Team:Cork Ireland/Practices
Outreach
Taking advantage of a medical summer elective at UCC, we decided as part of our project to send one of our members to an African hospital in Malawi, in order to investigate the usefulness of our detection system in a third world hospital lab as well as to increase the awareness of synthetic biology among the Malawian people. This was an opportunity to get up close and personal to investigate the logistic potential and receive feedback regarding our novel method of DNA diagnostics in a developing countries’ hospital laboratory.
Donnchadh spent the month of June in Malawi at Nkhoma Hospital. Nkhoma Mission Hospital is a 220-bed facility and includes all major departments. The hospital's primary catchment area is the surrounding rural population of 32,000 people, but it serves patients from all over Malawi and it’s neighbouring country Mozambique. It offers inpatient and outpatient care on site and conducts mobile clinics within its catchment area. The laboratory is an essential part of patient care at Nkhoma Hospital. It analyses samples from almost every patient that comes to the hospital.
The laboratory performs the following analysis: Haemoglobin, Malaria, Full Blood Count, Blood Transfusions, Sickle cell, Erythrocyte Sedimentation Rate, Urine & Stool Analysis, Pregnancy, HIV, Syphilis, Hepatitis B, Ascites, CSF and pleural fluid analysis, Meningococcal Antigen, and CD4 analysis. It also has a equipment which can perform multiple analyses on blood serum for liver function tests, Lactate, Glucose, Sodium, Potassium, Bilirubin, and many other beneficial chemical analyses.
Integrating Human Practices
When Donnchadh arrived at Nkhoma Hospital, his main goal was to identify a potential application for our novel DNA detection system. He spent the first few days at the Hospital speaking to the doctors, nursing staff and lab technicians about the diagnostic facilities available at there as well as other hospitals and health care clinics in Malawi.
It was evident that Tuberculosis (TB), an infectious disease caused predominantly by Mycobacterium tuberculosis, was a serious problem and one that our project needed to target. According to the World Health Organisation (WHO), one-third of the world's population is thought to have been infected with M. tuberculosis and new infections occur in about 1% of the population each year. WHO’s sixteenth global report on tuberculosis reported that there was between 1.3 and 1.5 million associated deaths and most of these were in developing countries. More people in the developing world contract tuberculosis largely due to high rates of HIV infection and the corresponding development of AIDS. Donnchadh was in constant communication with our iGEM team regarding the lab facilities available and the potential use and application of our DNA detection system. We decided to extensively research the requirements for and applications of an easy to use, low cost and reliable TB detector for use in third world hospital labs. Donnchadh’s feedback was very helpful but see what the lab technicians had to say below!
Our proposed Bacterial-DNA Detection System
We constructed a survey for the laboratory staff which explained our project, the detection system and its potential applications. We investigated what knowledge the laboratory staff had regarding synthetic biology and whether they thought that our detection system could be implemented in their laboratory. Click here to see the survey.
The feedback we received was very positive. As an initial impression it was felt that our project may ‘result in the development or use of highly sensitive and specific methods for detecting pathogens.. The method may also be time efficient’ and ‘It might help us to run tests quickly so our patients have results on time.
Knowledge regarding synthetic biology was diverse. Some saying that it is “using bacteria to make vaccines and drugs” and others explaining that they ‘don’t know anything about synthetic biology’.
There were no concerns regarding the use of synthetic biology except one lab assistant worrying about costs because ‘the use of technology is expensive; especially in developing countries’.
Everyone surveyed at Nkhoma Hosptial laboratory answered that they would like to use our new DNA detection system and that they felt there was potential for its implementation. Our detection system was seen as helpful because it’s ‘very fast, easy to use, cost efficient’... ’and people will be helped in getting treatment on time’.
Challenges
The Laboratory Manager pointed out potential barriers as he felt ‘it will be difficult to sustain the service’. He felt there would be ‘problems in terms of who to order the reagents’ and for the ’training of personnel on when to order and in what condition’ and also that ‘since it will be a new test, stigma will crop in’. He also felt that the biggest problems were with regard to ‘consumables, educators and training, logistic support, electricity, dust, protocol, and bio-safety’.
