Homework
Weekly homework submissions:
Week 6 HW: Genetic Circuits Part 1
HTGAA Week 6 Genetic circuit part 1 DNA Assembly 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 is a concentrated DNA polymerase solution containing a high fidelity reaction buffer, MgCI (Magnesium chloride) and dNTPs ( deoxynucleoside triphosphates). It is used in PCR as polymerase solution can help fill the gaps in the sequence cloned during Gibson or HiFi assembly. The reaction buffer serves as a stabilizer and MgCI and dNTPs serve as building blocks for PCR. Reference list BioChain Institute Inc. (2024). Biochain Institute Inc. [online] Biochain Institute Inc. Available at: https://www.biochain.com/blog/using-dntp-in-polymerase-chain-reaction-pcr/. New England Biolabs (2026). [online] Neb.com. Available at: https://www.neb.com/en-gb/products/m0531-phusion-high-fidelity-pcr-master-mix-with-hf-buffer [Accessed 23 Mar. 2026].
Week 7 HW: Genetic Circuits Part 2
HTGAA Week 7 Genetic circuits part 2 Part 1: Intracellular Artificial Neural Networks 1.What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? The advantage of IANNs over Boolean genetic circuits is their analog sensing and nonlinear processing capabilities, while traditional genetic circuits function as an On and Off system the IANNs can work in a continuous way due to its broader and stronger range of nonlinear inputs. Additionally, the IANNs have better pattern recognition and generalization technology, they can detect more complex patterns in data and can organise them better than the Boolean can.The IANNs are also less likely to fail and have a better error tolerance than the Boolean which is very susceptible to fail if there is a single issue with a gate. Moreover, the IANNs have a better scalable capacity due to the protein splicing mechanism allowing to create a multiple input-output circuit. The IANN technology can also better adapt and evolve to its environment compared to the Boolean which has a fixed function in its environment. Finally, IANNs have a strong memory quality that can be passed through to subsequent generations within the cell due stoichiometric cleavage and splicing which is irreversible.
HTGAA Week 9 Cell Free Systems Part A General and Lecture specific questions General Homework 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. Time : CFPS can be executed in very little time, a couple of hours however in vivo methods will take a few days to a few weeks. Time is a key part of efficient research as less time is wasted waiting to synthesize proteins to experiment on. System : CFPS is an open access system as it has no membrane and gives direct access to the molecule which one wants to work on, it offers more flexibility. It also allows for better control over the synthesis as one can specifically choose which components to input in a protein and better predict protein folding, this simplifies monitoring as well. Versus an in vivo method which has a membrane and therefore a closed system, this means the host and its other components will also react to any modification making it harder to control and direct, the cell’s functioning can often get in the way of the synthesis or create unpredicted issues. Tolerance: CFPS can tolerate high rates of toxic and difficult proteins as it is non living, however, in vivo technologies are more sensitive to toxins as it is likely to harm the host. CFPS also works using non-natural components offering a wider spectrum of possibilities. Complexity : CFPS is a simple PCR based procedure while in vivo requires more complex cloning and transformation steps. Reference List Silverman, A. D., et al. (2020). Quarto: A User’s Guide to Cell-Free Protein Synthesis. Nature Reviews Genetics. Gregorio, N. E., et al. (2019). Cell-free microbial synthesis of proteins. Frontiers in Bioengineering and Biotechnology.
Week 10 HW: Advanced imaging & measurement technology
HTGAA Week 10 Advanced imaging & measurement technology 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. As for this project I aim to use inaK for ice production I would like to measure the ice nucleation ratio and efficiency of the inaK protein. Additionally, I would like to measure the temperatures inaK can resist to, on its own and as a supplement to an ice sample. If my initial experiments are successful I would like to measure the inaK ratio innoculated into ice to find the most optimal inaK quantity needed.
Week 11 Bioproduction & Cloud Lab Part A - The 1.536 pixel art work canvas, collective artwork 1.Contribute at least one pixel to the global artwork I added early on a pixel towards the top left corner. I do not have much to say about this section of the work except maybe understanding the full purpose of this exercise.