week-07-hw-genetic-circuits-part-ii

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 allow biological systems to act as analog processors, mimicking neural network learning and offering higher versatility, precision, and robustness in synthetic biology applications. context-dependent responses rather than simple “on/off” outputs. mimic artificial neural networks using transcriptional regulators, allow for complex, nonlinear processing of multiple inputs, higher fault tolerance, and the ability to perform regression analysis, which is not possible with traditional digital genetic circuits.

2.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.

A useful application of IANN would be to detect early stage breast cancer. early stage breast cancer has elevated levels of mir-155 and mir-21.

Input : mir-21 (X2 ) ERN-(X1) output: killer protein

Increasing translation rate of endoribonuclease translation rate:

The negative element increases (X1)so we have more endoribonuclease and lower would be the output(killer protein) so decision boundary shifts left.

Increasing translation rate of output:killer protein

The positive element increases(X2), the decision boundary moves down.

With Bias:

Both inputs are high (X1 and X2) bias has a fixed value, output will also be high.( killer protein). This happens because X1 and X2 are both higher than the bias. Bias is negative.

In the case when X1 and X2 are low the output is low bercause both X1 and X2 are lower than the bias.

Only when X1 or X2 or combination of both are higehr than bias we get output(killer protein). This is called the high pass.

Low pass: The X1 And X2 are low and output is high.

The bias is positive and X1 and X2 are repressors so they are negative weights. The X1 and X2 are lower than the bias so the output is high. only when X1 and X2 in combiantion exceeds the bias will the output be low.

Two neurons would be required to create the dual region where the X1 and X2 would be positive weights in one neuron and negative weights in the other. the bias would also be positive and negative in the two neurons based on the positive and negative weights of inputs.

Bandpass: Three neurons would be required. X1 and X2 would be positive weights in one neuron and negative weights in the other, the bias would also be positive and negative in the two neurons based on the positive and negative weights of inputs. The output of this would be the input for the third neuron, which would have anegative weight and the bias would be positive. the output which is the negative weight if above the bias then teh final output is low otherwise the output is high.

Limitations

The intracellular environment is noisy and highly crowded. The IANN needs to be robust against degradation by cellular enzymes (nucleases).

The IANN components incorporated in vivo should not pose toxicity and generate immune response from patient.

The IANN produces output based on specific known cancer markers, what if the cancer cell mutates - they may fail.

3.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.

Neuron 1 X1- DNA encoding the endoribonuclease A (ERNA) which is the negative weight

X2- DNA encoding the endoribonuclease B(ERNB) which is teh positive weight as it controls the output.

Neuron 2

X3- DNA encoding blue fluorescent protein which is the positive weight

The output of neuron 1 (ERNB) is the input for neuron 2 and is the negative weight.

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

Fungal materials, primarily derived from mycelium (the root structure of fungi), are transforming industries by providing eco-friendly, biodegradable alternatives to plastics, leather, and construction materials. These materials are grown on agricultural or industrial waste, turning low-value byproducts into high-value, customizable composites.

Mycelium Packaging (Packaging Foam): Used to replace expanded polystyrene (EPS) or Styrofoam. It is molded into shapes to protect fragile goods during shipping. Myco-leather (Fungal Leather): A flexible, non-woven mat derived from mycelium (e.g., Mylo™, Mylea™, Reishi™) used in fashion for handbags, wallets, shoe soles, and clothing.Mycelium Insulation Boards: Panels created for thermal and acoustic insulation in building construction, providing fire resistance and soundproofing. MycoTree (Structural Material): Dense mycelium composites used to create structural components, such as self-supporting structures, furniture, and door cores. Mycoprotein Food Analogues: Filamentous fungi (e.g., Fusarium venenatum) are fermented to produce meat substitutes (e.g., Quorn™), providing a high-protein, low-fat sustainable food source

Fungal materials are eco-friendly, sustainable,biodegradable. Production cost is low and lower carbon footprint compared to plastic, ceramic, steel. They can be engineered to be surprisingly strong, with some pressed mycelium surpassing wood in tensile strength. higher fire resistance than synthetic foams, emitting fewer toxic fumes and taking longer to reach flashover. Fungi can grow into customized molds and even heal small damages in the material matrix.

2.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 would want to genetically engineer fungi to produce marine derived secondary metabolites against cancer.Their mechanism involves targeting multiple pathways simultaneously, inducing apoptosis, and inhibiting angiogenesis and metastasis with lower toxicity to healthy cells.

Fungi are eukaryotic, can be used to make eukayotic protein with proper folding and post translational modifications. Fungal fermentation occurs in acidic environments as compared to bacteria and can prevent bacterial contamination. Fungi have Biosynthetic gene clusters which they use to produce secondary metabolites like polyketides,terpenes.This capability enables the production of pharmaceuticals, pigments, and complex specialized chemicals. The filamentous fungi possess remarkable secretory pathways, helpful in secreting proteins at 10-100 fold higher quantities.

Assignment Part 3: First DNA Twist Order

This the sequence of interest to be incorporated in the plasmid.

The Twist Bioscience Order plasmid