Overview
Biocementing Bacteria
Bioreactors
Bioprinter
Software
Education
Inclusive Design Project
Entrepreneurship
Judging
Description

Description

meduCA is a modular platform that employs bacteria for on-site construction of living building materials in inhospitable environments. We leverage microbially-induced calcium carbonate precipitation (MICP) through the activity of carbonic anhydrases to convert greenhouse gases into carbon-negative bricks via biocementation. By harnessing bacterial surface-display mechanisms, our engineered cells enable stable expression of enzymes for bioremediation and construction, on Earth and beyond! Learn more about our project here.

Inclusive Perspective

Inclusive Perspective

Communities are a mosaic of different beliefs, opinions and thoughts. We strive to engage with different members of our community to ensure all perspectives are considered in our project, ranging from environmental to societal conversations.

Results

Results

This page summarizes meduCA’s technical results, highlighting our wet & dry lab goals, results, and future plans.

Team

Team

The people that made it all happen!

Biocementing Bacteria

Biocementing Bacteria

This page outlines the development of engineered microorganisms capable of microbially induced calcite precipitation (MICP) through surface-displayed carbonic anhydrase. By combining enzyme optimization, chassis selection, and surface localization strategies, we aim to create bacteria that can convert atmospheric CO₂ into stable calcium carbonate for sustainable biocementation on Earth and Mars.

Cyanobacteria

Cyanobacteria

Our project aims to develop a modular surface display system for Synechococcus elongatus UTEX 2973 to enable expression of proteins, such as carbonic anhydrases, for biocementation applications on Mars. By combining cyanobacterial expertise, rational construct design, and iterative testing, we engineered and validated a recombination-based vector, pRepv3, optimized for stable protein display and counterselection in UTEX. This work establishes a foundation for future cyanobacterial surface engineering and carbon capture strategies in space biotechnology.

Caulobacter

Caulobacter

Our project aims to engineer Caulobacter crescentus as a living platform for enzymatic surface display to support sustainable mine tailing remediation. By leveraging its crystalline S-layer system and resilience in harsh environments, we developed tools for displaying carbonic anhydrase (CA) and other functional proteins to enable calcium carbonate precipitation and biocementation in polluted sites.

E. coli

E. coli

To evaluate and compare surface display efficiency across species, E. coli was used as a benchmark chassis alongside Caulobacter crescentus and Synechococcus elongatus UTEX 2973. Using an established construct design from the distribution kit, we performed transformations and validation experiments to assess expression and functionality of the surface display system under standardized conditions.

Functional Validation

Functional Validation

This page outlines the experimental framework for validating surface-displayed carbonic anhydrase (CA) constructs across E. coli, Caulobacter crescentus, and Synechococcus elongatus UTEX. It connects molecular-level validation, protein localization and enzymatic activity, with biomineralization, establishing a full workflow from expression to microbially induced calcium carbonate precipitation (MICP).

Bioinformatics

Bioinformatics

To support our team’s wet lab, we investigated the evolutionary landscape and biochemical properties of carbonic anhydrases - the key enzyme in induced calcium carbonate precipitation. Our goal was to identify and characterize a diverse number of CA variants in order to optimally select one for extraterrestrial conditions. We conducted phylogenetic analysis using TreeSAPP on the alpha family and traced sequence motifs and functional divergence across variants that had high catalytic performances. This integrative approached allowed us to provide wet lab with crucial information for further testing.

Modelling

Modelling

To assist Wet Lab in selecting candidates for surface display, AlphaFold was used to generate 3D models of the fusion proteins. Structural alignment on PyMOL allowed for the investigation of conformational changes. Finally, the stability of the proteins were analyzed through molecular dynamics simulations with GROMACS.

Parts

Parts

To help other teams to create their own surface-displaying bacteria, we have created and submitted several parts to the iGEM Registry. Check them out here!

Protocols

Protocols
Lab Notebook: Biocementing Bacteria

Lab Notebook: Biocementing Bacteria
Bioreactor Overview

Bioreactor Overview

An iGEM classic, bioreactors are crucial to synthetic biology projects, providing and optimizing bacterial growth to increase wet lab stock and decreasing costs. This year, we built two bioreactors tailored towards our two chassis, C. crescentus and S. Elongatus. Our research questions for these two bioreactors explores the characteristics of each and how they affect our bioreactors’ conditions.

