Week 07 HW: Genetic Circuits Part II

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 can perform more complex computations than traditional genetic circuits, which are limited to Boolean functions. IANNs can process continuous inputs and produce continuous outputs, allowing for more nuanced control of gene expression. Additionally, IANNs can learn and adapt over time, making them more versatile and capable of handling dynamic environments.

2. 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.

One useful application for an IANN could be in the field of personalized medicine. An IANN can sense biomarkers from a patient’s blood and regulate the release of drugs in response to the biomarkers.

3. Below is a diagram depicting an intracellular single-layer perceptron where the X1 input is DNA encoding for the Csy4 endoribonuclease and the X2 input is DNA encoding for a fluorescent protein output whose mRNA is regulated by Csy4. Tx: transcription; Tl: translation. Draw a diagram for an intracellular multilayer perceptron where layer 1 outputs an endoribonuclease that regulates a fluorescent protein output in layer 2.

X1 (DNA encoding Csy4) --> Tx --> Csy4 mRNA --> Tl --> Csy4 protein
X2 (DNA encoding fluorescent protein) --> Tx --> fluorescent protein mRNA (regulated by Csy4) --> Tl --> fluorescent protein output

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-based materials used for packaging and insulation.

Advantages: sustainability, biodegradability, and low environmental impact.

Disadvantages: limited durability and potential for mold growth.

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?

Bioproduction of biofuels or other valuable chemicals. Fungi have the ability to break down complex organic materials, making them well-suited for this purpose. Fungi can grow in a wide range of environments, which makes them a more sustainable option compared to bacteria.