Week 7 HW: Genetic Circuits: Part II

Part 1: Intracellular Artificial Neural Networks (IANNs):

  1. What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? These IANNs have several advantages compared to traditional genetic circuits:
  • Continuous responses instead of binary outputs, which makes them more similar to real biological systems, where gene expression is not just “on or off” but varies in intensity.
  • Better handling of noisy biological environments, because IANNs can integrate multiple inputs and average signals, making them more robust to fluctuations caused by these noisy systems.
  • Ability to learn complex patterns compared to Boolean circuits that are limited to simple logic, while IANNs can approximate complex nonlinear functions allowing more sophisticated decision-making.
  • This neural-like architectures can be extended to multiple layers, enabling hierarchical processing.
  • IANNs are more biologically realistic, since gene regulatory networks in cells already behave more like analog systems.
  1. 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: Smart cancer cell detection and response system

  • An IANN could be engineered in mammalian cells to detect a specific combination of cancer biomarkers and trigger a therapeutic response. Input:
  1. Expression level of oncogene A
  2. Expression level of oncogene B
  3. Hypoxia signal

Processing: each input contributes with a weight, similar to neural networks. The system integrates all those signals and applies a threshold-like function to decide if the combined patterns whether matches or not a cancer profile. If it does, the output is activated.

Output: i. Expression of a pro-apoptotic protein (inducing cell death) OR ii. Expression of a fluorescent reporter for diagnosis Limitations: biological noise and variability in this cell systems may affect accuracy, as well as cross-talk with endogenous pathways causing unintended interactions. It may also be hard to precisely control gene expression levels and, since cancerous cells mutate all the time, this instability could break the system over time.

  1. 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.

Diagram showing a two-layer intracellular perceptron. In layer 1, the input X1 is transcribed and translated to produce the endoribonuclease Csy4, acting as the output of the first layer. Csy4 the regulates Layer 2 as the post-transcriptional level by cleaving the mRNA produced from input X”, which contains a Csy4 recognition site. In Layer 2, X2 is transcribed and translated to produce a fluorescent protein (Y). However, when Csy4 is present, it reduces mRNA stability, leading to lower protein expression. This system is considered a multiplayer perceptron because the output of the first layer controls the behavior of the second layer, allowing more complex signal processing.

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?
  • Some examples of fungal materials include biodegradable packing, eco-leather, and construction materials such as ecological bricks. Fungal packaging is typically produced using mycelium grown on agricultural waste, where it acts as a natural binder, forming a lightweight, foam-like composite material. This is used as a sustainable alternative to petroleum-based plastics and Styrofoam in protective packaging, as it can absorb impacts and be molded into specific shapes during growth. Mycelium-based leather is developed by controlling fungal growth to prodce dense, sheet-like structures. These materials are then processed (compressed, dried and sometimes chemically treated) to achieve mechanical properties similar to animal leather. They are used in fashion and textile industry for products such as shoes, bags and clothing. Fungal bricks are created by growing mycelium through lignocellulosic substrates, where it binds the particles into a solid composite. Once growth is complete, the material is dried to stop further biological activity. These bricks are lightweight, biodegradable and can provide thermal insulation. The main advantages of fungal materials include biodegradability, low environmental impact and the ability to use renewable feedstocks such as agricultural residues. Additionally, their production generally requires less energy compared to traditional materials. As limitations, their mechanical strength and long-term durability are often lower than those of conventional materials like plastics, concrete or treated leather. They can also be sensitive to moisture, biological degradation, and environmental variability, which may restrict their use in certain conditions or require additional processing to improve stability.
  1. 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?
  • One interesting application would be to engineer fungi to produce “self-healing” construction materials. These modified fungi could be able to respond to mechanical damage; such as cracks in a fungal brick. When damage occurs, the fungus could be activated to regrow its mycelial network and repair the structure. This could be achieved by engineering gene circuits that are activated by stress signals or exposure to oxygen and moisture. Additionally, fungi could be modified to produce extracellular polymers or bidngind proteins that improve the mechanical strength of the material during the repair process. As an advantage is possible to mention the fact that this would extend the lifetime of sustainable building materials and reduce the need for maintenance or replacement, making construction more environmentally friendly and cost-effective. Using fungi for this purpose is especially advantageous because their natural growth as filamentous networks allows them to penetrate and reconnect damaged areas, something that is difficult to achieve with bacteria. However, challenges include controlling fungal growth to prevent overproliferation, ensuring long-term stability, and designing genetic systems that respond reliably to environmental signals.