Team:ABSI Kenya
We Are ABSI Kenya
ABSI_Kenya is a team of young professionals with innovative ideas to solve local problems using synthetic biology.
ABOUT US
We are a team of young people from different universities and different dicsiplines, creating solutions to problems that affect us directly
About Our Project
Almost Half of Kenya’s population lacks clean drinking water and this has proved to be a serious health crisis. ABSI is developing a biosensor that detects common chemical and biological contaminants that can be used by people from the comfort of their homes. The biosensor will apply common engineering principles to work, and this will be a great step for affected communities to fight waterborne illnesses
About Our Project
Project Video Description
OUR PROJECT
Description
Our circuit would be engineered to detect multiple inputs (contaminants), amplify the signal and give an accurate signal. The focus should be on both microbial and chemical contaminants. Target chemical contaminants are Cadmium, Fluoride and Lead while microbial contaminants are E.coli H. Pylori and V. cholerae. We will additionally develop a device that will scan the bacteria genome for the Multidrug Resistance genes and report accurately. Currently, we have established a Cadmium biosensor which will obtained using the assembly of artificial translationally coupled cadR operons. The incorporation of combinatorial design measurement to obtain the best the optimum performace.
Design
Combinatorial Design
Signal amplification using T7RNAP to improve sensitivity & dynamic range. Addition of Zinc exporter to improve the selectivity of CadR10 repressor.
The development of this circuit will pave way for the integration of the other circuits and thereafter a multifaceted biosensor that aligns with our initial objectives.
Engineering
Engineering section Our desire is to design a biosensor with the following desired attributes of the biosensor design
- High selectivity
- Low detection limit
- Wide (output ) dynamic range
- Low leakiness
The last 3 attributes define the biosensor response curve
Our design is employing CadR.10Z ( this is a combined TF that has CadR gene + a ZitB gene that is a metal exporter that removes Zn from the cell cytoplasm thus improving selectivity). Low leakiness Low level of Cad Repressor is the design - means only low Cd ions will be needed to de -repressor the promoter to generate downstream protein expression. High level of Cad Repressor will mean that to generate downstream protein expression, then high Cd2+ ions will be needed for this to work Reducing the repressor concentration would therefore lower the specified demand on the inducer concentration, which effectively translates into a decreased LOD for the sensing module
Another strategy for improving the LOD of our biosensor could be the integration of CaDR repressor with a toggle switch. This is likely to modulate both the cadmium concentration and a LOD tuning ligand. This could be done after iGEM as we continue to work on our project. In biosensor design, if the transmembrane transporters for a ligand could be identified, the same outcome could be reproduced by overexpressing importers and knocking out exporters. For instance, disruption of the efflux transporters for Zn/Cd/Pb in P. putida strain KT2440 decreased the detection limits by up to 45-fold (Hynninen et al. 2010). In another example, an engineered E. coli biosensor achieved a lower LOD for Ni through the introduction of several foreign Ni-uptake systems
Our circuit would be engineered to detect multiple inputs (contaminants), amplify the signal and give an accurate readout signal. The focus should be on both microbial and chemical contaminants. Target chemical contaminants are Cadmium, Fluoride and Lead while microbial contaminants are E.coli H. Pylori and V. cholerae. We will additionally develop a device that will scan the bacteria genome for the Multidrug Resistance genes and report accurately. Currently, we have established a Cadmium gene circuit that is sensitive, specific and accurate. This is an improvement from the previous existing ones. Our approach focused on these 3 design principles:
- Transcription amplifier
- Multiple copy reporter gene
- Signal amplification
We applied Combinatorial Design to come up with different circuits and identify one that would yield the best performance. The work was divided into sections and handled one at a time. Therefore, we focused on: researching chemical and microbial water contaminants, market research on any available kits (none available locally), available genetic circuits of either of the contaminants of our focus and designing genetic circuits that senses and reports on cadmium contamination to identify the most sensitive and specific.
Design diagramsPARTS
| Part | Name | |
|---|---|---|
| Terminator | BBa_B0015 | double terminator |
| Metal Pump | WP_064701588.1 | Zinc Exporter |
| Polymerase 1 | BBa_I2032 | T7RNAP |
| Polymerase 2 | BBa_J04450 | mcherry |
| Polymerase 3 | CadR10 + PROTEASE TAG | |
| Promoter 2 | Bba_J23100 series | Constitutive promoters |
| Promoter 3 | BBa_J34814 | T7 promoter |
| Promoter 4 | PcadR10 | |
| Protease tag | BBa_M0051 | SsrA degradation tag |
| Repressor 1 | NZ_BDEP01000008.1 | CadR10 |
| Repressor 2 | BBa_M0051+ | CadR10-protease tag |
Constitive Promoter
| Name | Part | Source |
|---|---|---|
| Strong Promoter | BBa_J23100 | Anderson promoter collection |
| Medium Promoter | BBa_J23111 | |
| Weak Promoter | BBa_J23105 |
RBS
| STRENGTH | PART |
|---|---|
| Strong Promoter | BBa_K3137001 |
| Medium | BBa_B0032 |
| Weak | BBa_B0033 |
HUMAN PRACTICES
Market
Online research and groundwork, proved that there is currently no home-deployable biosensor in Kenya. The current field water testing kits, require certain reagents and cannot detect both chemical and microbial contaminants. This drove our interest to come up with a biosensor aimed at those living in poor conditions, those who rely on treating water, and other stakeholders to have access to clean water as they can easily test on their own and data that can inform decisions respectively.
