Week 7 HW: Genetic Circuits Part II

Intracellular Artificial Neural Networks (IANNs)

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

Variables input into Boolean functions are binary (either ON or OFF), whereas the variables input into IANNs can be continuous. Additionally, IANNs can input multiple variables at a time while Boolean functions (like a two-layer IANN) only integrate two variables.

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.

You could use an IANN to model cell fate decisions during embryonic development. The network could consider intracellular factors—such as gene expression—and extracellular influences—such as cell density and external signaling from morphogens or canonical signaling pathways—to predict the cell fate of a pluripotent or hemipotent cell during development. IANNs would provide a more representative in silico cell fate model than a Boolean function because, unlike the Boolean function, the IANN would be able to incorporate multiple influences (mentioned previously) that influence fate rather than one factor at a time. One limitation of the IANN in this application might be treating all cells in a developing embryo as homogeneous rather than incorporating noise and stochasticity into its fate predictions.

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

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Fungal Materials

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

Hinneberg et al. (2025) provide a recent review of existing fungal materials and exciting avenues for future innovation. Some examples of fungal material from the article include biodegradable packing, leather alternatives, and various strucutral components. Fungal materials are a sustainable alternative to many manufactured goods; however, the scalability of fungal material production is limited, and the process is time-consuming.

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 be interested in engineering a fungus to detect pH changes or other environmental changes in the water of the tanks where I keep my Xenopus laevis frogs for my research here at William & Mary. It would be interesting to have a biosensor that can demonstrate when the environment the frogs are kept in is outside of the standard physiological range so it can be adjusted for their health and well-being.

Unlike bacteria, fungi are eukaryotic, meaning they are a better model of the intracellular complexity of human cells than bacteria. In particular, protein folding in fungi follows the same processing (chromatin remodeling, endomembrane system, RNA processing such as post-translational modifications, etc.) as proteins in human cells. Additionally, as fungi are eukaryotic (multicellular), they are capable of responding to signaling from neighboring cells or external influences in a similar manner to human cells.

Final Project!

Project Title

Engineering a small molecule to target the βγ subunits of pre-Bötzinger Complex μ opioid receptors

Final Project Description

Renarcotization is a delayed consequence of naloxone administration after opioid consumption that occurs when an opioid re-binds to a receptor following release of naloxone from the μ opioid receptors (MOR) active site, resulting in delayed respiratory depression. Existing literature has identified the βγ subunits of the MOR as responsible for regulating the respiratory depression associated with opioid binding to MOR. In this project, I aim to design a small molecule that will bind to the βγ subunits of the MORs in the pre-Bötzinger complex (pre-BötzC) of M. musculus to target the respiratory depression associated with opioid administration without disrupting the analgesic effects associted with activation of the MOR α subunit.

Final Project Aim 1

The first aim of my final project is to design a small molecule capable of binding to βγ subunits of pre-BötzC MORs by utilizing the Boltz Lab Drug Discovery Platform introduced in Part B of the Week 5 homework assignment. Existing literature has identified Gallein as a small molecule capable of effectively binding to the MOR βγ subunit, but it was ineffective when applied in vivo. My first objective will be to modify this structure (then perhaps pursue alternative structures) to optimize targeting the specific MOR expressed in the pre-BötzC to prevent lethal off-target effects.