Team:Heidelberg/Notebook/Sensing Group/Notebook/1stweek

From 2008.igem.org

(Difference between revisions)
(→Wednesday, 08/06/2008)
(→Friday, 08/08/2008)
 
(31 intermediate revisions not shown)
Line 1: Line 1:
<html>
<html>
-
<link rel='stylesheet' href='http://igem-heidelberg.de/fileadmin/Wiki/Heidelberg2.css' type='text/css' />
+
 
-
<link rel="stylesheet" href="http://igem-heidelberg.de/fileadmin/Wiki/Menu.css" type="text/css"/>
+
 
-
<link rel="stylesheet"  href="http://igem-heidelberg.de/fileadmin/Wiki/MenuHD.css" type="text/css"/>
+
<style>
 +
h1.firstHeading { display: none; }
 +
 
 +
p {text-align: justify;}
 +
 
 +
a:link { color: #00b0e6; text-decoration: none}
 +
a:visited { color:#00b0e6; text-decoration: none}
 +
a:hover { color:#f29400; text-decoration: none}
 +
a:active { color:#f29400; text-decoration: none}
 +
 
 +
#bodyContent { padding: 10px auto; width: 910px; margin: auto; clear: none; }
 +
 
 +
table#team_members { text-align: justify; border: 0; }
 +
table#team_members h2, table#team_members h3 { clear: both; }
 +
 
 +
 
 +
/*-----------------------------------------------------------------------------------------------*/
 +
div.MenuBar ul li ul.DropDownMenu {
 +
  display: none; /* Hides all drop-down menus. */
 +
 
 +
}
 +
/*
 +
li:hover works in IE7 and FF2.
 +
a:hover works in IE6 and FF2.
 +
a:hover breaks li:hover in FF2.
 +
*/
 +
div.MenuBar ul li:hover ul.DropDownMenu li ul.SideMenu,
 +
div.MenuBar ul li a:hover ul.DropDownMenu li a ul.SideMenu {
 +
  display: none; /* Hides all side menus. */
 +
}
 +
/*------------------------------------------------------------------------------------- Menu Bar */
 +
div.MenuBar {
 +
  font: arial, helvetica, sans-serif;
 +
  height: 30px;
 +
  width: 910px;
 +
  /*width: 100%*/
 +
  margin: 0;
 +
  border-top: 0;
 +
  border-right: 0;
 +
  border-left: 0;
 +
  padding: 0;
 +
  background: black;
 +
 
 +
}
 +
div.MenuBar ul {
 +
  font: arial, helvetica, sans-serif;
 +
  text-align: center;
 +
  list-style-type: none;
 +
  margin: 0.5em auto;
 +
  border: 0;
 +
  padding: 0;
 +
  background: black;
 +
}
 +
div.MenuBar ul li {
 +
  font: arial, helvetica, sans-serif;
 +
  display: block;
 +
  padding: 0;
 +
  margin: 0;
 +
  font-size: 1.3em;
 +
  float: left;
 +
  background: black;
 +
  text-align: center;
 +
  width: 107px;
 +
  position: relative; /* Sets the positioning context for each drop-down menu. */
 +
}
 +
 
 +
div.MenuBar ul li a {
 +
  font: arial, helvetica, sans-serif;
 +
  display: block;
 +
  background: black;
 +
  height: 22px; /* Keep height + padding-top + padding-bottom sync with the menu bar height. */
 +
  color: #ffffff;
 +
  padding-top: 4px;
 +
  padding-bottom: 4px;
 +
  padding-left: 1em; /* Sets the left space between top-level items. */
 +
  padding-right: 1em; /* Sets the right space between top-level items. */
 +
  text-decoration: none;
 +
}
 +
 
 +
/*------------------------------------------------------------------------------ Drop-Down Menus */
 +
div.MenuBar ul li:hover ul.DropDownMenu,
 +
div.MenuBar ul li a:hover ul.DropDownMenu {
 +
  display: block;
 +
  width: 10em; /* Drop-down menu width.
 +
                  Use MenuTailor.css to customize. */
 +
  height: 1em;
 +
  padding: 1px; /* Sets the drop-down menu "effective border" width. */
 +
  position: absolute;
 +
  top: 23px; /* Places the drop-down menu under the menu bar.
 +
                Keep it sync with the menu bar height. */
 +
  left: 0; /* Aligns the drop-down menu to its top-level item. */
 +
  background-color: black; /* Selected item. */
 +
  color: #FFFFFF;
 +
 
