Team:Lyon-INSA/notebook

From 2012.igem.org

(Difference between revisions)
Line 3: Line 3:
<html xmlns="http://www.w3.org/1999/xhtml" xmlns:og="http://ogp.me/ns#" xmlns:fb="https://www.facebook.com/2008/fbml" >     
<html xmlns="http://www.w3.org/1999/xhtml" xmlns:og="http://ogp.me/ns#" xmlns:fb="https://www.facebook.com/2008/fbml" >     
-
<script>
+
                    <script>
-
var globalDay;
+
                        var globalDay;
-
var globalMonth;
+
                        var globalMonth;
-
var mutexTrans=0;
+
-
function bloqueTrans(){
+
                        /* MODIF LUCAS */
-
  mutexTrans=1;
+
-
}
+
 +
                        $(document).ready(function(){
 +
                            $("#noteBookTextContent").tinyscrollbar();
 +
                            $("#p-logo").find("img").attr("src","none");
-
function debloqueTrans(){
+
                            //initialisation au chargement de la page
-
  mutexTrans=0;
+
                            selectMonth($(".month:eq(0)").text(),"asc");
-
}
+
                            $("#monthDays ul li").has("a").eq(0).addClass("selected");
-
$(document).ready(function(){
+
                            $(".month").click(function(){
-
$("#noteBookTextContent").tinyscrollbar();
+
                                selectMonth($(this).text(),"asc");
-
$("#p-logo").find("img").attr("src","none");
+
                                $("#noteBookTextContent").tinyscrollbar_update();
 +
                                $(".textContent").transition({perspective: '500px',rotateX: '+=360deg'},700);
 +
                            });
-
$(".month").click(function(){
+
                            $("#jourPrecedent").click(function(){
 +
                                $(".textContent").transition({perspective: '500px',rotateY: '+=360deg'},700);
 +
                                switchDay(globalMonth,globalDay - 1);
 +
                                $("#noteBookTextContent").tinyscrollbar_update();
 +
                            });
-
selectMonth($(this).text(),"asc");
+
                            $("#jourSuivant").click(function(){
-
$("#noteBookTextContent").tinyscrollbar_update();
+
                                $(".textContent").transition({
-
          if (mutexTrans==0)
+
                                    perspective: '400px',rotateY: '-=360deg'
-
              { bloqueTrans();
+
                                },700);
-
                $(".textContent").transition({perspective: '500px',rotateX: '+=360deg'},700,function(){debloqueTrans()});}
+
                                switchDay(globalMonth,globalDay + 1);
-
});
+
                                $("#noteBookTextContent").tinyscrollbar_update();
-
 
+
                            });
-
  $("#jourPrecedent").click(function(){
+
-
          if (mutexTrans==0)
+
-
          {  bloqueTrans();
+
-
$(".textContent").transition({perspective: '500px',rotateY: '+=360deg'},700,function(){debloqueTrans()});}
+
-
previousDay(globalMonth,globalDay);
+
-
$("#noteBookTextContent").tinyscrollbar_update();
+
-
});
+
-
 
+
-
  $("#jourSuivant").click(function(){
+
-
          if (mutexTrans==0)
+
-
          {  bloqueTrans();
+
-
              $(".textContent").transition({  perspective: '400px',rotateY: '-=360deg'},700,function(){debloqueTrans()});
+
-
          }
+
-
nextDay(globalMonth,globalDay);
+
-
$("#noteBookTextContent").tinyscrollbar_update();
+
-
});
+
-
});
+
                        });
-
function selectMonth(month_name,type)
+
                        //fonction appelé lorsque l'on clique sur un jour (anime le texte et change les données affichées)
-
{
+
                        function selectDayAnimate(month_name,day, useDayNumber, dayLink) {
 +
                            $(".textContent").fadeOut('fast', function() {
 +
                                switchDay(month_name, day, useDayNumber);
 +
                            }).fadeIn();
 +
                            $("#monthDays .selected").removeClass("selected");
 +
                            $(dayLink).parent().addClass("selected");
 +
                            $("#noteBookTextContent").tinyscrollbar_update();
 +
                        }
 +
 
