Team:Kent/Attributions

Project Design


Team Kent along with our advisers decided on our project. After a series of brainstorming sessions, we decided on a project aimed to synthesise magnetite nanoparticles in E. coli ‘Mag-nano-tite’ was chosen. We felt that this would be a relevant project based on current research, that explores the numerous applications for magnetic nanoparticles including waste or heavy metal removal and drug delivery (Kumari et al 2015) (Berry et al 2003) (Estelrich et al 2015). We saw that some bacteria synthesise magnetosomes which are organelles that contain and synthesis magnetite crystals. Through our research we discovered Mam genes, these are a group of genes which encode proteins that aid in magnetite crystal formation (Schüler 2007). The limited literature on these encoded proteins eventually became a focus in our project.

Modelling


We have introduced a new type of mathematical modelling; this novel Big Data topic modelling approach has been introduced to iGEM for the purpose of human practices. Kritam, a team member, used topic modelling to uncover thematic structure in document collections. This provided a simple way to analyse large volumes of unlabelled text.

Wet Lab


Eight of the ten Team Kent members for iGEM this year are bioscience or chemistry students. Rita, Braulio, Jasmine, Sam, Hanya, Andrew, Rachel and Daniie together underwent a learning experience in the wet-lab. Together they carried out a vast range of experiments which included Gibson Assembly, PCR (Polymerase Chain Reaction), Ligation, TEM (Transmission Electron Microscopy) and AFM (Atomic Force Microscopy) imaging.

Protocols, experiments and results can be viewed here.

Integrated Human Practices


Human practices were explored by several members of Team Kent. Kritam, Braulio and Rita visited a secondary school to educate pupils about synthetic biology here, we gained perspective and external opinions on Mag-nano-tite. This provided a wider picture on the synthesis of our magnetite nano-particles which we had not previously considered synthesising chemically. Rachel, Braulio, Jasmine and Sam were ambassadors for iGEM at open days for University ofKent. Here, the team interacted with the public, shared our project ideas as well educating many on the iGEM competition. Daniie interviewed an expert in the magnetic nanoparticle area, who provided insight into the chemical synthesis of magnetite nanoparticles. Kritam, through topic modelling provided a novel means for quantify human practices in iGEM. More information on Human Practices can be found here.

Writing


Throughout the course of our iGEM project the Kent team have been carrying out research including reading related articles to our project. We have discovered that there is not a lot of background information on our chosen project, as well as lack of information on the proteins we have decided to engineer. We have had weekly meetings where we discuss, share thoughts and ideas, as well as make decisions for the benefit of this group. We have recorded the progress of this project in our notebook which can be found here. (hyperlink to notebook) We have designed posters, prepared presentations and written detailed explanations into our project that the whole team has contributed to. The wiki was organised by our team organiser Rachel, and coded by Aleksandra.

The Team


Kritam Thapa

Kritam’s main contributions was as a member of the Human Practice team. He was involved in the outreach aspect of the project. He gave an oral presentation at an outstanding school where he shared and received ideas from the students. Key information gathered from this event has proven central in some decisions we have made in the development of the project. Kritam developed the modelling for our project, he also wrote code for software to be used for the quantitative analysis for integrated human practice via LDA topic modelling.

Daniie Smith

Daniie’s main contributions to the team were as a wet lab member as well as her work for Human Practices. Her work provided a unique angle to this project which allowed us to investigate into alternate methods to chemically synthesise of magnetite nanoparticles. Daniie spoke to experts in the nanoparticle field which gave us crucial insight into the field, this made her a valuable member of the policy and practice team. As a wet lab team member her main contributions were in PCR and the EM imaging of nanoparticles.

Andrew Seaton

Andrew’s main contributions was as a member of the wet lab team and as a member of ‘The Protein Team’, carrying out the expressions of our proteins as well as the extraction and purification of our proteins. Andrew was involved in the validation of our proteins using SDS PAGE and photospectrometry.

Samantha Weetman

Sam’s main contributions was as a member of the wet lab team. She was a member of ‘The Protein Team’, carrying out the expressions of our proteins as well as the extraction and purification of our proteins. Sam was also involved in the characterisation and validation of our proteins using SDS PAGE and photospectrometry.

