Please put the Individual Final Project ideas after the slide of your node. Thanks.
More BioClub Logos. Feel free to use them on your slide.
BIOSCRIBE: Redefining Ink
Aim- To revolutionize sustainable design by creating self-replenishing, biologically powered ink pens, enabling continuous color production through biological processes, merging synthetic biology with practical, everyday applications in creative tools. It will help in reducing waste and reliance on synthetic chemicals, while paving the way for eco-friendly, living technologies in everyday products.
Genetically engineered bacteria can produce natural fluorescent ink. These bacteria grow and make pigments, so the pen can keep “recharging” itself.
Today’s pens use chemical inks that eventually dry up and get thrown away. This creates waste, pollution, and need for replacements.
What if we could replace that with a sustainable, self-renewing source of ink? This shows how synthetic biology can bring innovation even to simple things like stationery.
Overview- I will first design and edit DNA sequences of green fluorescent proteins aka GFP. These constructs will be inserted into E.coli via expression vector pGLO, forming genetic circuits that regulate pigment production. I’ll simulate this workflow computationally and explore protein design for unique color shades. If scaled for real-world use, bioproduction and cell-free systems could allow refillable cartridges.
By- Aprajita Shukla
To create a self-replenishing fluorescent pen using engineered bacteria.
Gene Selection and Codon Optimisation
Cloning into Vector
Transformation and Selection
Expression and Cultivation
Cartridge Loading
Fluorescent ink
Chatgpt 4.0 generated
FUTURE OF BIOSCRIBE AND BACTERIAL FLUORESCENCE
Systems like Raspberry pi can be used to log detection of toxins using fluorescence
Replacing traditional ink for sustainable stationery, Printer ink alternative (3D printing can form living structures)
Chatgpt 4.0 generated
Biodegradable display screens for bio-labs, eco-sensitive designs
Hansen Jonathan
AIMS
🧪 "Restoring marine sediments will have a direct and positive impact on mercury pollution,"� – Dr. Andrea G. Bravo, MER-CLUB
🌊 Meanwhile, microplastics sink and settle silently in ocean sediments (Clark et al., 2016).
Xue, Y., Du, P., Ibrahim Shendi, A. A., & Yu, B. (2022). Mercury bioremediation in aquatic environment by genetically modified bacteria with self-controlled biosecurity circuit. Journal of Cleaner Production, 337, 130524. https://doi.org/10.1016/J.JCLEPRO.2022.130524
Clark, J. R., Cole, M., Lindeque, P. K., Fileman, E., Blackford, J., Lewis, C., ... & Galloway, T. S. (2016). Marine microplastic debris: a targeted plan for understanding and quantifying interactions with marine life. Frontiers in Ecology and the Environment, 14(6), 317-324.
Directorate-General for Environment. (2024, November 13). Paving the way to mercury clean-up with marine bacteria - European Commission. https://environment.ec.europa.eu/news/paving-way-mercury-clean-marine-bacteria-2024-11-13_en
https://honorable-beryl-e1b.notion.site/Hansen-s-HTGAA-Journey-198944042f0e805c96aedb60a622130b?pvs=4
By Hansen Jonathan
Genetically Modified E. coli BL21 for Mercury and Microplastic Bioremediation with Biocontainment Contingency
1. Build Genetic Circuit for Mercury & Microplastic Bioremediation with E. coli BL21
2. Build Genetic Circuit for Biocontainment Effect with E. coli BL21
Hansen Jonathan
By Hansen Jonathan
Genetically Modified E. coli BL21 for Mercury and Microplastic Bioremediation with Biocontainment Contingency
Genetic Circuit as Proof of concept and upstream part of the research
Genetically Modified E. coli BL21 for Mercury and Microplastic Bioremediation with Biocontainment Contingency
Hansen Jonathan
Genetic Circuit as Proof of concept and upstream part of the research
-Made from strong and popular parts in iGEM and main journal reference
-Must be proven with wet lab experiments
Yash Sawant, Bioclub Tokyo, Mumbai, India
Synthetic Biology-Based Wearable Patch for Non-Invasive Volatile Organic Compound Detection in Diabetes Mellitus
Problem: �Diabetic patients emit Volatile Organic Compounds like acetone through the skin, but current monitoring relies on invasive glucose tests.
Solution:�A wearable, cell-free synthetic biology patch detects acetone from sweat and gives a fluorescence output — enabling non-invasive, real-time monitoring.
Yash Sawant, Bioclub Tokyo, Mumbai, India
Aim 1: Build the Sensing Circuit
2. Visualized the acetone-aptamer to �analyze binding sites and predict �conformational changes.
3. Integrated the acetone-binding aptamer �into a synthetic riboswitch model for� gene expression control.
1.Docking acetone with potential aptamers to predict binding affinity��Ligand used : Acetone�SMILES: CC(C)=O��Target Protein: 1ehz.pdb - Yeast phenylalanine tRNA, A known RNA aptamer structure (used as a model for the synthetic riboswitch)��Outcome:�Acetone binds within a plausible pocket on the aptamer model, supporting its use in riboswitch design.�The availability of several conformations with equivalent energies lends credence to the concept that the aptamer can bind acetone selectively, potentially triggering a conformational change required for riboswitch activation. (Experimental validation is pending)
− Acetone: Aptamer folded, RBS hidden → Translation OFF
+ Acetone: Aptamer unfolds, RBS exposed → Translation ON
TTTGTAGAGTCTTAA
Aptamer� sequence
Yash Sawant, Bioclub Tokyo, Mumbai, India
Aim 2: To experimentally confirm binding affinity of acetone and if the binding induces the predicted conformational change/ To overcome the limitations
Minimum free energy decreases from -276.40 kcal/mol to -253.61 kcal/mol in the presence of acetone, indicating that the structure becomes less stable. �high ensemble diversity indicates that the RNA is taking on numerous conformations, in the presence of Acetone�Validation of the binding affinity and conformation changes of Acetone-Aptamer experimentally using spectroscopic methods is needed.�There is an increase in acetone in diabetic sweat but it is still relatively less than breath, higher sensitivity has to be established
With Acetone
Without Acetone
Aim 3: To create a real-time, portable biosensing patch for non-invasive diabetes monitoring by coupling with Smartphone interface
Objectives and future prospects
(When acetone binds, local entropy peaks show areas with more structural flexibility, like the aptamer, while other areas stay stable)
1.Non-invasive & passive unlike breathe based
2. Programmable detection compared to traditional glucose detectors due to Syn-Bio
VOC profiles can indicate a spectrum of conditions not just Diabetes
3.Eventual integration into a smartphone interface for real time monitoring
Ischemia-Reperfusion (I/R) Injury and Mitochondria
I/R Injury: Blood supply restoration after ischemia can worsen damage instead of aiding recovery [1].
Calcium Overload & mPTP Opening: Reperfusion causes calcium influx, opening mPTP, disrupting membrane potential, stopping ATP synthesis, and triggering cell death [1].
Problem
CypD-Targeting Peptide for mPTP Inhibition in Ischemia-Reperfusion Injury
Active CypD
inActive CypD
1
Alireza Hekmati, Bio Club, Bujnord, Iran, AlirezaHekmati80@gmail.com
Problem
CypD-Targeting Peptide for mPTP Inhibition in Ischemia-Reperfusion Injury
Active CypD
inActive CypD
1
Alireza Hekmati, Bio Club, Bujnord, Iran, AlirezaHekmati80@gmail.com
I/R Injury
Problem
CypD-Targeting Peptide for mPTP Inhibition in Ischemia-Reperfusion Injury
Active CypD
inActive CypD
1
Alireza Hekmati, Bio Club, Bujnord, Iran, AlirezaHekmati80@gmail.com
Ischemia-Reperfusion (I/R) Injury and Mitochondria
I/R Injury: Blood supply restoration after ischemia can worsen damage instead of aiding recovery [1].
Alireza Hekmati, Bio Club, Bujnord, Iran, AlirezaHekmati80@gmail.com
Protocol
CypD target sequence in red and yellow in pymol
Benchling Plasmid
Peptide Binder to Red sequence
(Designed by AfDesign)
plddt 0.81 ptm 0.76 i_ptm 0.84
SSQEPSKQSMSKKSSPAGNGQAGQVNNPDASKRETSKSSHFENPASSCTHQETHWEFCERMKKYYEKERF
E. Coli Expression
Evaluation
Assay readout
Cell + peptide
Stress
2
Outcome
Each 30-minute delay in reperfusion therapy is associated with a 7.5% relative increase in 1-year mortality for patients [4]
During liver transplantation, I/R injury is a significant cause of graft dysfunction and failure. [3]
For more details visit my notion page
1. In silico
2. In vitro
3. In vivo
4.Clinical trials
“reperfusion alone can contribute up to 30% to 40% of total infarct size following coronary artery occlusion.” [5]
Ischemia-reperfusion (I/R) injury remains a critical challenge in myocardial infarction (MI) treatment, but no FDA-approved drugs specifically target this mechanism in current clinical protocols. [7]
Alireza Hekmati, Bio Club, Bujnord, Iran, AlirezaHekmati80@gmail.com
3
Other assays
Mitochondrial Swelling Assay
Mitochondrial Membrane Potential (ΔΨm) Measurement
mPTP Opening Assay (Calcein-AM/CoCl₂ Method)
Groups
Control 1 no treatment
Control 2 Cyclosporin A
Experiment Top design.
Measure
Aims
1 Design Computationally
2 Execute in the lab
3 Approved as treatment
Alireza Hekmati, Bio Club, Bujnord, Iran, AlirezaHekmati80@gmail.com
Lignin-Degrading Enzymes for Biomass Valorization
Azmine Toushik Wasi, Sylhet, Bangladesh (azminetoushik.wasi@gmail.com) | BioClub Tokyo, Japan
Motivation: Lignin, a complex and recalcitrant polymer, limits the efficient conversion of biomass into valuable biofuels and chemicals. This is because its rigid structure and chemical composition make it highly resistant to enzymatic degradation, hindering the overall efficiency of biomass conversion processes.
Background Research
ML Models
In-silico
Validation
Research, identify, and enerate enzyme scaffolds based on natural lignin-degrading enzymes using diffusion models.
Goal: Mimic natural enzyme structure while optimizing for efficiency.
Refine the generated enzyme scaffold sequences using ProteinMPNN/ other models.
Goal: Design robust, stable, and efficient enzyme sequences.
Perform enzyme-substrate docking and molecular dynamics simulations to validate performance.
Goal: Predict enzyme-substrate binding and catalytic efficiency.
Next Steps: Mass production of these lignin-degrading enzymes can be achieved by expressing them in high-yield microbial hosts like E. coli or Pichia pastoris using fermentation bioreactors. Optimized upstream (growth conditions, media composition) and downstream (purification, stabilization) processes ensure high enzyme yield and stability. Enzyme immobilization or formulation into enzyme cocktails can further enhance efficiency for large-scale industrial applications.
What’s’ next?
Farhani Syafwani ( farhanisyafwani@gmail.com )
Biodegradable Bioengineered Fiber for Sustainable Apparel
The fashion industry relies on fibers like polyester and nylon, which contribute to microplastic pollution and environmental degradation. There is a need for a sustainable alternative that combines the benefits of synthetic and natural fibers while remaining biodegradable.
Idea: Develop a synthetic natural fiber that is biodegradable and suitable for clothing.
Objective: To engineer biodegradable fiber hybrids suitable for clothing by integrating bacterial nanocellulose (BNC) with natural fibers, enhancing both environmental sustainability and material performance.
Engineer Komagataeibacter to enhance bacterial nanocellulose (BNC) production
BioClub Tokyo
Farhani Syafwani ( farhanisyafwani@gmail.com )
Farhani Syafwani ( farhanisyafwani@gmail.com )
Engineering Microbial Cell Factories for Sustainable Drug Production
Background:
Solution:
Chairunnisa Amanda, BioClub Tokyo, Jakarta, Indonesia (amandadermawan1@gmail.com)
Scalable Production of Marine Natural Products Using Genetically Engineered Yeast
Successful Example ->Artemisinin: An anti-malarial drug produced using engineered yeast
Aims
Aim 1: Computational Discovery of Biosynthetic Pathways
To identify a therapeutically relevant bioactive compound from a marine sponge and use available genomic and transcriptomic data to predict and analyse the biosynthetic gene clusters (BGCs) responsible for its production.
Aim 2: In Silico Design and Simulation of Synthetic Pathway
To design synthetic gene constructs optimized for yeast expression, simulate their integration into the host metabolism using computational tools, and develop a DNA assembly plan.
Bisucaberin B
Aims
Aim 3: Visionary – Towards Scalable Microbial Factories
To envision and outline the development of a scalable and sustainable microbial platform capable of producing sponge-derived natural products through genetically engineered yeast, ultimately replacing environmentally harmful harvesting practices and enabling broader applications in drug discovery.
A photochemical process developed by Sanofi and now operated by Huvepharma in Garessio, Italy, can produce 370-kg batches of semi-synthetic artemisinin.
Xinyao Ma, Beijing, China; BioClub Tokyo
DNA origami-based drug delivery
3D DNA origami containers & insulin (or other regulatory hormones/drugs) for timely delivery: in tandem with diagnostics + signal transduction, which makes origami scaffolds secrete synthesized hormone/drug.
*revision for insulin-origami idea: produce coagulants/anti-coagulants and release based on need. Thus we need a platform to detect blood clots AND we need locomotion
possible synthesis target: heparin?
the whole process would run like this: figure out origami & controlled release -> engineer bacteria producing target molecule and DNA origami -> figure out monitoring mechanism (platform) & locomotion (if needed) -> integrate suicide switch (for safety)
proof of concept include: origami secretion from chassis, controlled release from origami, origami durability, origami uncontrolled release risk
Xinyao Ma, BioClub Tokyo
Parkinson early diagnosis by detecting perillaldehyde (biomarker). By engineering a novel protein receptor.
protein LLM？tokenization & analysis of other non-biomolecule ligand binding proteins -> generate sequence -> use AlphaFold and PyMol dock for bioinfo analysis and screen for the best
*inspiration: iGEM 2024 Plasmid.AI
A Modular Metabolic Engineering Simulator for Biochemical Production Estimation
Cybergenetics, Machine Learning, Synthetic Biology, Bioengineering
Model
parameters data for training: part registry, BiGG Models, KEGG, MetaCyc; complexity -> computational load (algorithm effectiveness); scope (E.coli & S.cerevisiae?)
key components:
basis: genetic circuit modeling
literature review: Cello, iBioSim, OptFlux, COBRA, other models
methods: ODEs, COBRApy, RAVEN (matlab), kinetic models
integration
key principles: modularity (for genetic circuit parts),
validation: use studies
User Interface
graphical user interface with Python
Functions: input parameters, select genetic parts, choose metabolic pathways & chassis, visualize results
Nipada Srisereenuwat, Nakhon Ratchasima, Thailand, BioClub Tokyo
No Turning vs. Turning method
Problem (Why?)
https://images.app.goo.gl/PWGEfbqMReue8NbE9
How can we reduce composting time and effort through biological engineering tool?
Compost Accelerator for No-Turn Compost method
Turn leaves into compost
Aim 1: To develop accessible tool kit that allow people to engineer bacteria that can help make their compost faster
Aim 2: To increase number of people that make their own compost and reduce health problems from chemical fertilizer
Aim 3: To reduce fire hazard in forest property
| Turning Method | No-Turn method |
Time | 3-6 months (faster with consistent turning) | 6-18 months (slower due to limited oxygen) |
Effort | Requires physical labor to turn the pile regularly. | Minimal physical effort required after initial pile setup. |
Stakeholder: Land owner who wants to make their own quality compost
Solution: make cellulase enzymes able to break down a lot of cellulose (leaves, wood) in a short amount of time
PostApoc-D
PostApoc-D
Genetically Engineered Yeast to feed the world
Plant Waste (Cellulose) Food (Glucose)
Ergosterol Vitamin D2
S. cerevisiae engineered with UV-stable exoglucanase to generate glucose from cellulose. Treated with UV to produce Vit D producing a consumable
UV-B-radiation
Syed Tauheed Ahmad, BioClub Tokyo, Peshawar, Pakistan- tauheedsyed@hotmail.com
Designed instruction-set
Also contains:
Anushka Shinde, Bioclub Tokyo, Ahmedabad, India
HOW CAN I MAKE A ROOM TRULY A ‘LIVING ROOM’?
Can we collaborate with microorganism, and develop microorganism that may enable to grow ready-to-use products?
Slime molds grow in the direction of food supply. What if you can use that and design their path to create surface patterns, or industrially called CMF (colour, Material, Finish)?�Is this the CMF of future?
The Japan metro network is the best example of slime mold intelligence. �What other products may be generated in a similar way?�What materials will be used for this?�How does a future with products with a similar ideology look like?�Is it possible to manufacture or localize it?�Will synthetic microbes/plants/organisms be developed for this?
Anushka Shinde, Bioclub Tokyo, Ahmedabad, India
WHAT
WHY
HOW
WHERE
WHEN
Developing ‘living products’ using microbes/plants/materials that respond and evolve as per stimuli
This project is an enquiry on the future of materials and the shift in Human Centered Interaction which might occur due to the shift
Developing Biomaterials, wetlab work, (maybe) some SynBio, Biofabrication
Ahmedabad, India, National Institute of Design
Beginning now!
Meeting review: No literature on engineering slime mold yet. But bacteria/microbes can be engineered that may interact with the slime mold and determine its growth
Supanat Deawrattanakun, Bangkok, Thailand
Bioclub, Tokyo
design genetic circuit in benchling to detect serotonin then produce GFP
Aim 1 1
Synthetic Genetic Circuit for Serotonin Detection
Aim 3
Aim 2
Add more human’s emotion aspect in Human-Computer Interaction
The First Gene Circuit on Earth
Md Rasel Uddin, Jashore, Bangladesh
Then came the early organism with membrane and genetic material. Capable to reproduce.
First came the self-replicating molecules.
Then the hypothetical organism, Magna superstes (Great Survivor) came. It had two genes: gene A and gene B.
In tough conditions, gene A expresses and halts the reproduction.
In good or favourable conditions, gene B expresses which represses gene A, therefore reproduction continues.
Gene B became more special. Achieved a mutation that gave it DNA repair capability.
In bad situations, DNA breaks. So gene B goes busy repairing the DNA and not involved in repressing the gene A anymore. So, gene A expresses and gene A halts cell reproduction until the DNA is repaired.
These are all hypothetical and also stolen from David Sinclair’s book ‘Lifespan’.
If it is hypothetical and also Sinclair’s idea, then what is my input? I want to synthesize the circuit and I want to create the Magna superstes, in-silico and in-vivo.
Email: raseluddin.synbio@gmail.com
Plastic pollution is a growing environmental problem. Most biodegradable plastics depend on petroleum based or crop-derived sources, which makes them unsustainable
A possible solution for this could be: Engineer halophilic archaea (e.g., Halobacterium salinarum) to produce PHA/PLA;
It’s a scalable, low-resource system.
*PHA - polyhydroxyalkanoates, polyesters produced by some organisms naturally, through processes like bacterial fermentation etc
As most PHA producing bacteria require strict pH, oxygen and temperature control, archaea can be an alternative, as i ist more resistant to conditions’ fluctuations.
Why Archaea?
Experimental Design &Methodology
Methodology:
1. Gene Selection & Modification:
2. Strain Engineering & Growth Optimization:
3. Waste Utilization Testing:
4. PHA Extraction & Analysis:
Challenges
1. CRISPR in Archaea: Fewer genetic tools than in bacterial systems;
And overall compared to bacteria, there are much fewer established genetic tools and protocols for CRISPR modification in archaea. => we have to explore the protocols (e.g., suitable conditions first)
2. PHA Yield: Possibly lower efficiency than bacterial production;
Despite that using archaea is more cost effective, the efficiency might be lower, because their cell structure (such as ether linked membrane lipids) & adaptation to extreme environments may limit nutrient uptake => lowering the PHA yields
3. Limited knowledge of Archaea: archaeas are less studied compared to bacteria;
There are some gaps in understand their genetics and metabolism
https://biologydirect.biomedcentral.com/articles/10.1186/s13062-020-00262-7
Challenges
Regarding the PHA Yield more detailed,
As it can be seen from the picture, unlike bacteria bacteria, which have ester - linked membrane lipids, archaea possess ether -linked lipids/
These bonds, in turn, give greater stability and resistance to extreme conditions => results in reduced membrane fluidity and permeability
=> the rigidity can limit the transport of nutrients and metabolic intermediates across the membrane => potentially slowing down teg growth rates => reducing efficiency of metabolic processes like PHA synthesis
https://biologydirect.biomedcentral.com/articles/10.1186/s13062-020-00262-7
How far the mutant could change from the original
Anandita Amalia, Yogyakarta, Indonesia
During lectures and recitations, I learned a ton of bioinformatic tools and some concept about protein. Awesome!
I also learned about mutation in sequence that contribute in stability, specific function, and overall structure. Then, I just wondering how far the mutant could change from the original. Thus, in this final project, I would examine basic concept about mutation by using bioinformatic tools.
Try to mutate protein sequence by using Protein MPNN, ESM
Compare one candidate to the others using AlphaFold Multimer
Choose the ideal one and compare to the original in several parameter
Parameter for the comparison: sequence, protein structure, protein stability, and protein binding site
Brendah Namugamba, Bio Club Tokyo, Kampala , Uganda brendanamugamba30@gmail.com
Carbon-Negative tryptophan production using engineered Cyanobacteria
Objective
To engineer cyanobacteria
(Synechococcus
elongatus)
to convert atmospheric
carbon dioxide into
tryptophan
using a synthetic pathway.
Immune Regulation of Transplanted Organs Locally
Designing a local immune suppression system inspired by fetomaternal interface
Problem: Organ transplants need long immunosuppressive therapies to prevent rejections and current therapies have many side effects which can cause mortality & morbidity on the long run.
Solution: Engineering and implementing a local immunosuppressant system to the transplanted organ/tissue -as in human placenta- may prevent both organ rejections and systemic side effects of the state of art therapies.
Aim 1: Designing & engineering a protein that can induce immunosuppressive state as in the case of uterine microenvironment in pregnancy.
Aim 2: Optimization of the gene expression and the protein stabilization
Aim 3: Evaluation of the designed protein stability, expression & functionality in silico firstly, then in vitro and in vivo if it looks promising.
Elif Dilan Gündüz, Giresun Turkey, elifdilangndz@gmail.com
DALL·E 2025-03-13 14.17.42
Andrés Frankow - Buenos Aires, Argentina.
frankow@gmail.com
Algae-Based Detoxification System for Glyphosate Degradation
Develop a genetically engineered alga, Chlamydomonas reinhardtii, capable of detoxifying glyphosate and its derivatives in freshwater environments. This system aims to reduce contamination levels and improve ecosystem health.
Key Components & Strategy:
Yousif Graytee-Baghdad, Iraq
Targeting SETD8: Mechanisms, Inhibitor Development, and Therapeutic Potential
. SETD8 is a lysine methytrasnferase that monomethylates histone H4 at lysine 20
. Regulates chromatin compaction and transcriptional repression. Also controls cell cycle progression through interactions with p53. PCNA, and other proteins (methylates them)
.Protein is overexpressed in multiple cancers (ovarian, breast, prostate, etc..)
.Inhibitors have been identified and reported but they have limitations regarding potency, selectivity, and pharmacokinetic properties
.Goal is to identify novel SETD8 inhibitors and investigate their effects
.Screen drug-like molecules against SETD8’s catalytic domain and identify top candidates with strong binding affinity and specificity
Targeted Switchable Epigenome Editing
Drawbacks
Goals -
Rushda Parveen, Bhopal, India
Methyl/Acetyl transferase
BioClub Tokyo
{Ruchika Tekethotil, Pune, India} {Bioclub Tokyo Japan} {ruchikap2512@gmail.com}
BIOMINING POTENTIAL OF BACTERIAS TO RECYCLE COBALT FROM LITHIUM-ION BATTERIES
Objective: I aim to use geobacter’s resistance and nanoparticle coat formation from cobalt for biomining, via extraction of cobalt from spent lithium battery anodes
G. sulfurreducens exhibits a sophisticated, multi-faceted strategy for thriving in metal-rich environments. This includes metal sequestration, enhancing its growth in contaminated sites, and contributing to the sustainability of microbiomes dependent on cobamides. The bacterium’s ability to bio-mineralize cobalt offers new insights into microbial interactions with metals and the potential for biomining application.
Modulation of Microglial Activity by a synthetic protein
Abhilaya Makkuva, Hyderabad, Telangana
Bioclub Tokyo, Japan
Background: Microglia are resident immune cells of the brain, playing a key role in neuroinflammation and synaptic plasticity. In neurodegenerative disorders, microglial overactivation leads to excessive inflammation and neuronal damage.
Goal: To design a synthetic protein or modify an existing one that can bind to the microglia (microglial receptor) and either activate or suppress its signalling pathway leading to modulation of inflammation or phagocytosis
Step 1:
Through literature review, receptor selection, Protein design and structure prediction (alphafold)
Step 2:
Binding prediction and docking using autodock
Step 3:
Functional pathway analysis (still have to figure this out)
MaSp2 or major ampullate spidroin is a protein that make up spider dragline silk together with MaSp1. I select MaSp2 protein like what i choose in homework 1, because of its potential and promising physical properties that is superior. Therefore, it can be applicated to industrial, health, environment fields because of its biocompatible features (Yang et al., 2016). However, it is impossible to produce this protein from spider farming, so using synthetic biology we can integrate the genes and produce it in yeast or bacteria with fluorescent material for tissue engineering.
Hansen Jonathan
Kavya Sreekanth, Bengaluru, India
Kavya Sreekanth, Bengaluru, India
Kavya Sreekanth, Bengaluru, India
Dr. Data Cheuk Kwong NG, Hong Kong
Data@9lab.co
Modifying GFP as a biosensor to detect pet �(dogs or cats) ’s infection disease in their poop
Background:�Giardia intestinalis or Giardia lamblia, is a protozoan parasite that causes giardiasis, a common intestinal infection in dogs and cats. It is transmitted through the ingestion of cysts in contaminated water, food, or soil, and is a significant cause of diarrhea, weight loss, and malabsorption in pets Giardia in Pets.
Diagnosis typically involves fecal examination for cysts or trophozoites, antigen tests, or PCR-based methods.
Green Fluorescent Protein (GFP), originally isolated from the jellyfish Aequorea victoria, is a 27 kDa protein consisting of 238 amino acid residues that fluoresces green when excited by blue light.
Solution:
Using the modified GFP-tagged biosensor bind with antibodies to detect the Giardia ��- Target Antigens: Giardia cysteine proteases (CPs) are recognized as virulence factors and could serve as targets for GFP-tagged antibodies or peptides. Specifically, CP14019, CP16160, and CP16779 are key proteases involved in pathogenesis.�
- GFP Variants: Enhanced GFP (EGFP) (e.g. (U55762.1) with mutations F64L and S65T,
or split GFP could be used to create biosensors that bind specifically to these proteases or other Giardia antigens.
https://www.cdc.gov/giardia/about/index.html
Scope:
Similar Applications:
�Opportunities:
Most of the current solutions use PCR, culture, antigen kits. It takes days or very expensive to conduct the test for pets in vet.
Remediation system for heavy metal polluted water
Background
Arisa Tani, Bioclub Tokyo
Some plants, called hyperaccumulators can grow in contaminated soils and absorb the pollutants from the ground. A remediation technology using them is called phytoremediation. However, this method is not currently used because the plants grow too slowly, making it not very effective. I propose simulating the detoxification and accumulation processes of these plants in bacteria known to be safe to the human body to provide a temporary but quick and cost-effective method for drinking water remediation in contaminated areas.
