Team:Newcastle/Notebook

Notebook

Notebook

Week 1 - Bootcamp

Day 1 - 10/06/2019

Today was the first day of Newcastle iGEM 2019! We started the day right with a cup of tea and some lovely pastries. This was followed by a great introductory talk from Professor Frank Sargent who inducted us into iGEM and introduced the wide spanning capacity of SynBio. Jasmine Bird, Bradley Brown, and Alba Iglesias then gave the team a run through of the specifics of iGEM and important things to keep an eye on... particularly the wiki! We then spent the afternoon brainstorming and having a research of some winning projects from iGEMs past to prepare for a mini presentation tomorrow.

Day 2 - 11/06/2019

For day 2 of our iGEM bootcamp Jasmine Bird introduced us to the importance of measurement within a project to strengthen our results; sadly, we have ran out of snacks (sponsorships welcome!). We were then joined by Dr Colette Whitfield who gave us inspiration of how cell-free systems and hydrogels could be incorporated into our project. Dr Maria del Carmen Montero-Calasanz also dropped by to give a brief talk about her research in plant-microbe interactions and helped us expand on any ideas that may start to be forming in the back of our minds. Today we also gave our mini presentations on different projects that we liked - taking about 90 minutes to switch between users after each one.

Day 3 - 12/06/2019

The weather today was gloomy, typical Newcastle! We started the day off with an introductory talk from Alex Laverick and Dr Tom Howard about lab automation on how to carry out experiments more efficiently. Dr Harold Fellermann followed on with a talk on mathematical modelling and biodesign. We then had a gene construct design task set by Dr Jem Stach to test the presence of nitroxoline using GFP and to be compatible for BioBrick, which we only had two hours to complete! We initially added the wrong BioBrick prefix as there was no XbaI, which Dr Stach pointed out when we presented our results – we fixed this and added the correct prefix. We were successful although it was suggested we could change the restriction sites to be adapted to Type IIs and to use RFP for screening.

Highlight of the day - as we frantically tried to solve the task, we heard dogs barking next door…turns out there were therapy dogs visiting!

Day 4 - 13/06/2019

Day 4! Busy day today. We kicked off the day with a workshop with Professor Angharad Gatehouse discussing bio-economy and current ideas of an iGEM project this summer. Dr Maxim Kapralov then gave us a talk regarding climate change, increased CO2 levels and the potential of CO2 sequestration . After this we attended a seminar delivered by Dr Eileen Yu from the school of Engineering about bioelectrical chemical systems with academics from the school of Natural and Environmental Sciences. Dr Vas Andriotis presented us with his ideas about using metabolic pathways to detect oncoming drought in crops. Some of our team members were interested in using biofuels as alternatives to fossil fuels. Unfortunately, there were no talks scheduled in for the bootcamp about this topic. So, we asked Dr Ethan Hack to give a talk about using algae to make biofuels, which he graciously gave. It’s fair to say we have been worked today and developed some new ideas! Time for a nap…

Day 5 - 14/06/2019

The day started off with a talk from Dr Angel Goni-Monreno on behalf of Newcastle University's School of Computing. The concepts of cellular computing were introduced, with specific focus on engineering genetic circuits and how to approach standardisation within SynBio. Alba Iglesias Vilches then followed on with a preparation talk for the jamboree and how to make science accessible for all - highlighting the importance for diversity and inclusion within iGEM as a whole. The team then discussed our current ideas to tackle inclusion and accessibility. For example, using a single dyslexic-friendly font throughout the wiki. The morning was then concluded with a talk from Dr Martyn Dade-Robertson, a reader in Architectual Design Computation, who explored SynBio with an Architect’s approach to the design and manipulation of construction materials.
**cue cool and flashy design animations**

By noon the team were all rather tired and lacklustre. Unfortunately, the absence of a couple of team members only contributed to the mutual deflated feeling. To cheer ourselves up, but also as a pre-presentation treat, we headed to a local carvery for lunch!!

