Difference between revisions of "Team:Ecuador/Model"

 
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Line 1: Line 1:
 
{{Ecuador}}
 
{{Ecuador}}
 
<html>
 
<html>
 +
 
<head>
 
<head>
 
<meta charset="utf-8">
 
<meta charset="utf-8">
−
<title>C-lastin, Modeling</title>
+
<title>C-lastin, Interlab</title>
 
<style>
 
<style>
−
@charset "utf-8";
 
−
/* CSS Document */
 
−
@import url('https://fonts.googleapis.com/css?family=Raleway');
 
−
    *{
 
−
        margin: 0px;
 
−
        font-family: 'Raleway', sans-serif;
 
−
}
 
−
   
 
 
@charset "utf-8";
 
@charset "utf-8";
 
/* CSS Document */
 
/* CSS Document */
 
.ec--modeling--container{
 
.ec--modeling--container{
 
padding-top: 100px;
 
padding-top: 100px;
−
padding-right: 300px;
+
padding-right: 14%;
 
padding-bottom: 100px;
 
padding-bottom: 100px;
−
padding-left: 300px;
+
padding-left: 38%;
 
}
 
}
 
.ec--main--title{
 
.ec--main--title{
Line 36: Line 29:
 
}
 
}
 
.ec--modeling--items{
 
.ec--modeling--items{
 +
width: 270px;
 
display: block;
 
display: block;
 
position: fixed;
 
position: fixed;
−
float: right;
+
float: left;
−
right: 64px;
+
top: 250px; /*position: -webkit-sticky;
−
top: 200px;
+
position: sticky;
 +
padding-bottom: 0px;
 +
margin-top: 11.4em;*/
 +
left: 14%;
 +
line-height: 1.3;
 +
text-indent: inherit;
 +
}
 +
ul.circle {
 +
    list-style-type: circle;
 
}
 
}
 
.ec--biob--cont{
 
.ec--biob--cont{
Line 85: Line 87:
 
}
 
}
 
#leftBox {
 
#leftBox {
−
  float:left;
+
float: left;
−
  height:300px;
+
height: 300px;
−
  width: 390px;
+
width: 390px;
−
  margin:0;
+
margin: 0;
 
}
 
}
 
#rightBox {
 
#rightBox {
Line 101: Line 103:
 
padding-left: 25px;
 
padding-left: 25px;
 
}
 
}
−
 
+
.ec--h2{
−
</style>
+
font-size: 25px;
−
<style>
+
font-weight: bolder;
−
/*! normalize.css v3.0.1 | MIT License | git.io/normalize */
+
display: block;
−
 
+
margin-top: 15px;
−
/**
+
margin-bottom: 15px;
−
* 1. Set default font family to sans-serif.
+
clear: both;
−
* 2. Prevent iOS text size adjust after orientation change, without disabling
+
padding-top: 20px;
−
*    user zoom.
+
padding-bottom: 20px;
−
*/
+
color: black;
−
 
+
line-height: 40px;
−
html {
+
−
  font-family: sans-serif; /* 1 */
+
−
  -ms-text-size-adjust: 100%; /* 2 */
+
−
  -webkit-text-size-adjust: 100%; /* 2 */
+
 
}
 
}
−
 
+
.ec--p{
−
/**
+
display: block;
−
* Remove default margin.
+
line-height: 2;
−
*/
+
text-align: justify;
−
 
+
font-size: 16px;
−
body {
+
−
  margin: 0;
+
 
}
 
}
−
 
+
.ec--coll--video{
−
/* HTML5 display definitions
+
display: block;
−
  ========================================================================== */
+
clear: both;
−
 
+
text-align: center;
−
/**
+
padding-top: 30px;
−
* Correct `block` display not defined for any HTML5 element in IE 8/9.
+
padding-bottom: 30px;
−
* Correct `block` display not defined for `details` or `summary` in IE 10/11 and Firefox.
+
−
* Correct `block` display not defined for `main` in IE 11.
+
−
*/
+
−
 
+
−
article,
+
−
aside,
+
−
details,
+
−
figcaption,
+
−
figure,
+
−
footer,
+
−
header,
+
−
hgroup,
+
−
main,
+
−
nav,
+
−
section,
+
−
summary {
+
−
  display: block;
+
 
}
 
}
−
 
+
.ec--coll--letter{
−
/**
+
text-align: justify;
−
* 1. Correct `inline-block` display not defined in IE 8/9.
+
display: block;
−
* 2. Normalize vertical alignment of `progress` in Chrome, Firefox, and Opera.
+
margin-left: 20px;
−
*/
+
margin-right: 20px;
−
 
+
margin-top: 20px;
−
audio,
+
margin-bottom: 20px;
−
canvas,
+
width: 900px;
−
progress,
+
−
video {
+
−
  display: inline-block; /* 1 */
+
−
  vertical-align: baseline; /* 2 */
+
 
}
 
}
−
 
+
.ec--img--surv{
−
/**
+
top: 0;
−
* Prevent modern browsers from displaying `audio` without controls.
+
bottom: 0;
−
* Remove excess height in iOS 5 devices.
+
left: 0;
−
*/
+
right: 0;
−
 
+
margin: auto;
−
audio:not([controls]) {
+
padding-top: 20px;
−
  display: none;
+
padding-bottom: 20px;
−
  height: 0;
+
 
}
 
}
 +
.anchorOffset{
  
−
/**
+
display: block !important;
−
* Address `[hidden]` styling not present in IE 8/9/10.
+
position: relative !important;
−
* Hide the `template` element in IE 8/9/11, Safari, and Firefox < 22.
+
top: -135px !important;
−
*/
+
visibility: hidden !important;
  
−
[hidden],
 
−
template {
 
−
  display: none;
 
 
}
 
}
−
 
+
a.lateral{
−
/* Links
+
  color: black;
−
  ========================================================================== */
+
  text-decoration: inherit;
−
 
+
  opacity: 1;
−
/**
+
  color: gray;
−
* Remove the gray background color from active links in IE 10.
+
  font-weight: 500;
−
*/
+
   font-size: 16px;
−
 
+
−
a {
+
−
   background: transparent;
+
 
}
 
}
−
 
+
a.inner-link--active {
−
/**
+
   opacity: 1;
−
* Improve readability when focused and also mouse hovered in all browsers.
+
   animation: bulge .5s ease;
−
*/
+
   -webkit-animation: bulge .5s ease;
−
 
+
−
a:active,
+
−
a:hover {
+
−
  outline: 0;
+
−
}
+
−
 
+
−
/* Text-level semantics
+
−
  ========================================================================== */
+
−
 
+
−
/**
+
−
* Address styling not present in IE 8/9/10/11, Safari, and Chrome.
+
−
*/
+
−
 
+
−
abbr[title] {
+
−
  border-bottom: 1px dotted;
+
−
}
+
−
 
+
−
/**
+
−
* Address style set to `bolder` in Firefox 4+, Safari, and Chrome.
+
−
*/
+
−
 
+
−
b,
+
−
strong {
+
−
  font-weight: bold;
+
−
}
+
−
 
+
−
/**
+
−
* Address styling not present in Safari and Chrome.
+
−
*/
+
−
 
+
−
dfn {
+
−
  font-style: italic;
+
−
}
+
−
 
+
−
/**
+
−
* Address variable `h1` font-size and margin within `section` and `article`
+
−
* contexts in Firefox 4+, Safari, and Chrome.
+
−
*/
+
−
 
+
−
h1 {
+
−
  font-size: 2em;
+
−
  margin: 0.67em 0;
+
−
}
+
−
 
+
−
/**
+
−
* Address styling not present in IE 8/9.
+
−
*/
+
−
 
+
−
mark {
+
−
  background: #ff0;
+
−
  color: #000;
+
−
}
+
−
 
+
−
/**
+
−
* Address inconsistent and variable font size in all browsers.
+
−
*/
+
−
 
+
−
small {
+
−
  font-size: 80%;
+
−
}
+
−
 
+
−
/**
+
−
* Prevent `sub` and `sup` affecting `line-height` in all browsers.
+
−
*/
+
−
 
+
−
sub,
+
−
sup {
+
−
  font-size: 75%;
+
−
  line-height: 0;
+
−
  position: relative;
+
−
  vertical-align: baseline;
+
−
}
+
−
 
+
−
sup {
+
−
  top: -0.5em;
+
−
}
+
−
 
+
−
sub {
+
−
  bottom: -0.25em;
+
−
}
+
−
 
+
−
/* Embedded content
+
−
  ========================================================================== */
+
−
 
+
−
/**
+
−
* Remove border when inside `a` element in IE 8/9/10.
+
−
*/
+
−
 
+
−
img {
+
−
  border: 0;
+
−
}
+
−
 
+
−
/**
+
−
* Correct overflow not hidden in IE 9/10/11.
+
−
*/
+
−
 
+
−
svg:not(:root) {
+
−
  overflow: hidden;
+
−
}
+
−
 
+
−
/* Grouping content
+
−
  ========================================================================== */
+
−
 
+
−
/**
+
−
* Address margin not present in IE 8/9 and Safari.
+
−
*/
+
−
 
+
−
figure {
+
−
  margin: 1em 40px;
+
−
}
+
−
 
+
−
/**
+
−
* Address differences between Firefox and other browsers.
+
−
*/
+
−
 
+
−
hr {
+
−
  -moz-box-sizing: content-box;
+
−
  box-sizing: content-box;
+
−
  height: 0;
+
−
}
+
−
 
+
−
/**
+
−
* Contain overflow in all browsers.
+
−
*/
+
−
 
+
−
pre {
+
−
  overflow: auto;
+
−
}
+
−
 
+
−
/**
+
−
* Address odd `em`-unit font size rendering in all browsers.
+
−
*/
+
−
 
+
−
code,
+
−
kbd,
+
−
pre,
+
−
samp {
+
−
  font-family: monospace, monospace;
+
−
  font-size: 1em;
+
−
}
+
−
 
+
−
/* Forms
+
−
  ========================================================================== */
+
−
 
+
−
/**
+
−
* Known limitation: by default, Chrome and Safari on OS X allow very limited
+
−
* styling of `select`, unless a `border` property is set.
+
−
*/
+
−
 
+
−
/**
+
−
* 1. Correct color not being inherited.
+
−
*    Known issue: affects color of disabled elements.
+
−
* 2. Correct font properties not being inherited.
+
−
* 3. Address margins set differently in Firefox 4+, Safari, and Chrome.
+
−
*/
+
−
 
+
−
button,
+
−
input,
+
−
optgroup,
+
−
select,
+
−
textarea {
+
−
  color: inherit; /* 1 */
+
−
  font: inherit; /* 2 */
+
−
  margin: 0; /* 3 */
+
−
}
+
−
 
+
−
/**
+
−
* Address `overflow` set to `hidden` in IE 8/9/10/11.
+
−
*/
+
−
 
+
−
button {
+
−
  overflow: visible;
+
−
}
+
−
 
+
−
/**
+
−
* Address inconsistent `text-transform` inheritance for `button` and `select`.
+
−
* All other form control elements do not inherit `text-transform` values.
+
−
* Correct `button` style inheritance in Firefox, IE 8/9/10/11, and Opera.
+
−
* Correct `select` style inheritance in Firefox.
+
−
*/
+
−
 
+
−
button,
+
−
select {
+
−
  text-transform: none;
+
−
}
+
−
 
+
−
/**
+
−
* 1. Avoid the WebKit bug in Android 4.0.* where (2) destroys native `audio`
+
−
*    and `video` controls.
+
−
* 2. Correct inability to style clickable `input` types in iOS.
+
−
* 3. Improve usability and consistency of cursor style between image-type
+
−
*    `input` and others.
+
−
*/
+
−
 
+
−
button,
+
−
html input[type="button"], /* 1 */
+
−
input[type="reset"],
+
−
input[type="submit"] {
+
−
  -webkit-appearance: button; /* 2 */
+
−
  cursor: pointer; /* 3 */
+
−
}
+
−
 
+
−
/**
+
−
* Re-set default cursor for disabled elements.
+
−
*/
+
−
 
+
−
button[disabled],
+
−
html input[disabled] {
+
−
  cursor: default;
+
−
}
+
−
 
+
−
/**
+
−
* Remove inner padding and border in Firefox 4+.
+
−
*/
+
−
 
+
−
button::-moz-focus-inner,
+
−
input::-moz-focus-inner {
+
−
   border: 0;
+
−
  padding: 0;
+
−
}
+
−
 
+
−
/**
+
−
* Address Firefox 4+ setting `line-height` on `input` using `!important` in
+
−
* the UA stylesheet.
+
−
*/
+
−
 
+
−
input {
+
−
  line-height: normal;
+
−
}
+
−
 
+
−
/**
+
−
* It's recommended that you don't attempt to style these elements.
+
−
* Firefox's implementation doesn't respect box-sizing, padding, or width.
+
−
*
+
−
* 1. Address box sizing set to `content-box` in IE 8/9/10.
+
−
* 2. Remove excess padding in IE 8/9/10.
+
−
*/
+
−
 
+
−
input[type="checkbox"],
+
−
input[type="radio"] {
+
−
  box-sizing: border-box; /* 1 */
+
−
   padding: 0; /* 2 */
+
−
}
+
−
 
+
−
/**
+
−
* Fix the cursor style for Chrome's increment/decrement buttons. For certain
+
−
* `font-size` values of the `input`, it causes the cursor style of the
+
−
* decrement button to change from `default` to `text`.
+
−
*/
+
−
 
+
−
input[type="number"]::-webkit-inner-spin-button,
+
−
input[type="number"]::-webkit-outer-spin-button {
+
−
  height: auto;
+
−
}
+
−
 
+
−
/**
+
−
* 1. Address `appearance` set to `searchfield` in Safari and Chrome.
+
−
* 2. Address `box-sizing` set to `border-box` in Safari and Chrome
+
−
*    (include `-moz` to future-proof).
+
−
*/
+
−
 
+
−
input[type="search"] {
+
−
   -webkit-appearance: textfield; /* 1 */
+
−
  -moz-box-sizing: content-box;
+
−
  -webkit-box-sizing: content-box; /* 2 */
+
−
  box-sizing: content-box;
+
−
}
+
−
 
+
−
/**
+
−
* Remove inner padding and search cancel button in Safari and Chrome on OS X.
+
−
* Safari (but not Chrome) clips the cancel button when the search input has
+
−
* padding (and `textfield` appearance).
+
−
*/
+
−
 
+
−
input[type="search"]::-webkit-search-cancel-button,
+
−
input[type="search"]::-webkit-search-decoration {
+
−
  -webkit-appearance: none;
+
−
}
+
−
 
+
−
/**
+
−
* Define consistent border, margin, and padding.
+
−
*/
+
−
 
+
−
fieldset {
+
−
  border: 1px solid #c0c0c0;
+
−
  margin: 0 2px;
+
−
  padding: 0.35em 0.625em 0.75em;
+
−
}
+
−
 
+
−
/**
+
−
* 1. Correct `color` not being inherited in IE 8/9/10/11.
+
−
* 2. Remove padding so people aren't caught out if they zero out fieldsets.
+
−
*/
+
−
 
+
−
legend {
+
−
  border: 0; /* 1 */
+
−
  padding: 0; /* 2 */
+
−
}
+
−
 
+
−
/**
+
−
* Remove default vertical scrollbar in IE 8/9/10/11.
+
−
*/
+
−
 
+
−
textarea {
+
−
  overflow: auto;
+
−
}
+
−
 
+
−
/**
+
−
* Don't inherit the `font-weight` (applied by a rule above).
+
−
* NOTE: the default cannot safely be changed in Chrome and Safari on OS X.
+
−
*/
+
−
 
