HTGAA 2019

Final Projects

Team 1

A motley collection of ideas

Microbial gastronomy

• There’s been a lot of popular discussion around probiotics and fermentation lately, e.g. natto, kombucha, fish sauce, miso, kefir, sourdough, kimchi, cheese.
• Quite a few art projects also around cooking using human bodily bacteria (human cheese, vaginal yeast bread)
• These are all deeply traditional fermentation methods. Can we think of more experimental approaches to making food using microbes using the skills in HTGAA? Can we combine genetics from these traditional microbes into new forms of fermentation (e.g. hybrid cheese)?
• Making foods that carry the scent profile of a person using bacteria responsible for bodily odors?
• (https://en.wikipedia.org/wiki/Body_odour_and_sexual_attraction)
• Alternatively, find a microbial solution to unwanted body odor — a sort of permanent fragrance – or create bacterial perfumes.
• Using bacteria to synthesize flavours/make new tastes?
• A better stevia

Bee-gineering

• Can we influence honey by altering the kind of enzymes bees use? (Activity of salivary glands in secreting honey‐elaborating enzymes in two subspecies of honeybee (Apis melliferaL))
• Can we influence bee behaviour through altering or synthesizing their pheromones? (A Synthetic Pheromone Lure to Induce Worker Honeybees to Consume Water and Artificial Forage)
• Can we alter the composition of honey created by one hive/species by introducing microbes from another hive/species?
• Bee-based yeasts have also been used to brew beer. Perhaps we could grow yeast on bees, or combine yeasts from different hives for new fermentation strains.
• Can we solve the varroa mite problem by:
• Using RNAi?
• Altering western honeybee behavior to more resemble Asian honeybee when infected by mites? (Apis cerana Is Faster at Hygienic Behavior than A. mellifera)

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Other ideas!

What about some environmental sculpture that reveals something about the environment (something otherwise invisible), or a series of little sculptures as bio-sensors.

DIY biosensors for environmental testing (toxins, endocrine disruptors, etc?) in communities with no lab access. Open access molecules.

Bodily sensor that reveals something about you, living wearables?

Life/non-life, using viruses as a form of communication between people.

Microbial fuel cell robot that roams around demands to be fed.

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2/21/19 - Group 2 | Jelle, Lucy, Prathima

Cancer Cells as Building Material

2/21/19 - Group 2 | Jelle, Lucy, Prathima

Microbial Weaving

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2/21/19 - Group 2 | Jelle, Lucy, Prathima

Living Root bridges

2/21/19 - Group 2 | Jelle, Lucy, Prathima

Photosynthetic biofilms on architectural facades

2/21/19 - Group 2 | Jelle, Lucy, Prathima

Photosynthetic biofilm

2/21/19 - Group 2 | Jelle, Lucy, Prathima

Cultural Specific Gut Microbiome Supplements

2/21/19 - Group 2 | Jelle, Lucy, Prathima

Interspecies Communication & Co-Habitation

2/21/19 - Group 2 | Jelle, Lucy, Prathima

Environmental Specific Dye & Responsive Textile

Group 4 HTGAA Final Project Ideas

Rahma, Sara, Rae

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robo microbe gleaner

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collector that goes out to scavenge for diverse bacteria for people living in modern hermetically sealed air conditioned buildings and doesn’t have a dog. Special coating.

Self-assembling, deconstructable structures

DNA hydrogel have been shown to morph.

https://releases.jhu.edu/2017/09/15/dna-triggers-shape-shifting-in-hydrogels-opening-a-new-way-to-make-soft-robots/

Other protein, shape forming mechanisms?

Possible ideas

vag biosensor (ph monitor): engineer lactobacillus to excrete color when vag ecosystem ph is out of range (3.5-4).

biolube: Microbial oils, also called single cell oils, are produced by some oleaginous microorganisms, such yeast, fungi, bacteria and microalgae.

