Week 1 HW: Principles and Practices

source: wikimedia commons

Genetically Engineered Diatoms to Bind with Building Rubble/Waste

Building materials like cement and brick are difficult to reuse and natural weathering or active demolition leaves behind tons of waste material that remains under-recycled. In a previous project my team from graduate school developed a porous, bio receptive glass using glass waste and I would like to expand upon that research by bioengineering diatoms into a silica scaffold of cement and glass rubble/frits to fuse these waste materials into a new architectural material. Diatoms are an exciting prospect for architecture for their silica frustules, inherent translucency, and their lacy pore structure. I am curious to see if there would be a way to pattern their silica deposits for enhanced carbon sink and particle processing in urban spaces. It would also be beautiful to see the formation of silica deposits depending on sun patterns on site, filling in the rubble scaffold where there is more direct light. It would also be interesting to potentially engineer the directional strength of a diatom-rubble piece and the lace pattern, playing with the idea of directional bias in architecture more theoretically but also for building methods.

Goals:

• When speculating such panels, it is important to keep policy which mitigates the impact of the material creation and installation on the surrounding soil and water biodiversity through run off material and resources used to grow the diatom structures. Diatoms can overpower other microorganisms and limits on the volume of diatom production could help reduce the chances of local ecological harm and biological impact.

• Another goal is to secure a non-stress inducing method of cultivating and sourcing the diatoms for this scale of application.

• This material should be lessening the burden of the construction industry.

Concerns:

• Who would have access to this material?

• How does this material impact the local environment?

• Will users receive this material positively and use it? Or will it be demolished or underutilized?

• Will this create excess burden on access to an organism for this scale? What are the political realities of sourcing this material?

• How do diatoms react with materials like cement, brick, and glass? Are there any reactions between materials that can cause issues?

Actions:

• When casting the rubble diatom mixture, create reusable casts/equipment workflows when possible.

• Work directly with ecologists to determine the site for harvesting and to determine if the site for installation is appropriate in case of run-off or other biological interactions.

• One method of mitigating the environmental impact of sourcing and using diatoms at this large scale could be to focus on cultivation from local areas with diatom overgrowth so that this helps cut down on the environmental impact of current unhealthy ecology.

• Lab testing, especially longevity testing, would help clear up uncertainty regarding the impact of the material on site as it weathers and does through periods of high and low growth. This includes the potential toxicity of the rubble, the biological interactions of the diatoms, and how the ,odified diatoms may change over time through mutations and biomass buildup.

• Community workshops/exhibits as user studies to understand how people would interact with the material (biosecurity of sensory interaction), understand whether they would accept it in their built environment, and educate them on the material itself.

Week 2: DNA Read, Write, and Edit

Part 1: Benchling Gel Art

Part 3: DNA Design Challenge

When looking into proteins to explore further, I chose to focus on proteins related to the structure of diatom silica walls. These proteins would be exciting to understand to get a better picture of how diatoms would form the lacy micropatterns for the rubble-diatom material proposal for the final project. While there are a few different proteins key to the biosilica formation, and silaffins drive the lacy patterns and micropore structure.

In the NCBI database chose: silaffin protein (Thalassiosira pseudonana CCMP1335)

Week 3 - Lab Automation

Part 1: Opentrons Art

When creating this GUI art I created an image of cherries with a checkered background to see how common features in traditional drawing would translate to bacterial image creation including shading, regular patterning, thinner and thicker lines, as well as curved and straight forms. I downloaded the python script for the PCR plate system from this simulator.

created through Ronan’s Opentrons plate art simulator

Part 2: Python Script for Opentrons

Part 3: Opentrons Research and Potential Use of Automated Tools in Final Project

For the final project, if I were to pursue the diatom project idea, would be to use automated systems for cell seeding by scaning contruction rubble and detect the best spots to introduce diatoms into the rubble panel in response to the rubble placement, load bearing support, or areas that make easy bridges between rubble.

Salido et.al used automated technology for diatom identification:

Salido, J.; Sánchez, C.; Ruiz-Santaquiteria, J.; Cristóbal, G.; Blanco, S.; Bueno, G. A Low-Cost Automated Digital Microscopy Platform for Automatic Identification of Diatoms. Appl. Sci. 2020, 10, 6033. https://doi.org/10.3390/app10176033

Diatoms are traditionally identified and viewed using LM and SEM imaging, since they are invisible to the naked eye. Different species of diatoms have also remained unidentified due to these limitations. Automated technology and deep neural networks have assisted in the detection, classification, and counting which can be tricky due to the variety of shapes that diatoms may have.

