Team:Exeter/Notebook

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The story so far...

The first three weeks, commencing 28th May 2012 have been set aside to obtain a general biological background, particularly useful for the non-biologists in the team, the majority! This will be achieved through several short lectures, discussions and practical laboratory sessions. This allows every member of the team to have a suitable platform to create project designs.
Ideas will be put forward and built upon with the aim of making the final decision on Thursday 14th June 2012. The subsequent ten weeks are then for us to develop our project!

Wish us luck!

WEEK T-MINUS 2

28th May – 1st June 2012

The team arrived and Tom Howard, our project coordinator, began with a brief introduction to the iGEM competition. He then attempted, and in most cases succeeded in bringing everybody up to scratch on the basic biology we will need over this summer, predominantly PROMOTER – GENE – TERMINATOR (only mildly connected with the 1984 hit film, much to the disappointment of the physicists, its role is still to stop the process at all costs!).
John Love followed with a talk on synthetic biology and how cool the subject area is, not that we needed any convincing!
Orkun Soyer gave a talk on bio-stability which was well received by our in house mathematician and finally to end our day of talks Christine Sambles gave an introduction to the –omics.

More talks followed in the week. Clive Butler talked about Thauera selenatis and microbial nano-mineral synthesis. Nick Smirnoff spoke on metabolic engineering and this was followed by Nic Harmer talking about polysaccharides.
Tom spoke about his field of research which involves bio-fuel production, which was very interesting. George Littlejohn gave us a brief talk on biosensors and reporters. Rob Beardmore spoke about dynamic systems modelling.
Our final talk of the week was given by Peter Petrov on bacterial and artificial swimming. This featured many amazing videos showing different forms of swimming involving bacteria and how they could travel in a variety of methods! Most of the afternoons and evenings were set aside for brainstorming, below are a selection of some of the ideas.

Brainstorm of Initial Ideas

WEEK T-MINUS 1

4th - 8th June 2012

Cell Dilution

We had our first day in the labs this week. It started with an initial induction to the labs which included a very in depth health and safety talk.
We soon moved on to some basic lab techniques with plenty of pipette action which included gel preparation and creating single colonies, see photograph insert for the very respectable results from a Physicist!!
For a second consecutive day we were in the lab. We isolated DNA and then separated the DNA fragments using Gel Electrophoresis. The estimated sizes were then mapped and compared to expected maps. Another fun day!
Through many hours of brainstorming and discussion over the past two weeks the team has managed to create a short-list of five strong ideas to put forward as a potential project. The below ideas were presented to a range of relevant academics.

Phosphate Uptake Regulation – synthetically modifying Escherichia coli to significantly increase
the uptake of phosphates and being able to control the release through a mechanism.

Polysaccharide Synthesis – designer sugars. This would entail the creation of a biological toolkit
and the ability to know the physical properties of a polysaccharide by knowing the enzymes being
put into the system, and vice versa.

One - cell Cellulose Degradation (pac-man) – Find commonality for three types of cellulases and
affix to scaffold to improve the efficiency. Could have transfer sequence to cell exterior. This idea
stemmed from the ability of cows to eat grass and the usage of their 4 stomachs.

Logic-gated 'thinking' Bacteria – improve on what has already been done somehow. Should work
at level of proteins, not genes, for instant response. The potential for a counting device?

Biological Ionisation Radiation Detector (otherwise known as B. I. R. D) – a method of detecting
the strength of Gamma, X-ray and UV radiation through a biological system.

After further discussion, two ideas are to be taken forward to next week...
Polysaccharide Synthesis and Phosphate Uptake Regulation.

WEEK ZERO

11th-15th June 2012

Throughout the week we've all been super busy researching for the final presentation of our two ideas. We had to get our designs up to scratch for the scrutiny of a range of Professors and Researchers who really know their stuff! Freddie and Alice presented the two final ideas:

Phosphantastic: Phosphate supplies are going to be depleted within 30 years and because two thirds of the World population rely directly upon Phosphate-based fertiliser we feel it is a very important issue that needs to be tackled. We believe that through Synthetic modification we could create a two phase process where the cell, in response to a promoter, would uptake much more Phosphate than would naturally occur. The second phase looks at excreting the Phosphate so that it's ready for collection through a different control mechanism.

Sweet Shop: A Polysaccharide catalogue which could eventually lead to the ability to create designer Polysaccharides suitable for its specified use. For example being able to produce a polymer of ‘X’ size ‘Y’ tensile strength and ‘Z’ electrical charge by knowing the enzymes required. This idea, albeit a colossal challenge, if successful may change the outlook on Synthetic Biology and would lead to an entirely new field of research.

Freddie, Alex B and Raf preparing for the presentation

Both ideas are equally strong and most of us changed our minds multiple times before the day was out. After a discussion weighing up the pros and cons of each design and its potential impact, we had an anonymous vote ....SWEET SHOP is our project for the summer!

We're all super excited to get started!!

WEEK ONE

18th-22nd June 2012

Project planning began at 9am Monday morning with a huge whiteboard and tonnes of enthusiasm. It's a tall order to try and organise a ten week project between ten students from different backgrounds, but we're working on it!

We all met with Professor Winlove in the giant Physics building to discuss how our Polysaccharide Synthesis could be used in the real world. He gave us lots of food for thought, as well as great views of Exeter.

A few people began developing their coding knowledge and started working on the wiki page. Through reading lots of books and trawling the web for tutorials their knowledge expanded! They also started using Adobe Illustrator and Photoshop to develop images for the website. It was amazing to see that within a few days so much could visually change for the project.
After meeting with a graphic designer and battling with potential new names and ideas we re-branded our project with the name, e-candi. After showing us several logo concepts we had plenty to consider as we called it a night and went away to design our own.
The next day our new name was discussed with the rest of our group and it was agreed that it sounded better than the original "Sweet Shop". In the evening we had a mini presentation, which later turned into a mini competition (showing off our designing abilities), displaying our different logo ideas developed from concepts put forward by our graphic designer Marian. The outright winner by the way was Alex ... sorry Ryan.

Press-relations were considered and an outreach program began with Alex B creating a Polysaccharide based dominoes game which we can use to not only teach school children about our idea but also inspire them to continue studying science!
A Café Scientifique session has been organised in September for us to discuss both our project and Synthetic Biology as a whole to a wider audience.

Taking care not to neglect the Biology - Alex B, Freddie, Becca and Mary managed to find a massive list of 120 Glycosyltransferases to add to the database.
The design of how the biological system will work was produced.

"An Introduction to Systems Biology - Design Principles or Biological Circuits" by Uri Alon was read from cover to cover to help Liam with the modelling processes. The regulatory genetic network plasmid design was created through Tinkercell, with a view to have greater control over enzyme expression.

WEEK TWO

25th-29th June 2012

A meeting kicked off the week to find out where everyone's at within the project and to set targets for the week ahead. This helped us all to focus on the tasks in hand and to coordinate what individuals are doing.

The colossal list of 120 Glycosyltransferases has been narrowed to only 20 which can make viable pathways.

The Polysaccharides database plan began with a diagram of how the system works. It's a small step, but it had to be done. Liam, Alice and Andy discussed many different methods for implementing the database using programs from Microsoft Access to SQLite and Python. Liam started going through Python tutorials and managed to create a calculator in a couple of hours - pretty cool.

Novel uses for the Polysaccharides were considered:

Cotton is made from Polysaccharides but is currently produced in very damaging ways.
- Cotton farming accounts for 8-10% of the worlds pesticide use and in developing countries this is up to 50%. The World Health Organisation (WHO) says that there are several million cases of pesticide poisoning each year related to cotton causing between 20,000 and 40,000 deaths.
- To obtain about1 kg of cotton lint, which is about enough for a pair of jeans, 8500 litres of water is required. This is equivalent to 40 baths worth of water just for one pair of Levis.
- Due to irrigation of cotton the Aral Sea has decreased in size by 85% over the last 40 years leading to the destruction of ecosystems and biodiversity and the extinction of at least 24 native fish species. Due to cotton cultivation habitats are being destroyed all over the world. On top of all this the cotton industry is guilty of terrible working conditions. The India Committee of the Netherlands reported that nearly 450,000 children between 6 and 14 were employed in cotton fields in India during 2003-04.

Grow your own bridge - Hydrophobic domains repel the presence of water spontaneously creating a bridge over water. Hopefully I won't be the first person to walk across it!

Warm Wetsuit - incorporate Xylomannan (found in Alaskan Beetles) can be incorporated into wetsuit design to allow the user to resist below freezing temperatures.

Pressure Equaliser - using Hyaluronan to repel the pressure to allow divers to survive deeper depths.

After many tireless nights, the wiki became live at 2am on Thursday from Ryan's house! A very exciting day!

Tom, Alice, Andy and Ryan met with Ed Creed, a marketing executive from the University to help us advertise the project, as well as iGEM. We're looking forward to having many more hits on the wiki and hopefully we’ll get some press releases created next week.

WEEK THREE

2nd-6th July 2012

The group attended this month’s Café Scientifique to obtain a general feel for the type of talks and discussions that take place there. We soon realised it was a relaxed atmosphere where topical debate was frequent and encouraged, I’m sure we’ll have plenty to talk about when we do our talk in September!

Becca spent the week designing Gibson primers that unfortunately weren’t required due to a slight change in plan. She researched and designed the primers for Hyaluronan synthases (HAS) and the 3 other genes needed to get hyaluronan but currently it appears we can’t afford them. Gracefully she also assisted Alex in getting to grips with SacB and the primers for it.
This week we began investigating the ethics and impacts our project may have if successful. Alex B and Becca went to see Sabina Leonelli to obtain some extra guidance whilst Alex C has been investigating the potential impacts to pre-existing systems. We’ll be transferring everything we discover to their own corresponding wiki pages soon! Applications of SacB and HAS have also been explored whilst thinking how we can best display our triumph visually in the lab!

At the end of the week we’ve said goodbye to our engineer, Alice as she heads off for a lovely summer break in Budapest! But don’t despair she’ll be returning to help us out at a later date.

WEEK FOUR

9th-13th July 2012

We kicked off the week with our now routine group meetings where we discussed our change of plans and the division of labour in the labs. Each of our 4 biologists is now leading their own “mini” assignment whilst being supported by one another they have each also enlisted their very own physicist!

Finally our primers are sorted and have been ordered!

This week saw the team having a short tour of the labs that we’ll be stationed in for the duration of the summer by Dagmara.

Liam, after spending many an interesting hour in the library over the last few weeks has been trawling through plenty of online tutorials trying to make sense of coding with Python and using the SQLite3 module. A process I think he will admit that he has secretly enjoyed! With his wealth of obtained knowledge he has begun his first attempt at our database program.

He’s taken a modular approach to assembly, taking his time with each individual element. The first model consisted of a program that took 3 sugars as user input and produced 2 separate lists of potential enzymes that could be used to conjoin sugar 1 to 2 and 2 to 3 respectively. After his visit to John Rowe he was able to implement several quick improvements, for instance the addition of error messages if the combination is impossible.

Liam intends on making further improvements to his code with the hope of incorporating the ability to add any number of input sugars. The aim of the finished product which will hopefully be included in our wiki will require him learning code from another module called JPython... “Yay!”
For a more detailed evaluation of the Database please visit our section on the wiki.

Work in labs finally commenced by transforming Escherichia Coli to bulk up some promoters, terminators and other useful things for BioBrick assembly! The next morning our previous labour was checked to make sure everything had worked properly. Thankfully it had as Tom was unsure how he would deliver a pep talk had we of failed! The plated colonies were left in the fridge until the afternoon where they were transferred to broth culture for further incubation.
For full details of our work in the lab, please visit the Lab Book tab.

@@ Line 11: / Line 11: @@
 |}
 <br>
+<div align="justify">
 <font color = "FA8072"> <big><big><big>'''The story so far...'''</big></big></big><font color= black>
-<br>
+<br><br>
-The first three weeks, commencing 28th May 2012 have been set aside to obtain a general biological background, particularly useful for the non-biologists in the team, the majority! This will be achieved through several short lectures, discussions and practical laboratory sessions. This allows every member of the team to have a suitable platform to create project designs.
+The first three weeks, commencing 28th May 2012 have been set aside to obtain a general biological background, particularly useful for the non-biologists in the team, the majority! This will be achieved through several short lectures, discussions and practical laboratory sessions. This allows every member of the team to have a suitable platform to create project designs. <br>
-<br>
 Ideas will be put forward and built upon with the aim of making the final decision on Thursday 14th June 2012. The subsequent ten weeks are then for us to develop our project!
 <br>
@@ Line 22: / Line 21: @@
 <br>
-<font color = "FA8072"><big><big>'''WEEK ONE'''</big></big><font color = "black">
+<font color = "FA8072"><big><big>'''WEEK T-MINUS 2'''</big></big><font color = "black">
 <br><br>
 <big><u> 28th May – 1st June 2012 </u></big>
@@ Line 43: / Line 42: @@
 <br>
-<font color = "FA8072"><big><big>'''WEEK TWO'''<br></big></big><font color = "black">
+<font color = "FA8072"><big><big>'''WEEK T-MINUS 1'''<br></big></big><font color = "black">
 <br>
@@ Line 53: / Line 52: @@
 We had our first day in the labs this week. It started with an initial induction to the labs which included a very in depth health and safety talk. <br> We soon moved on to some basic lab techniques with plenty of pipette action which included gel preparation and creating single colonies, see photograph insert for the very respectable results from a Physicist!!<br>
 For a second consecutive day we were in the lab. We isolated DNA and then separated the DNA fragments using Gel Electrophoresis. The estimated sizes were then mapped and compared to expected maps. Another <b>fun</b> day!<br>
-Through many hours of brainstorming and discussion over the past two weeks the team has managed to create a short-list of five strong ideas to put forward as a potential project. The below ideas were presented to a range of relevant academics.<br>
+Through many hours of brainstorming and discussion over the past two weeks the team has managed to create a short-list of five strong ideas to put forward as a potential project. The below ideas were presented to a range of relevant academics.<br><br>
-*Phosphate Uptake Regulation – synthetically modifying <i>Escherichia coli</i> to significantly increase the uptake of phosphates and being able to control the release through a mechanism. <br>
+<div align="left">
+*Phosphate  Uptake  Regulation  –  synthetically modifying  <i>Escherichia coli</i>  to significantly increase<br>the uptake of phosphates and being able to control the release through a mechanism. <br>
-*Polysaccharide Synthesis – designer sugars. This would entail the creation of a biological toolkit and the ability to know the physical properties of a polysaccharide by knowing the enzymes being put into the system, and vice versa. <br>
+*Polysaccharide  Synthesis  –  designer sugars.  This would entail the creation of a biological toolkit<br> and the ability to know the physical properties of a polysaccharide by knowing the enzymes being<br>put into the system, and vice versa. <br>
-*One-cell Cellulose Degradation (pac-man) – Find commonality for three types of cellulases and affix to scaffold to improve the efficiency. Could have transfer sequence to cell exterior. This idea stemmed from the ability of cows to eat grass and the usage of their 4 stomachs. <br>
+*One - cell Cellulose Degradation (pac-man) – Find commonality for three types of cellulases and<br> affix to scaffold to improve the efficiency. Could have transfer sequence to cell exterior. This idea<br>stemmed from the ability of cows to eat grass and the usage of their 4 stomachs. <br>
-*Logic-gated 'thinking' Bacteria  –  improve on what has already been done somehow. Should work at level of proteins, not genes, for instant response.  The potential for a counting device?<br>
+*Logic-gated 'thinking' Bacteria  –  improve on what has already been done somehow. Should work<br>at level of proteins, not genes, for instant response.  The potential for a counting device?<br>
-*Biological Ionisation Radiation Detector (otherwise known as <b>B.I.R.D</b>) – a method of detecting the strength of Gamma, X-ray and UV radiation through a biological system. <br>
+*Biological Ionisation Radiation Detector (otherwise known as <b>B. I. R. D</b>) – a method of detecting<br>the strength of Gamma, X-ray and UV radiation through a biological system. <br><br>
+</div>
 <center>After further discussion, two ideas are to be taken forward to next week...<br><big><b>Polysaccharide Synthesis</b></big> and <big><b>Phosphate Uptake Regulation</b></big>.</center>
 <br>
-<font color = "FA8072"><big><big>'''WEEK THREE'''</big></big><font color = "black">
+<font color = "FA8072"><big><big>'''WEEK ZERO'''</big></big><font color = "black">
 <br><br>
 <big><u> 11th-15th June 2012</u></big>
@@ Line 80: / Line 80: @@
 <br>
 <center><b><big>We're all super excited to get started!! </big></b></center>
-<br><br>
-<font color = "FA8072"><big><big>'''WEEK FOUR'''</big></big><font color = "black">
+<font color = "FA8072"><big><big>'''WEEK ONE'''</big></big><font color = "black">
 <br><br>
 <big><u> 18th-22nd June 2012</u></big>
@@ Line 105: / Line 105: @@
 <br>
-<font color = "FA8072"><big><big>'''WEEK FIVE'''</big></big><font color = "black">
+<font color = "FA8072"><big><big>'''WEEK TWO'''</big></big><font color = "black">
 <br><br>
 <big><u> 25th-29th June 2012</u></big>
 <br><br>
-A meeting kicked off the week to find out where everyone is at within the project and to set targets for the week ahead. This helped us all to focus on the tasks in hand and to coordinate what everybody is doing. <br><br>
+A meeting kicked off the week to find out where everyone's at within the project and to set targets for the week ahead. This helped us all to focus on the tasks in hand and to coordinate what individuals are doing. <br><br>
 The colossal list of 120 Glycosyltransferases has been narrowed to only 20 which can make viable pathways. <br><br>
@@ Line 130: / Line 130: @@
 After many tireless nights, the wiki became live at 2am on Thursday from Ryan's house! A very exciting day! <br><br>
 Tom, Alice, Andy and Ryan met with Ed Creed, a marketing executive from the University to help us advertise the project, as well as iGEM. We're looking forward to having many more hits on the wiki and hopefully we’ll get some press releases created next week. <br><br>
+<br>
+<font color = "FA8072"><big><big>'''WEEK THREE'''</big></big><font color = "black">
+<br><br>
+<big><u> 2nd-6th July 2012</u></big>
+<br><br>
+The group attended this month’s Café Scientifique to obtain a general feel for the type of talks and discussions that take place there. We soon realised it was a relaxed atmosphere where topical debate was frequent and encouraged, I’m sure we’ll have plenty to talk about when we do our talk in September!<br>
+Becca spent the week designing Gibson primers that unfortunately weren’t required due to a slight change in plan. She researched and designed the primers for Hyaluronan synthases (HAS) and the 3 other genes needed to get hyaluronan but currently it appears we can’t afford them.  Gracefully she also assisted Alex in getting to grips with SacB and the primers for it. <br>
+This week we began investigating the ethics and impacts our project may have if successful. Alex B and Becca went to see Sabina Leonelli to obtain some extra guidance whilst Alex C has been investigating the potential impacts to pre-existing systems. We’ll be transferring everything we discover to their own corresponding wiki pages soon! Applications of SacB and HAS have also been explored whilst thinking how we can best display our triumph visually in the lab!<br><br>
+At the end of the week we’ve said goodbye to our engineer, Alice as she heads off for a lovely summer break in Budapest! But don’t despair she’ll be returning to help us out at a later date. <br><br>
+<font color = "FA8072"><big><big>'''WEEK FOUR'''</big></big><font color = "black">
+<br><br>
+<big><u> 9th-13th July 2012</u></big>
+<br><br>
+We kicked off the week with our now routine group meetings where we discussed our change of plans and the division of labour in the labs. Each of our 4 biologists is now leading their own “mini” assignment whilst being supported by one another they have each also enlisted their very own physicist! <br>
+Finally our primers are sorted and have been ordered! <br><br>
+This week saw the team having a short tour of the labs that we’ll be stationed in for the duration of the summer by Dagmara.<br><br>
+Liam, after spending many an interesting hour in the library over the last few weeks has been trawling through plenty of online tutorials trying to make sense of coding with Python and using the SQLite3 module. A process I think he will admit that he has secretly enjoyed! With his wealth of obtained knowledge he has begun his first attempt at our database program.<br>
+He’s taken a modular approach to assembly, taking his time with each individual element. The first model consisted of a program that took 3 sugars as user input and produced 2 separate lists of potential enzymes that could be used to conjoin sugar 1 to 2 and 2 to 3 respectively. After his visit to John Rowe he was able to implement several quick improvements, for instance the addition of error messages if the combination is impossible.  <br>
+Liam intends on making further improvements to his code with the hope of incorporating the ability to add any number of input sugars. The aim of the finished product which will hopefully be included in our wiki will require him learning code from another module called JPython... <b>“Yay!”</b><br>
+For a more detailed evaluation of the Database please visit our section on the wiki.
+<br><br>
+Work in labs finally commenced by transforming <i>Escherichia Coli</i> to bulk up some promoters, terminators and other useful things for BioBrick assembly! The next morning our previous labour was checked to make sure everything had worked properly. Thankfully it had as Tom was unsure how he would deliver a pep talk had we of failed! The plated colonies were left in the fridge until the afternoon where they were transferred to broth culture for further incubation. <br>
+For full details of our work in the lab, please visit the Lab Book tab.
+<br><br>