Week 7: Genetic Circuits II

Class Assignment

IANNs

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

IANNs can account for greater complexity, such as changing the level of output based on gradients or combinations of signals, which better reflects realistic biological 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.

IANNs could be used in therapeutic applications in a gut microbiome, such as to produce an anti-inflammatory cytokine inhibitor at low, medium, or high levels based on the intensity of several signals for inflammation (tetrathionate, nitric oxide, etc). This would however have high metabolic burden, and the engineered bacteria may struggle in the competitive gut microbiome.

  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.
diagram diagram

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 have been used for everything from fashion (as a leather-like material) to shipping (biodegradable packaging) to construction (insulation). They are biodegradable, which is a huge advantage over the counterparts they replace (like styrofoam) but are not are strong (more susceptible to moisture changes, can’t hold as much weight).

  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?

You could engineer fungi to have greater fiber strength for the above applications to address this weakness. Many fungi are eukaryotic and so are better at producing certain eukaryotic proteins than bacterial chassis and their multicellular capability expands potential applications (such as with fungal materials).

Twist Order

Insert sequence recorded in Benchling.