Part 4: Crit 1 Final Project Ideas

For the final project I would like to look closer at architectural materials and how they can respond to environmental stressors. Some of these ideas are a new perspective on previous ideas of mine, playing with how one concept can be explored through multiple fields.

Project 1: Diatoms and Rubble

This proposal looks into using diatoms to create a new aggregate material out of construction waste (ie cement) and diatoms to create a bioreceptive panel system. It plays with the way that diatoms create silica cell walls, leaving opalescent lacy micropatterns that could bring a new use to materials that are very hard to repurpose. By using diatoms with rubble, this ‘new’ material would create beautiful translucent seams that could potentially help host other organisms or itself help with nutrient filtration depending on the design application.

Project 2: Biopigment Stained Glass with Air Quality Indication

Stained glass has a history of storytelling for the masses, usually in churches and other religious spaces. It would be interesting to see if biopigments could:

1. stain glass without chemical inclusions
2. react to pollution levels and serve as a visual indicator for air quality in the area. This research would need to be further refined with the intensity of the color, how sensitive the reaction could be, and how the biofilm pigment could impact its environment in terms of microenvironments, both positive and negative.

Project 3: Brick Extremophiles

Looking back at a previous project where I studied brick walls and reimagined their structure, it would be interesting to see if there are certain prevalent extremophiles present in bricks especially in iron-rich clay areas. These extremophiles could be further designed to embody carbon and support environmental remediation.

Project 4: Bruising Homes

What if buildings bruised?

This is an idea that I pursued in a filmmaking studio in the past that I would like to unpack through alternative means. A touch-reactive biopigment could become a paint or biofilm that responds to the amount of pressure put onto the surface. Relating back to organisms like touch-me-not mimosa plants that are very sensitive to their environment, a paint like this could become an exploration into the permanence of human action, and document our relationship to our homes. The paint/biofilm would begin as a uniform color, and darken in reaction to pressure.

Week 1 HW: Slide Responses

Professor Jacobson:

1. The error rate for polymerase is 1:10^6. Compared to the length of the human genome of around 3.2Gbp (slide 10), the error rate is minute, occurring perhaps once in one genome. Biology deals with this discrepancy by proofreading the action before it is coded into the DNA.
2. There are 20 AA and 61 codons that specify amino acids (NHGRI), leading to different ways to code for an average human protein. Some reasons that all of these different codes don’t work for the protein of interest could be due to the physical structure of the protein, and the efficiency of each pathway. (not totally sure of this answer)

Dr.Leproust

1. The most common method for oligo synthesis is currently a chip based gene synthesis that couples the nucleotide with phosphonamidite. Historically, this has been a solid phase synthesis.
2. It’s difficult to make oligos longer than 200nt vir direct synthesis because of the surface and primarily the inefficiency of the current state of the art phosphonamidite method. Source: Yin Y, Arneson R, Yuan Y, Fang S. Long oligos: direct chemical synthesis of genes with up to 1728 nucleotides. Chem Sci. 2024 Dec 18;16(4):1966-1973. doi: 10.1039/d4sc06958g. PMID: 39759933; PMCID: PMC11694485.
3. You can’t make a 2000bp gene with direct olio synthesis because of the increased error rate in PCR. The new gene pool solution offers a 1 in 3,000 bp error rate which would allow for greater gene lengths to be processed. (slide 39)

Professor George Church

1. According to the NIH, the nine essential amino acids are histidine, isoleucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. This means that the Lysine Contingency is really already a contingency that all animals have upon receiving all nine of these AAs from their diet, not just lysine. (Fictional) dinosaurs are just like you and me, minus 8 more essential amino acids. Source: Lopez MJ, Mohiuddin SS. Biochemistry, Essential Amino Acids. Updated 2024 Apr 30. In: StatPearls Internet. Treasure Island (FL): StatPearls Publishing; 2025 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK557845/

Week 1 Lab: Pipetting

Individual Final Project

Group Final Project