 +
                        function selectMonth(month_name,type)
 +
                        {
-
        $(".textContent").text("");
+
                            $(".textContent").text("");
-
        var xmlDoc=document.getElementById("xmldata")
+
                            var xmlDoc=document.getElementById("xmldata")
-
        var day=0;
+
                            var day=0;
-
var x=xmlDoc.getElementsByTagName("month");
+
                            var monthIndex = -1;
-
for (i=0;i<x.length;i++)
+
                            var x=xmlDoc.getElementsByTagName("month");
-
{
+
                            for (i=0;i<x.length;i++)
-
  if (x[i].getAttribute("name")==month_name)
+
                            {
-
{  
+
                                if (x[i].getAttribute("name")==month_name)
-
                  if (type=="desc")
+
                                {  
-
                  {
+
                                    if (type=="desc")
-
                    day=x[i].getElementsByTagName("jour").length-1;
+
                                    {
-
                  }
+
                                        day=x[i].getElementsByTagName("jour").length-1;
-
  var jour=x[i].getElementsByTagName("jour");
+
                                    }
 +
                                    var jour=x[i].getElementsByTagName("jour");
  $(".textContent").append("<div class='dateExp'></div>");
  $(".textContent").append("<div class='dateExp'></div>");
  $(".dateExp").append(jour[day].getElementsByTagName("date")[0].childNodes[0].nodeValue);
  $(".dateExp").append(jour[day].getElementsByTagName("date")[0].childNodes[0].nodeValue);
Line 77: Line 78:
   $("#descExp"+j).append(jour[day].getElementsByTagName("description")[j].innerHTML);  
   $("#descExp"+j).append(jour[day].getElementsByTagName("description")[j].innerHTML);  
}   
}   
 +
                                    monthIndex = i;                                   
 +
                                }  
 +
                            }          
 +
                            //initialisation de la liste de jour pour le mois selectionné
 +
                            var dayCounter = 1;
 +
                            if (monthIndex != -1) {                               
 +
                                var monthSize = parseInt(x[monthIndex].getAttribute("size"));
 +
                                $("#monthDays ul").children().remove();
 +
                                for (j=0;j<jour.length;j++) {
 +
                                    var xmlDayNumber = jour[j].getAttribute("nb");
 +
                                    if (xmlDayNumber != null && dayCounter <= monthSize) {
 +
                                        // nombre seul
 +
                                        while(dayCounter != xmlDayNumber && dayCounter != monthSize + 1) {
 +
                                            $("#monthDays ul").append("<li>"+ dayCounter +"</li>");
 +
                                            dayCounter++;
 +
                                        }
 +
                                        //nombre avec un lien
 +
                                        $("#monthDays ul").append("<li><a href='#' onClick='selectDayAnimate(\""+ month_name + "\", " + xmlDayNumber + ", true, this);"
 +
                                                                                         
 +
                                                                                          + "return false;'>"
 +
                                                                                        + xmlDayNumber +"</a></li>");
 +
                                        dayCounter++;
 +
                                    } else {
 +
                                        $("#monthDays ul").append("<li>"+ dayCounter +"</li>");
 +
                                        dayCounter++;
 +
                                    }
 +
                                }
 +
                                while(dayCounter != (monthSize + 1) ) {
 +
                                    $("#monthDays ul").append("<li>"+ dayCounter +"</li>");
 +
                                    dayCounter++;
 +
                                }
 +
                            }
 +
                            else {
 +
                                //le mois m'existe pas dans le xml, la liste n'a pas de liens
 +
                              $("#monthDays ul").children().remove();
 +
                              while(dayCounter != 32) {
 +
                                    $("#monthDays ul").append("<li>"+ dayCounter +"</li>");
 +
                                    dayCounter++;
 +
                                }   
 +
                            }
-
}  
+
                            globalDay=day;
-
}          
+
                            globalMonth=month_name;
-
globalDay=day;
+
                        }
-
globalMonth=month_name;
+
-
}
+
-
function nextDay(month_name,day)
+
                        //fusion de previousday et nextday dans une seule fonction
-
{
+
                        //day peut etre l'index du jour dans le xml (utilisation de previous/next)
-
        $(".textContent").html("");
+
                        //ou le numéro du jour directement (indiqué par useDayNumber)
-
        var xmlDoc=document.getElementById("xmldata")
+
                        function switchDay(month_name,day, useDayNumber)
-
var newDay=day+1;
+
                        {
-
var x=xmlDoc.getElementsByTagName("month");
+
                            $(".textContent").html("");
-
for (i=0;i<x.length;i++)
+
                            var xmlDoc=document.getElementById("xmldata")
-
{
+
                            var x=xmlDoc.getElementsByTagName("month");                          
-
  if (x[i].getAttribute("name")==month_name)
+
                            for (i=0;i<x.length;i++)
-
{
+
                            {
-
var jour=x[i].getElementsByTagName("jour");
+
                                if (x[i].getAttribute("name")==month_name)
-
if (jour.length>newDay)
+
                                {
-
{
+
                                    var foundDay = false;
 +
                                    var jour=x[i].getElementsByTagName("jour");
 +
                                    if (useDayNumber) {
 +
                                        //parcours des jours
 +
                                        for (var j = 0; j < jour.length; j++) {
 +
                                           