CB2A Bioreactor: Requirements + Design

CB2A Bioreactor: Requirements + Design

The CB2A Bioreactor explores the optimization of Caulobacter crescentus given its cellular properties and growth factors. The research questions that we hope to answer with this project is how agitation methods affect CB2A, specifically impeller design and how we can reduce shear stress while optimizing cell growth.

CB2A Bioreactor: Build

CB2A Bioreactor: Build

The build process for CB2A Bioreactor involved implementing designs that met our requirements outlined in the previous page. We primarily used polylactic acid (PLA) to manufacture custom parts and used an Arduino to test the first few iterations. We also performed simulations in SolidWorks to explore shear stresses in silico.

CB2A Bioreactor: Validation

CB2A Bioreactor: Validation

To validate the CB2A bioreactor, we ran growth curves in our bioreactor and compared it to traditional methods that used culture flasks and shakers. We used the 30 °C temperature-controlled room and sampled using optical density at 600 nm at a frequency of 1 hour. Ultimately, we found that we were able to reach exponential phase quicker than wet lab, but heating issues stunted the curve later.

UTEX 2973 Bioreactor: Requirements + Design

UTEX 2973 Bioreactor: Requirements + Design

The bioreactor for UTEX 2973 strain is different from our previous bioreactors in the way it requires carbon dioxide delivery and light. Literature has shown that these two factors are critical in cellular growth and therefore their delivery system is a priority in the design. This page will outline how we will design these delivery systems.

UTEX 2973 Bioreactor: Build

UTEX 2973 Bioreactor: Build

This page outlines the UTEX Bioreactor build plan and how we implemented our critical CO2 and light delivery systems. Similar to the CB2A Bioreactor, we printed custom parts from polylactic acid (PLA) and tested early iterations on an Arduino microcontroller. Our CO2 delivery system consisted of a water-drip mechanism that evaporated dry ice and pumped into the system. Light was controlled using LED strips and interwoven around Mark 2.

UTEX 2973 Bioreactor: Validation

UTEX 2973 Bioreactor: Validation

Much like the CB2A Bioreactor, we validated the bioreactor by running growth curves and comparing it to traditional culture flasks. A key difference between these methods is the addition of sub-surface CO2 aeration. We utilized the CO2 chamber and pumped in CO2 through a thin copper tube. Overall, the growth curved reached higher optical densities quicker than wet lab methods.

UTEX 2973 Bioreactor: Media Optimization

UTEX 2973 Bioreactor: Media Optimization

To maximize the growth of UTEX 2973 in our bioreactors for optimal production of living building materials, we implemented flux balance analysis modelling to determine what the optimal BG-11 media composition and culture conditions are that maximizes UTEX 2973 growth rate.

Low-Gravity Bioreactor: Requirements + Design

Low-Gravity Bioreactor: Requirements + Design

The low gravity simulator is responsible for exploring bacteria behaviour and growth under low-gravity conditions found on Mars and in space. A key component of our research and conceptualization was considering how the project would be validated as it is difficult to measure acceleration in dynamics environment without having biased data. Our final concept is based off an RPM machine that spins in two axes.

Low-Gravity Bioreactor: Build

Low-Gravity Bioreactor: Build

Building the low gravity simulator presented a unique challenge in the importance of symmetry and dynamic movement. We ran into slight issues when 3D printed parts were slightly asymmetrical, causing imperfect revolution building mechanical stress into the structure. We included bearings and slip rings to counteract wire tangling and ensuring smooth rotation.

Low-Gravity Bioreactor: Validation

Low-Gravity Bioreactor: Validation

Validation for our low gravity simulator was particularly tricky because it was difficult to find a way where we could get unbiased quantitative data from the interior of the vessel during operation. Using literature, we adapted some qualitative tests that can indicate that low gravity may be present within the vessel.

Bioprinter: Overview

Bioprinter: Overview

We modified a 3D clay printer into a bioprinter compatible with our novel bioink. We created a biomaterial composition that can incorporate microbes to serve as a bioink for bioprinting 3D living building materials for Mars.

Bioink: Composition Testing

Bioink: Composition Testing

Before we incorporate any living organisms into the biomaterial, we wanted to optimize our protocol and determine the operable range of each component in the bioink. Learn more about our bioink composition and how it is created in this page!

