Contribution

"Plans to protect air and water, wilderness, and wildlife are in fact plans to protect human."

Taiwan's textile industry ranks third in the world in terms of output, making it a main global supplier of functional fabrics. However, massive production inevitably brings serious pollution. Large quantities of dyes are discharged into river and ocean during the garment making process. Those toxic dyes accumulated rapidly in the environment. That's why we wanted to clean up these water bodies with synthetic biology to achieve bioremediation. With the intention of decomposing excessive dyes with the function of microorganism, we came up with several innovative ideas among various fields. The contributions we've made this year are mainly about adding several new parts, designing new hardware and software. Although our design is not perfect and still has a long way to go, we firmly believe that our experience could be valuable to other iGEM teams or even companies; in the near future, this long-existing problem will be solved by a more feasible way, with the help of all pioneers.

Parts

—— Giving laccase infinite possibilities

BBa_K4618213, BBa_K4618500, BBa_K4618501, BBa_K4618502 are the sequences for secreting different kinds of laccase and NG Catcher.
BBa_K4618823is a sequence for secreting RK tails to wrap the surface of Catcher to form micron-level protein particles.
BBa_K4618105is the sequence for secreting hydrophobin and NG Tag.
Such design allows us to combine two different proteins with Catcher-Tag system to form a more functional protein complex. At first, we hoped to use laccase to achieve the purpose of color removal, but then we found that merely applying laccase is impossible to achieve our goal and the commercial value of it is quite low. That's why we apply the Catcher-Tag system to combine it with hydrophobin. Hydrophobin can increase the hydrophilicity of the PET paper surface, which is expected to help the protein complex adhere to the PET paper. Although we learned from the 3D protein structure that these two proteins are structurally unable to form a stable protein complex, we hope that laccase and NG Catcher-Tag system will have more applications in the future, and the new protein complex can completely solve the problem of color removal, both eco-friendly and economically affordable.

Hardware

—— Affordable and Precise Spectrophotometer

• Innovating Accessibility in Research and Education:

We've developed an economically and operationally accessible spectrophotometer, emerging as a pioneering tool within the iGEM community that is both budget-friendly and user-friendly, ensuring its applicability across diverse research and educational contexts.


• Evolution with Impact:

From Version 1 to Version 2, our design journey has seamlessly blended cost-effectiveness with enhanced precision and functionality, delivering a robust, economically viable solution for researchers and educators navigating financial constraints.


• A Stepping Stone for Inclusive Science:

Our hardware contribution not only offers a verified and affordable spectrophotometer but also stands as a testament to the potential for crafting precision with cost-efficiency, propelling forward the ethos of accessible and inclusive scientific research and education.

Fig 1. This 3D model is one of the elements of our spectrophotometer, which serves as a precursor of our real component.

Software

—— Introducing Espec: A Friendly Companion for Your Spectrophotometry Needs

• Making Things a Bit Easier with Espec:

We brought to life Espec - a friendly, straightforward software, aiming to just make things a little easier when working with our second-generation spectrophotometer hardware. It's all about reducing a few more steps, and a few less clicks in your research work.


• Simplicity and Ease in Every Click:

Espec is not here to change the world but to add a touch of convenience and simplicity to your experiments. It's designed with a cozy user interface, effortless trendline plotting, and easy control over RGB LEDs and testing processes. We hope it makes your data interpretation and experimental setup just a tad smoother.


• A Peek into Espec's Uncomplicated World:

Initiating Espec to visualizing data, we've tried to keep things neat and uncluttered. Engage with Arduino, choose your LED colors, and let the software gently guide you through your data, providing a helping hand without overcomplicating things.

• Step Towards Easier Research:

Espec might not be a giant leap, but we believe it's a small, friendly step towards making research and data analysis a bit more approachable and less daunting, especially for those just starting their journey into synthetic biology.

Documentation

This manual provides detailed information on using the Espec software and on building and aligning the spectrometer. In addition, the necessary CAD files are supplied in STL format. The materials required for this project are both inexpensive and easily accessible. Both the Ionic version and the web version of the Espec software can be downloaded and used from our GitHub repository.

Explore More on GitHub For comprehensive insights and further information about our project, visit our GitHub page: 2023.igem-csmu-taiwan Repository. This repository houses all the resources, updates, and collaborative opportunities associated with our iGEM Hardware & Software Open-Source Project. Your exploration and contributions are highly appreciated!

Model

Our Model Page

—— Contribution to Protein-Protein Interaction Modelling

• In-depth Exploration of the 'Tag' and 'Catcher' Concept:

Undertaking a nuanced exploration of protein-protein interactions, our model sought to elucidate the intricacies of a unique Tag and Catcher module. By adopting a bifurcated design strategy, we prioritized efficient bacterial expression whilst safeguarding vital interactive functionalities between the two entities.


• Employing Computational Tools for 3D Structural Insight:

Utilizing computational tools like AlphaFold and ClusPro, we navigated through the challenges of predicting and visualizing 3D structures and interactions of our proteins. This computational approach not only offered us preliminary insights into potential in vivo interactions but also delineated a pathway towards experimental validations.


• Addressing Challenges with Rigorous Model Refinement:

Confronted with challenges, notably the variability in Entity Two and initial docking impediments, our modelling trajectory was by no means linear. These challenges precipitated strategic refinements in our approach, affirming the importance of adaptive strategies in synthetic biology model development.


• A Calculated Foray into the Expansive Domain of Synthetic Biology:

While our modelling has shed light on pivotal aspects and provided directional insights, we acknowledge it as an incremental step in the expansive field of synthetic biology. Future endeavor may explore diverse paths, such as in vivo validations and application expansions, underlining our commitment to continuous exploration and development within the field.