Notebook

Week-by-week highlights, daily logs, pictures, and who did what.

Project Timeline

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01

Week 1

May 5–9, 2025

Completed
Highlights
  • Preliminary notebook template, scheduling, and mentor/prof coordination.
  • TMSD modelling research; enzyme–aptamer modelling; budget + SSAF application.
  • Inventory setup; Faculty Talk prep/presentation; wet-lab templates and protocols started.
Daily Log
May 5
  • Meagan (12–2 am): preliminary notebook template; TMSD modelling research; scheduling; meetings; availability tracker.
  • Ella: reviewed project proposal; TMSD review for specific sequence (in progress); presentation slides (in progress).
  • Jackson: compared enzyme sizes (β-gal vs HRP); worked on faculty talk slides; modelled β-gal & HRP with ptau ± substrates; added PDBs.
  • Durwyn: supported budget & finalized SSAF application.
  • Isabel: completed budget & itinerary for SSAF.
  • Ryland: LFA literature review (in progress); TMSD procedure revision (in progress).
  • Ria: aptamer literature review; protocol revisions; compared biotin/streptavidin vs PEG spacers vs other linkers; worked on slides.
  • Zehaan: generated ssDNA models for TMSD in Chimera; modelled duplex; saved PDBs.
May 6
  • Meagan: edited Faculty Talk slides; presented to Dr. Cairo; team meeting.
  • Ella: Faculty Talk script; toehold exchange sequence research; found TMSD sequences; presented to Dr. Cairo.
  • Jackson: created Faculty Talk script.
  • Mayuri: Faculty Talk presentation.
  • Durwyn: Faculty Talk visuals; LFA literature review.
  • Isabel: added substrate–enzyme protocol slides to Faculty Talk.
  • Ryland: LFA & attachment methods literature; wet-lab protocol slides.
May 7
  • Meagan: met lab tech; edited & presented Faculty Talk; emailed mentor; inventory template; sent protocols; wet-lab notebook template; team reminders; updated GANTT & contacts; scheduled meetings; many todos.
  • Ella: met lab tech; presented; finished slides; started organizing protocols.
  • Jackson: materials list.
  • Shade: enzyme/substrate binding lit review; Faculty Talk.
  • Durwyn: attended Faculty Talk; minutes and feedback notes.
  • Isabel: LFA lit review; slides on LFA–TMSD integration & enzyme/substrate validation; presented.
  • Ryland: edited protocols & slides; attended Faculty Talk; α-complementation review.
  • Ria: presented; edited wet-lab protocol slides; researched protocols; click-chemistry for enzyme–DNA attachment; planned diagrams.
May 8
  • Meagan: inventory; mentor meeting; brief TMSD modelling review.
  • Ella: inventory; reviewed safety certificates; daily experimental plans.
  • Durwyn: meeting; generated ssDNA/DNA models of updated TMSD in Chimera (exported PDB/PNG); to-dos on joining models; brief modelling review.
  • Isabel: control line protocols research (ongoing); mentor meeting notes (LFA integration, controls, enzyme–substrate reactions, modelling).
  • Ria: inventory; mentor meeting; lit review on EDC coupling to LFA membrane; click-chemistry protocol.
May 9
  • Meagan: inventory.
  • Ella: finished inventory; protocol review; created Week 1 summary.
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Week 2

May 12–16
Highlights
  • Wet-lab schedule; materials & equipment lists; protocol edits; attachment chemistry research.
  • In-silico SELEX scripting started; LFA attachment protocols explored.
Daily Log
May 12
  • Meagan: reviewed hours/protocols; emailed Ha.
  • Ella: created wet-lab schedule; protocol comments.
  • Jackson: finalized materials list; in-silico SELEX & sequence program research.
  • Shade: equipment list from protocols; LFA literature.
  • Ryland: NC membrane protein-binding; epoxide–thiol; diaminoalkane–glutaraldehyde; β-gal–NC attachment protocol.
  • Ria: protocol edits; functional-group attachment lit review.
  • Zehaan: in-silico SELEX with Jackson; docking software research (AutoDock, MOE, DockingServer).
May 13
  • Jackson: SELEX sequence generator (in progress); aptamer length review; materials list work.
  • Mayuri: materials list.
  • Durwyn: joined TMSD + literature aptamer models in Chimera; uploaded updated structures; LFA review (nucleic-acid aptamer-based).
  • Isabel: waste-disposal investigation.
  • Ria: HRP-to-DNA attachment literature.
May 14
  • Ria: completed HRP-to-DNA and TMB-to-DNA literature review; added to Attachment Methods → TMB/HRP.
  • Zehaan: Python script to generate SELEX banks; docking work continues.
May 15
  • Meagan: ordered materials; receipts to MindFuel; mentor meeting.
  • Ella: met Dr. Pandey; helped order materials.
  • Shade: LFA assembly procedure; mentor meeting.
  • Durwyn: mentor meeting.
  • Isabel: modelling software exploration; reviewed code from Zehaan & Jackson.
  • Ria: mentor meeting; pros/cons list for colorimetric pairs (started).
May 16
  • Meagan: MindFuel RSVP; Dr. Pandey meeting; lab orientation; emailed docs to Lindsay & Ha.
  • Ella: Dr. Pandey meeting.
  • Mayuri, Shade, Durwyn, Ryland, Ria, Zehaan: lab orientation (as listed).
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Week 3

