Week 7 Homework: Genetic Circuits Part II: Neuromorphic Circuits
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?
-Traditional genetic circuits typically operate on Boolean logic, which processes inputs as binary states (0 or 1). IANNs offer several advantages:
-Analog Integration - unlike Boolean circuits, IANNs can process graded signals, this allows cells to respond proportionally to varying concentrations of chemicals or light.
-Scalability - to achieve complex decision-making with Boolean logic, you need a massive number of gates, which places a heavy metabolic burden on the cell, IANNs can achieve classification or pattern recognition using fewer components by adjusting binding affinities or promoter strengths.
-Non-Linear Processing - IANNs utilize activation functions, this allows them to filter noise and handle non-linear relationships between inputs.
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.
Application: A cell designed to detect a specific cancer profile by sensing multiple microRNA (miRNA) biomarkers.
Input: The inputs ) are various miRNA sequences overexpressed in a specific tumor type. These inputs act as inhibitors or activators for the IANN.
Output: The output is the expression of a pro-apoptotic gene (causing cell death) or a secreted cytokine to alert the immune system. The output triggers only if the weighted sum of inputs exceeds a specific threshold
Limitations:
-Metabolic Load: High-level computation consumes cellular resources (ATP, ribosomes), potentially slowing cell growth.
-Signal Decay: Biological components degrade over time, which can shift the weights and lead to false positives.
3.Draw a diagram for an intracellular multilayer perceptron where layer 1 outputs an endoribonuclease that regulates a fluorescent protein output in layer 2.
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?
Fungal materials primarily utilize mycelium, the root-like structure of fungi.
| Material | Use | Adv | Disadv |
|---|---|---|---|
| Mycelium Packaging | Biodegradable alternative to Styrofoam | Fully compostable; low energy to produce | Lower impact resistance than some plastics |
| Fungal Leather | Sustainable textile for fashion | No animal cruelty; uses 90% less water than bovine leather | Consistency in texture can be difficult to scale. |
| Myco-Bricks | Sustainable construction | Naturally fire-resistant; excellent thermal insulation | Lower structural load-bearing capacity than concrete |
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?
Engineering fungi to biomineralize (deposit calcium carbonate) or secrete anti-microbial peptides. This could create “self-healing” buildings where cracks in fungal bricks are filled by the fungi themselves, or packaging that prevents food spoilage.
Advantages of Fungi vs. Bacteria:
-Fungi are eukaryotes, meaning they can perform complex post-translational modifications (like glycosylation) that bacteria (prokaryotes) cannot. This is essential for producing human-like proteins.
-The filamentous growth of mycelium provides a natural 3D scaffold. Bacteria usually form disorganized biofilms, whereas fungi create structural networks.
-Fungi are professional secretors. They are evolved to pump out massive amounts of enzymes to break down wood and organic matter, making them superior cell factories for harvesting products.
-Fungi can often thrive in more acidic or low-moisture environments where many industrial bacteria would perish.