This experiment is part of the iGEM 2019 Challenge Challenge Grant. Browse more projects

Spatially controlling attachment of functional proteins to bacterial cellulose using optogenetics

SoundBio Lab iGEM Team
Seattle, Washington
BiologyMaterials Science
Tax Deductible
DOI: 10.18258/13271
Grant: iGEM 2019 Challenge
$2,680
Raised of $2,500 Goal
107%
Funded on 6/21/19
Successfully Funded
  • $2,680
    pledged
  • 107%
    funded
  • Funded
    on 6/21/19

About This Project

The bacterium Komagataeibacter rhaeticus has the ability to naturally produce bacterial cellulose (BC) which possesses many unique, highly useful properties suitable for a wide range of applications. We hypothesize that an optogenetic circuit in an engineered strain of K. rhaeticus grown in an optimized bioreactor can spatially control attachment of proteins to the surface of BC membranes to enable fine-tuning of these properties for different applications.

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What is the context of this research?

While cellulose is best known as a plant product, some bacteria, most notably of the genus Acetobacter (a synonym for Komagataeibacter), can produce it as well. Bacterial cellulose (BC) is more pure than plant cellulose and possesses properties such as high porosity and moisture retention. These traits make BC attractive for wound dressing and tissue scaffolding compared to traditional materials.

Despite its innate benefits, BC does have shortcomings, such as lacking antimicrobicity. These shortcomings, however, can be solved by additional functionalization, such as by attaching antimicrobial peptides to the surface of BC. We plan to build off of Imperial College 2014 iGEM’s groundwork on functionalizing BC and use their genetic toolkit for engineering K. rhaeticus.

What is the significance of this project?

Bacterial cellulose (BC) has many applications, most notably in the fields of tissue engineering and biomedicine. The high tensile strength of cellulose microfibrils protects burn victims from bacterial infection as well as water loss through damaged skin tissue. BC is better at resisting tear than existing bandage materials on the market today, such as polyethylene and polyvinyl chloride. Precise spatial control of BC functionalization will allow for production of custom bandages that can modulate their properties to match the specific needs as they vary at different locations across a wound. Our functionalization mechanism may be utilized for a wide range of applications beyond biomed, such as environmentally-conscious production of textiles and other innovative alternative goods.

What are the goals of the project?

Our project aims to create a platform for precise, light-based control of bacterial cellulose functionalization. We will engineer K. rhaeticus to increase the functionality of BC by attaching fusion proteins via a cellulose binding domain. Levels of functionalization of the fusion proteins will be controlled with light via an optogenetic circuit. We will build a proof of concept that uses this process to spatially control the attachment of chromoproteins onto BC.

Production volumes will be improved through optimizing bioreactor conditions. Oxygen is a major limiting factor in production. Media enhancements, pH, and temperature optimization may also increase output. Additionally, we will explore metabolic engineering opportunities to increase production and reduce byproducts.

Budget

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Our budget is divided into three categories: lab operation, procedure costs, and bioreactor operation. Lab operation includes labware, lab consumables, and equipment maintenance.

The construction of our gene constructs, molecular cloning work, and production of bacterial cellulose in small-scale assays is a major development cost. This includes relevant molecular reagents, chemicals, gel and purification supplies, enzymes, and cells. Another part of our budget will go towards sequencing to confirm the assembly of our construct.

Lastly, construction of our bioreactor will incur significant costs - including parts and tubing, 3D printing filament, a simple control system, probes and sensors (for pH, dissolved oxygen, and temperature, etc.), and peristaltic pumps for nutrient delivery. There may be software costs for bioreactor and genetic modeling and control.

Endorsed by

The SoundBio team has set out an important--and achievable--project that has the potential to be a useful step forward for bacterial cellulose production. The team has a well thought-out plan and the expertise, motivation, and leadership to successfully carry it out.
I am the member of the team who first isolated this strain and developed the methods to engineer it. Beyond being exciting advances from the fundamental science point of view, the Soundbio iGEM team's project would allow for improvement bacterial cellulose production and the creation of new kinds of patterned biomaterials, in a way that is currently not possible. Their designed plans to reach this goal are scientifically sound and creative. I am excited for this project and hope to see their work come to fruition!

Flag iconProject Timeline

Our project will begin after training ends in June. The first month will focus on genetic construct and bioreactor design. Next, we will clone our constructs and demonstrate their functionality. BC will be produced and methods for optimizing material properties will be tested. By mid-summer, we plan to have a bioreactor prototype that produces large quantities of BC by optimizing conditions. Finally, we will investigate post-production modifications and prepare for the competition.

