Difference between revisions of "Team:IIT Kharagpur/Notebook"

 
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<html lang="en-US">
 
<html lang="en-US">
 
<head>
 
<head>
 +
<title>IGEM-IIT Kharagpur- Notebook</title>
 +
 +
 +
  
−
<title>IGEM-IIT Kharagpur- Protocol</title>
 
−
<meta charset="utf-8">
 
−
    <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
−
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−
<link rel="stylesheet" href="https://2016.igem.org/Template:IIT_Kharagpur/protocol_font_awesome?action=raw&ctype=text/css" />
 
−
 
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 +
<meta charset="utf-8">
 +
    <meta name="viewport" content="width=device-width, initial-scale=1.0">
 +
<link rel="stylesheet" href="https://2016.igem.org/Template:IIT_Kharagpur/notebook_bootstrap?action=raw&ctype=text/css" />
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<link rel="stylesheet" href="https://2016.igem.org/Template:IIT_Kharagpur/notebook_font_awesome_min?action=raw&ctype=text/css" />
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<link rel="stylesheet" href="https://2016.igem.org/Template:IIT_Kharagpur/notebook_fancy_buttons?action=raw&ctype=text/css" />
 
 
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<link href='http://fonts.googleapis.com/css?family=Raleway:600,400,300' rel='stylesheet' type='text/css'>
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<link href='http://fonts.googleapis.com/css?family=Open+Sans:400,300,600,700' rel='stylesheet' type='text/css'>
 +
<link href="http://fonts.googleapis.com/css?family=Roboto+Condensed:400,300,700" rel="stylesheet" type="text/css" />
 
<!--=== Other CSS files ===-->
 
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−
+
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<link rel="stylesheet" href="https://2016.igem.org/Template:IIT_Kharagpur/protocol_jquery_vegas?action=raw&ctype=text/css" />
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<link rel="stylesheet" href="https://2016.igem.org/Template:IIT_Kharagpur/notebook_jquery_vegas?action=raw&ctype=text/css" />
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<link rel="stylesheet" href="https://2016.igem.org/Template:IIT_Kharagpur/protocol_jquery_bxslider?action=raw&ctype=text/css" />
+
<link rel="stylesheet" href="https://2016.igem.org/Template:IIT_Kharagpur/notebook_jquery_bxslider?action=raw&ctype=text/css" />
 
 
 
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<!--=== Main Stylesheets ===-->
−
<link rel="stylesheet" href="https://2016.igem.org/Template:IIT_Kharagpur/protocol_style?action=raw&ctype=text/css" />
+
<link rel="stylesheet" href="https://2016.igem.org/Template:IIT_Kharagpur/notebook_style?action=raw&ctype=text/css" />
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<link rel="stylesheet" href="https://2016.igem.org/Template:IIT_Kharagpur/protocol_responsive?action=raw&ctype=text/css" />
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<link rel="stylesheet" href="https://2016.igem.org/Template:IIT_Kharagpur/notebook_responsive?action=raw&ctype=text/css" />
 
 
 
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<!--=== Color Scheme, three colors are available red.css, orange.css and gray.css ===-->
−
<link rel="stylesheet" id="scheme-source" href="https://2016.igem.org/Template:IIT_Kharagpur/protocol_gray?action=raw&ctype=text/css" />
+
<link rel="stylesheet" id="scheme-source" href="https://2016.igem.org/Template:IIT_Kharagpur/notebook_gray?action=raw&ctype=text/css" />
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<script src="http://oss.maxcdn.com/libs/respond.js/1.4.2/respond.min.js"></script>
 +
<![endif] -->
 
 
−
 
 
<style type="text/css">
 
<style type="text/css">
 
.logoigm{
 
.logoigm{
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     0%{ transform:rotate(0deg);  }
 
     0%{ transform:rotate(0deg);  }
 
     100%{ transform:rotate(360deg); }
 
     100%{ transform:rotate(360deg); }
 +
}
 +
.logobody{
 +
margin-left: 5%;
 +
 +
}
 +
.home_content{
 +
margin-top: -3%;
 
}
 
}
 
.icon{
 
.icon{
−
height: 26px;
+
height: 23px;
 
width: auto;
 
width: auto;
 
margin-right: 5px;
 
margin-right: 5px;
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#section-footer{
 
#section-footer{
 +
padding-top: 10px;
 
 
 
padding-bottom: 10px;
 
padding-bottom: 10px;
−
font-family: 'Dosis';
+
font-family: "Helvetica Neue",Helvetica,Arial,sans-serif;
 
color: white;
 
color: white;
 
}
 
}
 +
 
#logokgp{
 
#logokgp{
−
  padding-top: 15px;
+
    padding-top: 15px;
  
  
 
}
 
}
−
 
 
@media (max-width: 992px) {
 
@media (max-width: 992px) {
 
   #logokgp{
 
   #logokgp{
−
  padding-left: 10%;
+
    padding-left: 10%;
  
 +
}
 
}
 
}
 
}
 
}
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font-size: 15px;
 
font-size: 15px;
−
font-family: 'Dosis';
+
font-family: "Helvetica Neue",Helvetica,Arial,sans-serif;
−
line-height: 30px;
+
−
 
+
 
}
 
}
 
#mail{
 
#mail{
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     height: 40px;
 
     height: 40px;
 
     width: 80px;
 
     width: 80px;
−
    margin-top: -10px;
 
 
     font-size: 14px;
 
     font-size: 14px;
 
     font-weight: 400;
 
     font-weight: 400;
−
     font-family: 'Dosis';
+
     font-family: "Helvetica Neue",Helvetica,Arial,sans-serif;
 
     border-style: none;
 
     border-style: none;
−
    color: black;
 
 
}
 
}
 
.social{
 
.social{
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margin: .33em 0;
 
margin: .33em 0;
 
}
 
}
 +
 +
table {
 +
border-collapse: collapse;
 +
border-spacing: 0;
 +
}
 +
* {
 +
  margin: 0;
 +
  padding: 0;
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}
 +
 +
time {
 +
  color: white;
 +
  text-transform: uppercase;
 +
  font-weight: 300;
 +
  font-size: 38px;
 +
}
 +
time em {
 +
  display: block;
 +
  font-weight: 300;
 +
  font-style: normal;
 +
  font-size: 16px;
 +
}
 +
 +
header {
 +
  padding: 10px 0;
 +
  background: #4ecdc4;
 +
  text-align: center;
 +
  font-family: "Roboto Condensed", sans-serif;
 +
 +
}
 +
header a {
 +
  display: inline-block;
 +
  padding: 5px 20px;
 +
  border-radius: 20px;
 +
  background: #44b3ab;
 +
  color: white;
 +
  text-decoration: none;
 +
  text-transform: uppercase;
 +
  font-weight: 300;
 +
  font-size: 12px;
 +
  transition: all 0.3s ease-in-out;
 +
}
 +
header a:hover {
 +
  background: #249991;
 +
  color: #ccc;
 +
}
 +
 +
[role="main"] {
 +
  overflow: hidden;
 +
  padding: 15px;
 +
  background: white;
 +
  font-family: "Helvetica";
 +
}
 +
 +
section ul {
 +
  list-style-type: none;
 +
}
 +
section li {
 +
  position: relative;
 +
  display: inline-block;
 +
  float: left;
 +
  width: 25px;
 +
  height: 25px;
 +
  text-align: center;
 +
  line-height: 35px;
 +
  zoom: 1;
 +
  vertical-align: middle;
 +
  *display: inline;
 +
  margin-top: 2px ;
 +
  margin-left: 2px;
 +
 +
}
 +
 +
.l-date--event {
 +
  cursor: pointer;
 +
  transition: background 0.3s ease-in-out;
 +
}
 +
.l-date--event:hover {
 +
  background: #efefef;
 +
}
 +
 +
.m-bullet--event {
 +
  position: absolute;
 +
  top: 5px;
 +
  right: 5px;
 +
  display: block;
 +
  width: 5px;
 +
  height: 5px;
 +
  border-radius: 50%;
 +
  background: #ff6b6b;
 +
}
 +
 +
.m-box--weeks {
 +
  color: #e66b6b;
 +
  text-transform: uppercase;
 +
  font-weight: bold;
 +
  font-size: 10px;
 +
}
 +
 +
.m-box--date {
 +
  color: #555;
 +
  font-size: 14px;
 +
}
 +
 +
.l-date--passed {
 +
  color: #bababa;
 +
}
 +
 +
.eventTip {
 +
  position: absolute;
 +
  width: 150px;
 +
  left: 50%;
 +
  top: -125%;
 +
  margin-left: -75px;
 +
  background: #249991;
 +
  color: white;
 +
}
 +
.eventTip:before {
 +
  content: "▾";
 +
  position: absolute;
 +
  font-size: 25px;
 +
  color: #249991;
 +
  bottom: -19px;
 +
  left: 46%;
 +
}
 +
.calendar-patch{
 +
width: 220px;
 +
padding-top: 15px;
 +
}
 +
.content-calendar{
 +
color: white;
 +
padding-top: 10px;
 +
}
 +
 +
  
 
@font-face {
 
@font-face {
Line 140: Line 294:
 
}
 
}
  
 +
@font-face {
 +
font-family: 'Dosis';
 +
  font-style: normal;
 +
  font-weight: 400;
 +
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 +
}
  
 +
@font-face {
 +
font-family: 'Dosis';
 +
  font-style: normal;
 +
  font-weight: 500;
 +
  src: local("Dosis Medium"), local("Dosis-Medium"), url(http://fonts.gstatic.com/s/dosis/v6/obisuY-MenYRAFwd-r2NhfesZW2xOQ-xsNqO47m55DA.ttf) format("truetype");
 +
}
  
 +
@font-face {
 +
font-family: 'Dosis';
 +
  font-style: normal;
 +
  font-weight: 600;
 +
  src: local("Dosis SemiBold"), local("Dosis-SemiBold"), url(http://fonts.gstatic.com/s/dosis/v6/URSgP3aplSko3CQAzdXHwPesZW2xOQ-xsNqO47m55DA.ttf) format("truetype");
 +
}
  
 +
@font-face {
 +
font-family: 'Dosis';
 +
  font-style: normal;
 +
  font-weight: 700;
 +
  src: local("Dosis Bold"), local("Dosis-Bold"), url(http://fonts.gstatic.com/s/dosis/v6/Luunk03-uSz9LnB7oNEUuvesZW2xOQ-xsNqO47m55DA.ttf) format("truetype");
 +
}
  
 +
header:after, #timeline .timeline-item:after, header:before, #timeline .timeline-item:before {
 +
content: '';
 +
display: block;
 +
width: 100%;
 +
clear: both;
 +
}
  
−
body, html {
+
*, *:before, *:after {
−
height: 100%;
+
box-sizing: border-box;
 +
-webkit-box-sizing: border-box;
 +
-moz-box-sizing: border-box;
 
}
 
}
 +
 +
/*body, html {
 +
height: 100%;
 +
}*/
  
 
body {
 
body {
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font-weight: 500;
 
font-weight: 500;
 
}
 
}
−
.topcontainer{
+
 
−
color: white;
+
.project-name {
−
z-index: 12;
+
text-align: center;
−
position: relative;
+
padding: 10px 0;
 
}
 
}
  
 +
header {
 +
background: #2b2e48;
 +
padding: 10px;
 +
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 +
box-shadow: 0 3px 3px rgba(0, 0, 0, 0.05);
 +
}
  
−
.distance{
+
header .logo {
−
padding-top: 5px;
+
color: #ee4d4d;
 +
float: left;
 +
font-family: "Dosis", arial, tahoma, verdana;
 +
font-size: 22px;
 +
font-weight: 500;
 
}
 
}
−
.bluecolor{
+
 
−
background-color: #297b6e;
+
header .logo > span {
 +
color: #f7aaaa;
 +
font-weight: 300;
 
}
 
}
−
a{
+
 
 +
header .social {
 +
float: right;
 +
}
 +
 
 +
header .social .btn {
 +
font-family: "Dosis";
 +
font-size: 14px;
 +
margin: 10px 5px;
 +
}
 +
 
 +
#timeline {
 +
width: 100%;
 +
margin: 10px auto;
 
position: relative;
 
position: relative;
−
top: -5px;
+
padding: 0 5px;
 +
-webkit-transition: all 0.4s ease;
 +
-moz-transition: all 0.4s ease;
 +
-ms-transition: all 0.4s ease;
 +
transition: all 0.4s ease;
 +
z-index: 250;
 
}
 
}
−
.relativeposition{
+
 
 +
#timeline:before {
 +
content: "";
 +
width: 3px;
 +
height: 100%;
 +
background: #ee4d4d;
 +
left: 50%;
 +
top: 0;
 +
position: absolute;
 +
}
 +
 
 +
#timeline:after {
 +
content: "";
 +
clear: both;
 +
display: table;
 +
width: 100%;
 +
}
 +
 
 +
#timeline .timeline-item {
 +
margin-bottom: 50px;
 
position: relative;
 
position: relative;
−
top: -5px;
+
}
  
 +
#timeline .timeline-item .timeline-icon {
 +
background: #ee4d4d;
 +
width: 50px;
 +
height: 50px;
 +
position: absolute;
 +
top: 0;
 +
left: 50%;
 +
overflow: hidden;
 +
margin-left: -23px;
 +
-webkit-border-radius: 50%;
 +
-moz-border-radius: 50%;
 +
-ms-border-radius: 50%;
 +
border-radius: 50%;
 
}
 
}
−
.calendar{
+
 
−
font-family: "Dosis", arial, tahoma, verdana;
+
#timeline .timeline-item .timeline-icon svg {
−
padding-top: 45px;
+
position: relative;
−
background-color: white;
+
top: 14px;
−
font-size: 20px;
+
left: 14px;
−
line-height: 25px;
+
 
}
 
}
  
−
.panel-heading{
+
#timeline .timeline-item .timeline-content {
−
background-color: #82807f;
+
width: 45%;
 +
background: #fff;
 +
padding: 20px;
 +
-webkit-box-shadow: 0 3px 0 rgba(0, 0, 0, 0.1);
 +
-moz-box-shadow: 0 3px 0 rgba(0, 0, 0, 0.1);
 +
-ms-box-shadow: 0 3px 0 rgba(0, 0, 0, 0.1);
 +
box-shadow: 0 3px 0 rgba(0, 0, 0, 0.1);
 +
-webkit-border-radius: 5px;
 +
-moz-border-radius: 5px;
 +
-ms-border-radius: 5px;
 +
border-radius: 5px;
 +
-webkit-transition: all 0.3s ease;
 +
-moz-transition: all 0.3s ease;
 +
-ms-transition: all 0.3s ease;
 +
transition: all 0.3s ease;
 
}
 
}
−
.logobody{
 
−
margin-left: 4%;
 
  
 +
#timeline .timeline-item .timeline-content h2 {
 +
padding: 15px;
 +
background: #ee4d4d;
 +
color: #fff;
 +
margin: -20px -20px 0 -20px;
 +
font-weight: 300;
 +
-webkit-border-radius: 3px 3px 0 0;
 +
-moz-border-radius: 3px 3px 0 0;
 +
-ms-border-radius: 3px 3px 0 0;
 +
border-radius: 3px 3px 0 0;
 
}
 
}
−
.home_content{
+
 
−
margin-top: -2%;
+
#timeline .timeline-item .timeline-content:before {
 +
content: '';
 +
position: absolute;
 +
left: 45%;
 +
top: 20px;
 +
width: 0;
 +
height: 0;
 +
border-top: 7px solid transparent;
 +
border-bottom: 7px solid transparent;
 +
border-left: 7px solid #ee4d4d;
 
}
 
}
  
−
.tabledown{
+
#timeline .timeline-item .timeline-content.right {
 +
float: right;
 +
}
 +
 
 +
#timeline .timeline-item .timeline-content.right:before {
 +
content: '';
 +
right: 45%;
 +
left: inherit;
 +
border-left: 0;
 +
border-right: 7px solid #ee4d4d;
 +
}
 +
 
 +
.btn {
 +
padding: 5px 15px;
 +
text-decoration: none;
 +
background: transparent;
 +
border: 2px solid #f27c7c;
 +
color: #f27c7c;
 +
display: inline-block;
 
position: relative;
 
position: relative;
−
    top: 15em;
+
text-transform: uppercase;
 +
font-size: 12px;
 +
-webkit-border-radius: 5px;
 +
-moz-border-radius: 5px;
 +
-ms-border-radius: 5px;
 +
border-radius: 5px;
 +
-webkit-transition: background 0.3s ease;
 +
-moz-transition: background 0.3s ease;
 +
-ms-transition: background 0.3s ease;
 +
transition: background 0.3s ease;
 +
-webkit-box-shadow: 2px 2px 0 #f27c7c;
 +
-moz-box-shadow: 2px 2px 0 #f27c7c;
 +
-ms-box-shadow: 2px 2px 0 #f27c7c;
 +
box-shadow: 2px 2px 0 #f27c7c;
 
}
 
}
−
.well-come{
+
 
−
margin-top: 4em;
+
.btn:hover {
 +
box-shadow: none;
 +
top: 2px;
 +
left: 2px;
 +
-webkit-box-shadow: 2px 2px 0 transparent;
 +
-moz-box-shadow: 2px 2px 0 transparent;
 +
-ms-box-shadow: 2px 2px 0 transparent;
 +
box-shadow: 2px 2px 0 transparent;
 