 +
                                            if (day == jour[j].getAttribute("nb")) {  
 +
                                                foundDay = true;
 +
                                                changeNote(jour[j]);
 +
                                                globalDay=j; 
-
$(".textContent").append("<div class='dateExp'></div>");
+
                                            }
-
$(".dateExp").append(jour[newDay].getElementsByTagName("date")[0].childNodes[0].nodeValue);  
+
                                        }
 +
                                    }
 +
                                    else if (jour.length > day) {
 +
                                        //utilisation de day comme un index sur le xml
 +
                                        foundDay = true;
 +
                                        changeNote(jour[day]);
 +
                                        globalDay = day;
 +
                                    }
 +
                                    if (!foundDay) {
-
for (j=0;j<jour[newDay].getElementsByTagName("titre").length;j++)
+
                                        var monthIndexToTest = 0;
-
{
+
                                        var actionType;
-
  $(".textContent").append("<div class='titreExp' id='titreExp"+j+"'></div>");
+
                                        if (day - globalDay > 0) {
-
  $("#titreExp"+j).append(jour[newDay].getElementsByTagName("titre")[j].childNodes[0].nodeValue);
+
                                            //day bigger so going to next month
-
  $(".textContent").append("<div class='descExp' id='descExp"+j+"'></div>");
+
                                            monthIndexToTest = i + 1;
-
  $("#descExp"+j).append(jour[newDay].getElementsByTagName("description")[j].innerHTML);  
+
                                            actionType = "asc";
-
}
+
                                        }
 +
                                        else {
 +
                                            //day smaller so going to previous month
 +
                                            monthIndexToTest = i - 1;
 +
                                            actionType = "desc";
 +
                                        }
 +
                                        if (monthIndexToTest<x.length)
 +
                                        {                           
 +
                                            if (x[monthIndexToTest].getElementsByTagName("jour").length>0) {
 +
                                                selectMonth(x[monthIndexToTest].getAttribute("name"),actionType);
 +
                                            }     
 +
                                            else
 +
                                            {
 +
                                                globalDay=x[i].getElementsByTagName("jour").length;
 +
                                            }                   
 +
                                        }
 +
                                        else
 +
                                        {
 +
                                            globalDay=x[i].getElementsByTagName("jour").length;
 +
                                        }
 +
                                    }
 +
                                }
 +
                            }
 +
                        }
 +
                        //change du texte lors de la selection d'un jour
 +
                        function changeNote(xmlDayNode) {
 +
                            $(".textContent").append("<div class='titreExp'></div>");
 +
                            $(".titreExp").append(xmlDayNode.getElementsByTagName("titre")[0].childNodes[0].nodeValue);           
 +
                            $(".textContent").append("<div class='dateExp'></div>");
 +
                            $(".dateExp").append(" - " + xmlDayNode.getElementsByTagName("date")[0].childNodes[0].nodeValue);             
 +
                            $(".textContent").append("<div class='descExp'></div>");
-
        globalDay=newDay;
+
                            $(".descExp").append(xmlDayNode.getElementsByTagName("description")[0].innerHTML);  
-
         
+
                         }
                         }
-
else if (i+1<x.length)
 
-
{                           
 
-
                                if (x[i+1].getElementsByTagName("jour").length>0)
 
-
                                {selectMonth(x[i+1].getAttribute("name"),"asc");}     
 
-
                                else
 
-
                                {
 
-
            globalDay=x[i].getElementsByTagName("jour").length;
 
-
                                }                   
 
-
}
 
-
                        else
 
-
                        {
 
-
        globalDay=x[i].getElementsByTagName("jour").length;
 
-
                        }
 
-
}  
 
-
}
 
-
         
 
-
 
-
}
 
-
function previousDay(month_name,day)
+
                        /* //MODIF LUCAS */
-
{
+
                    </script>
-
        $(".textContent").html("");
 
-
        var xmlDoc=document.getElementById("xmldata")
 
-
var newDay=day-1;
 
-
var x=xmlDoc.getElementsByTagName("month");
 
-
for (i=0;i<x.length;i++)
 
-
  {
 
-
  if (x[i].getAttribute("name")==month_name)
 
-
  {
 
-
                        if (day>0)
 
-
                        {
 
-
  var jour=x[i].getElementsByTagName("jour");
 
-
  $(".textContent").append("<div class='dateExp'></div>");
 
-
  $(".dateExp").append(jour[newDay].getElementsByTagName("date")[0].childNodes[0].nodeValue);  
 
-
for (j=0;j<jour[newDay].getElementsByTagName("titre").length;j++)
 
-
{
 
-
  $(".textContent").append("<div class='titreExp' id='titreExp"+j+"'></div>");
 
-
  $("#titreExp"+j).append(jour[newDay].getElementsByTagName("titre")[j].childNodes[0].nodeValue);
 
-
  $(".textContent").append("<div class='descExp' id='descExp"+j+"'></div>");
 
-
  $("#descExp"+j).append(jour[newDay].getElementsByTagName("description")[j].innerHTML);
 
-
} 
 
-
 
 
-
     
 
-
     
 
-
                          globalDay=newDay;
 
-
                        }
 
-
                        else if (i>0)
 
-
        {                     
 
-
                          if (x[i-1].getElementsByTagName("jour").length>0)
 
-
                          {selectMonth(x[i-1].getAttribute("name"),"desc");}                     
 
-
                }
 
-
                        else
 
-
                        {
 
-
                            globalDay=-1;
 
