Week 1 Lab: Introduction to Pipetting and Dilutions

Overview

• • Date(s): 03/02/26 – 03/03/26
  • Notes: Reviewed lab materials outlined in ‘Overview’ protocol section (pipette types and tips, tubes, tube holders, and stock reagents) and concentration basics with Kate Carline (William & Mary Node TA). Discussed lab material functions and reviewed the basics of dilution math and pipetting technique.
  • Supporting Picture(s):
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Part 1: Mixing Color

• Prepared tubes with red, yellow, and blue food coloring solution
• Marked 6 tubes with red, yellow, blue, red/yellow, blue/yellow, and red/blue combinations
• Added 500 uL to each each red, yellow, blue, red/yellow, blue/yellow, and red/blue combination solution tube
• See above – made combinations by mixing colors
• See above
• See above
• Dispersed concentrations onto wax paper to make design in lieu of petri plate

  • Supporting Part 1 and Part 2 photos below

    

    Practiced basic pipetting, mixing colors, and performing serial dilution

Part 2: Performing Serial Dilution

• Performed serial dilutions on MS/food coloring
• Made a final serial dilution reaction based on the information in the pre-lab
  • See pictures above

Week 2: DNA Gel Art

DNA Gel Art

Protocol Part 0: Designing My Gel Art / Expected Results and Walkthrough

Created a virtual digest in Benchling as a basis for DNA Gel Art (see below)

Benchling Virtual Digest (A Hidden Hello)

Protocol Part 1a: Preparing a 1% Agarose Electrophoresis Gel

Preared a 1% Agarose Electrophoresis Gel (see below)

Protocol Part 1a: Restriction Digest

Ran Restriction Digest (see images below)

Protocol Part 2: Gel Run

Performed Gel Run (see mp4s below)

Protocol Part 3: Imaging My Results With a Transilluminator

Took gel and prepared to image results (see below)

Final Results

Final result (see below)

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Benchling Protocol Notes (sourced from Wiliam & Mary Node TA, Kate Carline)

NotI-HF: rCutSmart, incubates at 37C, 20,000 U/ml = 10 U/ul Kpn1 (Promega): Buffer J, incubates at 37C, 12,000 U/ml = 12 U/ul Sal1 (Promega): Buffer D, incubates at 37C. 10,000 U/ml = 20 U/ul

1.5 ug DNA 324 ng/ul of Kampy B 4.62 ul DNA for N and K 141.4 ng/ul Kampy C (Nanodrop after running out of Kampy B) 10.61 ul for S

15 units of enzyme 1.5 uL Not1-HF 1.25 ul Kpn1 0.75 ul Sal1

2 ul of each 10X Buffer

Remaining to 20 ul NFW 11.88 ul Not1 12.13 ul Kpn1 6.64 ul Sal1

Spin down briefly in picofuge

Incubated for 30 min at 37C

1% agarose gel 2 ul dye with 10 ul reaction 40 min 185 mA 150V //

Week 3 Lab: Opentrons Art

Opentrons Art Lab

Part 1: Flourescent Bacteria & Black Agar Script

See Flourescent Bacteria & Black Agar Script Colab Notebook Script here ^{1 2}

Part 2: Submission and Running Your Protocol

Traveled to William & Mary Node to complete this lab, as well as the Pipetting and DNA Gel Art Labs. During my time working this lab, I:

• Selected plates for the Opentrons robot
• Operated the Opentrons robot with the help of William & Mary students
• Ran my Opentrons code
• Dispensed Opentrons tips

Protocol photos and mp4 video loops shown below:

Part 3: Final Result

Here’s the final result, showing my Opentrons Art!

Week 4 Lab: Protein Design Part I

Lab Information

• Lab work can be found within the Week 4 HW Assignment in the hyperlink below ¹

Week 5 Lab: Protein Design Part II

Lab Information

• Lab work can be found within the Week 5 HW Assignment in the hyperlink below ¹

Week 6 Lab: Gibson Assembly

Gibson Assembly Lab

Pre-Lab: Primer and PCR (Part 1 of 3)

• Read this section and scanned the NuPack software hyperlink

Pre-Lab: Gibson Assembly (Part 2 of 3)

• Read this section

Pre-Lab: DpnI

• Read this section

Pre-Lab: Plasmid Transformation

• Read this section

Part 1: Polymerase Chain Reaction (PCR)

