Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Class Assignment — DUE BY START OF FEB 10 LECTURE Question 01 First, describe a biological engineering application or tool you want to develop and why. This could be inspired by an idea for your HTGAA class project and/or something for which you are already doing in your research, or something you are just curious about. According to the well-regarded popular science writer Matthew Cobb (2022), since the Asilomar conference in 1975, molecular biologists have been the vanguard in self-regulating when playing God. This means we refrain from conducting our research irresponsibly by deploying unnecessarily hazardous experimental methods. Alas, this also means that some of the most exciting genetic engineering is no longer done. Consider Dr. Oswald Avery’s transforming principle experiment. Blindly take a population of virulent pneumonia bacteria and feed them harmless kin until they lose their aggressive function and magically adapt into weak and indifferent pneumonia. Since Asilomar, this is indeed one kind of experiment that trustworthy principal investigators must abstain from. I get it, and still I contemplate. Wasn’t Avery the best of us, though? Between Schrodinger and Watson, Crick, and Franklin – Dr. Avery intuited DNA into existence with his transforming principle and used it effectively. Surely I didn’t name my oldest son after this man for nothing?
Week 2 HW: DNA Read Write and Edit
Table of contents Software used: Terminal, git, xcode, hugo, benchling, rcdonovan website, twist website. Objective: This week explores the read–write–edit toolkit: sequencing and synthesis workflows, restriction digests and gel electrophoresis, and early genome-editing frameworks.
Homework for HTGAA 2026 (Week 03): Lab Automation Table of contents Software used: Terminal, git, Opentrons, rcdonovan website, Google Colab. Objective: This week we get hands-on (or at least code-on) with pipetting robots.
Week 4 HW: Protein Design Part I
Homework: Protein Design I Assignment Objective: Learn basic concepts: amino acid structure, 3D protein visualization, and the variety of ML-based design tools. Brainstorm as a group how to apply these tools to engineer a better bacteriophage (setting the stage for the final project).
Week 5 HW: Protein Design Part ii
[] Homework — DUE BY START OF MAR 10 LECTURE Part A: SOD1 Binder Peptide Design (From Pranam) Superoxide dismutase 1 (SOD1) is a cytosolic antioxidant enzyme that converts superoxide radicals into hydrogen peroxide and oxygen. In its native state, it forms a stable homodimer and binds copper and zinc. Mechanis Mutations in SOD1 cause familial Amyotrophic Lateral Sclerosis (ALS). Among them, the A4V mutation (Alanine → Valine at residue 4) leads to one of the most aggressive forms of the disease. The mutation subtly destabilizes the N-terminus, perturbs folding energetics, and promotes toxic aggregation.
Week 6 HW: Genetic Circuits Part i
[]Homework — DUE BY START OF MAR 17 LECTURE Week 6 HW: Genetic Circuits Part 01 Assignment: DNA Assembly Protocol and Study Questions What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? A proprietary gold standard heat-stable DNA polymerase alternative to Taq reagent synthesized and sold by Thermo Fisher Scientific. Unlike Taq which was isolated from thermophilic bacteria, Phusion emulates an archaea-based enzyme that evolved in the hydrothermal vents from extremeophile species. They function as DNA polymerases essentially in a form biomimickry with minimal replication error. The purpose of Phusion is to amplify target DNA sequences in the PCR protocol. Phusion PCR is more expensive but worth the investment to increase the accuracy of the run.
Week 7 HW: Genetic Circuits Part 2
[]Homework — DUE BY START OF MAR 31 LECTURE at 2PM ET Week 7 HW: Genetic Circuits Part 2 Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? IANNs are ideal for the continuous transcriptomic-driven change observed in cells that are constantly moving and communicating in their intracellular environment – through analog computations. In contrast, much of the early synbio genetic circuit engineering was digital, with discrete logic gate switch programming or perhaps even through gene knock out (present versus absent) if such a connection would be permitted.