Customize: smell, taste.

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-“Empowering the vagina through biotechnology.”

Slow printing: Engineer homeobox genes of venus flower basket to grow different architecture in a tank of siliceous medium.

concepts

Logic circuits with synthetic biology

Depositing freeze dried bacteria on paper

Paper battery powered by bacteria

Giving “voice” to bacteria

Quorum sensing

Sonocytology

THANK YOU

GROUP 5 Priya, Yiqi, Andy, Mina

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Biosensing

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Bioactuation

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Additive 3D Biofab

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Growth-Based 3D Biofab

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APPLICATIONS

AND DESIGN

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Product Design

(biosensors for the home)

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Rapid Growth Agriculture

(https://fastplants.org/)

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BioBots

(solar energy/imaging)

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Wearable

(responsive material/

cognitive enhancing)

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ENABLING

TECHNOLOGIES

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instrument

food

tools

monitors

fashion

space

tatto

environmental

organ

digi-fab

electronics

additive manufacturing

material science

nanowire

vr/ar/mr

sensor tech

hci

Computer vision

Printed Bioactuators/sensors

Inspiration: BioLogic(biologically transforming structures).

Goal: Use embedded printing for biologically

powered braitenberg vehicles

• Senses light and induces actuation
• Other mechanisms: Temperature, Touch

Resources: Bioactuators, Open Source Embedded Printing, Soft Body Simulation

3D Cell Culturing/Biofabrication

Current Methods:

• Scaffolding/Bioinks deposited layer by layer (reference)
• Magnetic Cell Culture (reference)

Issue: Not taking advantage of biological capacities to make more complex structures.

Goal: Grow biological structures that can form complex shapes via genomic editing alone

GROUP 5 Priya, Yiqi, Andy, Mina

Team 3

Final Project Ideas

Bioessence

iGEM Bacteria that smell like Banana

Biological - Bioessence

Wearable BioTech

Epidermal Sticker

Mutant Paint / Bacterial Kusama

Team 1

Final Project Ideas

Project 1: Beehive contaminant detection

• “Contaminants in soil, air, and water come in contact with the surface structures and root systems of plants. The materials can become incorporated in leaves, flowers, and stems. Nectar and pollen, often brought back to the hives for processing can also contain pollutants which in turn are concentrated into bee products such as honey and wax.”
• Fabricate hives that are coated with substances that react to contaminants, such that there’s a color change when contaminants are brought back to the hive

https://thehoneybeeconservancy.org/bee-airport-biosensor/

https://www.nytimes.com/2010/06/29/business/29airports.html

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Fun Side Project: Bee Yeast Bread (Beast Bread!)

• Yeast from bees is being used to make artisanal beer; beer yeast and bread yeast are technically the same species
• Wikipedia: “In the 19th century, bread bakers obtained their yeast from beer brewers, and this led to sweet-fermented breads such as the Imperial Kaiser-Semmel roll”
• Bee saliva contains microbes that lacto-ferment pollen and nectar into bee bread (protein source)

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https://www.apidologie.org/articles/apido/pdf/1979/01/Apidologie_0044-8435_1979_10_1_ART0006.pdf

Project 2a: Engineering skin microbiome for BO reduction

Daniel Bawdon et al. Identification of axillary Staphylococcus sp. involved in the production of the malodorous thioalcohol 3-methyl-3-sufanylhexan-1-ol, FEMS Microbiology Letters https://doi.org/10.1093/femsle/fnv111 Also: Callewaert et al. Towards a bacterial treatment for armpit malodour. Exp Dermatol. 2017 May;26(5) https://www.ncbi.nlm.nih.gov/pubmed/27892611

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• Transform odorous species of Staphylococcus with plasmid for chromosomal deletion of the two genes
• Introduce conjugation mechanism such that the engineered bacteria conjugate other bacteria with plasmid
• Colonize axillary (armpit) skin with engineered bacteria
• Bonus: express pathway whereby the bacteria turns a sweat compound into something fragrant

Project 2b: Microbial scents

Microbes are increasingly common in scent production (Gingko, IFF) and many pathways are well known.

