Difference between revisions of "Team:SPSingapore/Safety"

Line 1: Line 1:
−
{{SPSingapore}}
 
 
<html>
 
<html>
−
<h2>Safety in iGEM</h2>
 
  
−
<p>Please visit <a href="https://2015.igem.org/Safety">the main Safety page</a> to find this year's safety requirements & deadlines, and to learn about safe & responsible research in iGEM.</p>
+
<head>
 +
<link rel="stylesheet" type="text/css"
 +
href="https://2015.igem.org/Team:SPSingapore/CSS/menu?action=raw&ctype=text/css" />
 +
<link rel="stylesheet" type="text/css"
 +
href="https://2015.igem.org/Team:SPSingapore/CSS/notebook?action=raw&ctype=text/css" />
 +
<link rel="stylesheet" type="text/css"
 +
href="https://2015.igem.org/Team:SPSingapore/CSS/sidemenu?action=raw&ctype=text/css" />
  
−
<p>On this page of your wiki, you should write about how you are addressing any safety issues in your project. The wiki is a place where you can <strong>go beyond the questions on the safety forms</strong>, and write about whatever safety topics are most interesting in your project. (You do not need to copy your safety forms onto this wiki page.)</p>
+
<style>
 +
#top_menu_under{display:none;}
 +
body{background-color:black;margin: 24px 0;padding: 0;text-align: center;font: 0.8em/1.3 Verdana, Arial, Helvetica, Sans-serif;}
 +
#content{
 +
padding: 0px 0px 0px 0px;
 +
border-left: 0px;
 +
border-right: 0px;
 +
background-color: ghostwhite;
 +
}
 +
table{
 +
background-color:ghostwhite;
 +
align:center;
 +
}
 +
.nbtable{background:transparent;border-collapse: collapse; border: 1px solid black;}
 +
.nbtable td{padding-left:15px;padding-right:15px;padding-top:3px;padding-bottom:3px;}
  
 +
h1 {
 +
display: block;
 +
font-size: 2em;
 +
margin-before: 0.67em;
 +
margin-after: 0.67em;
 +
margin-start: 0;
 +
margin-end: 0;
 +
font-weight: bold;
 +
border-bottom: 0px;
 +
}
  
−
<h4>Safe Project Design</h4>
+
h2 {
 +
display: block;
 +
font-size: 1.5em;
 +
margin-before: 0.83em;
 +
margin-after: 0.83em;
 +
margin-start: 0;
 +
margin-end: 0;
 +
font-weight: bold;
 +
border-bottom: 0px;
 +
}
  
−
<p>Does your project include any safety features? Have you made certain decisions about the design to reduce risks? Write about them here! For example:</p>
+
table{border:collapse;}
  
−
<ul>
+
.details td{
−
<li>Choosing a non-pathogenic chassis</li>
+
vertical-align:top;
−
Our chasssis organism is E coli strain Dh5-alpha
+
}
  
−
<li>Choosing parts that will not harm humans / animals / plants</li>
+
a,a:hover{text-decoration:none;color: #ff7f00;}
−
<li>Substituting safer materials for dangerous materials in a proof-of-concept experiment</li>
+
</style>
−
<li>Including an "induced lethality" or "kill-switch" device</li>
+
</head>
−
We have two switches, a QS dependent AND gate and an anaerobic promoter.
+
  
 +
 +
<body>
 +
 +
<! ------------------------LOGO and MENU START ----------------------------------->
 +
<div class = "logo">
 +
</div>
 +
 +
<div id='cssmenu'>
 +
<ul>
 +
  <li><a href='https://2015.igem.org/Team:SPSingapore/'><span>Home</span></a></li>
 +
  <li><a href='https://2015.igem.org/Team:SPSingapore/Team'><span>Team</span></a></li>
 +
  <li><a href='https://2015.igem.org/Team:SPSingapore/Project'><span>Project</span></a></li>
 +
  <li><a href='https://2015.igem.org/Team:SPSingapore/Protocol'><span>Protocol</span></a></li>
 +
  <li><a href='https://2015.igem.org/Team:SPSingapore/Parts'><span>Parts</span></a></li>
 +
  <li class = 'active'><a href='https://2015.igem.org/Team:SPSingapore/Notebook'><span>Notebook</span></a></li>
 +
  <li><a href='https://2015.igem.org/Team:SPSingapore/Practices'><span>Human Practices</span></a></li>
 +
  <li class='last'><a href='https://2015.igem.org/Team:SPSingapore/Safety'><span>Safety</span></a></li>
 
