Team:Minnesota/Templates

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UMN iGEM 2014

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Minnesota iGEM 2014




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Mercury is a neurotoxic heavy metal with the ability to biomagnify, therefore it is a significant issue in public health and environmental studies worldwide. Its levels are continually on the rise due to copper, nickel, and gold mining activities, the industrial use of mercury catalysts, mercurial fungicides in agriculture, and the burning of fossil fuels. This has resulted in the pollution of many marine ecosystems and water reservoirs worldwide, the cleanup of which using current technology, is either not feasible or incredibly costly. This study describes the use of engineered recombinant bacteria to facilitate the biological remediation of the neurotoxin methylmercury and hazardous mercury ions from an aquatic target site into less toxic form. This synthetic microbe was incorporated in novel encapsulation technology within a cost-effective, scalable water filtering column. The employment of this device could rigorously change the practices used in mercury decontamination efforts as well as pave the way for the switch to biological rather than chemical processes. Furthermore, this technology can be applied towards bioremediation and biosensing of various other heavy metals and organic toxins in the environment.





logo



Mercury is a neurotoxic heavy metal with the ability to biomagnify, therefore it is a significant issue in public health and environmental studies worldwide. Its levels are continually on the rise due to copper, nickel, and gold mining activities, the industrial use of mercury catalysts, mercurial fungicides in agriculture, and the burning of fossil fuels. This has resulted in the pollution of many marine ecosystems and water reservoirs worldwide, the cleanup of which using current technology, is either not feasible or incredibly costly. This study describes the use of engineered recombinant bacteria to facilitate the biological remediation of the neurotoxin methylmercury and hazardous mercury ions from an aquatic target site into less toxic form. This synthetic microbe was incorporated in novel encapsulation technology within a cost-effective, scalable water filtering column. The employment of this device could rigorously change the practices used in mercury decontamination efforts as well as pave the way for the switch to biological rather than chemical processes. Furthermore, this technology can be applied towards bioremediation and biosensing of various other heavy metals and organic toxins in the environment.





logo



Mercury is a neurotoxic heavy metal with the ability to biomagnify, therefore it is a significant issue in public health and environmental studies worldwide. Its levels are continually on the rise due to copper, nickel, and gold mining activities, the industrial use of mercury catalysts, mercurial fungicides in agriculture, and the burning of fossil fuels. This has resulted in the pollution of many marine ecosystems and water reservoirs worldwide, the cleanup of which using current technology, is either not feasible or incredibly costly. This study describes the use of engineered recombinant bacteria to facilitate the biological remediation of the neurotoxin methylmercury and hazardous mercury ions from an aquatic target site into less toxic form. This synthetic microbe was incorporated in novel encapsulation technology within a cost-effective, scalable water filtering column. The employment of this device could rigorously change the practices used in mercury decontamination efforts as well as pave the way for the switch to biological rather than chemical processes. Furthermore, this technology can be applied towards bioremediation and biosensing of various other heavy metals and organic toxins in the environment.





logo



Mercury is a neurotoxic heavy metal with the ability to biomagnify, therefore it is a significant issue in public health and environmental studies worldwide. Its levels are continually on the rise due to copper, nickel, and gold mining activities, the industrial use of mercury catalysts, mercurial fungicides in agriculture, and the burning of fossil fuels. This has resulted in the pollution of many marine ecosystems and water reservoirs worldwide, the cleanup of which using current technology, is either not feasible or incredibly costly. This study describes the use of engineered recombinant bacteria to facilitate the biological remediation of the neurotoxin methylmercury and hazardous mercury ions from an aquatic target site into less toxic form. This synthetic microbe was incorporated in novel encapsulation technology within a cost-effective, scalable water filtering column. The employment of this device could rigorously change the practices used in mercury decontamination efforts as well as pave the way for the switch to biological rather than chemical processes. Furthermore, this technology can be applied towards bioremediation and biosensing of various other heavy metals and organic toxins in the environment.