}
 
}
  
 +
@media screen and (max-width: 768px) {
 +
#timeline {
 +
margin: 30px;
 +
padding: 0px;
 +
width: 90%;
 +
}
  
 +
#timeline:before {
 +
left: 0;
 +
}
  
−
a:hover{
+
#timeline .timeline-item .timeline-content {
 +
width: 90%;
 +
float: right;
 +
}
 +
 
 +
#timeline .timeline-item .timeline-content:before, #timeline .timeline-item .timeline-content.right:before {
 +
left: 10%;
 +
margin-left: -6px;
 +
border-left: 0;
 +
border-right: 7px solid #ee4d4d;
 +
}
 +
 
 +
#timeline .timeline-item .timeline-icon {
 +
left: 0;
 +
}
 +
}
 +
 
 +
.calendar{
 +
background-color: #e0e0e0;
 +
padding-bottom: 5px;
 +
position: relative;
 +
z-index: 500;
 +
}
 +
.notebook-content{
 +
background-color: #f9f9f9;
 +
z-index: 250;
 +
position: relative;
 +
padding-top: 280px;
 +
}
 +
.topcontainer{
 
color: white;
 
color: white;
 +
z-index: 12;
 +
position: relative;
 +
}
 +
 +
 +
#sticky.stick {
 +
    margin-top: 0 !important;
 +
    position: fixed;
 +
    top: 0;
 +
    z-index: 10000;
 +
    border-radius: 0 0 0.5em 0.5em;
 +
}
 +
.distance{
 +
padding-top: 5px;
 +
}
 +
.bluecolor{
 +
background-color: #297b6e;
 +
}
 +
a{
 +
position: relative;
 +
top: -5px;
 +
}
 +
.relativeposition{
 +
position: relative;
 +
top: -5px;
 +
 +
}
 +
.affix{
 +
position: fixed;
 +
top: 30px;
 +
 
}
 
}
 
.footerimage{
 
.footerimage{
−
width: 100px;
+
  width: 100px;
−
height: auto;
+
  height: auto;
 
}
 
}
 
.dropbtn {
 
.dropbtn {
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     background-color: #3e8e41;
 
     background-color: #3e8e41;
 
}
 
}
−
 
−
.completefooter{
 
−
padding-top: 5px;
 
−
padding-bottom: 10px;
 
−
}
 
 
.igem-logo-top{
 
.igem-logo-top{
−
width: 55px;
+
  width: 55px;
−
height: auto;
+
  height: auto;
  
−
float: left;
+
  float: left;
−
position: relative;
+
  position: relative;
−
right: 12px;
+
  right: 12px;
 +
}
 +
#mail{
 +
background-color: #17bcb8 !important;
 +
-webkit-tap-highlight-color: transparent;
 +
    will-change: opacity, transform;
 +
    height: 40px;
 +
    width: 80px;
 +
    margin-top: -10px;
 +
    font-size: 14px;
 +
    font-weight: 400;
 +
    font-family: 'Dosis';
 +
    border-style: none;
 +
    color: black;
 +
    box-shadow: none;
 +
}
 +
.social{
 +
height: 40px;
 +
width: auto;
 +
}
 +
.logobody{
 +
margin-left: 4%;
 +
 
 +
}
 +
.home_content{
 +
margin-top: -2%;
 +
}
 +
.table{
 +
width: 200px;
 +
height: auto;
 +
 +
position: absolute;
 +
margin-left:-7.5em;
 +
margin-top: -1%;
 +
}
 +
.tabledown{
 +
position: relative;
 +
    top: 15em;
 +
}
 +
.well-come{
 +
margin-top: 4em;
 
}
 
}
 
.center_icon{
 
.center_icon{
Line 297: Line 723:
 
}
 
}
  
−
 
−
</style>
 
  
  
 +
</style>
  
  
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<!--=== Preloader section Ends ===-->
 
<!--=== Preloader section Ends ===-->
 
 
−
<!--=== Header section Starts ===-->
+
<!--=== Header section Starts ===-->
−
<div id="header" class="header-section">
+
  <div id="header" class="header-section">
−
<!-- sticky-bar Starts-->
+
    <!-- sticky-bar Starts-->
 
<div class="sticky-bar-wrap">
 
<div class="sticky-bar-wrap">
 
<div class="sticky-section">
 
<div class="sticky-section">
−
<div id="topbar-hold" class="nav-hold container">
+
<div id="topbar-hold" class="nav-hold container"><a href="https://2016.igem.org/Team:IIT_Kharagpur">
−
<img src="https://static.igem.org/mediawiki/2016/thumb/8/86/T--IIT_Kharagpur--logo.png/180px-T--IIT_Kharagpur--logo.png" class="igem-logo-top">
+
<img src="https://static.igem.org/mediawiki/2016/thumb/8/86/T--IIT_Kharagpur--logo.png/180px-T--IIT_Kharagpur--logo.png" class="igem-logo-top icon"></a>
 
<nav class="navbar" role="navigation">
 
<nav class="navbar" role="navigation">
 
<div class="navbar-header">
 
<div class="navbar-header">
Line 395: Line 820:
 
<div class="home_content">
 
<div class="home_content">
 
 
−
<h1 class="well-come" style="font-family:Dosis;">PROTOCOL</h1>
+
<h1 class="well-come" style="font-family:Dosis;">NOTEBOOK</h1>
−
<img src="https://static.igem.org/mediawiki/2016/7/74/T--IIT_Kharagpur--protocol_centre.png" class="center_icon">
+
<img src="https://static.igem.org/mediawiki/2016/c/cd/T--IIT_Kharagpur--notebook.png" class="center_icon">
 
 
−
<div class="col-md-8 col-md-offset-2 tabledown">
+
<!-- <div class="col-md-8 col-md-offset-2 tabledown">
 
<p class="intro-message" style="font-family:Dosis; font-size:20px; text-align:center;">HARD WORK JUST LIKE JUST MA AND PA TAUGHT US</p>
 
<p class="intro-message" style="font-family:Dosis; font-size:20px; text-align:center;">HARD WORK JUST LIKE JUST MA AND PA TAUGHT US</p>
−
</div>
+
</div> -->
 
<div class="home-buttons">
 
<div class="home-buttons">
 
 
Line 410: Line 835:
 
<!--=== Home Section Ends ===-->
 
<!--=== Home Section Ends ===-->
 
</div>
 
</div>
−
<div class="calendar col-md-12" id="sticky" >
 
−
<div class="panel-group" id="accordion" role="tablist" aria-multiselectable="true">
 
−
  <div class="panel panel-info">
 
−
    <div class="panel-heading" role="tab" id="headingOne">
 
−
      <h4 class="panel-title">
 
−
        <a role="button" data-toggle="collapse" data-parent="#accordion" href="#collapseOne" aria-expanded="true" aria-controls="collapseOne">
 
−
          <b style="font-family:Dosis;">PROTOCOL - TRANSFORMATION </b>
 
−
        </a>
 
−
      </h4>
 
−
    </div>
 
−
    <div id="collapseOne" class="panel-collapse collapse" role="tabpanel" aria-labelledby="headingOne">
 
−
      <div class="panel-body">
 
−
        <h3><b>Approximation time:</b></h3> 120 mins
 
−
        <h3><b>Material required:</b></h3>
 
−
        <ul>
 
−
        <li>70% ethanol</li>
 
−
        <li>Tissue paper</li>
 
−
        <li>Ice</li>
 
−
        <li>Container for ice</li>
 
−
        <li>Timer</li>
 
−
        <li>DH5alpha cells</li>
 
−
        <li>LB agar plates – Chloramphenicol, (kanamycin+ ampicillin), Kanamycin</li>
 
−
        </ul>
 
−
        <h3><b>Protocol:</b></h3>
 
−
        <p style="font-family:Dosis; font-size:20px;">1. Keep all materials on ice unless otherwise specified! This will help make the cells more competent and easier to transform.</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">2. Label a 2.0ml microcentrifuge tube as Transformation Control, another as Ligation: New Part, and one more as Ligation Control.
 
−
          (Add 20ul of the New Part ligation product into the Ligation: New Part tube.)
 
−
        </p>
 
−
<p style="font-family:Dosis; font-size:20px;">3. Place the tubes on ice to pre-chill them.</p>
 
−
<p style="font-family:Dosis; font-size:20px;">4.  Thaw one competent cell aliquot tube on ice (this takes about 5-8 minutes).</p>
 
  
−
<p style="font-family:Dosis; font-size:20px;">5.  Gently flick the tube of competent cells, then pipet 50ul of competent cells into each 2.0ml microcentrifuge tube.
+
−
(Try to keep the cells as cold as possible by holding just the top of the tube, not the bottom where the cells are.)
+
−
</p>
+
−
<p style="font-family:Dosis; font-size:20px;">6.    Incubate the DNA and cell mixtures on ice for 30 minutes. During this incubation, pre-heat the waterbath to 40°C.</p>
+
−
<p style="font-family:Dosis; font-size:20px;">7.    Place the tubes into the waterbath for 90 seconds. Immediately place the tubes back on ice for 10 minutes.</p>
+
−
<p style="font-family:Dosis; font-size:20px;">8.    Add 1000ul of LB media to each tube. Gently tap the tubes with your finger to mix.</p>
+
−
<p style="font-family:Dosis; font-size:20px;">9.    Incubate the tubes at 37°C for 1 hours. </p>
+
−
<p style="font-family:Dosis; font-size:20px;">10.  Pipet 200ul of the Transformation Control onto the appropriate plate. Spread evenly over the surface of the agar by gently shaking the plate back and forth. The beads will do the work for you!</p>
+
−
<p style="font-family:Dosis; font-size:20px;">11.  Repeat step 1 to 10 for the other two transformations.</p>
+
−
<p style="font-family:Dosis; font-size:20px;">12.  Place the agar plates into the incubator with the agar side facing up, lid facing down. Incubate the agar plates at 37°C for 12 - 14 hours. Alternately, incubate at room temperature for 24 hours.
+
−
+
−
</p>
+
−
<h3><b>Safety:</b></h3>
+
−
<p style="font-family:Dosis; font-size:20px;">● Gloves must be worn all the time.</p>
+
−
<p style="font-family:Dosis; font-size:20px;">● Every step must be done in the hood to avoid contamination and 4 degrees needs to be maintained during the procedure.
+
  
−
</p>
 
  
−
      </div>
+
<div class="calendar col-md-12" id="myaffix" hidden-xs hidden-sm hidden-md data-spy="affix" data-offset-top="730">
−
    </div>
+
<div class="calendar col-md-3 col-sm-3" >
−
  </div>
+
<div class="calendar-patch">
−
  <div class="panel panel-info">
+
<header role="banner">
−
    <div class="panel-heading" role="tab" id="headingTwo">
+
      <time>July<em>2016</em></time>
−
      <h4 class="panel-title">
+
     </header>
−
        <a class="collapsed" role="button" data-toggle="collapse" data-parent="#accordion" href="#collapseTwo" aria-expanded="false" aria-controls="collapseTwo">
+
     <section role="main">
−
          <b style="font-family:Dosis; font-size:20px;">PROTOCOL - RESTRICTION DIGEST</b>
+
       <ul class="m-box--weeks">
−
        </a>
+
          
−
      </h4>
+
         <li>
−
     </div>
+
          Mon
−
     <div id="collapseTwo" class="panel-collapse collapse" role="tabpanel" aria-labelledby="headingTwo">
+
         </li>
−
       <div class="panel-body">
+
        <li>
−
         <h3><b>Approxmation time:</b></h3>6hrs
+
          Tue
−
         <h3><b>Material required:</b></h3>
+
        </li>
−
         <ul>
+
        <li>
−
        <li>70% ethanol</li>
+
          Wed
−
        <li>Tissue paper</li>
+
        </li>
−
        <li>Ice</li>
+
        <li>
−
        <li>Container for ice</li>
+
          Thu
−
        <li>DNA sample</li>
+
        </li>
−
        <li>RFP Control </li>
+
        <li>
−
        <li>NEB buffer 2</li>
+
          Fri
−
        <li>NEB enzymes: EcoRI/SpeI/XbaI/PstI</li>
+
        </li>
−
        <li>pSB1C3/pSB1K3/pSB1A3/pSB1AK8( linearized plasmid backbone) </li>
+
        <li>
−
        <li>BSA</li>
+
          Sat
−
         </ul>
+
        </li>
−
         <h3><b>Protocol:</b></h3>
+
        <li>
−
         <p style="font-family:Dosis; font-size:20px;">1. Clean the lab bench by wiping down with 70% ethanol and paper towels.</p>
+
          Sun
−
        <p style="font-family:Dosis; font-size:20px;">2. Keep all enzymes and buffers used in this section on ice.</p>
+
        </li>
−
         <p style="font-family:Dosis; font-size:20px;">3. Thaw NEB Buffer 2 and BSA in room temperature water. Re-homogenize both by inverting the tubes, and flick/spin them to collect the liquid at the bottom of the tube.</p>
+
      </ul>
−
         <p style="font-family:Dosis; font-size:20px;">4. Label three 0.6 tubes: DNA sample, (pSB1C3/pSB1K3/pSB1A3/pSB1AK8) (linearized plasmid backbone), and RFP Control</p>
+
      <ul class="m-box--date">
−
        <p style="font-family:Dosis; font-size:20px;">5.    Add 500ng of DNA to the appropriate tube. Add distilled water to the tubes for a total volume of 42.5ul in each tube.</p>
+
        <li class="l-date--passed">
−
         <p style="font-family:Dosis; font-size:20px;">. Pipet 5ul of Buffer 2 to each tube.</p>
+
          <p class="relativeposition">27</p>
−
         <p style="font-family:Dosis; font-size:20px;">2. Pipet 0.5ul of BSA to each tube.</p>
+
         </li>
−
         <p style="font-family:Dosis; font-size:20px;">3. In the DNA sample: Add 1ul of EcoRI/SpeI/XbaI/PstI enzyme.</p>
+
         <li class="l-date--passed">
−
         <p style="font-family:Dosis; font-size:20px;">4. In the pSB1C3/pSB1K3/pSB1A3/pSB1AK8  tube: Add 1ul of restricted enzyme(EcoRI/SpeI/XbaI/PstI).</p>
+
          <p class="relativeposition">28</p>
−
        <p style="font-family:Dosis; font-size:20px;">5. In the RFP Control tube: Add 1ul of restricted enzyme(EcoRI/SpeI/XbaI/PstI).</p>
+
        </li>
−
        <p style="font-family:Dosis; font-size:20px;">6. The total volume in each tube should be approximately 50ul. Mix well by pipetting slowly up and down 5x. Be gentle, and do not vortex. Spin the samples for 5 seconds in a microcentrifuge, or flick them to collect all of the mixture to the bottom of the tube.</p>
+
         <li class="l-date--passed">
−
         <p style="font-family:Dosis; font-size:20px;">7. Incubate the restriction digests at 37°C for 30 minutes, then 80°C for 20 minutes. We use a thermocycler, but a waterbath and an accurate thermometer works well also!</p>
+
          <p class="relativeposition">29</p>
−
         <p style="font-family:Dosis; font-size:20px;">8.    The digested DNA can be stored at 4°C for a few days. For longer storage, keep at -20°C.
+
         </li>
−
                                                             
+
         <li class="l-date--passed">
−
</p>
+
          <p class="relativeposition">30</p>
−
      </div>
+
         </li>
−
    </div>
+
        <li >
−
  </div>
+
          <p class="relativeposition">1</p>
−
  <div class="panel panel-info">
+
         </li>
−
    <div class="panel-heading" role="tab" id="headingThree">
+
        <li>
−
      <h4 class="panel-title">
+
          <p class="relativeposition">2</p>
−
         <a class="collapsed" role="button" data-toggle="collapse" data-parent="#accordion" href="#collapseThree" aria-expanded="false" aria-controls="collapseThree">
+
         </li>
−
           <b style="font-family:Dosis; font-size:20px;">PROTOCOL - LIGATION</b>
+
        <li>
−
         </a>
+
          <p class="relativeposition">3</p>
−
      </h4>
+
         </li>
−
    </div>
+
      </ul>
−
    <div id="collapseThree" class="panel-collapse collapse" role="tabpanel" aria-labelledby="headingThree">
+
      <ul class="m-box--date">
−
      <div class="panel-body">
+
        <li>
−
         <h3><b>Approximation time:</b></h3>12hrs
+
          <p class="relativeposition">4</p>
−
         <h3><b>Materials required:</b></h3>
+
         </li>
−
        <ul>
+
         <li>
−
        <li>70% ethanol</li>
+
          <p class="relativeposition">5</p>
−
        <li>Paper towels</li>
+
        </li>
−
        <li>Distilled water </li>
+
        <li>
−
        <li>Ice</li>
+
          <p class="relativeposition">6</p>
−
        <li>Container for ice</li>
+
        </li>
−
        <li>T4 DNA Ligase Reaction Buffer</li>
+
         <li class="l-date--event" data-event="15:00 - New Haircut">
−
        <li>T4 DNA Ligase</li>
+
           <i class="m-bullet--event"></i> 7
−
        <li>Thermocycler, or waterbath </li>
+
         </li>
−
        <li>Restriction Digest: Part A and Part B</li>
+
        <li>
−
        <li>Restriction Digest: (pSB1K3/pSB1C3/pSB1A3/pSB1AK8)linearized plasmid backbone</li>
+
          <p class="relativeposition">8</p>
−
       
