Difference between revisions of "Team:Birkbeck/Notebook"

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<head>
 
<head>
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<h1>Sean is Editing!</h1>
+
<h1>The Big Birkbeck House</h1>
 +
</head>
 +
<h2>Notebook</h2>
 +
<div>
 +
<h3><b>Week 1 in the Big Birkbeck House</b></h3>
 +
<p><b>The Boot Camp</b</p>
 +
<br>
 +
<div>
 +
<p>A joint collaboration between the UCL, Biohackspace & Birkbeck iGEM teams were held in order to train team members in certain roles within each team. The organised boot camp took place over a week. Teams all met in mornings to carried out basic lab training. In afternoons, 3 specific training routes were followed; DIYbio, Software/Automation & extra lab. Members from each formed afternoon groups.</p>
 +
<IMG SRC="https://static.igem.org/mediawiki/2015/2/2f/BBKiGEM2015Labtraining%28WayneWorkingHard%29.jpg" ALT="Wayne Leading by example & working hard!" WIDTH=270 HEIGHT=480 align="right">
 +
</div>
 +
<br>
 +
<br>
 +
<h4>Monday 15<sup>th</sup> June<h4>
 +
<h5>Morning Lab</h5>
 +
<p>Monday morning consisted of a Lab safety induction & a discussion on the standardised cloning strategy to be applied throughout the iGEM competition. The common major feature of each plasmid backbone has a prefix (to the 5' end of the biobrick) & suffix (3' end of the biobrick). The prefix and suffix restriction sites are highlighted in <i>Figure 1</i>. The standardised engineering procedure works by cutting the vector backbone in the suffix region while inserts (if already cloned into a vector) are cut in the prefix and suffix (cartoon representation of reactions are displayed in <i>Figure 2</i>). The ligation of insert and vector backbone will yield a recombinant plasmid with a scar as the <i>XbaI</i> & <i>SpeI</i> sites anneal.</p>
 +
<br>
 +
<IMG SRC="https://static.igem.org/mediawiki/2015/9/9d/Prefix.Diagram.notebook.1.pdf" WIDTH=480 HEIGHT=480 Align="center">
 +
<p><i><b>Figure 1: Prefix & Suffix Restriction Sites</b></i>.</p>
 +
<br>
 +
<IMG SRC="https://static.igem.org/mediawiki/2015/2/28/Team.BBK.iGEM.2015.Cloning.Strategy_.pdf" WIDTH=580 HEIGHT=480 Align="center">
 +
<p><i><b>Figure 2: Cloning Strategy</b></i>.</p>
 +
</div><br>
 +
<div>
 +
<p> On the first day of the lab, each of the iGEM teams were split into 3 groups. Each sub team was investigating different promoters used in expressing <i>mrfp</i>;
 +
<br>
 +
<ul>
 +
<li><a href="http://parts.igem.org/partsdb/get_part.cgi?part=BBa_K823005"> Group 1 used pSB1C3 - BBa_J23101 as a vector.</a></li>
 +
<li><a href="http://parts.igem.org/partsdb/get_part.cgi?part=BBa_K823008"> Group 2 Used  pSB1C3 - BBa_J23106 as a vector.</a> </li>
 +
<li><a href="http://parts.igem.org/partsdb/get_part.cgi?part=BBa_K823013"> Group 3 Used  pSB1C3 - Bba_J23117 as a vector.</a></li>
 +
</ul>
 +
</p>
 +
</div>
  
