Contribution

Scientific Contribution

Our work advances the iGEM community through novel characterisation, data generation, and tool development in K. phaffii, a chassis essential for both academic discovery and industrial-scale protein production. Our contributions strengthen the open-source foundation for yeast synthetic biology by connecting molecular characterisation, data transparency, and computational optimisation in a unified framework.

We have characterised two previously unstudied genes central to K. phaffii’s sugar metabolism and secretion pathway, developed reproducible strain-provenance standards in collaboration with Change Bio, registered multiple new growth-factor expression constructs to the iGEM Registry, produced validated laboratory protocols for yeast handling and transformation, and released BioKernel — a no-code Bayesian optimisation tool for synthetic biologists.

Together, these contributions empower future iGEM teams to engineer K. phaffii more effectively, accelerate discovery cycles, and increase the reproducibility and transparency of yeast-based projects. Every construct, dataset, and workflow is documented in our lab notebook .

1. Characterisation of Hoc1: fixing a blind spot in K. phaffii engineering

We are the first iGEM team to attempt to characterise the Hoc1 gene in K. phaffii, a key factor in recombinant protein secretion. The Hoc1 gene encodes an α-1,6-mannosyltransferase, an enzyme responsible for building the outer mannan layer of the yeast cell wall. Despite its essential role in maintaining structural integrity, Hoc1 remains largely uncharacterised within industrially relevant protein-expression systems.

Through our work, we examined how Hoc1 influences exopolysaccharide (EPS) accumulation and downstream purification, revealing a trade-off between secretion yield and cell-wall robustness. Excess EPS increases viscosity and non-specific binding during purification, while overly weakened walls compromise cell viability. Our experimental assays sought to quantify this balance and provide concrete optimisation guidance for future strain designs.

These findings have practical implications for smoother purification workflows and higher-yield, lower-cost expression systems, particularly relevant to the cultivated meat and precision fermentation industries. By opening a previously neglected part of the K. phaffii genome, this work establishes a reference point for how modifying cell-wall biosynthesis can directly impact protein production efficiency.

All associated experimental data, design notes, and workflow documentation are archived in our lab notebook , allowing future iGEM teams to replicate and expand on our results.

2. First documented characterisation of Phosphomannose Isomerase (PMI)

The enzyme Phosphomannose Isomerase (PMI) catalyses the reversible conversion between fructose-6-phosphate and mannose-6-phosphate — a critical step in the GDP-mannose biosynthetic pathway. In K. phaffii, this process governs the flow of carbon into mannose-based glycans, influencing glycoprotein folding, secretion efficiency, and carbon-flux distribution.

Our work represents the first iGEM-level attempt to explore the consequences of PMI down-regulation on yeast physiology. We designed and constructed homologous recombination cassettes and guide RNAs to modulate PMI expression, aiming to redirect intracellular mannose pools toward central metabolism. This could enhance energy availability and reduce EPS overproduction, addressing two major bottlenecks in recombinant secretion systems.

By studying these metabolic effects, we established a framework for linking sugar-pathway regulation to protein-production performance. This contributes a systems-biology perspective to chassis design and provides a foundation for future studies into flux balancing, glycosylation co-regulation, and adaptive metabolic control.

Our data and constructs for PMI serve as the first open dataset connecting gene regulation to secretion efficiency in K. phaffii, creating opportunities for future synthetic biologists to refine energy use, improve yields, and streamline strain engineering.

3. Open provenance tracking of K. phaffii strains

To promote transparency and reproducibility in yeast synthetic biology, we partnered with ChangeBio to contribute practical validation data to their open-source framework, PhaffiiNet. This platform applies the Strain Provenance Protocol (SPP), a standardised method for documenting and tracing every genetic modification, transfer, and phenotype associated with a strain throughout its lifetime.

While we did not originate the SPP standard or its underlying scripts, our work offers one of the first practical validation case studies demonstrating how iGEM teams can integrate this system into real laboratory workflows. By embedding provenance tracking into routine design–build–test–learn cycles, we demonstrate how open documentation strengthens reproducibility and ethical transparency.

iGEM repositories already host sequences and parts, but rarely track the evolution of strains. With the growing scale of yeast engineering, ensuring version control for modified chassis has become a key ethical and technical priority. Our contribution lays the foundation for making provenance tracking a default part of strain management in academic and industrial projects.

