HTGAA 2026 · Week 12 · April 21, 2026
Week 12

Building Genomes

Designing, synthesizing, and editing whole genomes — from minimal cells to refactored microbes and synthetic chromosomes. Applied to the final design sprint of Füzi Poiesis.

George Church John Glass Jef Boeke CRISPR Metabolic Engineering Bioproduction
Week 12 · April 21–25, 2026

Lecture — Building Genomes

This week's lecture by George Church, John Glass, and Jef Boeke covered the frontier of whole-genome design and synthesis — from JCVI's minimal cell (JCVI-syn3.0, 473 genes) through the Sc2.0 synthetic yeast chromosome project and Church lab's recoded E. coli with expanded genetic codes. The recitation by Ice Kiattisewee focused on CRISPR-based metabolic engineering, directly relevant to Füzi Poiesis's auxotrophic deletion design.

John Glass — Minimal Cell
JCVI-syn3.0 and the question of sufficiency
Glass's work on JCVI-syn3.0 — a synthetic cell with the minimal gene set sufficient for life (473 genes, 531 kbp) — directly addresses a question central to Füzi Poiesis: what is the minimum genetic program required for a defined biological function? The 149 genes of unknown function in JCVI-syn3.0 represent the limit of current biological knowledge — essential for life but mechanistically uncharacterized. For Füzi Poiesis, the analogous question is what is the minimum consortium architecture sufficient for stable bioremediation under Lake Budi's conditions. The answer the project proposes — three strains, three deletion loci, one circular dependency — is a synthetic biology bet on sufficiency over redundancy.
Jef Boeke — Sc2.0
Synthetic chromosomes and designer genomes
The Sc2.0 project's approach to recoding a complete eukaryotic genome — replacing all TAG stop codons, removing transposable elements, adding SCRaMbLE recombination sites — demonstrates that genome-scale design is achievable when broken into modular chromosome-by-chromosome segments assembled by an international consortium. The SCRaMbLE system (Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution) is particularly relevant: it uses Cre-loxP recombination to generate combinatorial genome rearrangements on demand, accelerating directed evolution without knowing in advance which configurations are beneficial. The Nash Automaton concept in early Füzi Poiesis design drew from the same logic — automated iterative selection of consortium configurations — before the design simplified to a mathematically validated fixed topology.
George Church — Recoded organisms
Genomic recoding and virus-resistant cells
Church's work on recoded E. coli — replacing all 321 TAG stop codons with TAA and reassigning TAG/amber suppressor tRNAs to incorporate non-canonical amino acids — creates organisms that are inherently resistant to viral infection (phage cannot replicate using a code the host no longer uses) and dependent on synthetic amino acids for survival. This is a whole-genome implementation of the same containment principle underlying Füzi Poiesis's auxotrophic ring: dependency on an external supply that doesn't exist in the open environment. The difference in scale — 321 codon substitutions across the entire E. coli genome versus three gene deletions — reflects the difference between a research platform and a deployable bioremediation tool.
Recitation · Ice Kiattisewee

CRISPR-Based Metabolic Engineering

The recitation covered CRISPR-based metabolic engineering — using CRISPR interference (CRISPRi) and activation (CRISPRa) to modulate metabolic flux without permanent gene deletion, and CRISPR-mediated chromosomal editing for stable pathway integration. Both approaches are directly relevant to Füzi Poiesis Aim 2.

Connection to Füzi Poiesis

Auxotrophic deletions (ΔhisD, ΔtrpB, ΔleuB). The recitation's coverage of CRISPR-mediated chromosomal deletions maps directly to the three deletion events required for Füzi Poiesis's auxotrophic coupling. CRISPRi as an intermediate step — transcriptional silencing of hisD, trpB, and leuB before permanent deletion — provides a reversible validation layer: if silencing the gene in monoculture produces the expected auxotrophic phenotype (growth arrest without exogenous amino acid), the deletion can proceed with confidence. This reduces the risk of engineering a deletion that fails to produce the intended auxotrophy due to paralogous gene compensation.

Metabolic flux toward remediation outputs. CRISPRa upregulation of the mcjABCD operon (Strain A) and the sqr-pdo bicistronic cassette (Strain B) could increase remediation output beyond what constitutive promoter expression achieves, without increasing plasmid copy number or metabolic burden. This is an Aim 2 optimization strategy not explored in the Aim 1 computational design, where promoter strength was set to moderate expression to balance output with metabolic cost.

