Homework

Weekly homework submissions:

  • Week 1 HW: Principles and Practices

    For the raw text: https://docs.google.com/document/d/1u3VepFZVKRcZfB8QUowPQvQGaEuspPL8mM99Tzm679Y/edit?usp=sharing

  • Week 2 HW: DNA Read Write and Edit

      Homework week 2 - DNA READ, WRITE & EDIT   Part 1: Benchling & In-silico Gel Art Part 3: DNA Design Challenge 3.1. Choose your protein. Cocoonase, an enzyme capable of degrading silk protein sericin-2.   GenBank: AB604648.1 Rodbumrer P, Arthan D, Uyen U, Yuvaniyama J, Svasti J, Wongsaengchantra PY. Functional expression of a Bombyx mori cocoonase: potential application for silk degumming. Acta Biochim Biophys Sin (Shanghai). 2012 Dec;44(12):974-83. doi: 10.1093/abbs/gms090. PMID: 23169343.

  • Week 3 HW: Lab Automation

    Opentrons Artwork Post-Lab Questions Question 1.  My chosen article, entitled ‘AssemblyTron: flexible automation of DNA assembly with Opentrons OT-2 lab robots’, details novel development within the field of synthetic biology and automated lab operations in regards to DNA assembly.  Compared to other steps in the DBTL cycle of synbio, building has progressed the least in terms of automation, optimization and algorithmical performance. This step often involves DNA assembly, which continues to be done manually, with low throughput and often unreliable results. 

  • Week 4 HW: Protein Design Part 1

      Part A: Conceptual Questions Part A 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? A piece of meat weighing 500 grams contains approximately 100 to 160 grams of protein. 100 Daltons is equivalent to 1.66053907 × 10-22 grams If we divide the amount of protein by this number, it would mean that a piece of 500 grams of meat would contain between 6.0221407e+23 and 9.6354252e+23 amino acids. 

  • Week 5 HW: Protein Design Part 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. Original:  MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Mutated: MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ
  2. Generate four peptides of length 12 amino acids conditioned on the mutant SOD1 sequence, add the known SOD1-binding peptide FLYRWLPRSRRGG and record the perplexity scores of your generated binders. Binder

  • Week 6 HW: Genetic Circuits Part I

    Assignment: DNA Assembly What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? The Phusion High-Fidelity PCR Master Mix contains Phusion DNA Polymerase, nucleotides, and optimized reaction buffer including MgCl2. The DNA Polymerase synthesizes new strands of DNA by assembling nucleotides based on a template strand, the nucleotides are necessary for assembly and the optimized reaction buffers assure variable factors are optimised for PCR.  What are some factors that determine primer annealing temperature during PCR?

  • Week 7 HW: Genetic Circuits Part II

    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? One of the core advantages of IANNs over traditional genetic circuits is that IANNs can be used for complex computations whereas traditional genetic circuits are restricted to simpler digital operations. Moreover, IANNs have a higher predictability than traditional genetic circuits and can be modified to perform precise therapeutic functions. 

  • Week 9 HW: Cell Free Systems

    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 offers a number of advantages over traditional in vivo methods. An important advantage is the fact that cell-free systems are much more time efficient in comparison to their in-vivo counterparts. Cell-free systems also can operate using linear DNA fragments, whereas in-vivo systems necessitate the use of plasmid DNA.