Edinburgh/25 July 2008

From 2008.igem.org

(Difference between revisions)
(New page: <html> <head> <title>Edinburgh iGEM 2008</title> <script type="text/javascript"> //Drop Down Tabs Menu- Author: Dynamic Drive (http://www.dynamicdrive.com) //Created: May 16th, 07' var ta...)
 
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<html>
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<div id="header">{{Template:Team:Edinburgh/Templates/notebook-entry/header}}</div>
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<head>
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<title>Edinburgh iGEM 2008</title>
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<script type="text/javascript">
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//Drop Down Tabs Menu- Author: Dynamic Drive (http://www.dynamicdrive.com)
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//Created: May 16th, 07'
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var tabdropdown={
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:::: '''[[Edinburgh/24_July_2008|< Previous Entry]]'''
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enableiframeshim: 1, //1 or 0, for true or false
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//No need to edit beyond here////////////////////////
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== Week 6 ==
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dropmenuobj: null, ie: document.all, firefox: document.getElementById&&!document.all, previousmenuitem:null,
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=== Friday 25 July 08 ===
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currentpageurl: window.location.href.replace("http://"+window.location.hostname, "").replace(/^\//, ""), //get current page url (minus hostname, ie: http://www.dynamicdrive.com/)
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* Made maxiprep '''X4''' (pSB1A2+''crtB'' as M36; BBa_K118002) and '''X5''' (pSB1A2+''crtI'' as M42; BBa_K118003) (AH, XH)
-
var totaloffset=(offsettype=="left")? what.offsetLeft : what.offsetTop;
+
* Made ligations:
-
var parentEl=what.offsetParent;
+
** '''L19''': P12 (rbs+''dxs'') into Edinbrick1 to make pSB1A2+rbs+''dxs''
-
while (parentEl!=null){
+
** '''L20''': P15 (rbs+''appY'') into Edinbrick1 to make pSB1A2+rbs+''appY''
-
totaloffset=(offsettype=="left")? totaloffset+parentEl.offsetLeft : totaloffset+parentEl.offsetTop;
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** '''L21''': P28 (rbs+''crtB'') into Edinbrick1 to make pSB1A2+rbs+''crtB''
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parentEl=parentEl.offsetParent;
+
** '''L22''': P29 (rbs+''crtI'') into Edinbrick1 to make pSB1A2+rbs+''crtI''
-
}
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** '''L23''': P31 (''P<sub>zntA</sub>'') into Edinbrick1 to make (pSB1A2+''P<sub>zntA</sub>''). (Yan, OG)
-
return totaloffset;
+
* ''C. fimi'' Plate 48 appears to be contaminated (mix of opaque and clear colonies). The same culture was used for genomic DNA purification yesterday. This preparation is therefore inadequate for sequencing purpose but might be worth using for PCR. (AM)
-
},
+
* No growth of ''C. fimi'' on Plates 49 and 50, but ''C. fimi'' takes a relatively long time to form colonies so we should check again on Monday. (AM)
 +
* PCR '''P36''' of M43 (''glgC''-mut1,2) to excise the gene from BABEL and rectify its orientation and '''P37''' of ''crtY'' from ''P. ananatis'' (Plate 17) cell suspension - repeat of P27. (AM)
 +
** P36 and P37 run on '''Gel 25'''. P36 tentatively successful (larger than desirable smear in the region of interest), P37 failed. (AM)
 +
* Also did preparations to transfer ''crtE'' from BABEL2 vector to pSB1A2. This is necessary, because we are supposed to use Registry standard vectors for all BioBricks we make (in fact, we should even stop using pSB1A2 and move to pSB1A3). So digested the BABEL2+''crtE'' clone (that Douglas Leslie made) with EcoRI/PstI, and also Edinbrick1 - in both cases, 3μl in 20μl total volume. Ran both on a gel and excised the appropriate bands, eluted each to 10μl EB and set up a ligation ('''L24''') using 4μl of each in 10μl total volume. Ligated at 16°C. (CF)<br />
 +
<br />
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:::: '''[[Edinburgh/26_July_2008|Next Entry >]]'''
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this.dropmenuobj=document.getElementById(dropmenuID)
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this.dropmenuobj.onmouseout=function(e){tabdropdown.dynamichide(e, obj)}
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this.dropmenuobj.onclick=function(){tabdropdown.delayhidemenu(obj)}
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this.showhide(this.dropmenuobj.style, e, obj)
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this.dropmenuobj.style.top=this.dropmenuobj.y-this.clearbrowseredge(obj, "bottomedge")+obj.offsetHeight+1+"px"
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if (this.delayhide!="undefined")
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clearTimeout(this.delayhide)
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this.shimobject.style.height=this.dropmenuobj.offsetHeight+"px"
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this.shimobject.style.left=this.dropmenuobj.style.left
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this.shimobject.style.top=this.dropmenuobj.style.top
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}
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this.shimobject.style.display=(this.dropmenuobj.style.visibility=="visible")? "block" : "none"
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}
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hideshim:function(){
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if (this.enableiframeshim && typeof this.shimobject!="undefined")
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this.shimobject.style.display='none'
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},
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isSelected:function(menuurl){
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var menuurl=menuurl.replace("http://"+menuurl.hostname, "").replace(/^\//, "")
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return (tabdropdown.currentpageurl==menuurl)
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init:function(menuid, dselected){
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this.standardbody=(document.compatMode=="CSS1Compat")? document.documentElement : document.body //create reference to common "body" across doctypes
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var menuitems=document.getElementById(menuid).getElementsByTagName("a")
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for (var i=0; i<menuitems.length; i++){
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if (menuitems[i].getAttribute("rel")){
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var relvalue=menuitems[i].getAttribute("rel")
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document.getElementById(relvalue).firstlink=document.getElementById(relvalue).getElementsByTagName("a")[0]
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menuitems[i].onmouseover=function(e){
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var event=typeof e!="undefined"? e : window.event
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tabdropdown.dropit(this, event, this.getAttribute("rel"))
+
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}
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}
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if (dselected=="auto" && typeof setalready=="undefined" && this.isSelected(menuitems[i].href)){
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menuitems[i].parentNode.className+=" selected default"
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var setalready=true
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else if (parseInt(dselected)==i)
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menuitems[i].parentNode.className+=" selected default"
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}
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}
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+
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}
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</script>
+
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<style>
+
-
.ddcolortabs{
+
-
padding: 0;
+
-
width: 100%;
+
-
background: transparent;
+
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voice-family: "\"}\"";
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voice-family: inherit;
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}
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+
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.ddcolortabs ul{
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font: normal 11px Arial, Verdana, sans-serif;
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margin:0;
+
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padding:0;
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list-style:none;
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}
+
-
 