 +
}
 +
div.MenuBar ul li:hover ul.DropDownMenu li a,
 +
div.MenuBar ul li a:hover ul.DropDownMenu li a {
 +
  width: 10em; /* Keep it sync with the drop-down menu width.
 +
                            Use MenuTailor.css to customize. */
 +
  height: 1em;
 +
  padding-left: 0;
 +
  padding-right: 0;
 +
  background-color: black; /* Selected item. */
 +
  color: #FFFFFF;
 +
}
 +
ul.DropDownMenu li a span {
 +
  display: block;
 +
  padding-left: 0.75em; /* Sets the left space of each drop-down menu item. */
 +
  padding-right: 0.25em; /* Sets the right space of each drop-down menu item. */
 +
  text-align: right; /* Aligns the >> symbol to the right. */
 +
}
 +
ul.DropDownMenu li a span span {
 +
  float: left; /* Aligns the text (back) to the left. */
 +
  font: 12px arial, helvetica, sans-serif; /* Required for IE55. */
 +
  height: 20px;
 +
  color: #FFFFFF;
 +
}
 +
/*----------------------------------------------------------------------------------- Side Menus */
 +
div.MenuBar ul li:hover ul.DropDownMenu li:hover ul.SideMenu,
 +
div.MenuBar ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu {
 +
  display: block;
 +
  width: 11em; /* Side menu width.
 +
                  Use MenuTailor.css to customize. */
 +
  padding: 1px; /* Sets the side menu "effective border" width. */
 +
  position: absolute;
 +
  top: -1px; /* Aligns the side menu to its drop-down menu item.
 +
                Keep it sync with the side menu "effective border" width. */
 +
  left: 13em; /* Places the side menu to the right of the drop-down menu.
 +
                            Keep it sync with the drop-down menu width.
 +
                            Use MenuTailor.css to customize. */
 +
}
 +
div.MenuBar ul li:hover ul.DropDownMenu li:hover ul.SideMenu li a,
 +
div.MenuBar ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu li a {
 +
  width: 11em; /* Keep it sync with the side menu width.
 +
                            Use MenuTailor.css to customize. */
 +
  font: 12px arial, helvetica, sans-serif; /* Required for IE55. */
 +
  left: 13em; /* Places the side menu to the right of the drop-down menu.
 +
                            Keep it sync with the drop-down menu width.
 +
                            Use MenuTailor.css to customize. */
 +
}
 +
div.MenuBar ul li ul.DropDownMenu li ul.SideMenu li a span {
 +
  padding-left: 1.5em; /* Sets the left space of each side menu item. */
 +
  padding-right: 0.5em; /* Sets the right space of each side menu item. */
 +
  text-align: left;
 +
  font: 12px arial, helvetica, sans-serif; /* Required for IE55. */
 +
  left: 13em; /* Places the side menu to the right of the drop-down menu.
 +
                            Keep it sync with the drop-down menu width.
 +
                            Use MenuTailor.css to customize. */
 +
}
 +
/*----------------------------------------------------------------------------- Browser Specific */
 +
* html div.MenuBar ul li a {
 +
  float: left; /* Required for IE55 and IE6.
 +
                            Breaks O9.
 +
                            Hidden (* html) from non-IE browsers. */
 +
}
 +
* html ul.DropDownMenu li a:hover {
 +
  cursor: hand; /* Required for IE55.
 +
                  Hidden (* html) from non-IE browsers. */
 +
}
 +
ul.DropDownMenu li a:hover {
 +
  cursor: pointer; /* Required for IE6 and IE7.
 +
                      Hidding it (* html) from non-IE browsers breaks IE7!
 +
}
 +
* html div.MenuBar a:hover {
 +
  text-decoration: none; /* Required for IE55 and IE6.
 +
                            Hidden (* html) from non-IE browsers. */
 +
}
 +
* html div.MenuBar ul li table,
 +
* html div.MenuBar ul li table td {
 +
  border: 0; /* Required for IE55 and IE6.
 +
                Hidden (* html) from non-IE browsers. */
 +
}
 +
/*------------------------------------------------------------------------------- Default Colors */
 +
div.MenuBar {
 +
  background-color: Menu;
 +
  border-bottom: 1px solid ButtonShadow;
 +
}
 +
div.MenuBar a {
 +
  background-color: Menu; /* Top-level unselected items. */
 +
  color: MenuText;
 +
}
 +
div.MenuBar ul li:hover a,
 +
div.MenuBar ul li a:hover {
 +
  color: #ea7f16;
 +
  background-color: Highlight; /* Top-level selected item. */
 +
  color: HighlightText;
 +
}
 +
/*...............................................................................................*/
 +
div.MenuBar ul li:hover ul.DropDownMenu,
 +
div.MenuBar ul li a:hover ul.DropDownMenu {
 +
  background-color: ButtonShadow; /* Sets the drop-down menu "effective border" color. */
 +
}
 +
div.MenuBar ul li:hover ul.DropDownMenu li a,
 +
div.MenuBar ul li a:hover ul.DropDownMenu li a {
 +
  background-color: Menu; Drop-down menu unselected items.
 +
                            Sets the drop-down menu "effective background" color. */
 +
  color: MenuText;
 +
}
 +
div.MenuBar ul li:hover ul.DropDownMenu li:hover a,
 +
div.MenuBar ul li a:hover ul.DropDownMenu li a:hover {
 +
  background-color: Highlight; /* Drop-down menu selected item. */
 +
  color: HighlightText;
 +
}
 +
/*...............................................................................................*/
 +
div.MenuBar ul li:hover ul.DropDownMenu li:hover ul.SideMenu,
 +
div.MenuBar ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu {
 +
  background-color: ButtonShadow; /* Sets the side menu "effective border" color. */
 +
}
 +
div.MenuBar ul li:hover ul.DropDownMenu li:hover ul.SideMenu li a,
 +
div.MenuBar ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu li a {
 +
  background-color: Menu; /* Side menu unselected items.
 +
                            Sets the side menu "effective background" color. */
 +
  color: MenuText;
 +
}
 +
div.MenuBar ul li:hover ul.DropDownMenu li:hover ul.SideMenu li a:hover,
 +
div.MenuBar ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu li a:hover {
 +
  background-color: Highlight; /* Side menu selected item. */
 +
  color: HighlightText;
 +
}
 +
/*-----------------------------------------------------------------------------------------------*/
 +
/*Script-Free 3-Level Menu 1.2 Tailor
 +
  www.CesarDaniel.info
 +
/*-------------------------------------------------------------------------------------- General */
 +
body {
 +
  background: white;
 +
  color: black;
 +
  margin: 0;
 +
  border: 0;
 +
  padding: 0;
 +
}
 +
 
