Pre-June

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February

• Team Kent for iGEM 2016 was formed.
• We had our first iGEM meeting where we got acquainted with some of the team members.
• We also met with our team supervisor
• The iGEM timeline was discussed and key dates highlighted.
  • October 27-31 – iGEM Jamboree
  • Submissions deadline – 21 st October 2016
  • October 19 – Wiki-freeze
• We discussed our aims and goals for our project.
• Specific medal criteria – Bronze, Silver, Gold
• A team organiser and social media officer was appointed.

March

• Our iGEM team was complete 10 students, 2 supervisors and 3 advisors.
• We completed our official iGEM registration individually and as a team.
• We began establishing our plans for the summer.
  • We were appointed a space in the bioscience lab.
  • We would have weekly meeting from the start of our summer projects.
• We began brainstorming for our project.
  • Problem based approach - What problems needed to be addressed?
  • Are we inventing something novel? Are we improving something that has already been done?
  • How can we approach a problem that has already been addressed to get a different response?
  • Is this project feasible in the time available?
  • Is there a sensible approach for validation?
  • How will we explore this project?
• We viewed the track selections for iGEM
  • Which track would our project lay in?
• Tracks
  • Diagnostics
  • Energy
  • Environment
  • Food and nutrition
  • Information processing
  • Manufacturing
  • Therapeutics
  • Art and design
  • Hardware
  • Measurement
  • Software
• We began exploring previous iGEM projects by looking at previous team wikis.
• Our ideas
  • Bacterial Batteries
  • Magnetic bacteria
    • To conduct energy
    • Combat heavy metal poisoning
    • Lead
  • CRISPR – specific alteration of genomes
  • Material formation – with applications to fibre formation (continuation of nanowire project) (fibre formation an area of Dr Xue’s expertise)
  • Magnetic nanowires to conduct electricity?

April

• The brainstorming continued.
  • Bacteria that deals with free radicals
    • Fluorescent proteins that detect the radicals
  • Fluorescent proteins
    • For detection
  • Bacteria which grows hair
    • Clear applications to this
  • Swimming bacteria
  • Protein cages for drugs (be transported through Tat pathway)
  • Protein sculptures – visual
• We re-visited the idea of magnetic bacteria.
• We started researching magnetic bacteria species.

May

• We continued brainstorming ideas
  • Solar panels
    • Harnessing photosynthetic capability of bacteria
    • Phylum cyanobacteria (slow)
    • Researchers are thinking of modifying the bacteria
    • Current problems:
      • Removal of waste material (solar panel practically inaccessible after installation)
    • Efficiency of energy conversion, only 8% when solar panel gives 40%
    • Evolved to protect themselves from full sunlight, hence, low efficiency
  • Bacteria antimicrobial peptides (protein targeting)
    • To combat infections
    • Here, the protein is the drug
  • Bacteria preventing the growth of other bacteria

• Exam season!
• After months of brainstorming it was time to make a decision.
• We revisited an idea we had been discussion from our first brainstorming session.
• Magneto bacteria
  • It has been ‘tricked’ to bio-mineralizing crystals is which iron was replace with other metals
  • By growing the bacteria in a solution with a high concentration of both metals
  • Shown that it can incorporate manganese into the crystal structure of magnetite
  • Some success with cobalt
  • Uses: waste removal or drug delivery
• We started researching relevant literature relating to this topic
  • What are the key proteins? Can we obtain them?
  • Can it be incorporated into E.coli
  • What are the applications.
• We created a google drive where would feed in information throughout our project.

June

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May 31- June 5

• We began to gather scientific papers (PubMed, WebofKnowledge, Science Direct) to post on to our shared folder.
• We explored the iGEM archives for similar ideas identify Bio-bricks (Mam proteins?)
• Identify key words to search magnetosomes, MMS6 protein, nano-particles.

June 6 - June 12

• We began to plan how we would conduct our experiments.
  • What genes are relevant?
  • Can we obtain them
  • Do we need specific strains of E. coli?
  • Can we purchase these strains?
  • If not who do we speak to, to obtain these strains?
  • What safety risks do these pose?

June 13 - June 19

• We began to obtain sequences we would use.
• It was important here to start to identify the experiments we were going to use.

June 20 - June 26

• We continue reading through and understanding the relevant literature.
• We began to understand our safety implications of our project.

