Week 7 HW: Genetic Circuits Part II: Neuromorphic Circuits

Homework: IANNs and Fungal Materials

Assignment Part 1: Intracellular Artificial Neural Networks

1. Advantages of IANNs over traditional genetic circuits

IANNs can handle more than simple on/off behavior. Traditional genetic circuits often work like Boolean logic gates, where an input is either present or absent and the output is either low or high. In real cells, signals are usually more gradual than that. An IANN can combine several input levels and produce a more flexible output.

They are also useful when the cell needs to respond to a pattern of signals, not just one signal. This could make them better for sensing complex cell states, such as stress, disease, or changes in the environment.

2. Useful application for an IANN

A useful application would be an engineered cell that detects a disease-like environment. The inputs could be levels of inflammation, low oxygen, and a disease-associated molecule. The output could be a fluorescent reporter or a therapeutic protein.

This would be better than using only one input, because one marker alone might not be specific enough. The IANN could respond only when the full pattern looks correct. A limitation is that it may be hard to tune inside real cells, since gene expression is noisy and the circuit could behave differently in different cell types.

3. Diagram for a multilayer perceptron

Layer 1:

X1 DNA  -->  Tx  -->  Endoribonuclease
                         |
                         v
                    regulates mRNA

Layer 2:

X2 DNA  -->  Tx  -->  Fluorescent protein mRNA  -->  Tl  -->  Y

Assignment Part 2: Fungal Materials

1. Examples of existing fungal materials

One example is mycelium packaging, which can replace plastic foam packaging. Another example is mycelium leather, which is used as a leather-like material for fashion or textiles. Fungal materials are also being explored for insulation and acoustic panels.

The advantages are that these materials can be biodegradable and can sometimes be grown from agricultural waste. They can also be grown into useful shapes. The disadvantages are that they may not always be as strong, water-resistant, or consistent as traditional materials like plastic, foam, or animal leather.

2. What I might genetically engineer fungi to do

I would engineer fungi to make stronger and more water-resistant mycelium materials. For example, the fungus could produce extra structural proteins, natural pigments, or hydrophobic surface molecules. This could make the material more useful for packaging, leather-like sheets, or insulation.

The advantage of using fungi instead of bacteria is that fungi naturally grow as filamentous networks. That structure already looks more like a material. Bacteria are often easier to engineer, but they do not naturally form the same kind of large fibrous network. Fungi are better suited when the goal is to grow a physical material, not just produce a molecule.