 +
 
 +
div.MenuBar {
 +
  font: 13px arial, helvetica, sans-serif;
 +
}
 +
div.MenuBar ul {
 +
  font: 13px arial, helvetica, sans-serif; /* Required for IE55. */
 +
}
 +
/*--------------------------------------------------------------------------------------- Colors */
 +
div.MenuBar {
 +
  background-color: black; /* Selected item. */
 +
  color: #FFFFFF;
 +
  border-bottom: 1px solid ButtonShadow;
 +
}
 +
div.MenuBar a,
 +
div.MenuBar ul li:hover ul.DropDownMenu li a,
 +
div.MenuBar ul li a:hover ul.DropDownMenu li a,
 +
div.MenuBar ul li:hover ul.DropDownMenu li:hover ul.SideMenu li a,
 +
div.MenuBar ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu li a {
 +
  background-color: black; /* Selected item. */
 +
  color: #FFFFFF;
 +
}
 +
div.MenuBar ul li:hover a,
 +
div.MenuBar ul li a:hover,
 +
div.MenuBar ul li:hover ul.DropDownMenu li:hover a,
 +
div.MenuBar ul li a:hover ul.DropDownMenu li a:hover,
 +
div.MenuBar ul li:hover ul.DropDownMenu li:hover ul.SideMenu li a:hover,
 +
div.MenuBar ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu li a:hover {
 +
  background-color: #00b0e6; /* Selected item. */
 +
  color: #FFFFFF;
 +
}
 +
div.MenuBar ul li:hover ul.DropDownMenu,
 +
div.MenuBar ul li a:hover ul.DropDownMenu,
 +
div.MenuBar ul li:hover ul.DropDownMenu li:hover ul.SideMenu,
 +
div.MenuBar ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu {
 +
  background-color: ButtonShadow; /* Sets the drop-down and side menus "effective border" color. */
 +
}
 +
/*--------------------------------------------------------------------------------------- Widths */
 +
/*
 +
 
