Week 7 — Genetic Circuits Part II: Neuromorphic Circuits

This week covers neuromorphic genetic circuits, showing how engineered gene networks can implement neural-network “perceptron”-like computation and learning.

Assignment Part 1: Intracellular Artificial Neural Networks (IANNs)

  1. What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions?

IANNs (Intracellular Artificial Neural Networks) can handle analog, continuous signals instead of just on/off Boolean logic.They learn complex patterns through training, while traditional circuits need hand-designed logic gates. IANNs approximate nonlinear functions better than simple threshold-based genetic gates. They can generalize from noisy inputs, unlike rigid Boolean functions.

  1. Describe a useful application for an IANN; include a detailed description of input/output behavior, as well as any limitations an IANN might face to achieve your goal.

I could use an IANN to detect different glucose concentrations and output varying GFP fluorescence levels. Inputs would be glucose sensors (X1, X2) feeding into hidden nodes, with GFP as the output. Low glucose → low GFP, medium → medium GFP, high → high GFP for a smooth analog response. Limitation: slow response times due to transcription/translation delays, and sensitivity to cellular noise.

Assignment Part 2: Fungal Materials

  1. What are some examples of existing fungal materials and what are they used for? What are their advantages and disadvantages over traditional counterparts?

Mycelium pannels and tilling for home interior, fungal leather for fashion (replaces animal leather), mycelium packaging (replaces styrofoam). Mogu and Ecovative are actual companies selling those products. Advantages: biodegradable, grown from waste, carbon-negative; Disadvantages: different production pipeline, consumers rejection/fear/not used to it, problematics of producting out of living organisms.

  1. What might you want to genetically engineer fungi to do and why? What are the advantages of doing synthetic biology in fungi as opposed to bacteria?

I would engineer fungi to capture airborne pollutants even after the mycelium composite dries and dies. Many pollutants like VOCs (volatile organic compounds) and heavy metals remain in the air long-term, so I’d add genes for metallothioneins (metal-binding proteins) and enzymes like laccases that degrade pollutants. The dead mycelium would act like a passive filter that keeps working after growth stops.

I’d also make fungi more resistant to mechanical stress, water, and flame for stronger construction materials. For stress resistance, add genes for chitin synthase or hydrophobins to create a tougher outer cell wall. For water resistance, engineer hydrophobin overproduction to make a waterproof surface layer. For flame resistance, add phosphate accumulation genes could enhance the natural fire retardant capacities of the overgrowth outer layer.

Advantages of synthetic biology in fungi vs bacteria:

  • Better protein secretion: Fungi naturally secrete large amounts of enzymes and structural proteins into the environment
  • Eukaryotic modifications: Fungi properly fold and modify complex proteins like hydrophobins that need glycosylation
  • Scalable material production: Fungal mycelium grows on cheap waste substrates and forms bulk materials directly

Assignment Part 3: First DNA Twist Order

  1. Review the Individual Final Project documentation guidelines.
  2. Submit this Google Form with your draft Aim 1, final project summary, HTGAA industry council selections, and shared folder for DNA designs. DUE MARCH 20 FOR MIT/HARVARD/WELLESLEY STUDENTS
  3. Review Part 3: DNA Design Challenge of the week 2 homework. Design at least 1 insert sequence and place it into the Benchling/Kernel/Other folder you shared in the Google Form above. Document the backbone vector it will be synthesized in on your website.

Same as for the 6th, all the AI and comptute part took me a lot of time and therefore i’m quite late but I’ll catch up quick