Week 7 HW: Genetic Circuits Part II

Intracellular Artificial Neural Networks

  1. What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions?
  • Traditional genetic circuits operate on Boolean logic (AND, OR, NOT), which digitizes biological signals into strict ON (1) or OFF (0) states. IANNs, which operate on analog logic, allows for

  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.

  2. 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.

inhibitor ──⊣┐
              ├──→ output        output = excitatory AND NOT(inhibitor)
excitatory ──→┘

Layer 2 is an INHIBIT gate: X3 is the excitatory input (fluorescent protein mRNA), RNase2 from Layer 1 is the inhibitory input, and fluorescence only appears when X3 is present and Layer 1 has successfully suppressed RNase2 via RNase1.

X1 ──⊣┐
       ├──→ RNase2 ──⊣┐
X2 ──→┘                ├──→ ● Fluorescence
               X3 ──→─┘

An intracellular two-layer perceptron in which Layer 1 produces an endoribonuclease that post-transcriptionally regulates the Layer 2 fluorescent protein output.

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?
  • Most existing fungal materials are made from Mycelium, used for biopackaging, fungal leather/textile. The advantage is sustainability, given the biomaterial, mycelium is 100% compostable, and make efficient use of resources. The down side is that it’s susceptible to moisture, and the nature of the living biomaterial made standardization harder.
  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?
  • Fungi could be useful in tackling environmental issue, such as engineered to absorb and sequester heavy metals and radioactive waste from contaminated soil.
  • Fungi is better than bacteria because it’s a fun guy! (not funny..)