Week 7 Homework

Part A:

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

Intracellular artificial networks offer precise control over the output of an application, thus opening the gates for complex circuits where it is not only important that certain parameters exist, but also their quantity. Using IANNs it is possible to design a circuit whose output varies based on both the presence of x different molecules and their concentration.

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.

Creating a system that expresses 2 different protein based on the stimuli received by 3 other molecules. Input: molecule A (upragulates the expression of protein X & downregulates the expression of protein Y), molecule B upragulates the expression of protein Y & downregulates the expression of protein X, molecule C (upragulates the expression of protein X & upregulates the expression of protein Y - positive feedbak loop); Output: protein X, protein Y; Description of the circuit: The promoters of each gene are upregulated of downregulated by the 3 input molecules. We will consder that molecule A has an effect equal to the value 2 for upregulation and downregulation, molecule B has an effect of 1.5 on upregulation and 2.5 on downregulation and moelcule Chas an effect of 7.0 on upregulation. More molecule B willl be needed for the upregulation of molecule B when molecule A is present and more molecule A will be needed for upregulation in the presence of moelcule B, while moelcule C acts as a general upregulator that overwrites the other 2 molecules and amking sure that both genes will be expressed even though not in equal amounts.

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.

(Gemini Ai generated image by following a set of steps)

Part B:

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

Fungi have moved from the forest floor to the factory, particularly through the use of mycelium to create sustainable alternatives to traditional materials. Myco-leather offers an ethical substitute for animal hides, while mushroom packaging provides a biodegradable shield for electronics that competes with plastic foams. In architecture, myco-bricks utilize fungal growth to bond organic waste into fire-resistant structural elements. These biological materials are carbon-negative and non-toxic, providing a stark contrast to the high-polluting industries they aim to replace. However, the sheer scale of global demand remains a challenge, while millions of trees are felled every year to satisfy the timber and paper markets, the fungal industry is still scaling its production methods to reach that level of output. Furthermore, the porous nature of untreated mycelium means it currently lacks the inherent water-resistance and long-term durability found in chemically treated plastics or leathers, requiring further innovation in bio-coatings to match the lifespan of traditional goods.

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?

Designing strains for bioremediation that digest microplastics or sequester toxins from the soil, as well as infrastructure where fungal spores dormant in a wall grow to seal cracks autonomously when exposed to air. In medicine, the ability of fungi to produce complex human proteins could enable localized drug manufacturing in crisis zones; for instance, a portable bioreactor could synthesize a vital treatment for a patient before they are medevaced to a higher-level trauma center. Fungi hold a significant edge over bacteria in these tasks because, as eukaryotes, they possess specialized cellular machinery like the Golgi apparatus required for proper protein folding and modifications. They are also natural secretors, making it easier to harvest products compared to the destructive extraction methods often needed for bacteria. Research into these eukaryotic workhorses remains buoyed by the fact that they offer the structural strength of a multicellular network alongside the sophisticated chemical processing of higher life forms.