+
        </li>
−
         </ul>
+
         <li>
−
         <h3><b>Protocol:</b></h3>
+
          <p class="relativeposition">9</p>
−
         <p style="font-family:Dosis; font-size:20px;">1. Clean the lab bench by wiping down with 70% ethanol and paper towels.</p>
+
        </li>
−
         <p style="font-family:Dosis; font-size:20px;">2. Thaw T4 DNA Ligase Reaction Buffer at room temperature. Keep the T4 DNA Ligase in the freezer until you're ready to use it.</p>
+
         <li>
−
        <p style="font-family:Dosis; font-size:20px;">3.    Label one 0.6ml tube as New Part.
+
          <p class="relativeposition">10</p>
−
         <ul>
+
        </li>
−
        <li>1. Add 2ul from the (pSB1K3/pSB1C3/pSB1A3/pSB1AK8)linearized plasmid backbone digest.</li>
+
      </ul>
−
        <li>2. Add 3.3ul from the Part A digest.</li>
+
      <ul class="m-box--date">
−
        <li>3. Add 3.9ul from the Part B digest.</li>
+
        <li>
−
        <li>4. Add 1ul of T4 DNA Ligase Reaction Buffer.</li>
+
          <p class="relativeposition"> 11</p>
−
        <li>5. Add 0.5ul of T4 DNA Ligase (keep this at -20°C until use!).</li>
+
        </li>
−
        <li>6. Mix by gently pipetting up and down 3x. Do not vortex; this inactivates the enzymes. Place tube in microcentrifuge for a quick 5 second spin or flick the tube to collect the mixture at the bottom.</li>
+
        <li>
−
         </ul></p>
+
          <p class="relativeposition">12</p>
−
         <p style="font-family:Dosis; font-size:20px;">4.    Label one 0.6 tube as Ligation Control.
+
        </li>
−
        <ul>
+
        <li>
−
        <li>1. Add 2ul from the RFP Control digest.</li>
+
          <p class="relativeposition">13</p>
−
        <li>2. Add 6.5ul of distilled water.</li>
+
        </li>
−
        <li>3. Add 1ul of T4 DNA Ligase Reaction Buffer.</li>
+
        <li>
−
        <li>4. Add 0.5ul of T4 DNA Ligase.</li>
+
          <p class="relativeposition">14</p>
−
        <li>5. Mix by gently pipetting up and down 3x. Do not vortex; this inactivates the enzymes. Place tube in microcentrifuge for a quick 5 second spin or flick the tube to collect the mixture at the bottom.</li>
+
        </li>
−
         </ul></p>
+
        <li>
−
        <p style="font-family:Dosis; font-size:20px;">5. Incubate at 16°C for 30 minutes, then at 80°C for 20 minutes. We use a thermocycler, but a waterbath and thermometer combination works great too! The ligated products can be stored at -20°C.</p>
+
          <p class="relativeposition">15</p>
−
         <div class="container">
+
         </li>
−
        <table class="table table-bordered">
+
         <li>
−
        <thead>
+
          <p class="relativeposition">16</p>
−
        <tr>
+
        </li>
−
        <th>          </th>
+
         <li>
−
        <th>Ligation: New part</th>
+
          <p class="relativeposition">17</p>
−
        <th>Ligation: control</th>
+
         </li>
−
        </tr>
+
      </ul>
−
        <tr>
+
      <ul class="m-box--date">
−
        <td>Digest 1</td>
+
         <li>
−
        <td>2&micro;l backbone </td>
+
          <p class="relativeposition">18</p>
−
        <td>2&micro;l RFP control</td>
+
        </li>
−
        </tr>
+
        <li>
−
        <tr>
+
          <p class="relativeposition">19</p>
−
        <td>Digest 2</td>
+
        </li>
−
        <td>3.3&micro;l Part A</td>
+
        <li class="bluecolor">
−
        <td>-</td>
+
          <a data-scroll  href="#20july">20</a>
−
        </tr>
+
        </li>
−
        <tr>
+
        <li class="bluecolor">
−
        <td>Digest 3</td>
+
          <a data-scroll  href="#21july">21</a>
−
        <td>3.9&micro;l Part B</td>
+
         </li>
−
        <td>-</td>
+
         <li class="bluecolor">
−
        </tr>
+
          <a data-scroll  href="#22july">22</a>
−
        <tr>
+
        </li>
−
        <td>Distill water</td>
+
        <li>
−
        <td>0&micro;l</td>
+
          <p class="relativeposition">23</p>
−
        <td>6.5&micro;l</td>
+
        </li>
−
        </tr>
+
        <li>
−
        <tr>
+
          <p class="relativeposition">24</p>
−
        <td>T4 DNA Ligase</td>
+
         </li>
−
        <td>0.5&micro;l</td>
+
      </ul>
−
        <td>0.5&micro;l</td>
+
      <ul class="m-box--date">
−
        </tr>
+
         <li class="bluecolor">
−
        <tr>
+
          <a data-scroll  href="#july25">25</a>
−
        <td>T4 DNA Ligase buffer</td>
+
        </li>
−
        <td>1&micro;l</td>
+
        <li class="bluecolor">
−
        <td>1&micro;l</td>
+
           <a  data-scroll href="#july26">26</a>
−
        </tr>
+
        </li>
−
        </thead>
+
        <li class="bluecolor">
−
        </table>
+
          <a  data-scroll href="#july27">27</a>
−
        </div>
+
        </li>
−
      </div>
+
        <li class="bluecolor">
−
    </div>
+
          <a data-scroll  href="#july28">28</a>
−
  </div>
+
        </li>
 +
        <li>
 +
          <p class="relativeposition">29</p>
 +
        </li>
 +
        <li>
 +
          <p class="relativeposition">30</p>
 +
        </li>
 +
        <li>
 +
          <p class="relativeposition"> 31</p>
 +
        </li>
 +
      </ul>
 +
        <ul class="m-box--date">
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">1</p>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">2</p>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">3</p>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">4</p>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">5</p>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">6</p>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">7</p>
 +
        </li>
 +
      </ul>
 +
    </section>
 +
</div>
 +
</div>
  
−
  <div class="panel panel-info">
+
<div class="calendar col-md-3 col-sm-3" hidden-xs hidden-sm hidden-md >
−
    <div class="panel-heading" role="tab" id="headingFour">
+
<div class="calendar-patch">
−
       <h4 class="panel-title">
+
<header role="banner">
−
         <a class="collapsed" role="button" data-toggle="collapse" data-parent="#accordion" href="#collapseFour" aria-expanded="false" aria-controls="collapseFour">
+
      <time>August<em>2016</em></time>
−
           <b style="font-family:Dosis; font-size:20px;">PROTOCOL - PLASMID ISOLATION</b>
+
    </header>
−
            
+
    <section role="main">
−
             
+
       <ul class="m-box--weeks">
 +
       
 +
         <li>
 +
          Mon
 +
        </li>
 +
        <li>
 +
          Tue
 +
        </li>
 +
        <li>
 +
          Wed
 +
        </li>
 +
        <li>
 +
          Thu
 +
        </li>
 +
        <li>
 +
          Fri
 +
        </li>
 +
        <li>
 +
          Sat
 +
        </li>
 +
        <li>
 +
          Sun
 +
        </li>
 +
      </ul>
 +
      <ul class="m-box--date">
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">25</p>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">26</p>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">27</p>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">28</p>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">29</p>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">30</p>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">31</p>
 +
        </li>
 +
      </ul>
 +
      <ul class="m-box--date">
 +
        <li class="bluecolor">
 +
        <a data-scroll  href="#august1"> 1</a>
 +
        </li>
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#august2"> 2</a>
 +
        </li>
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#august3"> 3</a>
 +
        </li>
 +
        <li  class="bluecolor">
 +
          <a data-scroll  href="#august4"> 4</a>
 +
        </li>
 +
        <li>
 +
          <p class="relativeposition">5</p>
 +
        </li>
 +
        <li>
 +
          <p class="relativeposition">6</p>
 +
        </li>
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#august7">7</a>
 +
        </li>
 +
      </ul>
 +
      <ul class="m-box--date">
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#august8">8</a>
 +
        </li>
 +
        <li class="bluecolor">
 +
           <a data-scroll  href="#august9">9</a>
 +
        </li>
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#august10">10</a>
 +
        </li>
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#august11">11</a>
 +
        </li>
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#august12">12</a>
 +
        </li>
 +
        <li>
 +
           <p class="relativeposition">13</p>
 +
        </li>
 +
        <li>
 +
          <p class="relativeposition">14</p>
 +
        </li>
 +
      </ul>
 +
      <ul class="m-box--date">
 +
        <li>
 +
          <p class="relativeposition">15</p>
 +
        </li>
 +
       
 +
          <li class="bluecolor">
 +
          <a data-scroll  href="#august16">16</a></li></p>
 +
       
 +
       
 +
          <li class="bluecolor">
 +
          <a data-scroll  href="#august17">17</a></li></p>
 +
     
 +
       
 +
          <li class="bluecolor">
 +
          <a data-scroll  href="#august18">18</a></li></p>
 +
       
 +
        <li>
 +
          <p class="relativeposition">19</p>
 +
        </li>
 +
        <li>
 +
          <p class="relativeposition">20</p>
 +
        </li>
 +
        <li>
 +
          <p class="relativeposition">21</p>
 +
        </li>
 +
      </ul>
 +
      <ul class="m-box--date">
 +
       
 +
          <li class="bluecolor">
 +
          <a data-scroll  href="#august22">22</a></li></p>   
 +
       
 +
          <li class="bluecolor">
 +
          <a data-scroll  href="#august23">23</a></li></p>
 +
       
 +
       
 +
          <li class="bluecolor">
 +
          <a data-scroll  href="#august24">24</a></li></p>
 +
       
 +
       
 +
          <li class="bluecolor">
 +
          <a data-scroll  href="#august25">25</a></li></p>
 +
       
 +
       
 +
          <li class="bluecolor">
 +
          <a data-scroll  href="#august26">26</a></li></p>
 +
       
 +
        <li>
 +
          27
 +
        </li>
 +
        <li>
 +
          28
 +
        </li>
 +
      </ul>
 +
      <ul class="m-box--date">
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#august29">29</a>
 +
        </li>
 +
        <li>
 +
          30
 +
        </li>
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#august31">31</a>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">1</p>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">2</p>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">3</p>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">4</p>
 +
        </li>
 +
      </ul>
 +
    </section>
 +
</div>
 +
</div>
  
−
        </a>
 
−
      </h4>
 
−
    </div>
 
−
    <div id="collapseFour" class="panel-collapse collapse" role="tabpanel" aria-labelledby="headingFour">
 
−
      <div class="panel-body">
 
−
          <h3><b>Approximation time:</b></h3>3hrs
 
−
          <h3><b>Material required:</b></h3>
 
−
          <ul>Qiagen Miniprep Kit
 
−
          <li>Cell Culture</li>
 
−
          <li>1.6 ml Microcentrifuge tubes </li>
 
−
          <li>TE (1:10)</li>
 
−
          </ul>
 
−
          <h3><b>Protocol</b></h3>
 
−
          <p style="font-family:Dosis; font-size:20px;">1. Spin the cell culture in a centrifuge to pellet the cells, empty the supernatant (media) into a waste collection container.</p>
 
−
          <p style="font-family:Dosis; font-size:20px;">2. Resuspend pelleted bacterial cells in 250 µl Buffer P1 (kept at 4 °C) and transfer to a          microcentrifuge tube. No cell clumps should be visible after resuspension of the pellet.
 
  
−
          </p>
 
−
          <p style="font-family:Dosis; font-size:20px;">3. Add 250 μl Buffer P2 and gently invert the tube 4–6 times to mix. Do not vortex, as this will result in shearing of genomic DNA. If necessary, continue inverting the tube until the solution becomes viscous and slightly clear.</p>
 
−
            <p style="font-family:Dosis; font-size:20px;">4. Add 350 μl Buffer N3 and invert the tube immediately and gently 4–6 times. To avoid localized precipitation, mix the solution gently but thoroughly, immediately after addition of Buffer N3. Keep in ice for 10 minutes. </p>
 
−
            <p style="font-family:Dosis; font-size:20px;">5. Centrifuge for 25 min at 12,000 rpm in a  microcentrifuge. A White pellet will form.</p>
 
−
              <p style="font-family:Dosis; font-size:20px;">6. Load the supernant in QIAprep column and wait for 10 minutes. Discard the flow-through</p>
 
−
              <p style="font-family:Dosis; font-size:20px;">7. Wash QIAprep spin column by adding 0.75 ml Buffer PE and centrifuging for 1 minute.</p>
 
−
              <p style="font-family:Dosis; font-size:20px;">8. Discard the flow-through, and centrifuge for an additional 1 min at 10,000 rpm to remove residual wash buffer.</p>
 
−
              <p style="font-family:Dosis; font-size:20px;">9. Discard the flow-through, and centrifuge for an additional 2 min at 11,000 rpm. Discard the flow-through and transfer the column to fresh eppendorf tube.  </p>
 
−
              <p style="font-family:Dosis; font-size:20px;">10. Add 20 – 50&micro;L of Nuclease free water in the column. Centrifuge at 11000 rpm for 2 minutes for eluting the DNA bound to the Column.</p>
 
−
      </div>
 
−
    </div>
 
−
  </div>
 
  
−
 
+
<div class="calendar col-md-3 col-sm-3" >
 +
<div class="calendar-patch">
 +
<header role="banner">
 +
      <time>September<em>2016</em></time>
 +
    </header>
 +
    <section role="main">
 +
      <ul class="m-box--weeks">
 +
       
 +
        <li>
 +
          <p class="relativeposition">Mon</p>
 +
        </li>
 +
        <li>
 +
          <p class="relativeposition">Tue</p>
 +
        </li>
 +
        <li>
 +
          <p class="relativeposition">Wed</p>
 +
        </li>
 +
        <li>
 +
          <p class="relativeposition">Thu</p>
 +
        </li>
 +
        <li>
 +
          <p class="relativeposition">Fri</p>
 +
        </li>
 +
        <li>
 +
          <p class="relativeposition">Sat</p>
 +
        </li>
 +
        <li>
 +
          <p class="relativeposition">Sun</p>
 +
        </li>
 +
      </ul>
 +
      <ul class="m-box--date">
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">29</p>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">30</p>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">31</p>
 +
        </li>
 +
      <li class="bluecolor">
 +
          <a data-scroll href="#september1">1</a>
 +
        </li>
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#september2">2</a>
 +
        </li>
 +
        <li>
 +
          <p class="relativeposition">3</p>
 +
        </li>
 +
        <li>
 +
          <p class="relativeposition">4</p>
 +
        </li>
 +
      </ul>
 +
      <ul class="m-box--date">
 +
        <li>
 +
          <p class="relativeposition">5</p>
 +
        </li>
 +
        <li>
 +
          <p class="relativeposition">6</p>
 +
        </li>
 +
        <li>
 +
          <p class="relativeposition">7</p>
 +
        </li>
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#september8">8</a>
 +
        </li>
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#september9">9</a>
 +
        </li>
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#september10">10</a>
 +
        </li>
 +
        <li>
 +
          11
 +
        </li>
 +
      </ul>
 +
      <ul class="m-box--date">
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#september12">12</a>
 +
        </li>
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#september13">13</a>
 +
        </li>
 +
        <li>
 +
          <p class="relativeposition">14</p>
 +
        </li>
 +
        <li>
 +
          <p class="relativeposition">15</p>
 +
        </li>
 +
        <li>
 +
          <p class="relativeposition">16</p>
 +
        </li>
 +
        <li>
 +
          <p class="relativeposition">17</p>
 +
        </li>
 +
        <li>
 +
          <p class="relativeposition">18</p>
 +
        </li>
 +
      </ul>
 +
      <ul class="m-box--date">
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#september19">19</a>
 +
        </li>
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#september20">20</a>
 +
        </li>
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#september21">21</a>
 +
        </li>
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#september22">22</a>
 +
        </li>
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#september23">23</a>
 +
        </li>
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#september24">24</a>
 +
        </li>
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#september25">25</a>
 +
        </li>
 +
      </ul>
 +
      <ul class="m-box--date">
 +
      <li class="bluecolor">
 +
          <a data-scroll  href="#september26">26</a>
 +
        </li>
 +
      <li class="bluecolor">
 +
          <a data-scroll  href="#september27">27</a>
 +
        </li>
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#september28">28</a>
 +
        </li>
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#september29">29</a>
 +
        </li>
 +
        <li class="bluecolor">
 +
          <a data-scroll  href="#september30">30</a>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">1</p>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">2</p>
 +
        </li>
 +
      </ul>
 +
      <ul class="m-box--date">
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">3</p>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">4</p>
 +
        </li>
 +
        <li  class="l-date--passed">
 +
          <p class="relativeposition">5</p>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">6</p>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">7</p>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">8</p>
 +
        </li>
 +
        <li class="l-date--passed">
 +
          <p class="relativeposition">9</p>
 +
        </li>
 +
      </ul>
 +
    </section>
 +
</div>
 +
</div>
  