+
−
optgroup {
+
−
  font-weight: bold;
+
−
}
+
−
 
+
−
/* Tables
+
−
  ========================================================================== */
+
−
 
+
−
/**
+
−
* Remove most spacing between table cells.
+
−
*/
+
−
 
+
−
table {
+
−
  border-collapse: collapse;
+
−
  border-spacing: 0;
+
−
}
+
−
 
+
−
td,
+
−
th {
+
−
  padding: 0;
+
−
}
+
−
 
+
−
</style>
+
−
<style>
+
−
/*
+
−
* Ideal Image Slider v1.5.1
+
−
*
+
−
* By Gilbert Pellegrom
+
−
* http://gilbert.pellegrom.me
+
−
*
+
−
* Copyright (C) 2014 Dev7studios
+
−
* https://raw.githubusercontent.com/gilbitron/Ideal-Image-Slider/master/LICENSE
+
−
*/
+
−
 
+
−
.ideal-image-slider {
+
−
position: relative;
+
−
overflow: hidden;
+
 
}
 
}
−
.iis-slide {
+
.ec--h3{
 +
font-size: 22px;
 +
font-weight: bolder;
 
display: block;
 
display: block;
−
bottom: 0;
+
margin-top: 15px;
−
text-decoration: none;
+
margin-bottom: 15px;
−
position: absolute;
+
clear: both;
−
top: 0;
+
padding-top: 20px;
−
left: 0;
+
−
width: 100%;
+
−
height: 100%;
+
−
background-repeat: no-repeat;
+
−
background-position: 50% 50%;
+
−
background-size: cover;
+
−
text-indent: -9999px;
+
 
}
 
}
  
−
/* Slide effect */
 
−
.iis-effect-slide .iis-slide {
 
−
opacity: 0;
 
−
-webkit-transition-property: -webkit-transform;
 
−
  -moz-transition-property: -moz-transform;
 
−
-o-transition-property: -o-transform;
 
−
transition-property: transform;
 
−
-webkit-transition-timing-function: ease-out;
 
−
  -moz-transition-timing-function: ease-out;
 
−
-o-transition-timing-function: ease-out;
 
−
transition-timing-function: ease-out;
 
−
-webkit-transform: translateX(0%);
 
−
-ms-transform: translateX(0%);
 
−
transform: translateX(0%);
 
−
}
 
−
.iis-effect-slide .iis-current-slide {
 
−
opacity: 1;
 
−
z-index: 1;
 
−
}
 
−
.iis-effect-slide .iis-previous-slide {
 
−
-webkit-transform: translateX(-100%);
 
−
-ms-transform: translateX(-100%);
 
−
transform: translateX(-100%);
 
−
}
 
−
.iis-effect-slide .iis-next-slide {
 
−
-webkit-transform: translateX(100%);
 
−
-ms-transform: translateX(100%);
 
−
transform: translateX(100%);
 
−
}
 
−
.iis-effect-slide.iis-direction-next .iis-previous-slide,
 
−
.iis-effect-slide.iis-direction-previous .iis-next-slide { opacity: 1; }
 
  
−
/* Touch styles */
+
</style>
−
.iis-touch-enabled .iis-slide { z-index: 1; }
+
−
.iis-touch-enabled .iis-current-slide { z-index: 2; }
+
−
.iis-touch-enabled.iis-is-touching .iis-previous-slide,
+
−
.iis-touch-enabled.iis-is-touching .iis-next-slide { opacity: 1; }
+
−
 
+
−
/* Fade effect */
+
−
.iis-effect-fade .iis-slide {
+
−
-webkit-transition-property: opacity;
+
−
  -moz-transition-property: opacity;
+
−
-o-transition-property: opacity;
+
−
transition-property: opacity;
+
−
-webkit-transition-timing-function: ease-in;
+
−
  -moz-transition-timing-function: ease-in;
+
−
-o-transition-timing-function: ease-in;
+
−
transition-timing-function: ease-in;
+
−
opacity: 0;
+
−
}
+
−
.iis-effect-fade .iis-current-slide {
+
−
opacity: 1;
+
−
z-index: 1;
+
−
}
+
−
/* Captions */
+
−
.iis-has-captions .iis-slide { text-indent: 0; }
+
−
.iis-caption {
+
−
position: absolute;
+
−
left: 5%;
+
−
bottom: 5%;
+
−
max-width: 90%;
+
−
z-index: 10;
+
−
background: #000;
+
−
background: rgba(0,0,0,0.5);
+
−
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</head>
 
</head>
  
 
<body>
 
<body>
−
+
<div class="ec--modeling--container">
−
<div class="ec--modeling--container">
+
 
<div class="ec--first--section">
 
<div class="ec--first--section">
 
<div class="ec--main--title">
 
<div class="ec--main--title">
−
<a name="MOD"  style="text-decoration: none;"><h1>Collaborations</h1></a>
+
<a name="MOD"  style="text-decoration: none;"><a name="INT" style="text-decoration:none;"></a>
 +
<h1>
 +
MATHEMATICAL MODELING
 +
</h1>
 +
</a>
 
</div>
 
</div>
 
<div class="ec--modeling--items">
 
<div class="ec--modeling--items">
−
<ul>
+
<h3><a href="#INT" style="color:black; text-decoration: none">Index</a></h3>
−
<li><a href="#MOD">Modeling</a></li>
+
<ul class="circle">
−
<li><a href="#WWD">WHAT DID WE DO?</a></li>
+
<li><a href="#LOV" style="color:black; text-decoration: none">List of variables and  constants</a></li>
−
<li><a href="#HWD">HOW DID WE DO IT?</a></li>
+
                <li>I<a href="#IND3" style="color:black; text-decoration: none">PTG-inducible model</a></li>
−
<li><a href="#RES">RESULTS</a></li>
+
                <ul>
−
<li><a href="#EXP">EXPERIENCE</a></li>
+
                  <li><a href="#IND4" style="color:black; text-decoration: none">Entry of IPTG into the  cell</a></li>
−
<li><a href="#ACK">ACKNOWLEDGEMENT</a></li>
+
                  <li><a href="#IND5" style="color:black; text-decoration: none">CBD cipA-BMP2  expression</a></li>
 +
                  <li><a href="#IND6" style="color:black; text-decoration: none">Kinetic constants</a></li>
 +
                </ul>
 +
                <li><a href="#IND7" style="color:black; text-decoration: none">Results of the  IPTG-inducible model</a></li>
 +
                <ul>
 +
                  <li><a href="#IND8" style="color:black; text-decoration: none">Calculation of entry of  IPTG into the cell</a></li>
 +
                  <li>I<a href="#IND9" style="color:black; text-decoration: none">PTG-LacI repressor  interaction</a></li>
 +
                  <li><a href="#IND10" style="color:black; text-decoration: none">Calculation and  validation of CBD cipA-BMP2 expression</a></li>
 +
                </ul>
 +
                <li><a href="#IND11" style="color:black; text-decoration: none">Conclusions</a></li>
 
</ul>
 
</ul>
 
</div>
 
</div>
−
<div class="ec--img--home--slider">Reference image</div>
+
 
</div>
 
</div>
 
 
 
<div class="ec--nau--content">
 
<div class="ec--nau--content">
 
<div class="ec--sect--title">
 
<div class="ec--sect--title">
−
<h2><a name="I1" style="text-decoration: none;">1. 08 ABRIL 2018 MEXICO </a></h2>
 
−
                <p><a href="https://2018.igem.org/Team:TecCEM">https://2018.igem.org/Team:TecCEM</a></p>
 
−
                <p><br>
 
−
                </p>
 
−
              <p>Fue un honor haber tenido el primer  acercamiento con el equipo de Biología Sintética de México&nbsp;<a href="https://www.facebook.com/IgemTecMty/?__tn__=K-R&eid=ARAfb2E_6sxoGf4U-PxAIacXPEw8zbW5uHmz2rp4JDTxuw9QoSRDH1kJjKATRrqqhDqwW7prNtPdjth9&fref=mentions&__xts__%5B0%5D=68.ARCSxE4dTZUUKRVcQ5ejA987KvONVqpZm8oWOiQGmbtgfTM_-4M75OGo27BaI_kW1U_rIVi-dbkrqwEillzVDfO_u3nF_M8xmTZ_H_uilE7na8XTf_VdmNlvw5y7xRs3r2jofNMWsMHW1Fwk59pLx6RLQ_MVMLtf3MQGI8kOAZ-rwYYhJmQG">IGEM  Tec-Monterrey</a>&nbsp;con quienes iniciamos colaboraciones conjuntas con miras a la  competencia mundial (octubre-2018)<br>
 
−
              <p>Fue un honor haber tenido el primer  acercamiento con el equipo de Biología Sintética de México&nbsp;<a href="https://www.facebook.com/IgemTecMty/?__tn__=K-R&eid=ARAfb2E_6sxoGf4U-PxAIacXPEw8zbW5uHmz2rp4JDTxuw9QoSRDH1kJjKATRrqqhDqwW7prNtPdjth9&fref=mentions&__xts__%5B0%5D=68.ARCSxE4dTZUUKRVcQ5ejA987KvONVqpZm8oWOiQGmbtgfTM_-4M75OGo27BaI_kW1U_rIVi-dbkrqwEillzVDfO_u3nF_M8xmTZ_H_uilE7na8XTf_VdmNlvw5y7xRs3r2jofNMWsMHW1Fwk59pLx6RLQ_MVMLtf3MQGI8kOAZ-rwYYhJmQG">IGEM  Tec-Monterrey</a>&nbsp;con quienes iniciamos colaboraciones conjuntas con miras a la  competencia mundial (octubre-2018)<br>
 
−
                  El día de hoy tuvimos la oportunidad de  contactarnos con el equipo de&nbsp;<a href="https://www.facebook.com/BiosinEcuador/?__tn__=KH-R&eid=ARCfK2K3TZZH0ntl7nY_OhXTjadAxz6JDiAACcqOrm56w4y-GI1rUmAyQsNu7B02y2TXMrC-5yr8ghsF&fref=mentions&__xts__%5B0%5D=68.ARCSxE4dTZUUKRVcQ5ejA987KvONVqpZm8oWOiQGmbtgfTM_-4M75OGo27BaI_kW1U_rIVi-dbkrqwEillzVDfO_u3nF_M8xmTZ_H_uilE7na8XTf_VdmNlvw5y7xRs3r2jofNMWsMHW1Fwk59pLx6RLQ_MVMLtf3MQGI8kOAZ-rwYYhJmQG">IGEM  Ecuador - Biología Sintética</a>&nbsp;cuya participación es la primera en esta  competencia. Estamos muy entusiasmados en colaborar con ellos!!! #                                                                      &#127474;&#127485;    &#127466;&#127464; </p>
 
−
<div id="slider_Mexico">
 
−
<img src="res--2/collaborations/teccem1.jpg" data-src-2x="res--2/collaborations/teccem1.jpg" title="Estonia" alt="Reunion" />
 
−
<img data-src="res--2/collaborations/teccem2.jpg" data-src-2x="res--2/collaborations/teccem2.jpg" src="" title="Estonia" alt="From Ecuador" />
 
−
<img data-src="res--2/collaborations/teccem1.jpg" data-src-2x="res--2/collaborations/teccem1.jpg" src="" alt="Estonia" data-caption="Reunion" />
 
−
<img data-src="res--2/collaborations/teccem2.jpg" data-src-2x="res--2/collaborations/teccem2.jpg" src="" title="Estonia" alt="From Ecuador" />
 
−
</div>
 
 
 
−
  <a name="I2"><h2>2. 13 DE JULIO 2018 MEET UP LATINOAMERICA</h2></a>
+
<div class="ec--h2">
−
                <p><a href="https://2018.igem.org/Teams/Meetups#Latin_American_Meetup">https://2018.igem.org/Teams/Meetups#Latin_American_Meetup</a></p>
+
INTRODUCTION
−
              <p>Tecnológico de Monterrey,&nbsp; <br>
+
</div>
−
                  <strong>Description:</strong>&nbsp;​The participant  teams will present their projects in order to receive feedback from other teams  and experts on the subject. We are contacting different PhD ́s. who are  interested in participating and collaborating with the teams and can contribute  to the improvement of the projects. We are expecting the participation of the  teams from Tec Monterrey, Tec Guadalajara, Tec Chihuahua, Ecuador, Chile,  Brazil and Peru. In the case that any of the teams can not attend, then we will  designate a space for connecting with them via online.</p>
+
−
<div id="slider_Latin">
+
                <div class="ec--p">
−
<img src="res--2/collaborations/meet1.png" data-src-2x="res--2/collaborations/meet1.png" title="Estonia" alt="Reunion" />
+
                 
−
<img data-src="res--2/collaborations/meet2.png" data-src-2x="res--2/collaborations/meet2.png" src="" title="Estonia" alt="From Ecuador" />
+
                    This  is an IPTG-inducible model for the expression of the fusion protein CBD  cipA-BMP2 under the control of Plac promoter and cloned in psb1c3. The vector  does not contain the ORF of LacI and thus the LacI repressor protein concentration  is that in <em>E</em>. <em>coli</em> strains (10nM per cell).1<br>
−
<img data-src="res--2/collaborations/meet1.png" data-src-2x="res--2/collaborations/meet1.png" src="" alt="Estonia" data-caption="Reunion" />
+
                    <a name="LOV" style="text-decoration:none;"></a>The  model consists of systems of differential equations that were solved in Python  using Spyder 3.6 (Anaconda).
−
<img data-src="res--2/collaborations/meet2.png" data-src-2x="res--2/collaborations/meet2.png" src="" title="Estonia" alt="From Ecuador" />
+
</div>
−
</div>
+
−
                <a name="I3" style="text-decoration: none;">
+
<a name="LOV2" style="text-decoration:none;">
−
                <h2>3. 19 DE JULIO 2018 ESTONIA</h2></a>
+
<div class="ec--h2">
−
  <p> <a href="https://2018.igem.org/Team:Tartu_TUIT">https://2018.igem.org/Team:Tartu_TUIT</a> <br>
+
LIST OF VARIABLES AND CONSTANTS
−
Last week we had a conversation with IGEMers from&nbsp;<a href="https://www.facebook.com/iGEMEST/?__tn__=K-R&eid=ARDbjwtfdmVrhzasSaAN8PoUazw6HxWMGR7DFcDwC2hDpgjfIjHf_R0YIMxH0lrqLd0NZtRaOjY4IQvr&fref=mentions&__xts__%5B0%5D=68.ARAt7NWvD6E8WSiOiloQaCsq0JYd3t67eE7UuyCw5dOYNjNYbKha-iY2J3pryWplofx3LefxMVNb6rkGgWQQ2ETTHKp5F2tB8g06FFaFo5HuTlFdAV8RND74wKOhsD2q_l2d3dWNiREcaM-NBYVWqvf02wPwTo_oUP21WYOWHbsiF1l9zi1x">Estonia iGEM</a>&nbsp;for knowing more  about our projects and getting advice. We are also looking for a mutual  collaboration.&nbsp;<br>
+
</div>
−
La semana pasada tuvimos una charla con IGEMers  del equipo de Estonia para conocer más sobre nuestros proyectos y aconsejarnos.  Asimismo, tenemos en mira una colaboración mutua.</p>
+
</a>
−
             
