Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
1.Biological engineering tool/application I am trying to develop a dyeing method for fabrics and surfaces by using Physarum Polycephalum, or the slime mould as an activator. The aim is to let the slime mould create one-of-one designs by growing on the surface, letting a level of unpredictabiity of growth control the outcome. Slime moulds are very good at creating pathways while expanding in search of optimum survival conditons. During this travel, they tend to leave behind residual pigment, usually yellow in colour. After drying it looks something like this. In this bioengineered application, physarum polycephalum expresses a pigment forming enzyme(tyrosinase/laccase-type oxidase) that catalyzes the oxidation of benign phenolic or cathechol precursors into reactive quinones that polymerize into and insoluble melanin-like pigment.
Week 2 HW: DNA read-write-edit
Part 1: Gel Electrophoresis Due to no access to equipment and space for gel electrophoresis I simulated the same to understand the process on https://www.labxchange.org/library/items/lb:LabXchange:9548bee3:lx_simulation:1?fullscreen=true Workflow Design plasmid DNA with protein of interest →Transform bacteria with plasmid DNA→Get many copies of plasmid DNA→introduction of plasmid DNA to cells
1.Designing opentrons artwork I used https://opentrons-art.rcdonovan.com/ to design a four leaf clover design. Using the coordinates from the GUI and with assistance of Gemini in-built within Google colab, I came up with an Opentron code in python for actually creating the design. Google Colab - https://colab.research.google.com/drive/1rBH37jyag6naTs3t0gUx6asZEOQE1XjN#scrollTo=pczDLwsq64mk&line=107&uniqifier=1 The code was visualized and this is the result:
Week 4 HW: Protein Design Part 1
Part A: Questions by Shuguang Zhang How many molecules of amino acids do you take with a piece of 500 grams of meat? 500g divided by 100 Da gives you about 3 × 10²⁴ molecules. So there are roughly 3 trillion trillion amino acids in a single serving of meat.
Week 5 HW: Protein Design Part II
Human SOD1 sequence MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ After adding A4V mutation MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Therefore, produced peptides: index Binder Pseudo Perplexity 1 WLYVVAAVRWKX 23.320599604199636 2 WRYVAAAAAHKE 8.96053025308908 3 WLYVPAGLALWX 13.021677157633269 4 WLYYVVAVAHKX 15.430388570774006 5 FLYRWLPSRRGG 11.545571242285833 ##Part 2: Evaluating Binders with alpha fold3 The alpha fold results for some reason are not loading for me, despite multiple attempst and troubleshooting. Hence the results were analyzed with the help of Claude using PAE matrices peptide 1 ipTM 0.38 The PAE matrix shows a uniformly mid-green inter-chain strip with no distinct dark patch, indicating no preferred binding site and the peptide appears to be floating without specific engagement.
Week 6 HW: Genetic Circuits Part I
- What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? Phusion High-Fidelity PCR Master Mix contains most of the key ingredients needed for PCR, except the template DNA and primers. It is designed to make DNA amplification more accurate and easier to set up. Some of the main components are:
Week 7 HW: Genetic Circuits Part II
Part1: Intracellular Artificial Neural Networks What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Traditional genetic circuits treat inputs as binary. This works for simple logic but breaks down when you need nuanced, graded decisions based on multiple continuous signals. Biology itself is almost never binary; cells exist on spectrums of gene expression and signalling intensity. IANNs overcome this by operating in the analog domain. An IANN computes a weighted sum of all inputs and applies a nonlinear activation function, exactly like an artificial neuron. The same molecular parts can be reused to implement completely different decision boundaries just by changing the weights, without engineering new biological parts from scratch. IANNs can also be stacked into multiple layers, enabling hierarchical computation that is completely impossible with single-layer Boolean circuits.
General Questions 1. Explain the main advantages of cell-free protein synthesis over traditional in vivo methods, specifically in terms of flexibility and control over experimental variables. Name at least two cases where cell-free expression is more beneficial than cell production. Cell-free protein synthesis gives you a level of control over the reaction environment that you simply cannot get when working inside a living cell. Because there’s no cell membrane, you can directly add or remove components, adjust concentrations in real time, and introduce molecules that would be toxic to a living cell without worrying about killing your chassis. You also get direct access to the product without needing to lyse cells or purify through layers of cellular debris.
Week 10 HW: Imaging and Measurement
Waters Part I Molecular Weight Question 1: Based on the predicted amino acid sequence of eGFP (see below) and any known modifications, what is the calculated molecular weight? Using the ExPASy Compute pI/Mw tool with the provided eGFP sequence Theoretical MW = 28,006.60 Da