In the afternoon, we presented our long-list of project ideas to the team’s advisors, professors and PhD students who led talks with us throughout the week.

Our long-list of project ideas:

Soil disease biosensor (passive)
Lysteria bio-battery
Mycoplasma genitalium detection tool
Party-drug purity biosensor
Algae biofuel
Parkinson's biosensor
RuBisCo efficiency via carbonic anhydrase
Re-root aversion

After a brief Q&A the team received ample feedback for all of our proposed ideas. Some suggestions included changing our soil biosensor to a vector-disease detection system, as well as the modification of algae to produce specific high value product such as saffron. In addition, we were also asked to consider audience sensitivity with regards to drug-use and reasons behind purity detection. It was suggested that even changing it to the purity detection of alternatively sourced medical pharmaceuticals may be more suitable. Our audience was asked to vote for their three preferred ideas on an online anonymous poll. The top three choices are highlighted in bold on the long-list above.

The presentations and subsequent feedback was not nearly as daunting as originally thought. Though the team now has much to consider before we select our short-list of project ideas.

WE SURVIVED WEEK 1!!!

Week 2 - Bootcamp

Day 1 - 17/06/19

Second week of bootcamp! Today we had a talk from Dr Dana Ofiteru from the School of Engineering to tell us about mathematical modelling of microbial communities and she was very helpful in explaining the different types of models and gave examples for each. Also as a team, we decided on our three choices...

The results are:

Parkinson's biosensor
RuBisCo efficiency via carbonic anhydrase
Re-root aversion

Jasmine and Bradley set us a task to research previous iGEM teams modelling approaches. We used the iGEM 2018 Hamburg project as our modelling example. We then allocated our chosen projects between us to research and put together a project plan for each idea for our presentation on Friday.

Day 2 - 18/06/19

Today we continued our work on researching our 3 ideas. We primarily directed our focus on the Parkinson's biosensor as Connor and Karen made a few discoveries which meant we had to reconsider our approach. Just before lunch we had a quick Skype with the University of Waterloo over in Canada to learn about their project and discuss potential collaborations (thank you to them for getting up at 7am!) From this point, we spent the rest of the day exploring additional targets for our biosensor and discussing how Connor wasn't aware about the different breeds of cat.

Day 3 - 19/06/19

Today our research was focused on the carbonic anhydrase idea. We also had an ethics talk from Ken Taylor and Simon Woods, in this we found out certain aspects of our projects may be ethically questionable, and we would need to think a lot about how to tackle sensitive topics of discussion if we take our Parkinson's biosensor project forward. We will also need to consider the legal aspect of any of our project research.

Day 4 - 20/06/19

The penultimate day of bootcamp! Today we had a seminar presented by the NUSynBioNet committee. We had a presentation from Dr. Alice Banks regarding the use of computer modelling to optimise a cell free system. We also had a talk from Adnan Yaramis, a PhD candidate working in Dr Maria Del Carmen Montero-Calasanz’s lab on bioinoculants and how they affect plant growth. The rest of the day we spent finalising our 3 final ideas for our final short list presentation. We will be presenting these ideas to university researchers, lectures and members of the ethics committee. Hopefully we will decide what project we conduct for the summer. Wish us luck!

Day 5 - 21/06/19

The final day of bootcamp a.k.a presentation day.

Today the team presented our refined three shortlist project ideas to our PI's, instructors, plus any academics who had provided talks throughout the bootcamp. The presentations were followed by another Q&A feedback session and it became apparent that although engineering carbonic anhydrase to improve RuBisCo efficiency would be super cool and exciting, it was too complex and lengthy - not suitable for a summer iGEM project. After much debate and of course a cheeky Nando's, the team weighed up the pro's and con's for both our vector pathogen repellent (modified re-root aversion) and our Parkinson's Disease biosensor. We carried out an anonymous poll and it was a near even split. However, after some discussion regarding both the project plan and general direction, the entire team was in agreement.

