Team:Dundee/Team

From 2014.igem.org

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              <h1>Real world</h1>
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<h1>Once upon a time there was a team</h1>
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            <p class="lead">Taking It's First Steps</p>
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            <h3>Aleks Płochocka</h3>
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<b>Nickname:</b> Toothy MaGee
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<b>Described in 5:</b> Enthusiastic. Determined. Kind-hearted. Funny.Young’un.
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Aleks has a massive love for all things maths and physics. She puts everything she has in to the modelling and building the device, making her a multitasking genius! Aleks is great to be in the lab with as she is always so positive and upbeat about everything (even when it feels like nothing is working!).
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            <h3>Fatima Ulhuq</h3>
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<b>Nickname:</b> Miss Chief
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Since the L.A.S.S.O. was designed using input from the CF community we wanted them to let us know how well it worked. It was essential to the team that possible future users could use the prototype. Therefore, we took the L.A.S.S.O. back to the our local CF clinic in order to get possible future users to have a go at testing the device.
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<b>Described in 5:</b> Resourceful. Creative. Loyal. Inspiring. Passionate
 
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She is a talented Pharmacology Student who has just finished her final year. Not only great at cloning she is great at making smiles. From putting teammates faces on a range of images, with humorous results, to making witty comments that lighten the most stressful of days. A strong pillar of the group and the project could not be a success without her.
 
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            <h3>Robyn Shuttleworth</h3>
 
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<b>Nickname:</b> Sharp Shootin’ Shotgun Shuttleworth
 
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<b>Described in 5:</b> Knowledgeable. Caring. Motivated. Enthusiastic. Spirited.
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Michael, a Cystic Fibrosis patient, gives his view on the L.A.S.S.O.;
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A Raffish Bounty Hunter who teams with Gillian and Aleks to find the bacterial bandits binding behaviours in efforts to collect The Lung Ranger reward. Her aim and precision is widely acknowledged across the southern plains and her trusty companion Rou ensures she’s the fastest cowboy in the west. When she’s not out on the plains bounty huntin’, her propensity with numbers means she’s statistically the most likely to get a royal flush playing poker.
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<source src="https://2014.igem.org/File:DUN_Michael_and_the_Future_of_the_Lung_Ranger.ogg" type='video/ogg; codecs="theora, vorbis"'/>
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<source src="https://static.igem.org/mediawiki/2014/a/ad/DUN_Michael_and_the_Future_of_the_Lung_Ranger.mov" type='video/mp4'/>
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            <h3>Dave Burrell</h3>
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<b>Nickname:</b> Scarlet
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<b>Described in 5:</b> Easy-going. Witty. Honest. Ambitious. Inspirational.
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Dr Rogers giving her views on the L.A.S.S.O. Interface;
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Dave is probably one of the most chilled out people in the lab.Studying Computer Science; he’s the master of coding. With everything he does there’s the attitude of “when stuff will work”, not “if”. Aside from being the wiz behind the wiki he worked on the LASSO and dived into electronics with huge enthusiasm. Overall one of the best things about working on a team with Dave is the encouragement he gives you. He’s always motivating in terms of new ideas that come up and always there to crack a joke with in between.
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            <h3>Gillian Forsyth</h3>
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            <img class="person" data-alt-src="https://static.igem.org/mediawiki/2014/3/31/Gill_west2.png" src="https://static.igem.org/mediawiki/2014/1/15/Gillm.png" />                             
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We had an ISO 13485 certified auditor look through our documentation for the L.A.S.S.O. and perform a mock audit to highlight any additional steps we could take to have a product that is as industry-ready as possible. In addition to receiving suggestions about how to improve our documentation (which have been acted upon) we were informed of the following:
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    <b>Nickname:</b> Frisbeest
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<b>Described in 5:</b> Calm. Composed. Full of energy.
 
