Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
(The Challenge) Mastitis is an inflammation of the mammary gland in dairy cows, often caused by bacterial pathogens. It is a common and costly issue in dairy farms, leading to significant economic losses and affecting overall milk quality(Damasceno et al., 2025). The condition can arise from various factors, including poor hygiene, stress, and injuries to the udder. Common bacterial pathogens responsible for mastitis include Staphylococcus aureus, Escherichia coli, and Streptococcus uberis, which can enter the udder through damaged skin or during milking. Mastitis presents in either clinical or subclinical form. Coliforms from Escherichia coli, Klebsiella spp., and Enterobacter spp. account for 40% of clinical mastitis cases.
Week 2 HW: Read, write and Edit
Part 1: Benchling & In-silico Gel Art I began by signing into my Benchling account and creating a new folder called HTGAA-read, write, and edit I then added a new sequence that is the Lambda_NEB fasta sequence On the right-hand side, I used the icon that looks like scissors to enter the different restriction enzymes and then viewed the different digestion sites on the virtual digest tab. Below is the image from the virtual digest for the different enzymes.
Python Script for Opentrons Artwork I first designed the sunflower using the Opentrons-Art Website. For the design, I went with a sunflower design. https://opentrons-art.rcdonovan.com/?id=e3z1i8r73863y1k I then downloaded the Excel file, and on HTGAA26 Opentrons Colab, I leveraged Gemini assistance to be able to write the Python script. I uploaded the Excel sheet and promted gemini to assist in developing a script that would give me the sunflower design. Link to the Colab:https://colab.research.google.com/drive/1arsozAVNQhs-4Ol0LMIRKZ4QGVld0Kgf?usp=sharing
Week 4 HW: protein-design-part-i
Part A. Conceptual Questions How many molecules of amino acids in 500g of meat? A quick search shows that, for example, beef contains ~20–22g of protein per 100g of meat. Also, it would be good to mention that Raw meat contains more water, so the total weight of amino acids is lower per 100g compared to cooked meat, where water loss concentrates the nutrients (often increasing protein to 28–36g per 100g).
Week 5 HW:Protein-design-part-ii
Part 1: Generate binders with PepMLM Step 1 — Get the mutant SOD1 sequence Original SOD1 sequence from Uniprot sp|P00441|SODC_HUMAN Superoxide dismutase [Cu-Zn] OS=Homo sapiens OX=9606 GN=SOD1 PE=1 SV=2 MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ A4V mutant SOD1 sequence MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Step 2 — Run PepMLM Used google colab notebook for the step.
Week 6 HW: Genetic Circuits Part I: Assembly Technologies
DNA Assembly What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? What you add yourself (not in the master mix) Forward primer + Reverse primer — define what region to amplify Template DNA — the sequence to be copied Nuclease-free water — to bring the reaction to final volume
Week 7 HW: Genetic Circuits Part II: Neuromorphic Circuits
Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Integrated Artificial Neural Networks (IANNs) offer superior advantages over traditional Boolean genetic circuits by enabling analog processing, high-dimensional pattern recognition, and robust adaptability. Unlike Boolean circuits (on/off), IANNs handle continuous input levels, allowing complex decision-making, such as classifying disease states based on weighted molecular signatures rather than simple threshold switches.
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. In traditional in vivo (inside the cell) methods, the cell’s primary goal is its own survival. In CFPS, the goal is purely production.
Week 10 HW: Imaging and Measurement
Homework: Waters Part I — Molecular Weight We were analyzing an eGFP standard on a Waters Xevo G3 QTof MS system to determine the molecular weight of intact eGFP and observe its charge state distribution in the native and denatured (unfolded) states. The conditions for LC-MS analysis of intact protein cause it to unfold and be detected in its denatured form (due to the solvents and pH used for analysis).