[] Homework — DUE BY START OF Apr 7 LECTURE 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. Describe the main components of a cell-free expression system and explain the role of each component. Why is energy provision regeneration critical in cell-free systems? Describe a method you could use to ensure continuous ATP supply in your cell-free experiment. Let it be noted, I really want to use George AI to engage this question, but I am running out of time, so I am just pitching shots up on the green to try and finish off with a putter and I also recognize metaphors are symptomatic of a weak mind, so there you have it. This is why we need AI too. Most people are susceptible to weak-minded syndrome. Therefore, since my overall understanding of what I am describing here is dulled, please do not try any of this at home. The bioenergetic cycles we wish to reconstruct in the cell-free environment literally resemble a water mill. I start with these two examples because one makes sense to me, and the other appears to be the same engineering concept but now there are some critical features missing that makes it more difficult to reconstruct the working order of things. I believe the same problem challenges us with cell-free systems. We have all the parts and experiments are clearly designed but what sustains them? There are clearly hidden variables that cannot be intuited at first glance. Now I am afraid if just put up my next image it will be swept away do to copyright infringement laws since I didn’t personally take a picture of this biochemical pathway. The irony of course is that the water mill and whatever mill above were invented when Newton was still alive if not before, likely long before, anyway the cellular aerobic respiration cycle was discovered inside of living organisms on Earth. In addition, we should note that the cellular cycle is part of many interacting open systems, and the other two mills are closed systems embedded in open living systems. Infact, is there anything sadder than a watermill without water for there in the bones of brick and iron is a functionless relic of a time before atomic energy had been harnessed. Perhaps a time we will return to in the end, but enough conjecture.
Week 10 HW: Imaging and Measurement
Week 10 HW: Imaging and Measurement Homework: Final Project Homework is partly based on data that will be generated in the Waters Immerse Lab in Cambridge, MA. Students will characterize green fluorescent protein (eGFP, a recombinant protein standard) structure (primary, secondary/tertiary) in the lab using liquid chromatography and mass spectrometry, as well as Keyhole Limpet Hemocyanin (KLH) oligomeric states using charge detection mass spectrometry (CDMS). Data generated in the lab needed to do the homework is included both within this document and in the Appendix of the laboratory protocol. 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. Please describe all of the elements you would like to measure, and furthermore describe how you will perform these measurements. There are many measurements that could be taken. The DNA of the mites and their larva is a target. In addition the bacteria and other microbiota and parasites that capitalize on the infestation damage to the host epidermis. This ofcourse brings up the geometry of the host tissue and biochemical molecules all of which can be measured quantiatively or qualitatively. Specifically, when it comes to host cells there are living and deceased keratinocytes and corneocytes and the odd hair follicle, especially in most heavily infested cases. There is superinfection residues full of bacterial cocci and rods or periods and semi colons as Dr. Betsy Dyer writes. There crushed and desciated erythrocytes, platelets, and leukocytes. In addition there will be scattering fluctuations of neturophils, eosinophils, macrophages, and lymphocytes. In addition, goats are always on the move grazing when they’re not cuddled up in hay or dirt. Therefore there will be pollen grains, plant frags, seed husks and hay chaff, and plant hairs in addition to other ecotoparasites. What I want to measure most though is stress.
Homework — DUE BY START OF APR 28 LECTURE Week 11 HW Overview Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork [!info] Note that this homework is due a week later than it ordinarily would due to its release a week later than normal. [x] Contribute at least one pixel to this global artwork experiment before the editing ends on Sunday 4/19 at 11:59 PM EST.
Week 12 HW: Bioproduction and Cloud Labs
Week 12 HW Overview Assignment Part 1: Work on individual final project Reading & Resources
Week 13 HW: Bio Design Living Materials
Week 13 HW Overview Assignment Part 1: > Work on individual final project. Reading & Resources
Week 14 HW Overview Assignment Part 1: Work on individual final project. Reading & Resources