+
                  <table border="1" cellspacing="0" cellpadding="0" width="571">
−
<div id="slider_Estonia">
+
                    <tr>
−
<img src="res--2/Estonia.png" data-src-2x="res--2/Estonia.png" title="Estonia" alt="Reunion" />
+
                      <td width="142" nowrap valign="top"><div class="ec--p"><strong>Variable/Constant</strong></div></td>
−
<img data-src="res--2/estonia2.jpg" data-src-2x="res--2/estonia2.jpg" src="" title="Estonia" alt="From Ecuador" />
+
                      <td width="328" nowrap valign="top"><div class="ec--p"><strong>Definition</strong></div></td>
−
<img data-src="res--2/Estonia.png" data-src-2x="res--2/Estonia.png" src="" alt="Estonia" data-caption="Reunion" />
+
                      <td width="101" nowrap valign="top"><div class="ec--p"><strong>Unit/Value</strong></div></td>
−
<img data-src="res--2/estonia2.jpg" data-src-2x="res--2/estonia2.jpg" src=""title="Estonia" alt="From Ecuador" />
+
                    </tr>
−
</div>
+
                    <tr>
−
<a name="I4"><h2>4. 05 DE AGOSTO 2018 ESPAÑA</h2></a>
+
                      <td width="142" nowrap valign="top"><div class="ec--p">[IPTG] TOTAL</div></td>
−
          <p><a href="https://2018.igem.org/Team:Valencia_UPV">https://2018.igem.org/Team:Valencia_UPV</a></p>
+
                      <td width="328" nowrap valign="top"><div class="ec--p">Total IPTG    concentration in the medium</div></td>
−
              <p>Estamos  agradecidos con los iGEMers del equipo&nbsp;<a href="https://www.facebook.com/ValenciaUPViGEM/?__tn__=K-R&eid=ARD0cA9PuJETMIGKcNHtvkGKNKv-magkA2RuN1dCoZfG6opb0P9Z239Qby6DRjvQPBt1khYvel5EzVsZ&fref=mentions&__xts__%5B0%5D=68.ARB3rgHpEQxKSrOWMNmRBGY9wKZHLlLzfPoHoJKaVJAoECZuWQ22R3eG2tTaH8986gxy-e4Eevs-Le0PTYPGGyziolonhKZUukto62UfgW36Qx87z609dNDNHpiPHcigjXsS-mG7kO0kjcfQHLROm08g0ux7uR_43M6UBoRE9VqPITsfPkVQ">UPV  IGEM</a>&nbsp;por  la colaboración que han hecho con nosotros al enviarnos cepas de E. coli para  clonación que serán ensayadas nuestro proyecto. Conozcan su interesante  proyecto llamado PRINTERÍA&nbsp;<a href="http://www.upv.es/noticias-upv/noticia-10319-printeria-es.html" target="_blank">http://www.upv.es/noticias-…/noticia-10319-printeria-es.html</a>&nbsp;<br>
+
                      <td width="101" nowrap valign="top"><div class="ec--p">nM</div></td>
−
                We are grateful with the iGEMers from UPV IGEM  team for the collaboration by sending us E. coli cloning strains which will be  used in our project. Check out their project named PRINTERIA&nbsp;<a href="http://www.upv.es/noticias-upv/noticia-10319-printeria-es.html" target="_blank">http://www.upv.es/noticias-…/noticia-10319-printeria-es.html</a></p>
+
                    </tr>
−
<div id="slider_Valencia">
+
                    <tr>
−
<img src="res--2/collaborations/Valencia1.jpg" data-src-2x="res--2/collaborations/Valencia1.jpg" title="Estonia" alt="Reunion" />
+
                      <td width="142" nowrap valign="top"><div class="ec--p">[IPTG]ext</div></td>
−
<img data-src="res--2/collaborations/Valencia2.jpg" data-src-2x="res--2/collaborations/Valencia2.jpg" src="" title="Estonia" alt="From Ecuador" />
+
                      <td width="328" nowrap valign="top"><div class="ec--p">IPTG    concentration outside E. coli</div></td>
−
<img data-src="res--2/collaborations/Valencia1.jpg" data-src-2x="res--2/collaborations/Valencia1.jpg" src="" alt="Estonia" data-caption="Reunion" />
+
                      <td width="101" nowrap valign="top"><div class="ec--p">nM</div></td>
−
<img data-src="res--2/collaborations/Valencia2.jpg" data-src-2x="res--2/collaborations/Valencia2.jpg" src="" title="Estonia" alt="From Ecuador" />
+
                    </tr>
−
</div>
+
                    <tr>
−
              <h3><a name="I5"  style="text-decoration: none;"></a></h3>
+
                      <td width="142" nowrap valign="top"><div class="ec--p">[IPTG]int</div></td>
−
              <h2>5. 01 OCTUBRE 2018</h2>
+
                      <td width="328" nowrap valign="top"><div class="ec--p">IPTG    concentration inside E. coli</div></td>
−
              <p>Labs like you &amp; Moves like iGEM!!<br>
+
                      <td width="101" nowrap valign="top"><div class="ec--p">nM</div></td>
−
25 teams <br>
+
                    </tr>
−
Hey iGEMers!<br>
+
                    <tr>
−
This link is the final video we promised to send you. Thanks for contributing with this task, it&rsquo;s has been such an amazing experience working along with you, we have a lot of fun and we hope that you two.&nbsp;</p>
+
                      <td width="142" nowrap valign="top"><div class="ec--p">[IPTG]TOTAL</div></td>
−
              <p>Hope you like them, see you  in Boston!<br>
+
                      <td width="328" nowrap valign="top"><div class="ec--p">Total LacI    concentration in E. coli</div></td>
−
<iframe width="560" height="315" src="https://www.youtube.com/embed/R7vdiGLLJZA" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe>
+
                      <td width="101" nowrap valign="top"><div class="ec--p">nM</div></td>
 +
                    </tr>
 +
                    <tr>
 +
                      <td width="142" nowrap valign="top"><div class="ec--p">[LacI]act</div></td>
 +
                      <td width="328" nowrap valign="top"><div class="ec--p">Active LacI    concentration in E. coli</div></td>
 +
                      <td width="101" nowrap valign="top"><div class="ec--p">nM</div></td>
 +
                    </tr>
 +
                    <tr>
 +
                      <td width="142" nowrap valign="top"><div class="ec--p">[CB]mRNA</div></td>
 +
                      <td width="328" nowrap valign="top"><div class="ec--p">CBD-BMP2 mRNA    concentration in E. coli</div></td>
 +
                      <td width="101" nowrap valign="top"><div class="ec--p">nM</div></td>
 +
                    </tr>
 +
                    <tr>
 +
                      <td width="142" nowrap valign="top"><div class="ec--p">[CB]</div></td>
 +
                      <td width="328" nowrap valign="top"><div class="ec--p">CBD-BMP2    protein concentration in E. coli</div></td>
 +
                      <td width="101" nowrap valign="top"><div class="ec--p">nM</div></td>
 +
                    </tr>
 +
                    <tr>
 +
                      <td width="142" nowrap valign="top"><div class="ec--p">δ[CB]</div></td>
 +
                      <td width="328" nowrap valign="top"><div class="ec--p">Degradation    rate of CBD-BMP2 mRNA</div></td>
 +
                      <td width="101" nowrap valign="top"><div class="ec--p">min-1</div></td>
 +
                    </tr>
 +
                    <tr>
 +
                      <td width="142" nowrap valign="top"><div class="ec--p">β[CB]</div></td>
 +
                      <td width="328" nowrap valign="top"><div class="ec--p">Translational    rate of CBD-BMP2 protein</div></td>
 +
                      <td width="101" nowrap valign="top"><div class="ec--p">min-1</div></td>
 +
                    </tr>
 +
                    <tr>
 +
                      <td width="142" nowrap valign="top"><div class="ec--p">σ[CB]</div></td>
 +
                      <td width="328" nowrap valign="top"><div class="ec--p">Degradation    rate of CBD-BMP2 protein</div></td>
 +
                      <td width="101" nowrap valign="top"><div class="ec--p">min-1</div></td>
 +
                    </tr>
 +
                    <tr>
 +
                      <td width="142" nowrap valign="top"><div class="ec--p">t</div></td>
 +
                      <td width="328" nowrap valign="top"><div class="ec--p">time</div></td>
 +
                      <td width="101" nowrap valign="top"><div class="ec--p">min</div></td>
 +
                    </tr>
 +
                    <tr>
 +
                      <td width="142" nowrap valign="top"><div class="ec--p">α[CB]</div></td>
 +
                      <td width="328" nowrap valign="top"><div class="ec--p">Transcriptional    leakage of Plac promoter</div></td>
 +
                      <td width="101" nowrap valign="top"><div class="ec--p">%</div></td>
 +
                    </tr>
 +
                    <tr>
 +
                      <td width="142" nowrap valign="top"><div class="ec--p">kPlac</div></td>
 +
                      <td width="328" nowrap valign="top"><div class="ec--p">Maximum    transcription rate of Plac promoter</div></td>
 +
                      <td width="101" nowrap valign="top"><div class="ec--p">0.5 nM min-1</div></td>
 +
                    </tr>
 +
                    <tr>
 +
                      <td width="142" nowrap valign="top"><div class="ec--p">kIPTGupt</div></td>
 +
                      <td width="328" nowrap valign="top"><div class="ec--p">Rate constant    of IPTG uptake</div></td>
 +
                      <td width="101" nowrap valign="top"><div class="ec--p">0.92 min-1</div></td>
 +
                    </tr>
 +
                    <tr>
 +
                      <td width="142" nowrap valign="top"><div class="ec--p">kIPTGout</div></td>
 +
                      <td width="328" nowrap valign="top"><div class="ec--p">Rate constant    of IPTG output</div></td>
 +
                      <td width="101" nowrap valign="top"><div class="ec--p">0.05 min-1</div></td>
 +
                    </tr>
 +
                    <tr>
 +
                      <td width="142" nowrap valign="top"><div class="ec--p">KIPTG</div></td>
 +
                      <td width="328" nowrap valign="top"><div class="ec--p">Michaelis    constant of IPTG-LacI binding</div></td>
 +
                      <td width="101" nowrap valign="top"><div class="ec--p">600 nM</div></td>
 +
                    </tr>
 +
                    <tr>
 +
                      <td width="142" nowrap valign="top"><div class="ec--p"><a name="IND3"></a>hIPTG</div></td>
 +
                      <td width="328" nowrap valign="top"><div class="ec--p">Hill coefficient of IPTG-LacI binding </div></td>
 +
                      <td width="101" nowrap valign="top"><div class="ec--p">2</div></td>
 +
                    </tr>
 +
 
 +
                    <tr>
 +
                      <td width="142" nowrap valign="top"><div class="ec--p">HLacI</div></td>
 +
                      <td width="328" nowrap valign="top"><div class="ec--p">Hill coefficient of LacI-Plac promoter binding </div></td>
 +
                      <td width="101" nowrap valign="top"><div class="ec--p">2</div></td>
 +
                    </tr>
 +
                  </table>
 +
                  <div class="ec--h2"><strong><a name="IND4"></a>IPTG-INDUCIBLE MODEL FOR CBD CIPA-BMP2 PROTEIN EXPRESSION IN </strong><strong><em>E</em></strong><strong><em>. </em></strong><strong><em>coli</em></strong><strong> </strong></div>
 +
                  <div class="ec--p"><strong>Entry of IPTG into <em>E. coli</em></strong><br>
 +
                    Mimicking lactose, IPTG is a chemical widely used  in scientific research because it cannot be metabolized. IPGT induces the  expression of genes under the control of Plac promoter. </div>
 +
                  <div class="ec--p">IPTG enters into <em>E</em>. <em>coli</em> cells in a concentration dependent manner. This uptake is mediated by lactose permease and passive diffusion at low and high  concentrations respectively.2 The IPTG uptake through passive  diffusion can be described with the law of mass action expressing the balance  between IPTG concentration outside (IPTGext) and inside (IPTGint) of <em>E</em>. <em>coli</em> : 
 +
  <br><center>
 +
<img src="https://static.igem.org/mediawiki/2018/1/1a/T--Ecuador--Ecuacion1.jpg"/>
 +
  <br>Eq 1.
 +
</center>
 +
 
 +
  The first term on the right side of Eq 1  represents the forward rate where kIPTGupt is the rate constant of IPTG uptake (0.92 min-1)3 while the second term has negative sign because it represents the backward rate where kIPTGout is the rate constant of IPTG output (0.05 min-1).3 Because of [IPTG]ext = [IPTG]TOTAL - [IPTG]int, it can be replaced in equation 1 in order to have IPTGint as the unique independent variable:
 +
  <br><center>
 +
<img src="https://static.igem.org/mediawiki/2018/d/de/T--Ecuador--Ecuacion2.jpg"/>
 +
  <br>Eq 2.
 +
</center>
 +
  The LacI-IPTG interaction is assumed to be so  fast and when the IPTG concentration largely exceeds that of lacI. The LacI  active ([LacI]act), i.e that unbounded to IPTG, can be described with the Hill repression function.4,2<br>
 +
  <br><center>
 +
<img src="https://static.igem.org/mediawiki/2018/8/80/T--Ecuador--Ecuacion3.jpg"/>
 +
  <br>Eq 3.
 +
</center>
 +
 
 +
  Equation 3 (Eq 3) describes the amount of  unbounded LacI that actively repress the expression of a protein driven by the  Plac promoter; the expression of CBD cipA-BMP2 in the present study. <a name="IND5"></a>[LacI]TOTAL is the concentration of LacI inside <em>E</em>. <em>coli</em>, KIPTG is the Michaelis constant of IPTG-LacI binding (6000 M) 5 and hIPTG is the associated Hill coefficient (2).3,6</div>
 +
<div class="ec--p">&#160;</div>
 +
<div class="ec--p"><strong>CBD cipA-BMP2 EXPRESSION</strong></div>
 +
<div class="ec--p"><strong>            </strong><strong><u>CBD cipA-BMP2 mRNA</u></strong></div>
 +
<div class="ec--p">The CBD  cipA-BMP2 mRNA concentration ([CB]mRNA) at time t can be described as follows:</div>
 +
<br><center>
 +
<img src="https://static.igem.org/mediawiki/2018/1/1d/T--Ecuador--Ecuacion4.jpg"/>
 +
  <br>Eq 4.
 +
</center>
 +
 
 +
<div class="ec--p">The first term on the right side of the equation  2.6 represents the synthesis of mRNA. kPlac is the maximum transcriptional rate corresponding to the Plac promoter (0.5 nM min-1).3 αCEB+(1-αCEB) is the leakiness factor where αCEB is the  transcriptional leakage of Plac promoter.  is the repressing Hill function of Plac promoter where KLacI is the Michaelis constant of LacI-Plac promoter binding (6000 M), 3 and hLacI is the associated Hill coefficient(2).3 The second term  represents the degradation of the [CB]mRNA where δ[CB]<strong> </strong>is the degradation rate.3,6,7<br>
 +
  Because there is not constitutive expression of  LacI protein from the plasmid cloned in <em>E</em>. <em>coli</em> carrying the CBD cipA-BMP2 construct and based on our preliminary measurements of total  protein concentration using BCA method, the transcriptional leakage can be  taken to be 0.8 and thus the balance for [CB]mRNA becomes:
 +
<br><center>
 +
<img src="https://static.igem.org/mediawiki/2018/b/b2/T--Ecuador--Ecuacion5.jpg"/>
 +
  <br>Eq 5.
 +
</center>
  