</ul>
 
</ul>
 +
</div>
  
−
<h4>Safe Lab Work</h4>
+
<div id='sidemenu' style = "float:left">
 +
<ul>
 +
  <li class='last'><a href = "https://2015.igem.org/Team:SPSingapore/Notebook"><span>ENTRIES</span></a>
 +
<ul>
 +
        <li><a href = "https://2015.igem.org/Team:SPSingapore/Notebook-Week-1"><span>Week 1 (24/5 - 30/5) </span></a></li>
 +
        <li><a href = "https://2015.igem.org/Team:SPSingapore/Notebook-Week-2"><span>Week 2 (31/5 - 6/6)</span></a></li>
 +
        <li><a href = "https://2015.igem.org/Team:SPSingapore/Notebook-Week-3"><span>Week 3 (7/6 - 13/6)</span></a></li>
 +
        <li><a href = "https://2015.igem.org/Team:SPSingapore/Notebook-Week-4"><span>Week 4 (14/6 - 20/6)</span></a></li>
 +
        <li><a href = "https://2015.igem.org/Team:SPSingapore/Notebook-Week-5"><span>Week 5 (21/6 - 27/6)</span></a></li>
 +
        <li><a href = "https://2015.igem.org/Team:SPSingapore/Notebook-Week-6"><span>Week 6 (28/6 - 4/7)</span></a></li>
 +
        <li><a href = "https://2015.igem.org/Team:SPSingapore/Notebook-Week-7"><span>Week 7 (5/7 - 11/7)</span></a></li>
 +
        <li><a href = "https://2015.igem.org/Team:SPSingapore/Notebook-Week-8"><span>Week 8 (12/7 - 18/7)</span></a></li>
 +
        <li><a href = "https://2015.igem.org/Team:SPSingapore/Notebook-Week-9"><span>Week 9 (19/7 - 25/7)</span></a></li>
 +
        <li><a href = "https://2015.igem.org/Team:SPSingapore/Notebook-Week-10"><span>Week 10 (26/7 - 1/8)</span></a></li>
 +
        <li><a href = "https://2015.igem.org/Team:SPSingapore/Notebook-Week-11"><span>Week 11 (2/8 - 8/8)</span></a></li>
 +
        <li><a href = "https://2015.igem.org/Team:SPSingapore/Notebook-Week-12"><span>Week 12 (9/8 - 15/8)</span></a></li>
 +
        <li><a href = "https://2015.igem.org/Team:SPSingapore/Notebook-Week-13"><span>Week 13 (16/8 - 22/8)</span></a></li>
 +
        <li><a href = "https://2015.igem.org/Team:SPSingapore/Notebook-Week-14"><span>Week 14 (23/8 - 29/8)</span></a></li>
 +
        <li><a href = "https://2015.igem.org/Team:SPSingapore/Notebook-Week-15"><span>Week 15 (30/8 - 5/9)</span></a></li>
 +
        <li><a href = "https://2015.igem.org/Team:SPSingapore/Notebook-Week-16"><span>Week 16 (6/9 - 12/9)</span></a></li>
 +
        <li class = 'last'><a href = "https://2015.igem.org/Team:SPSingapore/Notebook-Week-17"><span>Week 17 (13/8 - 17/9)</span></a></li>
 +
      </ul>
 +
  </li>
 +
</ul>
 +
</div>
  
−
<p>What safety procedures do you use every day in the lab? Did you perform any unusual experiments, or face any unusual safety issues? Write about them here!</p>
+
<! ------------------------LOGO and MENU END ----------------------------------->
  