Heavy metals, which are toxic to many organisms including humans, are released from volcanic activity or industrial plants leading to large-scale pollution of water sources. It is expensive and labor-intensive to clear these pollutants, and traditional methods can be harmful.
Living Memory: DNA-Based Digital Storage (In Silico)
Aryan Choudhary, Delhi, India: Bioclub Tokyo
Project Goal:� To design a secure, efficient method to encode digital data into synthetic DNA sequences, enabling long-term, high-density storage with potential biosecurity applications.
Core Concept – Encoding Digital Data into DNA:
Additional Processing:
Genspace
Chaotically bioprinted noodles
Claudia Alarcón López Claudia.alarconlpz@gmail.com
Tec de Monterrey
Butter Synthesis Using Yeast
Ideas: Turn off unnecessary metabolism
Engineer expression of different enzymes (through both genetic and epigenetic methods) to create the appropriate protein concentration
Aim: Focus on one enzyme in TAG synthesis in oleaginous yeast to make it more efficient
Explore ways of making the TAG profile in oleaginous yeast proportional to that of butter
Yehuda Binik, NYC, GenSpace, ybinik1@gmail.com
Idea 1:
Context:
Automation in synthetic biology is streamlining repetitive lab-processes and reducing error, however as makers and designers enter the space, the rigid frameworks make reduce scope for creativity and “happy accidents”
Hypothesis:
Embracing craft-like interactions within certain contexts of the lab will help designers and makers to engage with synthetic biology
Opportunity:
Hybrid digital tools in synbio that embody intuitive craft-like interactions
Gibson-Assembly Tsugite
(Gibson Assembly processes inspired by wood joinery)
William Eliot
Aim 1:
Make Gibson Assembly more intuitive through interaction design
Aim 2:
Create a framework for making other syn bio techniques more intuitive
Idea 2:
Context:
Mealworms are being researched for their ability to digest polystyrene, which tae up 30% of the volume of landfill. This is due to exiguobacterium in their gut which breaks downs plastics. However, using mealworms to digest polystyrene is impractical and poses ethical concerns.
Hypothesis:
Being able to replicate exiguobacterium outside of the mealworm will make polystyrene waste reduction possible at scale.
Opportunity:
Creating an incubator to cultivate exiguobacterium so that it can survive outside the mealworm
Exiguobacterium polystyrene digester
William Eliot
Aim 1:
Extract key proteins from exiguobacterium for analysis and edit them to make them stable outside of the mealworm
Aim 2:
Design a container for processing waste polystyrene using exiguobacterium
Messages to the future
(I will be doing the above for an art show in April)
Nikhil Kumar, NYC, committed listener, Genspace
“Do we exist?”
“tat tvam asi”
Christina Cappelli
Genspace | Brooklyn, New York
E: christinacapp130@gmail.com
Food allergies, particularly to shellfish, can cause life-threatening reactions. This speculative concept aims to develop a rapid test. Using a lateral flow assay (LFA) designed to detect tropomyosin—a key allergenic protein in shellfish—within liquid food products such as sauces. Modeled after the design of a portable rapid test, the device would utilize antibodies that specifically bind to tropomyosin. The goal is to provide consumers and food professionals with an easy-to-use tool that enhances food safety and helps reduce the risk of allergic reactions by preventing their onset, rather than having to manage the reaction after it occurs.
Chien Lu, Jersey City, US | chien_lu@brown.edu | Week01 Notion Page
BACTERIAL-DRIVEN RESPONSIVE TEXTILES
(Smart Fabric with Living Materials / Bio-fiber Actuator)
*Projects I find interesting and inspiring are listed on the right, they’re linked in my W1 notion page as well.
Producing Ovalbumin with Yeast (Pichia Pastoris)
Sohum Patnaik / Genspace / NYC / sohumpatnaik@gmail.com
David Chau, New York, USA / ddcc@alum.mit.edu
Build a computer using cells
For his thesis, Jai Padmakumar implemented the MD5 hash function with logic gates built from E. coli!
I’d like to do a simpler version of this.
I’d be pretty happy to get even a single logic gate working.
(I haven’t finished reading the thesis yet.)
David Chau, New York, USA / ddcc@alum.mit.edu
Silly Idea #2: A Food De-Spicer
I can’t handle spicy food:
Design a protein that binds or cleaves capsaicin to neutralize it :)
(Though not sure how to do it with tools we have since capsaicin is not a protein.)
Sustainable Production of Renewable Diesel Using Bioengineered Candida antarctica Lipase B
Problems:
Solution:
Bioengineer a lipase that can perform exact same reaction but:
Methods:
Anastasia Bernaz, Abbotsford, Canada | Genspace | bernazstasy1902@gmail.com
Benefits:
Candida antarctica
Renewable diesel
Project aims are in slide notes
Biosynthesis of indigo or phytomining
-interested in indigo since the industry dye process is a petroleum-based process that’s harmful to the environment
-biosynthesis of indigo for biosensing of heavy metals means genetically modifying E. coli to produce indigo when there are heavy metals present in the environment
-example: Neri Oxman’s PHA shoe dyed with bacterial induced indigo (2025)
Research Publications:
"Production of Indigo by Recombinant Bacteria" by Fabara et al. (2023)
https://pmc.ncbi.nlm.nih.gov/articles/PMC11308077/
-interested in soil health / remediation techniques. I’m learning about phytomining while reading Soil Not Oil by Vandana Shiva about moving towards regenerative agriculture
-phytomining is the process of extracting metals from soil through plants
Research Publications:
"Soil Phytomining: Recent Developments—A Review" by Kumpiene et al. (2024)
Sequestering Radioactive Waste Through Engineered Microbes
Approach:
Heavy Metal Binding and Sequestration
Application:
Elliot Waxman, New York, NY | Genspace | elliot.verified@gmail.com
Making Polymers with Agricultural Waste
Challenge: genetically modifying microorganisms to overexpress proteins that produce NADH and NADPH. These coenzymes are crucial for the biosynthesis of biodegradable materials, such as bioplastics. The focus will be on using Pseudomonas fluorescens_, _Bacillus megaterium_, and _Cupriavidus necator_ (formerly known as _Ralstonia eutropha_ or _Wautersia eutropha
Organisms:
Oscar Schrag - 03/11/25
Aim (25 words):
To design and implement a bio-screen art system using a repressilator-based genetic circuit that enables bio-pixels to oscillate between different visual patterns in a controlled manner.
Method (50 words):
Engineered bacterial cells containing a repressilator circuit are arranged in a grid to form bio-pixels. Fluorescent proteins, controlled by the circuit, oscillate in phases to create dynamic images. Environmental tuning (e.g., chemical inducers) modulates synchronization. Time-lapse fluorescence microscopy captures the transitions, generating a bio-art display cycling through predefined images.
Tanisha Shaw, NYC, USA
GENERATIVE BIO ART
Microbial Art - Khush
Aim (25 words):�To design living microbial art by patterning fluorescent E. coli on bacterial cellulose, creating a customizable biomaterial for future biofabrication applications.
Method (50 words):
MoThief
Applications
- Abatement of Molybdenum from source and surface water, to discourage bacterial growth.
- Inhaled or Injected adjuvant therapeutic for various pulmonary bacterial infections (NTM & Pseudomonas aeruginosa) via reduction of bioavailable Molybdenum in sputum / lung tissue.
Background Info
- Molybdenum (& other trace metals) believed to play role in NTM & P. aeruginosa metabolisms.
- Source & surface water Mo levels greatest risk predictor for NTM infection in Cystic Fibrosis (CF) populations.
- Patients w/ pulmonary disease indications (CF & NCFB) have elevated sputum metal levels.
- Pulmonary NTM patients had significantly higher molybdenum blood serum concentrations (1.70 μg/L) compared to healthy controls (0.96 μg/L).
- Molybdenum sequestration (in-vivo or environmental) may improve NTM / other bacterial infection pathology or progression.
Project Overview
Step 1: Identify existing molybdenum-binding peptides and proteins to find workable template candidates and functional Motifs.
Step 2: Generate set of synthetic peptide sequences anticipated to have high affinity binding to Molybdenum via high-volume in-silico generation. Whittle down investigative candidate list based on overall predicted scoring metrics and predicted biocompatibility of candidate peptides (non-immunogenic + non-fouling + thermostable)
Step 3: Express and purify final candidate peptides for performance testing and application.
Step 4: Test candidate peptide performance via Molybdenum-bearing solution screening.
Step 5: Test final candidate peptide performance via in-vitro NTM / P. aeruginosa / sputum donor models, as well as in-vivo clinical trials in infected populations.
😭
Project Aims
Phase #1:
- In-silico design of peptide w/ high Molybdenum binding affinity, anticipated to be well-tolerated by human body.
Phase #2:
- Peptide synthesis + performance testing in Molybdenum-bearing solution.
- In-vitro testing of peptide performance in NTM / P. aeruginosa culture / sputum donor model.
Phase #3:
- Clinical testing of suite of metal abatement peptides (Mo, Zn, Cu, V, etc) in pulmonary NTM / Pseudomonas aeruginosa infected populations as adjuvant to antibiotic treatment.
Designed peptide which strongly binds to and sequesters Molybdenum (Mo), making it non-bioavailable to bacteria
Trevor Campbell, Cambridge, USA — tdcampnh@gmail.com
Nuke-a-Monas
Applications
- Inhaled therapeutic for treating pulmonary Pseudomonas aeruginosa infections and colonizations.
Background Info
- Pseudomonas aeruginosa is a common environmental bacteria, normally not harmful to humans.
- Pulmonologically immunosuppressed patients, like Cystic Fibrosis / NCFB and other pulmonary indications, can be susceptible to respiratory P. aeruginosa infection. In these populations, P. aeruginosa is the most harmful pathogen responsible for disease progression, lung function decline, and mortality.
- P. aeruginosa is difficult to treat with antibiotics due to infected patients’ underlying pulmonary disease pathology. It also has inherent and acquired resistance to many antibiotics, strong ability to form biofilms, and has significant genetic versatility.
- An engineered P. aeruginosa “Nuke-a-Monas” phage may provide an effective treatment option.
Project Overview
Step 1: Identify full library of known P. aeruginosa targeting Phages, as well as complete known proteome of Phage library. Also consider proteome / metabolome / excretome of bacterial species competitive or antagonistic to P. aeruginosa, as well as cooperative species.
Step 2: Identify solution space of most-optimal Phage trait characteristics and most-optimal trait combinations, and generate sequences for candidate Phage library across this space.
Step 3: Synthesize candidate Phages and test performance against in-vitro P. aeruginosa cultures.
Step 4: Test final candidate Phages in P. aeruginosa-bearing sputum donor models, as well as in-vivo clinical trials in infected populations.
Step 5: Develop tunable P. aeruginosa Phage platform which evaluates patient-specific culture / isolate, and delivers design of most-effective phage candidate(s) hyper-targeted to the present entities (as well as candidate(s) targeted to predicted drift-entities anticipated to emerge in response to treatment).
Project Aims
Phase #1:
- In-silico design of Phage candidates with anticipated optimal performance qualities.
Phase #2:
- Synthesis of Phage candidates + performance testing via in-vitro P. aeruginosa cultures.
Phase #3:
- Test final Phage candidates via in-vitro clinical trials in P. aeruginosa infected populations.
- Tunable P. aeruginosa Phage platform which can deliver computationally determined Phage candidate(s) with most-effective traits specific to patient culture / isolates. (Alternative to current large library screening approach)
Engineered phage which is hyper-effective at infecting and eliminating Pseudomonas aeruginosa
Trevor Campbell, Cambridge, USA — tdcampnh@gmail.com
Synthetic microbial consortia for coral resilience and thermal tolerance
Amparo Saavedra, Santiago, Chile, Genspace
Changing the format of a known binder
Aim: Throughout the pdb, several key therapeutic targets have known binders, these are often Mab’s,peptides/mini proteins etc. Further, papers like BindCraft have demonstrated the ability to generate peptide binders denovo. My goal would be to take a peptide known binder to a protein, graft it to the CDRs of a VHH/nanobody, express and test for binding.
Method:
1. Express EGFR Fragments for yeast/phage display
2. Use in silico design tools to convert a known binder to a VHH
3. Assemble a small library (~10-20) potential VHH CDR3s
3. Test for binding
Karmanya Aggarwal | Cambridge MA | karmanyaaggarwal@gmail.com
Bioluminescent Urban Lighting Fixture & Photobioreactor
Julia Almaraz, Arlington, Texas, USA
The proposed project envisions a bioluminescent urban lighting fixture that functions as a photobioreactor, integrating bioluminescent algae to enhance urban aesthetics and promote sustainability. By incorporating Pyrocystis fusiformis, a species known for its bioluminescent properties, the fixture aims to provide ambient lighting while contributing to environmental health. The algae's photosynthetic activity will absorb carbon dioxide and release oxygen, thereby improving air quality.
The design seeks to create a harmonious blend between urban infrastructure and natural processes, fostering a biodigital aesthetic that reflects a symbiotic relationship with modern ecology. Enhancing the luminescent properties of P. fusiformis through biological optimization of the proteins luciferase and luciferin could further improve the fixture's functionality and visual appeal.
Patrik Artell / Genspace / Lidingö / Sweden / patrikartell@gmail.com
Project Title: Targeting Disorder: AI-Driven Peptidomimetic Design for SIRT6 IDR Modulation in Aging and DNA Repair
Intrinsically disordered regions (IDRs) in proteins have traditionally been considered undruggable, yet they regulate critical functions in aging, cancer, and metabolism. Our project introduces a novel approach to precisely target the IDRs of SIRT6—a key longevity and DNA repair protein—with custom-designed peptides that modulate its function in a structure-informed manner.
Using computational analysis and insights from our MS2 L-protein disorder resilience work, we've designed peptides that target specific functional regions of SIRT6, including its N-terminal regulatory domain and C-terminal chromatin-binding region. These peptides are designed to alter SIRT6's interactions with DNA, influence its recruitment to damage sites, and potentially modulate its role in aging and genomic stability.
