week 7 HW: genetic circuits part II

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 can only read a signal as ON/OFF, even though molecules inside a cell exist at all kinds of intermediate concentrations. To build something complex out of ON/OFF switches, you have to layer many of them together, and each added layer introduces new opportunities for components to accidentally influence each other or fall out of sync. IANNs instead pass graded responses between nodes. Each node receives an actual concentration value, weighs it, and passes a continuous output forward. This means a single node carries far more information than an ON/OFF switch, so you need fewer of them to represent something complex, and there are fewer points at which things can go wrong.

  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.

A good use case is engineering bacteria to produce a drug. The bacteria need to balance how much raw material is available against how much final product has built up, since overproduction can stall or kill the cells. A Boolean circuit can only respond to whether the product level is above or below a fixed cutoff, shutting production on or off entirely. An IANN can instead read both signals as continuous values and smoothly adjust enzyme production in response, the same way a thermostat gradually responds to temperature rather than just cutting the heat off when a room gets warm.

  1. Draw a diagram for an intracellular multilayer perceptron where layer 1 outputs an endoribonuclease that regulates a fluorescent protein output in layer 2.
circuit_hw_7 circuit_hw_7

Layer 1 takes X₁ and X₂ as DNA inputs, each transcribed outside the cell. Inside, X₁ is translated into Csy4 (the inhibitory node, red) and X₂ is transcribed into FP mRNA. Both exit Layer 1 and enter Layer 2, where Csy4 represses translation of the FP mRNA while the mRNA itself drives it. The surviving signal is then translated by the output Tl node into the fluorescent protein.

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?

Packaging: Mycelium grown on agricultural waste like straw can be molded into compostable styrofoam alternatives, but costs more to produce and is harder to manufacture consistently at scale.

Insulation: Mycelium panels outperform synthetic foam on fire resistance and sound absorption and are fully biodegradable, but absorb moisture easily and aren’t strong enough for load-bearing applications.

  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?

If I were going to engineer fungi for materials, I’d want to tune the mycelium itself genetically to make it grow faster, more uniformly, and with better water resistance so that the material comes out of the growth process already having desireable properties, rather than having to add plastics or chemical treatments afterward to compensate.