One of the laboratory assistants felt that ‘since we don’t have any idea or knowledge how it works, doctors might not be able to accept the results unless they are oriented on how it works. We also need to be trained on the working principle’. She felt that the biggest problems that she could foresee were the ‘lack of educators, inadequate logistic support and insufficient monitoring of test quality’.
Despite the barriers that must be overcome, they felt that ‘this is a good development to our hospital and country since the test will require few reagents’ and that ‘the project is good’ and that there is ‘no need of big storage facilities’.
Including the Community
Donnchadh went to several out-reach clinics and schools to increase awareness of synthetic biology among the Malawian people. Donnchadh used a translator to communicate with the locals and gave a brief presentation to the mothers who used to come to the out-reach clinics for vaccinating their children. He explained to the iGEM team when he came back that ‘the outreach was a great chance to meet the locals and talk to them about the potential benefits of synthetic biology. I told them that we were hoping to use bacteria to detect viruses and the things that make people sick. They all seemed very positive about the project and about synthetic biology as a whole.
Donnchadh also went to the local primary and secondary schools. He gave a presentation to each of the classes. The teachers were happy to learn from the presentation too and informed Donnchadh after he left the school that he had augmented interest in science among the kids and that the presentation had ‘inspired the teachers to get more involved in the world of science and synthetic biology too’.
Witchdoctors and Basehunter
While at the outreach clinics and schools, Donnchadh learned about the culture of witchdoctors in Malawi- a strong tradition even to this day. The witchdoctors are very important in Malawi and have a lot of influence over the people and are seen as educators as well as healers.
Through the mission hospital, Donnchadh organised to meet the witchdoctor with a group a medics and a translator. The witchdoctor explained how her powers work and her role in society. She spoke about the herbal treatment she advises to the sick people who visit her.
Donnchadh spoke to her about synthetic biology and our DNA detection project. The witchdoctor thought the project was a great idea and noted the importance of science and education for the Malawian people. She also mentioned that she recommends visiting a medical professional to people that she will not be able to help.
An Adaptive Future
The feedback from the locals and lab technicians regarding synthetic biology and our project was extremely positive. The implementation of our DNA test kits at Nkhoma Mission Hospital is real possibility and welcomed by all.
‘My Malawian experience was fantastic, the people are so friendly and supportive of our work. I definitely see a role for our DNA detection system in resource poor hospitals not only in this hospital but hospitals all over Africa. Nkhoma a major hospital in Malawi but our project could be used in many other hospitals with poorer resourced labs as well. Now the next step the Giant Jamboree!’
Our Synthetic Biology Community Immersion Project
In the recent years, Cork has been identified as a global hub for synthetic biology and biotechnology. This is evident by the fact that 11 of the top 15 pharmaceutical companies in the world have a branch in Cork. IndieBio, formerly known as SynBio Axlr8r, is the world’s first synthetic biology accelerator programme and is one of the upcoming players in Cork’s synthetic biology community. This programme provides world class mentorship, state of the art labspace and seed funding of $50,000 to multiple synthetic biology startups each summer since May 2014. While we embarked on our iGEM journey at the UCC labs we took this opportunity to meet and get to know the nine biotech startups from around the world.
Forma Labs, Ireland’s first and only biomaker space was established in Cork this year. Despite formally being opened on the 3rd of September 2015 our team was involved since the very beginning. Our team was delighted to get involved and become pioneers in this upcoming community of synbio lovers! This movement is a great benefit for all involved and is a platform for learning and creativity.
We had the opportunity to get to know the UCL iGEM team when they came to visit Cork for the IndeBio Demo Dinner and Summer Party. We took this opportunity to show them Forma Labs and we talked about our vision for the community project. We learned about London Hacker Space and the potential for such an amazing community to work together in unique and modern ways. We can’t wait to see them at the Giant Jamboree!!
We spoke at the SynBio Future Conference about iGEM, synthetic biology and projects that were carried out by last years Cork iGEM team. We got to meet biohackers, academics, students and mentors from around the world who had come together to discuss synthetic biology. We were delighted to be invited to speak at a workshop for Masters students at the Cork Institute of Technology in April about the work we do as an iGEM team.
