Week 7 HW: Genetic Circuits Part II: Neuromorphic Circuits

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?

Traditional genetic circuits behave like simple ON/OFF switches (Boolean logic), but IANNs provide:

  1. Analog processing → Your construct’s aptamer-based 5′UTR already hints at graded responses (not just ON/OFF).
  2. Weighted inputs → Different regulators (e.g., RNA cleavage rates, promoter strengths) can tune output strength.
  3. Noise tolerance → Important in TX-TL systems where expression fluctuates.
  4. Complex decision-making → Enables pattern recognition rather than simple logic gates

2. Application of an IANN

Inputs
X1: Small molecule binding to aptamer in 5′UTR (affects translation efficiency)
X2: Endoribonuclease (e.g., Csy4) concentration regulating RNA stability
X3 (optional): T7 RNA polymerase concentration (transcription level)
Processing
Aptamer structure modulates ribosome access (weight 1)
Csy4 cleavage modulates mRNA degradation (weight 2)
Combined effects produce a graded sfGFP output
Output
Fluorescence intensity (sfGFP)
Represents a continuous function, not binary

Use case

  1. Environmental toxin detection
  2. Diagnostics (e.g., metabolite sensing)

Limitations

  1. Resource competition in TX-TL (limited ribosomes, ATP)
  2. Signal crosstalk between RNA regulators
  3. Difficulty tuning weights precisely
  4. Degradation variability in cell-free systems
  5. Scaling issues for deeper networks

3. Diagram

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Assignment Part 2: Fungal Materials

Examples of fungal materials-

  1. Mycelium-based packaging → alternative to Styrofoam
  2. Fungal leather → sustainable textile alternative
  3. Construction materials → bricks, insulation
  4. Filtration materials → water purification

Advantages over traditional materials

  1. Biodegradable
  2. Renewable and low-energy production
  3. Self-healing potential
  4. Carbon sequestration

Disadvantages

  1. Lower mechanical strength vs plastics/metals
  2. Moisture sensitivity
  3. Growth time variability
  4. Scaling challenges

We could engineer fungi to:

  1. Sense environmental toxins and fluoresce
  2. Produce functional biomolecules
  3. Self-heal structural materials

Why fungi over bacteria

  1. Multicellular structure → ideal for materials
  2. Secretion capability → easier protein harvesting
  3. Robust growth on waste substrates
  4. Better suited for large-scale physical materials

Part 3: First DNA Twist Order

Construct Summary

Name: T7-driven aptamer-regulated sfGFP cassette Backbone: pTwist Chlor (high copy)

Design Components

  1. T7 Promoter
  2. 5′ UTR with Aptamer
  3. RBS
  4. Reporter Gene
  5. Terminator

Benchling Link for the Twist Order: https://benchling.com/reet123/f_/DvufGAFHIG-final-project-construct/

Final Project Form also submitted-

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