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Gillian is our team Mathematical Biologist. While trying to come up with stochastic models, she’s making the perplexed biologists relive their nightmare of doing math! Usually, she’s quite calm and composed, until she finds a mini bicycle, and then she’s off! The rest of us might have all moved into the shade, injured by their burns, but Gillian will still be out and having fun! She loves variety in her life so to mix it up; she likes to hop on a space hopper!
 
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            <h3>Dimitrios Michailidis</h3>
 
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<b>Nickname:</b> Conchita Wurst
 
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<b>Described in 5:</b> Bewhiskered Bionic Beauty Battles BioBricks
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In Europe, to obtain a CE mark there are three devices directives:
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<li>Medical Device Directive </li>
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Science will never defeat him, it may knock him once...twice...three times (while going competent cells by the gallon full) but never will he surrender.He strives to do his very best, like no one ever has. To Biobrick the genes is his real test, to sequence them is his cause. He will travel across the labs, searching far and wide, each PostDoc to understand, the knowledge that’s inside. Gotta Biobrick them all. His life’s ambition is to be as successful as this year’s Eurovision song contest winner Conchita Wurst...do you think he has the potential?
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<li>Active Implantable Device Directive</li>
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<li>In Vitro Diagnostics (IVD) Directive </li>
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According to the auditor our device, while being “active”, is classed as an IVD and therefore if we were to optimise our device for uptake by a manufacturer we could streamline the process further by satisfying the criteria laid out in the IVD directive. This is being investigated currently.
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            <h3>Roddy McNeill</h3>
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<b>Nickname:</b> Violet
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<b>Described in 5:</b> A buffalo in a blizzard 
 
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Hailing from Glasgow's own Wild West end, Roddy brings a most necessary element of calm to the team - cool and collected in the face of results that might frazzle a softer scientist. Roddy has become our resident biochemist, absorbing the techniques of PhD students and PIs alike to become a one-gunned, sharp-eyed, no-horse-having, western-blotting hurricane. Roddy's extra mural activities also strengthen the team - his karate-honed reflexes mean he never drops the lunchtime frisbee and his time spent moonlighting as the lovely Violet has honed a thinly veiled talent for sass, which keeps the rest of us on our toes.
 
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            <h3>Jen Wood</h3>
 
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    <b>Nickname:</b> JeMCherry
 