Aleksandra Zawlocka

Aleksandra’s main contributions to our project were as the designer of our team identity, and she coded our wiki page. She expertly designed our logos, wrote code and prepared several visual assets for our page. Aleksandra also designed our posters and our team banner.

Jazzy Cornish

Jasmine’s main contributions to the team were as a wet lab member, in BioBrick construction and outreach. She used restriction enzyme cutting, Gibson assembly and ligation techniques to construct several of our BioBricks. Jasmine was part of the outreach team, where she attended speaking engagements at the University of Westminster and Kent, engaging with the public and fellow iGEM competitors. Jasmine also engaged in the improvement of previous project.

Braulio Carrillo

Braulio’s contributions to the team was as a wet lab member, he was involved in human practices and collaboration. Braulio was involved in the in vitro and in vivo protein expression, purification and imaging. Braulio was a key member of the human practices team, attending speaking engagements at Simon Langton Grammar School, University of Kent and the University of Westminster. Braulio will also present at the iGEM jamboree and was involved in the Team Kent iGEM collaboration with UEA.

Rita Adriani

Rita was a key member of the wet lab team, using ligation, Gibson assembly to form viable BioBricks as Rita also contributed to the improvement of a previous iGEM project. Rita was a member of the human practices team, she attended speaking engagements at Simon Langton Grammar School, University of Kent and the University of Westminster where she also presented.

Hanya Benotmane

Hanya’s main contributions were as the social media secretary for Mag-nano-tite. She was in charge of all social media outlets where she continually interacted with other iGEM teams around the world. As a result, Hanya led the collaboration for our team. She organised the collaboration with UEA, where she analysed samples for their project using AFM. She also worked with UC Davis collaborating on ideas for their website iGEMMatch.org. Hanya was also a wet lab member, involved in the AFM imaging of our samples as well as that of a previous iGEM project, she was also involved in human practices.

Rachel Adeyemi

Rachel’s main contribution to this project was as the organiser/team secretary. Rachel contributed as the safety officer, completing the safety documentation required for our project as well as ensuring the lab environment remained conducive for safe work. Rachel contributed with her writing, she aided in the organisation of our wiki, notebook and documented our weekly meetings and brainstorming sessions. Rachel was also a wet lab member undergoing techniques such as Gibson assembly and protein validation. Rachel was involved in human practices where she attended speaking engagements at the University of Kent.

Supervisors


  • Wei-Feng Xue
  • Mark Shephard

Advisors


  • Ben Blakeman
  • Rosie Gough
  • Lee Mun Ching

Acknowledgement


  • Dr. Marc Williamson (Nanoparticle expert)
  • Rokas Juodeikis (Magnetosome expert)
  • Radoslaw Kowalski (Topic Modelling expert)
  • School of Biosciences Lab Technical Support Team headed by Julian Cook and Dr Rosalyn Masterton – For their continuous support providing advice, materials and training in the correct use of equipment.
  • University of Kent – For providing us with the facilities and materials to conduct our project as well as funding for transportation.
  • SnapGene – For providing software that allowed us to visualise our plasmid sequences, primers and fragments. This valuable piece of software allowed us to annotate various features and design primers.
  • BBSRC, The Society for Experimental Biology, The Wellcome Trust - for providing the crucial funding for our project.
  • IDT - for providing us with the DNA fragments
  • Labster (Training software)
  • MathWorks (Matlab software)
  • iGEM Competition – For the vision behind this competition and providing this opportunity to experience, learn and grow.

References


1. Madhu Kumari, Charles U. Pittman Jr. and Dinesh Mohan. (2015). Heavy metals [chromium (VI) and lead (II)] removal from water using mesoporous magnetite (Fe3O4) nanospheres. Journal of Colloid and Interface Science. 442 (1), 120-132.

2. Catherine C. Berry and Adam S.G. Curtis. (2003). Functionalisation of magnetic nanoparticles for applications in biomedicine. JOURNAL OF PHYSICS D: APPLIED PHYSICS. 36 (1), 198-206.

3. Joan Estelrich, Elvira Escribano, Josep Queralt and Maria Antònia Busquets. (2015). Iron Oxide Nanoparticles for Magnetically-Guided and Magnetically-Responsive Drug Delivery. Internation Journal of Molecular Science. 16 (4), 8070-8101.

4. Dirk Schüler (2007). Magnetoreception and Magnetosomes in Bacteria. Berlin: Springer-Verlag. 3- 323.

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