Lab · April 23–24

Bioproduction — Beta-Carotene & Lycopene

The lab this week demonstrated metabolic engineering for bioproduction: engineering E. coli to produce beta-carotene and lycopene by introducing the mevalonate pathway and carotenoid biosynthesis genes from heterologous organisms. As a global student at the SynBio USFQ Node, wet-lab access was not available for this session. The conceptual connection to Füzi Poiesis is direct.

Global Student Note · Bioproduction Lab

The beta-carotene/lycopene bioproduction lab demonstrates the same design logic as Füzi Poiesis Strain B: heterologous pathway expression in E. coli for production of a compound not native to the chassis. The difference is output — carotenoids for visual detection versus SQR-mediated sulfide oxidation for environmental remediation. Both require codon optimization for E. coli K-12 expression, compatible promoter selection, and validation that the heterologous pathway doesn't create toxic metabolic bottlenecks. The MALDI-TOF and HPLC pipeline from Week 10 provides the analytical framework for confirming bioproduction at the protein level — exactly the approach planned for Füzi Poiesis Aim 2 biosafety validation at UFRO-BIOREN.

Final Project Progress · Week 12

Füzi Poiesis — Design Sprint

Week 12 was the primary design sprint week for Füzi Poiesis — finalizing the computational deliverables, completing the Benchling plasmid maps, and preparing the presentation. The following work was completed or finalized during this window.

Completed this week
pFP-C finalization and R-M shielding verification
The complete pFP-C plasmid (4,238 bp) — the primary DNA design deliverable of Aim 1 — was finalized in Benchling Academic during this week. R-M shielding was verified using REBASE + NEBcutter v3: zero internal EcoRI, SpeI, or XbaI sites confirmed in the expression cassette. The ts-ori (temperature-sensitive origin, cold-inactivating variant for Lake Budi's winter thermal regime below 15°C) is annotated as a placeholder for Aim 2 chassis selection. KanR selection marker documented with the constraint that it cannot interfere with the auxotrophic ring.
Completed this week
Six-equation ODE system — final figures
The dimensionless six-equation Monod ODE system (δ = 0.143, y = 0.45, K = 1) was finalized with all four simulation conditions: monoculture extinction, closed pair convergence, three-strain hypercycle convergence (n* ≈ 0.629, s* ≈ 0.628, Re(λ_max) ≈ −0.215), and cascade extinction after single-member removal at τ = 50. The Jacobian eigenvalue spectrum was computed symbolically using SymPy and evaluated numerically at the interior fixed point — all six eigenvalues with Re(λ) < 0, confirming asymptotic Lyapunov stability. The structural biocontainment figure (escaped strain exponential decay, t½ = 6.9 h) completes the four-figure proof-of-concept panel.
Completed this week
Presentation slides — final version
The three Google Slides for the Global Committed Listener presentation (May 13, 2026) were finalized: Slide 1 (consortium overview and Lake Budi crisis context), Slide 2 (Aim 1 computational proof — ODE results, AND-gate truth table, plasmid maps), Slide 3 (Aims 2 and 3 progression toward community-led restoration). The slide deck was copied into the shared HTGAA deck by the May 12 2PM ET deadline.
Reflection — Building Genomes and Füzi Poiesis

The lectures this week made one tension in Füzi Poiesis more visible: the gap between what genome-scale synthesis enables (arbitrary genetic programs, virus-resistant organisms, 473-gene minimal cells) and what is appropriate for deployment in a Lafkenche sacred lake. Building genomes is now technically feasible at scales that would have seemed impossible ten years ago. The question of what should be built — and where, and with whose consent — is the question that Füzi Poiesis tries to answer not by ignoring the power of the tools but by subordinating it to a framework of indigenous governance that precedes the technology.

George Church's recoded organism work is technically the most powerful biocontainment mechanism described this week — a cell that physically cannot be infected by natural viruses and cannot survive outside a synthetic amino acid supply. But it requires a fully recoded genome, years of engineering, and institutional infrastructure that doesn't exist in Temuco. The auxotrophic ring achieves a weaker but deployable version of the same principle — dependency on an external supply that doesn't exist in the open environment — with three gene deletions and three annotated plasmids in Benchling. That is the design constraint: not what is maximally powerful, but what is buildable, verifiable, and explainable to Lafkenche communities before any organism approaches Lake Budi.