-
                        }
 
-
                }  
 
-
    }  
 
-
       
 
-
}
 
-
</script>
 
-
<head>
 
-
</head>
 
-
<body>
+
                    </p><div id="projectBar" class="menuBar">
 +
                    <div class="boutonMenu" onclick="window.location=&#39;menu&#39;;">Menu</div>
 +
                    <div id="ongletBar">
 +
                        <div class="boutonOnglet" onclick="window.location=&#39;project&#39;;">Project description</div>
 +
                        <div class="boutonOnglet" onclick="window.location=&#39;modelling&#39;;">Modelling</div>
 +
                        <div class="boutonOnglet" onclick="window.location=&#39;safety&#39;;">Safety</div>
 +
                        <div class="boutonOnglet BOClicked">Notebook</div>
 +
                        <div class="boutonOnglet" onclick="window.location=&#39;protocol&#39;;">Protocol</div>
 +
                        <div class="boutonOnglet" onclick="window.location=&#39;datapage&#39;;">Data Page</div>
 +
                    </div>
 +
                </div>
 +
                <div id="bandeau"></div>
 +
                <div id="xml" style="display:none;">
 +
                    <xml id="xmldata" style="display:none;">
 +
                    <!--?xml version="1.0" encoding="ISO-8859-1"?-->
 +
                    <!-- Edited by XMLSpy -->
 +
                    <project>
 +
                    <month name="July"  size="31">
 +
                    <jour nb="2">
 +
                    <titre>For all purposes</titre>
 +
                    <date> Monday, July 2nd 2012</date>
 +
                    <description>Liquid culture (5 mL LB media) of NM 522 cells and overnight incubation under agitation at 37°C for later transformations.</description>
 +
                    </jour>
 +
                    <jour nb="3">
 +
                    <titre>For all purposes</titre>
 +
                    <date> Tuesday, July 3rd 2012</date>
 +
                    <description><p>Dilution of 100 µL saturated culture in  5 mL LB media. </p><br>
 +
                    <p>Incubation time : 2 hours (until O.D =0,3). </p><br>
 +
                    Transformation of the NM 522 strain  (this experiment was made 3 times) <br>
-
<div id="projectBar" class="menuBar">
+
                    For the positive control the pSB1C3 plasmid was used ;
-
    <div class="boutonMenu" onclick="window.location='menu';">Menu</div>
+
                    For the transformation, the pBBA_I742123 was used (well A2, 5th iGEM kit plate)
-
    <div id="ongletBar">
+
                    The transformed bacteria were selected on chloramphenicol plates.
-
        <div class="boutonOnglet"  onclick="window.location='project';">Project description</div>
+
                    </description>
-
        <div class="boutonOnglet"  onclick="window.location='modelling';">Modelling</div>
+
                    </jour>
-
        <div class="boutonOnglet"  onclick="window.location='safety';">Safety</div>
+
                    <jour nb="4">
-
        <div class="boutonOnglet BOClicked">Notebook</div>
+
                    <titre>For all purposes</titre>
-
        <div class="boutonOnglet" onclick="window.location='protocol';">Protocol</div>
+
                    <date> Wednesday, July 4th 2012</date>
-
        <div class="boutonOnglet"  onclick="window.location='datapage';">Data Page</div>
+
                    <description>
-
    </div>
+
                    Transformation analysis:<br><br>
-
</div>
+
                    <ul>
-
<div id="bandeau"></div>
+
                        <li>Positive control: lots of colonies</li>
-
<div id="xml" style="display:none;">
+
                        <li>Negative control: one of the three negative controls was contaminated (the correspondent transformed colonies were not used). No colonies were observed on the other two negative control plates.</li>
-
  <xml id='xmldata' style='display:none;'>
+
-
    <?xml version="1.0" encoding="ISO-8859-1"?>
+
-
<!-- Edited by XMLSpy -->
+
-
<project>
+
-
<month name="July">
+
-
<jour>
+
-
<titre>For all purposes</titre>
+
-
<date> Monday, July 2nd 2012</date>
+
-
<description>Liquid culture (5 mL LB media) of NM 522 cells and overnight incubation under agitation at 37°C for later transformations.</description>
+
-
</jour>
+
-
                <jour>
+
-
<titre>For all purposes</titre>
+
-
<date> Tuesday, July 3rd 2012</date>
+
-
<description><p>Dilution of 100 µL saturated culture in  5 mL LB media. </p><br />
+
-
<p>Incubation time : 2 hours (until O.D =0,3). </p><br />
+
-
Transformation of the NM 522 strain  (this experiment was made 3 times) <br />
+
-
For the positive control the pSB1C3 plasmid was used ;
+
                        <li>Test plate: between 1 and 8 were observed.</li></ul>
-
For the transformation, the pBBA_I742123 was used (well A2, 5th iGEM kit plate)
+
                    <br>
-
The transformed bacteria were selected on chloramphenicol plates.
+
                    4 liquid cultures (5mL LB media + 50 µL chloramphenicol) and 4 streaked chloramphenicol plates were made using isolated colonies likely to contain transformed bacteria.<br><br>
-
</description>
+
-
</jour>
+
-
                <jour>
+
-
<titre>For all purposes</titre>
+
-
<date> Wednesday, July 4th 2012</date>
+
-
<description>
+
-
Transformation analysis:<br/><br/>
+
-
<ul>
+
-
    <li>Positive control: lots of colonies</li>
+
-
  <li>Negative control: one of the three negative controls was contaminated (the correspondent transformed colonies were not used). No colonies were observed on the other two negative control plates.</li>
+
                    The antibiotic resistance (Ampicillin, Tetracyclin, Chloramphenicol and Kanamycin ) of the following strains was tested: BS 168, BS 168 MCherry, BS 168 GFP, BS 168 Lysostaphine, Staphylococcus epidermidis, BS Abrb.
 +
                    </description>
 +
                    </jour>
 +
                    <jour nb="5">
 +
                    <titre>For all purposes</titre>
 +
                    <date> Thursday, July 5th 2012</date>
 +
                    <description>
-
    <li>Test plate: between 1 and 8 were observed.</li></ul>
+
                    Antibiotics resistance tests :<br><br>
-
<br/>
+
                    <ul>
-
4 liquid cultures (5mL LB media + 50 µL chloramphenicol) and 4 streaked chloramphenicol plates were made using isolated colonies likely to contain transformed bacteria.<br/><br/>
+
                        <li>Bs 168 : no resistance</li>
-
The antibiotic resistance (Ampicillin, Tetracyclin, Chloramphenicol and Kanamycin ) of the following strains was tested: BS 168, BS 168 MCherry, BS 168 GFP, BS 168 Lysostaphine, Staphylococcus epidermidis, BS Abrb.
+
                        <li>Bs 168 M cherry : no resistance</li>
-
</description>
+
-
</jour>
+
-
                <jour>
+
-