May 22, 2019

Project Launched

Jul 01, 2019

Bioreactor and plasmid design

Jul 31, 2019

Cloning of our constructs, demonstrate plasmid functionality

Aug 08, 2019

Production of BC in small-scale culture, proof of light-controlled functionalization

Aug 15, 2019

Complete bioreactor prototype

Meet the Team

Zach Mueller
Zach Mueller
Co-founder

Affiliates

SoundBio Lab
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Kat Holo
Kat Holo
Student Lead
Sarah Alvi
Sarah Alvi
Student Lead
JJ Wheeler
JJ Wheeler
Student Lead
Sophie Liu
Sophie Liu
Student Lead
Charlie Anderson
Charlie Anderson
Student Lead
David Lu
David Lu
Student Lead
Regina Wu
Regina Wu
Advisor

Affiliates

SoundBio Lab
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Yoshitaka Goto
Yoshitaka Goto
Lab Manager, DirOps, iGEM Advisor

Affiliates

SoundBio Lab
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Claire Yang
Claire Yang
Student Lead
Aida Hidalgo A
Aida Hidalgo A
iGEM Advisor, Scientific Fellow (on a volunteer basis)

Affiliates

SoundBio Lab
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Anastasia Nicolov
Anastasia Nicolov
Washington iGEM Advisor, Scientist

Affiliates

SoundBio Lab, Just Biotherapeutics
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Sonia Yuan
Sonia Yuan
Student Lead

Team Bio

SoundBio iGEM is a high school synthetic biology team based out of the SoundBio Lab in Seattle, Washington. Since 2017, the SoundBio iGEM team has designed and developed their own synthetic biology projects addressing real-world problems such as LAL endotoxin assay improvement and PCB cleanup. This year, our team consists of 46 students from 16 schools in the Seattle area. Our members come from a wide range of grades, backgrounds, and experience and have highly interdisciplinary interests.

Zach Mueller

Zach is a biohacker based out of Seattle, Washington who is the co-founder of SoundBio Lab where he engages in community projects, advises their high school / community lab iGEM team, and oversees general operations. Although Zach has no formal background in biology, he is extremely passionate about synthetic biology and strengthening the power and network of DIY labs. When he is not working after hours in the lab, Zach can be found at his day job working as a Data Scientist at Amazon.

Kat Holo

As an aspiring biomedical engineer, Kat's experience in iGEM has been an amazing opportunity to not only learn, but to meet new people who are also dedicated and interested in synthetic biology. Outside of iGEM, she can be found procrastinating on her homework and searching for new music to listen to. She has thoroughly enjoyed working on SoundBio iGEM's project this year and is excited to see all the projects at the Giant Jamboree!

Sarah Alvi

Sarah Alvi enjoys reading, rowing, participating in her school’s jazz choir, and traveling. Her interest in genetics really peaked after she got the opportunity to explore Institute for Systems Biology. Since then, she has explored other fields but has always come back to biology. Being part of SoundBio iGEM for her third year has provided her with a great place where she can learn about topics that truly interest her, connect to the iGEM community, and have a good time!

JJ Wheeler

JJ has been interested in the amazing things that can be accomplished with synthetic biology for a long time and is always ready to learn new things. He used to dream of one day genetically engineering an actual, real, totally legit, fire-breathing dragon. Now that he’s actually learned a lot and gained that valuable experience through iGEM, his dream is becoming increasingly unrealistic because so far none of the science he’s done has involved dragons in any way, shape, or form; but there’s always next year.

Sophie Liu

As a member of the SoundBio iGEM team, Sophie Liu enjoys collaborating with her teammates to tackle real life issues using synthetic biology. If she's not reading a paper or designing primers, Sophie can be found at local badminton courts crushing her opponents or taking a long nap to escape her life problems.

Charlie Anderson

Synthetic biology has been a fascination of Charlie's since third grade, when his science class did a (very) brief unit on it and he decided he wanted to learn more. Being on an iGEM team has been a great opportunity for him to gain hands-on wetlab experience and meet some truly awesome people. Charlie hopes to eventually go into a career that somehow integrates synthetic biology, neuroscience, and machine learning. He also enjoys playing games and reading.

David Lu

David became recently passionate about synthetic biology when he took a biotechnology course his sophomore year. In his free time he enjoys sailing boats and playing piano. He also loves the color blue.

Regina Wu

Regina is an educator and curriculum designer based in Seattle at Fred Hutchinson Cancer Research Center where she works to develop robust protocols and curriculum material for high school teachers across Washington State. Prior to moving to Seattle, Regina was a primary and secondary school educator in Taiwan, teaching a range of levels and subjects including Elementary Life Sciences and Junior High Biology.