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<b>Described in 5:</b> Merry. Ambitious. Out-going. Energetic. Bubbly.
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A product life cycle is split into stages:
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Jen is the cheery-cherry of the group. Aside from sharing her singing with us in the lab, her passion for running has somehow rubbed off and even the un-fittest amongst us are running to raise money for the CF trust. Jen is our outreach goddess; she is very well connected and her enthusiasm and positivity is very infectious. Watch out our future medic will treat you with happiness and fantastic lemon cake!
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<li>Optimisation </li>
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<li>Verification </li>
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            <h3>Jess Martyn</h3>
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We are in the early stages of the above list, with Proof of concept/Feasibility being our main achievement thus far. Optimisation is being carried out currently by testing our device with variable levels of luminescent input. Verification will be carried out by clinical trials with homogenised sputum samples, a portion of which would be analysed by microbiological means (serial dilution and culturing for CFU count and sequencing/PCR for bacterial species identification) to ensure that our device is accurately and reproducibly giving readings of bacterial species and load.
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The audit concludes with some general questions on the use of the device. We have answered these below.
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<b>Q.</b> Microbiological concerns – are the specimen receptacles single use?  How long can they be stored before the bin needs to be emptied?  Will all the samples be from the same patient?
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<b>A.</b> The receptacles (plates containing our biological components) will be single use and will be emptied from the bin and disposed of following autoclaving on the day of use. The samples will not all necessarily be from the same patient, this will depend on the number of patients being visited in a day. Neither the team nor medical staff have identified any potential issues with this approach.
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<b>Q.</b> How will consistency be maintained between device batches?
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    <b>Nickname:</b> Mr Chief
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<b>Described in 5:</b> G<b>rrrrr</b>eat C<b>rrrrr</b>ackin Passionate Crazy Scientist 
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<b>A.</b> During the manufacture of our receptacles and prior to freeze-drying, each inoculum of our biological component will be measured carefully for optical density and a sample will be assayed for activity in the presence of a synthetic signalling molecule. The latter process would be scaled-down to the minimal reaction size required to give a significant result in order to be economically viable.
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<b>Q.</b> What kind of shelf-life/in-use stability are you looking at for this device?  How will it be transported and stored?
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"We’ll sneak in after she's left the lab and set everything up for her birthday!" . . . around about midnight Fatima and Aleks managed to get into the lab to set everything up. Jess is typically the first in, and last out of the lab; diligently pursuing the fluorescent read out from our little Lung Ranger. Bubbly, cheerful and always ready to play a prank (or two!) on unsuspecting members of the team, Jess is a stalwart of the wet lab. Everything she's involved in can generally be summed up as Crackin'!
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<b>A.</b> It is difficult to project a shelf–life for this device but based upon the simplicity of the majority of the hardware (plastic casings etc.), if the biennial maintenance checks suggested in our requirements  document are carried out for the electronic components, this product will potentially be viable for many years before replacement becomes necessary.
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<b>Q.</b> How can an operator check the test is working – will you provide calibrators or controls?
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<b>A.</b> Both a positive and a negative control would be supplied with the device. The negative control would be a plate that was identical to all other receptacles except that it would contain no bacterial culture and thus would also function as a reference measurement. The positive control would be a source of light such as an LED which would give a reliable intensity and wavelength of light. The light source should be of a very low light level so that it would be consistent with the level of light produced by the luciferase. The latter could be built in to future versions of the L.A.S.S.O. 
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Scott is a born synthetic biologist, and was in the lab the day after exams planning a cloning strategy. His long standing battle of attrition with colony PCRs has been costly, threatening to grind him down during long afternoons and evenings, and resorting to him pipetting with two Gilsons at a time. Yet his diligence and endurance has paid off, providing us with perfect clones for our devices. Scott’s sunny optimism often bolsters the team; during dark times, with no bands on gels, blank sequence results and no code on the computer, his “F*@k it; it’ll work” always lightens the mood and spurs people on! Scott’s musical expertise is undeniable; his highly anticipated iGEM mashup “Build Me Up Biobrick-All You Need is One (Resistant Colony)-Centrifuges Spin Me Right Round” is sure to make the headlines by the time Boston comes around.As one of the first in the team to present at the SULSA conference, and happy to ferry furniture to different offices when required, no job is too big or too small for Mr McCrimmon.
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Francois is very enthusiastic and passionate about science. He is always cool and collected in the lab; as well as on the football field!
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  <div class="col-md-10">  <p>  Karim has a talent for asking the questions which you haven’t even considered! He keeps us on our toes and helps us overcome any issues. With his help we are able to better understand our work and in turn progress with our project. Always popping his head in to see if there is anything he can help us with.       
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Avril is an iGEM veteran at the University of Dundee, having been a member of the 2012 team and stepping into an advisory role for the 2013 and 2014 teams.  Being a bit of a renaissance woman, Avril has helped us all out not only by contributing to our project-planning meetings at the start of the summer and helping to lay the groundwork in the lab, but also by creating some beautiful artwork for our wiki (including The Lung Ranger himself!). Not content with countless hours of brushstrokes, she has also been working on a wee musical iGEM treat… 
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    Tracy “Cactus ” Palmer is making her debut to the Jamboree this year after heading up the Dundee iGEM competition at home since 2011. Cactus Palmer is one of the most notorious outlaws of the Wild West, keeping her band of lawless students in check and making sure we don't stray from the path by running an 8mm gel for anything longer than 3 minutes... Tracy's famous skill at the cloning bench (it's a black art!) is envied by us all and we've spent the summer trying to develop our own magic hands. Although Tracy has been known to leave the team shaking in their little cowboy boots, her knowledge and experience is always on hand to settle things down when there's a fox in the iGEM henhouse!
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      Frank “Snakebite” Sargent is an iGEM veteran - with 3 competitions under his belt he returns to Boston this year on the poster judging panel, beware his eagle-eye! This poker-faced protein master has been mentoring the team over the summer by teaching us the way of the wild-western blot (with all the associated book-learnin’), helping us to design experiments to test our system, and by making an appearance as a scar-faced villain in our photoshoot.
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    Dyce is the dynamic driving force behind the dry lab. His high expectations of each team member bring out the best in us. Behind his formal attire is a comedian at heart and someone who is always prepared to ply us with coffee in our hours of need!   
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Revision as of 19:27, 17 October 2014

Dundee 2014

Real world

Taking It's First Steps

User Feedback

Since the L.A.S.S.O. was designed using input from the CF community we wanted them to let us know how well it worked. It was essential to the team that possible future users could use the prototype. Therefore, we took the L.A.S.S.O. back to the our local CF clinic in order to get possible future users to have a go at testing the device.

Michael, a Cystic Fibrosis patient, gives his view on the L.A.S.S.O.;



Dr Rogers giving her views on the L.A.S.S.O. Interface;



Audit

We had an ISO 13485 certified auditor look through our documentation for the L.A.S.S.O. and perform a mock audit to highlight any additional steps we could take to have a product that is as industry-ready as possible. In addition to receiving suggestions about how to improve our documentation (which have been acted upon) we were informed of the following:

In Europe, to obtain a CE mark there are three devices directives:

  • Medical Device Directive
  • Active Implantable Device Directive
  • In Vitro Diagnostics (IVD) Directive
According to the auditor our device, while being “active”, is classed as an IVD and therefore if we were to optimise our device for uptake by a manufacturer we could streamline the process further by satisfying the criteria laid out in the IVD directive. This is being investigated currently.

A product life cycle is split into stages:
  • Proof of concept/Feasibility
  • Optimisation
  • Verification
  • Validation
  • Launch
  • Post Market surveillance
  • Withdrawal from the market/end-of-life
We are in the early stages of the above list, with Proof of concept/Feasibility being our main achievement thus far. Optimisation is being carried out currently by testing our device with variable levels of luminescent input. Verification will be carried out by clinical trials with homogenised sputum samples, a portion of which would be analysed by microbiological means (serial dilution and culturing for CFU count and sequencing/PCR for bacterial species identification) to ensure that our device is accurately and reproducibly giving readings of bacterial species and load.

The audit concludes with some general questions on the use of the device. We have answered these below.
Q. Microbiological concerns – are the specimen receptacles single use? How long can they be stored before the bin needs to be emptied? Will all the samples be from the same patient?

A. The receptacles (plates containing our biological components) will be single use and will be emptied from the bin and disposed of following autoclaving on the day of use. The samples will not all necessarily be from the same patient, this will depend on the number of patients being visited in a day. Neither the team nor medical staff have identified any potential issues with this approach.
Q. How will consistency be maintained between device batches?

A. During the manufacture of our receptacles and prior to freeze-drying, each inoculum of our biological component will be measured carefully for optical density and a sample will be assayed for activity in the presence of a synthetic signalling molecule. The latter process would be scaled-down to the minimal reaction size required to give a significant result in order to be economically viable.
Q. What kind of shelf-life/in-use stability are you looking at for this device? How will it be transported and stored?

A. It is difficult to project a shelf–life for this device but based upon the simplicity of the majority of the hardware (plastic casings etc.), if the biennial maintenance checks suggested in our requirements document are carried out for the electronic components, this product will potentially be viable for many years before replacement becomes necessary.
Q. How can an operator check the test is working – will you provide calibrators or controls?

A. Both a positive and a negative control would be supplied with the device. The negative control would be a plate that was identical to all other receptacles except that it would contain no bacterial culture and thus would also function as a reference measurement. The positive control would be a source of light such as an LED which would give a reliable intensity and wavelength of light. The light source should be of a very low light level so that it would be consistent with the level of light produced by the luciferase. The latter could be built in to future versions of the L.A.S.S.O.