Our three-phase implementation strategy progresses from molecular characterization of peptide-IDR interactions (Phase A) to integration with bioelectric signaling (Phase B) and finally to quantum biological measurements (Phase C). This creates a complete framework connecting molecular disorder to quantum effects in a therapeutically relevant context.
The immediate focus is on Phase A experiments at Genspace, where we will validate peptide binding to SIRT6, assess cellular uptake and localization, and measure functional effects on DNA repair processes. This provides a solid foundation for subsequent phases while generating valuable standalone insights into IDR targeting as a therapeutic strategy.
Project Workflow Visualization
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Additional Implementation Notes
Patrik Artell / Genspace / Lidingö / Sweden / patrikartell@gmail.com
Project Title: Targeting Disorder: AI-Driven Peptidomimetic Design for SIRT6 IDR Modulation in Aging and DNA Repair
Intrinsically disordered regions (IDRs) in proteins have traditionally been considered undruggable, yet they regulate critical functions in aging, cancer, and metabolism. Our project introduces a novel approach to precisely target the IDRs of SIRT6—a key longevity and DNA repair protein—with custom-designed peptides that modulate its function in a structure-informed manner.
Using computational analysis and insights from our MS2 L-protein disorder resilience work, we've designed peptides that target specific functional regions of SIRT6, including its N-terminal regulatory domain and C-terminal chromatin-binding region. These peptides are designed to alter SIRT6's interactions with DNA, influence its recruitment to damage sites, and potentially modulate its role in aging and genomic stability.
Our three-phase implementation strategy progresses from molecular characterization of peptide-IDR interactions (Phase A) to integration with bioelectric signaling (Phase B) and finally to quantum biological measurements (Phase C). This creates a complete framework connecting molecular disorder to quantum effects in a therapeutically relevant context.
The immediate focus is on Phase A experiments at Genspace, where we will validate peptide binding to SIRT6, assess cellular uptake and localization, and measure functional effects on DNA repair processes. This provides a solid foundation for subsequent phases while generating valuable standalone insights into IDR targeting as a therapeutic strategy.
Project Workflow Visualization
Additional Implementation Notes
Biosensing Textiles for Physiological and Environmental Monitoring
Avantika Velho,
Boston, USA
avantikavelho1@gmail.com
86
Aim: This research explores integrating whole-cell biosensors into embroidered textile interfaces for the design of interactive wearables for physiological and environmental monitoring.
Method: In this experiment, I will design biosensor cells in-silico, culture a “placeholder”biosensor bacterial strain (engineered E.coli developed by Joshi Lab), encapsulate the cells in a sodium alginate hydrogel, and deposit them onto textile and biomaterial substrates. Using the Opentrons liquid-handling robot, I will dispense the hydrogel as microdroplets onto embroidered nodes before crosslinking them. Alternatively, I will coat individual threads with the cell-laden hydrogel and crosslink them to create uniform bioactive fibers and then embroider them. I will assess bacterial growth from fluorescence expression (via cuminic acid induction).
Schematic Project Overview
Biosensing Textiles for Physiological and Environmental Monitoring
Avantika Velho,
Boston, USA
avantikavelho1@gmail.com
87
Aim: This research explores integrating whole-cell biosensors into embroidered textile interfaces for the design of interactive wearables for physiological and environmental monitoring.
Lit Review:
Cai, L., Wang, L., Yu, Y., Zhao, W., & Rogers, J. A. (2024). Stitched textile-based microfluidics for wearable devices. Nature Communications, 15, Article 11599943. https://pmc.ncbi.nlm.nih.gov/articles/PMC11599943/
Kim, H., Patel, R., Zhang, X., & Balakrishnan, V. (2024). Advances in textile-based microfluidics for biomolecule sensing. Biosensors and Bioelectronics, 206, Article 11410389. https://pmc.ncbi.nlm.nih.gov/articles/PMC11410389/
Sahoo, A. K., Mishra, B., Nayak, S. K., & Ray, S. S. (2021). A review of textile-based electrodes developed for electrostimulation. Textile Research Journal, 91(1–2), 3–26. https://doi.org/10.1177/00405175211051949
Liu, Y., Kirell, R., Andrews, E., & Voigt, C. A. (2024). Integrating bioelectronics with cell-based synthetic biology. Nature Reviews Bioengineering, 2, 1–15. https://www.nature.com/articles/s44222-024-00262-6
Hudson, T. W., Liu, S. Y., Schmidt, C. E., & Boland, T. (2014). Composite living fibers for creating tissue constructs using textile techniques. Advanced Healthcare Materials, 3(12), 1931–1941. https://pmc.ncbi.nlm.nih.gov/articles/PMC4233137/
Aim 1:
Aim 2:
Aim 3:
Teddy Toussaint | Genspace | Cambridge, US | teddy@isibute.com
Background
As in silico design of proteins and other components of biology become more common, faster to produce, cheaper, and more accurate, there may be increased pressure to work through a growing backlog of experiments to verify designs in a manner that is cost-effective and timely. On one hand, we cannot afford to build out the number of labs it would take to keep up with the backlog of experiments required to validate computer generated designs. On the other hand, when each experiment might validate the safety and efficacy of a new life saving drug or lead to the better biomanufacturing of a much-needed commodity that is in short supply, we can not afford not to build out the lab infrastructure needed to validate our new biodesigns. This is why the development of lab-on-a-chip is so important. A lab-on-a-chip is a device that is able to perform one or more laboratory tasks (part of or whole experiments) on a space that ranges from square millimeters to a few square centimeters rather than the 10’s of square feet required for the smallest labs or 100K square feet need for the largest. The savings in real estate, consumables, and labor enabled by lab-on-a-chip could help us get through the backlog of experiments that could form with the improvement of in silico design without breaking the bank.
Aim 1
Attempt to design and fabricate lab-on-a-chip that can take in bacteriophage DNA as an input, transform it into E. coli, and perform and evaluate plaque assay.
Aim 2
Use lab-on-a-chip designed in aim 1 to increase throughput of HTGAA to test MS2 designs of all students.
Aim 3
Just as whole several thousand square foot computer mainframes from the late 1900’s are replaced by the computational power in your smartphone. Replace massive labs with a series of portable chips.
RhizoAlert:
A fluorescent biosensor for monitoring the health of your houseplants
Millions of people around the globe love plants and try to grow their own indoor plants in their apartments or houses… but unfortunately, many end up watching them wither and die without ever realizing the plant was missing some essential care.
I propose to modify Pseudomonas fluorescens, a species of rhizobacterium that inhabits many houseplants’ roots, with a genetic circuit that allows it to respond to abscisic acid (ABA), a plant stress hormone, and express red fluorescent protein (RFP) which, when combined with UV light of a specific wavelength, would allow users to detect early signs of stress in their precious plants, and be able to respond to it before it’s too late.
César Rubio, Santiago de Chile, cesar.rubio@ug.uchile.cl | Notion Page
AIM 1: Construct and clone a genetic circuit that enables Pseudomonas fluorescens to express RFP in response to the plant stress hormone abscisic acid (ABA).
AIM 2: Engineer Pseudomonas fluorescens with the designed circuit and validate its viability, colonization, and ABA-responsive RFP expression in both in vitro and plant-root environments.
AIM 3: Demonstrate the functionality of the biosensor under different plant stress conditions and evaluate its safety and practical implementation as a consumer-friendly home plant care kit.
Lifefabs Institute
Engineering HLA-G Protein for Enhanced Immune Tolerance and Reduced Graft Rejection
Folasewa Abdulsalam, Ramat-Gan, Israel|Lifefabs Institute|abdulsalammaryam381@gmail.com
Holly Adams, Barcelona, Spain - hollyadams2804@gmail.com
Living Second Skin
Protective Garment Grown from Genetically Engineered Microorganisms / Extremophiles
Providing a barrier between extreme external environmental conditions that could be generated from climate change and global warming
Cale Harrison | London, UK | Notion link | csh237@cornell.edu
Sustainable Bio-Engineered Leafware: Plates & Lunchboxes
Problems:
Solution:
Methods:
Irendra Wijewardana, Utrecht, The Netherlands | Lifefabs | irendraw1@gmail.com
Benefits:
I received a comment from Digby to think more about the other applications of this material. I am working on that.
Living Second Skin
Genetically engineered extremophiles grown into a biotextile for climate protection
Bioresponsive textile grown to the shape of the body from microorganisms that have adapted to survive in extreme environments - allowing for a eco barrier between us and the developing harsh climate. The second skin could also provide data about the environment through colour or pressure changes. Could this extremophile be encapsulated into a vessel allowing it to generate energy for the user as a byproduct of the harsh climate..
Holly Adams, Barcelona, Spain - hollyadams2804@gmail.com
Aims:
ENHANCING VOC DEGRADATION FOR INDOOR AIR QUALITY
Why: Reducing volatile organic compounds (VOCs) improves indoor air quality and decreases risks of irritations, asthma, and sometimes cancers.
Previous studies: Neoplants applied directed evolution to improve natural bacterial capabilities for breaking down benzene and toluene
CHLOE LEE | LONDON, UK | chloelee0207@gmail.com | Notion page
My approach: Genetically engineer bacteria to enhance VOC degradation
Self-dyeing of cellulose yarns using engineered bio-production of dyes.
Juan Pablo Guzman Alvarez | (Notion page) | juanpguz0709@gmail.com
How to Grow Almost Anything 2025 - London node, LifeFabs, UK.
The dyeing process is the most water-consuming step in the fabrication of a garment. Also, current industrial dye manufacturing relies on fossil fuels to cope with current demand. Bacterial dyes have proved potential to reduce dependency of fossil fuels in the supply chain and has successfully allowed the bio-production dyes (see Colorifix, Pili, Huue)
Regenerated cellulose has proved having a high potential for textile circularity by allowing to recycle waste textiles. Regenerated cellulose is manufactured through wet spinning of a cellulose pulp solution. My hypothesis is to modify the bacteria (or engineer the proteins directly) in a way that to allow growth in the pulp that can dye the thread in the manufacturing process.
Aim 1 - What I can do now with HTGAA:
Engineer the enzymes required in the bio-production of a selected dye and introduce them in a particular strain producing cellulose to reduce the thermal and pH sensitivity.
Aim 2 - Foreseeable future
Prototype the cellulose pulp solubilization process and embedding the engineered biologics testing for viability.
Aim 3 - The vision
Scaling up self-dyed garment production until reaching industrial scale.
Machoka Richard, Nairobi, Kenya | Lifelabs Institute | richmachoka@gmail.com
Target snake: Dendroaspis polylepis
Target snake venom component
Dendrotoxin 1
>1DEM_1|Chain A|DENDROTOXIN I|Dendroaspis polylepis polylepis (8620)
QPLRKLCILHRNPGRCYQKIPAFYYNQKKKQCEGFTWSGCGGNSNRFKTIEECRRTCIRK
Principle: Digital fabrication to control biological growth, using computational design to influence how and where the biological agent colonizes the structure.
Possible application:
Design a scaffold with variable porosity or integrated nutrient reservoirs that guide mycelium growth.
Aim 1: Develop an algorithmically generated CAD model of a scaffold designed to support and guide the growth of biological agents. If feasible, create an initial prototype to demonstrate the concept and explore how mycelium colonizes different textures and geometries.
Aim 2: Advance from conceptual modeling to a functional prototype using engineered mycelium-based material, tested in a real-world environment for a specific application e.g. shoe.
Aim 3: Establish a company that manufactures consumer products using living materials, bringing biohybrid design to everyday applications.
Tommaso Silluzio / Berlin / Germany / tom.silluzio@gmail.com
Smith, R.S., Bader, C., Sharma, S., Kolb, D., Tang, T., Hosny, A., Moser, F., Weaver, J.C., Voigt, C.A., & Oxman, N. (2019). Hybrid Living Materials: Digital Design and Fabrication of 3D Multimaterial Structures with Programmable Biohybrid Surfaces. Advanced Functional Materials, 30.
Neighbour-sensing model. In Wikipedia, The Free Encyclopedia. Retrieved 18:33, March 20, 2025, https://en.wikipedia.org/w/index.php?title=Neighbour-sensing_model&oldid=1183319541
Alaa Ali Elshazely,Giza,Egypt | Lifefabs Institute | alaaalielshazely@gmail.com
Genetic Circuit design for Self-Amplifying Immune Enhancement
The project aims design a genetic circuit that could detect and sense early immune signals like the inflammatory cytokines and in response it express immune-stimulatory molecules like the IL-12 which activate the immune response.
Project Workflow
Computational predictive modeling for ADHD treatment response
Objective: Develop a computational model predicting methylphenidate response in ADHD using multi-omics data.
Methodology:
1.Genomics: Incorporate DRD4 and SLC6A3 polymorphisms.
2.Proteomics: Use AlphaFold to predict dopamine transporter structure and simulate drug binding.
3.Neuroimaging: Integrate fronto-striatal fMRI connectivity metrics.
Tools & Techniques:
Machine Learning: SVM/Random Forest for baseline models; Graph Neural Networks (GNNs) for advanced modeling.
Data Integration: Federated learning for secure multi-site data pooling.
.
Sharvani Togata, kurnool, India, committed listener, life fabs node, sharvani.togata@gmail.com
Aim 1: Build a baseline computational pipeline using existing datasets and tools.
Aim 2: Develop a robust multi-omics predictive engine
Aim 3:Establish a global precision psychiatry platform for ADHD treatment optimization.
BioFlex Muscle Repair Patch: Enhanced Muscle Recovery Patch with Cell Engineering
u | | Lifefabs | vanesazabalo5656@gmail.com
Status Quo:
Muscle injuries, particularly hamstring strains, are prevalent in both athletes and the general population. In the Premier League's 2024–25 season, 24% of injuries were hamstring-related, with many leading to absences exceeding 30 days. (theguardian.com) Recovery times vary based on severity; mild strains may improve within days, while severe cases can take months. (Verywell Health) Notably, studies have found that hamstring strains have a 34% chance of recurrence within the same season. This high recurrence rate underscores the need for more effective and responsive treatment options to enhance muscle repair and prevent re-injury.
