Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Photosynthetic Image Generation (PIG) “Art cannot be separated from life. It is the expression of the greatest need of which life is capable, and we value art not because of the skilled product, but because of its revelation of a life’s experience.” -Robert Henri- Overview PIG is an experimental combination of biology, glassmaking, printmaking, and photography which produces a living, two dimmensional surface of bacteria cultured as graphic imagery. The research behind the process to date has produced a small series of images grown on a synthetic felt substrate.
Week 2 HW: Reading and Writing DNA Sequences
Start Your Homework! Part 1: Benchling & In-silico Gel Art Johnny Got His Gun -The sequence has been rearranged into the shape of a pistol. I wanted to keep the number of columns restricted to the original seven enzymes for this composition, but I’m sure the image could be improved with additional columns. Question? How many columns can be introduced to the gel matrix?
Do Your Homework!!! Links to Final Project Slides Photosynthetic Image Generation Surface Design Bryoculture Automation Reading Review: -Nature- Advancing sustainable agricultural transformation through the synergy of automated experimental platforms and living labs Forget the Opentron, it’s time for cranes, planes, and Agricutural Automation! Seriously though, not to hack on the Opentron, what an amazing tool for working in the lab. But let’s not forget about the outdoor living lab which is part of arguably one of the most important industries, Agriculture. The scale of an agricultural system can range from a backyard garden to industrial complexes spanning thousands of hectares. How can automation help manage systems across the scales of indusrty which ultimately translates into what does or doesn’t end up in our shopping carts?
Hi- It’s time to do your homework! Icosahedronic Molecular Modeling I -RCBeck Part A Questions: 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) Solve- How many Daltons are in 500 grams? 1g = 6.022173643E+23 Daltons (6.022173643E+23 x 500)/100 = 4.29 x 10E+18
Week 5 HW: Protein Design Part II
Time to do your homework- It’s always time to do homework in this course! Part A: SOD1 Binder Peptide Design Part 1: Generate Binders with PepMLM Starting with the human SOD1 sequence from UniProt (P00441), and then introducing the A4V mutation, we get the following sequence where the fourth amino acid in the sequences is changed from K to V:
Week 6 HW: Genetic Circuits Part I
Guess what. What? It’s time to do your homework. OMG!!! It’s never ending… I’m always doing my homework for HTGAA. Icosohedronic Molecular Model II -RCBeck Assignment: DNA Assembly Answer these questions about the protocol in this week’s lab What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? Answer: There are several components in the master mix. It contains - DNA polymerase, dNTP’s, reaction buffers, and MgCL2.
Week 7 HW: Gentetic Circuits Part II: Neuromorphic Circuits
After this assignment, it will finally not be time to do your homework for one day… Happy Spring Break! This is Your Brain on HTGAA- RCBeck Assignment Part 1: Intracellular Artificial Neural Networks What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? They can be weighted with high and low input values which gives them unique capabilities. Unlike a Bool - which is if this then that - the specificity of an IANN means they can be designed to produce more specific outcomes in cellular function by responding to multiple control parameters. Boolean functions have one input. Describe a useful application for an IANN; include a detailed description of input/output behavior, as well as any limitations an IANN might face to achieve your goal.
It’s that time again… RrrrrrraaAAHH!!! Glueless Icosahedron - RCBeck 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.
Week 10: Advanced Imaging and Measurment Technology
What happened to my brain? The Only Question -RCBeck Final Project Homework For your final project: 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. Aim One: Measurment Data The first aim of this project transforms a strain of Synechococcus elongatus 7942 (PCC7942) into the sucrose secreting, model organism S. elongatus cscB+. The original PCC7942 colony will need to be grown to an optical density (OD) 750 of ≥1 before transformation may take place. A spectrophotometer will be used to obtain this measurement. - First growth media needs to be prepared, which will require measuring agar, BG11 medium, AS Trace Elements, water, pH, and temperature of growth media. Plates are poured, streaked and incubated. Colonies are then selected and transfereed to new grow media. - Colonies are incubated until an OD of 750 is reached, then natural transformation may take place. - Transformed samples are then recultured with spectinomycin treated plates, which selects for only transformed model organisms.
Week 11: Bioproduction and Cloud Labs
OMG! Last One! Drawing Air (2026) Detail, Graphite on Paper -RCBeck Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork My contribution to the artwork was limited to one pixel, which was initially made to test interaction with the interface. I noticed how pixel contribution was rather competitive, where scripting was automatically writing over contributions. Unfortunately, this discouraged me from contributing any further, which lead me to focus on my final project alternatively.