−
              <p>1. iGEM IISER  Bhopa<br>
+
<div class="ec--p"><strong>&#160;</strong></div>
−
2. IGEM AFCM <br>
+
<div class="ec--p"><strong><u>CBD cipA-BMP2 protein</u></strong><br>
−
3. IGEM UNESP BRAZIL<br>
+
−
4. IGEM WASHINGTON<br>
+
−
5. IGEM Tust China <br>
+
−
6. iGEM team  Bielefeld-CeBiTec <br>
+
−
7. IISc-Bangalore  iGEM Team<br>
+
−
8. IGEM BRAZIL USP<br>
+
−
9. IGEM DUSSELDORF<br>
+
−
10. IGEM GRONINGEN<br>
+
−
11. IGEM DALHOUSIE<br>
+
−
12. IGEM LEIDEN<br>
+
−
13. Team UFLORIDA<br>
+
−
14. Tarta TUIT_IGEM<br>
+
−
15. Toulouse INSA  UPS<br>
+
−
16. IGEM MICHIGAN  STATE<br>
+
−
17. Team UCHILE_Biotec<br>
+
−
18. ECUADOR<br>
+
−
19. IGEM BRAZIL USP EEL<br>
+
−
20. Tec-Guadalajara<br>
+
−
21. Tec-Chihuahua<br>
+
−
22. UCSC IGEM<br>
+
−
23. TecCEM<br>
+
−
24.  iTESLA-SoundBio Team<br>
+
−
25. Tacoma  RainMakers Team</p>
+
−
              <h1>REVISTA</h1>
+
−
              <p><a href="https://2018.igem.org/Team:UChile_Biotec">https://2018.igem.org/Team:UChile_Biotec</a> <br>
+
−
                Magazine Latam</p>
+
−
              <h1>SURVEYS</h1>
+
−
              <p>Surveys  <a href="https://2017.igem.org/Team:Heidelberg/Collaborations#collaboration9">Development  within iGEM</a></p>
+
−
Dear iGEM Ecuador,<br>
+
−
<br>
+
−
<br>
+
−
My name is John and I am a member of iGEM Thessaloniki. I am contacting you to  let you know about the collaboration we are organising. More specifically, our  team is working on designing a system to increase robustness of measurements by  decoupling gene expression from copy number. So, if you would like to take part  in our Interlaboratory Collab all you have to do is to conduct measurements,  measuring fluorescence with our constructs in a plate reader. We will gather  and compare results from around the world and find out if our system diminishes  interlaboratory variations caused by differences in plasmid copy number.<br>
+
−
<br>
+
−
<br>
+
−
In addition, we have created a survey about synthetic biology, laboratory work,  safety and ethics that is addressed to experienced scientists working on the  synthetic biology field . We would appreciate it if you could forward this  survey to your PIs, instructors and advisors. You can find the survey here: <a href="https://goo.gl/forms/xigcfX3wmFpywlMo2" target="_blank">https://goo.gl/forms/xigcfX3wmFpywlMo2</a> <br>
+
−
<br>
+
−
<br>
+
−
<br>
+
−
Hope you see you in our Interlaboratory Collaboration. For more information  don&rsquo;t hesitate to contact us.<br>
+
−
<br>
+
−
<br>
+
−
Thank you in advance for your time.<br>
+
−
<br>
+
−
<br>
+
−
<br>
+
−
Best, <br>
+
−
<p>John Alexopoulos<br>
+
−
</p>
+
−
<img src="res--2/collaborations/survey1.png" width="1366" height="768" alt=""/>
+
−
<p>Dear iGEM Team Ecuador,<br>
+
−
  I&rsquo;m a member of this year&rsquo;s iGEM Team Bielefeld-CeBiTec (Germany) and we have a  little favor to ask. We prepared a survey on the topics Dual Use and Dual Use  Research of Concern for which we need your help! We already have many German  respondents and would be very happy to get a more international view - that&rsquo;s  why we would be pleased if as many of you as possible could participate! If we  can also do something for you, please do not hesitate to contact us <br>
+
−
  <br>
+
−
  See you in Boston &amp; best wishes!<br>
+
−
  Matthias<br>
+
 
   <br>
 
   <br>
 +
  The concentration of CBD cipA-BMP2 protein  ([CB]) can be described as follows:
 +
<br><center>
 +
<img src="https://static.igem.org/mediawiki/2018/d/d8/T--Ecuador--Ecuacion6.jpg"/>
 +
  <br>Eq 6.
 +
</center>
 +
  <a name="IND6"></a>The first term on the right side of the equation  6 represents the synthesis of [CB] where β[CB] is the translational rate of [CB]. The second term represents the degradation of [CB] where σ[CB] is the degradation rate.</div>
 +
 +
<div class="ec--p"><strong>KINETIC CONSTANTS</strong><br>
 +
  The time cell division of E. coli is function of factors such as pressure, temperature and culture medium  and ranging from 20-30 min under optimal conditions. Culturing in universal  common medium such as Nutrient Broth and Luria-Bertani at 35 ℃, the time cell division can be assumed to be 30  min.8,9,10<br>
 +
  The half life of mRNAs in E. coli has been well reported by Bernstein and coworkers who determined that it  depends of culture medium. In, LB 99% of mRNAs had a half-life time between  1-15 min with a mean of 5.2 min.11 Therefore, 5.2 min can be assumed as the  half-life time of CBD cipA -BMP2 mRNA. Consequently, δ[CB<strong>]</strong>= 0.226 min-1. <br>
 +
  In <em>E</em>. <em>coli</em> , the translation takes place at 12-21 amino  acids per second (aa s-1).12 We choose 19 aa s-1 because  the codon optimization. <a name="IND7"></a><strong><a name="IND8"></a></strong>Because CBD cipA-BMP2 contains 292 aa, β[CB]<strong> </strong>can be taken to be 3.904 min-1.The  half life of CBD cipA-BMP2 protein can be assumed to be 60 min-1, 13 consequently,  σ[CB]= 0.05min-1:</div>
 +
<div class="ec--h2">RESULTS OF THE IPTG-INDUCIBLE MODEL FOR CBD cipA-BMP2  PROTEIN EXPRESSION IN E. coli</div>
 +
<div class="ec--p"><strong>Calculation of entry of IPTG into </strong><strong><em>E</em></strong><strong><em>. </em></strong><strong><em>coli</em></strong><br>
 +
  Figure 1 is a rate balance plot derived from  Equation 1 whith both forward and backward rates as functions of the normalized  [IPTG]int concentration whose value in the equilibrium (steady  state) can be obtained where the two functions intersect. Analitically, this  point is [IPTG]int =0.9485[IPTG]TOTAL <br>
 +
<div>
 +
  <div class="ec--p">rate</div>
 +
<br><center>
 +
<img src="https://static.igem.org/mediawiki/2018/1/1f/T--Ecuador--rate.jpg"/>
 +
 +
</center>
 +
</div>
 +
<p><a name="IND9"></a>
 +
 
</p>
 
</p>
−
  <img src="res--2/collaborations/survey2.png" width="1366" height="768" alt=""/>
+
<p>&nbsp;</p>
−
<p>Dear team Ecuador<br>
+
</div>
−
   <br>
+
 
−
  Are you interested in contributing to the well being and prosperity for future  iGEM participants? All we need is your attention for 1 minute <br>
+
   <strong>Figure 1.</strong> Rate balance of IPTG diffusion through E. coli membrane. Forward and  backward rates are plotted versus normalized [IPTG]int </div>
−
  <br>
+
−
  We&rsquo;re the team from Lund University in Sweden. After talking with previous and  current iGEM students we&rsquo;ve come to the conclusion that iGEM can be a very  stressful and frustrating experience for many.<br>
+
<div class="ec--p"><strong>IPTG-LacI repressor interaction</strong><br>
−
  <br>
+
   Because of IPTG is the inducer, it is important to evaluate its interaction with LacI repressor at different initial concentrations added to the system ([IPTG]TOTAL). For these values the [LacI]act can be calculated with Equation 3 (Table 1). From table 1 and figure 4, it can be deduced that a concentration of IPTG = 0.1 mM is saturating because the solutions derived from higher IPTG values converge. </div>
−
   iGEM is multifaceted and challenges its participants in many ways. For many  individuals, it can become an overwhelming experience which in turn can cause mental health complications such as stress, anxiety and depression. Others members, such as the team leaders, might also face problems with managing the  team and ensuring that the project progresses in the right direction.<br>
+
<div class="ec--p">Table 1. [LacI]act for different initial IPTG concentrations. </div>
−
  <br>
+
<div align="center">
−
  We strongly believe that this can be changed with the proper tools and  guidance.<br>
+
   <table border="1" cellspacing="0" cellpadding="0" width="437">
−
  <br>
+
    <tr>
−
  As a part of our human practices initiative this year, we will be conducting a world-wide survey to map out self-fulfillment, motivation, stress, organization  and management, and group dynamics within the iGEM community. <br>
+
      <td width="212" nowrap valign="top">
−
  <br>
+
<div class="ec--p"><strong>[IPTG]TOTAL    (mM)</strong></div></td>
−
  This survey will serve as a foundation for a handbook written by us about  team-organization for future iGEM members and team leaders. The handbook will  skip all the theoretical jargon and dive straight into tools and practices the  teams can apply to improve their work flow and well-being.<br>
+
      <td width="225" nowrap valign="top"><div class="ec--p"><strong>[LacI]act (nM)</strong></div></td>
−
  <br>
+
    </tr>
−
   It would mean a lot to us if you could distribute our survey to as many people  as possible within your team. It takes less than 5 minutes to answer all the  questions.<br>
+
    <tr>
−
  <br>
+
      <td width="212" nowrap valign="top"><div class="ec--p">0,001</div></td>
−
  <a href="https://goo.gl/forms/MolMbkOuaKiXrWpB3" target="_blank">https://goo.gl/forms/MolMbkOuaKiXrWpB3</a> <br>
+
      <td width="225" nowrap valign="top"><div class="ec--p">9.7562</div></td>
−
  <br>
+
    </tr>
−
  Please don&rsquo;t hesitate to ask if there&rsquo;s anything our team could help you out  with.<br>
+
    <tr>
−
  <br>
+
      <td width="212" nowrap valign="top"><div class="ec--p">0,02</div></td>
−
  Warm regards,<br>
+
      <td width="225" nowrap valign="top"><div class="ec--p">0.9095</div></td>
−
  Albert Anis<br>
+
    </tr>
−
  iGEM Lund</p>
+
    <tr>
−
<p> </p>
+
      <td width="212" nowrap valign="top"><div class="ec--p">0,03</div></td>
−
  <img src="res--2/collaborations/survey3.png" width="1366" height="768" alt=""/>
+
      <td width="225" nowrap valign="top"><div class="ec--p">0.4257</div></td>
−
<p align="center">Dear Team Ecuador,<br>
+
    </tr>
−
  <br>
+
    <tr>
−
  Hello!<br>
+
      <td width="212" nowrap valign="top"><div class="ec--p">0.1</div></td>
−
  My name is Ayano Furuta, and I&rsquo;m a student at  Tokyo University of Science in Japan. I belong to Botchan Lab Tokyo, this  University&rsquo;s iGEM team, and I would like to ask you a favor.<br>
+
      <td width="225" nowrap valign="top"><div class="ec--p">0.0399</div></td>
−
  In this year, my team is planning to think  deeply about food issues through Human Practice, and we want to collect a data  which regard to awareness of food problem from different countries. <br>
+
    </tr>
−
  <br>
+
    <tr>
−
  If it&rsquo;s ok with you, please take a few minutes  to fill out the survey below. I want as many people as possible to fill out the  one, so if you can ask your friends or family, please ask them to answer the  questions.<br>
+
      <td width="212" nowrap valign="top"><div class="ec--p">1.0</div></td>
−
  <br>
+
      <td width="225" nowrap valign="top"><div class="ec--p">0.0004</div></td>
−
  I am really appreciate that you take your  precious time to read this.<br>
+
    </tr>
−
  If we can also do something for you, please do  not hesitate to contact us!<br>
+
   </table>
−
  I&rsquo;m looking forward to see you in Boston <br>
+
   <a name="IND10"></a></div>
−
  <br>
+
<div class="ec--p"></div>
−
  <a href="https://docs.google.com/forms/d/1Sx5q3K7PJTlJ4TNtTSLEfEPBmIsNgrYblHqRVWt8m_o/viewform?edit_requested=true" target="_blank">https://docs.google.com/forms/d/1Sx5q3K7PJTlJ4TNtTSLEfEPBmIsNgrYblHqRVWt8m_o/viewform?edit_requested=true</a><br>
+
<div class="ec--p"><br></div><div class="ec--p"><br></div>
−
  <br>
+
<div class="ec--p"><strong>&#160;</strong></div>
−
  Kind regards, <br>
+
<div class="ec--p"><strong>Calculation and validation of CBD cipA-BMP2  expression</strong></div>
−
  Ayano </p>
+
<div class="ec--p">The mathematical model for the expression of CBD  cipA-BMP2 is:
−
<p align="center"> </p>
+
<br><center>
−
  <img src="res--2/collaborations/survey4.png" width="1366" height="768" alt=""/>
+
<img src="https://static.igem.org/mediawiki/2018/4/4b/T--Ecuador--Ecuacion7.jpg"/>
−
<p align="center">&nbsp;</p>
+
  <br>Eq 7.
−
<p align="center">iGEM Tec Chihuahua 2018</p>
+
</center>
−
<p align="center">¡Saludos desde iGEM Tec-Chihuahua!<br>
+
−
  Estamos trabajando actualmente en un manual de  emprendimiento con el cual los equipos de iGEM podrían contar para el  desarrollo de la sección de emprendimiento de sus proyectos. Queremos que este  manual se pueda utilizar en las próximas ediciones de la competencia para que  los equipos puedan tener una guía adecuada en la cual se puedan basar para sacar  adelante el área.<br>
+
−
  <br>
+
−
  Es nuestra intención que esta guía incluya  situaciones que los diferentes equipos de iGEM de todo el mundo experimentan  mientras exploran el campo de emprendimiento. Por lo tanto, los invitamos a  colaborar con nosotros y con la comunidad de iGEM enviándonos sus preguntas y  preocupaciones que llegaron a surgirles al administrar esta sección de sus  proyectos. iGEM ​​Tec-Chihuahua consultará a diferentes expertos y  compartiremos con ustedes las mejores soluciones. También incluiremos sus  preguntas e inquietudes con sus respectivas respuestas en nuestro manual para  futura referencia.<br>
+
−
  <br>
+
−
  Adjunto a este mensaje, encontrarán un Google  Forms para recibir su apoyo en el desarrollo de este manual. Aquí incluimos  algunas preguntas para recopilar estadísticas sobre el emprendimiento en iGEM y  una sección para que ustedes nos compartan su opinión sobre este manual.<br>
+
−
  La fecha límite para completar este Google  Forms es <a href="https://www.facebook.com/BiosinEcuador/inbox/?mailbox_id=151919028838292&selected_item_id=100001373108487">el 8 de julio</a> y iGEM Tec-Chihuahua enviará las respuestas  correspondientes a cada equipo la primera semana de <a href="https://www.facebook.com/BiosinEcuador/inbox/?mailbox_id=151919028838292&selected_item_id=100001373108487">agosto</a>.<br>
+
−
  Le deseamos lo mejor para sus proyectos.<br>
+
−
   Muchas gracias!<br>
+
−
   <a href="https://l.facebook.com/l.php?u=https%3A%2F%2Fdocs.google.com%2Fforms%2Fd%2Fe%2F1FAIpQLSfooEx-ve4OCPklJeNpG8nAMcSc6Uyx-kIwyoFnOpaiFC3u_w%2Fviewform%3Fusp%3Dsf_link&h=AT0ujOVmRNt9sPeiyF1E7_Sk2cx6cAK4IuG1ifuzvqtlkBYyQsXDY_Jvd2q-FJ2PEP1WpJ0njIgyn02PV5y9u_xxI8ctsetoQsHYOqbJFJnXkGbdf1vJ5IoIRDm_y24f1w3F0A" target="_blank">https://docs.google.com/forms/d/e/1FAIpQLSfooEx-ve4OCPklJeNpG8nAMcSc6Uyx-kIwyoFnOpaiFC3u_w/viewform?usp=sf_link</a><br>
+
−
  En caso de que no puedan abrir el archivo,  háganoslo saber <br>
+
−
</p>
+
−
  <img src="res--2/collaborations/survey5.png" width="1366" height="768" alt=""/>
+
−
<p align="center">We thank all the teams  involved in these collaborations; for sharing their time with us, giving us  advice, supporting our project and making this experience more amusing. </p>
+
−
</div>
+
−
<div class="ec--sect--text"></div>
+
−
</div>
+
−
</div>
+
 