Objective:
Design a muscle regeneration patch using engineered cells to produce growth factors that accelerate athletic injury recovery and enhance muscle repair.
Concept:
Biodegradable:
Smart Responsiveness:
Delivery Method:
Archana Merla, London, UK // archana.merla@gmail.com
LifeFabs
Mycelium-Infused Toilet Paper for Wastewater Bioremediation
Problem + Objective
Pharmaceutical pollution is a growing crisis in the UK, with antidepressants, painkillers, antibiotics, and diabetes medications detected in 52 out of 54 rivers, harming ecosystems and contributing to antimicrobial resistance (AMR). Traditional wastewater treatment plants lack the enzymes to break down these pollutants, requiring a decentralized bioremediation approach.
FLUSHED is a bioengineered toilet paper infused with mycelium that activates upon flushing, using fungal enzymes to metabolize pharmaceuticals, hormones, and heavy metals in wastewater. By embedding remediation into a routine hygiene practice, FLUSHED provides a passive, scalable, and biodegradable solution to reduce water contamination.
What Can I Do Now In HTGAA
Explore mycelium strains capable of pharmaceutical degradation, focusing on white-rot fungi that produce laccases, peroxidases, and hydrolases.
Test different embedding methods for incorporating mycelium into toilet paper, including liquid culture infusion, mycelium-infused cellulose, freeze-dried mycelium layers, and electrospun mycelium fibers for controlled activation.
Foreseeable Future
Encapsulation technology to keep mycelium dormant until FLUSHED, ensuring controlled activation and longer shelf life. Additionally, I will experiment with genetically modified or selectively cultivated fungi to enhance pharmaceutical degradation efficiency.
Archana Merla, London, UK // archana.merla@gmail.com
LifeFabs
Bacterial-Driven Responsive Textiles
Problem + Objective
Current smart textiles rely on synthetic actuators, conductive coatings, or embedded circuits, which are energy-intensive, rigid, and non-biodegradable. They often require external power sources, limiting their sustainability and long-term viability, while also contributing to e-waste due to complex electronic components.
Biologically integrated textiles offer a self-sustaining, adaptive, and biodegradable alternative by using living bacteria as nanoactuators. Potential materials : bacterial cellulose, hydrogel-embedded microbes, or protein-based actuators.
This project aims to develop a bacterial-driven textile that uses biofiber actuators or nanoactuators to respond to light, humidity, airflow, pH, and biological signals by changing shape, stiffness, porosity, or color. Potential applications include self-ventilating wearables, wound-responsive bandages, breathable automotive interiors, and adaptive building facades. By offering a biodegradable, scalable alternative to conventional electronic-based smart fabrics, this project envisions a new paradigm for living, adaptive textiles.
https://skhadrao.cargo.site/RISDxHMG
Ethylene scavenging living materials for fruits preservation
Problem: 50% of food waste is fruits and vegetables.
Ali Khazem, Saarbruecken, Germany, Lifefabs, Ali.Khazem@leibniz-inm.de
Source: DOI: 10.1007/s10311-019-00938-1
Ethylene degrading biosticker
Freshness prolonged
Aim 1: Identify compatible microorganism
Aim 2: Develop metabolic pathway for ethylene degradation
Aim 3: Design biosafe sticker
Using E.coli to produce benzyl acetate from PET
Aims:
PET
Benzyl Acetate
Hana Urukalovic, Lifefabs, London, UK - hana.urukalovic@gmail.com
ALEKSANDR K. LONDON UK | LIFEFABS
info@aleksandk.co.uk
BIO-ENGINEERING PLATFORM FOR DISTRIBUTED FUNCTIONS�Construct synthetic consortia and program their behaviors for biotechnological applications
BIO-TOOLKIT
CONCEPT & APPLICATIONS
Biotechnologies
Bio-tools
Framework to program microbes to perform distributed tasks.
Quorum sensing systems can be used to coordinate coordination between organisms linking the production of a signaling molecule with corresponding receptors and promoters controlled by predesigned genetic circuits.
REFERENCES
Applications
ALEKSANDR K. LONDON UK | LIFEFABS
info@aleksandk.co.uk
AIM-1 Express GFP in-vivo/in-vitro via synthesis of AHL molecule
AIM-1: GFP & QS in vitro (Cell Free System)
LuxI – enzyme that synthesizes the QS molecule (AHL)
LuxR – transcription factor that binds AHL and activates the promoter
Design to express GFP:�- pLux promoter driving sfGFP
- RBS
- sfGFP
- Terminator
AIM-1.1: GFP & QS in vivo (E.coli)
Repeat the experiment but using e.coli
ALEKSANDR K. LONDON UK | LIFEFABS
info@aleksandk.co.uk
AIM-2, AIM-3
AIM-2: DNA Memory
AIM-3: “Leader” Election
Jon Somerscales, London/Bristol, UK (Lifefabs) jtsomerscales@gmail.com
(Generated with MidJourney)
Touch-me-not (mimosa pudica) biosensor button
A protein potentially involved in the touch-based reaction of the Touch-me-not plant (Generated with Swiss Model)
AIM 1: Identify key mechanisms and propose a feasible design to affect them using synthesis
AIM 2: Implement
AIM 3: Scale up the biosensor impact in areas of health and biodiversity
Next-Generation Synthetic Neural Circuits in Living Cells
What if cells could implement neural networks?
Rizik et. al (2022) asked the same question, as such an advancement could result in unprecedented synthetic and programmable processing and decision-making in living cells. In this spirit, they created the first implementation in living cells: the perceptgene
However, this implementation has multiple limitations, including:
Gaston Castillo Moro / Cordoba, Argentina / Lifefabs Institute, UK / gaston.castillom22@gmail.com
What if we can generate the next-generation of neuromorphic circuits based on designable, programmable & modular protein-protein interactions to overcome these limitations?
Aims:
Mona E.coLisa - Bioart platform
Aims:
Agarwal et al., 2023, https://doi.org/10.3390/microorganisms11030614
Gardner et al., 2012, https://doi.org/10.1016/j.cbpa.2012.04.010
Ariyanti et al., https://doi.org/10.1186/s12934-021-01621-3
Mikhail Bagirov, Maastricht, the Netherlands
m.bagirov@student.maastrichtuniversity.nl
Lifefabs Node, UK
Paula Rojas, Bogotá, Colombia | LIFEFABS
parojasguerrero@gmail.com
Bioremediation and biosensor for the reuse of rainwater/ wastewater
Objective:
Develop a biological system for detecting and degrading pollutants in rainwater and wastewater, making it safe for reuse in urban and rural settings.
Problem:
Water scarcity | Water pollution in rural areas | Climate change | Global warming | Pollution in rainwater
Aim 1: Immobilize Laccase protein for bioremediation. Engineering a enzymatic system capable of detecting and degrading at least one common water pollutant. Validate enzymatic activity and biosensing capabilities in a controlled experimental setup.
Aim 2: Optimize the bioremediation system by integrating multiple enzymes (e.g., laccase, peroxidases, cytochrome P450) into a functional biofilter.
Aim 3: Transform the technology into a scalable, modular water purification system that combines biosensors and bioengineered remediation for use in cities and rural communities. Develop portable or infrastructure-integrated biofilters for decentralized water treatment.
Mycelium pods - RISD researchers
Algae tiles - UCL
Fungi with Laccase enzyme
Extending Bee Lifespan – A Gateway to Understanding Longevity
Alexandru-Eugen Ioana, CL, Lifefabs Node, Timisoara, Romania, alex.46262@gmail.com
Increased lifespan for a whole new generation of bees in a colony in a isolated environment.
Aim 1: One colony (short-term)
Aim 2: Healthier apiary (medium-term)
Larger and more resilient population, scaling “the diet” to the whole apiary.
Aim 3: Human implications (long-term)
Explore human longevity links, testing MRJP1’s anti-aging potential across species.
Worker and queen larvae share the same DNA, yet queens live years while workers last 6 weeks. The difference? Diet. We will replicate key royal jelly proteins, MRJP1 (for longevity) and royalisin (for immunity) via PCR and Gibson Assembly to administer them to adult bees, not larvae, to avoid caste changes.
AI-GENERATED mRNA SEQUENCES FOR IN-CHIP RANDOMISED CRISPR-CAS13 MEDIATED MUTATIONS AND DE-NOVO IN SILICO SYNTHESIS OF ANTIBODY PARATOPES FOR METASTATIC CANCER RADIONUCLIDE-BEARING IMMUNOTHERAPY IN SILICO EVOLUTION AND DESIGN ENHANCEMENT.
HTGAA 2025 - Student: Federico Brunello - Naples, Italy - London Node - Email: federico.brunello-pharmatech@unina.it
PROBLEM STATEMENT: Immunotherapy in metastatic tumors is not always effective due to the immune escape of tumoral cells.
Constant mutations of tumoral cells can cause emergence of mutations causing resistance to treatment and metastasis. It is important to be able to devise AI-powered tools that can generate a set of randomly mutated antibodies which, based on the structure of existing immunotherapeutics, may be rapidly adapted to the constant epitope profile evolution of cancer cells, maximizing each treatment efficacy.
OBJECTIVE: to design a microfluidic device embedding CRISPR-CAS13, used to randomly insert AI-generated de novo synthesized mRNA sequences onto the mRNA sequences obtained off the paratopes (antigen-recognising areas) belonging to immunotherapeutics currently being used onto the patient. To translate the barcoded paratopes edited mRNA into proteins via ex vivo ribosomes embedded into the microfluidic chip and to assess the target affinity and specificity via quantum dots, and, finally, to functionalize the de novo generated antibodies with radionuclides or toxic compounds to selectively kill the cancerous cells. To perform directed evolution of randomly mutated anti-cancer antibodies so as to constantly be able to find paratopes mutations that are able to challenge the cancer cells mutations.
AIM 1: to identify the right sets of CRISPR-CAS13 and high processivity ribosomes to perform in-vitro RNA mutations and in vitro translation of antibody paratopes mRNA sequences. To implement a randomized mRNA sequence design and synthesis system, and to devise a multi chamber microfluidic chip fo in-vitro CRISPR-CAS13 mediated RNA insertions and translation of in silico edited paratorpes sequences. To identify, reverse-translate and synthesize the mRNA sequences of anti-cancer paratopes in existing anti-cancer antibody-based therapies
AIM 2: to build and test the microfluidic device and the ability of CRISPR-CAS13 to successfully introduce random RNA insertions within the mRNA of existing anti-cancer paratopes. To confirm synthetic ribosomes are able to successfully translate with the required fidelity and processivity the random mRNA insert and paratope mRNA complexes. Test the processivity of the fusion process between the paratope and the remaining part of the antibody, as well as the ability to functionalize the antibody with a quantum dot.
AIM 3: to assess the ability of the de-novo mutated antibodies to bind to the cancerous cell, to successfully screen within a microfluidic chip chamber on-target and off-target mutants, to functionalize the therapeutic antibodies and test them onto mutated cancer cells. To provide a feedback system allowing for the refinement of AI-generated mutations using successful Ab mutants as a training set for directed evolution.
AI-GENERATED mRNA SEQUENCES FOR IN-CHIP RANDOMISED CRISPR-CAS13 MEDIATED MUTATIONS AND DE-NOVO IN SILICO SYNTHESIS OF ANTIBODY PARATOPES FOR METASTATIC CANCER RADIONUCLIDE-BEARING IMMUNOTHERAPY IN SILICO EVOLUTON AND DESIGN ENHANCEMENT.
HTGAA 2025 - Student: Federico Brunello - Naples, Italy - London Node - Email: federico.brunello-pharmatech@unina.it
Background: among the key hallmarks of cancer (Weinberg et al, 2022) is the ability of tumoral cells to mutate and to evade immune destruction. As random genome mutations in cancer cells generate unpredictable epitope profile landscape alterations, the ability to predict and rapidly respond to the emergence of neoepitopes is paramount in order to successfully treat cancer with biologicals (Shiliang Ji et al., “Large-scale transcript variants dictate neoepitopes for cancer immunotherapy”.Sci. Adv, 2025). As random mutations accumulate within the cancer tumoral mass during immunotherapy treatment, some cells may be able to survive the treatment, leading to tumor relapse.
Goals and rationale: In this project, the combined effects of AI design of mRNAs, CRISPR-CAS13 random RNA insertion mutations and in vitro translation are harnessed within a microfluidic chip to generate synthetic mutations in the structure of antibody paratopes.and to subject them to an in-chip directed evolution process, to rapidly evolve a potential therapeutic candidate that may respond to emerging mutations. In-vitro mutated paratope mRNAs are translated in vitro within the microfluidic chip and then fused to the antibody non-variable structures. Neo-synthesized antibodies are bound to Quantum Dots and tested on cancer cells for their ability to bind to de-novo mutated cancer cells with the aid of a cytofluorimeter. Successful candidates are attached with cytotoxic or radionuclides and tested for their efficacy in treating tumoral cells bound onto a microfluidic chip.
Step by step process:
Overview: A biodegradable skin patch ("tattoo") that changes color when estradiol levels in sweat rise, signaling the approach of ovulation. By providing a non-invasive fertility indicator, this empowers users with body awareness and reproductive autonomy, without relying on invasive devices or third-party data storage.