• Genesis Node with Whole Genome Sequence: We submitted a reference K. phaffii genome, free from licensing restrictions, as a “genesis node” within PhaffiiNet — the foundation from which future modifications can be traced.
• Trusted, Fully Documented Origin: The node establishes a transparent and open origin for a new strain lineage, reducing duplication and enabling collaboration without IP barriers.
• Living Example of Provenance Tracking: Our characterisation of Hoc1 was logged as a “Modification Event,” followed by a “Snapshot Event” with phenotype data, serving as a concrete model of open genetic record-keeping.

Through these steps, we are turning K. phaffii from an opaque workhorse into a transparent, community-governed chassis. This collaboration shows how open-science practices can be implemented at every layer of the synthetic biology process — from construct design to strain validation.

In the long term, incorporating provenance systems like PhaffiiNet into iGEM’s infrastructure could allow for automated benchmarking of strain performance, transparent lineage tracking, and community-driven improvement across projects. Full records and our metadata entries are linked in our lab notebook.

4. Growth Factor Expression Constructs (HGF, IGF-1)

To expand the iGEM Parts Registry with practical, validated tools, we designed and registered two new expression constructs for human Hepatocyte Growth Factor (HGF) and Insulin-like Growth Factor 1 (IGF-1). These growth factors are central to cellular-differentiation and tissue-development pathways, making them highly relevant to regenerative medicine, tissue-engineering, and cultivated-meat research.

Each construct was assembled in a modular cloning framework that allows users to easily swap promoters, signal peptides, and terminators. Designs were verified in silico for codon optimisation in K. phaffii and annotated for cross-system compatibility. Using secretion tags and yeast-optimised regulatory elements, the constructs provide a plug-and-play platform for rapid expression of human growth factors in diverse biomanufacturing contexts.

By combining engineering efficiency with transparent documentation, these additions deliver biologically validated growth-factor parts that future iGEM teams can reuse without repeating the entire design process. Each plasmid is accompanied by promoter strength, secretion pathway, and tag data to ensure reproducibility and integration with other expression systems.

Collectively, these parts strengthen the open-source toolkit for recombinant protein production in yeast, an essential step toward animal-free biomanufacturing. Detailed construct maps, sequences, and validation notes are available in our lab notebook for direct reference and reuse.

5. Novel Ribosome Binding Sites (RBS) and Optimisation Elements

To complement our yeast-based constructs, we developed and characterised a suite of novel ribosome binding site (RBS) variants optimised for astaxanthin biosynthesis in E. coli. These elements were generated through an iterative computational–experimental workflow that balances translation efficiency with pathway flux control, reducing the need for random library screening.

Our RBS variants were designed using thermodynamic folding models and subsequently validated through controlled expression assays. The resulting library spans a wide range of translation-initiation strengths, allowing users to fine-tune expression ratios between pathway enzymes and maximise yield. All sequences and experimental results are documented in our lab notebook .

These data were integrated into our BioKernel optimisation software (see Software Contributions), which uses Bayesian optimisation to recommend the next most informative experiment. This synergy between computation and wet-lab testing provides an accessible model for future iGEM teams aiming to implement machine-learning-guided design in biological contexts.

We encourage future iGEM projects to expand this dataset across organisms such as S. cerevisiae and K. phaffii. Each RBS variant can be easily adapted thanks to our modular design principles, contributing to an open, reusable framework for quantitative expression control in synthetic biology.

6. Protocols and Documentation

Throughout our project, we established and refined a complete set of laboratory protocols for working with K. phaffii — from transformation and culture preparation to protein induction, purification, and analysis. Each protocol was written, tested, and annotated to ensure clear reproducibility for future iGEM teams regardless of resource availability.

To maintain consistency and accessibility, each procedure follows a defined structure: objective, materials, step-by-step protocol, expected results, and validation notes. Troubleshooting advice, reagent concentrations, and equipment substitutions were carefully included to accommodate teams with limited access to advanced facilities.