−
  <div class="panel panel-info">
+
−
    <div class="panel-heading" role="tab" id="headingSix">
+
−
      <h4 class="panel-title">
+
−
        <a class="collapsed" role="button" data-toggle="collapse" data-parent="#accordion" href="#collapseSix" aria-expanded="false" aria-controls="collapseSix">
+
−
          <b style="font-family:Dosis; font-size:20px;">PROTOCOL - PREPARATION OF COMPETENT CELLS (DH5&alpha;)</b>
+
−
        </a>
+
−
      </h4>
+
−
    </div>
+
−
    <div id="collapseSix" class="panel-collapse collapse" role="tabpanel" aria-labelledby="headingSix">
+
−
      <div class="panel-body">
+
−
        <h3><b>Approximation time:</b></h3>
+
−
        <h3><b>Material required:</b></h3>
+
−
        <ul>
+
−
        <li>100 mM CaCl2 </li>
+
−
        <li>200mL LB Media</li>
+
−
        <li>sterile centrifuge tubes </li>
+
−
        <li>Overnight DH5α culture</li>
+
−
        </ul>
+
−
        <h3><b>Protocol:</b></h3>
+
−
        <p style="font-family:Dosis; font-size:20px;">1. Add 200μl of overnight culture to 10ml of fresh LB medium for preparation of overday (O/D) culture.</p>
+
−
        <p style="font-family:Dosis; font-size:20px;">2. Keep the O/D culture in incubator(37°C) for 2.5 hours.</p>
+
−
        <p style="font-family:Dosis; font-size:20px;">3. Keep the O/D culture in refrigerator for some time and then transfer it to 15ml tubes.</p>
+
−
        <p style="font-family:Dosis; font-size:20px;">4. Centrifuge at 300 rpm and 4°C for 10 minutes.</p>
+
−
        <p style="font-family:Dosis; font-size:20px;">5. Decant the supernatant and gently resuspend each pellet in about 5mL of  100mM ice cold CaCl2.</p>
+
−
        <p style="font-family:Dosis; font-size:20px;">6. Again centrifuge the CaCl2 suspended cells at 4000rpm for 4 minutes at 4 degrees
+
−
And discard the supernatant. Add 1ml of CaCl2 and resuspend the cells and aliquote 100uL into sterile micro centrifuge tubes of 1.5ml tubes and store at 4 degrees for overnight. (Which  can be used to transform the ligated products)</p>
+
−
      </div>
+
−
    </div>
+
−
  </div>
+
  
  
−
  <div class="panel panel-info">
 
−
    <div class="panel-heading" role="tab" id="headingSeven">
 
−
      <h4 class="panel-title">
 
−
        <a class="collapsed" role="button" data-toggle="collapse" data-parent="#accordion" href="#collapseSeven" aria-expanded="false" aria-controls="collapseSeven">
 
−
          <b style="font-family:Dosis; font-size:20px;">PROTOCOL - AGAROSE GEL PERPARATION</b>
 
−
        </a>
 
−
      </h4>
 
−
    </div>
 
−
    <div id="collapseSeven" class="panel-collapse collapse" role="tabpanel" aria-labelledby="headingSeven">
 
−
      <div class="panel-body">
 
−
        <!-- <h3><b>Approximation time:</b></h3> -->
 
−
        <h3><b>Material required:</b></h3>
 
−
        <ul>
 
−
        <li>1X TAE buffer</li>
 
−
        <li>Ethidium bromide</li>
 
−
        </ul>
 
−
        <h3><b>Protocol:</b></h3>
 
−
        <p style="font-family:Dosis; font-size:20px;">1. Mix 0.4 grams of agarose with 40ml of TAE buffer in a conical flask.</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">2. Weigh the solution and then heat in the oven for 2 mins.</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">3. Add 4 µl (10mg/ml) of EtBr in the solution.</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">4. Weigh it again and add the TAE buffer to make it 250ml add pour in the tray.</p>
 
−
      </div>
 
−
    </div>
 
−
  </div>
 
  
 +
<div class="calendar col-md-3 col-sm-3">
 +
<div class="calendar-patch">
 +
<header role="banner">
 +
      <time>October<em>2016</em></time>
 +
    </header>
 +
    <section role="main">
 +
      <ul class="m-box--weeks">
 +
       