Elsa Donovan | Paris, France | Lifefabs | elsa.k.donovan@gmail.com
SomaSignal: Bio-Tattoo for Fertility
Aims:
Components: estradiol detection mechanism, biodegradable patch, visual color indicator
ioana ferariu, bucharest, romania : lifelabs : notion : ioana.fery@gmail.com
purePeel
the fruit detox spray
coolBiome
the cooling probiotic
breatheWear
the misting fabric
a probiotic supplement that helps your body naturally tolerate and manage heat better, reducing heat stress and keeping you cooler for longer
a bioactive rinse that removes pesticide residues and harmful chemicals from fruits & vegetables before you eat them—leaving you with produce that’s as clean as organic
a bio-responsive textile that mimics sweating—absorbing body heat and releasing moisture to cool you down, just like human skin does
engineered Lactobacillus strains → produce heat shock proteins (HSPs) in body → help cells withstand higher temperatures
temporary biofilm → made of engineered bacteria or enzymes → bind to and break down pesticides
→ wash with water
fabric fibers → infused with engineered microbial biofilms → secrete cooling hydrogels or evaporative fluids → based on body temperature
Describe expression problem
Enzyme to produce, source organism, required cofactors, pH, Temperature, pressure, RedOx potential…
Not every enzyme can be produced in existing systems…not everything can grow in a Petri dish
Time for upgrade
Tweak the chosen system - describe the features to modify, genes to add, conditions to use for growth and expression for the maximum yeld of the enzyme/protein of interest
Generate a protocol, add steps to enhance the automation - bind protein folding and design tool for functions lacking in expression system…Sugerate how Opentrons could be use to handle complicate pippeting
Choosing the best existing expression system
Weight the constraints and choose the best commercially available expression system.
03
01
02
Andrita Orbandi/London, England, UK/LifeFabs/andrita.project@gmail.com
Enhancing photoprotective ability of bacterial nanocellulose by inducing engineered L-Tyrosine enzyme to kickstart melagonesis of Eumelanin
Aim 1
Run a co-culture protocols of bacterial nanocellulose and engineered yeast
Aim 2
Aim 3
Ayça Esma Subaşi, İstanbul, Türkiye, Lifefabs Node, aesubasi.tr@gmail.com
Genetic Protection in Space:
Modeling Solutions for Astronaut Health
Methodology: Computational Modeling Approach
Simulation of Problems:
Computational Solutions:
Astronauts face serious genetic risks during space missions due to exposure to microgravity and radiation. These conditions can damage DNA, affect cells, and speed up aging, which may harm their health and mission success. This project focuses on developing a computer model to better understand these genetic challenges and explore potential solutions. By analyzing the effects of space conditions on the human genome, this research will help develop ways to protect astronaut health and make their bodies more resistant to space conditions.
Project Phases:
(CRISPR-Cas9, epigenetic modifications, gene therapy) to observe their effects on mitigating genetic damage.
Developing a probiotic drink against uropathogenic E.coli
Vaginal Suppository
Main goal: Modify probiotic strains to express mannose-like receptors that competitively bind UPEC’s FimH adhesins, preventing attachment to bladder cells.
Lactobacillus strains (found in the vaginal microbiome) to produce antimicrobial peptides that kill or block uropathogenic bacteria
Clara Costea, Warwick, UK- claratheocost@gmail.com
Engineering the Skin Microbiome: Boosting Wound Healing
FINAL PROJECT IDEA
Problem: For people suffering from particular medical conditions (e.g. Type II diabetes, hemophilia, etc.), small deep wounds are often healed very slowly and risk infection by pathogens. Also, extensive skin injuries resulting from burns or chemicals can be lead to significant water loss and leave the body’s interface with the environment unprotected for hours to days.
Aim 1: A) Investigating the physiology of wounds in normal, hemophilic, and diabetic individuals and choosing the target population of patients for which the therapy will be designed. B) Finding or creating a model of the natural human skin microbiome along with its major actors. B) Designing transformation vectors for the expression of recombinant Factor VIII (for hemophilia A patients), acidic metabolites (for lowering pH), immunostimulants/immunomodulators (e.g. flagellin proteins), and/or growth factors (e.g. Wnt/Beta-catetenin agonists), using BioBrick genetic circuit parts and SBOL in the process. C) (Might be skipped/modified) Metabolic modelling of the transformed strains, focusing on their function or pathways of interest. D) Systems modelling of the cross-talk between the native species and the newly-introduced or engineered strain. SBML, COPASI, or Python may be the methods of choice.
Aim 2: A) Implementing the single and consortium-based microbiome engineering design using murine, porcine, or cell culture biosystems, assessing each of the proposed designs in Aim 1 for their predicted efficacy vs. their real-world systems-wide effects on the skin microbiome with the inclusion of positive (i.e. healthy) and negative (i.e. wounded) controls. B) Finding and investigating efficient modes of delivery, such as biocellulose (BC; produced by the Komagataeibacter spp.) dressing integrations or other hydrogels.
Aim 3+: A) Trying to formulate a long-term engineering approach (e.g. engineering commensals like S. epidermidis) as well as a short-term topical solution (e.g. using Lactoplantibacillus plantarum). B) Personalizing the therapy by using adaptable neuromorphic genetic circuits like perceptgene in the engineered microorganisms. C) Integrate/switch to protocellular/cell-free systems for noise-free genetic circuit function and greater biosafety. D) Deliver phage therapies or mycoviral therapies as an alternative. E) Create textile-integrated, cell-free microbiome modulators for rapid healing bondages. F) Create solutions for melanoma prevention, skin rejuvenation, smell modulation, acne reduction, and cancer therapies.
Kourosh Afshinjoo | LifeFabs Node | kshafshinjoo@gmail.com
Native commensals
Introduced strains
Propionibacterium acnes
Staphylococcus epidermidis
Corynebacterium amycolatum
Lactobacillus reuteri
Lactoplantibacillus plantarum
Target population
Strain selection
In silico design
In silico systems modelling and response prediction
Biosecurity design
Cellsius
San Francisco
Muhamad Muhamad Alkriz, Biotechnology, University of Aleppo, Syria, muhammadkriz22@gmail.com
Esraa Alkhalil, Biotechnology, University of Aleppo, Syria, esraaalkhalil2000@gmail.com
Targeting EpCAM Using Phytochemicals: A Structure-Based Drug Discovery Approach
EpCAM as a Cancer Marker: EpCAM is overexpressed in many epithelial cancers and plays a key role in proliferation and metastasis, making it a promising therapeutic target.
Data Analysis and Visualization
Top 8 compounds were analyzed via BIOVIA for interaction profiles; 4 were selected based on hydrogen bonding and stability, supported by CASTp pocket mapping.
Tools and Workflow
We docked 30 phytochemicals from PubChem to EpCAM’s N-terminal domain (PDB: 4ZMV) using AutoDock Vina after preparing ligands and protein with Open Babel and AutoDock Tools.
Next Steps and Extensions
ADMET analysis and MM-GBSA scoring will further assess drug-likeness and binding strength; future experimental validation is planned.
Objective of the Idea: This study aims to identify potential phytochemical inhibitors targeting the N-terminal domain of EpCAM, a cell surface protein overexpressed in various epithelial cancers. Using a structure-based drug discovery approach, 30 plant-derived compounds were selected from PubChem and screened via molecular docking (AutoDock Vina) against the EpCAM structure (PDB: 4ZMV). The objective is to highlight lead compounds with favorable binding energies and multiple interactions with key residues. This computational screening provides a foundation for future experimental validation and supports the development of natural, targeted therapies against EpCAM-expressing tumors.
Quantum Computing & AI for Endometriosis
Cindy Catherine Orbegoso-Barrantes, Cambridge(UK). Lifelabs, London
cindycatherine.orbegoso@gmail.com
Problem statement
Aim:
Predict endometriosis using gene expression data and compare classical AI models with quantum-enhanced models (Quantum SVM).
Phases:
Developing mRNA vaccines and assessing their immune efficacy for treating
Wafaa Aldarwish, Idleb, Syria | Bioclub London | wafaa.aldarwish.2002@gmail.com
László Cseresznyés, Lisbon, Portugal�laszlo.cseresznyes6@gmail.com
LIFELAB�LONDON
SENSEABLE STRESS
Measuring stress VOC of humans and plants
- > Urban design and policy making�- > Awareness�- > Art
I.�Engineering basic genetic circuit in bacteria:
extracellular receptors - > concentration in cytoplasm - > expression of gene
II. �Engineering complete genetic circuit:
VOC receptors - > protein synthesis of chromoprotein��III.�Urban installation:�Visible - sensitive - safe�
André Trindade, Lisbon, Portugal�andre@bytheendofmay.com
LIFELAB�LONDON
Reishi mushrooms as air quality sensors
Reishi mushrooms grow differently according to CO2 concentrations
>2000 ppm: fruit as antler-like formations�<800 ppm: develop normal caps�
I.�Modifying genetic circuit to be sensitive to local range of CO2 concentration
II.�Modifying genetic circuit to be reactive to other pollutant particles or introducing bacteria that respond to these. �
III.
Integrating it to urban objects, surfaces or growing new urban structures�(Bus stops, benches, etc)
Engineering an HIV Vaccine with AI-driven Neoantigen Discovery & Design
Leonardo de la Parra | Monterrey, Mexico | Lifefabs Institute, UK | leodelaparra1@gmail.com
Overview: HIV remains a major global health challenge due to its rapid mutation rate and immune evasion strategies. This project aims to use deep learning models to identify HIV neoantigens, optimize them with stabilizing scaffolds and potent adjuvants for the development of a next-generation vaccine.
MHC binding prediction
Novel peptides
Genetically Modified Plants for Phytoremediation of Heavy Metals
Why?
Heavy metal contamination, especially mercury (Hg²⁺), is a major environmental issue.Traditional phytoremediation is slow and limited by plant tolerance. Animals need something to eat while we clean the soil. If we upload plants that do not have mercury, animals will not bioaccumulate it. Its important to clean and support the areas affected by mercury pollution as well as their native flora and fauna.
How?
We will insert a transcriptional construct of the Mer operon with some modifications. The Mer operon comes from mercury-resistant bacteria and allows the reduction of oxidized mercury to elemental mercury, which is its less toxic form. We will truck the experiment with the expression of GFP.
Alejandro Menca Castellanos (AMC) | Spain | Alejandro.Mena1@alu.uclm.es
Figure 2. Schematic representation of the implementation of heavy metal transporters to the extracellular space, creating a circuit where the cell absorbs heavy metals, typically via co-transporters of assimilable light metals such as calcium, potassium, and sodium. This diagram illustrates the regulation of low mercury concentrations in a soil contaminated by the heavy metal. The protein generated through genetic editing functions to export mercury ions present in the cytoplasm.
Figure 1. Confocal images show GFP-ATM1
(IQ-tail) distribution on lateral root. Golomb, Lior & Abu-Abied, Mohamad & Belausov, Eduard & Sadot, Einat. (2008).
Genetically Modified Plants for Phytoremediation of Heavy Metals
Alejandro Menca Castellanos (AMC) | Spain | Alejandro.Mena1@alu.uclm.es
Figure 2. Schematic representation of phytoremediation strategies used by plants to mitigate mercury contamination. The diagram illustrates mechanisms such as mercury uptake by roots, translocation to shoots, and detoxification processes including chelation, compartmentalization, and enzymatic reduction to elemental mercury.
Figure 1. Confocal images show GFP-ATM1
(IQ-tail) distribution on lateral root. Golomb, Lior & Abu-Abied, Mohamad & Belausov, Eduard & Sadot, Einat. (2008).
Alejandro Menca Castellanos (AMC) | Spain | Alejandro.Mena1@alu.uclm.es
Figure 4: Materials used in floral dip transformation. Adapted from Scientific Journal of Biological Sciences, 2023,
Genetically Modified Plants for Phytoremediation of Heavy Metals: Walkthrough
Figure 3: Schematic representation of the mer operon and its function in mercury resistance. In the presence of mercury, the mer operon is activated, leading to the expression of genes responsible for mercury detoxification. This process involves the reduction of mercury to its less toxic form, which is then retained within the cell, preventing further damage.Adapted from Scientific Journal of Biological Sciences, 2023,
Alejandro Menca Castellanos (AMC) | Spain | Alejandro.Mena1@alu.uclm.es
Genetically Modified Plants for Phytoremediation of Heavy Metals: Walkthrough
Figure 5. Decrease in absorbance at 340 nm indicating the oxidation of NADPH to NADP⁺ during the enzymatic reduction of Hg²⁺ to elemental mercury (Hg⁰) by the MerA enzyme from the mer operon. The rate of NADPH consumption is proportional to the amount of Hg²⁺ present in the reaction. Soderberg, T. (2016). Monitoring Hydrogenation and Dehydrogenation Reactions by UV Spectroscopy. In Organic Chemistry with a Biological Emphasis (Vol. 2.0).
Figure 6. Representation of the protein MerA surface in PyMOL. Residues near cofactors are highlighted in red, while potential cavity-forming residues are shown in blue. The analysis identified five theoretical binding pockets.
Figure ref: Kwak, S.-Y., Giraldo, J. P., Wong, M. H., Koman, V. B., Lew, T. T. S., Ell, J., Weidman, M. C., Sinclair, R. M., Landry, M. P., Tisdale, W. A., & Strano, M. S. (2017). A Nanobionic Light-Emitting Plant. Nano Letters, 17(12), 7951–7961. https://doi.org/10.1021/acs.nanolett.7b04369
Cell-free Luciferase system for brighter bio-lighting
Defne Karagul, LifeFabs, London, UK
defnekaragul@gmail.com
In 2017, Kwak et al. made nanobionic luciferase plants that gave dim lighting for up to 4 hours, which could eventually replace electric lighting.
Why go cell-free?
Aim 1: express the luciferin-luciferase system in a cell-free framework
Aim 2: introduce mutations that would achieve brighter reactions
Aim 3: incorporate photosynthetic machinery so that the system can provide its own energy
I will also use Gaussia luciferase instead of firefly luciferase because this is an ATP-independent luminescence system, therefore the energy can be saved purely for DNA replication, transcription and translation.
ScentCapsule: A Paper-based Scent Generator
AIM 1 (Scent Designer)�Develop a computational model to design biological circuits that produce specific scents.
AIM 2 (The ScentCapsule)
Develop a Cell-free paper based device with a porous mesh acting as scent memory, multiple compartments to store/ produce different scents, and an activation method to trigger scent release.