All experimental records are linked to the corresponding part entries in the iGEM Registry, ensuring that every construct can be traced from sequence to result. This structure bridges the gap between wet-lab data and registry documentation, making replication and verification seamless for future contributors.

For transparency and open-science continuity, every validated protocol, dataset, and experimental log is available in our lab notebook . There, readers can access downloadable versions, notes from optimisation rounds, and direct cross-references to specific constructs or genes described in this page.

These resources form a growing foundation for open-standard documentation in yeast synthetic biology — helping future iGEM teams work faster, more efficiently, and more reproducibly across global labs.

7. Parts Table

Below is a list of some of the genetic parts we designed, constructed, and registered. Each part includes a description, context of use, and its novelty within iGEM. All sequences are linked to experimental validation and are documented in our lab notebook .

Together, these parts represent a toolkit designed to improve protein secretion, enhance metabolic balance, and strengthen open-source collaboration in yeast synthetic biology. Each construct’s validation data and full procedural notes can be found in our lab notebook .

Software Contributions – BioKernel

Addressing the challenge of optimising biological systems under limited experimental capacity, we created BioKernel — a no-code software platform that uses Bayesian optimisation to intelligently suggest the next most informative experiment. It enables teams to navigate complex design spaces while saving time, reagents, and effort.

Unlike conventional optimisation tools, BioKernel models non-constant measurement uncertainty, allowing it to handle the high variability typical of biological experiments. It translates advanced statistical concepts into a visual, intuitive interface designed specifically for synthetic biologists with little or no coding experience.

The platform follows the Design–Build–Test–Learn (DBTL) workflow:

• Design: Users input experimental parameters, objectives, and constraints (e.g., promoter strength, enzyme ratio, media composition).
• Build & Test: BioKernel recommends experiments that maximise information gain based on its probabilistic model.
• Learn: New results update the model in real time, refining predictions and improving accuracy for subsequent runs.

This adaptive loop maximises learning per experiment, allowing teams to extract maximum insight from limited data. Interactive visualisations display convergence and uncertainty maps, helping researchers balance exploration and exploitation in decision-making.

BioKernel was used in our project to optimise RBS variants for astaxanthin production, reducing experimental overhead while maintaining predictive robustness (see RBS & Optimisation). Future iGEM teams can use it to optimise growth media, promoter combinations, or bioproduction conditions across chassis.

Built with accessibility and collaboration in mind, BioKernel is open-source, modular, and fully documented. Users can extend it with their own features — from batch experiment modules to pathway-specific optimisation schemes. The codebase, usage guide, and step-by-step examples are hosted on GitHub and accessible via our lab notebook.

Ultimately, BioKernel represents a step toward AI-assisted laboratory workflows that merge computational learning with biological experimentation. It empowers small teams to achieve data-driven insight normally reserved for large-scale industrial labs, accelerating discovery across the iGEM community.

Educational Contributions

Education was at the heart of our outreach mission. We aimed to make synthetic biology more approachable, inclusive, and inspiring for learners of all ages — from children discovering science for the first time to university students shaping the field’s future. Our educational efforts combined hands-on learning, creativity, and accessibility across formats.

Team, Career & Community Toolkit

We developed a comprehensive toolkit to help student teams start, manage, and grow their synthetic biology initiatives. This includes our “Getting Started with iGEM” handbook, outlining how to form a team, plan a project, and navigate the competition. We also created Careers in Synthetic Biology guides, adaptable to different countries, that highlight diverse paths in academia, industry, and entrepreneurship.

To strengthen the community beyond competition, we built the SynBio Circle Community Guide — a resource for forming supportive networks across institutions. Additionally, our Mini-Jamboree Event Manual offers templates for hosting regional synbio gatherings, including logistics, budgeting, and workshop outlines.

Resources Contributed: Open-source handbooks, community toolkits, and event manuals that enable future iGEM teams to organise effectively, secure funding, and sustain long-term collaborative communities.

Hands-on & Creative Learning Resources

To make learning engaging and accessible, we designed interactive, age-adaptable resources that blend creativity with biology. These include the Sir Loin plushie kit, which helps explain cultivated meat to children through storytelling and play; our colouring and picture books introducing cell biology concepts; and classroom activities like the Marble Yeast Game and The Overlab, which teach teamwork in scientific environments.