May 19–23
Highlights
  • This week the group worked together to create a project presentation, poster, and video to present at the MindFuel TFC competition. This included us creating an overview of where we have gotten to this point with modeling and concept review.
  • The dry lab continued modeling and creating the Python code for our in-silico SELEX experiments.
Daily Log
May 19 (Victoria Day)
  • Meagan: revised 2024 GANTT; DNA biosensor research.
  • Shade: completed LFA literature review.
May 20
  • Ella: compiled prior notes; outlined MindFuel prototype; reviewed mentor minutes; updated wet-lab schedule (new start).
  • Jackson: organized judges' notes from MindFuel pitch.
  • Durwyn: finished substrate & aptamer LFA models; uploaded; finished nucleic-acid LFA review.
  • Ryland: protocol work.
May 21
  • Ella, Jackson, Mayuri, Durwyn, Isabel: MindFuel slide work (visuals, models, outline for prototype video).
May 22
  • Ella: confirmed in-lab schedules; slides; poster planning.
  • Durwyn: slides; presented at mentor meeting.
  • Isabel: BioRender image; proposal update.
  • Ria: slides; presented at mentor meeting.
May 23
  • Ella: edited MindFuel slides from feedback; weekly summary; poster & wet-lab schedule.
  • Jackson: salivary biomarkers document.
  • Ria: edited MindFuel slides/scripts to be concise.
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Week 4

May 26–30
Highlights
  • This week we worked to finish our presentation, poster, and video for Mondfuel TFC. We then presented our work in person! We received the award for Biggest Pivot Since Pitch for $500! This was a great opportunity to enhance our presentation skills for the BIOMOD competition and get valuable feedback from mentors and judges on our project design and concept.
Daily Log
May 26
  • Meagan: week planning; meetings (Ella, Faeez).
  • Ella: week planning; poster/video script work.
  • Jackson: IDT ordering research.
  • Durwyn: MindFuel video script outline finalized.
  • Ryland: reviewed v5 proposal comments.
  • Ria: video script.
May 27
  • Ella: poster for MindFuel; recorded script.
  • Durwyn: video editing; finished & uploaded MindFuel prototype video.
  • Isabel: BioRender images; poster creation.
  • Ryland: protocols updated w/ substrate–enzyme pair.
May 28
  • Ella: transport materials list.
  • Durwyn: finished modelling script for prototype presentation; uploaded video + description.
  • Isabel: MindFuel presentation work.
  • Ryland: HRP research.
  • Ria: presented to mentor; follow-up research.
May 29
  • Durwyn: mentor meeting; finished project display.
  • Isabel: mentor meeting; patent on new AD biomarkers.
  • Ria: mentor meeting; HRP vs β-gal pros/cons.
May 30
  • Isabel: memorized MindFuel script; slide/script edits.
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Week 5

June 2–6
Highlights
  • This week we focused on the move into our new lab. We were able to move all of our materials and disposables over and begin organizing them. It is starting to get exciting as we should be able to start experimentation in the lab shortly!
Daily Log
June 2
  • Ella: created prior-week summary.
June 3
  • Ella: edited experimental schedule; reviewed protocol comments.
  • Jillian: addressed judges' RBC filtration comments.
  • Durwyn: protocol work; LoD research for blood/saliva biomarkers.
  • Isabel: proposal edits.
  • Ryland, Ria: protocol work.
June 4
  • Ella: worked on proposal v5.
  • Ria: reviewed protocol comments.
June 5
  • Meagan, Ella, Jillian, Zehaan: transported materials.
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Week 6

June 9–13
Highlights
  • This week we worked hard on finalizing the sequences for our project so that we can order them as soon as possible and start experimentation with them. These sequences are important for our project to ensure that the toehold exchange will work properly and to ensure our aptamer properly changes confirmation allowing our colorimetric substrate/ enzyme pair to come into contact.
Daily Log
June 9
  • Ella: weekly summary; team-bonding planning; protocol-confirming literature.
  • Ria: protocol edits based on comments.
June 11
  • Ria: qPCR techniques; Cell-SELEX aptamer article shared; biomarker research.
June 12
  • Ryland: edited protocols to use HRP; HRP application research.
June 13
  • Ryland: continued HRP protocol edits & research.
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Week 7