 +
/*
 +
Menu Bar 1
 +
Drop-Down Menu #2
 +
*/
 +
div.MenuBar#navi ul li:hover ul.DropDownMenu#MB1-DDM4,
 +
div.MenuBar#navi ul li a:hover ul.DropDownMenu#MB1-DDM4,
 +
div.MenuBar#navi ul li:hover ul.DropDownMenu#MB1-DDM4 li a,
 +
div.MenuBar#navi ul li a:hover ul.DropDownMenu#MB1-DDM4 li a {
 +
  width: 11em; /* Drop-down menu width. */
 +
}
 +
div.MenuBar#navi ul li:hover ul.DropDownMenu#MB1-DDM5,
 +
div.MenuBar#navi ul li a:hover ul.DropDownMenu#MB1-DDM5,
 +
div.MenuBar#navi ul li:hover ul.DropDownMenu#MB1-DDM5 li a,
 +
div.MenuBar#navi ul li a:hover ul.DropDownMenu#MB1-DDM5 li a {
 +
  width: 12em; /* Drop-down menu width. */
 +
}
 +
 
 +
/*...............................................................................................*/
 +
/*
 +
Menu Bar 1
 +
Drop-Down Menu #2
 +
Side Menu #1
 +
*/
 +
div.MenuBar#navi ul li:hover ul.DropDownMenu li:hover ul.SideMenu#MB1-DDM2-SM1,
 +
div.MenuBar#navi ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu#MB1-DDM2-SM1 {
 +
  left: 15.5em !important; /* Places the side menu to the right of the drop-down menu.
 +
                            Keep it sync with the drop-down menu width. */
 +
}
 +
div.MenuBar#navi ul li:hover ul.DropDownMenu li:hover ul.SideMenu#MB1-DDM2-SM1,
 +
div.MenuBar#navi ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu#MB1-DDM2-SM1,
 +
div.MenuBar#navi ul li:hover ul.DropDownMenu li:hover ul.SideMenu#MB1-DDM2-SM1 li a,
 +
div.MenuBar#navi ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu#MB1-DDM2-SM1 li a {
 +
  width: 10em; /* Side menu width. */
 +
}
 +
/*...............................................................................................*/
 +
/*
 +
Menu Bar 1
 +
Drop-Down Menu #2
 +
Side Menu #2
 +
*/
 +
div.MenuBar#navi ul li:hover ul.DropDownMenu li:hover ul.SideMenu#MB1-DDM2-SM2,
 +
div.MenuBar#navi ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu#MB1-DDM2-SM2 {
 +
  left: 15.5em  !important; /* Places the side menu to the right of the drop-down menu.
 +
                            Keep it sync with the drop-down menu width. */
 +
}
 +
div.MenuBar#navi ul li:hover ul.DropDownMenu li:hover ul.SideMenu#MB1-DDM2-SM2,
 +
div.MenuBar#navi ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu#MB1-DDM2-SM2,
 +
div.MenuBar#navi ul li:hover ul.DropDownMenu li:hover ul.SideMenu#MB1-DDM2-SM2 li a,
 +
div.MenuBar#navi ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu#MB1-DDM2-SM2 li a {
 +
  width: 10em; /* Side menu width. */
 +
}
 +
/*...............................................................................................*/
 +
/*
 +
Menu Bar 1
 +
Drop-Down Menu #2
 +
Side Menu #3
 +
*/
 +
div.MenuBar#navi ul li:hover ul.DropDownMenu li:hover ul.SideMenu#MB1-DDM2-SM3,
 +
div.MenuBar#navi ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu#MB1-DDM2-SM3 {
 +
  left: 15.5em  !important; /* Places the side menu to the right of the drop-down menu.
 +
                            Keep it sync with the drop-down menu width. */
 +
}
 +
div.MenuBar#navi ul li:hover ul.DropDownMenu li:hover ul.SideMenu#MB1-DDM2-SM3,
 +
div.MenuBar#navi ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu#MB1-DDM2-SM3,
 +
div.MenuBar#navi ul li:hover ul.DropDownMenu li:hover ul.SideMenu#MB1-DDM2-SM3 li a,
 +
div.MenuBar#navi ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu#MB1-DDM2-SM3 li a {
 +
  width: 10em; /* Side menu width. */
 +
}
 +
/*...............................................................................................*/
 +
 