We also developed multimedia content — including a 2000s-style tabloid magazine, a Webtoon storybook, and a visual dictionary of synthetic biology terms — to merge science communication with design and media literacy. These formats encourage creative learning and can be reused for outreach events, school visits, or public festivals.

Resources Contributed: Printable kits, illustrated storybooks, and creative games that promote interactive science learning and can be freely adapted by educators and teams worldwide.

Ethics, Media & Cross-Team Engagement

To complement scientific education, we built ethics and media engagement tools that foster critical thinking. Our web-based bioethics quiz, The Moral Code, guides players through moral dilemmas in biotechnology, exploring themes of consent, enhancement, and environmental responsibility.

We supported the quiz with essay prompts, discussion packs, and classroom debate guides, enabling its integration into both secondary and higher education. Our podcast series extends this reflection, featuring stories from scientists, artists, and iGEM alumni at the intersection of ethics and innovation.

Alongside this, we launched the Digital Postcard Initiative, connecting iGEM teams globally through visual storytelling. Cross-team mentoring and international webinars further encouraged dialogue and peer learning across cultures.

Resources Contributed: Playable ethics quizzes, recorded podcasts, and collaborative outreach templates that promote reflection, communication, and interdisciplinary engagement across teams and communities.

Human Practices Contributions

Our Human Practices strategy connected every technical choice in the lab with its ethical, industrial, and societal implications. By embedding stakeholder input and expert validation into our design process, we transformed Human Practices into a genuine decision-making framework that guided our scientific and entrepreneurial directions.

The insights we gathered — from researchers, bioprocess engineers, entrepreneurs, and policymakers — helped us ensure our project was both scientifically sound and societally relevant. We summarised our findings into practical rules and reproducible workflows to aid future iGEM teams in bridging the gap between science and application.

• Technical decision rules: How the choice of chassis, such as K. phaffii, cascades into downstream consequences — from secretion behaviour to purification strategy and facility design. This framework helps teams integrate manufacturability early in their design phase.
• Practical lab workflows: We compiled verified CRISPR, transformation, and expression protocols for yeast, including tips on ΔKu70 strains, electroporation, and strain burden management. These methods reduce trial-and-error time for future teams and improve reproducibility.
• Downstream & scale-up guidance: Consultations with industry professionals provided insight into purification bottlenecks, scale-up validation, and realistic bioreactor design expectations. These were condensed into a set of milestones for scale-readiness.
• Regulatory, IP & commercial playbook: Through interviews with legal advisors and startup mentors, we mapped key hurdles — from GRAS certification to IP protection and licensing of microbial strains. This analysis also informed our support of open initiatives like PhaffiiNet for transparent, traceable biotechnology.
• Network & resource map: We built a curated database of academics, companies, and government bodies who supported our research validation. This network provides a reusable entry point for future iGEM teams engaging similar stakeholders.
• Stakeholder engagement templates: Our framework for stakeholder mapping, structured interviews, and ethical impact assessment ensures that feedback loops are systematic and results can directly influence project design.

Collectively, these contributions turn Human Practices into a strategic design discipline rather than a reporting requirement. They help future iGEM teams approach their projects holistically — combining ethical awareness, industrial feasibility, and scientific excellence.

All transcripts, workflow templates, and guidance materials are available in our lab notebook , where they can be freely accessed and adapted. We hope these resources empower upcoming teams to design responsibly, act transparently, and build technologies that genuinely serve people and the planet.

Closing Reflections

Together, our scientific, educational, and human practices contributions form a complete ecosystem of open science — from foundational genetic parts and yeast tools to ethical, creative, and collaborative frameworks for future teams. By integrating technical rigor with thoughtful outreach and reproducible documentation, we aim to leave a legacy of transparency, curiosity, and community within iGEM.

Every resource, dataset, and workflow we produced is available for reuse and expansion through our lab notebook . We invite future teams to build upon these foundations, continue exploring K. phaffii as a powerful chassis, and advance the shared mission of open, ethical synthetic biology.