 +
<br>
 +
<p>This interlab study aims at using the same protocol in expression of <i>rfp</i> in <i>E. coli</i> cells. With reference to <i>Figure 3</i>, the 2006 Berkeley iGEM team characterised each of the promoters. iGEM teams across the globe will quantitatively measure the fluorescence of RFP & GFP with respect to each promoter listed. This will generate a large data set and therefore a statistically more reliable conclusion of the original experiments.</p>
 +
<IMG SRC="https://static.igem.org/mediawiki/2015/b/bc/Team.bbk.2015.iGEM.notebook.week1.interlab.fig2.pdf" WIDTH=580 HEIGHT=480 Align="center">
 +
<br>
 +
<div>
 +
<p><i><b><li><a href="http://parts.igem.org/Part:BBa_J23101">Figure 3: Results of the Berkeley 2006 iGEM Team</i></b></a>.</p>
 +
</div>
 +
<br>
 +
<p>On day 1, the main goal in the morning lab was to make a ligation reaction ready for transformation on day 2. The backbone (pSB1C3 based) had to be cut with <i>SpeI</i> & <i>PstI</i> which linearised the vector backbone by cutting into the suffix(as highlighted in <i>Figures 1</i> & <i>Figures 2</i>). The insert dervived from pSB1A2 by a double restriction digest using <i>XbaI</i> & <i>PstI</i>. In order to verify reactions had worked, each of the double digests were ran on a 1% (wt/vol) agarose gel (100 V for 1 hr) and visualised by ethidium bromide staining and visualising bands using a U.V. light source.</p>
 +
<br>
 +
<p>After reaction verification, a ligation was performed by using ~75 ng of insert to 25 ng of vector. The reaction was carried out at room temperature for 30 minutes and the heat killed at 80°C for 20 mins. Reactions were stored at 4°C overnight for transformation.</p>
 +
<br>
 +
<h5>Meet & Greets</h5>
 +
<br>
 +
<p>All team members were invited to the anatomy building of UCL to meet each other. After a brief 30 minutes of introductions, A skype talk was help with Randy Rettberg (the president of the iGEM foundation). The talk consisted of Randy Rettbergs general background, interest in synthetic biology & the origins of the iGEM competition. A Q & A session was held after the talk.</p>
 +
<br>
 +
<p>A previous iGEM team member (UCL 2014, Georgia Bondy) held an interactive talk on the division of labour. Emphasis was placed on the need for team members to take responsibility for <b>one aspect</b> of the project. The "babies" had to be nurtured by the team member who chooses to be responsible for each task.</p>
 +
<h4>Tuesday 16<sup>th</sup> June</h4>
 +
<h5>Mornin Lab</h5>
 +
<br>
 +
<p></p>
 +
<br>
 +
<h5>Software</h5>
 +
<br>
 +
<p></p>
 +
<br>
 +
<h5>DIY Bio</h5>
 +
<br>
 +
<p></p>
 +
<br>
 +
<h5>Extra Lab</h5>
 +
<br>
 +
<p></p>
 +
<br>
 +
<h4>Wednesday 17<sup>th</sup> June</h4>
 +
<h5>Mornin Lab</h5>
 +
<br>
 +
<p></p>
 +
<br>
 +
<h5>Software</h5>
 +
<br>
 +
<p></p>
 +
<br>
 +
<h5>DIY Bio</h5>
 +
<br>
 +
<p></p>
 +
<br>
 +
<h5>Extra Lab</h5>
 +
<br>
 +
<p></p>
 +
<br>
 +
<h4>Thursday 18<sup>th</sup> June</h4>
 +
<h5>Mornin Lab</h5>
 +
<br>
 +
<p></p>
 +
<br>
 +
<h5>Software</h5>
 +
<br>
 +
<p></p>
 +
<br>
 +
<h5>DIY Bio</h5>
 +
<br>
 +
<p></p>
 +
<br>
 +
<h5>Extra Lab</h5>
 +
<br>
 +
<p></p>
 +
<br>
 +
<h4>Friday 19<sup>th</sup> June</h4>
 +
<h5>Mornin Lab</h5>
 +
<br>
 +
<p></p>
 +
<br>
 +
<h5>Software</h5>
 +
<br>
 +
<p></p>
 +
<br>
 +
<h5>DIY Bio</h5>
 +
<br>
 +
<p></p>
 +
<br>
 +
<h5>Extra Lab</h5>
 +
<br>
 +
<p></p>
 +
<br>
 +
<br><hr><br>
 +
 +
 +
<h3>Week 2 in the Big Birkbeck House</h3>
 +
<h4>The Science Busk</h4>
 +
<p></p>
 +