The Newcastle iGEM 2019 project is... **prolonged dramatic music** ... THE PARKISON'S BIOSENSOR!!

Our PD biosensor was inspired by Joy Milne a "super smeller" with the unique ability to "smell" PD on her late husband. Joy described her husband Les as smelling “musky” up-to 10 years prior to his PD diagnosis. After further research, we discovered that the odour Joy was detecting was actually Malassezia fungal growth associated with seborrheic dermatitis, a non-motor symptom of PD due to immune deficiency. We are now attempting to develop a triplet biomarker system, each biomarker will run independently, and only a collective positive result for all three tests will result in a confirmed need for a diagnosis of PD.

Week 3

As of now we're moving to weekly updates! Check back weekly for progress reports!

This week we finalised our wiki design plans as well as assembling the sequences of our gene constructs. When finalising wiki design plans we focused heavily on balancing the appearance with accessibility. With members of the team who are colourblind and also dyslexic we thought this was a primary concern. Taking inspiration from Parkinson's UK colour schemes we opted for a scheme including a variety of blues with a splash of grey. Blue is colourblind friendly while also reducing contrast enough to minimise impact on those with dyslexia. Below you'll see a behind the scenes picture of how we chose more final versions of the colours we wanted to use. Thankfully, Karen decided to wear this blouse today!!

Week 1

Today was our fortnightly presentation to update the instructors, PIs and advisors on our project. This week has involved getting gene constructs checked, booking flights to Boston for the Jamboree, and attempting to arrange meetings for the Human Practices section of our project. We contacted Vivienne Rogerson from Parkinson’s UK, who informed us of ‘Parkinson’s Café’ events for people with Parkinson’s to socialise and exercise classes such as yoga and dance, to help people with Parkinson’s stay active. She also recommended we contact Professor Richard Walker, an expert in Parkinson's research.

Week 2

This week we designed our gene constructs and made them compatible to Type IIs. We ordered them on Tuesday, now we just have to wait for them to arrive and get started in the labs! As well as designing and finalising our gene constructs, for human practices, we submitted our ethics form and formatted a briefing and debrief sheet along with the ethics form. Emily and Alice attended the 'Parkinson's Café' meet up at Newcastle Eldon Square and met the lovely coordinator Vivienne Rogerson and socialised with people with Parkinson's. We also contacted Professor Richard Walker and have agreed to meet up when he is available.

Week 3

At the start of the week we received our IDT order for our different DNA constructs, this prompted us to start looking into and understanding the protocols that we will be needing to use in the coming weeks. We also finalised our chemical safety forms and were able to order our chemicals for the use in the biosensor testing as well as our collaboration with Waterloo. In the mid-week, Alice, Emily and Matt visited another Parkinson's UK meetup. Connor and Karen also worked further on our collaborations with calls between the Waterloo and Grenoble Alpes teams. Daniel also had the delightful task of starting to shift our wiki design from the GitHub onto our main wiki; we currently fear for his code in the transition. On Thursday we had one of our typical bi-weekly presentations which were, as ever, great for further developing our project. We also got our lab strain DH5alpha from Alba so we finally started in the lab, finally!

Week 4

The week started with a win for the human practices sub-team as they had received written project approval from Newcastle University's internal ethics department SAgE. Not long after Alice was able to arrange an interview in the near future with Dr Dow Smith, a recently retired General Practitioner from Oxford Terrace and Rawling Road Medical Group, Gateshead. Matt has also had a successful start to the week by completing all cell competency tests. Unfortunately, Newcastle has had a sweltering heatwave this past week with the labs getting as hot as 38ºC. This has proven difficult for all team members and any of Karen's wet-lab cell transformations. Sadly we will have to repeat this all when the labs become cooler.

The week was concluded with a project review with a few of the team's PI's and instructors present. It was a productive meeting which included the finalisation of a new colour scheme and gave the opportunity to mull around with some project names based around core associations to Parkinson's Disease like 'brain' and 'memory'. Through a little google we discovered that in old Norse mythology a pair of ravens Huginn of "thought" and Muninn of "memory" would collect information from across the world and deliver it to the God Odin. After much discussion and a democratic vote, the team approved 'muninn' as our project name.

Week 5 - The national iGEM meet-up!

This week has been a busy one. Connor and Karen have been busy organising the annual UK iGEM meet-up which kicked off here at Newcastle University on Tuesday 30th. The UK meet-up was attended by the likes of Edinburgh OG and UG, Exeter, King’s, Manchester Nottingham, Oxford, Sheffield, St Andrews, UCL, Warwick and Westminster University - a full house.

In the morning, Matt and Emily ran a competitive team building session in which mixed teams had to decipher an amino acid code then organise a science related anagram. The second activity was a ‘describe and draw’ task of a complex gene circuit. The rest of the day and the morning following consisted of team project presentations chaired by Alice. At the end of the presentations on the second day, all the teams voted for a team to represent UK iGEM at the Designer Biology conference 2019. The winner was Sheffield University with their 'OPENLUX’' hardware project, an open source plate reader providing a cheaper alternative to current industry technologies. After a poster presentation and plenty of opportunity to network, the teams departed on a tour of the local brewary, Wylam.

Back at the office, our preliminary modelling results we have identified the need to alter the expressions of enzymes such as ChaC to make our model more responsive. This gives us a good predication of how our lab system may respond.

The team are exhausted.

Week 1

Happy August all! After a busy week from the iGEM UK meetup and the Designer Biology conference, we were looking forward to getting back to normal iGEM life. On Sunday the 4th, Alice and Matt attended one of the largest Parkinson’s UK meetups in North East England. It was a rewarding experience, giving us insight into the range of therapies Parkinson’s UK have to offer. We even got to try out one of these therapies at the meetup… singing! We all got the chance to have a group sing along, it was great fun.

On the Tuesday, Matt and Alice interviewed Professor Richard Walker from North Tyneside General Hospital, an expert in Parkinson’s disease. Our main focus was to understand the method of Parkinson’s diagnosis, the ranges of treatments, the changes needed in treatment/ diagnostics and feedback on our project.

For the wetlab, the team continued with transforming bacteria with the gene constructs. Three of which worked successfully, as confirmed from sequencing plasmids extracted from transformed bacteria. So, we can start with some data gathering! We also received the bacteria containing the CRISPR Cas13a (Connor was very happy). The lab work is well under way now. Hopefully next week will be just as successful.

Week 2

This week involved a lot of work in the wet lab, we also set up a GoFundMe for Parkinson’s UK to collect donations, CLICK HERE TO DONATE!Working with them showed to us how much of a difference they make to the lives of people living with Parkinson’s Disease, and how necessary the organisation is. Alongside this we have decided to take part in the Annual Geoff Cobbing Cycle Ride set up by Parkinson’s UK as a memorial and a fundraiser. Whilst speaking to people living with Parkinson’s disease we found that healthcare systems were not all consistent with the information given out to patients, meaning that some did not have access to all the support offered by charities such as Parkinson’s UK, and because of this we emailed the National Institute for Health and Care Excellence (NICE), to enquire as to whether they could possibly review their guidelines and include more information about such organisations.

Week 3

On Wednesday we had our first bake sale to raise some money for Parkinson’s UK for the Geoff Cobbing Cycle Ride. We successfully raised £161 - a massive thank you to everyone who supported and donated! Our next bake sale is planned for Monday 2nd September and we can’t wait to get the whisks out again! Earlier in the week, Karen contacted Promega for a sample of the NADH assay kit for characterising our part for the bronze criteria. On Friday she met with Paul Banks from Promega and discussed a potential sponsorship. In the labs, we were having some difficulties with the CRISPR Cas13a as it seemed like it could not be expressed in E. coli BL21 (DE3). We needed to have a rethink and decided our goal for next week was to try and transform our Cas13a into E. coli Rosetta 2(pLysS) cells.