Generally Escherichia coli or yeast such as Saccharomyces cerevisiae is engineered for isoprenoid production by insertion of one or two genetic pathways used by plants to make terpene precursors. The microbe also gets genes coding for an enzyme terpene synthase that makes a particular terpene from one or more precursors. The resulting terpene can be functionalized through hydroxylation, isomerization, oxidation, reduction or acylation.

https://medcraveonline.com/JMEN/JMEN-02-00034

An iGEM project! Making banana or wintergreen scent with E. Coli.

https://openwetware.org/wiki/IGEM:MIT/2006/Blurb

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Project 2c: Synthesizing human scent in plants

Natural human body odor derives from eccrine and apocrine glands which produce sweat containing proteins which are broken down by bacteria.

Synthetic blends of human odor chemicals have been produced to experiment with attraction for mosquitos.

Plants produce scent through “scent genes” and enzymes which create volatile compounds of terpenoid or phenylpropanoid/benzenoid. These pathways are somewhat known in model organisms (e.g. Rose, Petunia).

Can the scent pathways of a plant be affected to produce a synthetic human scent compound?

(Puchersky, Dudereva, Scent engineering: toward the goal of controlling how flowers smell: https://www.sciencedirect.com/science/article/pii/S0167779907000182)

Gene transfer to plants using agrobacterium. (https://link.springer.com/chapter/10.1007/978-3-642-60234-4_2)

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Team 4

Final Project Ideas

Signal

Bacteria-activated Rube Goldberg - overview

Signal

(Animated)

Bacteria can respond to many signals, including:

• Light: proteorhodopsin, a light-driven proton pump
• Chemical gradient: chemotaxis
• Bacterial signals: quorum sensing

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Cyborg petri-dishes: enhanced with motors, wheels, sensors..

Interspecies communication

• Across scales, impossible meetings
• Plants and bacteria sympoiesis
• What does bacteria sound like?

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Final Project Ideas

Team 5: Priya, Yiqi, and Andy

Idea 1: Biosensors/Actuators/Robot

Goal: System that can provide closed-loop sensing+control

Inspiration: light activated robots

Three parts:

• Sensing+Actuation Circuit
• Modeling
• Fabrication

(Robot will have to be quite small / thin)

Sensing + Actuation Circuit

Prior Work:

Light to Color:

Need new circuit to combine sensing + actuation (aquaporin?)

Sensing + Response

Actuators (Bacillus Subtilis)

Modeling

• Have ability to model soft, actuated structures
• Framework is differentiable for easier design optimization
• Goal: Given a biological actuator, optimize shape and cell placement for optimal motion

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Alternative Idea: Ballglena

Fabrication

• Currently-process of growing cellulose biomaterial with bacteria (Kombucha scoby; Suzanne Lee Bacterial Leather)
• Can we make a biomaterial that incorporates a protein into it?
• Protein modify GFP/other exciting protein to have a cellulose binding domain which would attach GFP to the material

Other ideas

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robo microbe gleaner

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collector that goes out to scavenge for diverse bacteria for people living in modern hermetically sealed air conditioned buildings and doesn’t have a dog. Special coating.

biovazard

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biosensor (ph monitor): engineer lactobacillus to excrete color when vag ecosystem ph is out of range (3.5-4).

biolube: Microbial oils, also called single cell oils, are produced by some oleaginous microorganisms, such yeast, fungi, bacteria and microalgae.

Customize: smell, taste.

Venus basket glass printer

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Engineer homeobox genes of venus flower basket to grow different architecture in a tank of siliceous medium.

Microbial ethics

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What do they want? How do we give them voice without speaking for them? How do we engage with their agency, in their own terms?