iGEM 2015 2015 Cooper Union Summer STEM Program - - PowerPoint PPT Presentation

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iGEM 2015 2015 Cooper Union Summer STEM Program - - PowerPoint PPT Presentation

Nov 25, 2022 355 likes •894 views

iGEM 2015 2015 Cooper Union Summer STEM Program http://www.cmu.edu/bio/research/undergrad_research/summer/igem/images/igem.png Biosensors An analytical device that detects a substance, and is made from biological parts that are based on or

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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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Biosensors

An analytical device that detects a substance, and is made from biological parts that are based on or derived from living

  • rganisms

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

  • f 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 detector

Our 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

product

  • 2 designs - Petri dish & drill

attachment

  • 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 Problem

In 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/Overview

Why 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
  • Created pYeaR promoter
  • Bristol iGem 2010
  • Used PyeaR to detect nitrates and nitrites
  • NsrR used as a regulatory protein
  • Rice University 2015
  • Creating biosensor that detects nitrates, phosphates, and

potassium

  • Currently trying to work with 3 promoters
  • SVA/NYC 2015
  • 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)

  • responsive to nitrate,

nitrite, and nitric oxide

  • pSB1C3 Vector
  • Primers
  • Rainbow Kit
  • GFP, medium RBS

Plasmid Map

http://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
  • Rainbow Kit misassembly
  • Very Strong RBS
  • Overproduction of amilGFP
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Future Goals

  • Increase the sensitivity of the biosensor
  • Altering the ORI, reporter, and promoter
  • 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