 
 +
<div class="ec--p">The stability of the system can be analyzed with the  Jacobian matrix associated to the system of differential equations:<br>
 +
<div>
 +
  <div class="ec--p">JACOBIAN</div>
 +
<br><center>
 +
<img src="https://static.igem.org/mediawiki/2018/2/22/T--Ecuador--Jacobian.jpg"/>
 +
</center>
 
 
−
<!-->IdealImageSlider<!-->
+
</div>
−
<script type="text/javascript">
+
−
var IdealImageSlider = (function() {
+
−
"use strict";
+
  
−
/*
+
  Because the two igenvalues (λ1= -0.226 y λ2 = -0.05) are negative, the equilibrium point is a  stable node.</div>
−
* requestAnimationFrame polyfill
+
<div class="ec--p">&#160;</div>
−
*/
+
<div class="ec--p"><strong>          <u>Time step selection and phase plane</u></strong><br>
−
var _requestAnimationFrame = function(win, t) {
+
  A reasonable error less than 0.01 for both mRNA and  protein concentrations was obtained with a time step Dt=0.1/8. Therefore, this Dt was considered to evaluate a phase plane plot  which indicates the equilibrium points of the mathematical model. To determine  the maximum concentrations of CBD cipA-BMP2 mRNA and CBD cipA-BMP2 protein, a  saturating concentration of IPTG (IPTG=0.1 mM) was evaluated. This is a  monostable system where the equilibrium point at the steady state (Figure 2) is  2.21 nM and 172.69nM for CBD cipA-BMP2 mRNA and CBD cipA-BMP2 protein  respectively.</div>
−
return win["r" + t] || win["webkitR" + t] || win["mozR" + t] || win["msR" + t] || function(fn) {
+
<div class="ec--p">
−
setTimeout(fn, 1000 / 60);
+
<div>
−
};
+
  <div class="ec--p">Plano </div>
−
}(window, 'equestAnimationFrame');
+
<br><center>
−
 
+
<img src="https://static.igem.org/mediawiki/2018/5/55/T--Ecuador--Plano.jpg"/>
−
/**
+
</center>
−
* Behaves the same as setTimeout except uses requestAnimationFrame() where possible for better performance
+
−
* @param {function} fn The callback function
+
−
* @param {int} delay The delay in milliseconds
+
−
*/
+
−
var _requestTimeout = function(fn, delay) {
+
−
var start = new Date().getTime(),
+
−
handle = {};
+
−
 
+
−
function loop() {
+
−
var current = new Date().getTime(),
+
−
delta = current - start;
+
−
 
+
−
if (delta >= delay) {
+
−
fn.call();
+
−
} else {
+
−
handle.value = _requestAnimationFrame(loop);
+
−
}
+
−
}
+
−
 
+
−
handle.value = _requestAnimationFrame(loop);
+
−
return handle;
+
−
};
+
−
 
+
−
/*
+
−
* Helper functions
+
−
*/
+
−
var _isType = function(type, obj) {
+
−
var _class = Object.prototype.toString.call(obj).slice(8, -1);
+
−
return _and_f(_and_f(obj !== undefined, obj !== null),_class === type);
+
−
};
+
 
 
−
var _and_f =function(parameter1, parameter2) {
+
</div>
−
    return !(!parameter1 || !parameter2);
+
</div>
−
}
+
−
 
+
−
var _isInteger = function(x) {
+
−
return Math.round(x) === x;
+
−
};
+
−
 
+
−
var _deepExtend = function(out) {
+
−
out = out || {};
+
−
for (var i = 1; i < arguments.length; i++) {
+
−
var obj = arguments[i];
+
−
if (!obj)
+
−
continue;
+
−
for (var key in obj) {
+
−
if (obj.hasOwnProperty(key)) {
+
−
if (_and_f(_isType('Object', obj[key]), obj[key] !== null))
+
−
_deepExtend(out[key], obj[key]);
+
−
else
+
−
out[key] = obj[key];
+
−
}
+
−
}
+
−
}
+
−
return out;
+
−
};
+
−
 
+
−
var _hasClass = function(el, className) {
+
−
if (!className) return false;
+
−
if (el.classList) {
+
−
return el.classList.contains(className);
+
−
} else {
+
−
return new RegExp('(^| )' + className + '( |$)', 'gi').test(el.className);
+
−
}
+
−
};
+
−
 
+
−
var _addClass = function(el, className) {
+
−
if (!className) return;
+
−
if (el.classList) {
+
−
el.classList.add(className);
+
−
} else {
+
−
el.className += ' ' + className;
+
−
}
+
−
};
+
−
 
+
−
var _removeClass = function(el, className) {
+
−
if (!className) return;
+
−
if (el.classList) {
+
−
el.classList.remove(className);
+
−
} else {
+
−
el.className = el.className.replace(new RegExp('(^|\\b)' + className.split(' ').join('|') + '(\\b|$)', 'gi'), ' ');
+
−
}
+
−
};
+
−
 
+
−
var _toArray = function(obj) {
+
−
return Array.prototype.slice.call(obj);
+
−
};
+
−
 
+
−
var _arrayRemove = function(array, from, to) {
+
−
var rest = array.slice((to || from) + 1 || array.length);
+
−
array.length = from < 0 ? array.length + from : from;
+
−
return array.push.apply(array, rest);
+
−
};
+
−
 
+
−
var _addEvent = function(object, type, callback) {
+
−
if (object === null || typeof(object) === 'undefined') return;
+
−
 
+
−
if (object.addEventListener) {
+
−
object.addEventListener(type, callback, false);
+
−
} else if (object.attachEvent) {
+
−
object.attachEvent("on" + type, callback);
+
−
} else {
+
−
object["on" + type] = callback;
+
−
}
+
−
};
+
−
 
+
−
var _loadImg = function(slide, callback) {
+
−
if (!slide.style.backgroundImage) {
+
−
var img = new Image();
+
−
img.setAttribute('src', slide.getAttribute('data-src'));
+
−
img.onload = function() {
+
−
slide.style.backgroundImage = 'url(' + slide.getAttribute('data-src') + ')';
+
−
slide.setAttribute('data-actual-width', this.naturalWidth);
+
−
slide.setAttribute('data-actual-height', this.naturalHeight);
+
−
if (typeof(callback) === 'function') callback(this);
+
−
};
+
−
}
+
−
};
+
−
 
+
−
var _isHighDPI = function() {
+
−
var mediaQuery = "(-webkit-min-device-pixel-ratio: 1.5),(min--moz-device-pixel-ratio: 1.5),(-o-min-device-pixel-ratio: 3/2),(min-resolution: 1.5dppx)";
+
−
if (window.devicePixelRatio > 1)
+
−
return true;
+
−
if (_and_f(window.matchMedia , window.matchMedia(mediaQuery).matches))
+
−
return true;
+
−
return false;
+
−
};
+
−
 
+
−
var _translate = function(slide, dist, speed) {
+
−
slide.style.webkitTransitionDuration =
+
−
slide.style.MozTransitionDuration =
+
−
slide.style.msTransitionDuration =
+
−
slide.style.OTransitionDuration =
+
−
slide.style.transitionDuration = speed + 'ms';
+
−
 
+
−
slide.style.webkitTransform =
+
−
slide.style.MozTransform =
+
−
slide.style.msTransform =
+
−
slide.style.OTransform = 'translateX(' + dist + 'px)';
+
−
};
+
−
 
+
−
var _unTranslate = function(slide) {
+
−
slide.style.removeProperty('-webkit-transition-duration');
+
−
slide.style.removeProperty('transition-duration');
+
−
 
+
−
slide.style.removeProperty('-webkit-transform');
+
−
slide.style.removeProperty('-ms-transform');
+
−
slide.style.removeProperty('transform');
+
−
};
+
−
 
+
−
var _animate = function(item) {
+
−
var duration = item.time,
+
−
end = +new Date() + duration;
+
−
 
+
−
var step = function() {
+
−
var current = +new Date(),
+
−
remaining = end - current;
+
−
 
+
−
if (remaining < 60) {
+
−
item.run(1); //1 = progress is at 100%
+
−
return;
+
−
} else {
+
−
var progress = 1 - remaining / duration;
+
−
item.run(progress);
+
−
}
+
−
 
+
−
_requestAnimationFrame(step);
+
−
};
+
−
step();
+
−
};
+
−
 
+
−
var _setContainerHeight = function(slider, shouldAnimate) {
+
−
if (typeof shouldAnimate === 'undefined') {
+
−
shouldAnimate = true;
+
−
}
+
−
 
+
−
// If it's a fixed height then don't change the height
+
−
if (_isInteger(slider.settings.height)) {
+
−
return;
+
−
}
+
−
 
+
−
var currentHeight = Math.round(slider._attributes.container.offsetHeight),
+
−
newHeight = currentHeight;
+
−
 
+
−
if (_and_f(slider._attributes.aspectWidth, slider._attributes.aspectHeight)) {
+
−
// Aspect ratio
+
−
newHeight = (slider._attributes.aspectHeight / slider._attributes.aspectWidth) * slider._attributes.container.offsetWidth;
+
−
} else {
+
−
// Auto
+
−
var width = slider._attributes.currentSlide.getAttribute('data-actual-width');
+
−
var height = slider._attributes.currentSlide.getAttribute('data-actual-height');
+
−
 
+
−
if (_and_f(width , height)) {
+
−
newHeight = (height / width) * slider._attributes.container.offsetWidth;
+
−
}
+
−
}
+
−
 
+
−
var maxHeight = parseInt(slider.settings.maxHeight, 10);
+
−
if (_and_f(maxHeight , newHeight > maxHeight)) {
+
−
newHeight = maxHeight;
+
−
}
+
−
 
+
−
newHeight = Math.round(newHeight);
+
−
if (newHeight === currentHeight) {
+
−
return;
+
−
}
+
−
 
+
−
if (shouldAnimate) {
+
−
_animate({
+
−
time: slider.settings.transitionDuration,
+
−
run: function(progress) {
+
−
slider._attributes.container.style.height = Math.round(progress * (newHeight - currentHeight) + currentHeight) + 'px';
+
−
}
+
−
});
+
−
} else {
+
−
slider._attributes.container.style.height = newHeight + 'px';
+
−
}
+
−
};
+
−
 
+
−
var _touch = {
+
−
 
+
−
vars: {
+
−
start: {},
+
−
delta: {},
+
−
isScrolling: undefined,
+
−
direction: null
+
−
},
+
−
 
+
−
start: function(event) {
+
−
if (_hasClass(this._attributes.container, this.settings.classes.animating)) return;
+
−
 
+
−
var touches = event.touches[0];
+
−
_touch.vars.start = {
+
−
x: touches.pageX,
+
−
y: touches.pageY,
+
−
time: +new Date()
+
−
};
+
−
_touch.vars.delta = {};
+
−
_touch.vars.isScrolling = undefined;
+
−
_touch.vars.direction = null;
+
−
 
+
−
this.stop(); // Stop slider
+
−
 
+
−
this.settings.beforeChange.apply(this);
+
−
_addClass(this._attributes.container, this.settings.classes.touching);
+
−
},
+
−
 
+
−
move: function(event) {
+
−
if (_hasClass(this._attributes.container, this.settings.classes.animating)) return;
+
−
// Ensure swiping with one touch and not pinching
+
−
if (event.touches.length > 1 || _and_f(event.scale , event.scale !== 1) ) return;
+
−
 
+
−
var touches = event.touches[0];
+
−
_touch.vars.delta = {
+
−
x: touches.pageX - _touch.vars.start.x,
+
−
y: touches.pageY - _touch.vars.start.y
+
−
};
+
−
 
+
−
if (typeof _touch.vars.isScrolling == 'undefined') {
+
−
_touch.vars.isScrolling = !!(_touch.vars.isScrolling || Math.abs(_touch.vars.delta.x) < Math.abs(_touch.vars.delta.y));
+
−
}
+
−
 
+
−
// If user is not trying to scroll vertically
+
−
if (!_touch.vars.isScrolling) {
+
−
event.preventDefault(); // Prevent native scrolling
+
−
 
+
−
_translate(this._attributes.previousSlide, _touch.vars.delta.x - this._attributes.previousSlide.offsetWidth, 0);
+
−
_translate(this._attributes.currentSlide, _touch.vars.delta.x, 0);
+
−
_translate(this._attributes.nextSlide, _touch.vars.delta.x + this._attributes.currentSlide.offsetWidth, 0);
+
−
}
+
−
},
+
−
 
+
−
end: function(event) {
+
−
if (_hasClass(this._attributes.container, this.settings.classes.animating)) return;
+
−
 
+
−
var duration = +new Date() - _touch.vars.start.time;
+
−
 
+
−
// Determine if slide attempt triggers next/prev slide
+
−
var isChangeSlide = _and_f(Number(duration) < 250 , Math.abs(_touch.vars.delta.x) > 20) || Math.abs(_touch.vars.delta.x) > this._attributes.currentSlide.offsetWidth / 2;
+
−
 
+
−
var direction = _touch.vars.delta.x < 0 ? 'next' : 'previous';
+
−
var speed = this.settings.transitionDuration ? this.settings.transitionDuration / 2 : 0;
+
−
 
+
−
// If not scrolling vertically
+
−
if (!_touch.vars.isScrolling) {
+
−
if (isChangeSlide) {
+
−
_touch.vars.direction = direction;
+
−
 
+
−
if (_touch.vars.direction == 'next') {
+
−
_translate(this._attributes.currentSlide, -this._attributes.currentSlide.offsetWidth, speed);
+
−
_translate(this._attributes.nextSlide, 0, speed);
+
−
} else {
+
−
_translate(this._attributes.previousSlide, 0, speed);
+
−
_translate(this._attributes.currentSlide, this._attributes.currentSlide.offsetWidth, speed);
+
−
}
+
−
 