 +
        <li>    <p class="relativeposition">      Mon </p>        </li>        <li>      <p class="relativeposition">    Tue</p>
 +
</li>        <li>        <p class="relativeposition">  Wed </p>        </li>        <li>          <p class="relativeposition">Thu</p>
 +
</li>        <li>        <p class="relativeposition">  Fri    </p>    </li>        <li>          <p class="relativeposition">Sat</p>
 +
</li>        <li>          <p class="relativeposition"> Sun    </p>    </li>      </ul>      <ul
 +
class="m-box--date">        <li class="l-date--passed">          <p class="relativeposition"> 26</p>
 +
</li>        <li class="l-date--passed">          <p class="relativeposition">27    </p>    </li>
 +
<li class="l-date--passed">          <p class="relativeposition">28        </p> </li>        <li
 +
class="l-date--passed">          <p class="relativeposition"> 29  </p>    </p>  </li>        <li class="l-date--
 +
passed">          <p class="relativeposition"> 30  </p>      </li>        <li class="bluecolor">
 +
          <a data-scroll  href="#october1">1</a>
 +
        </li>
 +
<li class="bluecolor">
 +
          <a data-scroll  href="#october2">2</a>
 +
        </li>
 +
              </ul>
 +
                      <ul class="m-box--date">
 +
<li>          3        </li>        <li>          4        </li>
 +
<li>          5        </li>        <li class="l-date--event" data-
 +
event="15:00 - New Haircut">          <i class="m-bullet--event"></i> 6
 +
</li>        <li>          7        </li>        <li>          8
 +
</li>        <li>          9        </li>      </ul>      <ul
 +
class="m-box--date">        <li>          10        </li>        <li>
 +
11        </li>        <li>          12        </li>        <li>
 +
13        </li>        <li>          14        </li>        <li>
 +
15        </li>        <li>          16        </li>      </ul>      <ul
 +
class="m-box--date">        <li>          17        </li>        <li>
 +
18        </li>        <li>          19        </li>        <li>
 +
20        </li>        <li>          21        </li>        <li>
 +
22        </li>        <li>          23        </li>      </ul>      <ul
 +
class="m-box--date">        <li>          24        </li>        <li>
 +
25        </li>        <li>          26        </li>        <li>
 +
27        </li>        <li>          28        </li>        <li>
 +
29        </li>        <li>          30        </li>      </ul>      <ul
 +
class="m-box--date">        <li>          31        </li>        <li
 +
class="l-date--passed">          1        </li>        <li class="l-date--
 +
passed">          2        </li>        <li class="l-date--passed">
 +
3        </li>        <li class="l-date--passed">          4        </li>
 +
<li class="l-date--passed">          5        </li>        <li
 +
class="l-date--passed">          6        </li>      </ul>    </section>
 +
</div>    </div>
 +
 +
 +
 +
 +
</div>
 +
 +
 +
 +
<div class="notebook-content">
 +
 +
 +
 +
 +
 +
 +
<div class="container" id="content">
 +
    <h2 class="project-name">WEEK ONE - ( 20th July - 22th July )</h1>
 +
<div id="timeline">
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="20july">
 +
<h2>20th july, Wednesday</h2>
 +
<p class="distance">
 +
DH5 alpha competent cells were prepared for transformation experiments.
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<g>
 +
<path fill="#FFFFFF" d="M17.92,3.065l-1.669-2.302c-0.336-0.464-0.87-0.75-1.479-0.755C14.732,0.008,7.653,0,7.653,0v5.6
 +
c0,0.096-0.047,0.185-0.127,0.237c-0.081,0.052-0.181,0.06-0.268,0.02l-1.413-0.64C5.773,5.183,5.69,5.183,5.617,5.215l-1.489,0.65
 +
c-0.087,0.038-0.19,0.029-0.271-0.023c-0.079-0.052-0.13-0.141-0.13-0.235V0H2.191C1.655,0,1.233,0.434,1.233,0.97
 +
c0,0,0.025,15.952,0.031,15.993c0.084,0.509,0.379,0.962,0.811,1.242l2.334,1.528C4.671,19.905,4.974,20,5.286,20h10.307
 +
c1.452,0,2.634-1.189,2.634-2.64V4.007C18.227,3.666,18.12,3.339,17.92,3.065z M16.42,17.36c0,0.464-0.361,0.833-0.827,0.833H5.341
 +
l-1.675-1.089h10.341c0.537,0,0.953-0.44,0.953-0.979V2.039l1.459,2.027V17.36L16.42,17.36z"/>
 +
</g>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="21july">
 +
<h2>21st July, Thursday</h2>
 +
<p>
 +
Transformation of the prepared competent cells was carried out.
 +
The plasmids used for transformation  were YFP (BBa_K592101), HIV cleavage site (BBa_I712015), and the protease construct (BBa_K743013)
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="22july">
 +
<h2>22nd July, Friday</h2>
 +
<p>
 +
Replication plating for above transformed parts was done. This including the three sets of  transformed cells containing the plasmids YFP (BBa_K592101), the HIV cleavage site (BBa_I712015), and the protease construct (BBa_K743013).
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
</div>
 +
</div>
 +
 +
 +
<div class="container" id="content">
 +
    <h2 class="project-name">WEEK TWO - ( 25th July - 30th July )</h1>
 +
<div id="timeline">
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="july25">
 +
<h2>25th july, Monday</h2>
 +
<p class="distance">
 +
1 litre of LB media was prepared and duly autoclaved.
 +
5 plates each of the antibiotics chloramphenicol, ampicillin and ampicillin+Kanamycin were prepared.
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<g>
 +
<path fill="#FFFFFF" d="M17.92,3.065l-1.669-2.302c-0.336-0.464-0.87-0.75-1.479-0.755C14.732,0.008,7.653,0,7.653,0v5.6
 +
c0,0.096-0.047,0.185-0.127,0.237c-0.081,0.052-0.181,0.06-0.268,0.02l-1.413-0.64C5.773,5.183,5.69,5.183,5.617,5.215l-1.489,0.65
 +
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 +
c0,0,0.025,15.952,0.031,15.993c0.084,0.509,0.379,0.962,0.811,1.242l2.334,1.528C4.671,19.905,4.974,20,5.286,20h10.307
 +
c1.452,0,2.634-1.189,2.634-2.64V4.007C18.227,3.666,18.12,3.339,17.92,3.065z M16.42,17.36c0,0.464-0.361,0.833-0.827,0.833H5.341
 +
l-1.675-1.089h10.341c0.537,0,0.953-0.44,0.953-0.979V2.039l1.459,2.027V17.36L16.42,17.36z"/>
 +
</g>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="july26">
 +
<h2>26th July, Tuesday</h2>
 +
<p>
 +
20ml Cultures were prepared for the plasmid extraction of each of YFP (BBa_K592101), the HIV cleavage site (BBa_I712015) and the protease construct (BBa_K743013).
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
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 +
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 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="july27">
 +
<h2>27th July, Wednesday</h2>
 +
<p>
 +
Plasmid  extraction was done for  YFP (BBa_K592101), the HIV cleavage site (BBa_I712015), and the protease construct (BBa_K743013) using mini-prep plasmid DNA extraction kit.
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<g>
 +
<path fill="#FFFFFF" d="M17.92,3.065l-1.669-2.302c-0.336-0.464-0.87-0.75-1.479-0.755C14.732,0.008,7.653,0,7.653,0v5.6
 +
c0,0.096-0.047,0.185-0.127,0.237c-0.081,0.052-0.181,0.06-0.268,0.02l-1.413-0.64C5.773,5.183,5.69,5.183,5.617,5.215l-1.489,0.65
 +
c-0.087,0.038-0.19,0.029-0.271-0.023c-0.079-0.052-0.13-0.141-0.13-0.235V0H2.191C1.655,0,1.233,0.434,1.233,0.97
 +
c0,0,0.025,15.952,0.031,15.993c0.084,0.509,0.379,0.962,0.811,1.242l2.334,1.528C4.671,19.905,4.974,20,5.286,20h10.307
 +
c1.452,0,2.634-1.189,2.634-2.64V4.007C18.227,3.666,18.12,3.339,17.92,3.065z M16.42,17.36c0,0.464-0.361,0.833-0.827,0.833H5.341
 +
l-1.675-1.089h10.341c0.537,0,0.953-0.44,0.953-0.979V2.039l1.459,2.027V17.36L16.42,17.36z"/>
 +
</g>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="july28">
 +
<h2>28th July, Thursday</h2>
 +
<p>
 +
DNA quantification was done using Nano Drop.
 +
YFP: 250 ng/ul<br>
 +
Protease: 170 ng/ul<br>
 +
Cleavage Site: 120 ng/ul<br>
 +
1% agarose gel was prepared  for screening of the plasmids extracted by the mini prep kit.<br>
 +
The FRET construct was kept for overnight digestion at the restriction sites E and P.
 +
<br>
 +
Digestions with E and P for YFP, Protease and Cleavage Site<table>
 +
<tr><th></th><th>YFP</th><th>Protease</th><th>Cleavage Site</th></tr>
 +
<tr><th>Component</th><th>Volume(ul)</th><th>Volume(ul)</th><th>Volume(ul)</th></tr>
 +
<tr><td>DNA</td><td>2</td><td>3</td><td>3.5</td></tr>
 +
<tr><td>2.1 Buffer</td><td>2</td><td>2</td><td>2</td></tr>
 +
<tr><td>ECoRI</td><td>0.5</td><td>0.5</td><td>0.5</td></tr>
 +
<tr><td>Psti</td><td>0.5</td><td>0.5</td><td>-</td></tr>
 +
<tr><td>Nf H2O</td><td>15</td><td>14</td><td>14</td></tr>
 +
</table>
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
 +
</div>
 +
</div>
 +
 +
 +
<div class="container" id="content">
 +
    <h2 class="project-name">WEEK THREE - ( 1st August - 7th August )</h1>
 +
<div id="timeline">
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="august1">
 +
<h2>1st August, Monday</h2>
 +
<p class="distance">
 +
3ml cultures made for the preparation of competent cells of DH5 alpha cells.
 +
20ml culture prepared for the construct BBa_K844004. (MaSP without ATG)
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<g>
 +
<path fill="#FFFFFF" d="M17.92,3.065l-1.669-2.302c-0.336-0.464-0.87-0.75-1.479-0.755C14.732,0.008,7.653,0,7.653,0v5.6
 +
c0,0.096-0.047,0.185-0.127,0.237c-0.081,0.052-0.181,0.06-0.268,0.02l-1.413-0.64C5.773,5.183,5.69,5.183,5.617,5.215l-1.489,0.65
 +
c-0.087,0.038-0.19,0.029-0.271-0.023c-0.079-0.052-0.13-0.141-0.13-0.235V0H2.191C1.655,0,1.233,0.434,1.233,0.97
 +
c0,0,0.025,15.952,0.031,15.993c0.084,0.509,0.379,0.962,0.811,1.242l2.334,1.528C4.671,19.905,4.974,20,5.286,20h10.307
 +
c1.452,0,2.634-1.189,2.634-2.64V4.007C18.227,3.666,18.12,3.339,17.92,3.065z M16.42,17.36c0,0.464-0.361,0.833-0.827,0.833H5.341
 +
l-1.675-1.089h10.341c0.537,0,0.953-0.44,0.953-0.979V2.039l1.459,2.027V17.36L16.42,17.36z"/>
 +
</g>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="august2">
 +
<h2>2nd August, Tuesday</h2>
 +
<p>
 +
11 vials of DH5 alpha competent cells were prepared.
 +
Plasmid extraction done for the construct BBa_K844004 (MaSP without ATG).
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="august3">
 +
<h2>3rd August, Wednesday</h2>
 +
<p>
 +
As a part of the iGEM 2016 interlab study, transformations were done for the following:<br>
 +
Test device1<br>
 +
Test device2<br>
 +
Test device3<br>
 +
Positive control<br>
 +
Negative control<br>
 +
Also, transformed cells were prepared with the part BBa_K844008 (MaSP with ATG)
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<g>
 +
<path fill="#FFFFFF" d="M17.92,3.065l-1.669-2.302c-0.336-0.464-0.87-0.75-1.479-0.755C14.732,0.008,7.653,0,7.653,0v5.6
 +
c0,0.096-0.047,0.185-0.127,0.237c-0.081,0.052-0.181,0.06-0.268,0.02l-1.413-0.64C5.773,5.183,5.69,5.183,5.617,5.215l-1.489,0.65
 +
c-0.087,0.038-0.19,0.029-0.271-0.023c-0.079-0.052-0.13-0.141-0.13-0.235V0H2.191C1.655,0,1.233,0.434,1.233,0.97
 +
c0,0,0.025,15.952,0.031,15.993c0.084,0.509,0.379,0.962,0.811,1.242l2.334,1.528C4.671,19.905,4.974,20,5.286,20h10.307
 +
c1.452,0,2.634-1.189,2.634-2.64V4.007C18.227,3.666,18.12,3.339,17.92,3.065z M16.42,17.36c0,0.464-0.361,0.833-0.827,0.833H5.341
 +
l-1.675-1.089h10.341c0.537,0,0.953-0.44,0.953-0.979V2.039l1.459,2.027V17.36L16.42,17.36z"/>
 +
</g>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="august4">
 +
<h2>4th August, Thursday</h2>
 +
<p>
 +
Colonies were seen for all six of the transformed plates. The transformation procedure was hence successful.
 +
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="august7">
 +
<h2>7th August, Sunday</h2>
 +
<p>
 +
20ml Culture was prepared for the screening of BBa_K844008 (MaSP with ATG).
 +
Also, 20ml cultures were prepared for each of test device 1, test device 2, and test device 3 for the interlab study.
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
 +
 +
 +
</div>
 +
</div>
 +
 +
<div class="container" id="content">
 +
    <h2 class="project-name">WEEK FOUR - ( 8th August - 12th August )</h1>
 +
<div id="timeline">
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="august8">
 +
<h2>8th August, Monday</h2>
 +
<p class="distance">
 +
PPlasmid extraction performed for the screening of the parts BBa_K844008 (MaSP with ATG); and test device 1, test device 2, test device 3 for the interlab study.
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<g>
 +
<path fill="#FFFFFF" d="M17.92,3.065l-1.669-2.302c-0.336-0.464-0.87-0.75-1.479-0.755C14.732,0.008,7.653,0,7.653,0v5.6
 +
c0,0.096-0.047,0.185-0.127,0.237c-0.081,0.052-0.181,0.06-0.268,0.02l-1.413-0.64C5.773,5.183,5.69,5.183,5.617,5.215l-1.489,0.65
 +
c-0.087,0.038-0.19,0.029-0.271-0.023c-0.079-0.052-0.13-0.141-0.13-0.235V0H2.191C1.655,0,1.233,0.434,1.233,0.97
 +
c0,0,0.025,15.952,0.031,15.993c0.084,0.509,0.379,0.962,0.811,1.242l2.334,1.528C4.671,19.905,4.974,20,5.286,20h10.307
 +
c1.452,0,2.634-1.189,2.634-2.64V4.007C18.227,3.666,18.12,3.339,17.92,3.065z M16.42,17.36c0,0.464-0.361,0.833-0.827,0.833H5.341
 +
l-1.675-1.089h10.341c0.537,0,0.953-0.44,0.953-0.979V2.039l1.459,2.027V17.36L16.42,17.36z"/>
 +
</g>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="august9">
 +
<h2>9th August, Tuesday</h2>
 +
<p>
 +
Gel Electrophoresis with 1% agarose gel was done for BBa_K844008 (MaSP with ATG), test device 1, test device 2, test device 3 for screening.
 +
The run was not successful due to gel over flow.
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="august10">
 +
<h2>10th August, Wednesday</h2>
 +
<p>
 +
20ml Culture was prepared for screening of BBa_K844008 (MaSP with ATG), test device 1, test device 2, test device 3.
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<g>
 +
<path fill="#FFFFFF" d="M17.92,3.065l-1.669-2.302c-0.336-0.464-0.87-0.75-1.479-0.755C14.732,0.008,7.653,0,7.653,0v5.6
 +
c0,0.096-0.047,0.185-0.127,0.237c-0.081,0.052-0.181,0.06-0.268,0.02l-1.413-0.64C5.773,5.183,5.69,5.183,5.617,5.215l-1.489,0.65
 +
c-0.087,0.038-0.19,0.029-0.271-0.023c-0.079-0.052-0.13-0.141-0.13-0.235V0H2.191C1.655,0,1.233,0.434,1.233,0.97
 +
c0,0,0.025,15.952,0.031,15.993c0.084,0.509,0.379,0.962,0.811,1.242l2.334,1.528C4.671,19.905,4.974,20,5.286,20h10.307
 +
c1.452,0,2.634-1.189,2.634-2.64V4.007C18.227,3.666,18.12,3.339,17.92,3.065z M16.42,17.36c0,0.464-0.361,0.833-0.827,0.833H5.341
 +
l-1.675-1.089h10.341c0.537,0,0.953-0.44,0.953-0.979V2.039l1.459,2.027V17.36L16.42,17.36z"/>
 +
</g>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="august11">
 +
<h2>11th August, Thursday</h2>
 +
<p>
 +
Plasmid extraction for the screening of BBa_K844008 (MaSP with ATG), test device 1, test device 2, test device 3 was done.
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="august12">
 +
<h2>12th August, Friday</h2>
 +
<p>
 +
Gel electrophoresis with 1% agarose gel was done for BBa_K844008 (MaSP with ATG), test device 1, test device 2, test device 3.
 +
 +
<img src= "https://static.igem.org/mediawiki/2016/e/e2/T--IIT_Kharagpur--12_aug.jpg" height="200px" width="200px">
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
 +
 +
 +
</div>
 +
</div>
 +
 +
 +
<div class="container" id="content">
 +
    <h2 class="project-name">WEEK FIVE - ( 15th August - 18th August )</h1>
 +
<div id="timeline">
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="august16">
 +
<h2>16th August, Tuesday</h2>
 +
<p class="distance">
 +
Plasmid extraction of BBa_K844008 (MaSP with ATG), test device 1, test device 2, and test device 3 was done with mini-prep kit.
 +
Digestion of above obtained plasmids with E And P was carried out.
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<g>
 +
<path fill="#FFFFFF" d="M17.92,3.065l-1.669-2.302c-0.336-0.464-0.87-0.75-1.479-0.755C14.732,0.008,7.653,0,7.653,0v5.6
 +
c0,0.096-0.047,0.185-0.127,0.237c-0.081,0.052-0.181,0.06-0.268,0.02l-1.413-0.64C5.773,5.183,5.69,5.183,5.617,5.215l-1.489,0.65
 +
c-0.087,0.038-0.19,0.029-0.271-0.023c-0.079-0.052-0.13-0.141-0.13-0.235V0H2.191C1.655,0,1.233,0.434,1.233,0.97
 +
c0,0,0.025,15.952,0.031,15.993c0.084,0.509,0.379,0.962,0.811,1.242l2.334,1.528C4.671,19.905,4.974,20,5.286,20h10.307
 +
c1.452,0,2.634-1.189,2.634-2.64V4.007C18.227,3.666,18.12,3.339,17.92,3.065z M16.42,17.36c0,0.464-0.361,0.833-0.827,0.833H5.341
 +
l-1.675-1.089h10.341c0.537,0,0.953-0.44,0.953-0.979V2.039l1.459,2.027V17.36L16.42,17.36z"/>
 +
</g>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="august17">
 +
<h2>17th August, Wednesday</h2>
 +
<p>
 +
1% agarose gel was prepared for digested plasmids
 +
PCR of protease construct for HIV site primers was done
 +
PCR parameters:<br>
 +
{95 degree 2 minutes<br>
 +
[95 degree 30 seconds<br>
 +
60 degrees 30 sec<br>
 +
68 degree 2 min] X35 cycles<br>
 +
68 degree 10 min}<br>
 +
 +
PCR products run in 1% agarose gel.<br>
 +
Amplification not upto expectation.<br>
 +
Repetition of the experiment, with different conditions suggested.<br>
 +
Note: Too many non specific products were observed that is why the same was repeated next week.
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="august18">
 +
<h2>18th August, Thursday</h2>
 +
<p>
 +
PCR of protease construct for HIV site primers was done.<br>
 +
PCR products were run in 1% agarose gel.
 +
<img src= "https://static.igem.org/mediawiki/2016/0/03/T--IIT_Kharagpur--18_aug.jpg" height="100px" width="100px"> <br>
 +
 +
PCR Parameters:<br>
 +
{95 degree 2 minutes<br>
 +
[95 degree 20 seconds<br>
 +
62 degrees 30 sec<br>
 +
68 degree 2 min 15 sec] X35 cycles<br>
 +
68 degree 10 min}<br>
 +
Amplification not upto expectation.<br>
 +
Repetition of the experiment, with different conditions suggested.
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
 +
 +
 +
 +
</div>
 +
</div>
 +
 +
<div class="container" id="content">
 +
    <h2 class="project-name">WEEK SIX - ( 22nd August - 26th August )</h1>
 +
<div id="timeline">
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="august22">
 +
<h2>22th August, Monday</h2>
 +
<p class="distance">
 +
PCR for both fret and silk constructs at two conditions was done.<br>
 +
<img src= "https://static.igem.org/mediawiki/2016/9/90/T--IIT_Kharagpur--22_aug.jpg" height="200px" width="200px"> <br>
 +
 +
Condition 1<br>
 +
{95 degree 5 minutes<br>
 +
Taq DNA polymerase is added.<br>
 +
[95 degree 30 seconds<br>
 +
57.5 degrees 40 sec<br>
 +
68 degree 40 sec] X35 cycles<br>
 +
68 degree 10 min}<br>
 +
Condition 2<br>
 +
{95 degree 2 minutes<br>
 +
[95 degree 30 seconds<br>
 +
58 degrees 1 min<br>
 +
68 degree 2 min] X35 cycles<br>
 +
68 degree 10 min}<br>
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<g>
 +
<path fill="#FFFFFF" d="M17.92,3.065l-1.669-2.302c-0.336-0.464-0.87-0.75-1.479-0.755C14.732,0.008,7.653,0,7.653,0v5.6
 +
c0,0.096-0.047,0.185-0.127,0.237c-0.081,0.052-0.181,0.06-0.268,0.02l-1.413-0.64C5.773,5.183,5.69,5.183,5.617,5.215l-1.489,0.65
 +
c-0.087,0.038-0.19,0.029-0.271-0.023c-0.079-0.052-0.13-0.141-0.13-0.235V0H2.191C1.655,0,1.233,0.434,1.233,0.97
 +
c0,0,0.025,15.952,0.031,15.993c0.084,0.509,0.379,0.962,0.811,1.242l2.334,1.528C4.671,19.905,4.974,20,5.286,20h10.307
 +
c1.452,0,2.634-1.189,2.634-2.64V4.007C18.227,3.666,18.12,3.339,17.92,3.065z M16.42,17.36c0,0.464-0.361,0.833-0.827,0.833H5.341
 +
l-1.675-1.089h10.341c0.537,0,0.953-0.44,0.953-0.979V2.039l1.459,2.027V17.36L16.42,17.36z"/>
 +
</g>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="august23">
 +
<h2>23rd August, Tuesday</h2>
 +
<p>
 +
PCR for FRET construct was done.
 +
PCR Parameters:<br>
 +
{95 degree 2 minutes<br>
 +
[95 degree 30 seconds<br>
 +
57 degrees 40 sec<br>
 +
68 degree 2 min] X35 cycles<br>
 +
68 degree 10 min}<br>
 +
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="august24">
 +
<h2>24th August, Wednesday</h2>
 +
<p>
 +
Gel run for FRET construct was performed.
 +
 +
<img src="https://static.igem.org/mediawiki/2016/e/e0/T--IIT_Kharagpur--24_aug.jpg" height="200px" width="200px">
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<g>
 +
<path fill="#FFFFFF" d="M17.92,3.065l-1.669-2.302c-0.336-0.464-0.87-0.75-1.479-0.755C14.732,0.008,7.653,0,7.653,0v5.6
 +
c0,0.096-0.047,0.185-0.127,0.237c-0.081,0.052-0.181,0.06-0.268,0.02l-1.413-0.64C5.773,5.183,5.69,5.183,5.617,5.215l-1.489,0.65
 +
c-0.087,0.038-0.19,0.029-0.271-0.023c-0.079-0.052-0.13-0.141-0.13-0.235V0H2.191C1.655,0,1.233,0.434,1.233,0.97
 +
c0,0,0.025,15.952,0.031,15.993c0.084,0.509,0.379,0.962,0.811,1.242l2.334,1.528C4.671,19.905,4.974,20,5.286,20h10.307
 +
c1.452,0,2.634-1.189,2.634-2.64V4.007C18.227,3.666,18.12,3.339,17.92,3.065z M16.42,17.36c0,0.464-0.361,0.833-0.827,0.833H5.341
 +
l-1.675-1.089h10.341c0.537,0,0.953-0.44,0.953-0.979V2.039l1.459,2.027V17.36L16.42,17.36z"/>
 +
</g>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="august25">
 +
<h2>25th August, Thursday</h2>
 +
<p>
 +
PCR for silk construct was done with the following parameters:<br>
 +
{95 degree 2 minutes<br>
 +
[95 degree 30 seconds<br>
 +
57 degrees 40 sec<br>
 +
68 degree 2 min] X35 cycles<br>
 +
68 degree 10 min}<br>
 +
 +
<img src="https://static.igem.org/mediawiki/2016/e/ee/T--IIT_Kharagpur--25_aug.jpg" height="200px" width="200px">
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="august26">
 +
<h2>26th August, Friday</h2>
 +
<p>
 +
PCR for FRET construct was done.<br>
 +
PCR Parameters:<br>
 +
{95 degree 2 minutes<br>
 +
[95 degree 30 seconds<br>
 +
58 degrees 1 min<br>
 +
68 degree 2 min] X35 cycles<br>
 +
68 degree 10 min} <br>
 +
 +
<img src="https://static.igem.org/mediawiki/2016/3/33/T--IIT_Kharagpur--26_aug.jpg" height="200px" width="200px">
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
 +
 +
 +
</div>
 +
</div>
 +
 +
<div class="container" id="content">
 +
    <h2 class="project-name">WEEK SEVEN - ( 29th August - 2nd September )</h1>
 +
<div id="timeline">
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="august29">
 +
<h2>29th August, Monday</h2>
 +
<p class="distance">
 +
Nano drop analysis for pSB1K3( Kanamycin backbone) was done.
 +
Result:Obtained concentration was 192.6mg/ul.
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<g>
 +
<path fill="#FFFFFF" d="M17.92,3.065l-1.669-2.302c-0.336-0.464-0.87-0.75-1.479-0.755C14.732,0.008,7.653,0,7.653,0v5.6
 +
c0,0.096-0.047,0.185-0.127,0.237c-0.081,0.052-0.181,0.06-0.268,0.02l-1.413-0.64C5.773,5.183,5.69,5.183,5.617,5.215l-1.489,0.65
 +
c-0.087,0.038-0.19,0.029-0.271-0.023c-0.079-0.052-0.13-0.141-0.13-0.235V0H2.191C1.655,0,1.233,0.434,1.233,0.97
 +
c0,0,0.025,15.952,0.031,15.993c0.084,0.509,0.379,0.962,0.811,1.242l2.334,1.528C4.671,19.905,4.974,20,5.286,20h10.307
 +
c1.452,0,2.634-1.189,2.634-2.64V4.007C18.227,3.666,18.12,3.339,17.92,3.065z M16.42,17.36c0,0.464-0.361,0.833-0.827,0.833H5.341
 +
l-1.675-1.089h10.341c0.537,0,0.953-0.44,0.953-0.979V2.039l1.459,2.027V17.36L16.42,17.36z"/>
 +
</g>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="august31">
 +
<h2>31st August, Wednesday</h2>
 +
<p>
 +
Digestion for Kanamycin backbone and FRET PCR with E And P
 +
<table>
 +
<tr><th></th><th>K backbone</th><th>FRET PCR</th></tr>
 +
<tr><th>Component</th><th>Volume(ul)</th><th>Volume(ul)</th></tr>
 +
<tr><td>DNA</td><td>6</td><td>2.3</td></tr>
 +
<tr><td>2.1 Buffer</td><td>2</td><td>2</td></tr>
 +
<tr><td>ECoRI</td><td>1</td><td>1</td></tr>
 +
<tr><td>Psti</td><td>1</td><td>1</td></tr>
 +
<tr><td>Nf H2O</td><td>10</td><td>13.7</td></tr>
 +
</table>
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="september1">
 +
<h2>1st September, Thursday</h2>
 +
<p>
 +
Ligation for Kanamycin backbone and FRET PCR with E and P was done
 +
Vector:Insert=1:3
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<g>
 +
<path fill="#FFFFFF" d="M17.92,3.065l-1.669-2.302c-0.336-0.464-0.87-0.75-1.479-0.755C14.732,0.008,7.653,0,7.653,0v5.6
 +
c0,0.096-0.047,0.185-0.127,0.237c-0.081,0.052-0.181,0.06-0.268,0.02l-1.413-0.64C5.773,5.183,5.69,5.183,5.617,5.215l-1.489,0.65
 +
c-0.087,0.038-0.19,0.029-0.271-0.023c-0.079-0.052-0.13-0.141-0.13-0.235V0H2.191C1.655,0,1.233,0.434,1.233,0.97
 +
c0,0,0.025,15.952,0.031,15.993c0.084,0.509,0.379,0.962,0.811,1.242l2.334,1.528C4.671,19.905,4.974,20,5.286,20h10.307
 +