Bioink: Model Validation

Bioink: Model Validation

We devised a protocol to incorporate UTEX 2973 into the MGS-1 alginate gel, for which we can adopt in the future for validating the formation of bricks from calcium carbonate crystals. Here, we also introduce Design of Experiments, a modelling approach we can use to optimize our bioink composition for UTEX 2973 viability and calcium carbonate formation in the future.

Bioink: Calcium Diffusion Modelling

Bioink: Calcium Diffusion Modelling

This page details the computational approach for simulating diffusion and crosslinking processes in alginate-based ink formulations.

Bioprinter: Requirements + Design

Bioprinter: Requirements + Design

This adapted bioprinter will be used to test and characterise the bioink produced for meduCA. In this page, we’ll outline the modifications and requirements we need to sufficiently meet these goals. We used a TronXY Moore 1 and modified it with a syringe pump for extrusion and added a holder for bioink.

Bioprinter: Build

Bioprinter: Build

Building the bioprinter was a multi-team process coordinating both the bioink composition team and hardware team. We considered the user interface and limitations of our modifications and compromised to produce a prototype that could extrude the bioink. Our next steps would controlling the bioprinter environment to optimize sterility and cell viability.

Bioprinter: Validation

Bioprinter: Validation

Validating the bioprinter involved the completed and optimized bioink to produce basic geometric structures and testing their strengths. We will be testing its capabilities by printing at slow speeds in 2D and 3D squares, comparing the results to experiments conducted by the bioink team as a control.

Lab Notebook: Bioprinter & Bioink

Lab Notebook: Bioprinter & Bioink

Lab notebook entries related to developing the bioink and bioprinter.

Software

Software

Innovative software tools that power meduCA and accelerate breakthroughs in synthetic biology.

dagger

dagger

A library that empowers developers to painlessly build high-performance parallel applications.

maestro

maestro

A task orchestration framework for reproducible, distributable bioinformatic workflows.

miso

miso

A framework to develop intuitive user interfaces for meduCA’s bioreactors and the next generation of hardware in iGEM.

Education

Education

The Education subteam focuses on delivering synthetic biology programming and fostering community awareness through impact-driven initiatives. Learn more about how we developed our educational curriculum in this page!

Educational Programming & Outreach

Educational Programming & Outreach

Educational programming and outreach sought to introduce synthetic biology concepts to community members through hands-on workshops and interactive activities. Learn more about the wide range of workshops and community programs we hosted in this page!

UBC iGEM 2025 SynBio Case Competition

UBC iGEM 2025 SynBio Case Competition

From skill-building workshops and a life sciences research panel to a unique opportunity to tackle a pressing issue, the UBC iGEM 2025 SynBio Case Competition engages local high school students to gain exposure to synthetic biology and critical problem-solving. Learn more about how we organized the Case Competition and developed an engaging case study in this page!

Synthetic Biology Children’s Storybook

Synthetic Biology Children’s Storybook

The Synthetic Biology Children’s Storybook engages young readers with space exploration and scientific research. Learn more about how we designed our storybook in this page!

Inclusivity

Inclusivity

We ask all those who work or have worked in a wet lab; what would your life look like if something happened to your hands?

Understanding our User’s Needs

Understanding our User’s Needs

Our project begins with literature review to establish baseline weighted decision matrices and preliminary c-sketches to validate with our user. Designs were then screened against requirements and affirmed by iHPs before extending it to the greater MSK community.

Fine-tuning our Understanding

Fine-tuning our Understanding

Concept generation never comes easy; after many failed designs, user conversations, and changes to evaluation criteria, learn about our first successful preliminary design and the screening process involved.

Iterative DBTL Cycles

Iterative DBTL Cycles

This step in our design process begins our 3D modelling and printing stage. Prototypes were welcomed, such as custom clay molds to better understand our user’s comfort and quantify thicknesses. Many DBTL cycles were required to reach a viable product.

Project Outcomes

Project Outcomes

During our final meeting with our user, we provided her with the add on that now perfectly fit her pipette and qualitatively evaluated her comfort and level of upper-limb strain with and without the pipette. We saw a visible reduction in her use of her wrist tendons, and to quantify this value, we conducted tests with EMG electrodes. Despite having limitations such as a lack of pipette knob support, non-squishy material and a smooth surface (our user prefers a textured pipette to increase her grip), this add on was able to reduce our user’s hand intensity when handling her pipette while also being lightweight and sterilizable, all of which make it a helpful tool that can be further iterated to make optimal to many individuals that have upper-limb musculoskeletal disorders.