June 16–20
Highlights
  • Focused on primer sequences and finalized all TMSD and aptamer sequences, confirmed via online software by dry lab team.
  • Investigated the best biomarker for our project: part of the team performed literature review, while dry lab evaluated docking and modeling to confirm compatibility.
Daily Log
June 16
  • Jackson: AutoDock docking research; PDBs for p-T181 & p-T231; phosphorylating tau with Zehaan (ChimeraX/PyMOL).
  • Ryland: primer design research.
  • Ria: primer sequences + materials tab + Tm values.
June 17
  • Jackson: primer details (Tm/dimers/ΔG etc.); how-to doc for in-silico SELEX.
June 18
  • Jillian: aptamer docking controls.
June 19
  • Jackson: WinCoot setup; phosphorylation workflow.
  • Jillian: aptamer docking controls.
  • Durwyn: BIOMOD wiki design concept; photo scheduling; team questions & form.
June 20
  • Jackson: materials list check; phosphorylation research.
  • Ryland: protocol reviewing.
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Week 8

June 23–27
Highlights
  • Dry lab continued focusing on biomarker choice using software to phosphorylate tau (181 and 231) for simulation.
  • Started designing our BIOMOD website, comparing previous iGEM and BIOMOD winners, and planning layout and features creatively.
Daily Log
June 23
  • Jackson: phosphorylating tau in WinCoot; SU Conference funding application work.
June 24
  • Durwyn: "Meet the Team" form; wiki design; SU funding application.
June 25
  • Jackson: coordinated WinCoot phosphorylation with Zehaan; SU funding application.
June 26
  • Meagan: completed phosphorylated tau (181/231) in WinCoot; emails; commercialization/photo when2meets; wiki profile.
  • Isabel: surveyed past iGEM/BIOMOD wikis (incl. best-website winners).
  • Ria: developed aptamer-TMSD sequences; researched alternative columns & unmodified oligo options.
June 27
  • Isabel: continued wiki survey.
  • Ryland: protocol reviewing; team description form.
  • Ria: worked on SU funding application (June 28).
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Week 9

June 30–July 4
Highlights
  • Started lab work by creating buffers—a crucial first step before beginning experiments.
  • Dry lab progressed on BIOMOD website creation, focusing on formatting, features, and design.
Daily Log
June 30
  • Jackson: primer review + primer design doc; protocol & materials review.
  • Isabel, Ryland, Ria, Zehaan: SU funding application completed.
July 1 (Canada Day)
  • —
July 2
  • Ella: weekly summary & schedule updates; meeting minutes.
  • Mayuri: materials list — justification & protocol comparison.
  • Ryland, Ria: asymmetric PCR reading; pricing & sequence updates; outreach to 2024 BIOMOD for PCR help; team meeting.
July 3
  • Mayuri: Chimera interview questions; materials list; started Tris buffers.
  • Jillian, Durwyn, Isabel, Ryland: Chimera interview questions work (various).
July 4
  • —
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Week 10

July 7–11
Highlights
  • Team photos and headshots taken, great opportunity to connect and discuss the competition.
  • Lab work continued with preparation of buffers to be used in upcoming experiments.
Daily Log
July 7
  • Jillian: novelty review.
  • Ryland: asymmetric PCR + purification methods reading; protocols for asymmetric PCR & denaturing PAGE; ongoing λ-exonuclease ssDNA purification protocol.
July 8
  • Mayuri & Durwyn: made 1 L Tris pH 7.5 (calibrated pH meter; diluted HCl; titration to pH 7.49); started 500 mL Tris pH 8.0.
July 9
  • Mayuri: finished 50 mM Tris-HCl pH 8.0 (500 mL); documented titration & corrections.
  • Jillian: novelty review.
July 10
  • Mayuri: updated notebook for lab work; materials list review.
July 11
  • Mayuri: Chimera interview questions.
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Week 11

July 14–18
Highlights
  • Finalized project sequences, confirmed correct interactions via dry lab testing.
Daily Log
July 14
  • Mayuri: lit review — TBE vs Tris-HCl buffer.
July 17
  • Meagan: PI meeting; sequence spreadsheet edits (internal amino-mod for TMB; folding behavior; concentration & purification fixes).
  • Jackson: prepared aptamer + ligand docking files for pTau181 & pTau231.
July 18
  • Mayuri: TBE vs Tris-HCl lit review (continued).
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Week 12

July 21–25
Highlights
  • Created additional buffers in preparation for incoming materials.
Daily Log
July 21
  • Mayuri: prepared 1× TBE buffer (500 mL).
July 22
  • Jackson, Zehaan: molecular docking work.
July 24
  • Jackson: molecular docking.
July 25
  • Jackson: finished docking; downloaded & organized files.
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Week 13

July 28–August 4
Highlights
  • Collected SDS information for incoming materials to ensure lab safety and proper documentation.
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Week 14

August 11–15
Highlights
  • No wet lab activities this week.
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Week 15

August 18–22
Highlights
  • No wet lab activities this week.
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Week 16

August 25–29
Highlights
  • No wet lab activities this week.
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Week 17

September 1–5
Highlights
  • Started lab work by creating a colorimetric standard curve with HRP and TMB.
  • Faced roadblocks due to a defective pH meter, plan to continue experiments next week.
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Week 18

September 8–12
Highlights
  • Continued efforts to create a standard curve for our colorimetric output.
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