+
−
_requestTimeout(_touch.transitionEnd.bind(this), speed);
+
−
} else {
+
−
// Slides return to original position
+
−
if (direction == 'next') {
+
−
_translate(this._attributes.currentSlide, 0, speed);
+
−
_translate(this._attributes.nextSlide, this._attributes.currentSlide.offsetWidth, speed);
+
−
} else {
+
−
_translate(this._attributes.previousSlide, -this._attributes.previousSlide.offsetWidth, speed);
+
−
_translate(this._attributes.currentSlide, 0, speed);
+
−
}
+
−
}
+
−
 
+
−
if (speed) {
+
−
_addClass(this._attributes.container, this.settings.classes.animating);
+
−
_requestTimeout(function() {
+
−
_removeClass(this._attributes.container, this.settings.classes.animating);
+
−
}.bind(this), speed);
+
−
}
+
−
}
+
−
},
+
−
 
+
−
transitionEnd: function(event) {
+
−
if (_touch.vars.direction) {
+
−
_unTranslate(this._attributes.previousSlide);
+
−
_unTranslate(this._attributes.currentSlide);
+
−
_unTranslate(this._attributes.nextSlide);
+
−
_removeClass(this._attributes.container, this.settings.classes.touching);
+
−
 
+
−
_removeClass(this._attributes.previousSlide, this.settings.classes.previousSlide);
+
−
_removeClass(this._attributes.currentSlide, this.settings.classes.currentSlide);
+
−
_removeClass(this._attributes.nextSlide, this.settings.classes.nextSlide);
+
−
this._attributes.currentSlide.setAttribute('aria-hidden', 'true');
+
−
 
+
−
var slides = this._attributes.slides,
+
−
index = slides.indexOf(this._attributes.currentSlide);
+
−
 
+
−
if (_touch.vars.direction == 'next') {
+
−
this._attributes.previousSlide = this._attributes.currentSlide;
+
−
this._attributes.currentSlide = slides[index + 1];
+
−
this._attributes.nextSlide = slides[index + 2];
+
−
if (_and_f(typeof this._attributes.currentSlide === 'undefined' ,
+
−
typeof this._attributes.nextSlide === 'undefined')) {
+
−
this._attributes.currentSlide = slides[0];
+
−
this._attributes.nextSlide = slides[1];
+
−
} else {
+
−
if (typeof this._attributes.nextSlide === 'undefined') {
+
−
this._attributes.nextSlide = slides[0];
+
−
}
+
−
}
+
−
 
+
−
_loadImg(this._attributes.nextSlide);
+
−
} else {
+
−
this._attributes.nextSlide = this._attributes.currentSlide;
+
−
this._attributes.previousSlide = slides[index - 2];
+
−
this._attributes.currentSlide = slides[index - 1];
+
−
if (_and_f(typeof this._attributes.currentSlide === 'undefined' ,
+
−
typeof this._attributes.previousSlide === 'undefined')) {
+
−
this._attributes.currentSlide = slides[slides.length - 1];
+
−
this._attributes.previousSlide = slides[slides.length - 2];
+
−
} else {
+
−
if (typeof this._attributes.previousSlide === 'undefined') {
+
−
this._attributes.previousSlide = slides[slides.length - 1];
+
−
}
+
−
}
+
−
 
+
−
_loadImg(this._attributes.previousSlide);
+
−
}
+
−
 
+
−
_addClass(this._attributes.previousSlide, this.settings.classes.previousSlide);
+
−
_addClass(this._attributes.currentSlide, this.settings.classes.currentSlide);
+
−
_addClass(this._attributes.nextSlide, this.settings.classes.nextSlide);
+
−
this._attributes.currentSlide.setAttribute('aria-hidden', 'false');
+
−
 
+
−
_setContainerHeight(this);
+
−
this.settings.afterChange.apply(this);
+
−
}
+
−
}
+
−
 
+
−
};
+
−
 
+
−
/*
+
−
* Slider class
+
−
*/
+
−
var Slider = function(args) {
+
−
// Defaults
+
−
this.settings = {
+
−
selector: '',
+
−
height: 'auto', // "auto" | px value (e.g. 400) | aspect ratio (e.g. "16:9")
+
−
initialHeight: 400, // for "auto" and aspect ratio
+
−
maxHeight: null, // for "auto" and aspect ratio
+
−
interval: 4000,
+
−
transitionDuration: 700,
+
−
effect: 'slide',
+
−
disableNav: false,
+
−
keyboardNav: true,
+
−
previousNavSelector: '',
+
−
nextNavSelector: '',
+
−
classes: {
+
−
container: 'ideal-image-slider',
+
−
slide: 'iis-slide',
+
−
previousSlide: 'iis-previous-slide',
+
−
currentSlide: 'iis-current-slide',
+
−
nextSlide: 'iis-next-slide',
+
−
previousNav: 'iis-previous-nav',
+
−
nextNav: 'iis-next-nav',
+
−
animating: 'iis-is-animating',
+
−
touchEnabled: 'iis-touch-enabled',
+
−
touching: 'iis-is-touching',
+
−
directionPrevious: 'iis-direction-previous',
+
−
directionNext: 'iis-direction-next'
+
−
},
+
−
onInit: function() {},
+
−
onStart: function() {},
+
−
onStop: function() {},
+
−
onDestroy: function() {},
+
−
beforeChange: function() {},
+
−
afterChange: function() {}
+
−
};
+
−
 
+
−
// Parse args
+
−
if (typeof args === 'string') {
+
−
this.settings.selector = args;
+
−
} else if (typeof args === 'object') {
+
−
_deepExtend(this.settings, args);
+
−
}
+
−
 
+
−
// Slider (container) element
+
−
var sliderEl = document.querySelector(this.settings.selector);
+
−
if (!sliderEl) return null;
+
−
 
+
−
// Slides
+
−
var origChildren = _toArray(sliderEl.children),
+
−
validSlides = [];
+
−
sliderEl.innerHTML = '';
+
−
Array.prototype.forEach.call(origChildren, function(slide, i) {
+
−
if (slide instanceof HTMLImageElement || slide instanceof HTMLAnchorElement) {
+
−
var slideEl = document.createElement('a'),
+
−
href = '',
+
−
target = '';
+
−
 
+
−
if (slide instanceof HTMLAnchorElement) {
+
−
href = slide.getAttribute('href');
+
−
target = slide.getAttribute('target');
+
−
 
+
−
var img = slide.querySelector('img');
+
−
if (img !== null) {
+
−
slide = img;
+
−
} else {
+
−
return;
+
−
}
+
−
}
+
−
 
+
−
if (typeof slide.dataset !== 'undefined') {
+
−
_deepExtend(slideEl.dataset, slide.dataset);
+
−
if (slide.dataset.src) {
+
−
// Use data-src for on-demand loading
+
−
slideEl.dataset.src = slide.dataset.src;
+
−
} else {
+
−
slideEl.dataset.src = slide.src;
+
−
}
+
−
 
+
−
// HiDPI support
+
−
if (_and_f(_isHighDPI() , slide.dataset['src-2x'])) {
+
−
slideEl.dataset.src = slide.dataset['src-2x'];
+
−
}
+
−
} else {
+
−
// IE
+
−
if (slide.getAttribute('data-src')) {
+
−
slideEl.setAttribute('data-src', slide.getAttribute('data-src'));
+
−
} else {
+
−
slideEl.setAttribute('data-src', slide.getAttribute('src'));
+
−
}
+
−
}
+
−
 
+
−
if (href) slideEl.setAttribute('href', href);
+
−
if (target) slideEl.setAttribute('target', target);
+
−
if (slide.getAttribute('className')) _addClass(slideEl, slide.getAttribute('className'));
+
−
if (slide.getAttribute('id')) slideEl.setAttribute('id', slide.getAttribute('id'));
+
−
if (slide.getAttribute('title')) slideEl.setAttribute('title', slide.getAttribute('title'));
+
−
if (slide.getAttribute('alt')) slideEl.innerHTML = slide.getAttribute('alt');
+
−
slideEl.setAttribute('role', 'tabpanel');
+
−
slideEl.setAttribute('aria-hidden', 'true');
+
−
 
+
−
slideEl.style.cssText += '-webkit-transition-duration:' + this.settings.transitionDuration + 'ms;-moz-transition-duration:' + this.settings.transitionDuration + 'ms;-o-transition-duration:' + this.settings.transitionDuration + 'ms;transition-duration:' + this.settings.transitionDuration + 'ms;';
+
−
 
+
−
sliderEl.appendChild(slideEl);
+
−
validSlides.push(slideEl);
+
−
}
+
−
}.bind(this));
+
−
 
+
−
var slides = validSlides;
+
−
if (slides.length <= 1) {
+
−
sliderEl.innerHTML = '';
+
−
Array.prototype.forEach.call(origChildren, function(child, i) {
+
−
sliderEl.appendChild(child);
+
−
});
+
−
return null;
+
−
}
+
−
 
+
−
// Create navigation
+
−
if (!this.settings.disableNav) {
+
−
var previousNav, nextNav;
+
−
if (this.settings.previousNavSelector) {
+
−
previousNav = document.querySelector(this.settings.previousNavSelector);
+
−
} else {
+
−
previousNav = document.createElement('a');
+
−
sliderEl.appendChild(previousNav);
+
−
}
+
−
if (this.settings.nextNavSelector) {
+
−
nextNav = document.querySelector(this.settings.nextNavSelector);
+
−
} else {
+
−
nextNav = document.createElement('a');
+
−
sliderEl.appendChild(nextNav);
+
−
}
+
−
 
+
−
_addClass(previousNav, this.settings.classes.previousNav);
+
−
_addClass(nextNav, this.settings.classes.nextNav);
+
−
_addEvent(previousNav, 'click', function() {
+
−
if (_hasClass(this._attributes.container, this.settings.classes.animating)) return false;
+
−
this.stop();
+
−
this.previousSlide();
+
−
}.bind(this));
+
−
_addEvent(nextNav, 'click', function() {
+
−
if (_hasClass(this._attributes.container, this.settings.classes.animating)) return false;
+
−
this.stop();
+
−
this.nextSlide();
+
−
}.bind(this));
+
−
 
+
−
// Touch Navigation
+
−
if (('ontouchstart' in window) || _and_f(window.DocumentTouch , document instanceof DocumentTouch)) {
+
−
this.settings.effect = 'slide';
+
−
previousNav.style.display = 'none';
+
−
nextNav.style.display = 'none';
+
−
_addClass(sliderEl, this.settings.classes.touchEnabled);
+
−
 
+
−
_addEvent(sliderEl, 'touchstart', _touch.start.bind(this), false);
+
−
_addEvent(sliderEl, 'touchmove', _touch.move.bind(this), false);
+
−
_addEvent(sliderEl, 'touchend', _touch.end.bind(this), false);
+
−
}
+
−
 
+
−
// Keyboard Navigation
+
−
if (this.settings.keyboardNav) {
+
−
_addEvent(document, 'keyup', function(e) {
+
−
e = e || window.event;
+
−
var button = (typeof e.which == 'number') ? e.which : e.keyCode;
+
−
if (button == 37) {
+
−
if (_hasClass(this._attributes.container, this.settings.classes.animating)) return false;
+
−
this.stop();
+
−
this.previousSlide();
+
−
} else if (button == 39) {
+
−
if (_hasClass(this._attributes.container, this.settings.classes.animating)) return false;
+
−
this.stop();
+
−
this.nextSlide();
+
−
}
+
−
}.bind(this));
+
−
}
+
−
}
+
−
 
+
−
// Create internal attributes
+
−
this._attributes = {
+
−
container: sliderEl,
+
−
slides: slides,
+
−
previousSlide: typeof slides[slides.length - 1] !== 'undefined' ? slides[slides.length - 1] : slides[0],
+
−
currentSlide: slides[0],
+
−
nextSlide: typeof slides[1] !== 'undefined' ? slides[1] : slides[0],
+
−
timerId: 0,
+
−
origChildren: origChildren, // Used in destroy()
+
−
aspectWidth: 0,
+
−
aspectHeight: 0
+
−
};
+
−
 
+
−
// Set height
+
−
if (_isInteger(this.settings.height)) {
+
−
this._attributes.container.style.height = this.settings.height + 'px';
+
−
} else {
+
−
if (_isInteger(this.settings.initialHeight)) {
+
−
this._attributes.container.style.height = this.settings.initialHeight + 'px';
+
−
}
+
−
 
+
−
// If aspect ratio parse and store
+
−
if (this.settings.height.indexOf(':') > -1) {
+
−
var aspectRatioParts = this.settings.height.split(':');
+
−
if (_and_f(_and_f(aspectRatioParts.length == 2 , _isInteger(parseInt(aspectRatioParts[0], 10))) , _isInteger(parseInt(aspectRatioParts[1], 10)))) {
+
−
this._attributes.aspectWidth = parseInt(aspectRatioParts[0], 10);
+
−
this._attributes.aspectHeight = parseInt(aspectRatioParts[1], 10);
+
−
}
+
−
}
+
−
 
+
−
_addEvent(window, 'resize', function() {
+
−
_setContainerHeight(this, false);
+
−
}.bind(this));
+
−
}
+
−
 
+
−
// Add classes
+
−
_addClass(sliderEl, this.settings.classes.container);
+
−
_addClass(sliderEl, 'iis-effect-' + this.settings.effect);
+
−
Array.prototype.forEach.call(this._attributes.slides, function(slide, i) {
+
−
_addClass(slide, this.settings.classes.slide);
+
−
}.bind(this));
+
−
_addClass(this._attributes.previousSlide, this.settings.classes.previousSlide);
+
−
_addClass(this._attributes.currentSlide, this.settings.classes.currentSlide);
+
−
_addClass(this._attributes.nextSlide, this.settings.classes.nextSlide);
+
−
 
+
−
// ARIA
+
−
this._attributes.currentSlide.setAttribute('aria-hidden', 'false');
+
−
 
+
−
// Load first image
+
−
_loadImg(this._attributes.currentSlide, (function() {
+
−
this.settings.onInit.apply(this);
+
−
_setContainerHeight(this, false);
+
−
}).bind(this));
+
−
// Preload next images
+
−
_loadImg(this._attributes.previousSlide);
+
−
_loadImg(this._attributes.nextSlide);
+
−
};
+
−
 
+
−
Slider.prototype.get = function(attribute) {
+
−
if (!this._attributes) return null;
+
−
if (this._attributes.hasOwnProperty(attribute)) {
+
−
return this._attributes[attribute];
+
−
}
+
−
};
+
−
 
+
−
Slider.prototype.set = function(attribute, value) {
+
−
if (!this._attributes) return null;
+
−
return (this._attributes[attribute] = value);
+
−
};
+
−
 
+
−
Slider.prototype.start = function() {
+
−
if (!this._attributes) return;
+
−
this._attributes.timerId = setInterval(this.nextSlide.bind(this), this.settings.interval);
+
−
this.settings.onStart.apply(this);
+
−
 
+
−
// Stop if window blur
+
−
window.onblur = function() {
+
−
this.stop();
+
−
}.bind(this);
+
−
};
+
−
 
+
−
Slider.prototype.stop = function() {
+
−
if (!this._attributes) return;
+
−
clearInterval(this._attributes.timerId);
+
−
this._attributes.timerId = 0;
+
−
this.settings.onStop.apply(this);
+
−
};
+
−
 
+
−
Slider.prototype.previousSlide = function() {
+
−
this.settings.beforeChange.apply(this);
+
−
_removeClass(this._attributes.previousSlide, this.settings.classes.previousSlide);
+
−
_removeClass(this._attributes.currentSlide, this.settings.classes.currentSlide);
+
−
_removeClass(this._attributes.nextSlide, this.settings.classes.nextSlide);
+
−
this._attributes.currentSlide.setAttribute('aria-hidden', 'true');
+
−
 