+
-
.ddcolortabs li{
+
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display:inline;
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margin:0 2px 0 0;
+
-
padding:0;
+
-
text-transform:uppercase;
+
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}
+
-
 
+
-
 
+
-
.ddcolortabs a{
+
-
float:left;
+
-
color: white;
+
-
background: black url(media/color_tabs_left.gif) no-repeat left top;
+
-
margin:0 2px 0 0;
+
-
padding:0 0 1px 3px;
+
-
text-decoration:none;
+
-
letter-spacing: 1px;
+
-
}
+
-
 
+
-
.ddcolortabs a span{
+
-
float:left;
+
-
display:block;
+
-
background: transparent url(media/color_tabs_right.gif) no-repeat right top;
+
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padding: 4px 8px 2px 7px;
+
-
}
+
-
 
+
-
.ddcolortabs a span{
+
-
float:none;
+
-
}
+
-
 
+
-
.ddcolortabs a:hover{
+
-
background-color: #591f20;
+
-
}
+
-
 
+
-
.ddcolortabs a:hover span{
+
-
background-color: #591f20;
+
-
}
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-
 
+
-
.ddcolortabs .selected a, #ddcolortabs .selected a span{ /*currently selected tab*/
+
-
background-color: #591f20;
+
-
}
+
-
 