 +
</style>
 +
 
<body>
<body>
Line 52: Line 393:
</li>
</li>
<li>
<li>
-
<a href="https://2008.igem.org/Team:Heidelberg/Chemotaxis" style="color: white">Modeling<!--[if gt IE 6]><!--></a><!--<![endif]-->
+
<a href="https://2008.igem.org/Team:Heidelberg/Modeling" style="color: white">Modeling<!--[if gt IE 6]><!--></a><!--<![endif]-->
<!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
<!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
<ul class="DropDownMenu" id="MB1-DDM3">
<ul class="DropDownMenu" id="MB1-DDM3">
Line 62: Line 403:
</li>
</li>
<li>
<li>
-
<a href="https://2008.igem.org/Team:Heidelberg/Notebook/Sensing_Group/Notebook" style="color: white">Notebook<!--[if gt IE 6]><!--></a><!--<![endif]-->
+
<a href="https://2008.igem.org/Team:Heidelberg/Notebook/Overview" style="color: white">Notebook<!--[if gt IE 6]><!--></a><!--<![endif]-->
<!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
<!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
<ul class="DropDownMenu" id="MB1-DDM5">
<ul class="DropDownMenu" id="MB1-DDM5">
Line 98: Line 439:
</li>
</li>
<li style="width: 160px">
<li style="width: 160px">
-
<a href="https://2008.igem.org/Team:Heidelberg/Project/General_information" style="color: white">Human Practice<!--[if gt IE 6]><!--></a><!--<![endif]-->
+
<a href="https://2008.igem.org/Team:Heidelberg/Human_Practice/Project_Overview" style="color: white">Human Practice<!--[if gt IE 6]><!--></a><!--<![endif]-->
<!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
<!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
<ul class="DropDownMenu" id="MB1-DDM4">
<ul class="DropDownMenu" id="MB1-DDM4">
Line 106: Line 447:
                               <li><a href="https://2008.igem.org/Team:Heidelberg/Human_Practice/Surveys"><span><span>Surveys</span></span></a></li>
                               <li><a href="https://2008.igem.org/Team:Heidelberg/Human_Practice/Surveys"><span><span>Surveys</span></span></a></li>
                               <li><a href="https://2008.igem.org/Team:Heidelberg/Human_Practice/Open_Day"><span><span>Open Day</span></span></a></li>
                               <li><a href="https://2008.igem.org/Team:Heidelberg/Human_Practice/Open_Day"><span><span>Open Day</span></span></a></li>
-
                               <li><a href="https://2008.igem.org/Team:Heidelberg/Human_Practice/Nobel_Prize"><span><span>Nobel Prize</span></span></a></li>
+
                               <li><a href="https://2008.igem.org/Team:Heidelberg/Human_Practice/Nobel_Prize"><span><span>Nobel Prize</span></span></a></li>
 +
</ul>
</ul>
<!--[if lte IE 6]></td></tr></table></a><![endif]-->
<!--[if lte IE 6]></td></tr></table></a><![endif]-->
Line 126: Line 468:
=== Preparations ===
=== Preparations ===
-
Preparations were done at the end of the week before
+
Preparations were started at the end of the week before
-
* Transformation of pDK48 and pTrc99a in ''E. coli'' DH5a (0.5 µl plasmid-DNA + 50 µl competent cells)
+
* Transformation of pDK48 and pTrc99alpha plamids in ''E. coli'' strain DH5α (0.5 µl plasmid-DNA + 50 µl competent cells)
* Glycerol-stock of ''Vibrio harveyi'' BB120, BB886, mm30, BB178, BB125
* Glycerol-stock of ''Vibrio harveyi'' BB120, BB886, mm30, BB178, BB125
-
* picked pTrc99a and pDK48 cultures and inoculated in 3 ml LB overnight
+
* pick pTrc99α and pDK48 colonies and then incubated in 3 ml LB at 37 overnight
-
* ''V. harveyi'' cultured on LB+-Agar plate
+
* ''V. harveyi'' cultured on LB plate
-
* MiniPrep of pTrc99a and pDK48 from DHha
+
* MiniPrep of pTrc99α and pDK48 from DH5α
== Tuesday, 08/05/2008 ==
== Tuesday, 08/05/2008 ==
=== Cloning of LuxP ===
=== Cloning of LuxP ===
[[Image:HD_080805-LuxP_PCR.png|thumb|150px|LuxP colony PCR]]
[[Image:HD_080805-LuxP_PCR.png|thumb|150px|LuxP colony PCR]]
-
<div style="float: right; clear:none">[[Image:HD 080805-LuxQ S PCR.png|right|thumb|200px|LuxQ, LuxS PCR]]</div>
+
<div style="float: right; clear:none;">[[Image:HD 080805-LuxQ S PCR.png|right|thumb|200px|LuxQ, LuxS PCR]]</div>
-
* PCR of LuxP from ''V. harveyi'' colony
+
 