<p>On Wednesday 24th June the Birkbeck 2015 iGEM team visited Canonbury Primary School in order to carry out a “scientific” busk. The Birkeck team and other current students/graduates of Birkbeck College presented on a wide variety of scientific topics.</p>
 +
<p></p>
 +
<p>There were 3 talks;</p>
 +
<p></p>
 +
<ol>
 +
<li> The importance of cleanliness and application of microbes in industry.
 +
<br>
 +
Kids took part in an activity using glitter to illustrate the epidemiology of bacteria being passed in a population through contact. Clapping & shouting was involved in this activity which the kids animatedly took part in.</p6>
 +
<p></p>
 +
<p6>b. It was also explained that not all microbes are bad & that in fact some are actually used in the production of food.</p6>
 +
<br>
 +
<p></p>
 +
<p6>2. Imaging, Geology & Planetary Science.</p6>
 +
<br>
 +
<p6>a. Kids interacted enthusiastically with an activity involving piecing together an image of a planet. </p6>
 +
<br>
 +
<p6>b. Real geological samples were on display, with a Birkbeck Geology graduate describing the fossil & rock samples on show.</p6>
 +
<br>
 +
<p6>3. Genetic Inheritance, DNA Structure & DNA function.</p6>
 +
<br>
 +
<p6>a. The use of coloured beans (to represent genes) and paper flowers (to represent the phenotype) was used in an activity to show the nature of inheritance.</p6>
 +
<br>
 +
<p6>b. Kids took part in formin a human DNA double helix.</p6>
 +
<br>
 +
<p6>c. Kids took the role of detectives in the “Break the Code” DNA game. Paper models of a DNA with a secret code was used to illustrate the different functions of DNA based on the sequence and reinforce the structure of DNA.</p6>
 +
<br>
 +
<br>
 +
<p6>Along with teaching the kids a little science (although the level of understanding & knowledge the kids had was grossly under estimated) an important message was conveyed by each group. “What actually interested each individual in science?”, was used to try to inspire the kids into perhaps studying science at degree level. Many people presenting were from all walks of life, ages and reasons for being enthusiastic about their specialized subject area.</p6>
 +
<br>
 +
<h4>Lab Training</h4>
 +
<br>
 +
<p7>On Thursday 25th of June, the OwligOs were inducted into Lab303/307 at the main building at Birkbeck College (Mallet Street). The induction involved training with lab equipment (such as centrifuges, pH meter, plate readers & PCR machines), the disposal of waste materials, procedures to follow in emergencies,  staff members to contact for particular problems & location of consumables (including logging consumable usage).</p7>
 +
</div2><br><hr><br>
 +
<div3>
 +
<h3>Week 3 in the Big Birkbeck House</h3>
 +
<p1>Enter Text</p1>
 +
</div3>
 +
<br><hr><br>
 +
<div4>
 +
<h3>Week 4 in the Big Birkbeck House</h3>
 +
<p1>Enter Text</p1>
 +
</div4>
 +
<br><hr><br>
 +
<div5>
 +
<h3>Week 5 in the Big Birkbeck House</h3>
 +
<p1>Enter Text</p1>
 +
</div5>
 +
<br><hr><br>
 +
<div6>
 +
<h3>Week 6 in the Big Birkbeck House</h3>
 +
<p1>Enter Text</p1>
 +
</div6>
 +
<br><hr><br>
 +
<div7>
 +
<h3>Week 7 in the Big Birkbeck House</h3>
 +
<p1>Enter Text</p1>
 +
</div7>
 +
<br><hr><br>
 +
<div8>
 +
<h3>Week 8 in the Big Birkbeck House</h3>
 +
<p1>Enter Text</p1>
 +
<br><hr><br>
 +
</div8>
 +
<div9>
 +
<h3>Week 9 in the Big Birkbeck House</h3>
 +
<p1>Enter Text</p1>
 +
</div9>
 +
<br><hr><br>
 +
<div10>
 +
<h3>Week 10 in the Big Birkbeck House</h3>
 +
<p1>Enter Text</p1>
 +
</div10>
 +
<br><hr><br>
 