This year, three of our members gained invaluable experience interning for IndieBio during the summer. This opportunities was only made possible because our iGEM team is recognised as an enthusiastic, hardworking and motivated team looking to get involved in the local synthetic biology community.
The internships were varied, stimulating and expanded our horizons regarding synthetic biology on a global level. Donnchadh interned as an Event Manager to organise the globally publicised Summer Party and Demo Dinner, Shama interned as Assistant Director and Timothy interned with one of the companies that participated in the accelerator, Biocellection, who aim to make a sustainable fish food.
Shama worked closely with the nine biotech startups administering, organising and mentoring these groups. We learned a lot about the biotech world ranging from distinguished mentors and advisors to partners and investors. Having spent every day in the lab with these enthusiastic young synbio startups, many of whom were previous iGEM team members, was very exciting and inspired us for own futures. Daily lab life included a mixture of lab work, research and mentorship while the startup teams worked in one lab. Shama even got to interview the teams and learn more about how their synthetic biology companies are going to change the world for the better!
Timothy learnt a lot from BioCellection. Miranda and Jeanny, the founders, are both final year university students in the University of Pennsylvania and University of Toronto respectively. Miranda took part in iGEM last year. BioCellection is working toward creating a by-catch free fish food made from yeast and algae . Their yeast eats plastic and produces all the components required for good quality fish food. Their aim is to save the world oceans by preventing over fishing and getting rid of the ever accumulating plastic waste pollution. This is an excellent example of how synthetic biology has the potential to help our planet and we were more than happy to help them out too!
When Donnchadh returned to Ireland after carrying out the outreach for our detector in Malawi, he teamed up with Shama to organise the Summer Party and Demo Dinner that took place on the 12th of August. This event was attended by the hundreds, viewed by thousands and took place in the historic Cork City Gaol. The teams delivered amazing pitches to an audience that consisted of investors, mentors, academics, friends and family. Cork iGEM were instrumental in making this event a success. We welcomed and registered the guests and talked about iGEM & synthetic biology to everyone who would listen - even Cork City’s Lord Mayor wasn’t an exception. We watched how far these teams have progressed, admired their success and wish them the best in the future.
These internships unveiled the global synthetic biology community and how iGEM plays a foundational part in it. We spent the summer with people who shared the same enthusiasm and understanding of synthetic biology, genetics and biotechnology. We learnt about what's involved in creating a biotech startup, inspiring our own futures! Despite the challenge of working on our iGEM project and carrying out these internships, we immersed ourselves in Cork’s synthetic biology community and had an amazing summer. Our iGEM project was not just a research project - we became part of the community and have helped it to grow.
Interviews
Interview with Cathal Garvey
As we have mentioned above, IndieBio EU is a startup accelerator focused on biotechnology and synthetic biology based in Cork City. The Cork iGEM team and the Indie Bio wet labs are both based in University College Cork. IndieBio is an example of how the theoretical, ideological aspects of synthetic biology can become a practical and commercially-viable reality through funding and mentorship. This is interview is an attempt to learn about the person who runs the programme.
Cathal Garvey is the Director of IndieBio EU.
His work includes co-founding Forma Labs, a community lab in Cork City and Ireland’s first biohacker space and working as curator of Grow Your Own, an exhibit on DIY biology at the Science Gallery Dublin. He is also known as the inventor of the DremelFuge, a small 3D printable centrifuge. The plans are online for anyone to access.
Cathal discussing how he first got involved in DIY Biology
At the same time that he was feeling "dissatisfied" with his PhD work in cancer biology, Cathal encountered the DIY biology community online. "...I saw that there were people around the world just getting involved in biology under the heading DIY Bio and a lot of these people had not gone to university like I had. Now there’s two ways you can approach this – a lot of people who have become card carrying professors of whatever often feel that when their discipline gets co-opted outside academia, outside industry, or outside the normal strictures I think that they feel a bit threatened. They think, ‘I became an expert at this …and I became the sort of person that generalists come and talk to by working really hard for years so you shouldn’t be able to call yourself a molecular biologist without going through the same difficulty that I did. So… the other way of approaching this is ‘I love my field and I want to see it become more important in society and that’s never going to happen as long as people can only get involved after eight years in college."
