Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices & Lecture 2 Prep
Can flashes of light be used to grow a computer? The idea is to shine light at cells to get them to produce proteins that reconfigure the structure that surrounds the cell. I’m curious if cells can produce proteins that cause interactions in their surrounding environment. #Goal: Maintain Biodiversity. Reduce Proliferation Inhibit self-replication ability Action 1: Create Biological Testing Grounds. Researchers across academia and private sectors partner with municipal governments to set aside land via legislation that can be used for testing how cell-computers interact with their environment.
Part 1 Hi. I used the KPNI enzyme repeatedly in the virtual digest. Is it possible to re-use enzymes? I think not. The DNA will have already been cut up. Part 3 I chose the protein phytochrome, which is found in plants and which detects red light. I chose phytochrome because I wanted to use a protein that’s found in plants. Initially I thought about choosing a protein that’s in asparagus. I learned that asparagus is green because of chlorophyll not because of a protein.
import random radius = 40 xloc = -20 yloc = -20 cursor = center_location.move(types.Point(0,0)) # Aspirate pipette_20ul.pick_up_tip() pipette_20ul.aspirate(20, location_of_color('Green')) for num in range(15): xloc += 2.5 yloc += 2.5 randomNum = random.randint(0,20) cursor = center_location.move(types.Point(xloc, yloc)) dispense_and_detach(pipette_20ul, 1, cursor) pipette_20ul.drop_tip()
Part 2: The generated peptide with the sequence WRYYAVGAAHKK has an ipTM score of 0.43, which is greater than the SOD1 binding protein’s ipTM score of 0.34. Part 3: Peptides with higher ipTM do not show stronger predicted binding affinity. Peptide with the sequence WRYYAVGAAHKK has the highest ipTM of 0.43, but the first two peptides have lower ipTMs and stronger predicted binding affinities. All three peptides are soluble. I don’t know what therapeutic properties are.
Week 7 HW: Genetic Circuits Part II: Neuromorphic Circuits
IANNs have components that check whether two values are similar in magnitude, as opposed to just checking whether the values are HIGH or LOW. In other words, they can perform analog computations. Here is a sample application for an IANN: Help calm down an allergic reaction to peanuts. Input: peanut protein, white blood cells Output: anti-inflammatory signals Limitations: There might be an allergic reaction happening at a site that’s not near the cell with a genetic circuit, in which case the circuit won’t get triggered.
Week 9 HW: Week 9 — Cell-Free Systems
General Qs: One advantage of cell-free protein synthesis is that the reaction can be freeze-dried to decrease its sensitivity to storage conditions. Freeze-dried cell-free protein synthesis mixture is sehlf-stable for a year. CFPS is also sometimes faster because all the energy of the system is directed at producing a protein. The main components of a cell-free expression system are: DNA: contains code for protein of interest RNA polymerase: produces RNA