Week 7 HW: 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?

I found really interesting and maybe usefull for my final proyect. IANNs have an important advantage over traditional genetic circuits because while traditional circuits act like simple on/off switches, IANNs can process multiple input signals and produce a gradual and smooth response. This type of circuit can generate intermediate levels of expression, such as weak, medium, or strong fluorescence, depending on the value of the signal. This allows the cell to make finer and more complex decisions, such as better distinguishing between closely related conditions, something Boolean circuits cannot do with the same level of precision.

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.

Following this idea that this type of circuit could be useful for my final project, a useful application for an IANN that comes to mind is a pH sensor inside a bacterium, where the intensity of a color (for example, fluorescence) indicates the pH value. In this case, the inputs of the IANN would be the molecular signals associated with pH, and the output would be the amount of fluorescent protein produced. With a traditional circuit, the color would only turn on once the pH passes a certain threshold, and you would not see the difference between a moderately high pH and a very high pH. In contrast, with an IANN the color becomes progressively more intense as the pH changes, allowing you to see whether the value is continuously increasing or decreasing.

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.

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?

In recent years, materials made from living organisms, especially fungi, have started to gain a lot more visibility in everyday life. Most of these materials are based on mycelium, which is basically the root system of fungi. It acts as a natural binder, feeding on organic waste and growing into dense, compact structures.

These materials are already being used in different ways. For example, they can be used to create biodegradable packaging that replaces traditional plastic or cardboard. They also have good sound insulation properties, which makes them useful for things like acoustic panels.

More recently, this type of material has started to appear in the fashion industry as well. Companies like MycoWorks are working on developing leather-like materials made from mycelium, offering an alternative that avoids the environmental and ethical costs of animal leather.

image source: https://vegnews.com/south-carolina-sustainable-vegan-mushroom-leather

Advantages: One of the clear advantages of mycelium-based materials compared to traditional ones is that they are sustainable and biodegradable, so they don’t create long-term waste. Moreover, they can be grown using organic waste matter, which makes the production process more environmentally friendly. Another benefit is that they require less energy and fewer resources than conventional materials.

Disadvantages: However, there are still some limitations. One of them is that these materials are not always as strong or durable as conventional ones, especially for heavy-duty uses. Another major disadvantage is that the production process can be slower, since it depends on biological growth, which can increase costs and require more storage space. Finally, scalability is also an issue, as it can be difficult to produce these materials on a large industrial scale.

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?

Fungi are already some of nature’s best decomposers, but what I find really interesting is the idea of taking that a step further through genetic engineering. You could imagine a fungal material that stays stable and strong while it’s being used, but once it ends up in a landfill or a compost environment, some kind of genetic “switch” activates. Instead of just breaking itself down, it could be engineered to release enzymes that also help degrade surrounding waste, like microplastics or even certain toxic substances, much faster than they would normally break down.

From what I understand, and also just based on how I see it, doing this with fungi could actually be more effective than using bacteria in some cases. Bacteria are great, but they usually stay at a very small scale, like in lab conditions or Petri dishes. Fungi, on the other hand, grow as mycelium, which means they can form much larger, three-dimensional structures.