Week 7 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?

  • Continuous signal processing: Unlike Boolean circuits that operate in binary (On/Off), IANNs can process graded inputs and outputs, enabling more nuanced cellular responses.

  • Integration of multiple inputs: IANNs can combine many signals simultaneously and compute a weighted response, similar to an artificial neural network.

  • Instead of being limited to simple logic gates (and, or, not), IANNs can model nonlinear relationships between inputs and outputs.

  • Parameters like the promoter strength, binding affinity and degradation rates can be tuned to adjust how strongly each input influences the output.

  • Cells can make context - dependent decisions rather than rigid binary responses.

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.

A useful application of an intracellular artificial neural network (IANN) is the classification of cancer cells based on microRNA expression profiles. In this system, the inputs are the intracellular concentrations of specific microRNAs (for example, miR-21 or miR-34), which are differentially expressed in cancerous cells. These microRNAs regulate gene expression by repressing or permitting translation of target mRNAs, effectively acting as weighted inputs in the network.

The output is the expression of a reporter or therapeutic gene, such as a fluorescent protein or an apoptosis-inducing factor. The IANN integrates the multiple microRNA inputs and produces a response only when the combined signal exceeds a threshold, similar to a perceptron. However, this approach faces several limitations because biological noise in gene expression can reduce accuracy and unintended interactions may interfere with circuit behavior. Additionally, there are constraints on the number of inputs that can be reliably implemented. Finally, delivering such engineered systems into patients remains a significant practical limitation.

Reference:

Xie, Z., Wroblewska, L., Prochazka, L., Weiss, R., & Benenson, Y. (2011). Multi-input RNAi-based logic circuit for identification of specific cancer cells. Science (New York, N.Y.), 333(6047), 1307–1311. https://doi.org/10.1126/science.1205527

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.

This diagram I made on Canva represents an intracellular artificial neural network composed of two layers. In Layer 1, the inputs X₁ and X₂ are transcribed (Tx) and translated (Tl) to produce an endoribonuclease (E), which acts as an intermediate regulatory signal. This enzyme then interacts with Layer 2, where inputs X₃ and X₄ are transcribed into mRNA. The endoribonuclease E negatively regulates this layer by cleaving the mRNA, thereby reducing its availability for translation. As a result, the production of the fluorescent protein Y is modulated at the translational level. This design mimics a multilayer perceptron, where the first layer processes inputs to generate a hidden signal (E), and the second layer integrates both direct inputs and regulatory signals to determine the final 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?

Fungal materials are primarily based on mycelium, the filamentous network of fungi, which can bind organic matter into solid structures. One of the most well-known examples is mycelium-based packaging, used as an alternative to polystyrene foam for protecting goods during shipping. These materials are lightweight, biodegradable, and can be molded into custom shapes. Another example is mycelium leather, a sustainable alternative to animal leather, used in fashion and upholstery. Additionally, fungal materials are used in construction, such as insulation panels and biodegradable bricks, due to their thermal resistance and low density. Some applications also include acoustic panels and biocomposites for furniture. Fungal materials are biodegradable, renewable, and can be grown using agricultural waste, which significantly reduces environmental impact compared to plastics or synthetic foams. Their production typically requires less energy and generates fewer emissions. Furthermore, they exhibit useful properties such as thermal insulation, fire resistance, and lightweight structure. However, there are also limitations as fungal materials generally have lower mechanical strength compared to plastics or metals, which restricts their use in load-bearing applications. They can be sensitive to moisture and environmental conditions if not properly treated. Additionally, scaling production while maintaining consistency can be challenging, and their durability over long periods may be lower than that of conventional 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?

CategoryDescriptionWhy it matters
Stronger materialsEngineer fungi to produce enhanced structural proteins or denser mycelium networksImproves mechanical strength for construction, packaging, and durable biomaterials
Water resistanceModify fungi to synthesize hydrophobic compoundsIncreases durability in humid environments and expands real-world applications
Self-healing materialsProgram fungi to regrow and repair damaged structuresExtends lifespan of materials and reduces maintenance costs
Antimicrobial propertiesEngineer production of antimicrobial compoundsPrevents contamination and increases safety in medical or packaging uses
Responsive (smart) materialsEnable fungi to respond to stimuli (light, temperature, chemicals)Allows development of adaptive or sensing materials

Fungi vs Bacteria in Synthetic Biology

FeatureFungiBacteria
Cell structureMulticellular, filamentous (mycelium)Unicellular
Material formationNaturally forms 3D structuresCannot form structures without scaffolds
Protein secretionHigh secretion capacityLimited secretion
Substrate useCan degrade complex biomass (e.g., agricultural waste)Prefer simpler substrates
Growth speedSlowerFaster
Genetic manipulationMore complexEasier
Best use caseLiving materials, biomaterials, structure-based applicationsFast production of molecules, simple genetic circuits

References: