HCD: Genomics Research
Collaboration: University of Eastern Africa - Baraton
The goal of this collaboration is to provide students with real world scenarios in which they attempt to successfully develop sustainable commercial applications. Students perform work under close faculty supervision and CSTI facilitates the identification of and interaction with expert mentors.
Each cohort will go through multiple phases of trial and error until success is achieved. In addition to the project outcomes, the students will be gaining rapid prototyping skills that increase their employability upon graduation.
Participating students also become CSTI Ambassadors in their communities. As Ambassadors their primary cross pollination function is to demystify science in a way that stimulates engagement in scientific research and innovation.
University of East Africa Baraton Faculty members (not in picture):
DEPARTMENT CHAIR BIOLOGICAL SCIENCE DEPARTMENT: MICHAIAH OGOLA OJUNGA
Senior Lecturer Microbiology, Biotechnology and Bioinformatics: Mr. Frank Onyango Combo
Baraton Cohort Student Coordinator (not in picture):
Arthur O. Allela
Research Focus-Computational genomics
BSc Network & Communications – Senior
Mobile Geo-spatial system: KIPI Patent application No. KE/P/2012/001673
Mobile transaction processing merchant platform- KIPI PATENT : KE/P/2009/000872.
CSTI Habitat Patch Philosophy
We provide a safe space for real world scenario experimentation. Students are treated as if they were working professionals in a chemical factory. Students are expected to figure out as much as possible on their own.
CSTI sets use case parameters and product design specifications. External mentors provide specification boundaries for commercial product development and experienced insights on what can go wrong. Baraton faculty provide close supervision and supplementary training.
External Volunteer Mentor Institutions
University of Nairobi Institute for Climate Change and Adaptation (ICCA)
University of Nairobi Centre of Biotechnology & Bioinformatics (CEBIB)
The pedagogical style is Action Learning based on a combination of the Socratic Method and Montessori Method (for adults). No we are not running a structured educational experiment. We are actually just winging it to see how well this works. You can find a proper Montessori for Adults research study here.
Students are allowed to follow their natural curiosity. Weekly CSTI updates are delivered by Arthur (project manager and we finally got him on camera in December 2017).
Update reports highlight methodological progress, technical needs and skills gaps. However, most of the exchanges are focused on philosophical issues or socio-environmental challenges that need to be addressed. Students are pushed to defend their decision making every step of the way.
Students keep making an inexplicable reference to Training Day only tougher with repeated mentions of brain cells melting because we keep reminding them of everything that can go wrong while demanding behavior and solutions remain at high academic standards of ethics.
Training Day at CSTI means Dunia ni maabara: the world is a laboratory where various experiments are going on/ Our translation: you can fail but don't break anything.
Just because something can be done is no excuse for doing it. There must be a significant social benefit in addition to ecological technological and commercial benefit.
"This is the way everyone else would solve it"/"This is normative behavior and what can be expected under the circumstances" is not an option. The only option is to perform as if the problem was not pressuring you to behave otherwise.
Did we mention church attendance is a Baraton weekly requirement (grin)?
Mindfullness and meditation are daily practices for all involved (including CSTI Board Members and Baraton Faculty).
After students finish filling up on Faith we tell them to use Reasoning. Everyone participating is working, in addition to regular studies or workload. On average Faculty and CSTI Board Members are spending 1hr daily (often 2hrs on weekends). External Mentors spend up to 4 hours a month. Students are spending at least 10hrs a week in addition to studies.
We do monitor for burn out and demand students take breaks. However students defied us by working through the 2017 December holidays. We are not sure transference of the "workaholic gene" is a good thing but students say they are enjoying the experience. Testimonials to follow...
2017 Eureka Moment
Genomics is an exciting combination of scientific and technological innovation that makes biotechnology research more affordable. Specifically, DNA sequencing can now be performed in the equivalent of a portable school laboratory (Scientific American, 2017).
A scientist's dream is that every human on the planet is equipped with the skills to fully understand scientific discoveries. Innovation is maximized by the richness of diverse perspectives and insights. Social media allows for the cross pollination of ideas.
Genomics tools such as CRISPR and QPCR can be used to develop a new era of science for good in which citizens and scientists use open innovation platforms to solve community challenges.
As the Science Magazine (2016) video showcases, there may be a few technical glitches in the implementation of this idea...
2017 Bio-Polymer Cohort
Students face multiple challenges: improve the attractiveness of cassava as an agricultural crop by developing an industrial value chain use case for counterfeit proof cassava bioplastic that can be used as PLA 3D printing filament as well as in the development of a wearable biosensor.
Use locally available materials
Use university lab
Ensure maximum affordability
Scan literature for guidance on best industrial use blend
Maximum time available to develop first prototype = 6 months (1 semester)
Cassava biopolymer was created.
Sorbitol and Glycerol were to be tested as plasticizers.
4 factor Randomized Complete Block Design (RCBD)
Biopolymer density standard ASTM 792-91
First prototype developed in 3 months (1/2 of anticipated time) which caused a lot of internal celebration
Sorbitol was not readily available and difficult to procure. Fructose used instead.
Regulating oven temperature is key or you get squishy plastic. This took a significant amount of time and repeated trials.
Still working on completing the above product specification requirements
University of East Africa Baraton Students:
BSc in Agriculture (General Agriculture Option)-Junior
Kirika Miriti Kivuti
BSc in Chemistry (Biochemistry Option)-Senior
Bsc in Biotechnology-Senior
2017 Eco-Immunology and Oncovirus Cohort
Students were instructed to use a metagenomics approach to examine an ecological issue. The product use case is the affordable wearable biosensor. Technical specifications on what proteins or method to use were not given. Instead general boundaries were set:
Stay focused on DNA analysis.
Always choose the simplest method.
Innovation is about adaptation, not invention.
No medical intervention or treatment.
Focus on detection.
Figure out how to perform the research with tools and equipment available in a standard university laboratory.
Whatever your initial costs turn out to be, reduce these by 50%, ideally 75%.
Minimize risk and harm.'
Stay focused on the end user needs
This is an applied research project, not a theoretical research project. Hence, the only technical prowess that will impress is the ability to develop a commercial ready prototype within 12 months instead of the standard 2-3yrs
Where are you going to conduct clinical trials?
Cynanobacteria selected as the micro-organism (metagenomics). Response from mentors - approved as long as you spend time reading about cyanotoxins and explain how you are going to reduce risks and harm.
Breast Cancer selected as the use case. Response from mentors: you are making your life difficult. Aflatoxins and liver damage would be easier. Proceed knowing you will not have lab access for genomic sequencing. You must justify the environmental focus because CSTI is not a medical research facility, our focus is environmental research.
Working on cell free paper based method for biomarker protein identification.
Building on lessons from Ghanian researchers
iGem 2017 Ghanian team write up
Behind the scenes
Building on less
Finding a workable use case and gene sequence is a lot harder when human genes are the focus of investigation
Stay tuned for updates ...
University of East Africa Baraton Students:
Musvosvi Bliss Rutendo
BSc in Public Health-Senior
BSc in Biology (Biomedical Option)-Senior
Student Laboratory Assistant for Histology
Ochuodho Harrison Ouko
MSc in Biology (Biomedical Option)-In progress
BSc in Biology (Biomedical Option)
Published work: Microbial analysis of raw and boiled milk sold at Baraton center in Nandi
Position: Laboratory Assistant for Human Anatomy & Physiology and Medical Microbiology.
Kombe Jasco Nzai
BSc in Biology (Biomedical Option)-Senior
Student Laboratory Assistant for Microbiology and Molecular Biology
Cilia Ivy Kenyanya
BSc in Nursing-Junior
Nairobi Innovation Week 2018 Pitch
Ours Africa - Breast Cancer Biosensor
Cell free paper based genomic protein detection
Goal: Affordable Testing
Equipment partners welcome!