Project

  • Dry Lab  
  • dry dry
  • dry dry dry
  • Wet Lab
    • wet wet
    • wet wet








Encapsulation








The main goal of EncapsuLab was to create a system for the preservation and protection of the bacteria in our system, as well as physically separating them from the outside environment. To achieve this, we created a water-porous silica matrix using techniques developed by the Aksan and Wackett labs at the U of M. Furthermore, we developed a device to work as a proof of concept for the use of encapsulated bacteria in a real water-cleaning system. In addition to this, we conceptualized a scaling-up of our system for larger water-cleaning problems. Lastly, we developed a mathematical model to compare our experimental data in order to better understand the biochemical networks behind our work.
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Encapsulation Procedure

Mathematical Modeling

Mathematical Modeling

Mathematical Modeling

Planets merR merT merP merA merB

Dry Lab

dry dry dry dry dry dry











Wet Lab

wet wet wet wet

Biobrick Assembly

phsABC

Biobrick Assembly

Biosafety

Results Hg2

Results MethyllHg

Results phsABC




Meet The Team






Policies & Practices

Our Policy and Practices approach this year has focused on establishing an effective two-way discourse between our team and the public in order to inform our design, educate the public, and illuminate ethical issues related to both our project and integration of public opinion into project implementation. We focused our discussion on safety, ethics, and sustainability in order to design a project that fits the needs of the public while maintaining technical viability. Our team did extensive educational outreach in addition to educating ourselves on public perception of our work. We used this input to inform our device design such that it could be implemented in a way that addresses the major concerns of both scientists and consumers. We also took steps to protect our intellectual property and to educate ourselves about the patent process. Finally, our team sought to investigate ethical issues brought up by our discourse with the public by discussing both our work and ethics related to the project with a variety of experts and ethicists.

Educational Outreach

Building on past successes, our team has been devoted to volunteering our services to the community in a number of educational venues. The team took our curriculum, first developed in 2013, and improved the structure and delivery of our lesson plans in the hopes of encouraging awareness and education on topics in synthetic biology. Since 2013 our educational outreach group ECORI (Educating Communities On Research Innovation) has taught our [[File:original, interactive classroom curriculum]] to over 200 students (K-12) and their teachers. This year we also created a mobile exhibit form of our curriculum along with a layman’s introduction to our project that we displayed on over half a dozen weekends to visitors of all ages at the Science Museum of Minnesota. Our curriculum has also been brought to several other STEM fairs and family fun events in the Twin Cities area including the 3M Science Day Fair for 3M employees and their families, UMN Biodiversity Fair, CSE Family Fun Fair, and the Middle School STEM Fair hosted by the Association of Multicultural Students at UMN. Finally, the team designed a Synthetic Biology Game Show that was presented on stage with 30 participants at the Minnesota State Fair to assess the general public’s knowledge of the subject and teach hundreds of passers-by in a way that was both engaging and interactive. Winners were rewarded with reusable bags, magnets, and gift cards donated by our sponsors. In the spirit of science, our curriculum has been ever evolving to constantly address salient topics and educational materials. The variable versions of our curriculum allow it to be flexible and practical in various settings.

Public Perception

Our team sought to inform the majority stakeholders in our community concerning the scope of our project. This year our team chose to have an exhibit catered towards adult residents at the Minnesota State Fair (the largest statewide annual gathering with over 1.8 million visitors each year) to learn how we can best design our technology to meet the needs and concerns of the people whose waters we hope to bioremediate. We delivered a short synopsis of our device, the synthetic biology involved, and safety precautions we have outlined for our project. We then presented visitors with a five question survey using a Likert Scale to gauge public perception of both our device, and the synthetic biology methods used. The survey was a huge success with over 320 participants. With such a diverse attendance, our survey captured a great cross-section of the Minnesota community that would be impacted by the implementation of our device. The results of our survey, illustrated below, informed how and where the public would be most comfortable with implementing our device, and illustrated the need for catered education addressing the public’s major concerns prior to applying our device in the environment. Our model for gauging public perception allowed for a wide, diverse crowd to be accessed. This model can be used upon request.

Intellectual Property

Documentary



We compiled this documentary in order to inform those unfamiliar with the problem of global mercury contamination and to discuss the bioethical questions of synthetic biology as they related to our device implementation. We have conducted interviews with specialists from environmental toxicology, biotechnology, and philosophy at the University of Minnesota. Through our collaboration with the 2014 Colombia iGEM Team, we further examined the current methylmercury contamination in Colombia and around the globe.

Safety in the Lab

1. Your Training



a) Safety trainings
DEHS Introduction: Research Safety DEHS Chemical Safety DEHS Waste Management

Safety in the Lab

2. Our Local Rules and Regulations Who is responsible for biological safety at our institution? The project was discussed with the Department of Environmental Health and Safety at our university, and a plan was devised for mercury waste disposal based on their input. General biosafety guidelines found at https://www.dehs.umn.edu/bio.htm, http://www.dehs.umn.edu/bio_pracprin.htm and http://www.cdc.gov/biosafety/publications/bmbl5/bmbl.pdf were followed.

