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?

IANNs are great for analog computation, while also being scalable in deployment and useful for approximating functions.

  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.

Disease diagnostics. Inputs would be expressions levels of biomarkers and signals deemed harmful. Outputs could be in the form of a gene with a strong signal or that is therapetic in nature. Strong limitations could come from unintended interactions with the output, as well as cross-talk generated. Noise within the biological system could affected outputs as well.

  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.Draw a diagram for an intracellular multilayer perceptron where layer 1 outputs an endoribonuclease that regulates a fluorescent protein output in layer 2.

The diagram can be found below:

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?

Some examples of fungal materials are mycelium packaging and fungal leather.

Mycelium packaging can be regrown, replace styrofoam, is biodegradable, and can be sustainably generation. Disadvantages can come in resistance to degrdation under moisture.

Myceliucum leather can be produeced animal free and has the earlier mentioned advantages. Mycelium leather may not be as durable as animal counterparts, but it may be engineered to one day meet or exceed that duability.

  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?

I might genetically engineer fungi to eat waste products or grow as shielding or building material. In either case, the fungi can serve as a meaningful redesinging of the environment. Advantages of doing synthethic biology with fungi are at least three fold: A) you can perform unique protein modications and syntheses that you can’t yet easily do with bacteria, you can take advantage of more complex molecular regulatory systems within fungi, in some cases they may be more safely scalable, and you get easy “Last of Us” Jokes.

Assignment Part 3: First DNA Twist Order

Objectives of this were as follows:

  1. Review the Individual Final Project documentation guidelines.

Done

  1. Submit this Google Form with your draft Aim 1, final project summary, HTGAA industry council selections, and shared folder for DNA designs.

Done.

  1. Review Part 3: DNA Design Challenge of the week 2 homework. Design at least 1 insert sequence and place it into the Benchling/Kernel/Other folder you shared in the Google Form above. Document the backbone vector it will be synthesized in on your website.

This was done as well. The backbone chosen was pSB1C3 (High Copy). As a student without lab access, I was allowed to be exempt from the actual order.