c1.452,0,2.634-1.189,2.634-2.64V4.007C18.227,3.666,18.12,3.339,17.92,3.065z M16.42,17.36c0,0.464-0.361,0.833-0.827,0.833H5.341
 +
l-1.675-1.089h10.341c0.537,0,0.953-0.44,0.953-0.979V2.039l1.459,2.027V17.36L16.42,17.36z"/>
 +
</g>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="september2">
 +
<h2>2nd September, Friday</h2>
 +
<p>
 +
Transformation for Kanamycin backbone and FRET PCR with E and P failed.<br>
 +
 +
Note: Reason was determined to be inadequate amount of the PCR product
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
 +
 +
 +
 +
</div>
 +
</div>
 +
 +
<div class="container" id="content">
 +
    <h2 class="project-name">WEEK EIGHT - ( 8th September - 10th September )</h1>
 +
<div id="timeline">
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="september8">
 +
<h2>8th September, Thursday</h2>
 +
<p class="distance">
 +
2 ml culture of CFP and YFP was prepared.<br>
 +
 +
PCR done for FRET construct and silk construct<br>
 +
Digestion with E and P of FRET PCR product was done.<br>
 +
<table>
 +
<tr><th></th><th>FRET PCR</th></tr>
 +
<tr><th>Component</th><th>Volume(ul)</th></tr>
 +
<tr><td>DNA</td><td>19</td></tr>
 +
<tr><td>2.1 Buffer</td><td>2.5</td></tr>
 +
<tr><td>ECoRI</td><td>1</td></tr>
 +
<tr><td>PstI</td><td>1</td></tr>
 +
<tr><td>NF H2O</td><td>1.5</td></tr>
 +
</table>
 +
 +
<img src="https://static.igem.org/mediawiki/2016/8/87/T--IIT_Kharagpur--8_sep.jpg" height="200px" width="200px">
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<g>
 +
<path fill="#FFFFFF" d="M17.92,3.065l-1.669-2.302c-0.336-0.464-0.87-0.75-1.479-0.755C14.732,0.008,7.653,0,7.653,0v5.6
 +
c0,0.096-0.047,0.185-0.127,0.237c-0.081,0.052-0.181,0.06-0.268,0.02l-1.413-0.64C5.773,5.183,5.69,5.183,5.617,5.215l-1.489,0.65
 +
c-0.087,0.038-0.19,0.029-0.271-0.023c-0.079-0.052-0.13-0.141-0.13-0.235V0H2.191C1.655,0,1.233,0.434,1.233,0.97
 +
c0,0,0.025,15.952,0.031,15.993c0.084,0.509,0.379,0.962,0.811,1.242l2.334,1.528C4.671,19.905,4.974,20,5.286,20h10.307
 +
c1.452,0,2.634-1.189,2.634-2.64V4.007C18.227,3.666,18.12,3.339,17.92,3.065z M16.42,17.36c0,0.464-0.361,0.833-0.827,0.833H5.341
 +
l-1.675-1.089h10.341c0.537,0,0.953-0.44,0.953-0.979V2.039l1.459,2.027V17.36L16.42,17.36z"/>
 +
</g>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="september9">
 +
<h2>9th September, Friday</h2>
 +
<p>
 +
PCR purification of digested FRET PCR product was done.
 +
Plasmid isolation of YFP and CFP was performed.<br>
 +
YFP: 250 ng/ul<br>
 +
CFP: 218 ng/ul<br>
 +
Glycerol stock for CFP and YFP was prepared.<br>
 +
Restriction digestion(overnight) of YFP and cleavage site was done.<br>
 +
<table>
 +
<tr><th></th><th>YFP</th></tr>
 +
<tr><th>Component</th><th>Volume(ul)</th></tr>
 +
<tr><td>DNA</td><td>5</td></tr>
 +
 +
<tr><td>ECoR buffer</td><td>2</td></tr>
 +
<tr><td>ECoRI</td><td>1</td></tr>
 +
<tr><td>NF H2O</td><td>12</td></tr>
 +
</table>
 +
 +
<table>
 +
<tr><th></th><th>Cleavage Site</th></tr>
 +
<tr><th>Component</th><th>Volume(ul)</th></tr>
 +
<tr><td>DNA</td><td>10</td></tr>
 +
<tr><td>3.1 Buffer</td><td>2</td></tr>
 +
<tr><td>ECoRI</td><td>1</td></tr>
 +
<tr><td>Xbal</td><td>1</td></tr>
 +
<tr><td>NF H2O</td><td>6</td></tr>
 +
</table>
 +
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="september10">
 +
<h2>10th September, Saturday</h2>
 +
<p>
 +
PCR purification of YFP digested with E was done.
 +
Digestion of purified YFP was done with S for 4 hrs at 37 degrees.
 +
<table>
 +
<tr><th></th><th>YFP</th></tr>
 +
<tr><th>Component</th><th>Volume(ul)</th></tr>
 +
<tr><td>DNA</td><td>20</td></tr>
 +
<tr><td>Cutsmart Buffer</td><td>2.5</td></tr>
 +
<tr><td>Spel</td><td>1</td></tr>
 +
<tr><td>NF H2O</td><td>1.5</td></tr>
 +
</table>
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
 +
</div>
 +
</div>
 +
 +
<div class="container" id="content">
 +
    <h2 class="project-name">WEEK NINE - ( 12th September - 13th September )</h1>
 +
<div id="timeline">
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="september12">
 +
<h2>12th September, Monday</h2>
 +
<p class="distance">
 +
22 ml cultures of CFP, YFP, HIV site, MASP with ATG and MASP without ATG was prepared.
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<g>
 +
<path fill="#FFFFFF" d="M17.92,3.065l-1.669-2.302c-0.336-0.464-0.87-0.75-1.479-0.755C14.732,0.008,7.653,0,7.653,0v5.6
 +
c0,0.096-0.047,0.185-0.127,0.237c-0.081,0.052-0.181,0.06-0.268,0.02l-1.413-0.64C5.773,5.183,5.69,5.183,5.617,5.215l-1.489,0.65
 +
c-0.087,0.038-0.19,0.029-0.271-0.023c-0.079-0.052-0.13-0.141-0.13-0.235V0H2.191C1.655,0,1.233,0.434,1.233,0.97
 +
c0,0,0.025,15.952,0.031,15.993c0.084,0.509,0.379,0.962,0.811,1.242l2.334,1.528C4.671,19.905,4.974,20,5.286,20h10.307
 +
c1.452,0,2.634-1.189,2.634-2.64V4.007C18.227,3.666,18.12,3.339,17.92,3.065z M16.42,17.36c0,0.464-0.361,0.833-0.827,0.833H5.341
 +
l-1.675-1.089h10.341c0.537,0,0.953-0.44,0.953-0.979V2.039l1.459,2.027V17.36L16.42,17.36z"/>
 +
</g>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="september13">
 +
<h2>13th September, Tuesday</h2>
 +
<p>
 +
Glycerol stock and plasmid extraction of  CFP, YFP, HIV site, MASP with ATG and MASP without ATG was performed.<br>
 +
CFP:437.5 ng/ul<br>
 +
YFP: 286.7 ng/ul<br>
 +
HIV Cleavage Site: 357.1 ng/ul<br>
 +
MaSP with ATG: 268.2 ng/ul<br>
 +
MaSP w/o ATG: 123ng/ul<br>
 +
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
 +
 +
 +
 +
 +
</div>
 +
</div>
 +
 +
 +
 +
 +
<div class="container" id="content">
 +
    <h2 class="project-name">WEEK TEN - ( 19th September - 24th September )</h1>
 +
<div id="timeline">
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="september19">
 +
<h2>19th September, Monday</h2>
 +
<p class="distance">
 +
PCR for FRET (2 sets)
 +
Digestion with E and X for HIV site and E for CFP was successfully done.<br>
 +
<table>
 +
<tr><th></th><th>CFP</th></tr>
 +
<tr><th>Component</th><th>Volume(ul)</th></tr>
 +
<tr><td>DNA</td><td>20</td></tr>
 +
 +
<tr><td>ECoR buffer</td><td>2</td></tr>
 +
<tr><td>ECoRI</td><td>1</td></tr>
 +
<tr><td>NF H2O</td><td>14.7</td></tr>
 +
</table>
 +
 +
<table>
 +
<tr><th></th><th>Cleavage Site</th></tr>
 +
<tr><th>Component</th><th>Volume(ul)</th></tr>
 +
<tr><td>DNA</td><td>2.8</td></tr>
 +
<tr><td>3.1 Buffer</td><td>2</td></tr>
 +
<tr><td>ECoRI</td><td>1</td></tr>
 +
<tr><td>Xbal</td><td>1</td></tr>
 +
<tr><td>NF H2O</td><td>13.2</td></tr>
 +
</table>
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<g>
 +
<path fill="#FFFFFF" d="M17.92,3.065l-1.669-2.302c-0.336-0.464-0.87-0.75-1.479-0.755C14.732,0.008,7.653,0,7.653,0v5.6
 +
c0,0.096-0.047,0.185-0.127,0.237c-0.081,0.052-0.181,0.06-0.268,0.02l-1.413-0.64C5.773,5.183,5.69,5.183,5.617,5.215l-1.489,0.65
 +
c-0.087,0.038-0.19,0.029-0.271-0.023c-0.079-0.052-0.13-0.141-0.13-0.235V0H2.191C1.655,0,1.233,0.434,1.233,0.97
 +
c0,0,0.025,15.952,0.031,15.993c0.084,0.509,0.379,0.962,0.811,1.242l2.334,1.528C4.671,19.905,4.974,20,5.286,20h10.307
 +
c1.452,0,2.634-1.189,2.634-2.64V4.007C18.227,3.666,18.12,3.339,17.92,3.065z M16.42,17.36c0,0.464-0.361,0.833-0.827,0.833H5.341
 +
l-1.675-1.089h10.341c0.537,0,0.953-0.44,0.953-0.979V2.039l1.459,2.027V17.36L16.42,17.36z"/>
 +
</g>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="september20">
 +
<h2>20th September, Tuesday</h2>
 +
<p>
 +
PCR purification of CFP digested with E was done.
 +
Digestion with S of purified product was done for 6 hours at 37 degrees.
 +
 +
<table>
 +
<tr><th></th><th>CFP</th></tr>
 +
<tr><th>Component</th><th>Volume(ul)</th></tr>
 +
<tr><td>DNA</td><td>20</td></tr>
 +
<tr><td>Cutsmart Buffer</td><td>2.5</td></tr>
 +
<tr><td>Spel</td><td>1</td></tr>
 +
<tr><td>NF H2O</td><td>1.5</td></tr>
 +
</table>
 +
 +
<br>
 +
Gel extraction of digested CFP and HIV site was successfully performed.
 +
The gel pieces stored at 4 degrees
 +
 +
<img src="https://static.igem.org/mediawiki/2016/4/49/T--IIT_Kharagpur--20_sep.jpg" height="200px" width="200px">
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="september21">
 +
<h2>21st September, Wednesday</h2>
 +
<p>
 +
Gel extraction of stored gel pieces
 +
Amount of extracted DNA too low to proceed to ligation step
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<g>
 +
<path fill="#FFFFFF" d="M17.92,3.065l-1.669-2.302c-0.336-0.464-0.87-0.75-1.479-0.755C14.732,0.008,7.653,0,7.653,0v5.6
 +
c0,0.096-0.047,0.185-0.127,0.237c-0.081,0.052-0.181,0.06-0.268,0.02l-1.413-0.64C5.773,5.183,5.69,5.183,5.617,5.215l-1.489,0.65
 +
c-0.087,0.038-0.19,0.029-0.271-0.023c-0.079-0.052-0.13-0.141-0.13-0.235V0H2.191C1.655,0,1.233,0.434,1.233,0.97
 +
c0,0,0.025,15.952,0.031,15.993c0.084,0.509,0.379,0.962,0.811,1.242l2.334,1.528C4.671,19.905,4.974,20,5.286,20h10.307
 +
c1.452,0,2.634-1.189,2.634-2.64V4.007C18.227,3.666,18.12,3.339,17.92,3.065z M16.42,17.36c0,0.464-0.361,0.833-0.827,0.833H5.341
 +
l-1.675-1.089h10.341c0.537,0,0.953-0.44,0.953-0.979V2.039l1.459,2.027V17.36L16.42,17.36z"/>
 +
</g>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="september22">
 +
<h2>22nd September, Thursday</h2>
 +
<p>
 +
S digestion of CFP and X digestion of HIV
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="september23">
 +
<h2>23rd September, Friday</h2>
 +
<p>
 +
PCR purification of above digested followed by E digestion of both for 6 hrs at 37 degrees
 +
Gel extraction after completion of digestion followed by ligation of E and X digested HIV site and E and S digested CFP at 16 degrees overnight
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="september24">
 +
<h2>24th September, Saturday</h2>
 +
<p>
 +
Transformed DH5 alpha cells with ligation mix and plating on A+K plates
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
 +
 +
 +
</div>
 +
</div>
 +
 +
<div class="container" id="content">
 +
    <h2 class="project-name">WEEK ELEVEN - ( 25th September - 2nd October )</h1>
 +
<div id="timeline">
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="september25">
 +
<h2>25th September, Sunday</h2>
 +
<p class="distance">
 +
Colonies observed on incubated plates
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<g>
 +
<path fill="#FFFFFF" d="M17.92,3.065l-1.669-2.302c-0.336-0.464-0.87-0.75-1.479-0.755C14.732,0.008,7.653,0,7.653,0v5.6
 +
c0,0.096-0.047,0.185-0.127,0.237c-0.081,0.052-0.181,0.06-0.268,0.02l-1.413-0.64C5.773,5.183,5.69,5.183,5.617,5.215l-1.489,0.65
 +
c-0.087,0.038-0.19,0.029-0.271-0.023c-0.079-0.052-0.13-0.141-0.13-0.235V0H2.191C1.655,0,1.233,0.434,1.233,0.97
 +
c0,0,0.025,15.952,0.031,15.993c0.084,0.509,0.379,0.962,0.811,1.242l2.334,1.528C4.671,19.905,4.974,20,5.286,20h10.307
 +
c1.452,0,2.634-1.189,2.634-2.64V4.007C18.227,3.666,18.12,3.339,17.92,3.065z M16.42,17.36c0,0.464-0.361,0.833-0.827,0.833H5.341
 +
l-1.675-1.089h10.341c0.537,0,0.953-0.44,0.953-0.979V2.039l1.459,2.027V17.36L16.42,17.36z"/>
 +
</g>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="september26">
 +
<h2>26th September, Mondayy</h2>
 +
<p>
 +
18 colonies from the 1:3 plate were put into 1 ml media overnight for screening<br>
 +
14 colonies from the 1:5 plate were put into 1 ml media overnight for screening<br>
 +
Digestion of YFP with X and P<br>
 +
Digestion of HIV site with S and P
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="september27">
 +
<h2>27th September, Tuesday</h2>
 +
<p>
 +
PCR for FRET (2 sets)<br>
 +
Gel extraction for PCR products and digestion with P<br>
 +
Digestion of K backbone with P<br>
 +
Screening for  18 colonies from the 1:3 plate and 14 colonies from the 1:5 plate<br>
 +
Colonies 1, 4, 7, 10 from 1:3 plate showed a shift<br>
 +
Colonies 1, 5, 11 from 1:5 plate showed a shift<br>
 +
 +
<img src="https://static.igem.org/mediawiki/2016/a/aa/T--IIT_Kharagpur--27_sep.jpg" height="200px" width="200px">
 +
Ligation of YFP digested with X and P with HIV site digested with S and P<br>
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<g>
 +
<path fill="#FFFFFF" d="M17.92,3.065l-1.669-2.302c-0.336-0.464-0.87-0.75-1.479-0.755C14.732,0.008,7.653,0,7.653,0v5.6
 +
c0,0.096-0.047,0.185-0.127,0.237c-0.081,0.052-0.181,0.06-0.268,0.02l-1.413-0.64C5.773,5.183,5.69,5.183,5.617,5.215l-1.489,0.65
 +
c-0.087,0.038-0.19,0.029-0.271-0.023c-0.079-0.052-0.13-0.141-0.13-0.235V0H2.191C1.655,0,1.233,0.434,1.233,0.97
 +
c0,0,0.025,15.952,0.031,15.993c0.084,0.509,0.379,0.962,0.811,1.242l2.334,1.528C4.671,19.905,4.974,20,5.286,20h10.307
 +
c1.452,0,2.634-1.189,2.634-2.64V4.007C18.227,3.666,18.12,3.339,17.92,3.065z M16.42,17.36c0,0.464-0.361,0.833-0.827,0.833H5.341
 +
l-1.675-1.089h10.341c0.537,0,0.953-0.44,0.953-0.979V2.039l1.459,2.027V17.36L16.42,17.36z"/>
 +
</g>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="september28">
 +
<h2>28th September, Wednesday</h2>
 +
<p>
 +
PCR purification of P digested K backbone and FRET PCR followed by E digestion
 +
Gel Extraction of the digested products followed by ligation
 +
Colonies observed of ligated YFP and HIV site observed
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
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 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="september29">
 +
<h2>29th September, Thursday</h2>
 +
<p>
 +
25 colonies from the ligated YFP and HIV site plate picked for screening
 +
X and P digestion for CFP+ HIV
 +
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="september30">
 +
<h2>30th September, Friday</h2>
 +
<p>
 +
Screening of YFP + HIV<br>
 +
Gel run X and P digested CFP + HIV<br>
 +
20 ml cultures for plasmid extraction of K-backbone, CFP+HIV and HIV Site, YFP+HIV (colony 7) and YFP+HIV (colony 13)
 +
 +
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="october1">
 +
<h2>1st October, Saturday</h2>
 +
<p>
 +
Plasmid extractions for the above cultures<br>
 +
Digestion with X and P for YFP+HIV (colony 7) and CFP+HIV<br>
 +
Gel run for the digested YFP+HIV (colony 7) and CFP+HIV<br>
 +
Digestion with X of YFP+HIV<br>
 +
Digestion with S of CFP
 +
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
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 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="october2">
 +
<h2>2nd October, Sunday</h2>
 +
<p>
 +
PCR purification of the digested products<br>
 +
Digestion with E of S digested CFP and X digested YFP+HIV<br>
 +
Gel extraction of the digested product<br>
 +
Ligation of E and S digested CFP and E and X digested YFP+HIV<br>
 +
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div></div></div>
 +
<div class="container" id="content">
 +
    <h2 class="project-name">WEEK TWELVE - ( 3rd October - 9th October )</h1>
 +
<div id="timeline">
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="october3">
 +
<h2>3rd October, Monday</h2>
 +
<p class="distance">
 +
Transformation of the Ligated product onto A+K plates.
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
c-0.329-0.825-1.5-0.825-1.83,0L7.476,5.611c-0.132,0.346-0.462,0.578-0.824,0.61L0.894,6.766C0.035,6.848-0.312,7.921,0.333,8.499
 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="october4">
 +
<h2>4th October, Tuesday</h2>
 +
<p class="distance">
 +
Growth was observed on both the plates. <br>
 +
1 ml culture was given for 14 colonies of each of the plates, for the purpose of screening.
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
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 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="october5">
 +
<h2>5th October, Wednesday</h2>
 +
<p class="distance">
 +
 +
1% Agarose gel was run for the plasmids extracted from the overnight cultures.<br>
 +
Sufficient number show the desired shift.<br>
 +
20 ml culture was given for miniprep extraction of CFP+HIV+YFP  form colony 10 and 15 of the 1:3 ligation plate
 +
 +
 +
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
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 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="october6">
 +
<h2>6th October, Thursday</h2>
 +
<p class="distance">
 +
 +
PCR was run (2 sets)<br>
 +
The PCR product was run on 1% agarose gel for extraction.<br>
 +
Amount too low to continue.<br>
 +
 +
Miniprep for CFP+HIV+YFP<br>
 +
Colony 10: 187.5 ng/ul<br>
 +
Colony 15: 185 ng/ul<br>
 +
Digestion with X and P for the isolated plasmid (overnight)<br>
 +
<table>
 +
<tr><th></th><th>CFP+HIV+YFP</th></tr>
 +
<tr><td>Components</td><td>Volume(&micro;l)</td></tr>
 +
<tr><td>DNA</td><td>6</td></tr>
 +
<tr><td>3.1 Buffer</td><td>2</td></tr>
 +
<tr><td>Xba1</td><td>1</td></tr>
 +
<tr><td>Pstl</td><td>1</td></tr>
 +
<tr><td>NF H2O</td><td>10</td></tr>
 +
</table>
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
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 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="october7">
 +
<h2>7th October, Friday</h2>
 +
<p class="distance">
 +
 +
1% agarose gel was run for the digested product.<br>
 +
Bands appear as expected
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
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 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="october8">
 +
<h2>8th October, Saturday</h2>
 +
<p class="distance">
 +
 +
20 ml culture for plasmid extraction of CFP+HIV+YFP (Colony 10)
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
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 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content right" id="october9">
 +
<h2>9th October, Sunday</h2>
 +
<p class="distance">
 +
 +
Mini prep extraction of CFP+HIV+YFP<br>
 +
 +
CFP+HIV+YFP:  94 ng/&micro;l<br>
 +
 +
PCR was done (2 sets) for FRET<br>
 +
No amplification was seen
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
</div>
 +
</div>
 +
<div class="container" id="content">
 +
    <h2 class="project-name">WEEK THIRTEEN - ( 11th October - 16th October )</h1>
 +
<div id="timeline">
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
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 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
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 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="october11">
 +
<h2>11th October, Tuesday</h2>
 +
<p class="distance">
 +
PCR was done (2 sets) for FRET<br>
 +
No amplification was seen
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
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 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="october13">
 +
<h2>13th October, Thursday</h2>
 +
<p class="distance">
 +
Digestions with X and P of CFP in pSB1C3 backbone and CFP+HIV, YFP+HIV and CFP+HIV+YFP all in pSB1AK8 backbone.
 +
<table>
 +
<tr><th></th><th>CFP+HIV+YFP</th><th>CFP+HIV</th><th>HIV+YFP</th><th>CFP</th></tr>
 +
<tr><td>Component</td>Volume (&micro;l)<td>Volume (&micro;l)</td><td>Volume (&micro;l)</td><td>Volume (&micro;l)</td><td>Volume (&micro;l)</td></tr>
 +
<tr><td>DNA</td><td>6</td><td>4</td><td>6</td><td>3</td></tr>
 +
<tr><td>3.1 Buffer</td><td>2</td><td>2</td><td>2</td><td>2</td></tr>
 +
<tr><td>Xba1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr>
 +
<tr><td>Pstl</td><td>1</td><td>1</td><td>1</td><td>1</td></tr>
 +
<tr><td>NF H2O</td><td>10</td><td>12</td><td>10</td><td>13</td></tr>
 +
</table>
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
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 +
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 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="october14">
 +
<h2>14th October, Friday</h2>
 +
<p class="distance">
 +
1% Agarose gel for extraction of all above.<br>
 +
Significant amount observed only in the digested CFP, whereas all the rest proved unsuccessful.<br>
 +
 +
20 ml cultures given for extraction of CFP+HIV, YFP+HIV and CFP+HIV+YFP.
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
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 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
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 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="october15">
 +
<h2>15th October, Saturday</h2>
 +
<p class="distance">
 +
Mini prep done for CFP+HIV, YFP+HIV and CFP+HIV+YFP.<br>
 +
 +
CFP+HIV:  84 ng/ul<br>
 +
HIV+YFP:  92 ng/ul<br>
 +
CFP+HIV+YFP:  87 ng/ul<br>
 +
 +
X and P digestions set up for all three isolated plasmids<br>
 +
<table>
 +
<tr><th></th><th>CFP+HIV+YFP</th><th>CFP+HIV</th><th>HIV+YFP</th></tr>
 +
<tr><td>Components</td><td>Volume (&micro;l)</td><td>Volume (&micro;l)</td><td>Volume (&micro;l)</td></tr>
 +
<tr> <td>DNA</td> <td>13</td> <td>13</td> <td>13</td> </tr>
 +
<tr> <td>3.1 Buffer</td> <td>2</td> <td>2</td> <td>2</td> </tr>
 +
<tr> <td>Xbal</td> <td>1</td> <td>1</td> <td>1</td> </tr>
 +
<tr> <td>Pstl</td> <td>1</td> <td>1</td> <td>1</td> </tr>
 +
<tr> <td>NF H2O</td> <td>3</td> <td>3</td> <td>3</td> </tr></table>
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
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 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
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 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="october16">
 +
<h2>16th October, Sunday</h2>
 +
<p class="distance">
 +
1% agarose gel run for gel extraction of digested products.<br>
 +
 +
Digestion with X and P of CFP and C+H+Y
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
 +
 +
 +
 +
 +
 +
</div>
 +
</div></div></div>
 +
 +
<div class="container" id="content">
 +
    <h2 class="project-name">WEEK FOURTEEN - ( 17th October - 23rd October )</h1>
 +
<div id="timeline">
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
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 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="october17">
 +
<h2>17th October, Monday</h2>
 +
<p class="distance">
 +
% Agarose gel run for Gel Extraction of digested product. <br>
 +
Ligation with ratio 1:3 done using the backbone from CFP and Insert from CFP+HIV+YFP<br>
 +
 +
30 ml culture given for plasmid extraction of CFP+HIV+YFP.
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
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 +
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 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
c-0.081-0.365,0.035-0.729,0.313-0.975l4.34-3.811C21.219,7.921,20.855,6.848,19.998,6.766z"/>
 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="october19">
 +
<h2>18th October, Tuesday</h2>
 +
<p class="distance">
 +
Mini Prep for CFP+HIV+YFP<br>
 +
 +
CFP+HIV+YFP:  275 ng/ul<br>
 +
 +
X and P digestion of the CFP and CFP+HIV+YFP<br>
 +
1% Agarose Gel for Gel Extraction of the above digested products<br>
 +
 +
Quick Ligation was set up for the the digested CFP backbone and CFP+HIV+YFP<br>
 +
1:3 ratio was used<br>
 +
Transformation was done on Cam plates<br>
 +
 +
Overnight Ligation set up for CFP and CFP+HIV+YFP in the ratio 1:3<br>
 +
 +
Transformation done for the previously set overnight ligation<br>
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
 +
<div class="timeline-item">
 +
<div class="timeline-icon">
 +
<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
 +
width="21px" height="20px" viewBox="0 0 21 20" enable-background="new 0 0 21 20" xml:space="preserve">
 +
<path fill="#FFFFFF" d="M19.998,6.766l-5.759-0.544c-0.362-0.032-0.676-0.264-0.822-0.61l-2.064-4.999
 +
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 +
l4.338,3.811c0.279,0.246,0.395,0.609,0.314,0.975l-1.304,5.345c-0.199,0.842,0.708,1.534,1.468,1.089l4.801-2.822
 +
c0.313-0.181,0.695-0.181,1.006,0l4.803,2.822c0.759,0.445,1.666-0.23,1.468-1.089l-1.288-5.345
 +
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 +
</svg>
 +
 +
</div>
 +
<div class="timeline-content" id="october19">
 +
<h2>19th October, Wednesday</h2>
 +
<p class="distance">
 +
%No colonies observed on the quick ligated plate<br>
 +
 +
Colonies observed on plate whose ligation was done on 17th october<br>
 +
1 ml Cultures for 16 colonies of the plate given overnight<br>
 +
 +
 +
Transformation done for the ligated products from 18th October.
 +
 +
 +
 +
</p>
 +
 +
</div>
 +
</div>
  