A portable device for storage and release of custom scents on demand. Leveraging genetic circuits and cell-free based expression.
Youssef Abdelmaksoud | Paris, France, yosefmhmod@gmail.com | Lifelab
Image created with Playground
🔹Conventional exosomes contain uncontrolled bioactive molecules, posing risks of inflammation, tumorigenesis, and infection.� 🔹 Solution: Engineered Exosomes – precisely modified to deliver targeted molecules to Dermal Papilla Cells (DPCs) for enhanced hair regeneration.
✅ Customized cargo (growth factors, miRNA, proteins) to stimulate DPC function� ✅ Elimination of harmful components (inflammatory cytokines, tumorigenic factors)� ✅ Enhanced targeting for specific uptake by DPCs, ensuring localized action
Engineering Exosomes for Hair Loss – Targeting Dermal Papilla Cells
Kasidet Khimnae , Berlin , Germany
flyfframa11@gmail.com
Why Targeting DPCs with Engineered Exosomes?
🔬 Challenges with Natural Exosomes
🚀 The Engineered Exosome Advantage
🔍 Future Directions:
Project Proposal: Spirulina-Based Bio-Active Wearables and Regenerative Textiles
Auda Sakho, Lifelab nodes, London, UK
infoaudadesignsite@gmail.com
Spirulina (Arthrospira platensis), a nutrient-dense cyanobacterium, is renowned for its high protein content and bioactive compounds. Recent advancements suggest its potential in developing sustainable, bio-active textiles that not only serve functional purposes but also contribute positively to the environment.
Objectives:
• Bio-Active Wearables: Develop textiles capable of releasing oxygen, absorbing CO₂, and delivering skin-nourishing nutrients.
• Regenerative Fashion: Create spirulina-based textiles that are biodegradable, returning nutrients to the soil, thus supporting a circular fashion system.
2. Bio-Active Wearables
Concept:
Integrate living Spirulina cells into textiles to harness their photosynthetic ability, enabling CO₂ absorption and oxygen release. Additionally, utilize Spirulina’s bioactive components to promote skin health.
Key Project Goals:
1. Develop a functional spirulina-polymer composite
• Experiment with different formulations, such as spirulina biomass + PLA/PHA.
• Optimize mechanical properties (flexibility, strength, biodegradability).
Sustainable Bio-Interactive Wearable Sensors
This fabric has multiple potential applications:
Applications:
Health Monitoring Wearables: Embedding biological sensors in fabric to track health indicators like heart rate, body temperature, and pH levels.
Sustainable Biomaterials: Using biodegradable materials (e.g., bacterial cellulose) to create eco-friendly smart fabrics in fashion.
Aims:
Aim 1: Develop a biological sensor that can be integrated into clothing to monitor sweat pH levels using electrochemical, bio-fluorescent, or color-changing mechanisms.
Aim 2: Enhance sensor performance to create smart fabrics with wireless data transmission capabilities.
Aim 3: Build a sustainable brand combining fashion, health, and technology. This involves creating customizable smart clothing lines for different user groups like athletes, patients, and fashion consumers. Additionally, improving the production of eco-friendly, biodegradable, and renewable smart fabrics.
Serenity,Lifefabs,London,UK
svea_xuzhihan@126.com
LAST SLIDE
LIFEFABS
SLIDE DECK
Cellsius Final Projects�SF Node
De Novo designed antivenoms
Implement this paper end to end: https://www.nature.com/articles/s41586-024-08393-x
Bio-Sponge for Targeted Toxin Removal
Concept: A genetically engineered bio-sponge designed to capture and neutralize harmful proteins at a targeted site in the body.
Etai Sapoznik/Cellsius/SF/USA/etai.sapoznik@gmail.com
Bio-sponge Genetic Circuit
Genetic Circuit Components:
Etai Sapoznik/Cellsius/SF/USA/etai.sapoznik@gmail.com
Bio-Sponge Additional Considerations
Scaffold Choice: avoid aggregation
Ferritin-based – Find a variant with low iron binding
Exosome-based – Using a surface protein (e.g., CD63) for target binding
Target Choice:
SpyTag/SpyCatcher
Nanobody
Etai Sapoznik/Cellsius/SF/USA/etai.sapoznik@gmail.com
The Vision for a healthier Global Microbiome
To create a more balanced, healthier microbiome. To that end, create a communication and visualization interface that tracks individual and global microbiome health and interactions over time. This would include a simpler, cost-effective way to repeatedly diagnose and analyze our biomes. It would help people understand how and which lifestyle changes, interventions, and/or environmental exposures affect their microbiome composition and function, and what they could do to rebalance the biome.
The Project
Focus on the continued health of people’s oral microbiome. Devise a bioengineered probiotic to detect and destroy the main pathogen of the oral microbiome consortium. The human subgingival plaque harbors more than 500 bacterial species. Research has shown that Porphyromonas gingivalis is the major etiologic agent which contributes to chronic periodontitis.
https://pmc.ncbi.nlm.nih.gov/articles/PMC4746253/
Periodontal disease caused an estimated loss of $154.06B in the US and €158.64B in Europe, in 2018. These results show that the economic burden of periodontal disease is significant.
https://pubmed.ncbi.nlm.nih.gov/34053082/
Creating a Bioengineered Probiotic to Detect and Destroy Porphyromonas Gingivalis
Heike Rapp | San Francisco, CA | heike.here@gmail.com
Enhancing carbon sequestration with extremophile genes
‘CHONKUS’ ie. UTEX 3222
OCEAN CARBON REMOVAL
TRANSPLANTING THE CARBON STORAGE GRANULE GENE
Microscopy image of UTEX 3222 via Wyss Institute at Harvard University
THE GOAL?
PROJECT PROPOSAL BY MAKENNA MAHRER
This extremophile cyanobacteria, lovingly dubbed ‘Chonkus’ for its high affinity for carbon storage, has a unique ability to convert ambient carbon dioxide into large carbon storage granules.
First and foremost, I’m interested in identifying the gene(s) responsible for the high sequestration rates in UTEX 3222. Once accomplished, these genes might serve as novel tools to enhance carbon sequestration potentials of terrestrial plants, algae, or other industrial bacteria, with implications for biofuels and other target metabolite production.
The biological carbon pump is naturally adept at sequestering atmospheric carbon dioxide in the deep ocean, and figuring out a way to use this gene(s) to enhance that process safely could have massive impacts in the climate space.
Isolate the gene responsible for large carbon storage granules and achieve transgene expression in a model organism.
https://doi.org/10.1128/aem.00841-24
mmahrer23@cmc.edu
Soylent Genes
Mickey McManus
Space Silk
Mickey McManus
Through synthetic biology a lab in china has now been able to design a silk worm that produces spider silk. Spidroin the protein that spider’s make has enhanced properties beyond classic silk worm fibroin, but has been historically very hard to scale up by convincing cannibalistic spiders to play nice and sit still for milking on industrialized spider farms.
Silk is uniquely biocompatible and water soluble as well as antimicrobial. And if factored in with the strength of spider silk has structural properties. In space we need structures for living and ways to close the loop so that the waste material can be used for other purposes. Space silk may be the secret solution to weaving space habitats. Could we merge a good zero gravity plant or organism with the powers of silk?
Cell free super sensing and personal biome tuning
Mickey McManus
How might we use solid state bioprinting to dramatically increase the sensing of our body’s media?
How might we close the loop to personal biome tuning by building a cell-free bioprinter?
&
Rnai based therapeutics revised
Saad ahmad | Individual project
Dominant-Negative Mutations:
SPECIFICITY ISSUE/OFF TARGETING
Violeta Vilcapoma|Cellsius|Lima| Peru| violeta.vilcapoma@pucp.edu.pe
One of the limitations for colonizing Mars focuses on the living conditions that can be provided, so it is necessary to be able to guarantee the capacity of oxygen that can be generated according to environmental conditions that can vary abruptly.
-> Currently, filamentous fungi, biominerals such as calcium carbonate, and diazotrophic cyanobacteria are used. However, various biopolymers could also be incorporated to filter the Martian environment, retaining only oxygen particles for storage. Additionally, they could contribute to converting Mars' CO₂ into oxygen.
This idea is a nanoparticle-based drug delivery system for immunocompromised patients, could provide targeted and controlled medication release to boost immune responses or modulate immune activity as needed.
-> It seeks to be a controlled drug release system based on nanoparticles designed to encapsulate antivirals or antibiotics, with the aim of regulating and controlling the immune system in immunocompromised patients. In addition, it would be integrated with artificial intelligence (AI) to analyze clinical history and generate predictive immunological markers, allowing personalized dosing and adaptation of treatment in real time.
OxyMars : Biomaterial for Oxygen Production on Mars
ImmunoTher: Drug delivery system for immunocompromised patients
Since cancer is one of the diseases with the highest number of patients in the world, being able to create a microfluidic system in which brain cancer can be detected would be essential and would help reduce health gaps.
-> Idea inspiration:
Augustine R, Aqel AH, Kalva SN, Joshy KS, Nayeem A, Hasan A. Bioengineered microfluidic blood-brain barrier models in oncology research. Transl Oncol [Internet]. 2021;14(7):101087. Disponible en: http://dx.doi.org/10.1016/j.tranon.2021.101087
Microfluidic for cancer detection
Divya Srinivasan | Cellsius
1. Electricity from Bacteria
Inspired by some papers I read, certain bacteria (geobacter sulfurreducens) generate electricity when they feed on acetate, and this could potentially be turned into a sensor of sorts, by engineering the bacteria to generate electrons in a certain condition (such as body temperature, to create a “touch” sensor).
https://www.teresavandongen.com/Spark-of-Life
https://www.dezeen.com/2023/10/02/renewable-biodegradable-power-bacteria/
Microbial biofilms for electricity generation from water evaporation and power to wearables
https://pubs.acs.org/doi/10.1021/acssynbio.9b00506
divya_srinivasan@berkeley.edu
Divya Srinivasan | Cellsius
2. Bacteria Tarot
More of a fun/random experimentation, I was inspired by a project on generating typography from different bacteria that grows/merges traditional and modern Hebrew script together with bacteria (paenibacillus vortex) and its food source. I think it could be an interesting idea for “tarot” where a question/prompt is given in one medium, and fed with another input that then creates a visual that can be interpreted.
divya_srinivasan@berkeley.edu
Exploring development of structural predictor focused towards DNA nanostructures | Packaging DNA/RNA into compact shapes to improve cellular uptake and localized delivery | Rolling Circle Amplification to enable largescale self-folding DNA. |
While alpha fold has excellent prediction capabilities for proteins it is limited for the prediction of DNA nanostructures as the no. of strands that can be input are limited. In a sense, DNA nanostructure prediction is theoretically simpler since the primary interaction is only DNA base pairing. Taking sequence complementarity into account should help verify the accuracy further. This is particularly useful because multiple sets of orthogonal sequences can result in the same structure. | Several works have shown that DNA nanostructures can enhance cellular uptake. Designing modular structures that can latch on to different strands and act as envelopes to deliver messages (DNA strands) to desired location. The same envelope can be used for different kinds of messages. | Rolling circle amplification creates long repetetive copies of input strands. Certain strand sequences have the capability of self folding into a variety of shapes. Choosing the shapes cleverly such that they are capable of assembling further via blunt end stacking or base pairing to further form macroscale assemblies. This is analogous to primary and secondary structure seen in proteins where the primary structure is that of the building block which interact to form the secondary structures. |
Anirudh Sampath, West Lafayette, USA
Arvind Bhallamudi
Cellsius
Interested in using fungi species for plastic bioremediation : including laccases, peroxidases, esterases (like cutinases and lipases), and potentially PETase and MHETase, to break down plastic polymers into simpler compounds.
Examples of fungi species:
SynBioGenetics
Rodrigo Tamayo | SynBioGenetics | CL | Santiago, Chile | rodrigo.tamayo.b@gmail.com
De Novo Production of Brassinosteroids in Yarrowia lipolytica
500 USD 10mg
Rodrigo Tamayo | SynBioGenetics | CL | Santiago, Chile | rodrigo.tamayo.b@gmail.com
Engineered Peptide + Exosomes as a treatment for hair-loss
AR
DHT
Rodrigo Tamayo | SynBioGenetics | CL | Santiago, Chile | rodrigo.tamayo.b@gmail.com
Automatic dispenser of neuromodulators
GABA
Serotonin
Dopamine
Molecular modeling and in silico validation of peptide inhibitors of MDM2-p53 interaction as a strategy to restore p53 antitumor activity in cancer cells.
Cancer remains one of the leading causes of mortality worldwide, largely due to therapies with low specificity and high side effects. One of the key pathways involved in multiple types of cancer is the interaction between MDM2 and p53, where MDM2 blocks the tumor suppressor activity of p53. This project proposes to design inhibitory peptides capable of disrupting this interaction, allowing the restoration of p53 anti-tumor function. Unlike small inhibitors such as Nutlin-3a, computationally designed peptides offer the potential to be more specific, less toxic and customizable, justifying the development of new therapeutic strategies based on artificial intelligence.
Jorge Moreano, Quito, Ecuador.
jluismoreano@gmail.com
Objective
To design and structurally predict peptide inhibitors of MDM2-p53 interaction using generative models and artificial intelligence, evaluating their binding affinity in silico as a basis for future therapeutic applications against cancer.
Vanessa Romero, Quito, Ecuador.
vromero@usfq.edu.ec
Soylent Genes
Through synthetic biology a lab in china has now been able to design a silk worm that produces spider silk. Spidroin the protein that spider’s make has enhanced properties beyond classic silk worm fibroin, but has been historically very hard to scale up by convincing cannibalistic spiders to play nice and sit still for milking on industrialized spider farms.