<titre>For all purposes</titre>
+
-
<date> Thursday, July 5th 2012</date>
+
-
<description>
+
-
Antibiotics resistance tests :<br/><br/>
+
                        <li>Bs 168 GFP : no resistance</li>
-
<ul>
+
-
    <li>Bs 168 : no resistance</li>
+
-
    <li>Bs 168 M cherry : no resistance</li>
+
                        <li>Bs abrB : Cm resistant</li>
-
    <li>Bs 168 GFP : no resistance</li>
+
                        <li>Bs 168 lysostaphine PWG100 : no resistance</li>
-
    <li>Bs abrB : Cm resistant</li>
+
                        <li>S. Epidermidis : Tet resistant</li>
 +
                    </ul>
 +
                    <br>
 +
                    Extraction of 4 clones containing the pBBA_I742123 plasmid. Verification by gel electrophoresis (after EcoR1 digestion)
-
    <li>Bs 168 lysostaphine PWG100 : no resistance</li>
+
                    </description>
 +
                    </jour>
 +
                    <jour nb="6">
 +
                    <titre>For all purposes</titre>
 +
                    <date> Friday, July 6th 2012</date>
 +
                    <description>
-
    <li>S. Epidermidis : Tet resistant</li>
+
                    Telephonic conference with Romain Briandet<br><br>
-
</ul>
+
-
<br/>
+
-
Extraction of 4 clones containing the pBBA_I742123 plasmid. Verification by gel electrophoresis (after EcoR1 digestion)
+
-
</description>
+
                    Terminator was retrieved from the plate 1 well 13D<br><br>
-
</jour>
+
                    Long meeting
-
                <jour>
+
-
<titre>For all purposes</titre>
+
-
<date> Friday, July 6th 2012</date>
+
-
<description>
+
-
Telephonic conference with Romain Briandet<br/><br/>
+
                    </description>
 +
                    </jour>
 +
                    <jour nb="9">
 +
                    <titre>For all purposes</titre>
 +
                    <date> Monday, July 9th 2012</date>
 +
                    <description>
 +
                    <ul>
 +
                        <li>pBBa_I742123 was put in storage (under the reference pBK1);</li>
-
Terminator was retrieved from the plate 1 well 13D<br/><br/>
+
                        <li>a liquid culture of NM522/pBK1 transformed cells was made so we could extract more plasmid DNA (50 mL LB media + 500 µL Cloramphenicol + 500 µL liquid culture of transformed bacteria );</li>
-
Long meeting
+
-
</description>
+
                        <li>we had the 3 genes coding for lysostaphin, dispersin and lacI repressor in pUC57 Ampicillin resistant plasmid delivered;</li>
-
</jour>
+
-
                <jour>
+
-
<titre>For all purposes</titre>
+
-
<date> Monday, July 9th 2012</date>
+
-
<description>
+
-
<ul>
+
-
    <li>pBBa_I742123 was put in storage (under the reference pBK1);</li>
+
-
    <li>a liquid culture of NM522/pBK1 transformed cells was made so we could extract more plasmid DNA (50 mL LB media + 500 µL Cloramphenicol + 500 µL liquid culture of transformed bacteria );</li>
+
                        <li>transformation of NM522 strain with pUC57-Lyso, pUC57-Disp and pUC57-sfp;</li>
-
    <li>we had the 3 genes coding for lysostaphin, dispersin and lacI repressor in pUC57 Ampicillin resistant plasmid delivered;</li>
+
                        <li>200 µL of each transformed strains were spread on LB media Ampicillin resistant plates
 +
                        liquid cultures of the following strains were made: Bs 168 in BL, Bs abrB in BL media supplemented with Chloramphenicol, S. epidermidis in BL media supplemented with Tetracyclin</li></ul>
-
    <li>transformation of NM522 strain with pUC57-Lyso, pUC57-Disp and pUC57-sfp;</li>
+
                    </description>
 +
                    </jour>
 +
                    <jour nb="10">
 +
                    <titre>For all purposes</titre>
 +
                    <date> Tuesday, July 10th 2012</date>
 +
                    <description>
 +
                    the following parts were put in storage:
 +
                    <ul>
 +
                        <li>Lysostaphin in pUC57 Amp resistant (pBK2);</li>
-
    <li>200 µL of each transformed strains were spread on LB media Ampicillin resistant plates
+
                        <li>Dispersin in pUC57 Amp resistant (pBK3);</li>
-
    liquid cultures of the following strains were made: Bs 168 in BL, Bs abrB in BL media supplemented with Chloramphenicol, S. epidermidis in BL media supplemented with Tetracyclin</li></ul>
+
-
</description>
+
                        <li>Surfactin part 2 (RBS-lacI-terminator) dans pUC57 Amp resistant (pBK4)</li>
-
</jour>
+
                    </ul>
-
                <jour>
+
-
<titre>For all purposes</titre>
+
-
<date> Tuesday, July 10th 2012</date>
+
-
<description>
+
-
    the following parts were put in storage:
+
-
<ul>
+
-
        <li>Lysostaphin in pUC57 Amp resistant (pBK2);</li>
+
-
        <li>Dispersin in pUC57 Amp resistant (pBK3);</li>
+
                    and the following strains:
 +
                    <ul> 
 +
                        <li>S epi on BL + Tet (BK1)</li>
-
        <li>Surfactin part 2 (RBS-lacI-terminator) dans pUC57 Amp resistant (pBK4)</li>
+
                        <li>Bs abrB on BL + Cm (BK2)</li>
-
</ul>
+
-
  and the following strains:
+
                        <li>Bs 168 on BL (BK3)</li>
-
<ul>
+
                    </ul>
-
        <li>S epi on BL + Tet (BK1)</li>
+
                    ligation of  Dispersin and Lysostaphin biobricks:
 +
                    <ul>
 +
                        <li>digestion of pBK2 with the restriction enzymes EcoRI and SpeI;</li>
-
        <li>Bs abrB on BL + Cm (BK2)</li>
+
                        <li>digestion of pBK3 with the restriction enzymes PstI and XbaI;</li>
-
        <li>Bs 168 on BL (BK3)</li>
+
                        <li>digestion of pBK4 with the restriction enzymes EcoRI and PstI;</li>
-
</ul>
+
-
    ligation of  Dispersin and Lysostaphin biobricks:
+
-
<ul>
+
-
        <li>digestion of pBK2 with the restriction enzymes EcoRI and SpeI;</li>
+
-
        <li>digestion of pBK3 with the restriction enzymes PstI and XbaI;</li>
+
                        <li>3A ligation of the digested parts;</li>
-
        <li>digestion of pBK4 with the restriction enzymes EcoRI and PstI;</li>
+
                        <li>electrophoresis control showed the expected fragment for lysostaphin and dispersin (2,1 kb). However, the digested backbone plasmid had 3 fragments instead of 2.<br>
 +
                        <strong>Plasmid A2 extraction with a midiprep (pBK5) and digestion → 3 stripes are observed : PROBLEM. Digestion is made again with E, P and E+P → There are 2 Pst1 sites !!! WRONG PLASMID</strong></li>
-
        <li>3A ligation of the digested parts;</li>
+
                        <li>transformation of NM522 strain with the part BBa_K606061 Chloramphenicol resistant;</li>
-