−
We work in a BSL2 Lab. In order to ensure no leak of bacteria, proper sterile technique is practiced and all bacterial work in done in a Biosafety Cabinet. Liquid Biohazard waste is deactivated using Presept Tablets (bleach) and solid biohazard waste is incinerated
+
<br>
  
 +
<! ------------------------------- Main Content START --------------------------------------------->
 +
<div id = "maincontent">
 +
<center>
 +
<table>
 +
<tr>
 +
<td colspan=1 style = "box-shadow: 0 0 0; padding:0;border-top:5px white;font-size:15px">
 +
<h1>Research Notebook</h1></td>
 +
</tr>
 +
</table>
 +
</center>
 +
 +
<center>
 +
<table><tr><td>
 +
<div style = "border-top: 5px solid blue; width:750px; text-align:justify;margin-bottom: 20px; line-height:normal;">
 +
<h3 style ="margin-left:20px;">Week 3 (7/6 - 13/6)</h3>
 +
 +
 +
 +
<!----------------------- Entry Start ------------------------>
 +
<center>
 +
<table style = "width:700px; border-collapse: collapse;">
 +
 +
<tr class = "tablenotebook"><td><p class = "paper">
 +
8th June 2015
 +
<br><br>
 +
<strong>Yi Han</strong>
 +
<br><br>
 +
&bull; Miniprep of gfp plasmids, preparation of samples for sequencin
 +
<br>
 +
</p>
 +
</td>
 +
</tr>
 +
 +
<tr class = "tablenotebook"><td><p class = "paper">
 +
9th June 2015
 +
<br><br>
 +
<strong>Yi Han</strong>
 +
<br><br>
 +
&bull; All gfp plasmids had a correct sequence<br>
 +
&bull; Yun Ting kept glycerol stocok for all, and inoculation of 3mL of gfp3 into 100mL LB+amp for midiprep<br>
 +
</p>
 +
</td>
 +
</tr>
 +
 +
<tr class = "tablenotebook"><td><p class = "paper">
 +
10th June 2015
 +
<br><br>
 +
<strong>Yi Han & Yun Ting</strong>
 +
<br><br>
 +
&bull; Midiprep of gfp plasmid
 +
<br>
 +
&bull; PCR of gfp with KpnI-gfp and XhoI-gfp primers
 +
</p>
 +
</td>
 +
</tr>
 +
 +
<tr class = "tablenotebook"><td><p class = "paper">
 +
11th June 2015
 +
<br><br>
 +
<strong>Yun Ting & Duy</strong>
 +
<br><br>
 +
&bull; Nanodrop of gfp product &rarr; 595.5ng/ul
 +
<br>
 +
&bull; RE digest of EsaR vector with KpnI/XHoI<br>
 +
&bull; Gel electrophoreseis at 1000V for 30min<br>
 +
&bull; Gel extraction: 3.9ng/ul and 6.9ng/ul for Esa fragment and GFP --&gt; low yield<br>
 +
</p>
 +
</td>
 +
</tr>
 +
 +
<tr class = "tablenotebook"><td><p class = "paper">
 +
12th June 2015
 +
<br><br>
 +
<strong>Yun Ting</strong>
 +
<br><br>
 +
&bull; Gel extraction using Promega binding solution to melt gel, followed by thermo scientific kit
 +
<br><br>
 +
<strong>Adrian</strong>
 +
<br><br>
 +
&bull; Gel extraction optimisation
 +
<br>
 +
&bull; Hypothesised that the Binding buffer has a problem/DNA does not bind to column
 +
<br>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 +
1: 2X promega binding buffer volume<br>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 +
2: Increase incubation time for binding to 5min
 +
<br>
 +
&bull; Switch binding buffer to that of thermo scientific PCR purification kit<br>
 +
&bull; Use sodium acetate if available? To facilitate stronger binding to column
 +
<br>
 +
<u>Results:</u><br>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1: ~10ng/ul<br>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2: ~9ng/ul<br>
 +
&bull;Further optimisation-&gt; warm buffer, incubate for 5min<br>
 +
&bull;Elute in 30/20ul smaller volumes<br>
 +
</p>
 +
</td>
 +
</tr>
 +
 +
<tr class = "tablenotebook"><td><p class = "paper">
 +
13th June 2015
 +
<br><br>
 +
<strong>Yi Han</strong>
 +
<br><br>
 +
1: Thermoscientific miniprep columns with 2XThermoscientific binding buffer
 +
<br>
 +
2: Thermoscientific PCR purification kit 2X buffer
 +
<br>
 +
3: Promega kit 2X buffer
 +
<br><br><br>
 +
</p>
 +
</td>
 +
</tr>
 +
 +
</table>
 +
</center>
 +
<!------------------------------------------------------ Team End ---------------------------------------------------->
  
