iGEM 2015

2015 Cooper Union Summer STEM Program

http://www.cmu.edu/bio/research/undergrad_research/summer/igem/images/igem.png

BiosensorsAn analytical device that detects a substance, and is made from

biological parts that are based on or derived from living

organisms

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http://www.abpischools.org.uk/res/coResourceImport/modules/infectiousdiseases_immunity/en-

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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

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

Group A

Ethylene Gas Biosensor: A Fruit Ripening Detector

Anna McNeil, Orenna Brand, Misha Kotlik, Makda Fekade, Rageeb Mahtab

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

Food waste data1

1Food and Agriculture Organization of the United Nations

Solution:

Improved purchase and

consumption planning

Ethylene and fruit ripening

Ethylene gas (C2H4):

natural plant hormone

A: tomato

B: kiwifruit

Plants in Action, Australian Society of Plant Scientists

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.

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

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.)

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

Thanks to...

Lipshitz Consulting Group

Group C

Vitamin B12 Riboswitch

Gina Kim, Jee Hae Han, Ariella Himelstein, Sonal Kumar

Vitamin B12

Rationale

Vitamin B12 deficiency is a huge problem in

developing countries

Why?

Our Project

● The aim of our project is to use a riboswitch to detect B12 in

food

RDP Compliance Manual

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

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

Our Product

Available to the everyday consumer

Group T

Lead and Arsenic Biosensors

Cooper Union Summer STEM 2015 iGEM

Group T

Ayelet Senderowicz, Sarah Araten, Gabrielle Amar and Sam

Shersher

Introduction

❖ Element #82 on Periodic Table

❖ Naturally toxic to humans

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

Introduction: Arsenic

❖ Element #33

❖ Metalloid

❖ Two forms

The Problem

❖ Common in bedrock

❖ Symptoms of arsenic

poisoning:

➢ vomiting

➢ cardiac issues

➢ skin changes

Our Biosensors

Future Plans

● Designing and constructing physical producto 2 designs - Petri dish & drill

attachmento Biodegradable, disposable material

Group U

Nitrate Biosensor

Sofia Gereta, Maira Khan, Tina Lu, Aolanie Vargas

Group U

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

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/

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

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

PyeaR - GFP Composite

Source: http://2010.igem.org/Team:BCCS-Bristol/Wetlab/Part_Design/BioBricks/PyeaR

Experimentation

● Control: PyeaR composite

● Experimental: iGem Kit with medium RBS

● Measured fluorescence levels at varying nitrate concentrations using spectrophotometer

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

Results & Discussion (cont.)

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

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

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amazon.com/images/I/61s2MgB%2BkiL._S

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Group G

BIOBLOCK: ULTRAVIOLET BIOSENSOR

Group G, featuring Akiva Lipshitz, Steve Rebollo,

Jarrod Sinibaldi, and Shaina Zafar

Cooper Union Summer STEM

iGem Competition 2015

Professor Medvedik

BACKGROUND

BIOSENSOR MAP OVERVIEW

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

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/

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.

Q&A