        <li>electrophoresis control showed the expected fragment for lysostaphin and dispersin (2,1 kb). However, the digested backbone plasmid had 3 fragments instead of 2.<br/>
+
                        <li>transformation of NM522 strain with the part BBa_B0010 Ampicillin resistant;</li>
-
    <strong>Plasmid A2 extraction with a midiprep (pBK5) and digestion → 3 stripes are observed : PROBLEM. Digestion is made again with E, P and E+P → There are 2 Pst1 sites !!! WRONG PLASMID</strong></li>
+
-
    <li>transformation of NM522 strain with the part BBa_K606061 Chloramphenicol resistant;</li>
+
                        <li>transformation of NM522 strain with the part BBa_K606040 Chloramphenicol resistant;</li>
 +
                        <li>design and order of the primers for the constitutive promotor (part BBa_K143012)</li>
 +
                    </ul>
 +
                    </description>
 +
                    </jour>
 +
                    <jour nb="11">
 +
                    <titre>For all purposes</titre>
 +
                    <date> Wednesday, July 11th 2012</date>
 +
                    <description>
 +
                    <ul>
 +
                        <li>Extraction of part BBa_K606061 (RBS) Chloramphenicol resistant from transformed NM522 strain;</li>
 +
                        <li>Extraction of part BBa_B0010 (terminator) Ampicillin resistant from transformed NM522 strain; <i>(nb : the clones were pink which means that the part contains a RFP gene)</i></li>
 +
                        <li>Extraction of part BBa_K606040 (pLacI)  from transformed NM522 strain;</li>
 +
                        <li>Extraction of  pUC57-Lyso/pUC57-Disp/pUC57-lacI from transformed NM522 strains;</li>
 +
                        <li>Transformation of NM522 strain with the part BBa_0010 Ampicillin resistant. The observed phenotype does not correspond to the description found in the registry (the colour of the colonies is pink). We decided to make another transformation with the same part, only this time the 2011 kit was used.</li>
 +
                    </ul>
 +
                    </description>
 +
                    </jour>
-
    <li>transformation of NM522 strain with the part BBa_B0010 Ampicillin resistant;</li>
+
                    <jour nb="12">
 +
                    <titre>For all purposes</titre>
 +
                    <date> Thursday, July 12th 2012</date>
 +
                    <description>
 +
                    <ul>
 +
                        <li>PCR product electrophoresis  of Promoter PCR : the product is not the good one.</li>
 +
                        <li>Reception and storage of the primers (for the amplification of the BBa_K143012 part);</li>
 +
                        <li>The transformed NM522 strain with the part BBa_0010 Ampicillin resistant from the 2011 iGEM kit shows the same phenotype as the part found in the 2012 kit;</li>
 +
                        <li>Extractions with a miniprep kit are made :
 +
                        <ul>
 +
                            <li>4 clones containing the pLac promotor (1,2,3,4)</li>
 +
                            <li>4 clones containing the Bacillus subtilis RBS (1,2,3,4)</li>
 +
                            <li>3 clones containing theTerminator 1,2,3</li>
 +
                            <li>4 clones containing the gene for Dispersin</li>
 +
                            <li>4 clones containing the gene for Lysostaphin</li>
 +
                            <li>4 clones containing the gene for lacI</li>
 +
                        </ul>
 +
                        Then a digestion is made on a 0.7% agarose gel.</li>
-
    <li>transformation of NM522 strain with the part BBa_K606040 Chloramphenicol resistant;</li>
+
                    </ul>
-
    <li>design and order of the primers for the constitutive promotor (part BBa_K143012)</li>
+
                    </description>
-
</ul>
+
                    </jour>
-
</description>
+
-
</jour>
+
-
<jour>
+
-
<titre>For all purposes</titre>
+
-
<date> Wednesday, July 11th 2012</date>
+
-
<description>
+
-
<ul>
+
-
      <li>Extraction of part BBa_K606061 (RBS) Chloramphenicol resistant from transformed NM522 strain;</li>
+
-
      <li>Extraction of part BBa_B0010 (terminator) Ampicillin resistant from transformed NM522 strain; <i>(nb : the clones were pink which means that the part contains a RFP gene)</i></li>
+
-
      <li>Extraction of part BBa_K606040 (pLacI)  from transformed NM522 strain;</li>
+
-
      <li>Extraction of  pUC57-Lyso/pUC57-Disp/pUC57-lacI from transformed NM522 strains;</li>
+
-
      <li>Transformation of NM522 strain with the part BBa_0010 Ampicillin resistant. The observed phenotype does not correspond to the description found in the registry (the colour of the colonies is pink). We decided to make another transformation with the same part, only this time the 2011 kit was used.</li>
+
-
</ul>
+
-
</description>
+
-
</jour>
+
-
<jour>
+
                    <jour nb="13">
-
<titre>For all purposes</titre>
+
                    <titre>Kill</titre>
-
<date> Thursday, July 12th 2012</date>
+
                    <date> Friday, July 13th 2012</date>
-
<description>
+
                    <description>
-
<ul>
+
                    <ul>
-
    <li>PCR product electrophoresis  of Promoter PCR : the product is not the good one.</li>
+
                        <li>PCR of the constitutive promotor (part BBa_K143012); → the PCR did not work so we ran a new PCR with a more diluted promotor solution.</li>
-
    <li>Reception and storage of the primers (for the amplification of the BBa_K143012 part);</li>
+
                        <li>The following strains are put in storage:
-
    <li>The transformed NM522 strain with  the part  BBa_0010 Ampicillin resistant from the 2011 iGEM kit shows the same phenotype as the part found in the 2012 kit;</li>
+
                        <ul>
-
    <li>Extractions with a miniprep kit are made :
+
                            <li>NM522 containing lacI-pUC57</li>
-
    <ul>
+
                            <li>NM522 containing rbs-pUC57 </li>
-
            <li>4 clones containing the pLac promotor (1,2,3,4)</li>
+
                            <li>NM522 containing dsp-pUC57</li>
-
            <li>4 clones containing the Bacillus subtilis RBS (1,2,3,4)</li>
+
                        </ul>
-
            <li>3 clones containing theTerminator 1,2,3</li>
+
                        </li></ul>
-
            <li>4 clones containing the gene for Dispersin</li>
+
                        </description>
-
            <li>4 clones containing the gene for Lysostaphin</li>
+
                        </jour>
-
            <li>4 clones containing the gene for lacI</li>
+
-
    </ul>
+
-
Then a digestion is made on a 0.7% agarose gel.</li>
+
-
</ul>
+
                        <jour nb="16">
-
</description>
+
                        <date> Monday, July 16th 2012</date>
-
</jour>
+
-
 