−
  <div class="panel panel-info">
 
−
    <div class="panel-heading" role="tab" id="headingEight">
 
−
      <h4 class="panel-title">
 
−
        <a class="collapsed" role="button" data-toggle="collapse" data-parent="#accordion" href="#collapseEight" aria-expanded="false" aria-controls="collapseEight">
 
−
          <b style="font-family:Dosis; font-size:20px;">PROTOCOL - PLASMID ISOLATION FOR SCREENING</b>
 
−
        </a>
 
−
      </h4>
 
−
    </div>
 
−
    <div id="collapseEight" class="panel-collapse collapse" role="tabpanel" aria-labelledby="headingEight">
 
−
      <div class="panel-body">
 
−
        <h3><b>Approximation time:</b></h3>
 
−
        <h3><b>Material required:</b></h3>
 
−
        <ul>
 
−
        <li></li>
 
−
        </ul>
 
−
        <h3><b>Protocol:</b></h3>
 
−
        <p style="font-family:Dosis; font-size:20px;">1. Centrifuge cells at 1000 rpm for 6 minutes.</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">2. Discard suspension and resuspend pellet in 200 µl of P1 and vortex it.</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">3. Add 200 µl of P2 and invert mix it 4 to 6 minutes.</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">4. Add 200 µl of P3 and invert mix it .Keep on ice for 10 minutes.</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">5. Centrifuge at 12000 rpm for 25 minutes at 4 °C.</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">6. Transfer supernatant into a fresh tube and add equal volume of chloroform. Invert mix it. Centrifuge at 1000 rpm for 10 minutes at 4 °C.</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">7. Aspirate supernatant and add ethanol to it.Mix and keep at -20°C for 1 hour.</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">8. Centrifuge at 1200 rpm for 15 minute at 4°C.</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">9. Resuspend pellet in 70% alcohol and centrifuge at 1200 rpm for 10 min at 4°C.</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">10. Discard supernatant and allow the pellet to dry. Add milli Q water.</p>
 
−
    </div>
 
−
  </div>
 
−
  </div>
 
  
  
−
  <div class="panel panel-info">
 
−
    <div class="panel-heading" role="tab" id="headingNine">
 
−
      <h4 class="panel-title">
 
−
        <a class="collapsed" role="button" data-toggle="collapse" data-parent="#accordion" href="#collapseNine" aria-expanded="false" aria-controls="collapseNine">
 
−
          <b style="font-family:Dosis; font-size:20px;">PROTOCOL- CULTURING, STREAKING AND PLATING  </b>
 
−
        </a>
 
−
      </h4>
 
−
    </div>
 
−
    <div id="collapseNine" class="panel-collapse collapse" role="tabpanel" aria-labelledby="headingNine">
 
−
      <div class="panel-body">
 
−
        <h3><b>Approxmiation time:</b></h3>
 
−
        <h3><b>Material required:</b></h3>
 
−
        <ul>
 
−
        <li>Mixed culture of bacteria</li>
 
−
        <li>Sterile petri dish with appropriate bacterial media</li>
 
−
        <li>Inoculating loop </li>
 
−
        <li>Bunsen burner</li>
 
−
        </ul>
 
−
        <h3><b>Protocol</b></h3>
 
−
        <p style="font-family:Dosis; font-size:20px;">1. Label the petri dishes including organism ,type of agar ,date and name on the bottom</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">2. Sterilise the transfer loop by flaming it in the bunsen burner and let the loop cool down.</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">3. Flame the neck of the test tube.</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">4. Insert the loop into the culture broth and withdraw. At all times hold the loop as still as possible.</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">5. Flame the neck of the test tube again.</p>
 
−
        <p style="font-family:Dosis;font-size:20px;">6. Replace the cap/ cotton wool plug of the test tube using the little finger of your right hand. Place the test tube in a rack. For a liquid culture, dip the loop into the broth, or for solid media, lightly touch a colony with the loop.</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">7. Partially lift the lid of the Petri dish containing the solid medium.</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">8. Place a loopful of the culture on the agar surface on a area and then drag it rapidly several times across the surface of area.</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">9. Turn the dish 90°C anticlockwise and streak the area hitting last area several times. Repeat the step three more time.</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">10. Remove the loop and close the Petri dish.</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">11. Tape the plate closed and incubates the plate in an inverted position in an incubator for 24-48 hours.</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">12. Flame the loop before putting it aside.</p>
 
−
      </div>
 
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−
    <div class="panel-heading" role="tab" id="headingTen">
 
−
      <h4 class="panel-title">
 
−
        <a class="collapsed" role="button" data-toggle="collapse" data-parent="#accordion" href="#collapseTen" aria-expanded="false" aria-controls="collapseTen">
 
−
          <b style="font-family:Dosis; font-size:20px;">PROTOCOL - POLYMERASE CHAIN REACTION</b>
 
−
        </a>
 
−
      </h4>
 
−
    </div>
 
−
    <div id="collapseTen" class="panel-collapse collapse" role="tabpanel" aria-labelledby="headingTen">
 
−
      <div class="panel-body">
 
−
        <h3><b>Approximation time:</b></h3>2-4hrs
 
−
        <h3><b>Material required:</b></h3>
 
−
        <ul>
 
−
        <li>10x Amplification buffer</li>
 
−
        <li>dNTP solution containing all four dNTPs </li>
 
−
        <li>Thermostable DNA polymerase</li>
 
−
        <li>Nucleic Acids and Oligonucleotides</li>
 
−
        <li>Template DNA</li>
 
−
        <li>PCR tubes</li>
 
−
        <li>Primers(Foward & Reverse)</li>
 
  
−
        </ul>
 
−
        <h3><b>Protocol:</b></h3>
 
−
        <p style="font-family:Dosis; font-size:20px;">1. In the amplification tube,add and mix in the order
 
−
        <div class="contianer">
 
−
        <table class="table table-bordered">
 
−
        <tr>
 
−
        <td>10x PCR buffer</td>
 
−
        <td>5&micro;l</td>
 
−
        </tr>
 
−
        <tr>
 
−
        <td>20mM solution of four dNTPs</td>
 
−
        <td>1&micro;l</td>
 
−
        </tr>
 
−
        <tr>
 
−
        <td>10 pmol/&micro;l forward primer</td>
 
−
        <td>3&micro;l</td>
 
−
        </tr>
 
−
        <tr>
 
−
        <td>10 pmol/&micro;l reverse primer</td>
 
−
        <td>3&micro;l</td>
 
−
        </tr>
 
−
        <tr>
 
−
        <td>Thermostable DNA polymerase mix</td>
 
−
        <td>0.5 - 1 &micro;l</td>
 
−
        </tr>
 
−
        <tr>
 
−
        <td>Template DNA</td>
 
−
        <td>6&micro;l</td>
 
−
        </tr>
 
−
        <tr>
 
−
        <td>water</td>
 
−
        <td>31&micro;l</td>
 
−
        </tr>
 
  
−
        </table>
 
−
        </div></p>
 
−
        <p style="font-family:Dosis; font-size:20px;">2. If the thermal cycler is not fitted with a heated lid, overlay the reaction mixtures with 1 drop (approx. 50 μl) of light mineral oil. Alternatively, place a bead of wax into the tube if using a hot start protocol. Place the tubes or the micro titer plate in the thermal cycler.</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">3. Amplify the nucleic acids using the denaturation, annealing, and polymerization times and temperatures listed below.
 
