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

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 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

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 Promoter = gene switch RBS = binds the protein-building machine Protein coding region = codes for actual protein Terminator = stop sign http://2009.igem.org/wiki/images/thumb/7/78/II09_GC_Key.png/425px-II09_GC_Key.png

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 data 1 1 Food and Agriculture Organization of the United Nations

Solution: Improved purchase and consumption planning

Ethylene and fruit ripening Ethylene gas (C 2 H 4 ): natural plant hormone A: tomato B: kiwifruit Plants in Action, Australian Society of Plant Scientists

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 C 2 H 4 .

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 (Synbiota TM ) ● 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 product o 2 designs - Petri dish & drill attachment o Biodegradable, disposable material

Group U

Nitrate Biosensor Sofia Gereta, Maira Khan, Tina Lu, Aolanie Vargas Group U

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. http://www.i-study.co.uk/IB_ES/IB_unit5_pollution_management.html Nitrogen is a main component of fertilizer, yet when excessively applied they pollute the local waters through a process called eutrophication .

Introduction/Overview Why is it important? Happy Environment! 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. http://www.clipart- box.com/cliparts/MEQEUAbc4fW6aa2b/

Previous Research ● Edinburgh 2009 o Created pYeaR promoter ● Bristol iGem 2010 https://upload.wikimedia.org/wikipe o Used PyeaR to detect nitrates and nitrites dia/commons/3/3b/HandsInSoil.jpg 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

Materials; Our Biobrick ● Nitrate cassette with PyeaR promoter (BBa_K381001) o responsive to nitrate, nitrite, and nitric oxide ● pSB1C3 Vector ● Primers ● Rainbow Kit o http://beta.labgeni.us/registries/parts_re Plasmid Map GFP , medium RBS 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 http://ecx.images- amazon.com/images/I/61s2MgB%2BkiL._S L1000_.jpg

Group G

BIOBLOCK: ULTRAVIOLET BIOSENSOR Cooper Union Summer STEM Group G, featuring Akiva Lipshitz, Steve Rebollo, iGem Competition 2015 Jarrod Sinibaldi, and Shaina Zafar 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