Education
● Ongoing publication paper (Richard’s presentation)
Collaborations
● Translation of (ASTWS) China team game.
● Survey?
Integrated Human Practices
- Participation in Inaugural International Synthetic Biology and Biosecurity Conference in Africa
- Engagement with research experts and various stakeholders.
- Engaging with Hatem. Presentation of an ongoing paper & pitch by Richard
- Synthetic Biology Conference Dec 1st
Inclusivity
Multidisciplinary team and engagements
Team formation saw the involvement of various disciplines ranging from engineering to biology to all come experience synthetic biology as a new.
Collaboration with local universities and scientists
Through partnership and involving various stakeholders, we were introduced to other university students new to synthetic biology. This collaboration helped foster knowledge exchange and future plan on capacity building.
Ongoing publication paper (Richard’s presentation)
The focus of this paper is to show that synthetic biology cannot survive on its own. Fostering its progress and growth will require involving every single person to be informed and aware of it.
OUR TEAM
Richard Machoka
Team Leader
Field of Study: BSc. Biomedical Science
Kelly Nyachama
Communication
Field of Study: BSc. MicroBiology
Mary Muturi
Human Practices
Field of Study: BSc. Biomedical Science
Bukhosi Masuku
Science Lead
Field of Study: BSc. Biomedical Science & Biotechnology
Enock Chebu
Wiki Page Development
Field of Study: B.Eng Chemical & Process Engineering
ATTRIBUTION
Primary Investigators
Dr. Faith Onditi
Senior Scientist
Institute of Primate Research
She is the primary PI of our team she helped evaluate our project for feasibility and practicability. She helped us with project design and provided our team with the lab space to execute our project. She has guided us in searching for and applying for funding to enable us execute the project.
Dr. Jael Obiero
Head Reproductive Health Biology
Institute of Primate Research
Dr. Jael is Research Scientist in Reproductive Health and currently the Head of Reproductive Health & Biology at the Institute of Primate Research. Dr. Obiero holds a BSc from Egerton University, both MSc (Physiology) and PhD (Medical Microbiology) from the University of Nairobi. She has participated in mentoring both undergraduate and post graduate students and is an author of Cochrane Systematic Reviews in Collaboration with the South African Cochrane Centre. She helped us with the laboratory space
Primary Investigators
Jacob Kittinya
Lecturer
Master of Technology in Chemical Engineering, Tshwane University of Technology (TUT) Pretoria, South Africa
Mr. Kittinya is a PhD student at Tshwane University of Technology and lecturers at the Technical University of Kenya and a chemical engineer. He was very instrumental in the conceptualizing and designing of the gene circuit. He helped in the mathematical modelling of the gene circuit using the Computer Aided Design tools. Together with other members of the team, he helped in designing and populating the wiki page as well as provided a lab space for the chemical tests experiments that were required.
Kenneth Waititu
Mr .Waititu holds an MSc in Microbiology from Kenya Polytechnic. He was very instrumental in setting up the laboratory space and ensuring the laboratory is able to conduct a Synthetic Biology research. He helped in identifying and procuring laboratory reagents needed for the work as well as helping in the organization of a general laboratory safety training and orientation for the rest of the team members. He helped in the experimental designs and development of the SOPs. Working with other team members he helped in the wet lab and supervised all laboratory activities.
Professionals/ Mentor
Hatem Mohamed Gaber
Mr Hatem is a research assistant at Zewail City of Science and Technology. He is also An iGEM judge, an iGEM mentor and a member of the iGEM Engineering Committee, iGEM Foundation M.Sc. student at Faculty of Science, Cairo University. He guided us in all aspects of designing, modelling and simulating our gene circuit. He generously donated his valuable time to and met us for 3 hours every week and sometimes even more in order to help the team in our project. Synthetic Biology is quite new in Kenya and to most team members so his guidance was invaluable.
Harry Akligoh
He’s has been our mentor from the EPIC iGem 2021, and has been supportive along the way for even process outside the competition..
Volunteer
Sylvester Asare Sarpong
Helped with the wiki page development
CONTACT US
Contact Us Via Any of The Methods Below
CONTACT INFO
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Address:
Nairobi, Kenya -
Mail Us: info@africabiosynthetic.co.ke
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Phone:
+254 725 909775