Week 4

An eventful week. For the wet-lab, Matt has been able to complete two more successful bacterial transformations; we now have a total of 5 assembled E. coli plasmids. Karen has ordered some more DNA constructs from IDT and made competent Rosetta 2 DE3 pLysS cells. Emily has begun digitising the lab-books and protocols for the wiki. Alice has started developing a computational neuroinformatic animation for the use at the Jamboree in conjunction with Newcastle University’s computer science school. The team has been particularly small as this week as both Connor and Daniel have had time off. Nonetheless, the Newcastle team has been officially registered for the Giant Jamboree, the pressure of Boston is on!.

Week 1

Yet another week and yet another month at iGEM here in Newcastle. This week was mostly a week of admin but both Connor and Daniel return from their adventures. Connor returned to begin work on the final safety form and finish up our CRISPR SHERLOCK kinetics model after following advice from our collaborators at the University of Waterloo as well as turning out some drafts for our abstract. Matt continued his quest to assemble all of our constructs to varying levels of success whilst Karen had fun at a wedding and Alice explored Paris. Daniel continued to do what Daniel does best, cleaning up everyone's wiki messes while making steady progress towards our end wiki product. The theme of a small team continues... anyone know how to get E. coli to do all the work themselves?

Week 2

With the majority of the team back from their adventures, we continued working through our to do lists. Matt was in the labs characterising our Eicosanol-RFP part using different alcohols. Connor was doing lots of PCR's to get the Cas13a out its storage plasmid and the primers for our CRISPR work arrived, so our CRISPR SHERLOCK work has been progressing. Karen was busy doing admin work and planning bronze criteria related lab work.

Week 3

As the theme of a small team continues, we discovered our plan for the bronze part criteria would not be considered for bronze and we had to rethink our approach. As much as we were disappointed, we quickly solved our problem and came up with a solution and we are back on track with fulfilling our bronze requirement. Karen has been tasked on characterising parts for bronze. Connor has been working hard on the CRISPR model and writing up the model and CRISPR results. Matt has been busy in the labs doing more assemblies and transformation, with some hopefully successful results coming back next week. Alice has been busy training for freshers week to welcome in the students of 2019 and Daniel has been busy working on the design of our banner.

Week 4

With less than a month until wiki freeze, Karen and Matt have been working hard this past week in the labs and Connor has been busy designing Cas13a for Gibson assembly. To say we are not stressed would be an understatement, but we are working through our workload before uni and lectures officially start. Matt has been busy characterising his glycine biosensor and Karen has been busy working on His-tagged eGFP and His-tagged mCherry. Daniel was busy working on the banner and submitted it on Friday, keep an eye out for our banner at the jamboree!

Week 1

OFFICIALLY THE MONTH OF WIKI FREEZE! With the academic year starting, the team have been busy with university work. Matt and Connor have six hour labs every day practicing their molecular techniques; Alice has been busy starting her final year (exciting yet daunting) and Daniel and Emily have been settling into second year. Karen has been busy working in the labs doing iGEM work and achieved a standard curve of the His-tagged eGFP. In his spare time, Matt has been working on the glycine biosensor and got some good results.

Week 2

This week, Daniel was tasked to design our flyer and merchandise to take to Boston, keep an eye out for our t-shirts and hoodies at the jamboree! Karen and Matt have been busy finalising the lab work and have been busy putting up content on the wiki. Connor has been writing up the modelling and results pages whilst being busy in masters labs. Slowly but surely, progress is made as we are getting closer and closer to wiki freeze. The next week will be busy with writing up and finalising everything, coffee and naps will definitely be on the agenda!

Week 3

ONE WEEK UNTIL WIKI FREEZE! Last minute experiments, long nights of write up and endless coffee to keep us going. The team have been busy working on the wiki and finalising all content. A group trip to the library on Saturday was very productive and lots of boxes were ticked. All the stress and sleepless nights will pay off - not long to go now! The team can't wait to go to Boston to show everyone what we have been up to all summer!