+
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.ddcolortabsline{
+
-
clear: both;
+
-
padding: 0;
+
-
width: 100%;
+
-
height: 8px;
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-
line-height: 8px;
+
-
background: black;
+
-
border-top: 1px solid #fff; /*Remove this to remove border between bar and tabs*/
+
-
}
+
-
 
+
-
/* ######### Style for Drop Down Menu ######### */
+
-
 
+
-
.dropmenudiv_a{
+
-
position:absolute;
+
-
top: 0;
+
-
border: 1px solid black; /*THEME CHANGE HERE*/
+
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border-top-width: 8px; /*Top border width. Should match height of .ddcolortabsline above*/
+
-
border-bottom-width: 0;
+
-
font:normal 12px Arial;
+
-
line-height:18px;
+
-
z-index:100;
+
-
background-color: white;
+
-
width: 200px;
+
-
visibility: hidden;
+
-
}
+
-
 
+
-
 
+
-
.dropmenudiv_a a{
+
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width: auto;
+
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display: block;
+
-
text-indent: 5px;
+
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border-top: 0 solid #678b3f;
+
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border-bottom: 1px solid #678b3f; /*THEME CHANGE HERE*/
+
-
padding: 2px 0;
+
-
text-decoration: none;
+
-
color: black;
+
-
}
+
-
 
+
-
* html .dropmenudiv_a a{ /*IE only hack*/
+
-
width: 100%;
+
-
}
+
-
 
+
-
.dropmenudiv_a a:hover{ /*THEME CHANGE HERE*/
+
-
background-color: #8a3c3d;
+
-
color: white;
+
-
}
+
-
</style>
+
-
</head>
+
-
 
+
-
<!-- CSS for Drop Down Tabs Menu #1 -->
+
-
<link rel="stylesheet" type="text/css" href="ddcolortabs.css" />
+
-
 
+
-
<div id="colortab" class="ddcolortabs">
+
-
<ul>
+
-
<li><a href="https://2008.igem.org/Team:Edinburgh" title="Home"><span>Home</span></a></li>
+
-
<li><a href="https://2008.igem.org/Team:Edinburgh/Project" title="Project" rel="dropmenu1_a"><span>The Project</span></a></li>
+
-
<li><a href="https://2008.igem.org/Team:Edinburgh/Team" title="Team" ><span>The Team</span></a></li>
+
-
<li><a href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2008&group=Edinburgh" title="Project" rel="dropmenu1_a"><span>BioBrick Parts</span></a></li>
+
-
<li><a href="https://2008.igem.org/Team:Edinburgh/Modeling" title="Modelling" rel="dropmenu2_a"><span>Modelling</span></a></li>
+
-
<li><a href="https://2008.igem.org/Team:Edinburgh/Notebook" title="Notebook"><span>Notebook</span></a></li>
+
-
</ul>
+
-
</div>
+
-
<div class="ddcolortabsline">&nbsp;</div>
+
-
<div id="dropmenu1_a" class="dropmenudiv_a">
+
-
<a href="https://2008.igem.org/Team:Edinburgh/Team">Overview</a>
+
-
<a href="https://2008.igem.org/Team:Edinburgh/Team">Step1</a>
+
-
<a href="https://2008.igem.org/Team:Edinburgh/Team">Step2</a>
+
-
</div>
+
-
<script type="text/javascript">
+
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//SYNTAX: tabdropdown.init("menu_id", [integer OR "auto"])
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tabdropdown.init("colortab", 3)
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</script>
+
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</html>
+
-
 