July

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June 27 th – 3 rd July (Week 1)

Day 1

• We received our lab induction. We received training on how to use unfamiliar equipment.
• Having already researched the different protocols we would be using during our project we conducted risk assessments.
• We received training on the correct use and disposal of waste and materials.
• We were appointed different plasmids:
  • pET3a mamX/mamT/mamP
  • pET23B SecS mamX/ mamT/ mamP
  • pSB1A3 RFP
  • pEC86
  • pSB1c3 RFP
  • pET3a
  • pSB1C3
• We began writing our project descriptions for the upcoming deadline.
• We set up our social media accounts: Twitter,
• Facebook and Instagram.

Day 2

• We made LB plates and broth ensuring to add the relevant antibiotics (ampicillin or chloramphenicol).

Day 3

• Parts from our distribution kits were re-suspended.
• Our plasmids were transformed in top10 cells and left overnight for 15-18hours incubation.

Day 4

• Re-streaks were performed on successful transformations.
• Unsuccessful transformations were repeated.
• The writing of our project was continued.
• Registration for a student account for Enthought Canopy,

• Tutorials were completed on TutorialSpoint/Python
• We attempted to ‘scrape’ one iGEM wiki

July 4 th – July 10 th (Week 2)

Day 5

• Liquid cultures were prepared frim our transformed cells.
• Using SnapGene we carried out plasmid map analysis using Snapgene to identify compatible restriction sites on our individual plasmids.

Day 6

• Our plasmids were purified from the overnight liquid cultures.
• The concentration of the DNA of our individual plasmids were determined.
• Restriction enzyme digests were conducted based on the restriction sites identified on the plasmid maps including the appropriate buffer.
  • pET3a – Xbal, HindIII, promega E
  • pET3a mamP – Xbal, EcoRI, promega H
  • pET3a mamT – Xbal, HindIII, promega E
  • pET3a mamX – Xbal, HindIII, promega E
  • pET23b mamP – NdeI, EcoRV, promega D
  • pET23b mamT – XbaL, PstI, promega H
  • pET23b mamX – NdeI, EcoRV, promega D
  • pET23b mamP – NdeI, EcoRV, promega D
  • pEC86 – Ndel, EcoRV, promega D

Day 7

• Agarose gels were conducted to validate our various plasmids.
• We uploaded our project description onto our wiki
• Gels were imaged.

Day 8

• Troubleshooting began who electrophoresis gels which were unsuccessful.

Day 9

• pSB1C3 RFP and pSB1A3 RFP plasmids were validated.

July 11 th – July 17 th (Week 3)

Day 10

• Gel extraction protocols were used to purify validated plasmids.
• Liquid cultures were prepared to form glycerol stocks from validated plasmids.
• We prepared our outreach presentations for Simon
• Langton Grammar School for Boys Canterbury.

Day 11

• We successfully gave outreach presentations at Simon
• Langton Grammar School for Boys Canterbury.
• Two presentations delivered to physics and biology classes respectively.
• Questions from both physics classes were documented.

Day 12

• We continued with the validation of our individual plasmids with the aim to validate all our plasmids.
• Gel electrophoresis gels were continued.
• Plasmids pET3a and pET23b sec.S mamT/ mamP/ mamX were validated.

Day 13

• Plasmids pET3a and pET23b sec.S mamT/ mamP awere transformed into BL21 cells.
• Liquid cultures were prepared from the Top10 constructs of Plasmids pET3a and pET23b SecS mamT/ mamP

Day 14

• Glycerol stocks were made for pet3aMamT and psb1c3, pSB1C3 RFP and pSB1A3 RFP.
• Liquid cultures were made for these plasmids
• Plasmid purification was done for the necessary plasmids to build up the DNA stocks

July 18 th – July 24 th (Week 4)

Day 15

• Liquid cultures from BL21 cells containing SecS.MamX/MamT/MamP plasmids.
• Using SnapGene we looked at primer sequences in preparation for PCR.
• We began brainstorming for the iGEM meet up at the University of Westminster on August 17-19 th

Day 16

• We gathered detailed the sequences of the Mam proteins using their respective SnapGene
• We ensure that we validated the sequences UniProt data and found the correct open reading frames.
• We began growing up liquid cultures in preparation for the purification of our proteins MamP and MamT.

Day 17

• We finished gathering possible primer sequences for our Mam proteins.
• We began protein preparations for protein expression and purification.
• MamP, MamX and MamT grown in

Day 18

• Buffers were prepared.
  • Lower Tris buffer prepared using: 1.5M Tris, 0.4% SDS, pH 8.8
  • Upper Tris buffer prepared using: 1M Tris, 0.4% SDS, pH 6.8
  • Tris-Glycine running buffer prepared – 30g Tris base, 144g Glycine, 150ml SDS (1.5% w/v)
• Liquid cultures from BL21 cells were made from transformed MamX, MamT and MamP cells and incubated overnight.