 +
* PCR of LuxP from ''V. harveyi'' colony with the primers LuxPc and LuxPd with Taq polymerase Mastermix. 5min @ 95°C || 30s @ 95°C | 30s @ 58 °C | 2min @ 72°C || 10min @ 72°C | 4°C hold (30 cycles)
* Gel Purification of LuxP eluted in 30 µl H<sub>2</sub>O
* Gel Purification of LuxP eluted in 30 µl H<sub>2</sub>O
-
* Digestion of LuxP with SalI and NotI of pDK48 and LuxP-Gel-Purification product: 2 µl NEB-Buffer 3 + 0.5 µl SalI/NotI + 10 µl DNA + 7 µl H<sub>2</sub>O
+
* Digestion of LuxP with SalI and NotI of pDK48 and LuxP-Gel-Purification product: 2 µl NEB-Buffer 3 + 0.5 µl SalI & NotI + 10 µl DNA + 6 µl H<sub>2</sub>O
-
* Ligation with vector:insert ratio 1:3 and 1:1
+
* Ligation with vector:insert ratio 2µl:6µl  and 5µl:5µl
=== Cloning of LuxS ===
=== Cloning of LuxS ===
-
* PCR of ''V. harveyi'' genome and PCR purification
+
* PCR of ''V. harveyi'' genome with primers LuxSa and LuxSb and PCR purification 5min @ 95 °C || 30s @ 95°C | 30s @ 58 °C | 2min @ 72°C || 10min @ 72°C | 4°C hold (30 cycles) with Tag polymerase Mastermix
-
* digestion of LuxS and pTrc99a with BamHI/NcoI
+
* digestion of LuxS and pTrc99α with BamHI/NcoI (NEBuffer 3 + BSA)
-
* Ligation with vector:insert ratio 1:3 and 1:1
+
* Ligation with vector:insert ratio 2µl:6µl and 5µl:5µl
<br style="clear: both;"/>
<br style="clear: both;"/>
== Wednesday, 08/06/2008 ==
== Wednesday, 08/06/2008 ==
-
* 5 colonies of LuxQ,S,P transformation (1:1 ligation) picket and used for colony-PCR
+
* 5 colonies of LuxQ,S,P transformation (1:1 ligation) picked and analyes with colony-PCR
-
* Colony-PCR to check for insert
+
* Colony-PCR to check for insert. 5min @ 95°C || 30s @ 95°C | 30s @ 58 °C | 2min @ 72°C || 10min @ 72°C  | 4°C hold (30 cycles)
[[Image:HD 080806-LuxQ P S ColonyPCR.png|center|thumb|500px|Colony PCR of LuxQ, LuxS and LuxP]]
[[Image:HD 080806-LuxQ P S ColonyPCR.png|center|thumb|500px|Colony PCR of LuxQ, LuxS and LuxP]]
 +
* preparation of O/N cultures for Miniprep
== Thursday, 08/07/2008 ==
== Thursday, 08/07/2008 ==
 +
* Miniprep of samples Q#1-5, S#1-5, P#1-5
 +
* PCR from Minipreps to confirm inserts. Same programme as yesterday
 +
[[Image:HD 080807-LuxQ P S miniPCR.png|center|thumb|500px|PCR to confirm insert from Minipreps. LuxQ no. 3 seems to be posivite. For LuxS and LuxP all samples are positive.]]
 +
* 10 new colonies of LuxQ-plate were picked and checked via colony-PCR
 +
[[Image:HD_080807-LuxQ_ColonyPCR.png|center|thumb|500px|LuxQ colony PCR of 10 new colonies.]]
 +
* Sequencing of LuxS,P,Q positive clones at GATC
 +
Sequencing Results
 +
LuxS: correct sequence
 +
LuxP: all clones contain mutations, cloning has to be repeated
 +
LuxQ: no insert in the picked colonies
== Friday, 08/08/2008 ==
== Friday, 08/08/2008 ==
 +
* Miniprep of overnight-cultures of the picked colonies Q#6-15
 +
* In silico cloning of LuxQ, S in pTrc99α and LuxP in pDK48
 +
* Test-Digestion of LuxQ with XbaI --> positive result for Q3, 7, 9, 11, 14
 +
 +
 +
[[Team:Heidelberg/Notebook/Sensing_Group/Notebook/2ndweek | Go to 2nd week]]