−
<h4>Safe Shipment</h4>
 
  
−
<p>Did you face any safety problems in sending your DNA parts to the Registry? How did you solve those problems?</p>
 
  
  
 
</div>
 
</div>
 +
</td></tr></table>
 +
 +
<! ------------------------------- Main Content END --------------------------------------------->
 +
 +
<! ------------------------------- Footer START ------------------------------------------------>
 +
 +
<div id="footer1">
 +
<br>
 +
<div class="left_sec">
 +
<p>
 +
<img src = "https://static.igem.org/mediawiki/2015/a/ab/SPSingapore_Team-Logo-New.png" height = "80px">
 +
</p>
 +
</div>
 +
<div class="right_sec">
 +
<p>
 +
<img src = "https://static.igem.org/mediawiki/2015/0/05/SPSingapore_NUS-Logo.png" height = "60px" style = "margin-top:10px;margin-right:30px;padding-right:30px;border-right: 3px solid lightgrey;">
 +
<img src = "https://static.igem.org/mediawiki/2015/7/72/SPSingapore_SPS-Logo.png" height = "60px" style = "margin-top:10px;margin-right:50px;"></a>
 +
</p>
 +
</div>
 +
</div>
 +
<br><br>
 +
 +
<! ------------------------------Footer END ---------------------------------------------------->
 +
 +
</body>
 +
 +
 +
 +
 
</html>
 
</html>

Revision as of 18:48, 12 September 2015


Research Notebook

Week 3 (7/6 - 13/6)

8th June 2015

Yi Han

• Miniprep of gfp plasmids, preparation of samples for sequencin

9th June 2015

Yi Han

• All gfp plasmids had a correct sequence
• Yun Ting kept glycerol stocok for all, and inoculation of 3mL of gfp3 into 100mL LB+amp for midiprep

10th June 2015

Yi Han & Yun Ting

• Midiprep of gfp plasmid
• PCR of gfp with KpnI-gfp and XhoI-gfp primers

11th June 2015

Yun Ting & Duy

• Nanodrop of gfp product → 595.5ng/ul
• RE digest of EsaR vector with KpnI/XHoI
• Gel electrophoreseis at 1000V for 30min
• Gel extraction: 3.9ng/ul and 6.9ng/ul for Esa fragment and GFP --> low yield

12th June 2015

Yun Ting

• Gel extraction using Promega binding solution to melt gel, followed by thermo scientific kit

Adrian

• Gel extraction optimisation
• Hypothesised that the Binding buffer has a problem/DNA does not bind to column
       1: 2X promega binding buffer volume
       2: Increase incubation time for binding to 5min
• Switch binding buffer to that of thermo scientific PCR purification kit
• Use sodium acetate if available? To facilitate stronger binding to column
Results:
       1: ~10ng/ul
       2: ~9ng/ul
•Further optimisation-> warm buffer, incubate for 5min
•Elute in 30/20ul smaller volumes

13th June 2015

Yi Han

1: Thermoscientific miniprep columns with 2XThermoscientific binding buffer
2: Thermoscientific PCR purification kit 2X buffer
3: Promega kit 2X buffer