Day 19

• SDS page gels was made.
• Samples taken from the liquid cultures were boiled to denatured protein.
• Samples obtained were run on an SDS-page gel.
• The gel was stained with comassie blue over the duration of the weekend.

July 25 th – July 31 st (Week 5)

Day 20

• We decided on the team name ‘Mag-nano-tite’

• A collaboration was formed between Team Kent and UC Davis
• We wrote code for a search bar on iGEMMatch.org
• SDS PAGE gel de-stained using methanol on shaker for ~3 hours.
• Gel was imaged and proved unsuccessful.
• Troubleshooting began.

Day 21

• Continued work on ideas/concepts for the upcoming Westminster presentation and poster.
• Nickel column B and wash buffers were made and set to the correct pH.
• overnight liquid
• Liquid cultures were also prepared from SecS.MamX, MamP, MamT and pET3a Top10 cells.

Day 22

• The plasmids were purified from the liquid cultures made the previous day and the concentrations determined
• We contacted the iGEM team at the University of Westminster team regarding the meet up and continued work to the presentation.

Day 23

• we conducted an inventory to determine which plasmids still required transformation, or repeats.
• pEC86 was transformed into BL21 cells.

Day 24

• We attempted co-transformation into BL21 cells using plasmids secS mamP & pec86) and incubated over the weekend.

August

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August 1st – August 7th (Week 6)

Day 25

• We began preparing for the iGEM deadline on August 12th.
• We began compiling information for our abstract
• Co-transformed plasmids pEC86 + SecS MamP were made into BL21 DE3 competent cells.
• SecS MamP were transformed in BL21 in DE3 competent cells.

Day 26

• SecS MamX were transformed in BL21 in DE3 competent cells.
• We created a code which measures the frequency of a key word for our Topic modelling programme.

Day 27

• Competent cells were created for pEC86 and SecS MamX were, measured into 0.5mL aliquoted and stored in the -80°C deep freezer.

• We received our primers,

Day 28

• The primers were re-suspended.
• We carried out our first PCR using the Mam genes (SecS and insoluble) to amplify our DNA.
• The PCR products were purified.

Day 29

• An electrophoresis gel was conducted to validate the PCR products. This gel was unsuccessful, and the PCR was repeated adjusting the temperatures in a bid to correct the errors from the first PCR.
• Prepared Mam proteins were analysed using an SDS-page gel. They were stained using coomasie-blue for the duration of the weekend

August 8th – August 14th (Week 7)

Day 30

• SDS PAGE gels were de-stained; resulting image shown below.
• The team delivered a mock presentation in preparation for Westminster conference.
• Final adjustments were made for iGEM deadline for track Selections and project abstract

Day 31

• Mam proteins were isolated using His-tag purification.
• After a third failed attempt to gain the correct PCR products, PCR was repeated using different enzymes.
• Plasmid maps were view to select new primers. primers.

Day 32

• pET3a plasmid validated.
• We had a meeting with team and supervisors to discuss direction of our project and set targets to achieve Gold medal criteria
• PCR was repeated using new primers

Day 33

• We began researching the literature relating to the chemical synthesis of magnetic nano-particles.
• We spoke to a chemical expert in the field of nano-particles.
• We liaised with teams for a possible collaboration.

Day 34

• iGEM deadline met, abstract submitted and track selection completed – New Applications.
• We continued sourcing the materials for the chemical synthesis of chemical nano-particles.
• Preparation for the Westminster meet-up continued.

August 15th – August 21st (Week 8)

Day 35

• We began working on an outline for our wiki page.
• A Gibson assembly was performed and fragment sup35nm was re-suspended.
• We finalised our presentations and posters for the University of Westminster conference.

Day 36

• We started identifying improvements we could make of the previous years’ project.
• Liquid culture was prepared from pEC86 + MamP and MamT
• We observed that the induced liquid culture when spun down was red in colour likely due to the cytochrome C domain in the protein binding iron.

Day 37

• We developed our Topic modelling programme to read multiple text files.
• Members of the iGEM team presented our poster at the University of Westminster iGEM conference
• Using nickel ion chromatography, we purified out MamX, MamT, MamP proteins

Day 38

• Members of the iGEM team gave a spoken presentation at the University of Westminster iGEM conference

Day 39

• We began compiling our data, results in preparation for our wiki.

August 22nd – August 28th (Week 9)

Day 40

• We reflected on the presentations given at the Westminster
• Gibson assemblies were performed.
• We double digested pSB1C3 and ran a gel to validated,
• We transformed NEB 5-alpha competent E. coli cells with 2ul of the Gibson reaction mixture.

Day 41

• Colonies from plates were Re-streaked some white colonies and made liquid cultures.

