Week 7 HW: Genetic Circuits Part II

Part 1. Intracellular Artificial Neural Networks (IANNs)

Q1. What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions?

IANNs can process inputs in a more continuous and analog way. This allows them to respond to gradual changes in input levels and produce more complex behaviors, such as weighted integration, thresholding, and pattern classification. Because of this, IANNs are better for tasks where biological signals are noisy and not strictly binary. They can also represent more complicated decision boundaries than traditional logic-gate-based circuits.

Q2. 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.

An IANN can be used for disease sensing in mammalian cells. It could integrate multiple signals, such as inflammation, hypoxia, and cancer-related RNAs, and produce an output only when the overall pattern matches a disease state. The output could be a fluorescent reporter or a therapeutic protein. A key limitation is that IANNs can be difficult to design and tune because of noise, cell-to-cell variability, and unpredictable interactions between components.

Q3. Draw a diagram for an intracellular multilayer perceptron where layer 1 outputs an endoribonuclease that regulates a fluorescent protein output in layer 2.

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?

Existing fungal materials include mycelium packaging, insulation, leather-like materials, and mycelium composites for products or building panels. They are used as alternatives to plastic foam, synthetic leather, and some lightweight construction materials. Their advantages are that they are renewable, biodegradable, lightweight, and can be grown from waste. Their disadvantages are that they may have lower durability, lower water resistance, and less consistent mechanical properties than traditional materials.

2. 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 want to genetically engineer fungi to create a higher-performance biofilament for 3D printing. For example, fungi could be engineered to improve the filament’s mechanical strength, flexibility, printability, and stability. This would be useful because it could make fungal materials more practical for fabrication while still being sustainable. Fungi are advantageous over bacteria because they naturally grow as filamentous networks, which makes them more suitable for forming continuous material structures. They are therefore a promising platform for developing stronger and more functional bio-based materials for 3D printing.