rationale
Vitamin B12 deficiency is a huge problem in
developing countries
Why?
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Our Project
● The aim of our project is to use a riboswitch to detect B12 in
food
RDP Compliance Manual
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iGEM Kit Assembly
Edwards, Andrea L., B.S., and Robert T. Batey, Ph.D. "Riboswitches: A Common RNA Regulatory Element." Nature. Nature Education, 2010. Web. 10 Aug. 2015
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Results
● Our colonies grew● We encountered a problem because the B12
is naturally red and we weren’t able to determine the difference between the B12 color or the RFP
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Our Product
Available to the everyday consumer
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Group T
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Lead and Arsenic Biosensors
Cooper Union Summer STEM 2015 iGEM
Group T
Ayelet Senderowicz, Sarah Araten, Gabrielle Amar and Sam
Shersher
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Introduction
❖ Element #82 on Periodic Table
❖ Naturally toxic to humans
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The Problem
❖ In 1976, a ban was issued on all paint containing lead
❖ However, there are still many inhabited houses painted before 1976 whose paint is a health hazard
❖ This paint falls into soil and contaminates all growth
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Introduction: Arsenic
❖ Element #33
❖ Metalloid
❖ Two forms
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The Problem
❖ Common in bedrock
❖ Symptoms of arsenic
poisoning:
➢ vomiting
➢ cardiac issues
➢ skin changes
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Our Biosensors
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Future Plans
● Designing and constructing physical producto 2 designs - Petri dish & drill
attachmento Biodegradable, disposable material
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Group U
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Nitrate Biosensor
Sofia Gereta, Maira Khan, Tina Lu, Aolanie Vargas
Group U
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Introduction/Overview: The Nitrate ProblemIn order to create a biosensor capable of detecting nitrate levels in soils, we are amplifying the cassette created by the
BCCS-Bristol 2010 iGem team, with modifications.
Nitrogen is a main component of fertilizer, yet when excessively applied they pollute the local waters through a
process called eutrophication.
http://www.i-study.co.uk/IB_ES/IB_unit5_pollution_management.html
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Introduction/OverviewWhy is it important?
Why is it interesting?
A biosensor capable of detecting
nitrogen levels in soil would allow
for more efficient use of fertilizer,
and can potentially decrease
chemical contamination in the
environment.
Happy Environment!
http://www.clipart-
box.com/cliparts/MEQEUAbc4fW6aa2b/
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Previous Research
● Edinburgh 2009
o Created pYeaR promoter
● Bristol iGem 2010
o Used PyeaR to detect nitrates and nitrites
o NsrR used as a regulatory protein
● Rice University 2015
o Creating biosensor that detects nitrates, phosphates, and
potassium
o Currently trying to work with 3 promoters
● SVA/NYC 2015
o Device that displays soil nutrient levels for in home use
https://upload.wikimedia.org/wikipe
dia/commons/3/3b/HandsInSoil.jpg
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Materials; Our Biobrick● Nitrate cassette with PyeaR
promoter (BBa_K381001)
o responsive to nitrate,
nitrite, and nitric oxide
● pSB1C3 Vector
● Primers
● Rainbow Kit
o GFP, medium RBS Plasmid Maphttp://beta.labgeni.us/registries/parts_re
gistry/?part=BBa_K216005
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PyeaR - GFP Composite
Source: http://2010.igem.org/Team:BCCS-Bristol/Wetlab/Part_Design/BioBricks/PyeaR
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Experimentation
● Control: PyeaR composite
● Experimental: iGem Kit with medium RBS
● Measured fluorescence levels at varying nitrate concentrations using spectrophotometer
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Results & Discussion
● No growth from very strong RBS iGEM Kit
● iGem Kit with medium RBS showed growth
● Nitrate composite (BBa_K381001) grew in high
amounts
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Results & Discussion (cont.)
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Problems & Setbacks
● Possible Contamination
● Low concentrations of DNA
● Time - unable to run additional trials
● Lack of growth of transformed bacteria
o Rainbow Kit misassembly
o Very Strong RBS
o Overproduction of amilGFP
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Future Goals
● Increase the sensitivity of the biosensor
o Altering the ORI, reporter, and promoter
o Using regulatory proteins
● Detecting other fertilizer chemicals such
as phosphates and potassium from other sources
● Creating a compact device; Commercial and
Individual Use
○ Form a pH strip, simple chemical test
http://ecx.images-
amazon.com/images/I/61s2MgB%2BkiL._S
L1000_.jpg
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Group G
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BIOBLOCK: ULTRAVIOLET BIOSENSOR
Group G, featuring Akiva Lipshitz, Steve Rebollo,
Jarrod Sinibaldi, and Shaina Zafar
Cooper Union Summer STEM
iGem Competition 2015
Professor Medvedik
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BACKGROUND
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BIOSENSOR MAP OVERVIEW
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RESULTS
2 Experiments
• Controlled/Simulated Experiment: using a Blak-Ray 100 Long Wave UV
Length Lamp
• Direct UV Ray Experiment: using direct sunlight
2 Controls
• Positive Control: constitutive rainbow kit promoter PR4
• Negative Control: same parts; placed in dark room
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OUR PRODUCT
• Bioblock: “spray on bacteria”
• Past product: AOB(Ammonia-Oxidizing Bacteria) soaps and mists.
• Convenient, cost effective, raises awareness, and informative.
Artwork by Dan Cassaro. Photograph by Jens Mortensen for The New York Times http://thekiddsplace.com/screening-the-sunscreens/
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FUTURE APPLICATIONS
• The replacement of the LacZ reporter with melanin would make this
product more consumer friendly.
• Melanin either absorbs or scatters UVR light, allowing the product to be
used as a sunscreen. The longer the sunscreen is exposed to UVR, the more
melanin will be produced.
• Reduce the risk of contracting skin cancer; temporarily even out tans.
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Q&A