Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
What I would like developing a Microbial Oxytocin-Sensing Network，a decentralized, “invisible” biosensing system designed for non-invasive ecological monitoring. These “living sentinels” utilize chimeric GPCRs to detect mammalian oxytocin and record signals via CRISPR-genomic storage. To maintain ecological integrity, the data is expressed through near-infrared bioluminescence, creating an interface that is sensory yet non-intrusive to the local fauna.
Week 10 HW: Imaging and Measurement
Homework: Final Project 1. Measurement Object (Elements to be Measured) In this project, I will focus on measuring the following three interrelated indicators to verify the success of the conversion of heart rate data into biological signals: A luorescence Emission Intensity: This is a core measurement item. It directly corresponds to the intensity or frequency of the heartbeat signal. By measuring the brightness of fluorescence within a unit area or volume, it verifies whether the biological system has generated corresponding visual feedback based on the input heartbeat data.
Week 11 HW: Imaging and Measurement
Part B: Cell-Free Protein Synthesis | Cell-Free Reagents Recording to Gemini： Component Roles in CFPS E. coli Lysate (BL21 (DE3) Star): Provides the essential molecular machinery, including ribosomes and chaperones, while the T7 RNA Polymerase drives the transcription of DNA into mRNA. HEPES-KOH pH 7.5: Functions as a chemical buffer to maintain a stable pH, ensuring that enzymes and proteins remain folded and active throughout the reaction.
Week 2 HW：Dna Read Write and Edit
Part 1 Benchling & In-silico Gel Art Limbda Sequence Import
Python Script for Opentrons Artwork My Inspiration In taxonomy, Bucardo belongs to the genus Capra (goats). In my Opentrons practice, I discovered that the mosaic pattern formed by fluorescent bacteria blurred the boundaries between specific species and macroscopic classification. I am not depicting an exact sheep, but rather using the universality of the “Capra” attribute to reconstruct an image of “Resurrection for 7 Minutes”. This mosaic-like visual language is not only a numerical metaphor for Bucardo’s shattered life, but also a vague expression about ’existence and disappearance’ that transcends species classification.
Week 4 HW: Protein design part 1
Part A. Conceptual Questions 1.Why do humans eat beef but do not become a cow, eat fish but do not become fish? Because the human body completely breaks down exogenous proteins into free amino acids. And the DNA re-directs these amino acids to be arranged in the human sequence, rather than the sequence of cows or fish.
Week 5 HW：Protein Design Part-ii
Part A: SOD1 Binder Peptide Design Part 1: Generate Binders with PepMLM Generate four peptides of length 12 amino acids conditioned on the mutant SOD1 sequence. Among the generated sequences, WRYPAAAAELKK (7.61) stands out the most. It has a lower perplexity than the other generated sequences, indicating that it may be more compatible with the pocket of the SOD1 A4V mutation site in terms of chemical environment and geometric conformation.
Week 6 HW: Genetic Circuits Part 1
Assignment: DNA Assembly 1.What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? Phusion is an enzyme commonly used for high-precision cloning. Its Master Mix typically contains the following core components:Phusion DNA Polymerase: The core enzyme. It possesses 3’→5’ exonuclease activity (proofreading function), ensuring high fidelity DNA replication with an extremely low error rate. dNTPs (dATP, dTTP, dCTP, dGTP): The “raw materials” for building new DNA strands.Mg²⁺ (usually MgCl₂): A cofactor for the polymerase. It stabilizes primer-template binding and activates the enzyme’s catalytic center. Buffer: Maintains a constant pH and provides suitable ionic strength to ensure enzyme activity.
Week 7 HW: Genetic Circuits Part 1
Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) 1.IANNs vs. Traditional Genetic Circuits (Boolean Functions) Traditional genetic circuits are typically Boolean logic (0 or 1), meaning the output is only triggered when both inducers reach high concentrations simultaneously. In contrast, IANNs offer the following advantages: Analog/Graded Response Processing: Traditional circuits are prone to abrupt changes near a threshold. IANNs can handle analog inputs, achieving “weighted summarization,” allowing cells to respond linearly or with finer nonlinear responses to subtle changes in signal strength.
Homework Part A: General and Lecturer-Specific 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. Advantages:1.Flexibility and Control: You can directly adjust the reaction system, such as changing pH, ion concentration, or adding non-natural amino acids, without worrying about “killing” cells.2.Openness: The system is open; you can monitor the reaction process in real time or directly add linear DNA without constructing complex plasmids.