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.

  • Week 3 HW: Lab Automation

    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).