+
-
<jour>
+
-
<titre>Kill</titre>
+
-
<date> Friday, July 13th 2012</date>
+
-
<description>
+
-
<ul>
+
-
    <li>PCR of the constitutive promotor (part BBa_K143012); → the PCR did not work so we ran a new PCR with a more diluted promotor solution.</li>
+
-
    <li>The following strains are put in storage:
+
-
    <ul>
+
-
            <li>NM522 containing lacI-pUC57</li>
+
-
            <li>NM522 containing rbs-pUC57 </li>
+
-
            <li>NM522 containing dsp-pUC57</li>
+
-
    </ul>
+
-
</ul>
+
-
</description>
+
-
</jour>
+
-
 
+
-
<jour>
+
-
<date> Monday, July 16th 2012</date>
+
                         <titre>Kill</titre>
                         <titre>Kill</titre>
-
<description>
+
                        <description>
-
<ul>
+
                        <ul>
-
    <li>PCR of constitutive promoter  → it didn’t work. A new PCR is run with modifications of settings. The annealing temperature was modified from 50°C to 57°C, and 3 solutions with different concentration were tested, however the concentration did not affect the yield.</li>
+
                            <li>PCR of constitutive promoter  → it didn’t work. A new PCR is run with modifications of settings. The annealing temperature was modified from 50°C to 57°C, and 3 solutions with different concentration were tested, however the concentration did not affect the yield.</li>
-
    <li>Purification of the PCR product.</li>
+
                            <li>Purification of the PCR product.</li>
-
    <li>Gel electrophoresis of lysostaphin.</li>
+
                            <li>Gel electrophoresis of lysostaphin.</li>
-
</ul>
+
                        </ul>
-
</description>
+
                         <titre>For all purposes</titre>
                         <titre>For all purposes</titre>
-
<description>
+
                        <ul>
-
<ul>
+
                            <li>Transformation of B0015 terminator.</li>
-
      <li>Transformation of B0015 terminator.</li>
+
                            <li>Strains BK13 (Bs arbB), BK10 (Bs 168 GFP) and BK11 (Bs 168 mCherry) are put in storage.</li>
-
      <li>Strains BK13 (Bs arbB), BK10 (Bs 168 GFP) and BK11 (Bs 168 mCherry) are put in storage.</li>
+
                        </ul>
-
</ul>
+
                        </description>
-
</description>
+
                        </jour>
-
</jour>
+
-
<jour>
+
                        <jour nb="17">
-
<date> Tuesday, July 17th 2012</date>
+
                        <date> Tuesday, July 17th 2012</date>
                         <titre>For all purposes</titre>
                         <titre>For all purposes</titre>
-
<description>
+
                        <description>
-
<ul>
+
                        <ul>
-
    <li>Long morning meeting to discuss results and to write some posters in a frenetic psychopath way in order to remember our tasks.</li>
+
                            <li>Long morning meeting to discuss results and to write some posters in a frenetic psychopath way in order to remember our tasks.</li>
-
    <li>Ligation of promoter-rbs-GFP in plasmid.</li>
+
                            <li>Ligation of promoter-rbs-GFP in plasmid.</li>
-
    <li>Bs’ genomic DNA extraction: buffers preparation.</li>
+
                            <li>Bs’ genomic DNA extraction: buffers preparation.</li>
-
    <li>Failure of B0015 transformation.</li>
+
                            <li>Failure of B0015 transformation.</li>
-
</ul>
+
                        </ul>
-
</description>
+
                         <titre>Kill</titre>
                         <titre>Kill</titre>
-
<description>
+
                        <ul>
-
<ul>
+
                            <li>Cloning of the constitutive promoter in front of the disp part (the gene coding for Dispersin) and RBS/GFP (of Ecoli) using a 3A ligation followed by transformation of the ligation in the NM522 strain;</li>
-
      <li>Cloning of the constitutive promoter in front of the disp part (the gene coding for Dispersin) and RBS/GFP (of Ecoli) using a 3A ligation followed by transformation of the ligation in the NM522 strain;</li>
+
                            <li>Extraction of pUC57-lysostaphin. Gel electrohporesis showed a shaded DNA → forgetting of RNase during the extraction.</li>
-
      <li>Extraction of pUC57-lysostaphin. Gel electrohporesis showed a shaded DNA → forgetting of RNase during the extraction.</li>
+
                        </ul>
-
</ul>
+
                        </description>
-
</description>
+
                         </jour>
-
</jour>
+
-
 
