Homework

Weekly homework submissions:

  • 1.Describe a biological engineering application or tool you want to develop and why. I want to engineer a bacteria to produce enzymes to convert plastic wastes to a fertilizer. Microbes secrete extracellular enzymes—such as PETase, MHETase, cutinases, lipases, and esterases—to hydrolyze (break) the chemical bonds of plastics, releasing monomers (e.g., ethylene glycol, terephthalic acid) and oligomers. I want to create a bacteria that can combine these two functions by engineering it to produce enzymes for break down of both plastics and glasses and convert to useful biofertilizers for plants. I want to develop such an organism because both plastic and seem to pose serious threats as being non biodegradable for ages.
  • Part 1: Benchling & In-silico Gel Art Import lambda DNA Courtesy:NCBI - O’Leary NA, Cox E, Holmes JB, Anderson WR, Falk R, Hem V, Tsuchiya MTN, Schuler GD, Zhang X, Torcivia J, Ketter A, Breen L, Cothran J, Bajwa H, Tinne J, Meric PA, Hlavina W, Schneider VA. Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets. Sci Data. 2024 Jul 5;11(1):732. doi: 10.1038/s41597-024-03571-y. PMID: 38969627; PMCID: PMC11226681.
  • Create a Python file to run on an Opentrons liquid handling robot. 1.Generate an artistic design using the GUI at opentrons-art.rcdonovan.com. 2.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. You may use AI assistance for this coding — Google Gemini is integrated into Colab (see the stylized star bottom center); it will do a good job writing functional Python, while you probably need to take charge of the art concept. If you’re a proficient programmer and you’d rather code something mathematical or algorithmic instead of using your GUI coordinates, you may do that instead.
  • Homework: Protein Design I Part A. Conceptual Questions 1.Why are there only 20 natural amino acids? The 20 natural amino acids evolved as optimal sets very early, during the RNA world (4 billion years ago). The format was not changed and became frozen because it would disrupt all proteins and also due to tRNA recognition limitations further expansion was prohibited.
  • Homework: Protein Design II Part A: SOD1 Binder Peptide Design (From Pranam) Part 1: Generate Binders with PepMLM 1.Begin by retrieving the human SOD1 sequence from UniProt (P00441) and introducing the A4V mutation.
  • Assignment: DNA Assembly Answer these questions about the protocol 1.What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? The components of Phusion High-Fidelity PCR Master Mix contains Phusion DNA Polymerase (high-accuracy, 50x higher than Taq), dNTPs (nucleotide building blocks), and optimized reaction buffer with MgCl2(essential for enzyme activity).
  • Assignment 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 allow biological systems to act as analog processors, mimicking neural network learning and offering higher versatility, precision, and robustness in synthetic biology applications. context-dependent responses rather than simple “on/off” outputs. mimic artificial neural networks using transcriptional regulators, allow for complex, nonlinear processing of multiple inputs, higher fault tolerance, and the ability to perform regression analysis, which is not possible with traditional digital genetic circuits.
  • Homework Part A: General and Lecturer-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.
  • Homework: Final Project For your 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 the final project the presence of specific AMR gene is detected using aptamer fluorescence.The fluorescence intensity is directly proportional to the amount of the gene present at the site.
  • Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork 2.Make a note on your HTGAA webpages including: a.What you contributed to the community bioart project (e.g., “I made part of the DNA on the bottom right plate”) I made the upper triangle part before it was modified.8 pixels.