+
-
=== Week 6 ===
+
-
==== Friday 25 July 08 ====
+
-
 
+
-
* Made maxiprep '''X4''' (pSB1A2-''crtB'' as M36; BBa_K118002) and '''X5''' (pSB1A2-''crtI'' as M42; BBa_K118003) (AH, XH)
+
-
* Ligation of P29 into Edinbrick1 to make '''L22''' (pSB1A2+rbs+''crtI''). (Yan, OG)
+
-
* Ligation of P28 into Edinbrick1 to make '''L21''' (pSB1A2+rbs+''crtB''). (Yan, OG)
+
-
* Ligation of P12 into Edinbrick1 to make '''L19''' (pSB1A2+rbs+''dxs''). (Yan, OG)
+
-
* Ligation of P15 into Edinbrick1 to make '''L20''' (pSB1A2+rbs+''appY''). (Yan, OG)
+
-
* Ligation of P31 into Edinbrick1 to make '''L23''' (pSB1A2+pZntA). (Yan, OG)
+
-
* ''C. fimi'' Plate 48 appears to be contaminated (mix of opaque and clear colonies). The same culture was used for genomic DNA purification yesterday ~ this preparation is therefore inadequate for sequencing purpose but might be worth using for PCR. (AM)
+
-
* No growth of ''C. fimi'' on Plates 49 and 50, but ''C. fimi'' takes a relatively long time to form colonies so we should check again on Monday. (AM)
+
-
* PCR '''P36''' of M43 (''glgC''-mut1,2) to excise the gene from BABEL and rectify its orientation and '''P37''' of ''crtY'' from ''P. ananatis'' (Plate 17) cell suspension - repeat of P27.
+
-
** P36 and P37 run on '''Gel 25'''. P36 tentatively successful (larger than desirable smear in the region of interest), P37 failed.
+
-
* Also did preparations to transfer ''crtE'' from BABEL2 vector to pSB1A2. This is necessary, because we are supposed to use Registry standard vectors for all BioBricks we make (in fact, we should even stop using pSB1A2and move to pSB1A3). So, digested the BABEL2+''crtE'' clone that Douglas Leslie made with EcoRI and PstI, and also Edinbrick1 - in both cases, 3μl in 20μl total volume. Ran both on a gel and excised the appropriate bands, eluted each to 10μl EB and set up a ligation using 4μl of each in 10μl total volume. Ligated at 16°C. (CF)
+

Latest revision as of 20:36, 29 October 2008

< Previous Entry

Week 6

Friday 25 July 08

  • Made maxiprep X4 (pSB1A2+crtB as M36; BBa_K118002) and X5 (pSB1A2+crtI as M42; BBa_K118003) (AH, XH)
  • Made ligations:
    • L19: P12 (rbs+dxs) into Edinbrick1 to make pSB1A2+rbs+dxs
    • L20: P15 (rbs+appY) into Edinbrick1 to make pSB1A2+rbs+appY
    • L21: P28 (rbs+crtB) into Edinbrick1 to make pSB1A2+rbs+crtB
    • L22: P29 (rbs+crtI) into Edinbrick1 to make pSB1A2+rbs+crtI
    • L23: P31 (PzntA) into Edinbrick1 to make (pSB1A2+PzntA). (Yan, OG)
  • C. fimi Plate 48 appears to be contaminated (mix of opaque and clear colonies). The same culture was used for genomic DNA purification yesterday. This preparation is therefore inadequate for sequencing purpose but might be worth using for PCR. (AM)
  • No growth of C. fimi on Plates 49 and 50, but C. fimi takes a relatively long time to form colonies so we should check again on Monday. (AM)
  • PCR P36 of M43 (glgC-mut1,2) to excise the gene from BABEL and rectify its orientation and P37 of crtY from P. ananatis (Plate 17) cell suspension - repeat of P27. (AM)
    • P36 and P37 run on Gel 25. P36 tentatively successful (larger than desirable smear in the region of interest), P37 failed. (AM)
  • Also did preparations to transfer crtE from BABEL2 vector to pSB1A2. This is necessary, because we are supposed to use Registry standard vectors for all BioBricks we make (in fact, we should even stop using pSB1A2 and move to pSB1A3). So digested the BABEL2+crtE clone (that Douglas Leslie made) with EcoRI/PstI, and also Edinbrick1 - in both cases, 3μl in 20μl total volume. Ran both on a gel and excised the appropriate bands, eluted each to 10μl EB and set up a ligation (L24) using 4μl of each in 10μl total volume. Ligated at 16°C. (CF)


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