Team:Sheffield/Attributions

Attributions



Project Conceptualisation

Initially, the idea of the project came from one of our team members Ruby Kell and one of our advisors Mateusz Jurga. However, later on Piotr Janas, redirected the idea from examining both MRSA and UTIs, to just UTIs. This was to eliminate any false positives from commensals appearing in our sample. Urine is considered sterile, therefore culture urine and focus on UTIs.

  • Ruby Kell (Student)
  • Lucy Barnett (Student)
  • Piotr Janas (Student)
  • Mateusz Jurga (Advisor)
  • Dimitrios Michailidis (Supervisor)

Project Design (Science)

All Biologists (Harindi Jayakody, Ruby Kell, Thea Chrysostomou, Piotr Janas) researched current diagnostic tests and what was already in the field, and then collaborated with the rest of the Sheffield iGEM team to produce our final device. The team was guided by the supervisor Dimitrios Michailidis. During the development of the project, they all helped to arrange and attend meetings with relevant academics at the university of Sheffield, clinicians from abroad and microbiologists to ensure that the biology behind the idea was sound. They then went on to produce some antibiotic resistant bacterial strains by transformation of iGEM biobricks. These were initially used to produce bacterial growth curves, and then used for the 96 well plate reader experiments, which were then analysed. We have used Kanamycin, Chloramphenicol, Carbenicillin and wild type (control) as strains and we tested whether E. coli is resistant or sensitive to the particular antibiotics. Then using the well plate reader we obtained our results and analysed them.

  • Harindi Jayakody (Student)
  • Ruby Kell (Student)
  • Thea Chrysostomou (Student)
  • Piotr Janas (Student)
  • Dimitrios Michailidis (Supervisor)

Device

All engineers (Lucy Barnett, Emily Ingham and Caleb Parikh) researched previous methods for the estimation and detection of bacterial growth. Our aim was to construct a cheap device which was relatively easy to build and is able provide automated readings of a bacterial sample. During the development of this device meetings were arranged with academic supervisors to seek advice about the circuit construction and software implementation of the device. Once prototyping of the device had begun a lot of time was spent troubleshooting and making adjustments to the device, including additions such as the external casing was made. Software implementation was also being developed along the device with the aim of constructing a user-friendly interface for quick data interpretation.

  • Lucy Barnett (Student)
  • Emily Ingham (Student)
  • Caleb Parikh (Student)
  • Dimitrios Michailidis (Supervisor)

Modelling

For modelling our engineers (Lucy Barnett, Emily Ingham and Caleb Parikh) looked into the questions that we wanted to know about our device that we didn’t have time to find out with experiments. In the respect of investigating the bacterial growth response, we wanted to know what sort of time we would be expecting to wait for different starting inoculums of bacteria. Some meeting with advisor were arranged to discuss which would be the simplest and most effective way to answer this question. Some simple in lab experiments began, and a simple linear model was constructed to estimate the time it would take growth to be noticed depending on the initial inoculum.

  • Lucy Barnett (Student)
  • Emily Ingham (Student)
  • Caleb Parikh (Student)

Wiki

Uddhav Agarwal was the developer of the wiki, following the design provided by Dimitrios Michailidis.

Human Practices

Our supervisor Dimitrios lead our Human Practices campaign. A list of people and organisations that we have interviewed as part of our Humans Practices is provided.

Clinical Laboratories

  • Dr. Dimitris Sokratous- ANALYSIS-LAB in Cyprus (7/6) has given us insight how we should improve our biological techniques using (eucast.org) and that there is an existing machine in the market named Vitek.
  • Dr. Rohini Wandanamby in Sri Lanka (7/11) - recommended a liquid media to use (BHI broth) and which organism to use E.coli.
  • Barbara Bakalorz- Slaskie Laboratoria Analityczne in Poland (7/7) - GPs in broad EU use 2nd generation cephalosporins instead of trimethoprim/nitrofurantoin, suggested to apply our AMR detection system to veterinary labs and make sure you have a control system for contamination because very often urine is contaminated.

Academics

  • Robin Purhouse (6/22) - Recommended to look at photo-voltaic models, at optical properties of cell culture and how this will have an effect on our system.
  • David Hornby (7/3) - explained how urine samples are taken in hospitals (Mid stream urine culture), stated the main causes of increasing AMR worldwide and that quinolones are widely used in community for UTI treatment.
  • Graham Stafford (7/4) - has suggested to research NICE website to find relevant antibiotics for UTI.
  • Robert Poole (7/5) -put us in contact with a phd student specialising on AMR and advised to talk to the biosafety officer/surveillance department regarding the potential experiments we are going to run.
  • Hannah Southam (7/14) - mentioned that we need to know how many cells we put into the well plate. Also, pick where to use our device and then decide which antibiotics to use according to that, as different countries use different antibiotics as first line treatment for UTIs.eg, Poland, Greece/Cyprus use second generation cephalosporins but UK uses trimethoprim and nitrofurantoin.
  • Dr. Jim Gilmour (7/19) - told us to think about how we can determine whether bacteria start dying using just growth curves and use MIC to find out the minimal

Hospitals

  • Prevent X Diagnostic Lab (8/8)
  • Royal Hallamshire Hospital (7/8)
  • Urology Clinic (9/8)
  • Royal Liverpool Hospital(23/8)
  • Northern General Hospital (17/10)

Lab Space & Consumables

  • Molecular Biology & Biotechnology Department for allowing us to use the Perak Laboratories 1, after our supervisor Dimitrios Michailidis made the arrangements.
  • Dr Melanie Stapleton (Senior Lab Technician) and Sarah Noble - for general lab support and equipment.

Finance Support

  • The following people helped us with financial procedures.
    • James Bollington
    • Jenny Miller
    • Rachel Hammond
    • Mark Johnson

Management & Fundraising

  • Our supervisor Dimitrios Michailidis raised the funds for our project, organised recruitment and run the team. Mateusz Jurga provided general support with financial transcations. Lukas Jasaitis helped organise recruitment, and weekly management of the team.
    • Dimitrios Michailidis
    • Mateusz Jurga
    • Lukas Jasaitis

Presentation & Poster

The team worked on the presentation and poster for Boston guided by Dimitrios Michailidis.

Outreach

Ruby designed the outreach plans following the Sheffield iGEM 2016 manual created by Wesley Man Jessey. A few of our members helped execute the outreach event where they paired up with student teams and helped them design their own projects. The team invited students from secondary schools around Sheffield, provided them with an introduction to Synthetic Biology and thereafter gave them the opportunity to develop their own projects.

We would also like to thank the following people for liaising with colleges and helping with the organisation of the outreach event.

  • Ruby Kell (student)
  • Lucy Barnett (student)
  • Thea Chrysostomou (student)
  • Emily Ingham (student)
  • Caleb Parikh (student)
  • Lukas Jasaitis (advisor)
  • Dimitrios Michailidis (supervisor)
  • Michael Goudreault
  • Emma-Jayne Russell

General Support

We would like to thank the following people for helping us by providing general advice on our project.

  • Dr Stuart Casson
  • Prof Stephen Matcher
  • Helen Wright
  • Craig Bacon
  • Palmer Dasha
  • Prof Kathryn Ayscough