Latest revision as of 14:01, 29 October 2008

Back to the overview

Contents

Monday, 08/04/2008

Preparations

Preparations were started at the end of the week before

  • Transformation of pDK48 and pTrc99alpha plamids in E. coli strain DH5α (0.5 µl plasmid-DNA + 50 µl competent cells)
  • Glycerol-stock of Vibrio harveyi BB120, BB886, mm30, BB178, BB125
  • pick pTrc99α and pDK48 colonies and then incubated in 3 ml LB at 37 overnight
  • V. harveyi cultured on LB plate
  • MiniPrep of pTrc99α and pDK48 from DH5α

Tuesday, 08/05/2008

Cloning of LuxP

LuxP colony PCR
LuxQ, LuxS PCR
  • PCR of LuxP from V. harveyi colony with the primers LuxPc and LuxPd with Taq polymerase Mastermix. 5min @ 95°C || 30s @ 95°C | 30s @ 58 °C | 2min @ 72°C || 10min @ 72°C | 4°C hold (30 cycles)
  • Gel Purification of LuxP eluted in 30 µl H2O
  • Digestion of LuxP with SalI and NotI of pDK48 and LuxP-Gel-Purification product: 2 µl NEB-Buffer 3 + 0.5 µl SalI & NotI + 10 µl DNA + 6 µl H2O
  • Ligation with vector:insert ratio 2µl:6µl and 5µl:5µl

Cloning of LuxS

  • PCR of V. harveyi genome with primers LuxSa and LuxSb and PCR purification 5min @ 95 °C || 30s @ 95°C | 30s @ 58 °C | 2min @ 72°C || 10min @ 72°C | 4°C hold (30 cycles) with Tag polymerase Mastermix
  • digestion of LuxS and pTrc99α with BamHI/NcoI (NEBuffer 3 + BSA)
  • Ligation with vector:insert ratio 2µl:6µl and 5µl:5µl


Wednesday, 08/06/2008

  • 5 colonies of LuxQ,S,P transformation (1:1 ligation) picked and analyes with colony-PCR
  • Colony-PCR to check for insert. 5min @ 95°C || 30s @ 95°C | 30s @ 58 °C | 2min @ 72°C || 10min @ 72°C | 4°C hold (30 cycles)
Colony PCR of LuxQ, LuxS and LuxP
  • preparation of O/N cultures for Miniprep

Thursday, 08/07/2008

  • Miniprep of samples Q#1-5, S#1-5, P#1-5
  • PCR from Minipreps to confirm inserts. Same programme as yesterday
PCR to confirm insert from Minipreps. LuxQ no. 3 seems to be posivite. For LuxS and LuxP all samples are positive.
  • 10 new colonies of LuxQ-plate were picked and checked via colony-PCR
LuxQ colony PCR of 10 new colonies.
  • Sequencing of LuxS,P,Q positive clones at GATC 
Sequencing Results
LuxS: correct sequence
LuxP: all clones contain mutations, cloning has to be repeated
LuxQ: no insert in the picked colonies

Friday, 08/08/2008

  • Miniprep of overnight-cultures of the picked colonies Q#6-15
  • In silico cloning of LuxQ, S in pTrc99α and LuxP in pDK48
  • Test-Digestion of LuxQ with XbaI --> positive result for Q3, 7, 9, 11, 14


Go to 2nd week

Retrieved from "http://2008.igem.org/Team:Heidelberg/Notebook/Sensing_Group/Notebook/1stweek"