Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
A1. I want develop a living biological tool that works like a chromatography instrument. I have been thinking since a long time that what if we could use 3D bioprinting to create a living tissue (I like to call it an ‘organstrument’) that can selectively bind and separate ions/molecules. I propose it could work similar to a ion-exchange / affinity chromatography columns but instead of using mechanical parts, it would be bio-engineered. It would be made of cells and biomaterials that do the separation biologically.
Week 10 HW: Imaging and Measurement
Homework: Final Project What will I measure? My final project involves modifying an existing flowering plant species to enhance anthocyanin pigment production. So that’s metric number one. How much production is occurring. Now the reason we’re tweaking anthocyanin production is to turn the petals of the plant into reliable pH indicators. I would also need to measure the change in color, the rate of deterioration of pigment after plucking the petal. The correlation between temperature and pigment concentration and also the overall pigment concentration in petals, if it can be even roughly standardized (all petals might not have exact amount for it to function as intended. so we tweak and see if at least all petals have similar concentration and if not then what is the limiting factor (specific env. conditions?))
Week 2 HW: DNA Read, Write & Edit
Week 2 : Pre-HW Professor Jacobson: A1. DNA polymerase with proofreading has an error rate of about 1 error per 10⁶ bases (10⁻⁶). This is due to its proofreading and exonuclease activity. The human genome is about 3.2 billion base pairs. At a raw error rate of 10⁻⁶, replication would introduce thousands of errors per genome copy, which is unacceptable. Biology deals with this via multiple layers of correction, DNA Polymerase proofreading, post replication mismatch repair and other such systems.
Assignment : Python Script for Opentrons Artwork I had to write a Python script for a art design. I chose to create a silhouette of the Indian subcontinent, with my city being highlighted. I did that using the Opentrons Artwork website. I thought I will make a pattern of sorts with code but I realized that would time consuming and not very symbolic as such. I got a clipart of India from google and cropped it and then used that too generate my artwork. It didn’t look very good, I had to fiddle around with the contrast, brightness and other values to make it work. It still wasn’t looking how I’d expected it too. I decided to redo it.
Part A : Conceptual Questions 1. 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) Amino Acids are protein building blocks, so whatever percent of protein the meat contains is technically the AA content. A quick google search tells me that most cooked meats contain 20%-30% protein by weight. I’ll take 25% as my number. Now, 25% of 500g is 125g. (500/4)
Part A: SOD1 Binder Peptide Design Part 1: Generating Binders with PepMLM Part 2: Evaluating Binders with AlphaFold3 Part 3: Evaluate Properties of Generated Peptides in the PeptiVerse Part 4: Generate Optimized Peptides with moPPIt Part B: BRD4 Drug Discovery Platform Tutorial Part C: Final L Protein Mutants
DNA Assembly What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? The Phusion Hi-Fi PCR Master Mix has multiple components like the Phusion Hot Start II DNA Polymerase is the central enzyme. It is a polymerase enzyme with 3’ to 5’ exonuclease activity that corrects mismatched bases and therefore has low error rates than Taq polymerase. The ‘Hot Start’ part in the name refers to the modification done to enzyme to keep it inactive until the initial denaturation step so that the polymerase doesn’t amplify some other DNA at room temperature. The mix also contains dNTPs which is a given as the nucleotides are the building blocks used for extension. Another component is MgCl2 which is a cofactor required for polymerase activity, The magnesium ion helps in catalysis of the phosphodiester bond formation between nucleotides. Magnesium ions are also important to form active substrate from dNTPs which is recognized by polymerase. (The magnesium ions neutralize some of the charge of the triphosphate group so they can fit into the active site of the polymerase without hindrance) Other components in the mix are Reaction Buffer and Stabilizers. The buffer maintains the optimal pH and Ionic strength for enzyme activity. What are some factors that determine primer annealing temperature during PCR?
Week 7 HW: Genetic Circuits II
What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Traditional genetic circuits are boolean, like the question says. Therefore, they can be either ‘on’ or ‘off’ and only can compute boolean functions. Limiting the cell’s computational ability. IANNs are different in the way that they produce continuos signals, they can take in multiple inputs. I think the benefits of IANNs over conventional genetic circuits are synonymous to the benefits of a neural network over a hard-coded solution. IANNs can react to novel inputs whereas the conv. genetic circuits can only respond to the input they were designed for. 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.
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. Compare prokaryotic versus eukaryotic cell-free expression systems. Choose a protein to produce in each system and explain why. How would you design a cell-free experiment to optimize the expression of a membrane protein? Discuss the challenges and how you would address them in your setup. Imagine you observe a low yield of your target protein in a cell-free system. Describe three possible reasons for this and suggest a troubleshooting strategy for each. Homework question from Kate Adamala Design an example of a useful synthetic minimal cell as follows: