Section Six - References & Budget

Author: Eric Schneider · 2026a-eric-schneider Node: Genspace NYC Affiliation: BioArt Studio, MakerSpace Charlotte

Form Prompts

List all references cited in your project documentation.

Provide a budget for your project. Include all costs associated with your project, including materials, equipment, and any other expenses. If you have not yet incurred any costs, provide an estimated budget.

References

All references ordered by first appearance across Sections 1–5. See Appendix A (separate file: biolight_appendixA_optogenetic_systems.md) for optogenetic systems evaluation table and associated references R17–R21.

Section 2 — Aims

• R1. Li X, Zhang C, Xu X, Miao J, Yao J, Liu R, Zhao Y, Chen X & Yang Y. A single-component light sensor system allows highly tunable and direct activation of gene expression in bacterial cells. Nucleic Acids Research 48(6):e33 (2020). doi:10.1093/nar/gkaa044 · PMC7102963 · PMID 31989175 (eLightOn — BioLightV5 molecular ancestor. Primary citation.) Link to eLightOn

• R2. Jin X & Riedel-Kruse IH. Biofilm Lithography enables high-resolution cell patterning via optogenetic adhesin expression. PNAS 115(14):3698–3703 (2018). doi:10.1073/pnas.1720676115 · RRID:Addgene_107741 (pDawn-sfGFP control construct — Addgene #107741.)

Section 3 — Background

• R3. Kuldell N, Bernstein R, Ingram K, Hart KM. BioBuilder: Synthetic Biology in the Lab. O’Reilly Media (2015). ISBN 978-1491904299. https://www.oreilly.com/library/view/biobuilder/9781491904299/ (Karen Ingram co-author and scientific illustrator — introduced HTGAA 2026, leading to the BioLight project.)

• R4. Levskaya A, Chevalier AA, Tabor JJ, Simpson ZB, Lavery LA, Levy M, Davidson EA, Scouras A, Ellington AD, Marcotte EM, Voigt CA. Synthetic biology: Engineering Escherichia coli to see light. Nature 438(7067):441–442 (2005). doi:10.1038/nature04405 · PMID 16306980 (Foundational bacterial photography — Cph8 chimeric receptor. Primary citation 1.)

• R5. Tabor JJ, Salis HM, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD. A Synthetic Genetic Edge Detection Program. Cell 137(7):1272–1281 (2009). doi:10.1016/j.cell.2009.04.048 · PMID 19563759 · PMC2775486 (Tabor Lab edge detection — bacterial photography lineage.)

• R6. Tabor JJ, Levskaya A, Voigt CA. Multichromatic Control of Gene Expression in Escherichia coli. J. Mol. Biol. 405(2):315–324 (2011). doi:10.1016/j.jmb.2010.10.038 (Tabor Lab CcaS/CcaR multichromatic — inline reference.)

• R7. Teller E (Astro Teller, Captain of Moonshots, X / Google X). Quoted by Thomas L. Friedman in: Thank You for Being Late: An Optimist’s Guide to Thriving in the Age of Accelerations. Farrar, Straus and Giroux (2016). ISBN 978-0374273538. (“Today is the slowest rate of change we will ever experience.”)

• R8. Gartner Research. Term “citizen data scientist” introduced ca. 2016. https://www.gartner.com/en/information-technology/glossary/citizen-data-scientist

• R9. Mace RL. Universal Design: Barrier-Free Environments for Everyone. Designers West 33(1):147–152 (1985). Center for Universal Design, North Carolina State University College of Design. https://design.ncsu.edu/research/center-for-universal-design/ (Ron Mace coined Universal Design — mentor to Eric Schneider at NCSU.)

• R10. The MIT License. Massachusetts Institute of Technology. https://opensource.org/licenses/MIT (Open-source license governing Photoplasm hardware, software, and protocol releases.)

Section 4 — Experimental Design

• R11. Tabor JJ. Plate-based assays for light-regulated gene expression systems. Methods in Enzymology 497:373–391 (2011). doi:10.1016/B978-0-12-385075-1.00015-9 (Agarose slab embedding method — foundational protocol for bacteriography.)

• R12. Sanders ER. Aseptic laboratory techniques: plating methods. Journal of Visualized Experiments (JoVE) 63:e3064 (2012). doi:10.3791/3064 (Bacterial plating methodology.)

• R13. IDT Codon Optimization Tool. Integrated DNA Technologies. https://www.idtdna.com/CodonOpt (Used for RsLOV protein sequence → E. coli K12 codon-optimized DNA conversion during BioLightV5 design.)

• R14. Addgene plasmid #107741 — pDawn-sfGFP. Deposited by Ingmar Riedel-Kruse Lab. RRID:Addgene_107741. https://www.addgene.org/107741/ (Control construct for Aim 2 — Test & Analyze. See also R2.)

Section 5 — Results & Validation

• R15. Hurter F & Driffield VC. Photochemical investigations and a new method of determination of the sensitiveness of photographic plates. Journal of the Society of Chemical Industry 9:455–469 (1890). (H&D curve — foundational sensitometry. Conceptual framework for the bacterial H&D curve deliverable of Aim 2.)

• R16. Li X, Zhang C, Xu X, Miao J, Yao J, Liu R, Zhao Y, Chen X & Yang Y. A single-component light sensor system allows highly tunable and direct activation of gene expression in bacterial cells. Nucleic Acids Research 48(6):e33 (2020). doi:10.1093/nar/gkaa044 (Full author list verified against published article. See also R1.)

Appendix A References

R17–R21 listed in full in biolight_appendixA_optogenetic_systems.md.

Reference Count Summary

Budget

Section 1 — BioLightV5 Plasmid & Genspace Lab Protocol

Section 1 Subtotal: ~$612 + TBD (membership)

Section 2 — Photoplasm Device Hardware

Section 2 Subtotal: ~$528

Total Project Budget Summary

TBD = Genspace community lab membership — prorated community member rate, to be confirmed at orientation May 28, 2026. Several Genspace consumable line items (1.03–1.12) may be available from Genspace lab stock at reduced or no cost — to be confirmed at orientation. Separate optical component sourcing alternatives are deferred to Aim 3 — Learn & Refine (Visionary) as community-driven hardware innovation. All estimates subject to revision as actuals are received.

Status key:

• ✅ Purchased — actual cost incurred
• ✅ Ordered — committed, actual confirmed
• ⏳ Ordered — committed, awaiting delivery
• ⏳ Pending — not yet ordered, confirmation needed
• ⏳ Planned — scheduled for future aim phase
• ⏳ In progress — design underway, cost estimated