Yoshitaka Goto

I am currently the Director of Operations and Lab Manager at SoundBio Lab, and an advisor for the SoundBio iGEM and Washington iGEM teams. A graduate of University of Washington Bioengineering, I was part of the iGEM team there for three years. I am also actively involved in After iGEM initiatives, ran by iGEM Alumni. An avid supporter of iGEM, as well as the fields of synthetic and systems biology, I'm inspired by biotech, and I hope to inspire future biotechnologists!

Claire Yang

Claire loves discovering new ideas and meeting cool people to discuss them with. She wants to further explore the the field of biology and use that knowledge to help others and improve the world. Being a part of the SoundBio iGEM team has been a great way to start. Claire also loves to dance, draw, spend time with her two sisters, or look through the Internet's endless supply of biology memes.

Aida Hidalgo A

I am a scientific fellow volunteer at SoundBio Lab and belong to the SoundBio iGEM advisors' team. I hold a BSc in Food Chemistry from UNAM, Mexico, a MSc in Clinical Microbiology from the University of Nottingham, UK and a PhD in bacterial genetics from the University of Birmingham, UK. I worked as a research scientist in different NHS Reference Laboratories in the UK and completed the NHS Scientist Training Programme in Clinical Microbiology in Bristol, England.

When not volunteering in SoundBio Lab and advising its iGEM team, I volunteer in different community organisations tackling public health issues in Seattle. I also enjoy spending time with my family and building Playmobil and Lego cities with my little Son.

Anastasia Nicolov

A native of Seattle, I completed a B.S in Bioengineering and a B.M in Violin Performance at the University of Washington in 2017. I currently work as a bioreactor scientist at Just Biotherapeutics working on optimization of protein drug production.

I am an advisor for both the SoundBio iGEM team and the Washington iGEM team, facilitating training, coaching students on engineering design, and helping manage administrative and fundraising efforts.

Outside of iGEM, I am also an avid performer in local orchestras and chamber groups. In my limited spare time, I enjoy running my Etsy jewelry business and traveling with my family.

Sonia Yuan

Sonia is a senior at Ingraham High School. She had no idea synthetic biology was a thing until she joined iGem, she just knew she liked linking & applying concepts between seemingly unrelated situations. Needless to say, she's having a blast making genetic circuits and designing experiments. When she's not doing iGem, she enjoys binge-reading fantasy novels and running cross country.

Additional Information

This year, our team consists of 42 students from 16 schools in the Seattle area. Our members come from a wide range of grades, backgrounds, and experience and have highly interdisciplinary interests.

Bellevue HS
Alice Wang (Sophomore)
Cedarcrest HS
Hayden Bhavsar (Junior)
Eastlake HS
Emma Huang (Sophomore)
Garfield HS
Alyssa Tou (Sophomore), Forest Tschirhart (Sophomore)
Homeschooled
Cameron Olson (Sophomore), Claris Winston (Junior), Liana Wood (Junior)
Ingraham HS
Arya Gharib (Freshman), Maya Landry-Livshetz (Freshman), Sonia Yuan (Junior)
Inglemoor HS
Cathy Zhao (Sophomore)
International School
Annie Tu (Junior) , Daniel Koo (8th) , Gargi Panatula (Junior) , Leodis Lee (Freshman), Sabreen Moazzam (Freshman), Sarah Alvi (Senior, Leadership), Sofia Alvi (8th)
Interlake HS
Kat Holo (Junior, Leadership), Mahathi Mangipudi (Sophomore)
Juanita HS
Keemia Mohammadi (Junior)
Lakeside School
Belle Pan (Sophomore), Charlie Anderson (Sophomore, Leadership), Collin Dong (Sophomore), Eric Xia (Sophomore), Hari Koneru (Sophomore), Minsoo Kwon (Junior)
Newport HS
Alex Richardson (Junior), Amy Lin (Sophomore), JJ Wheeler (Senior, Leadership), Kaya Schroeder (Junior), Rachel Gao (Senior), Sophie Liu (Junior, Leadership)
North Creek HS
Vrishab Sathish Kumar (Senior)
Redmond HS
Keerthana Thammana (Junior)
Roosevelt HS
David Lu (Junior, Leadership), Kevin Lu (Freshman)
Tesla STEM HS
Ananya Nandula (Sophomore), Claire Yang (Sophomore, Leadership)


Project Backers

  • 31Backers
  • 107%Funded
  • $2,680Total Donations
  • $86.45Average Donation
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