+
−
var slides = this._attributes.slides,
+
−
index = slides.indexOf(this._attributes.currentSlide);
+
−
this._attributes.nextSlide = this._attributes.currentSlide;
+
−
this._attributes.previousSlide = slides[index - 2];
+
−
this._attributes.currentSlide = slides[index - 1];
+
−
if (_and_f(typeof this._attributes.currentSlide === 'undefined' ,
+
−
typeof this._attributes.previousSlide === 'undefined')) {
+
−
this._attributes.currentSlide = slides[slides.length - 1];
+
−
this._attributes.previousSlide = slides[slides.length - 2];
+
−
} else {
+
−
if (typeof this._attributes.previousSlide === 'undefined') {
+
−
this._attributes.previousSlide = slides[slides.length - 1];
+
−
}
+
−
}
+
−
 
+
−
// Preload next image
+
−
_loadImg(this._attributes.previousSlide);
+
−
 
+
−
_addClass(this._attributes.previousSlide, this.settings.classes.previousSlide);
+
−
_addClass(this._attributes.currentSlide, this.settings.classes.currentSlide);
+
−
_addClass(this._attributes.nextSlide, this.settings.classes.nextSlide);
+
−
this._attributes.currentSlide.setAttribute('aria-hidden', 'false');
+
−
 
+
−
_addClass(this._attributes.container, this.settings.classes.directionPrevious);
+
−
_requestTimeout(function() {
+
−
_removeClass(this._attributes.container, this.settings.classes.directionPrevious);
+
−
}.bind(this), this.settings.transitionDuration);
+
−
 
+
−
if (this.settings.transitionDuration) {
+
−
_addClass(this._attributes.container, this.settings.classes.animating);
+
−
_requestTimeout(function() {
+
−
_removeClass(this._attributes.container, this.settings.classes.animating);
+
−
}.bind(this), this.settings.transitionDuration);
+
−
}
+
−
 
+
−
_setContainerHeight(this);
+
−
this.settings.afterChange.apply(this);
+
−
};
+
−
 
+
−
Slider.prototype.nextSlide = function() {
+
−
this.settings.beforeChange.apply(this);
+
−
_removeClass(this._attributes.previousSlide, this.settings.classes.previousSlide);
+
−
_removeClass(this._attributes.currentSlide, this.settings.classes.currentSlide);
+
−
_removeClass(this._attributes.nextSlide, this.settings.classes.nextSlide);
+
−
this._attributes.currentSlide.setAttribute('aria-hidden', 'true');
+
−
 
+
−
var slides = this._attributes.slides,
+
−
index = slides.indexOf(this._attributes.currentSlide);
+
−
this._attributes.previousSlide = this._attributes.currentSlide;
+
−
this._attributes.currentSlide = slides[index + 1];
+
−
this._attributes.nextSlide = slides[index + 2];
+
−
if (_and_f(typeof this._attributes.currentSlide === 'undefined' ,
+
−
typeof this._attributes.nextSlide === 'undefined')) {
+
−
this._attributes.currentSlide = slides[0];
+
−
this._attributes.nextSlide = slides[1];
+
−
} else {
+
−
if (typeof this._attributes.nextSlide === 'undefined') {
+
−
this._attributes.nextSlide = slides[0];
+
−
}
+
−
}
+
−
 
+
−
// Preload next image
+
−
_loadImg(this._attributes.nextSlide);
+
−
 
+
−
_addClass(this._attributes.previousSlide, this.settings.classes.previousSlide);
+
−
_addClass(this._attributes.currentSlide, this.settings.classes.currentSlide);
+
−
_addClass(this._attributes.nextSlide, this.settings.classes.nextSlide);
+
−
this._attributes.currentSlide.setAttribute('aria-hidden', 'false');
+
−
 
+
−
_addClass(this._attributes.container, this.settings.classes.directionNext);
+
−
_requestTimeout(function() {
+
−
_removeClass(this._attributes.container, this.settings.classes.directionNext);
+
−
}.bind(this), this.settings.transitionDuration);
+
−
 
+
−
if (this.settings.transitionDuration) {
+
−
_addClass(this._attributes.container, this.settings.classes.animating);
+
−
_requestTimeout(function() {
+
−
_removeClass(this._attributes.container, this.settings.classes.animating);
+
−
}.bind(this), this.settings.transitionDuration);
+
−
}
+
−
 
+
−
_setContainerHeight(this);
+
−
this.settings.afterChange.apply(this);
+
−
};
+
−
 
+
−
Slider.prototype.gotoSlide = function(index) {
+
−
this.settings.beforeChange.apply(this);
+
−
this.stop();
+
−
 
+
−
_removeClass(this._attributes.previousSlide, this.settings.classes.previousSlide);
+
−
_removeClass(this._attributes.currentSlide, this.settings.classes.currentSlide);
+
−
_removeClass(this._attributes.nextSlide, this.settings.classes.nextSlide);
+
−
this._attributes.currentSlide.setAttribute('aria-hidden', 'true');
+
−
 
+
−
index--; // Index should be 1-indexed
+
−
var slides = this._attributes.slides,
+
−
oldIndex = slides.indexOf(this._attributes.currentSlide);
+
−
this._attributes.previousSlide = slides[index - 1];
+
−
this._attributes.currentSlide = slides[index];
+
−
this._attributes.nextSlide = slides[index + 1];
+
−
if (typeof this._attributes.previousSlide === 'undefined') {
+
−
this._attributes.previousSlide = slides[slides.length - 1];
+
−
}
+
−
if (typeof this._attributes.nextSlide === 'undefined') {
+
−
this._attributes.nextSlide = slides[0];
+
−
}
+
−
 
+
−
// Load images
+
−
_loadImg(this._attributes.previousSlide);
+
−
_loadImg(this._attributes.currentSlide);
+
−
_loadImg(this._attributes.nextSlide);
+
−
 
+
−
_addClass(this._attributes.previousSlide, this.settings.classes.previousSlide);
+
−
_addClass(this._attributes.currentSlide, this.settings.classes.currentSlide);
+
−
_addClass(this._attributes.nextSlide, this.settings.classes.nextSlide);
+
−
this._attributes.currentSlide.setAttribute('aria-hidden', 'false');
+
−
 
+
−
if (index < oldIndex) {
+
−
_addClass(this._attributes.container, this.settings.classes.directionPrevious);
+
−
_requestTimeout(function() {
+
−
_removeClass(this._attributes.container, this.settings.classes.directionPrevious);
+
−
}.bind(this), this.settings.transitionDuration);
+
−
} else {
+
−
_addClass(this._attributes.container, this.settings.classes.directionNext);
+
−
_requestTimeout(function() {
+
−
_removeClass(this._attributes.container, this.settings.classes.directionNext);
+
−
}.bind(this), this.settings.transitionDuration);
+
−
}
+
−
 
+
−
if (this.settings.transitionDuration) {
+
−
_addClass(this._attributes.container, this.settings.classes.animating);
+
−
_requestTimeout(function() {
+
−
_removeClass(this._attributes.container, this.settings.classes.animating);
+
−
}.bind(this), this.settings.transitionDuration);
+
−
}
+
−
 
+
−
_setContainerHeight(this);
+
−
this.settings.afterChange.apply(this);
+
−
};
+
−
 
+
−
Slider.prototype.destroy = function() {
+
−
clearInterval(this._attributes.timerId);
+
−
this._attributes.timerId = 0;
+
−
 
+
−
this._attributes.container.innerHTML = '';
+
−
Array.prototype.forEach.call(this._attributes.origChildren, function(child, i) {
+
−
this._attributes.container.appendChild(child);
+
−
}.bind(this));
+
−
 
+
−
_removeClass(this._attributes.container, this.settings.classes.container);
+
−
_removeClass(this._attributes.container, 'iis-effect-' + this.settings.effect);
+
−
this._attributes.container.style.height = '';
+
−
 
+
−
this.settings.onDestroy.apply(this);
+
−
};
+
−
 
+
−
return {
+
−
_hasClass: _hasClass,
+
−
_addClass: _addClass,
+
−
_removeClass: _removeClass,
+
−
Slider: Slider
+
−
};
+
  
−
})();
+
<div class="ec--p"><strong>Figure 2.</strong> Phase plane plot of the molecular species of CBD cipA-BMP2 with IPTG=0.1 mM as saturating concentration. The stable  equilibrium point is at 2.21 nM and 172.69 nM for [CB]mRNA and [CB], respectively. </div>
−
var div = document.getElementById("textDiv");  
+
<div class="ec--p"><strong>          </strong><strong><u>Expression at different IPTG inducer concentrations</u></strong><strong><u> </u></strong><br>
−
    div.textContent = "my text";  
+
  Different values of [LacI]act cause a different effect in the mathematical model for expression of [CB]mRNA and [CB]. Figure 3 and Figure 4 show the  concentrations of [CB]mRNA and [CB], respectively, as functions of time with a time step size Dt=0.1/8. It is worth to note that the higher IPTG dosage  the higher [CB]mRNA and [CB] until the saturating level of IPTG = 0.1 mM.</div>
−
    var text = div.textContent;
+
<div class="ec--p">
−
</script>
+
<div>
 +
  <div class="ec--p">RNA</div>
 
 
−
<!-->Captions Extension v1.0.1<!-->
+
<br><center>
−
<script>
+
<img src="https://static.igem.org/mediawiki/2018/0/09/T--Ecuador--RNA.jpg"/>
−
/*
+
</center>
−
  * Ideal Image Slider: Captions Extension v1.0.1
+
</div>
−
*
+
</div>
−
* By Gilbert Pellegrom
+
<div class="ec--p"><strong>Figure 3.</strong> CBD cipA-BMP2 mRNA concentration as function of time. The concentration is dependent of levels of  IPTG inducer until the saturating  concentration (IPTG=0.1 mM). <br>
−
* http://gilbert.pellegrom.me
+
<div>
−
*
+
  <div class="ec--p">CB protein</div>
−
* Copyright (C) 2014 Dev7studios
+
<br><center>
−
* https://raw.githubusercontent.com/gilbitron/Ideal-Image-Slider/master/LICENSE
+
<img src="https://static.igem.org/mediawiki/2018/9/9e/T--Ecuador--CB_protein.jpg"/>
−
*/
+
</center>
 +
</div>
 +
&#160;<a name="IND11"></a>
 +
</div>
  
−
(function(IIS) {
+
<div class="ec--p"><strong>Figure 4.</strong> CBD cipA-BMP2 protein concentration  as function of time. The concentration is dependent of the IPTG  inducer until the saturating level (IPTG=0.1 mM).</div>
−
"use strict";
+
<div class="ec--p">&#160;</div>
−
 
+
<div class="ec--h2">CONCLUSIONS</div>
−
IIS.Slider.prototype.addCaptions = function() {
+
<div class="ec--p">The present IPTG-inducible mathematical model,  where a fusion protein CBD cipA-BMP2 was cloned in psb1c3, can be analyzed in  two stages. First, the concentration of the IPTG inducer added to the culture  medium interacts with the repressor protein LacI following the Hill equation. Then, the expression of CBD cipA-BMP2 becomes relieved, and at saturating  concentrations of IPTG ≥ 0.1 mM it reaches the highest value (CBD  cipA-BMP2 protein = 172.69nM, CBD cipA-BMP2 mRNA=2.21 nM).</div><br>
−
IIS._addClass(this._attributes.container, 'iis-has-captions');
+
<div class="ec--p">
−
 
+
The IPTG concentration inside E. coli is 94,845% of the total IPTG added to the culture  medium. Moreover, the phase line analysis of the ODE representing the IPTG  concentration inside <em>E</em><em>. </em><em>coli</em> as function of time showed that the equilibrium point  is stable.</div>
−
Array.prototype.forEach.call(this._attributes.slides, function(slide, i) {
+
  The linearization of the mathematical model revealed  an stable equilibrium point for the expression of CBD cipA-BMP2 because two  negative igenvalues,</div>
−
var caption = document.createElement('div');
+
<div class="ec--p">&#160;</div>
−
IIS._addClass(caption, 'iis-caption');
+
<div class="ec--p">&#160;</div>
−
 
+
<div class="ec--h2">REFERENCES</div>
−
var captionContent = '';
+
<div class="ec--p">
−
if (slide.getAttribute('title')) {
+
  1. Oehler, S. (2009). Feedback Regulation of Lac Repressor Expression in <em>Escherichia coli</em>. Journal of Bacteriology, 191(16), 5301–5303.  http://doi.org/10.1128/JB.00427-09<br>
−
captionContent += '<div class="iis-caption-title">' + slide.getAttribute('title') + '</div>';
+
  2. Ukkonen, K.  Vasala, A. (2015). Protein expression by IPTG autoinduction in EnPresso  B:Protocol with minimal manual work and superior yields compared to other  media.BioSilta. Retrieved on june 24th, 2018 from  https://bioscience.co.uk/userles/pdf/Application%20Note%20-%20Protein%20expression%20by%20IPTG%20autoinduction%20in%20EnPresso%20B.pdf.<br>
−
}
+
  3. Team TUDelft. (2009).Bacterial Relay Race.  International Genetically Enginereed Machines. Retrieved on june 25th, 2018  from https://2009.igem.org/Team:TUDelft.</div>
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<div class="ec--p">4. Semsey, S., Jaured, L., Csiszovszki, Z.,  Erdssy, J., Stger, V., Hansen, S. Krishna, S. (2014).The effect of LacI  autoregulation on the performanceof the lactose utilization system in <em>Escherichia coli</em>. <em>Nucleic Acids Research</em>,41 (13),6381?6390.https://academic.oup.com/nar/article/41/13/6381/1120421.</div>
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<div class="ec--p">5.  University of California Berkeley.(2006).Berkeley. International  Genetically Enginereed Machines.Retrieved on july 14th, 2018 from  https://2006.igem.org/wiki/index.php/Berkeley<br>
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  6. Ozbudak, E., Thattai, M., Lim, H., Shraiman,  B. Van Oudenaarden, A. (2004).Multistability in the lactose utilization network  of <em>Escherichia coli</em>. Nature, 427  (1476-4687), 737?740.https://www.nature.com/articles/nature02298.</div>
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<div class="ec--p">8. Moulton, G. (2014). Fed-Batch Fermentation A  Practical Guide to Scalable Recombinant Protein Production in Escherichia coli. Retrieved from <a href="https://books.google.com.ec/books?id=MTpYc3fAyICpg=20lpg=PA20dq=doubling+time+recombinant+e+coli+30+minutessource=ots=97TxFmAXwsig=W3OJJYLqLEF5Z48fXRfVTPqPP4hl=essa=Xved=ahUKEwi505aivqTcAhVSuVkKHVaDTgQ6AEwCHoECAgQAQv=onepageq=20-30">Google Books</a>.</div>
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<div class="ec--p">10. Hovgaard, L., Frokjaer, S. van de Weert, M.  (2013).Pharmaceutical Formulation Development of Peptides and Proteins. Second  Edition. Retrieved from <a href="https://books.google.com.ec/books?id=MTpYc3fAyICpg=PA20lpg=20dq=doubling+time+recombinant+e+coli+30+minutessource_blots=p97TxFmAXwsig=W3OJJYLqLEF5Z48fXRfVTPqPP4hl=essa=Xved=ahUKEwi505aivqTcAhVSuVkKHVaDTgQ6AEwCHoECAgQAQv=onepageq=20-30">Google Books</a>. </div>
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−
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<div class="ec--p">13. Team PKU  Beijing.(2009).PKU IGEM . International Genetically Enginereed Machines.  Retrieved on july 16th, 2018 from://2009.igem.org/Team:PKU  Beijing/Modeling/Parameters</div>
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                  <div class="ec--p">The main goal of our work is to develop a functionalized cellulose-based biomaterial for bone and cartilage regeneration in order to allow a faster injuries recovery time and overcome remaining challenges in repairing these connective tissues. In biomedicine, emergent strategies have focused the use biomaterials loaded with drugs.1-3 We aimed to use bacterial cellulose, a biocompatible biomaterial, as scaffold for the delivery of the human bone morphogenetic protein 2 (BMP2). It is worth to note that the diffusion of a drug far of the action site can become ectopic tissue formation, representing a serious problem. Therefore, we focused to attach the BMP2 by the use of a cellulose binding domain (CBD). We choose the CBD of the scaffolding protein of C. thermocellum (CBD cipA) because the higher affinity compared to other CBDs, reported by the Team Imperial_2014. Moreover, in an effort for a longer broad application of a functionalized bacterial cellulose, such as wound healing, we also fused the CBD cipA with an elastin like polypeptide (ELP_C5) derived from the ELP- [V-150].</div>
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Latest revision as of 22:53, 19 November 2018

iGEM ECUADOR
C-lastin, Interlab

MATHEMATICAL MODELING

Index

INTRODUCTION
This is an IPTG-inducible model for the expression of the fusion protein CBD cipA-BMP2 under the control of Plac promoter and cloned in psb1c3. The vector does not contain the ORF of LacI and thus the LacI repressor protein concentration is that in E. coli strains (10nM per cell).1
The model consists of systems of differential equations that were solved in Python using Spyder 3.6 (Anaconda).
LIST OF VARIABLES AND CONSTANTS
Variable/Constant
Definition
Unit/Value
[IPTG] TOTAL
Total IPTG concentration in the medium
nM
[IPTG]ext
IPTG concentration outside E. coli
nM
[IPTG]int
IPTG concentration inside E. coli
nM
[IPTG]TOTAL
Total LacI concentration in E. coli
nM
[LacI]act
Active LacI concentration in E. coli
nM
[CB]mRNA
CBD-BMP2 mRNA concentration in E. coli
nM
[CB]
CBD-BMP2 protein concentration in E. coli
nM
δ[CB]
Degradation rate of CBD-BMP2 mRNA
min-1
β[CB]
Translational rate of CBD-BMP2 protein
min-1
σ[CB]
Degradation rate of CBD-BMP2 protein
min-1
t
time
min
α[CB]
Transcriptional leakage of Plac promoter
%
kPlac
Maximum transcription rate of Plac promoter
0.5 nM min-1
kIPTGupt
Rate constant of IPTG uptake
0.92 min-1
kIPTGout
Rate constant of IPTG output
0.05 min-1
KIPTG
Michaelis constant of IPTG-LacI binding
600 nM
hIPTG
Hill coefficient of IPTG-LacI binding
2
HLacI
Hill coefficient of LacI-Plac promoter binding
2
IPTG-INDUCIBLE MODEL FOR CBD CIPA-BMP2 PROTEIN EXPRESSION IN E. coli
Entry of IPTG into E. coli
Mimicking lactose, IPTG is a chemical widely used in scientific research because it cannot be metabolized. IPGT induces the expression of genes under the control of Plac promoter.
IPTG enters into E. coli cells in a concentration dependent manner. This uptake is mediated by lactose permease and passive diffusion at low and high concentrations respectively.2 The IPTG uptake through passive diffusion can be described with the law of mass action expressing the balance between IPTG concentration outside (IPTGext) and inside (IPTGint) of E. coli :

Eq 1.
The first term on the right side of Eq 1 represents the forward rate where kIPTGupt is the rate constant of IPTG uptake (0.92 min-1)3 while the second term has negative sign because it represents the backward rate where kIPTGout is the rate constant of IPTG output (0.05 min-1).3 Because of [IPTG]ext = [IPTG]TOTAL - [IPTG]int, it can be replaced in equation 1 in order to have IPTGint as the unique independent variable:

Eq 2.
The LacI-IPTG interaction is assumed to be so fast and when the IPTG concentration largely exceeds that of lacI. The LacI active ([LacI]act), i.e that unbounded to IPTG, can be described with the Hill repression function.4,2


Eq 3.
Equation 3 (Eq 3) describes the amount of unbounded LacI that actively repress the expression of a protein driven by the Plac promoter; the expression of CBD cipA-BMP2 in the present study. [LacI]TOTAL is the concentration of LacI inside E. coli, KIPTG is the Michaelis constant of IPTG-LacI binding (6000 M) 5 and hIPTG is the associated Hill coefficient (2).3,6
 
CBD cipA-BMP2 EXPRESSION
CBD cipA-BMP2 mRNA
The CBD cipA-BMP2 mRNA concentration ([CB]mRNA) at time t can be described as follows:


Eq 4.
The first term on the right side of the equation 2.6 represents the synthesis of mRNA. kPlac is the maximum transcriptional rate corresponding to the Plac promoter (0.5 nM min-1).3 αCEB+(1-αCEB) is the leakiness factor where αCEB is the transcriptional leakage of Plac promoter. is the repressing Hill function of Plac promoter where KLacI is the Michaelis constant of LacI-Plac promoter binding (6000 M), 3 and hLacI is the associated Hill coefficient(2).3 The second term represents the degradation of the [CB]mRNA where δ[CB] is the degradation rate.3,6,7
Because there is not constitutive expression of LacI protein from the plasmid cloned in E. coli carrying the CBD cipA-BMP2 construct and based on our preliminary measurements of total protein concentration using BCA method, the transcriptional leakage can be taken to be 0.8 and thus the balance for [CB]mRNA becomes:

Eq 5.
 
CBD cipA-BMP2 protein

The concentration of CBD cipA-BMP2 protein ([CB]) can be described as follows:

Eq 6.
The first term on the right side of the equation 6 represents the synthesis of [CB] where β[CB] is the translational rate of [CB]. The second term represents the degradation of [CB] where σ[CB] is the degradation rate.
KINETIC CONSTANTS
The time cell division of E. coli is function of factors such as pressure, temperature and culture medium and ranging from 20-30 min under optimal conditions. Culturing in universal common medium such as Nutrient Broth and Luria-Bertani at 35 ℃, the time cell division can be assumed to be 30 min.8,9,10
The half life of mRNAs in E. coli has been well reported by Bernstein and coworkers who determined that it depends of culture medium. In, LB 99% of mRNAs had a half-life time between 1-15 min with a mean of 5.2 min.11 Therefore, 5.2 min can be assumed as the half-life time of CBD cipA -BMP2 mRNA. Consequently, δ[CB]= 0.226 min-1.
In E. coli , the translation takes place at 12-21 amino acids per second (aa s-1).12 We choose 19 aa s-1 because the codon optimization. Because CBD cipA-BMP2 contains 292 aa, β[CB] can be taken to be 3.904 min-1.The half life of CBD cipA-BMP2 protein can be assumed to be 60 min-1, 13 consequently, σ[CB]= 0.05min-1:
RESULTS OF THE IPTG-INDUCIBLE MODEL FOR CBD cipA-BMP2 PROTEIN EXPRESSION IN E. coli
Calculation of entry of IPTG into E. coli
Figure 1 is a rate balance plot derived from Equation 1 whith both forward and backward rates as functions of the normalized [IPTG]int concentration whose value in the equilibrium (steady state) can be obtained where the two functions intersect. Analitically, this point is [IPTG]int =0.9485[IPTG]TOTAL
rate

 

Figure 1. Rate balance of IPTG diffusion through E. coli membrane. Forward and backward rates are plotted versus normalized [IPTG]int
IPTG-LacI repressor interaction
Because of IPTG is the inducer, it is important to evaluate its interaction with LacI repressor at different initial concentrations added to the system ([IPTG]TOTAL). For these values the [LacI]act can be calculated with Equation 3 (Table 1). From table 1 and figure 4, it can be deduced that a concentration of IPTG = 0.1 mM is saturating because the solutions derived from higher IPTG values converge.
Table 1. [LacI]act for different initial IPTG concentrations.
[IPTG]TOTAL (mM)
[LacI]act (nM)
0,001
9.7562
0,02
0.9095
0,03
0.4257
0.1
0.0399
1.0
0.0004


 
Calculation and validation of CBD cipA-BMP2 expression
The mathematical model for the expression of CBD cipA-BMP2 is:

Eq 7.
The stability of the system can be analyzed with the Jacobian matrix associated to the system of differential equations:
JACOBIAN

Because the two igenvalues (λ1= -0.226 y λ2 = -0.05) are negative, the equilibrium point is a stable node.
 
Time step selection and phase plane
A reasonable error less than 0.01 for both mRNA and protein concentrations was obtained with a time step Dt=0.1/8. Therefore, this Dt was considered to evaluate a phase plane plot which indicates the equilibrium points of the mathematical model. To determine the maximum concentrations of CBD cipA-BMP2 mRNA and CBD cipA-BMP2 protein, a saturating concentration of IPTG (IPTG=0.1 mM) was evaluated. This is a monostable system where the equilibrium point at the steady state (Figure 2) is 2.21 nM and 172.69nM for CBD cipA-BMP2 mRNA and CBD cipA-BMP2 protein respectively.
Plano

Figure 2. Phase plane plot of the molecular species of CBD cipA-BMP2 with IPTG=0.1 mM as saturating concentration. The stable equilibrium point is at 2.21 nM and 172.69 nM for [CB]mRNA and [CB], respectively.
Expression at different IPTG inducer concentrations
Different values of [LacI]act cause a different effect in the mathematical model for expression of [CB]mRNA and [CB]. Figure 3 and Figure 4 show the concentrations of [CB]mRNA and [CB], respectively, as functions of time with a time step size Dt=0.1/8. It is worth to note that the higher IPTG dosage the higher [CB]mRNA and [CB] until the saturating level of IPTG = 0.1 mM.
RNA

Figure 3. CBD cipA-BMP2 mRNA concentration as function of time. The concentration is dependent of levels of IPTG inducer until the saturating concentration (IPTG=0.1 mM).
CB protein

 
Figure 4. CBD cipA-BMP2 protein concentration as function of time. The concentration is dependent of the IPTG inducer until the saturating level (IPTG=0.1 mM).
 
CONCLUSIONS
The present IPTG-inducible mathematical model, where a fusion protein CBD cipA-BMP2 was cloned in psb1c3, can be analyzed in two stages. First, the concentration of the IPTG inducer added to the culture medium interacts with the repressor protein LacI following the Hill equation. Then, the expression of CBD cipA-BMP2 becomes relieved, and at saturating concentrations of IPTG ≥ 0.1 mM it reaches the highest value (CBD cipA-BMP2 protein = 172.69nM, CBD cipA-BMP2 mRNA=2.21 nM).

The IPTG concentration inside E. coli is 94,845% of the total IPTG added to the culture medium. Moreover, the phase line analysis of the ODE representing the IPTG concentration inside E. coli as function of time showed that the equilibrium point is stable.
The linearization of the mathematical model revealed an stable equilibrium point for the expression of CBD cipA-BMP2 because two negative igenvalues,
 
 
REFERENCES
1. Oehler, S. (2009). Feedback Regulation of Lac Repressor Expression in Escherichia coli. Journal of Bacteriology, 191(16), 5301–5303. http://doi.org/10.1128/JB.00427-09
2. Ukkonen, K. Vasala, A. (2015). Protein expression by IPTG autoinduction in EnPresso B:Protocol with minimal manual work and superior yields compared to other media.BioSilta. Retrieved on june 24th, 2018 from https://bioscience.co.uk/userles/pdf/Application%20Note%20-%20Protein%20expression%20by%20IPTG%20autoinduction%20in%20EnPresso%20B.pdf.
3. Team TUDelft. (2009).Bacterial Relay Race. International Genetically Enginereed Machines. Retrieved on june 25th, 2018 from https://2009.igem.org/Team:TUDelft.
4. Semsey, S., Jaured, L., Csiszovszki, Z., Erdssy, J., Stger, V., Hansen, S. Krishna, S. (2014).The effect of LacI autoregulation on the performanceof the lactose utilization system in Escherichia coli. Nucleic Acids Research,41 (13),6381?6390.https://academic.oup.com/nar/article/41/13/6381/1120421.
5. University of California Berkeley.(2006).Berkeley. International Genetically Enginereed Machines.Retrieved on july 14th, 2018 from https://2006.igem.org/wiki/index.php/Berkeley
6. Ozbudak, E., Thattai, M., Lim, H., Shraiman, B. Van Oudenaarden, A. (2004).Multistability in the lactose utilization network of Escherichia coli. Nature, 427 (1476-4687), 737?740.https://www.nature.com/articles/nature02298.
7. Michel, D. (2013). Kinetic approaches to lactose operon induction and bimodality. Journal of Theoretical Biology 325, 6275.https://www.sciencedirect.com/science/article/pii/S0022519313000659?via
8. Moulton, G. (2014). Fed-Batch Fermentation A Practical Guide to Scalable Recombinant Protein Production in Escherichia coli. Retrieved from Google Books.
9. Galli, E., Midonet, C., Paly, E. Barre, F. (2017).Pressure and Temperature Dependence of Growth and Morphology of Escherichia coli:Experiments and Stochastic Model. Plos Genetics,13(3):e1006702.https://doi.org/10.1371/journal.pgen.1006702. ://jour-nals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006702
10. Hovgaard, L., Frokjaer, S. van de Weert, M. (2013).Pharmaceutical Formulation Development of Peptides and Proteins. Second Edition. Retrieved from Google Books.
11. Bernstein, J., Khodursky, A., Lin, P., Chao, S. Cohen, S. (2002). Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two color fluorescent DNA microarrays. Proceedings of the National Academy of Sciences of the United States of America. 99 (15) 9697-9702. ://www.pnas.org/content/99/15/9697
12. Bremer, H., Dennis, P. P. (1996) Modulation of chemical composition and other parameters of the cell by growth rate. Neidhardt, et al. eds. Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd ed. chapter 97, pp. 1559, Table 3
13. Team PKU Beijing.(2009).PKU IGEM . International Genetically Enginereed Machines. Retrieved on july 16th, 2018 from://2009.igem.org/Team:PKU Beijing/Modeling/Parameters
 
The main goal of our work is to develop a functionalized cellulose-based biomaterial for bone and cartilage regeneration in order to allow a faster injuries recovery time and overcome remaining challenges in repairing these connective tissues. In biomedicine, emergent strategies have focused the use biomaterials loaded with drugs.1-3 We aimed to use bacterial cellulose, a biocompatible biomaterial, as scaffold for the delivery of the human bone morphogenetic protein 2 (BMP2). It is worth to note that the diffusion of a drug far of the action site can become ectopic tissue formation, representing a serious problem. Therefore, we focused to attach the BMP2 by the use of a cellulose binding domain (CBD). We choose the CBD of the scaffolding protein of C. thermocellum (CBD cipA) because the higher affinity compared to other CBDs, reported by the Team Imperial_2014. Moreover, in an effort for a longer broad application of a functionalized bacterial cellulose, such as wound healing, we also fused the CBD cipA with an elastin like polypeptide (ELP_C5) derived from the ELP- [V-150].
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