Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Biological Engineering application Bioremediation with Developmental control General purposal: Engineered bacteria that sculpt the rhizosphere for enhanced bioremediation I want to develop a biological engineering tool designed to enhance the natural process of phytoremediation, where plants are used to extract or break down soil contaminants. The core idea is to create specially engineered soil bacteria that act as biological boosters for ordinary plants. This would enable plants to clean contaminated environments far more effectively. The tool is inspired by natural systems like the plant pathogen Agrobacterium tumefaciens, a microbe that hijacks plant development to create tumors. However, here I would redesign this concept for a beneficial purpose, that involves this: instead of causing disease in the plant, the engineered bacteria would send beneficial signals to the plant, first by these bacteria being able to express morphogens and then instructing the plant to grow a more extensive root system, in addition to further activate internal contaminants uptake and potencial degradation pathways.
Week 2 HW: DNA read, write, and edit
Homework Questions Nature’s machinery for copying DNA is called polymerase. What is the error rate of polymerase? How does this compare to the length of the human genome. How does biology deal with that discrepancy? Polymerase has a very low error rate of approximately 10^{-4} to 10^{-6} errors per nucleotide without proofreading. Thus, comparing to the human genome length of approximately 3 billion base pair, it represents a minimal part. Thanks to other molecular features, errors produced by the sythesis machinery can be corrected by mechanisms applied like read proof, including the polymerase’s intrinsic proofreading domain, post-replication mismatch repair (MMR) pathways involving proteins like MutS and MutL that scan and excise mismatches, and DNA damage response mechanisms such as base excision repair (BER) and nucleotide excision repair (NER).
Assignment: Python Script for Opentrons Artwork Python file to run on an Opentrons liquid handling robot Opentrons Colab https://colab.research.google.com/drive/1FSLFjeZfWudyaujskQb60dIuhlPAv9Nq?usp=sharing Python Script from GUI OTDesign_02-24-26_10-43-25.py
Week 4 HW: Protein Design Part I
Homework Questions Part A. Conceptual Questions Why humans eat beef but do not become a cow, eat fish but do not become fish? Because digestion breaks proteins into individual amino acids, so it means it destroys the cow’s structure and information. We absorb the amino acids and then our ribosomes rebuild human proteins based on human DNA. To make it clear, biological identity comes from genetic information, not raw material.
Week 5 HW: Protein Design Part II
Part A. SOD1 Binder Peptide Design Part 1 Design short peptides that bind mutant SOD1 Which are worth advancing for therapy Human SOD1 sequence MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ SOD1 A5V sequence MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Binder 1: WHYPAVAVALGX Perplexity: 8.190170 Binder 2: KRYYVVGVRHKE Perplexity: 31.759185
Week 6 HW: Genetic Circuits Part I: Assembly Technologies
DNA Assembly Part 1. What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? The Phusion High-Fidelity PCR Master Mix key components include: Phusion DNA Polymerase: This is a fusion protein comprising a traditional Pfu-like DNA polymerase and a processivity-enhancing domain. Its purpose is to synthesize new DNA strands with exceptionally high fidelity (due to its inherent 3’→5’ proofreading exonuclease activity) and high speed.
Week 7 HW: Genetic Circuits Part II: Neuromorphic Circuits
Part 1: Intracellular Artificial Neural Networks What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? 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. 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.
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Cell Free Artwork Experimental Loop I made this fish-like shape at the second quadrant (on the right side of the plate) I liked that this project brings our creative side, and we use fluorescent protein expression to reflect artistry. For next collaborative project there could be done in modified bacteria grown in different growth media (so as to see different color expression)