</div>
 
</div>
 
</html>
 
</html>
 +
</div>
 +
<br><hr><br>
 +
<--!
 +
<p>During our first week on the project, the OwligO team was invited to take part in a training week kindly organised by UCL. This involved all training aspects of the project from Lab work to writing this wiki page! The weeks training also involved members of the OwligO team travelling to the London BioHackspace and being given training on DIYBiology. From each of the teams, people were divided into 3 groups to take part in three workshops.</p>
 +
<p> Document the dates you worked on your project.</p>
 +
 +
<h5>What should this page have?</h5>
 +
<ul>
 +
<li>Chronological notes of what your team is doing.</li>
 +
<li> Brief descriptions of daily important events.</li>
 +
<li>Pictures of your progress. </li>
 +
<li>Mention who participated in what task.</li>
 +
</ul>
 +
 +
 +
<h4>Inspiration</h4>
 +
<p>You can see what others teams have done to organize their notes:</p>
 +
 +
<ul>
 +
<li><a href="https://2014.igem.org/Team:ATOMS-Turkiye/Notebook">2014 ATOMS-Turkiye</a></li>
 +
<li><a href="https://2014.igem.org/Team:Tec-Monterrey/ITESM14_project.html#tab_notebook">2014 Tec Monterrey</a></li>
 +
<li><a href="https://2014.igem.org/Team:Kyoto/Notebook/Magnetosome_Formation#title">2014 Kyoto</a></li>
 +
<li><a href="https://2014.igem.org/Team:Cornell/notebook">2014 Cornell</a></li>
 +
</ul>
 +
<p>The lab training involved the cloning of rfp into pXXXXXXX using the rfc10 biobrick assembly protocol. There were 3 promoters cloned from pX, pY & pZ. Each construct would have been used for the interlab study.</p>
 +
<br>
 +
<p>In the group doing the DIY biology constructed a spectrophotometer using a LED light source and 3D printing. These workshops were all carried out at the London BioHackspace community lab.</p>
 +
<br>
 +
<p>The "software" group had workshops in modelling, coding & wiki design.</p>
 +
<br>
 +
<p>And at the end of a hard weeks iGEM training, wine, beer & nibbles were kindly provided :)</p>
 +
</div>
 +
<div2>

Revision as of 21:04, 1 July 2015

The Big Birkbeck House

Notebook

Week 1 in the Big Birkbeck House

The Boot Camp

A joint collaboration between the UCL, Biohackspace & Birkbeck iGEM teams were held in order to train team members in certain roles within each team. The organised boot camp took place over a week. Teams all met in mornings to carried out basic lab training. In afternoons, 3 specific training routes were followed; DIYbio, Software/Automation & extra lab. Members from each formed afternoon groups.

Wayne Leading by example & working hard!


Monday 15th June

Morning Lab

Monday morning consisted of a Lab safety induction & a discussion on the standardised cloning strategy to be applied throughout the iGEM competition. The common major feature of each plasmid backbone has a prefix (to the 5' end of the biobrick) & suffix (3' end of the biobrick). The prefix and suffix restriction sites are highlighted in Figure 1. The standardised engineering procedure works by cutting the vector backbone in the suffix region while inserts (if already cloned into a vector) are cut in the prefix and suffix (cartoon representation of reactions are displayed in Figure 2). The ligation of insert and vector backbone will yield a recombinant plasmid with a scar as the XbaI & SpeI sites anneal.


Figure 1: Prefix & Suffix Restriction Sites.


Figure 2: Cloning Strategy.


On the first day of the lab, each of the iGEM teams were split into 3 groups. Each sub team was investigating different promoters used in expressing mrfp;


This interlab study aims at using the same protocol in expression of rfp in E. coli cells. With reference to Figure 3, the 2006 Berkeley iGEM team characterised each of the promoters. iGEM teams across the globe will quantitatively measure the fluorescence of RFP & GFP with respect to each promoter listed. This will generate a large data set and therefore a statistically more reliable conclusion of the original experiments.



On day 1, the main goal in the morning lab was to make a ligation reaction ready for transformation on day 2. The backbone (pSB1C3 based) had to be cut with SpeI & PstI which linearised the vector backbone by cutting into the suffix(as highlighted in Figures 1 & Figures 2). The insert dervived from pSB1A2 by a double restriction digest using XbaI & PstI. In order to verify reactions had worked, each of the double digests were ran on a 1% (wt/vol) agarose gel (100 V for 1 hr) and visualised by ethidium bromide staining and visualising bands using a U.V. light source.


After reaction verification, a ligation was performed by using ~75 ng of insert to 25 ng of vector. The reaction was carried out at room temperature for 30 minutes and the heat killed at 80°C for 20 mins. Reactions were stored at 4°C overnight for transformation.


Meet & Greets

All team members were invited to the anatomy building of UCL to meet each other. After a brief 30 minutes of introductions, A skype talk was help with Randy Rettberg (the president of the iGEM foundation). The talk consisted of Randy Rettbergs general background, interest in synthetic biology & the origins of the iGEM competition. A Q & A session was held after the talk.