Day 42

• Re-streaks showing white colonies were mini-prepped.
• QIAprep protocol to purify the plasmids.

Day 43

• We focused on dry lab tasks such as planning the mock questions for future presentations.

Day 44

• We continued compiling information the wiki
• Planned future experiments

September

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August 29 th – September 4 th (Week 10)

Day 45

• The AFM imaging of samples commenced.

• Double digest of PSB1C3 RFP with Sup35nm using Ecor1 and Pst1
• PCR using usual protocol (with double digested template DNA) and original long primer on pET23B SecS genes.
• Prepared 500ml LB in 2L Baffled flasks for protein expression

Day 46

• Repeated agarose gels
• New forward primers arrived therefore PCR was done using normal protocol (with annealing temp at 52 degree and double digested template DNA).
• We set up 4ml overnight liquid cultures containing double antibiotics, 2 for each Pet23b Sec.S MamT, MamP, and MamX with pEC86 using the same colony.
• Made fresh antibiotic samples.

Day 47

• Made 1ml glycerol stocks using 500ul of liquid culture for Sec.S MamP, MamT and MamX with Pec86 in BL21’s.
• Using the remaining 3.5ml to inoculate 500ml LB in the Baffled flasks.
• We grew up the cells and induced with IPTG for protein expression.
• Ligation and transformations carried out.

Day 48

• We finalised our plans for collaboration with UEA over skype conference. It was agreed that we would carry out some AFM images of their S. oneidensis cells on a variety of different surfaces.
• SDS gels carried for MamP SecS, MamX SecS, MamT SecS and stained overnight.

Day 49

• De-strained SDS page gels and imaged them.
• In preparation, we shipped off AFM sample discs to UEA in Norwich in preparation for collaboration the following week.

September 5 th - September 11 th (Week 11)

Day 50

• We prepared liquid cultures with all Mam pET23B genes.
• Using plasmid maps we designed new primers.

Day 55

• Mini-prepped liquid cultures and ran undigested verification gels
• Re-attempted PCR
• Web design progress for our wiki.
• We used the absorbance reading at 280nm and extinction coefficient 8.73 mM -1 cm -1 to estimate the concentration of mam P as 27.4 µM.
• We used the absorbance reading at 280 and extinction coefficient 27.32 mM -1 cm -1 to estimate the concentration of mam P as 39.2 µM

Day 56

• Using SnapGene plasmid map sequences we designed new SecS primers
• We carried out spin columns for protein purification of mamP/T/X
• Using the absorbance reading at 280 nm and extinction coefficients, we estimated the concentrations for mamP/X/T for subsequent anaerobic reaction vessels.

• Carried out the reaction using purified proteins with iron solutions within anaerobic reaction vessel.

Day 57

• Reactions between purified proteins and iron solutions were placed onto EM grids and prepared for imaging (in vivo).

September 12 th – September 18 th (Week 12)

• The team logo and banner were designed for review by the team.
• We collaborated UEA to AFM image with samples.
• We continued making our final constructs.

September 19 th - September 25 th (Week 13)

• The team logo and banner were finalised.
• We continued writing
• AFM imaging of our samples continued.

October

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September 26th – October 2nd

• Semester resumes
• We began planning our outreach presentation for the University of Kent summer student Bioscience Symposium.
• We prepared a presentation using updated information about our project and updated results
• We continued imaging our samples to validate our constructs, these constructs include: pSB1A3-[AraC- pBAD]-[CsgA- SS-Sup35NM- 1-61], pSB1A3-[AraC- pBAD]-[CsgA- SS-Sup35NM- 1-61- Cytb562], pSB1A3-[AraC- pBAD]-[CsgA- SS-Sup35NM]

October 3rd – October 9th

• We continued writing up our results and compiling information for our wiki.
• The team attended a University of Kent Bioscience open day. We spoke to the public about our iGEM project, the iGEM competition and its future applications.
• We continued the AFM imaging of samples.
• The final construct of pSB1A3 mamOPXT transformed.

October 10th – October 16th

• pSB1A3 mamOPXT
• We continued the AFM imaging of our samples.
• E. coli cells were induced containing the mamOPXT plasmid, we did this by growing the cells in a liquid media containing arabinose, IPTG and Ferric Citrate.
• Electron microscopy grids prepped for imaging.

• Writing for wiki continued.

October 17th – October 23rd

• The team Completed content for our wiki
• Wiki freeze.
• Final electron microscopy images produced.
• Prepared our posters, banner and presentation for the jamboree
• Outreach at second University of Kent open day.

October 24th – October 31st

• iGEM Jamboree in Boston.