On getting a license for the Biosafty Level 1 lab he set up in his parents' home
Cathal was granted a license from Ireland’s Environmental Protection Agency to create genetically modified microbes in his parents' home. His is the only such license in Ireland held by an individual, all others being held by academic or industrial labs. "I set up a lab there and invited the EPA out to take a look and them… they gave me the license. They took their time thinking about it, I understand it went to high levels of the EPA to get a sign off on it and ultimately they decided to take a risk on me and I’m grateful for that because in the end I didn’t cause any problems for them. I ran a pretty normal molecular biology lab at the lowest category of risk. I tried to generate a few open source biotechnology products, I had some mixed results, nothing marketable and ultimately the start-up failed. I learned a lot from that failure and looking back I did everything wrong. So you know, nothing that would upset a regulator."
Cathal on Synthetic Biology's impact on industry
"Synthetic Biology brings down that risk by allowing much more rapid development times and a much more fine-grained control over the design of your product or bio-product."
Advice for prospective Biotech start-ups
After setting up his lab, Cathal founded his own biotech/synthetic biology company called GlowBiotics. Although it failed, his experience has proved useful in his current role as director of the IndieBio EU programme. Now he advises startups going through IndieBio on mistakes they should avoid in order to be successful. This is his advice to anyone considering creating a biotech start-up. "Don’t go it alone, don’t be too risk-averse."
"I would never recommend that anyone go out and do a start-up on their own, because this was too much, there’s paperwork, there’s regulations, there’s tax returns and accountancy. And then there’s the actual science, and that science can be very time-critical; it can occupy your time. And then there’s marketing; what good is a product if you don’t have customers. You need to be able, at the very first stage you need to know who your customer is, find them, meet them, build up this relationship before you ever have a product to sell them and find out what they want. That is too much work for one person to do all these different things, wear all these different hats.
You also have to have someone who checks your ideas and says what you’re doing is really stupid, you know, that [going it alone] probably would have been the single biggest thing that led to my failure."
"...if you go out to become a start-up in biotech you are basically doing an applied engineering project now that’s not pure science, you don’t need p-values as long as you know the thing works."
Interview With Glow Diagnostics
GlowDx are a biotech startup that participated in the IndieBio EU accelerator in Cork this summer. They aim to deliver new diagnostic platforms to the developing world with their main target being tropical diseases like dengue.
Over the summer, we got to know the founders of GlowDx, Blaine Doyle, Yensi Flores and Aisling Finn as the IndieBio labs are based only minutes away from us. We were quite lucky to build such a fantastic relationship with a diagnostic company as they gave us a lot of insight into building Basehunter in a realistic and user-friendly way.
Shama and TImothy got a chance to interview CEO, Blaine Doyle and find out more about GlowDx and their thoughts on Basehunter.
How would you describe GlowDx? What is the goal of GlowDx?
GlowDx is a diagnostics company that employs novel molecular biology to provide developing countries with high quality diagnostic tests; focusing on neglected tropical diseases. We are creating a DNA-computer in a test-tube; which can diagnose human disease. Molecular logic gates allow us to provide increased sensitivity & specificity while reducing costs. Meaning our “appropriate technology” is accessible to those who need it most.
What motivated you and your fellow co-founders to start working on GlowDx?
It started out when Yensi, Aisling and I were sitting down and talking about infectious disease in developing countries like Honduras where Yensi is from. Dengue has affected Yensi personal life as well as her professional life.
Yensi got Dengue when she was 8 years of age and she also nearly lost her dad who was travelling between Honduras and Geneva at the time. He had been infected with Dengue earlier that week, recovered and decided it was safe to travel. It turned out that it wasn't and during the flight experienced a hemorrhagic fever and the airport had an ambulance waiting for him in Geneva. That was a horrible experience for him.