A previous iGEM team member (UCL 2014, Georgia Bondy) held an interactive talk on the division of labour. Emphasis was placed on the need for team members to take responsibility for one aspect of the project. The "babies" had to be nurtured by the team member who chooses to be responsible for each task.

Tuesday 16th June

Mornin Lab


Software


DIY Bio


Extra Lab


Wednesday 17th June

Mornin Lab


Software


DIY Bio


Extra Lab


Thursday 18th June

Mornin Lab


Software


DIY Bio


Extra Lab


Friday 19th June

Mornin Lab


Software


DIY Bio


Extra Lab




Week 2 in the Big Birkbeck House

The Science Busk

On Wednesday 24th June the Birkbeck 2015 iGEM team visited Canonbury Primary School in order to carry out a “scientific” busk. The Birkeck team and other current students/graduates of Birkbeck College presented on a wide variety of scientific topics.

There were 3 talks;

  1. The importance of cleanliness and application of microbes in industry.
    Kids took part in an activity using glitter to illustrate the epidemiology of bacteria being passed in a population through contact. Clapping & shouting was involved in this activity which the kids animatedly took part in.

    b. It was also explained that not all microbes are bad & that in fact some are actually used in the production of food.

    2. Imaging, Geology & Planetary Science.
    a. Kids interacted enthusiastically with an activity involving piecing together an image of a planet.
    b. Real geological samples were on display, with a Birkbeck Geology graduate describing the fossil & rock samples on show.
    3. Genetic Inheritance, DNA Structure & DNA function.
    a. The use of coloured beans (to represent genes) and paper flowers (to represent the phenotype) was used in an activity to show the nature of inheritance.
    b. Kids took part in formin a human DNA double helix.
    c. Kids took the role of detectives in the “Break the Code” DNA game. Paper models of a DNA with a secret code was used to illustrate the different functions of DNA based on the sequence and reinforce the structure of DNA.

    Along with teaching the kids a little science (although the level of understanding & knowledge the kids had was grossly under estimated) an important message was conveyed by each group. “What actually interested each individual in science?”, was used to try to inspire the kids into perhaps studying science at degree level. Many people presenting were from all walks of life, ages and reasons for being enthusiastic about their specialized subject area.

    Lab Training


    On Thursday 25th of June, the OwligOs were inducted into Lab303/307 at the main building at Birkbeck College (Mallet Street). The induction involved training with lab equipment (such as centrifuges, pH meter, plate readers & PCR machines), the disposal of waste materials, procedures to follow in emergencies, staff members to contact for particular problems & location of consumables (including logging consumable usage).

    Week 3 in the Big Birkbeck House

    Enter Text

    Week 4 in the Big Birkbeck House

    Enter Text

    Week 5 in the Big Birkbeck House

    Enter Text

    Week 6 in the Big Birkbeck House

    Enter Text

    Week 7 in the Big Birkbeck House

    Enter Text

    Week 8 in the Big Birkbeck House

    Enter Text

    Week 9 in the Big Birkbeck House

    Enter Text

    Week 10 in the Big Birkbeck House

    Enter Text

</div>



<--!

During our first week on the project, the OwligO team was invited to take part in a training week kindly organised by UCL. This involved all training aspects of the project from Lab work to writing this wiki page! The weeks training also involved members of the OwligO team travelling to the London BioHackspace and being given training on DIYBiology. From each of the teams, people were divided into 3 groups to take part in three workshops.

Document the dates you worked on your project.

What should this page have?
  • Chronological notes of what your team is doing.
  • Brief descriptions of daily important events.
  • Pictures of your progress.
  • Mention who participated in what task.


Inspiration

You can see what others teams have done to organize their notes:

The lab training involved the cloning of rfp into pXXXXXXX using the rfc10 biobrick assembly protocol. There were 3 promoters cloned from pX, pY & pZ. Each construct would have been used for the interlab study.


In the group doing the DIY biology constructed a spectrophotometer using a LED light source and 3D printing. These workshops were all carried out at the London BioHackspace community lab.


The "software" group had workshops in modelling, coding & wiki design.


And at the end of a hard weeks iGEM training, wine, beer & nibbles were kindly provided :)

</div> <div2>