Safety in the Lab

3. Risks of Your Project Now To mitigate risks to the safety and health of team members, or other people working in the lab: Gloves are used in any protocol that utilizes Ethidium Bromide, including gel electrophoresis. Lab coat, gloves, and full face shields are used when cutting gel fragments in proximity of ultraviolet light. For handling mercury, a lab coat, inner and outer (long cuffed) nitrile gloves, lab goggles and face shields will be used, and used materials will be disposed of by the University of Minnesota Department of Environmental Health and Safety. There are assigned incubators, hoods, and disposal containers for hazardous materials like mercury chloride. Design features to minimize risk kill switch proposal that would not allow the bacteria to survive outside of the encapsulation or even device holding the cells Air tight? non pathogenic lab strains

Attributions


Wet Lab:

Mercury Project Design:
Basem, Aunica

Mercury Ion Testing:
Aunica, Sarah, Cassandra, Camilo, Srijay, Jennifer, Suzie

Methylmercury testing:
Nater Lab, Aunica, Nicholas, Srijay, Patrick, Suzie, Basem

Cadmium, Zinc, Copper project design:
Basem, Stephen, Aunica

Cadmium, Zinc, Copper Testing:
Aunica, Cassandra, Jessica

Kill Switch Proposal:
David, Sarah, Camilo, Stephen, Basem

pDU1358 received from Dr. Anne O. Summers, University of Georgia
pSB74 received through addgene from Keasling Lab

Composite parts:
mer operon:
Primer design: Basem, Stephen
Parts cloning: Basem, Jennifer, Stephen, Valeriu

phsABC:
Primer design: Basem, Stephen
Parts cloning: Basem, Stephen, Valeriu

Single parts:
merR:

Primer design: Basem, Stephen
Parts cloning: Cassandra
merT:
Primer design: Stephen, Basem
Parts cloning: Sarah, Jennifer
merP:
Primer design: Basem, Stephen
Parts cloning: Camilo, Logan
merA:
Primer design: Stephen, Basem
Parts cloning: Valeriu, Jessica
Characterization: Cassandra, Sarah
merB:
Primer design: Basem, Stephen
Parts cloning: Logan, David

Chassis Transformations:
Pseudomonas putida: Basem
Shewanella oneidensis: Basem
E. coli K12: Basem, David

Rhodopseudomonas
Project design: Basem, Stephen
Parts cloning: Stephen, Basem

Dry lab:

EncapsuLab:
Protocol Design: Srijay, Patrick, David, Nicholas
Cell encapsulation: Nicholas, Patrick, Srijay, David, Basem, Suzie
Cell Viability Testing: Patrick, David, Nicholas
SEM encapsulation imaging: Nicholas, UofM imaging center
Device design: Roxana, Nicholas
Mathematical modelling: Di, Zhiyi, Patrick, David

Policies and Practices:

Outreach, presentations, public perception studies

School Curriculum design: Basem, Suzie
Science Museum Curriculum Design: everybody
Middle School Classroom outreach: Jess, Basem, Cassandra, Jennifer, Suzie
Science Museum outreach: Jess, Jen, David, Sarah, Cassandra, Basem, Srijay, Di, Holly, Logan
3M presentation: Suzie, Basem, Cassandra, Stephen, Jess
Cargill presentation: ???
State Fair outreach:
tabling & survey: Cassandra Taylor Jess Jen Basem Suzie Nicholas Stephen Roxana Di
Srijay Patrick Holly Logan
Survey statistics: Taylor
slideshow: Jess, David, Logan
giveaways: CBS, local businesses gift cards, Rob Rakow
survey content: everyone
State Fair game show presentation: Cassandra, Taylor

Ethics :
blog: Basem, Cassandra, Logan, Jen
Documentary: Jennifer, David, Colombia iGEM team

Business Plan:
Justin, Tanner, Basem, Tamara, ?

Economic Analysis: ??? + IP team at OTC

Colombia collaboration: (magnetic stirrer) Stephen
Other collaborations??

Wiki development
Design: Mari, Chris, Aaron, Basem, ??
Icons, figures development: Mari, Basem, Nicholas, ???
Coding, CSS, javascript: Aaron, Chris,
Lab notebook: Sarah Lucas

Poster:
Basem

Team Logo
Nicholas

Administrative forms, IP, safety:
Basem

Parts Submission form & shipping
Stephen

Public relations and team contact
Basem, Jessica

Grant writing, fundraising
Basem, Jess, David, Cassandra





Sponsors




  • Platinum

  • Gold

  • Silver






Gold Medal Requirements

Gold Medal Requirements

Gold Medal Requirements