Prepared PCR (see photos below)

Part 1a: DpnI Digest

Completed DpnI Digest (see photos below)

Part 1b: DNA Purification and Quantification

Purified and quantified DNA. It seems at this point that I did something wrong in one of the proceeding protocol stages with my non-Blue chosen color, so instead of proceeding with both colors, I only proceeded with Blue, as the other color did not have an adequate concentration. See photos below for more documentation of this protocol step

Part 2a: Gibson Assembly

Completed Gibson Assembly. Incubated reaction per protocol (see photo below)

Part 2b: Transformation

Completed Transformation protocol step

Final Results

LOREM

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Supporting prompts for analyzing the lab protocol listed below for reference

Week 7 Lab: Neuromorphic Circuits

Neuromorphic Circuits Lab

Downloaded Neuromorphic Wizard

Completed Circuit Design and Simulation in Neuromorphic Wizard

• See Neuromorphic Wizard Result Screenshots Below

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Completed Google Sheet Template

Week 9 Lab: Cell-Free Systems

Cell-Free Systems Lab

• Was unable to perform this Lab protocol at the William & Mary Node Wet Lab, as this protocol was not performed at the Lab as part of William & Mary’s HTGAA engagement this semester. However I did review the related ‘Cell-Free Systems Laboratory’ protocol. Answers to the questions found in the ‘Homework questions’ section of the protocol can be found in my Week 9 Homework in the ‘Part A: General Homework Questions’ section ¹

Week 10 Lab: Mass Spectrometry

Mass Spectrometry Lab

• Was unable to perform this Lab protocol at the William & Mary Node Wet Lab, as this protocol was not performed at the Lab as part of William & Mary’s HTGAA engagement this semester. However I did review the related ‘Mass Spectrometry’ protocol.

Week 11 Lab: Introduction to Cloud Laboratories

Introduction to Cloud Laboratories

• See Week 11 and Week 12 Homework assignments for answers and documentation regarding all related questions ¹²

Week 12 Lab: Bioproduction of Beta-Carotene and Lycopene

Bioproduction of Beta-Carotene and Lycopene Lab

• Was unable to perform this Lab protocol at the William & Mary Node Wet Lab, as this protocol was not performed at the Lab as part of William & Mary’s HTGAA engagement this semester. However I did review the related ‘Bioproduction of Beta-Carotene and Lycopene Lab’ protocol. Answers to the questions found in the ‘Post Lab Questions’ section of the protocol can be found below:

  • Which genes when transferred into E. coli will induce the production of lycopene and beta-carotene, respectively?
    • The Erwinia herbicola crtE, crtI, crtB, and crtY genes induce respective lycopene and beta-carotene production
  • Why do the plasmids that are transferred into the E. coli need to contain an antibiotic resistance gene?
    • Antibiotic resistance genes help researchers identify which E. coli bacteria successfully took the plasmid. This is necessary because a lot of the time E. coli bacteria do not successfully take plasmids
  • Whast outcomes might we expect to see when we vary the media, presence of fructose, and temperature conditions of the overnight cultures?
    • We might expect different levels of lycopene and beta-carotene production (i.e., different levels of biosynthesis, difficult absorption, and/or potentially different shades of produced pigments by varying overnight culture media, presence of fructose, and temperature conditions
  • Generally describe what “OD600” measures and how it can be interpreted in this experiment
    • OD600 measuress cell concentration and peak absorption for respective samples post-cellular culture incubation. It can be interpreted to determine whether or not we actually produced the desired forms of lycopene and beta-carotene with the appropriate pigmentation because we can compare our experimental absorption results form our cultures with previously established lycopene and beta-carotene absorption results in the literature
  • What are other experimental setups where we may be able to use acetone to separate cellular matter from a compound we intend to measure?
    • It would appear that acetone would be useful for experimental setups like separating out certain proteins from a larger mixture
  • Why might we want to engineer E. coli to produce lycopene and beta-carotene pigments when Erwinia herbicola naturally produces them?
    • Likely because we want more control over production of said pigments than Erwinia herbicola naturally provides. Control in this case might extend to pigment shade, concentration, or production time

All supporting prompts for this section listed below

Week 13 No Lab

No Lab for Week 13

Week 14 Lab: No Lab

No Lab for Week 14