She set up the first molecular biology lab in Honduras and has past experience in running that lab. People who visited just could not be diagnosed or would end up misdiagnosed because they wouldn’t have a proper procedure for the diseases. She also noticed the lack of supply chain for diagnostics, those suppliers that could provide diagnostics had to charge massive prices to make a profit. So we decided to set up the company to provide diagnostics for developing countries and give them access to quick and accurate diagnostics.
Describe the concept of a diagnostic DNA computer?
All of the current molecular diagnostic products on the market have three things in common; they require specialized training, a lab fitted with expensive equipment and an end-user who has the buying power.
Isothermal amplification technologies have been developed to tackle these issues but many have been proven to have high false positive rates and under-perform in the field.
Using DNA-Computing we can modify the performance of these isothermal amplification technologies, eliminating false positives but not further complicating the protocol.
How will your product be used once it’s fully developed?
Any type of laboratory or clinic can diagnose a wide range of diseases quickly by taking a single blood sample and placing it in the reaction tube; this tube contains our DNA computer! If the pathogen is present the tube will glow giving a rapid and reliable result.
Why is so important to get an accurate diagnosis of a disease before treatment can start?
Many diseases can present initially with similar symptoms such as a headache, body ache or fatigue; but medically they are different. A treatment that could cure one type of illness could potentially be harmful in another. Molecular diagnostic tests allow us to distinguish between diseases and result in the patient getting the correct treatment.
What advantages will your product have over other diagnostic methods?
Our product is designed to work in low resource settings, regardless of specialized equipment or trained personnel. Using our DNA-computing technology, the cost of a single test is 10 times cheaper than current molecular tests on the market. Using the test is simple; determining the results even simpler! The tube glows to show a positive result!
How much will this diagnostic cost?
At the moment, the cost of 1 test in Honduras is $113 whereas the average Honduran only earns $80 a week which put these diagnostic tests far from their reach. Our test costs $3, yes that’s right, $3.
For each reaction, our reagents cost $1.56, tubes cost $0.46 and fluorochrome costs $0.76 which gives a total cost of $2.78. Our kit will be able to run 56 reactions and the price of this kit will be $132.94.
Where do you eventually hope to see your product being used?
We will deliver reliable diagnostics to the poorest & most remote areas of Central America & then the World!
When do you hope your product will reach the market?
Validation kicks off in November, rounding off right in time for dengue season next year!
Where do you see GlowDx in the future?
As a leader in developing diagnostic tests, tailored to the low resource regions of the world. We are first targeting neglected tropical diseases but will expand our portfolio into diagnosing diseases that universally affect humanity.
What do you think of iGEM and the buzzing synthetic biology community in Cork?
It’s great that one of the diseases you have targeted is Tuberculosis because it is so hard to culture, you are using clever molecular methods along with basic culture methods which get a rapid diagnosis of Tuberculosis compared to the available methods, this is the gold standard all over the world and is applicable to almost every lab.
For example, when I was in Honduras, they had a microbiology lab in the main hospital and they would have to common culturing methods but they were still using very slow growing methods for culturing TB.
In the last 5 years the WHO and The Foundation of Renovated Diagnostics have put an emphasis on investment into diagnostics for developing countries. Diagnostics are central to an intervention with the patient. Unless they have a suitable diagnostic, there won’t be any progress and they won’t get the correct treatment on the other side. For a student team to be able to create this can have a massive impact on the world.
From what I’ve seen over the summer, this year’s iGEM team is very diverse and each of you have an area of expertise and traits that you bring to the team. You are a very talented group of students. Good luck in Boston!
Advice from Dr. Brigid Lucey
In our talks with experienced biomedical scientist, Dr. Brigid Lucey, we found that a niche exists even in developed labs for a rapid diagnostic for TB. As Mycobacterium tuberculosis is slow growing, it is difficult to culture. For this reason, lab results are often delayed even weeks for a confirmation of results. Basehunter could provide a simple and rapid method to identify M. tuberculosis in samples. For this reason we designed a Mycobacterium tuberculosis detector and began to verify that it functions as well as the other detectors. In this way, our Human practices investigations highlighted a real world problem that we sought to address.