Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Bioindicator for Microplastic Contamination in Agricultural Soils 1. Biological Engineering Application Project Description The proposed biological engineering application is the development of a bioindicator for detecting contamination by microplastics and their chemical additives in agricultural soils.
Week 2 HW: DNA read, write and edit.
Part I: Benchling & In-silico Gel Art Begin by importing your DNA sequence and use the Digests tool to test the effects of different restriction enzyme(s). Export your final design as a png and compare with your lab results on your Notion page. See the images below for where to find the Digests tool, selecting the “NEB 2-log” ladder in the Virtual Digest tab, and how to have multiple Digests appear in the same Virtual Digest.
WEEK 3 — LAB AUTOMATION LAB PROTOCOL 1. Review of Materials First, I reviewed the available documentation on HTGAA (LAB–Week 3 – Opentrons Art). Key information required to prepare the design was found at the beginning of the Google Colab notebook, including technical constraints and recommended parameters for droplet spacing and volume.
Week 4 HW: Protein Design - Part I
Part A. Conceptual Questions How many molecules of amino acids do you take with a piece of 500 grams of meat? First, I researched how much protein the meat contains. I assumed it was beef, and I saw that the amount of protein per gram varies depending on the cut (FEN, 2012). I calculated the average protein content of 10 cuts and got 19.46, which I rounded up to 20g per 100g.
Week 5 HW: Protein Design Part II
Part 1: Generate Binders with PepMLM 1. Begin by retrieving the human SOD1 sequence from UniProt (P00441) and introducing the A4V mutation. Superoxide Dismutase 1 (SOD1) is a human enzyme that plays a critical role in protecting cells from oxidative stress by catalyzing the conversion of superoxide radicals into oxygen and hydrogen peroxide. It is a small, 154-amino-acid protein that typically forms a stable homodimer and contains a β-βarrel core structure with metal cofactors, copper and zinc, essential for its catalytic activity. Mutations in SOD1, such as the A4V variant, are associated with familial amyotrophic lateral sclerosis (ALS), a neurodegenerative disorder. SOD1 is widely expressed in the cytoplasm and is a key model protein for studying protein folding, aggregation, and targeted protein degradation strategies.
Week 6 HW: Genetic Circuits: Part I
Answer these questions about the protocol in this week’s lab:
- What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? Components of the Phusion High-Fidelity PCR Master Mix and their purpose: Phusion DNA polymerase – a high-fidelity DNA polymerase that synthesizes new DNA strands with a low error rate during PCR. Primers (forward and reverse) – short DNA sequences that bind to the target DNA and define the region that will be amplified. dNTPs (dATP, dTTP, dCTP, dGTP) – the nucleotide building blocks used by the polymerase to synthesize new DNA strands. Reaction buffer – maintains optimal pH and ionic conditions for proper enzyme activity. Mg²⁺ ions – an essential cofactor required for DNA polymerase catalytic activity. Nuclease-free water – maintains the correct reaction volume and prevents degradation of DNA. 2. What are some factors that determine primer annealing temperature during PCR?
Week 7 HW: Genetic Circuits: Part II
Week 7 — Genetic Circuits Part II: Neuromorphic Circuits 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 offer several advantages over traditional genetic circuits with Boolean input/output behavior:
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. Cell-free protein synthesis (CFPS) has several advantages compared to in vivo methods because it is an open system and we can control everything better.
Week 10 HW: Advanced Imaging & Measurement Technology
PART A: Final Project 1. Please identify at least one (ideally many) aspect(s) of your project that you will measure. It could be the mass or sequence of a protein, the presence, absence, or quantity of a biomarker, etc. In this project, it would be recommended to measure several aspects related to microbial adhesion proteins involved in biofilm formation on microplastics. These include the molecular weight and amino acid sequence of candidate adhesion proteins, as well as their relative abundance. It would also be useful to measure the presence and quantity of biofilm formation on synthetic polymer surfaces. Additionally, evaluating protein–surface interactions, such as binding affinity to plastics, would provide insight into adhesion mechanisms. Finally, physicochemical properties such as hydrophobicity and surface charge could be analyzed, as they are known to influence protein adhesion behavior.
Week 11 HW: Bioproduction & Cloud Labs
Cloud laboratories are making science accessible, affordable, and reproducible. Our aim this semester is to showcase how they can enable human creativity at scale, and how they provide a platform for collaboration and community. How To Grow (Almost) Anything is about synthetic biology, bioengineering, robotics, automation, art, and AI. But it is also about friendship, shared purpose, and the freedom to build beyond what we know and to be inspired by what can be. To that end, the goal with this cloud lab unit and homework assignment is to inspire collaboration and creativity while designing a scientifically rigorous cell-free fluorescent protein optimization experiment together.