In the classic 1960’s [science fiction story] (https://en.wikipedia.org/wiki/Make_Room!_Make_Room!) and 1970’s movie Soylent Green the world by the year 2022 was entering a hothouse run away global warming catastrophe combined with overpopulation crisis. The masses were offered a breakthrough new food wafer called Soylent Green made ostensibly of plankton. The company who produced it didn’t actually tell folks that Soylent Green was actually made of people (well that’s one way to get rid of extra humans).
Now that synthetic biologists have created a way to not only make fibroin but also spidroin via silkworms, it made me wonder “how we might dramatically increase the production output of silkworm?” Planting many more mulberry trees and fostering far more sericulture is one approach (and it’s got a triple bottom line in that it sequesters carbon in the soil, provides shade, silk, feed, and fertilizer (when the silk moths or worms die). But that limits us to climates that can support mulberry trees (silk worms have been domesticated over thousands of years to only eat mulberry tree leaves.)
I’d like to actually edit plankton so that they grow white mulberry tree leaves (and or the proteins that provide the signals and nutrients that a silk worm needs to thrive). That way we could create Soylent Gene powered food wafers for silk worms. Silk worms are attracted to the jasmine smell of the white mulberry tree and get all their nutrition from the leaves. By editing plankton to produce silkworm food we can spread the benefits of silk worm production to coastal areas that have abundant sea water, or scale up solar powered bioreactor factories of phytoplankton.
The species of the mulberry tree is called Morus alba, it is diploid and has 28 chromosomes. The species of plankton would be the model organism that has already been well studied for various alternative production methods called Synechocystis.
An Alternative approach would be to edit other fast growing plant species that could provide nutrients to silk worms but that grow in a wider range of climates. In either case we need to consider how to get the key factors that drive silk worms wild with delight when they are given white mulberry tree leaves. Of course if I were taking the movie completely seriously we’d edit the silk worms themselves to love the taste of silk moths and close the loop entirely but my science teachers taught me that perpetual motion machines don’t exist and that cannibalism isn’t nice.
Anahí Ñacato
Production of recombinant Dispersin B to trait Staphylococcus aureus and Pseudomonas aeruginosa Biofilms in a cell-free system
Production of recombinant Dispersin B to trait Staphylococcus aureus and Pseudomonas aeruginosa Biofilms in a cell-free system
1. Self-Assembling Peptides for Cultivated Meat Scaffolding
Objective:
Design self-assembling peptides that form bioactive scaffolds, enhancing cell adhesion, proliferation, and differentiation in cultivated meat. These scaffolds will mimic the extracellular matrix (ECM) and improve tissue maturation.
2. Fetal Hemoglobin for Enhanced Oxygen Transport in Cultivated Meat
Objective:
Engineer and produce fetal hemoglobin (HbF) in yeast to enhance oxygen transport in cultivated meat, improving cell survival and tissue viability.
3. Co-Culturing Cultivated Meat with Probiotic Bacteria for Scaffolding and Antimicrobial Properties
Objective:
Develop a co-culture system integrating probiotic bacteria with cultivated meat to enhance scaffold formation, improve texture, and naturally inhibit microbial contamination, using genetic circuits.
The path towards an accessible Cultivated Meat
María José Méndez, Cali, Colombia m.mendezv97@gmail.com
Mycoplasma Biosensor for cell culture
Present at least one final project idea! Can be more than one if you like :)
Supporting text and images welcome :)
Natalie Edwards, Santiago Chile natalie.edwards@ug.uchile.cl
Mycoplasma spp. is a common contaminant of cell cultures, undetectable to the naked eye and capable of passing through 0.22 µm filters used for culture media filtration. This type of contamination can spread to cell cultures, as it lacks a cell wall and does not respond to antibiotic treatments, affecting cell viability and the integrity of the studies conducted.This contamination is not noticeable to the naked eye, and can be detected when the amount of cells is high.
Detection includes PCR test wich takes several hours and treatment to remove these contaminants include antibiotics, which do not always work and there is a risk treated cultures can always spread contamination. ��Objective: I propose the use of a highly sensitive cell free system biosensor for early detection of contamination to avoid harmful effects in the long run.
Damaris Ganchozo| Guayaquil, Ecuador | Synbio Genetics | damarismichaelle@gmail.com
In vivo monitoring of hydrocarbon contamination in coastal ecosystems
Problem
There are many oil spills in coastal areas where it takes a long time to delimit the affected areas, especially when it gets dark at night.
Solution
The idea relies in the creation of a biosensor module powered by bioluminescent bacteria with the intent of the monitoring and mapping of environmental hazards. Under toxic conditions, the bioluminescence is reduced and can be measured by a luminometer.
Buoys could be deployed in high-risk areas, such as shipping lanes and oil drilling sites, for continuous monitoring.
Aims:
More info here
Problem
Babies have a developing immune system, which makes them more susceptible to the ingestion of contaminated food, causing symptoms such as vomiting, diarrhea, fever and their ability to fight pathogens is limited, which increases the risk of serious complications.
Damaris Ganchozo| Guayaquil, Ecuador | Synbio Genetics | damarismichaelle@gmail.com
Solution
Design a skin patch incorporating a biosensor capable of detecting changes in skin temperature and the presence of specific biomarkers associated with rashes (by high levels of histamine) and fever.
Aim 1 Identify a flexible, non toxic material that can adhere to the skin.
Aim 2. Design an enzymatic biosensor based on aptamers, which are DNA or RNA sequences designed to bind to specific molecules, such as histamine, and emit colorimetric signals to detect food poisoning at an early stage.
Aim 3 Create a network cloud where data can be stored and shared in real time with parents and doctors.
BabyPatch: Rapid testing of histamine levels in babies.
More info here
More Informatión Here: https://mini-cotton-2a7.notion.site/FINAL-PROYECT-1b6d9ae1b02a802ca7c6dd0e22f2fece?pvs=4
Victoria Makerspace, BC, Canada
GUSTAVO M. MARCHANI Calgary, AB, Canada | gamm2000.gm@gmail.com
Improved Luz (Fungal Luciferase)
“Fluorescence”-Activated Cell Sorting (FACS)
Use bioinformatics approach to engineer the enzyme to have better qualities and is functional in cytosolic form
Effect of Microgravity on DNA Origami
Development of a DNA Origami System for Targeted Delivery of Doxorubicin in Breast Cancer Cells
Andrea Tambo, La Paz, Bolivia | and.andreatambo17@gmail.com | Victoria Makerspace Node
Andrea Tambo, La Paz, Bolivia | and.andreatambo17@gmail.com | Victoria Makerspace Node
Methodology
Design & Synthesis
Functionalization
Drug Loading
Controlled Release
Cytotoxicity Tests
Udomprasert, A., & Kangsamaksin, T. (2017). DNA origami applications in cancer therapy. Cancer Science, 108(8), 1535-1543. https://doi.org/10.1111/cas.13290
Project idea 1: In-Silico Engineering of Cyclin-Dependent Kinase (CDK) Peptide Inhibitors
Develop small peptide inhibitors for CDKs to regulate cell cycle in cancer cells.
Design & Simulation: Use PyMOL & AutoDock for peptide design and docking.
Optimization: Refine peptides using GROMACS simulations.
Validation: Partner with labs for in vitro testing of peptide efficacy.
Potential Novel therapeutic approach for cancer treatment through targeted CDK inhibition.
Jerome Bright Ogenrwot, Kampala, Uganda. Victoria node.
Designer Cells Lab�Ahmad Hader, Faculty of medicine, Yarmouk university�ahmaduni.a10@gmail.com
Design PAN HLA-I Binder
Why a New HLA‑Class I Binder?
Project Approach & Aims
Impact & Broader Value
Designer Cell Labs, Korea
Xavier Alexandro Rios Salinas
Sucre, Bolivia
Lithium is a metal used in the production of batteries but also for medical drugs used in psychiatric disorders
Current methods for lithium extraction are large scale water consumption technologies which is a harm for environment, especially for local communities. At the same time, when lithium is used by patients, it has the risk to produce adverse effect by its toxicity, so it needs to be constantly monitored in patient´s serum.
A possible solution for this could be: cell free biosensor of lithium capable of a dual use in biomining and medicine.
EXtended Chemosensory Array for Lateral Ion Biosensing and Ultimate Recovery
“EXCALIBUR”
A riboswitch is a RNA sequence capable of adhering directly to Li+ ions and function as a promoter at translational level.
Dual use?
https://www.nature.com/articles/s41598-022-20695-6
Designer Cell Labs, Korea
Xavier Alexandro Rios Salinas
Sucre, Bolivia
Designer Cell Labs, Korea
Xavier Alexandro Rios Salinas
Sucre, Bolivia
xavier.alexandro.rios.salinas@gmail.com
Experimental Design &Methodology
Methodology:
Designer Cell Labs, Korea
Hyunseo kwon, Incheon, Korea
kwonhspresent@yonsei.ac.kr
Background Information
Western populations, such as those in the United States and Europe, tend to have a higher abundance of Bacteroides species, which are associated with high-fat, high-protein diets. (1)
In contrast, non-Western populations, such as those in Africa and Asia, often exhibit a higher prevalence of Prevotella species, which are linked to high-fiber, plant-based diets. (2)
These differences are thought to be driven by dietary habits.
Japanese populations have been found to have lower alpha and beta diversity compared to other populations, with a high abundance of Bifidobacterium and a low abundance of potentially pathogenic bacteria. This may be attributed to the unique dietary habits of the Japanese population, which include a high intake of soy, seafood, and fermented foods.(3)
Designer Cell Labs, Korea
Hyunseo kwon, Incheon, Korea
kwonhspresent@yonsei.ac.kr
Question Mark?! - 1 -
How about difference within Korea?
Designer Cell Labs, Korea
Hyunseo kwon, Incheon, Korea
kwonhspresent@yonsei.ac.kr
(1) Lim MY, Hong S, Bang SJ, Chung WH, Shin JH, Kim JH, Nam YD. Gut Microbiome Structure and Association with Host Factors in a Korean Population. mSystems. 2021 Aug 31;6(4):e0017921. doi: 10.1128/mSystems.00179-21. Epub 2021 Aug 3. PMID: 34342532; PMCID: PMC8407462.
Designer Cell Labs, Korea
Hyunseo kwon, Incheon, Korea
kwonhspresent@yonsei.ac.kr
Question Mark ?!
How about difference within Korea?
How about relationship with Soil microbiome?
Designer Cell Labs, Korea
Hyunseo kwon, Incheon, Korea
kwonhspresent@yonsei.ac.kr
FINAL Idea
Soil Microbiome &
Gut Microbiome
Relationship
Gut Microbiome
Relationship within Korean
Final Goal : Understand Interrelation between microbiome to understand �the significance of pathogenesis and progression of human disease
Designer Cell Labs, Korea
Anastasia Arkhipenkova, Incheon, Korea
anastasia.rkh@yonsei.ac.kr
Openbioscience
Ottawa Node
XOS Project: SynBio Enzyme Soil Restoration
What?
Alexander Proaño, La Armenia, Openbioscience Ottawa Node
Why?
How?
In the future?
Advantages
https://www.notion.so/New-individual-project-1d8a68cfac3f8099a476d6696d20fade
Bio Fashion Design - Kate Melanson
Valeria Rodriguez Espinoza�Munich, Germany �valeriarodres@gmail.com
Addressing Pollution from Fabrics
The textile industry is the most polluting industry in Europe, and recycling textiles remains a major challenge due to the complex supply chain and the diversity of materials. Synthetic fibers accounts for 70% of global fiber use, where 9 out 10 are polyester.
While there are solutions for collection and sorting, the biggest leverage point lies in production. What if we would design recyclable and biodegradable textiles from the start?
This project enables the production of textiles that can self-degrade, shifting the current standards of the fashion and textile industries toward a truly circular economy.
This will be achieved by automating the molecular biology, and fermentation steps using Opentrons to produce enzymes capable of breaking down synthetic fibers made out of polyester.
Polyethylene terephthalate (PET) is the chemical name for polyester. Polyester textiles are semi-crystalline monomeric structural units linked by ester bonds. There are some fungal hydrolytic enzymes are capable of breaking down PET like esterases, lipases, cutinases, hydrolases and keratinases.
Cutinases and Estereases are of industrial applications interest because they remain active in the absence of an oil–water interface. Industrial scale has been developed to break down bottles PET into fiber PET, nevertheless textile fiber-to-fiber recycling is still in lab scale—where the major challenges are the energy cost-effectiveness. Therefore, the biggest lever comes at the scale up production.
For this Proof Of Concept, I I will focus on designing an entire fermentation workflow with minimal human assistance using Opentron to scape up to 25 ml. For this I have selected Leaf-Branch Compost Cutinases (EC 3.1.1.74), as it has the ability to break down semi-crystalline PET, and have demonstrated promising results at lab scale. Although this project focuses on cutinases, this technology can be adapted for other enzymes.
How to hydrolyze PET?
Cutinase
Valeria Rodriguez Espinoza�Munich, Germany �valeriarodres@gmail.com
Aim 2
Create a PoC by expressing cutinase into E. coli
Transforming Production for Circular Textiles
Aim 1�Design an entire fermentation workflow with minimal human assistance using OPENTRON
Aim 3
Create a Textile PoC by embedding the protein in a fabric.
Valeria Rodriguez Espinoza�Munich, Germany �valeriarodres@gmail.com
Regenerative Therapy for Motor Neuron Recovery in Amyotrophic Lateral Sclerosis
Mariana Valdez, Puebla, México marianavaldez2001@gmail.com
Design a genetic circuit for neural stem cells that promotes:
The circuit will activate the expression of genes related to neuronal protection and remyelination to slow motor neuron degeneration.
Goal: New enzymes for the Reclone open DNA collections!
T4 Ligase & Bsal
Ethan Itovitch, Montreal, QC
Context
Goal
T4 Ligase
Protocol
Bsal
Considerations
Protocol
TdT murine for miRNAs synthesis
Berenice Ferruzca
Querétaro, México
ferruzca.berenice@gmail.com
LAST SLIDE OF THE
COMMITTED LISTENERS
FINAL PROJECT SLIDES