Week 07 HW: Genetic Circuits Part II

Part 1: Intracellular Artificial Neural Networks 1: What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? IANNs process analog signals instead of only ON/OFF outputs. They handle noisy data better and perform complex decisions using fewer genetic parts.

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. An IANN can be used in cancer therapy cells. The cell detects tumor biomarkers and releases a killing protein only when signal levels match cancer conditions. A limitation is high energy use, which may slow growth or cause mutations.

4: 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.

The first layer produces Csy4, which controls the second layer by inhibiting fluorescence output. Protein Y is produced only after both layers process the signals together.

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? 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? Fungal materials include mycelium leather and bio-composites for packaging and construction. They are biodegradable and low-cost but are less durable and sensitive to humidity compared to traditional materials.

Fungi can be engineered to sense environmental conditions like pH or nutrients and respond accordingly. Fungi are better than bacteria for complex proteins and strong 3D biomaterials because they are eukaryotic and form hyphal networks.

Assignment Part 3: First DNA Twist Order Have designed multiple twist orders for the final individual project and has been discussed with TA.