Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
- Describe a biological engineering application or tool you want to develop and why. Throughout my previous research as a new biodesigner, I have been particularly drawn to two themes: the intricate relationship between the gut microbiota and its effects on human physical and mental health, and the fascinating world of fungi and their broader implications for planetary health. I have deepened my research into psilocybin and related tryptamine alkaloids (substances that activate serotonin 5-HT receptors), which are already being investigated clinically for neuropsychiatric conditions (Xi et al., 2023), but what especially interests me is emerging evidence that some of their effects may be mediated by the gut microbiota rather than the brain alone (Caspani et al., 2024). There is still a lack of research on the precise impact that serotonergic psychedelics have on the structure and composition of the gut microbiota, even though animal studies suggest possible links (Császár-Nagy et al., 2022). A survey of wild‑type rats has shown changes in the abundance of spore‑forming gut bacteria following oral administration of serotonin, suggesting that serotonergic compounds such as psilocybin could directly or indirectly reshape microbial communities (Fung et al., 2019).
Week 2 HW: Dna-Read-Write-and-Edit
Part 1: Benchling & In-silico Gel Art I simulated the Restriction Enzyme Digestion in Benchling to create a design. I found it initially difficult to visualise patterns or images with the 7 restriction enzymes. I therefore decided to mix certain enzymes in the same wells to generate more DNA fragments and explore shapes further. Part 3: DNA Design Challenge 3.1 Which protein have you chosen and why? Using one of the tools described in the recitation (NCBI, UniProt, Google), obtain the protein sequence for the protein you chose. Name of protein: psiH (tryptamine 4-monooxygenase)
Assignment: Python Script for Opentrons Artwork 1) Generate an artistic design using the GUI at opentrons-art.rcdonovan.com. My OpenTron design is inspired by the nudibranch (sea slug) from the Mollusca phylum. Image source: Siewert, I. (2014). Nudibranch - Marine Life in Thailand. [online] Diving in Phuket Thailand. Available at: https://www.diving-thailand-phuket.com/nudibranch-marine-life-thailand/. Using the coordinates from the GUI, follow the instructions in the HTGAA26 Opentrons Colab to write your own Python script which draws your design using the Opentrons.
Part A. Conceptual Questions
- How many molecules of amino acids do you take with a piece of 500 grams of meat? (on average, an amino acid is ~100 Daltons) There are a variety of meats depending on the kind. Let’s take an average of about 20% of protein by mass of meat (Day, 2016). This would therefore mean that 500g of meat would contain roughly 100g of protein. The average molecular weight of an amino acid residue is 100 Daltons, which translates to about 100g per mole of the amino acid unit (100g/100g/mol = 1 mole of amino acid units) (ProPrep, 2019). 1 mole contains 6.022 x 1023 (Avogadro’s number) amount of particles (The ChemTeam, 2026). Therefore, if you consume 500g of meat, you are also ingesting approximately 6 x 1023 amino acid residues.
Part 1: Generate Binders with PepMLM 1. Begin by retrieving the human SOD1 sequence from UniProt (P00441) and introducing the A4V mutation. Human SOD1 Sequence (154AA per monomer - 308AA): MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQMATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ A4V mutation: The alanine to valine mutation at codon 4 (A4V) of SOD1 causes a rapid and progressive form of amyotrophic lateral sclerosis (ALS). In Uniprot, however, it appears that the sequence starts with Methionine, making the mutation from Alanine to Valine actually at codon 5.
Week 6 HW: Genetic Circuits Part I: Assembly Technologies
Assignment: DNA Assembly 1. What are some components in the Phusion High-Fidelity PCR Master Mix, and what is their purpose? Phusion High-Fidelity PCR Master Mix offers high fidelity and performance for PCR. It consists of Phusion DNA polymerase (1), deoxynucleotides and reaction buffer that has been optimised and also includes MgCl2 (New England Biolabs, 2026). The DNA Polymerase allows for the rapid synthesis of a new DNA strand with high accuracy, as it generates long templates with a single enzyme (Thermo Scientific, 2018). The deoxynucleotides are the essential building blocks for the DNA polymerase to proceed with the synthesis of a new DNA strand, whilst the buffer is what provides the ideal environment for the DNA polymerase to function, resulting in high-yield and fidelity.
Week 7 HW: Genetic Circuits Part II: Neuromorphic Circuits
Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) 1) What advantages do IANNs have over traditional genetic circuits, whose input/output behaviours are Boolean functions? The main limitation of traditional genetic circuits is their restricted control over the strength, timing, and cellular context of therapeutic effects, as their input–output behaviour is usually constrained to simple Boolean logic. In contrast, IANNs can provide finer control of gene expression and cellular behaviour by tuning promoters, repressors, and other genetic components, and they can also sum and weight multiple inputs within a single network, rather than relying on many individually wired logic gates, which become complex and error‑prone.
Week 9 HW: Cell - free systems
Homework Part A: General and Lecturer-Specific Questions General homework questions
- 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 provides greater flexibility and control compared to traditional in vivo expression, as the reaction occurs outside living cells, allowing factors such as DNA concentration and energy components to be adjusted without affecting cell viability. In in vivo expression methods, amplifying the bacterial plasmid, sequencing it, expressing the strain, and purifying the protein must be done separately for every single protein in the pathway. In contrast, in cell-free protein expression using a synthetic cell, proteins can be expressed directly from linear PCR fragments without the need for plasmid construction. This makes the process much more time‑efficient and allows results to be obtained within hours. Furthermore, all proteins can be expressed in one pot by adjusting the concentrations of the DNA, unlike in vivo systems that require different promoters for each protein and expression level.
Week 10 HW: Advanced Imaging & Measurment Technology
Homework: Final Project 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. For my project, I want to measure the activity of the CotA laccase from Bacillus subtilis (whose gene is inserted into my pETite‑based plasmid) against PAH compounds using ABTS as a colour‑indicating substrate. I will measure the initial reaction rate of CotA, expressed as the change in absorbance over time, under different conditions, such as pH and temperature, to determine the enzyme’s optimal working range.