Week 7 — Genetic Circuits Part II: Neuromorphic Circuits

Assignment Part 1: Intracelluar Artificial Neural Networks (IANNs)

IANNs Advantages

What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions?

  • More closely mirror most natural genetic circuits where responses are naturally anolog.
  • In cases where you have analog input and output, which is many biological situations, the number of components required to transform to digital, do a digital computation, and then encode back in an analog output is often very large. This is not a big deal for digital circuits because we have figured out how to make each component so small and cheap that the flexiblity and debugability of boolean circuits is a huge win. For a biological circuit where even a 1000 components spread across many different cells is ambitious it is not clear this trade off is worth it in all cases.
  • Biological circuits are noisy and different proteins have different max and min expressoin levels, this makes it much harder to digitize the underlying analog signals than in a digital circuit where the highs and lows are same across the circuit and we can safely digitize by saying the signal is “near” high or “near” low without too much of a chance of cross over (though we still need to worry about transient states, which is why we often have a clock).

Application

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.

Not sure I have enough knowledge to come up with a really great application. Based on the lecture and what I know of simple neural nets I think they would be useful for siutations where you want to do multi-dimensional edge-detection. That is you have several different analog inputs, like oxygen level, light level etc and you want to have a variable response based on some complicated combination of them. For example, maybe an engineered bacteria that is added to canned/jarred food that fluoreces/turns color when conditions are favorable for botulism spores to reproduce.

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.

Fungal Materials

What are some examples of existing fungal materials and what are they used for? What are their advantages and disadvantages over traditional counterparts?

  • Looking at the mycelium materials wikipedia page for background. It looks like there applications for mycellium leather replacements and also building materials.
  • A cool project with mycelium I remembered from past reading is using mycleium to grow materials/buildings on the moon or Mars that NASA is studying

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 have a very broad range of chemistries they have figured out that other domains can’t, i.e. decomposing lignin from trees.
  • Fungi naturally emit substantces as part of their external digestion which can make extraction easier and more scalable.
  • Fungi are eukaryotes so they can do complex post-translational modfifications that bacteria can’t, which could be needed in some applications, e.g. drugs for people.