Alternative Inclusive Design Projects

Alternative Inclusive Design Projects

We explored various project ideas to improve accessibility for different lived experiences, before ultimately pursuing musculoskeletal disorders. Nonetheless, a lot was learned from reflecting on why our other projects didn’t work out, and how they can be a starting place for other teams.

Best Practices for Inclusive Design Project

Best Practices for Inclusive Design Project

The Inclusive Lab Space is an intended framework for the iGEM community to conduct their own inclusive design projects. Walk through our design process and learn about areas where our team performed or diverged from the best practices, and how to approach challenging aspects of an inclusive design project.

Needs Finding

Needs Finding

What commercializable issue is currently unresolved in the market, and who would want such a solution?

Market Research

Market Research

What is the market like for our proposed product? Where should we begin and what growth potential do we have?

Strategic Planning

Strategic Planning

What is our core business model and how can we grow our business in terms of customers and funding?

Business Development

Business Development

What does our roadmap look like for the immediate future and how can we continuously improve?

Long Term Growth

Long Term Growth

What is the ultimate goal of the business? What long-term plans do we have for the business, and its impacts on society?

Medal Criteria

Medal Criteria

To help demonstrate our team’s achievements to the judges, we put together a judging summary page to guide you to each deliverable!

Contributions

Contributions

Check out UBC Vancouver’s 2025 contributions to the iGEM community!

Human Practices

Human Practices

Our Human Practices page displays all expert & stakeholder interviews which helped drive meduCA forward across our deliverables!

Engineering

Engineering

Our Engineering Success page lays out the Design-Build-Test-Learn (DBTL) cycles that each subteam iterated on in relation to their main deliverables this season.

Attributions

Attributions

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Generating a Dry Cell Weight Curve

Objective

Author(s): Pattarin Blanchard

This protocol will produce a curve that quantifies cell biomass at a given OD.

Materials

Procedure

OD measurements

  1. For ease of working and to avoid contamination, aliquot just over 5 mL of liquid culture into a 15 mL falcon tube.

  2. Under a flame, make the following dilutions of liquid culture in PBS in appropriately labelled microcentrifuge tubes. Use the aliquoted liquid culture.

    Tube12345678910
    Liquid culture (µL)05010020030050060075010001500
    PBS (µL)1500145014001300120010009007505000

  3. Blank the spectrophotometer with Milli-Q water at the appropriate wavelength for the organism.

    1. E. coli, CB2A: 600 nm
    2. UTEX: 750 nm

  4. Measure the OD of each tube starting from tube 1, wiping the cuvette with a kimwipe before each measurement. After each measurement, discard the contents in a waste beaker, rinse 3 times with water, then leave face-down on a paper towel soaking with ethanol or disinfectant if not reusing right away.

Dry cell weight

  1. Aliquot 25 mL of liquid culture into a 50 mL centrifuge tube and centrifuge at 10000G for 5 mins.

  2. In the meantime, weigh the drying dish in the analytical balance.

  3. Remove supernatant and resuspend with 10 mL PBS and centrifuge again at 10000G for 5 mins.

  4. Repeat step 3 once.

  5. Remove supernatant and resuspend with 3-5 mL water, try to recover all of the pellet. Pour into the drying dish.

  6. Place the drying dish in an oven and come back the next day to weigh the dish.

  7. Calculate the dry cell “weight” (per mL) from the obtained measurements:

    ρ=mdry−mempty25 mL\rho = \frac{m_{dry}-m_{empty}}{25 \text{ mL}}

Dry cell weight curve

  1. Use the value from the previous step to calculate the dry cell weight at each dilution:

    DCW=ρ⋅Vculture1.5 mLDCW=\frac{\rho \cdot V_{culture}}{1.5 \text{ mL}}

  2. Calculate true OD by subtracting each value with the OD of PBS only (tube 1).

  3. Plot true OD vs. DCW, it should be approximately linear between OD 0.1-1.

  4. Perform a linear regression on the data points in the linear region. The reciprocal of the slope is the desired quantity and has the units g/mL⋅AU\text{g/mL}\cdot \text{AU}.