−
        <div class="contianer">
 
−
        <table class="table table-bordered">
 
−
        <thead>
 
−
        <tr>
 
−
        <th>Cycle Number</th>
 
−
        <th>Denaturation</th>
 
−
        <th>Annealing</th>
 
−
        <th>Polymerisation</th>
 
−
        </tr>
 
−
        </thead>
 
−
        <tr>
 
−
        <td>35</td>
 
−
        <td>30 sec at 94 °C</td>
 
−
        <td>1 min at 58 °C</td>
 
−
        <td>2 mins at 68°C</td>
 
−
        </tr>
 
−
        </table>
 
−
        </div></p>
 
−
        <p style="font-family:Dosis; font-size:20px;">4. Withdraw a sample (5-10 μl) from the test reaction mixture and the four control reactions, analyze them by electrophoresis through an agarose gel, and stain the gel with ethidium bromide or SYBR Gold to visualize the DNA. A successful amplification reaction should yield a readily visible DNA fragment of the expected size.</p>
 
−
        <p style="font-family:Dosis; font-size:20px;">5. If mineral oil was used to overlay the reaction (Step 2), remove the oil from the sample by extraction with 150 μl of chloroform. The aqueous phase, which contains the amplified DNA, will form a micelle near the meniscus. The micelle can be transferred to a fresh tube with an automatic micropipette.</p>
 
−
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Latest revision as of 01:04, 20 October 2016

IGEM-IIT Kharagpur- Notebook

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WEEK ONE - ( 20th July - 22th July )

20th july, Wednesday

DH5 alpha competent cells were prepared for transformation experiments.

21st July, Thursday

Transformation of the prepared competent cells was carried out. The plasmids used for transformation were YFP (BBa_K592101), HIV cleavage site (BBa_I712015), and the protease construct (BBa_K743013)

22nd July, Friday

Replication plating for above transformed parts was done. This including the three sets of transformed cells containing the plasmids YFP (BBa_K592101), the HIV cleavage site (BBa_I712015), and the protease construct (BBa_K743013).

WEEK TWO - ( 25th July - 30th July )

25th july, Monday

1 litre of LB media was prepared and duly autoclaved. 5 plates each of the antibiotics chloramphenicol, ampicillin and ampicillin+Kanamycin were prepared.

26th July, Tuesday

20ml Cultures were prepared for the plasmid extraction of each of YFP (BBa_K592101), the HIV cleavage site (BBa_I712015) and the protease construct (BBa_K743013).

27th July, Wednesday

Plasmid extraction was done for YFP (BBa_K592101), the HIV cleavage site (BBa_I712015), and the protease construct (BBa_K743013) using mini-prep plasmid DNA extraction kit.

28th July, Thursday

DNA quantification was done using Nano Drop. YFP: 250 ng/ul
Protease: 170 ng/ul
Cleavage Site: 120 ng/ul
1% agarose gel was prepared for screening of the plasmids extracted by the mini prep kit.
The FRET construct was kept for overnight digestion at the restriction sites E and P.
Digestions with E and P for YFP, Protease and Cleavage Site

YFPProteaseCleavage Site
ComponentVolume(ul)Volume(ul)Volume(ul)
DNA233.5
2.1 Buffer222
ECoRI0.50.50.5
Psti0.50.5-
Nf H2O151414

WEEK THREE - ( 1st August - 7th August )

1st August, Monday

3ml cultures made for the preparation of competent cells of DH5 alpha cells. 20ml culture prepared for the construct BBa_K844004. (MaSP without ATG)

2nd August, Tuesday

11 vials of DH5 alpha competent cells were prepared. Plasmid extraction done for the construct BBa_K844004 (MaSP without ATG).

3rd August, Wednesday

As a part of the iGEM 2016 interlab study, transformations were done for the following:
Test device1
Test device2
Test device3
Positive control
Negative control
Also, transformed cells were prepared with the part BBa_K844008 (MaSP with ATG)

4th August, Thursday

Colonies were seen for all six of the transformed plates. The transformation procedure was hence successful.

7th August, Sunday

20ml Culture was prepared for the screening of BBa_K844008 (MaSP with ATG). Also, 20ml cultures were prepared for each of test device 1, test device 2, and test device 3 for the interlab study.

WEEK FOUR - ( 8th August - 12th August )

8th August, Monday

PPlasmid extraction performed for the screening of the parts BBa_K844008 (MaSP with ATG); and test device 1, test device 2, test device 3 for the interlab study.

9th August, Tuesday

Gel Electrophoresis with 1% agarose gel was done for BBa_K844008 (MaSP with ATG), test device 1, test device 2, test device 3 for screening. The run was not successful due to gel over flow.

10th August, Wednesday

20ml Culture was prepared for screening of BBa_K844008 (MaSP with ATG), test device 1, test device 2, test device 3.

11th August, Thursday

Plasmid extraction for the screening of BBa_K844008 (MaSP with ATG), test device 1, test device 2, test device 3 was done.

12th August, Friday

Gel electrophoresis with 1% agarose gel was done for BBa_K844008 (MaSP with ATG), test device 1, test device 2, test device 3.

WEEK FIVE - ( 15th August - 18th August )

16th August, Tuesday

Plasmid extraction of BBa_K844008 (MaSP with ATG), test device 1, test device 2, and test device 3 was done with mini-prep kit. Digestion of above obtained plasmids with E And P was carried out.

17th August, Wednesday

1% agarose gel was prepared for digested plasmids PCR of protease construct for HIV site primers was done PCR parameters:
{95 degree 2 minutes
[95 degree 30 seconds
60 degrees 30 sec
68 degree 2 min] X35 cycles
68 degree 10 min}
PCR products run in 1% agarose gel.
Amplification not upto expectation.
Repetition of the experiment, with different conditions suggested.
Note: Too many non specific products were observed that is why the same was repeated next week.

18th August, Thursday

PCR of protease construct for HIV site primers was done.
PCR products were run in 1% agarose gel.
PCR Parameters:
{95 degree 2 minutes
[95 degree 20 seconds
62 degrees 30 sec
68 degree 2 min 15 sec] X35 cycles
68 degree 10 min}
Amplification not upto expectation.
Repetition of the experiment, with different conditions suggested.

WEEK SIX - ( 22nd August - 26th August )

22th August, Monday

PCR for both fret and silk constructs at two conditions was done.

Condition 1
{95 degree 5 minutes
Taq DNA polymerase is added.
[95 degree 30 seconds
57.5 degrees 40 sec
68 degree 40 sec] X35 cycles
68 degree 10 min}
Condition 2
{95 degree 2 minutes
[95 degree 30 seconds
58 degrees 1 min
68 degree 2 min] X35 cycles
68 degree 10 min}

23rd August, Tuesday

PCR for FRET construct was done. PCR Parameters:
{95 degree 2 minutes
[95 degree 30 seconds
57 degrees 40 sec
68 degree 2 min] X35 cycles
68 degree 10 min}

24th August, Wednesday

Gel run for FRET construct was performed.

25th August, Thursday

PCR for silk construct was done with the following parameters:
{95 degree 2 minutes
[95 degree 30 seconds
57 degrees 40 sec
68 degree 2 min] X35 cycles
68 degree 10 min}

26th August, Friday

PCR for FRET construct was done.
PCR Parameters:
{95 degree 2 minutes
[95 degree 30 seconds
58 degrees 1 min
68 degree 2 min] X35 cycles
68 degree 10 min}

WEEK SEVEN - ( 29th August - 2nd September )

29th August, Monday

Nano drop analysis for pSB1K3( Kanamycin backbone) was done. Result:Obtained concentration was 192.6mg/ul.

31st August, Wednesday

Digestion for Kanamycin backbone and FRET PCR with E And P

K backboneFRET PCR
ComponentVolume(ul)Volume(ul)
DNA62.3
2.1 Buffer22
ECoRI11
Psti11
Nf H2O1013.7

1st September, Thursday

Ligation for Kanamycin backbone and FRET PCR with E and P was done Vector:Insert=1:3

2nd September, Friday

Transformation for Kanamycin backbone and FRET PCR with E and P failed.
Note: Reason was determined to be inadequate amount of the PCR product

WEEK EIGHT - ( 8th September - 10th September )

8th September, Thursday

2 ml culture of CFP and YFP was prepared.
PCR done for FRET construct and silk construct
Digestion with E and P of FRET PCR product was done.

FRET PCR
ComponentVolume(ul)
DNA19
2.1 Buffer2.5
ECoRI1
PstI1
NF H2O1.5

9th September, Friday

PCR purification of digested FRET PCR product was done. Plasmid isolation of YFP and CFP was performed.
YFP: 250 ng/ul
CFP: 218 ng/ul
Glycerol stock for CFP and YFP was prepared.
Restriction digestion(overnight) of YFP and cleavage site was done.

YFP
ComponentVolume(ul)
DNA5
ECoR buffer2
ECoRI1
NF H2O12
Cleavage Site
ComponentVolume(ul)
DNA10
3.1 Buffer2
ECoRI1
Xbal1
NF H2O6

10th September, Saturday

PCR purification of YFP digested with E was done. Digestion of purified YFP was done with S for 4 hrs at 37 degrees.

YFP
ComponentVolume(ul)
DNA20
Cutsmart Buffer2.5
Spel1
NF H2O1.5

WEEK NINE - ( 12th September - 13th September )

12th September, Monday

22 ml cultures of CFP, YFP, HIV site, MASP with ATG and MASP without ATG was prepared.

13th September, Tuesday

Glycerol stock and plasmid extraction of CFP, YFP, HIV site, MASP with ATG and MASP without ATG was performed.
CFP:437.5 ng/ul
YFP: 286.7 ng/ul
HIV Cleavage Site: 357.1 ng/ul
MaSP with ATG: 268.2 ng/ul
MaSP w/o ATG: 123ng/ul

WEEK TEN - ( 19th September - 24th September )

19th September, Monday

PCR for FRET (2 sets) Digestion with E and X for HIV site and E for CFP was successfully done.

CFP
ComponentVolume(ul)
DNA20
ECoR buffer2
ECoRI1
NF H2O14.7
Cleavage Site
ComponentVolume(ul)
DNA2.8
3.1 Buffer2
ECoRI1
Xbal1
NF H2O13.2

20th September, Tuesday

PCR purification of CFP digested with E was done. Digestion with S of purified product was done for 6 hours at 37 degrees.

CFP
ComponentVolume(ul)
DNA20
Cutsmart Buffer2.5
Spel1
NF H2O1.5

Gel extraction of digested CFP and HIV site was successfully performed. The gel pieces stored at 4 degrees

21st September, Wednesday

Gel extraction of stored gel pieces Amount of extracted DNA too low to proceed to ligation step

22nd September, Thursday

S digestion of CFP and X digestion of HIV

23rd September, Friday

PCR purification of above digested followed by E digestion of both for 6 hrs at 37 degrees Gel extraction after completion of digestion followed by ligation of E and X digested HIV site and E and S digested CFP at 16 degrees overnight

24th September, Saturday

Transformed DH5 alpha cells with ligation mix and plating on A+K plates

WEEK ELEVEN - ( 25th September - 2nd October )

25th September, Sunday

Colonies observed on incubated plates

26th September, Mondayy

18 colonies from the 1:3 plate were put into 1 ml media overnight for screening
14 colonies from the 1:5 plate were put into 1 ml media overnight for screening
Digestion of YFP with X and P
Digestion of HIV site with S and P

27th September, Tuesday

PCR for FRET (2 sets)
Gel extraction for PCR products and digestion with P
Digestion of K backbone with P
Screening for 18 colonies from the 1:3 plate and 14 colonies from the 1:5 plate
Colonies 1, 4, 7, 10 from 1:3 plate showed a shift
Colonies 1, 5, 11 from 1:5 plate showed a shift
Ligation of YFP digested with X and P with HIV site digested with S and P

28th September, Wednesday

PCR purification of P digested K backbone and FRET PCR followed by E digestion Gel Extraction of the digested products followed by ligation Colonies observed of ligated YFP and HIV site observed

29th September, Thursday

25 colonies from the ligated YFP and HIV site plate picked for screening X and P digestion for CFP+ HIV

30th September, Friday

Screening of YFP + HIV
Gel run X and P digested CFP + HIV
20 ml cultures for plasmid extraction of K-backbone, CFP+HIV and HIV Site, YFP+HIV (colony 7) and YFP+HIV (colony 13)

1st October, Saturday

Plasmid extractions for the above cultures
Digestion with X and P for YFP+HIV (colony 7) and CFP+HIV
Gel run for the digested YFP+HIV (colony 7) and CFP+HIV
Digestion with X of YFP+HIV
Digestion with S of CFP

2nd October, Sunday

PCR purification of the digested products
Digestion with E of S digested CFP and X digested YFP+HIV
Gel extraction of the digested product
Ligation of E and S digested CFP and E and X digested YFP+HIV

WEEK TWELVE - ( 3rd October - 9th October )

3rd October, Monday

Transformation of the Ligated product onto A+K plates.

4th October, Tuesday

Growth was observed on both the plates.
1 ml culture was given for 14 colonies of each of the plates, for the purpose of screening.

5th October, Wednesday

1% Agarose gel was run for the plasmids extracted from the overnight cultures.
Sufficient number show the desired shift.
20 ml culture was given for miniprep extraction of CFP+HIV+YFP form colony 10 and 15 of the 1:3 ligation plate

6th October, Thursday

PCR was run (2 sets)
The PCR product was run on 1% agarose gel for extraction.
Amount too low to continue.
Miniprep for CFP+HIV+YFP
Colony 10: 187.5 ng/ul
Colony 15: 185 ng/ul
Digestion with X and P for the isolated plasmid (overnight)

CFP+HIV+YFP
ComponentsVolume(µl)
DNA6
3.1 Buffer2
Xba11
Pstl1
NF H2O10

7th October, Friday

1% agarose gel was run for the digested product.
Bands appear as expected

8th October, Saturday

20 ml culture for plasmid extraction of CFP+HIV+YFP (Colony 10)

9th October, Sunday

Mini prep extraction of CFP+HIV+YFP
CFP+HIV+YFP: 94 ng/µl
PCR was done (2 sets) for FRET
No amplification was seen

WEEK THIRTEEN - ( 11th October - 16th October )

11th October, Tuesday

PCR was done (2 sets) for FRET
No amplification was seen

13th October, Thursday

Digestions with X and P of CFP in pSB1C3 backbone and CFP+HIV, YFP+HIV and CFP+HIV+YFP all in pSB1AK8 backbone.

Volume (µl)
CFP+HIV+YFPCFP+HIVHIV+YFPCFP
ComponentVolume (µl)Volume (µl)Volume (µl)Volume (µl)
DNA6463
3.1 Buffer2222
Xba11111
Pstl1111
NF H2O10121013

14th October, Friday

1% Agarose gel for extraction of all above.
Significant amount observed only in the digested CFP, whereas all the rest proved unsuccessful.
20 ml cultures given for extraction of CFP+HIV, YFP+HIV and CFP+HIV+YFP.

15th October, Saturday

Mini prep done for CFP+HIV, YFP+HIV and CFP+HIV+YFP.
CFP+HIV: 84 ng/ul
HIV+YFP: 92 ng/ul
CFP+HIV+YFP: 87 ng/ul
X and P digestions set up for all three isolated plasmids

CFP+HIV+YFPCFP+HIVHIV+YFP
ComponentsVolume (µl)Volume (µl)Volume (µl)
DNA 13 13 13
3.1 Buffer 2 2 2
Xbal 1 1 1
Pstl 1 1 1
NF H2O 3 3 3

16th October, Sunday

1% agarose gel run for gel extraction of digested products.
Digestion with X and P of CFP and C+H+Y

WEEK FOURTEEN - ( 17th October - 23rd October )

17th October, Monday

% Agarose gel run for Gel Extraction of digested product.
Ligation with ratio 1:3 done using the backbone from CFP and Insert from CFP+HIV+YFP
30 ml culture given for plasmid extraction of CFP+HIV+YFP.

18th October, Tuesday

Mini Prep for CFP+HIV+YFP
CFP+HIV+YFP: 275 ng/ul
X and P digestion of the CFP and CFP+HIV+YFP
1% Agarose Gel for Gel Extraction of the above digested products
Quick Ligation was set up for the the digested CFP backbone and CFP+HIV+YFP
1:3 ratio was used
Transformation was done on Cam plates
Overnight Ligation set up for CFP and CFP+HIV+YFP in the ratio 1:3
Transformation done for the previously set overnight ligation

19th October, Wednesday

%No colonies observed on the quick ligated plate
Colonies observed on plate whose ligation was done on 17th october
1 ml Cultures for 16 colonies of the plate given overnight
Transformation done for the ligated products from 18th October.