+
-
<jour>
+
-
<date> Wednesday, July 18th 2012</date>
+
-
                         <titre>For all purposes</titre>
+
-
<description>
+
-
<ul>
+
-
    <li>Extraction and digestion (E & P) of strain Bs 168 GFP’s plasmid. Gel electrohporesis showed absence of non digested plasmid → extraction failure.</li>
+
-
    <li>Bs 168’s genomic DNA extraction (Kit Genomic DNA from tissue) .</li>
+
-
    <li>Transformation of pBK5 in <i>B. subtilis</i> abrB failed.</li>
+
-
</ul>
+
-
</description>
+
-
                      <titre>Kill</titre>
+
-
<description>
+
-
<ul>
+
-
      <li>The transformation results of the 3A ligation ([disp+RBS/GFP+pSB1T3]) was unsuccessful, so it was repeated, this time with both a positive control (strain 39) and a negative one with NM522 culture ;</li>
+
-
      <li>Addition of RNase to the miniprep from pUC57-lysostaphin clones. Gel electrophoresis: there is still a layered cut. However, the bands are as expected.</li>
+
-
</ul>
+
-
</description>
+
-
</jour>
+
-
<jour>
+
                        <jour nb="18">
-
<date> Thursday, July 19th 2012</date>
+
                        <date> Wednesday, July 18th 2012</date>
                         <titre>For all purposes</titre>
                         <titre>For all purposes</titre>
-
<description>
+
                        <description>
-
<ul>
+
                        <ul>
-
    <li>TSS tests are also made to be sure that all TSS solutions that we have are ok because some transformations did not work;</li>
+
                            <li>Extraction and digestion (E &amp; P) of strain Bs 168 GFP’s plasmid. Gel electrohporesis showed absence of non digested plasmid → extraction failure.</li>
-
    <li>A 50ug/mL erythromycin solution is made in order to test the strains’ resistance;</li>
+
                            <li>Bs 168’s genomic DNA extraction (Kit Genomic DNA from tissue) .</li>
-
    <li>Transformation of yfp, gfp et cfp (from iGEM plates) in NM522;</li>
+
                            <li>Transformation of pBK5 in <i>B. subtilis</i> abrB failed.</li>
-
    <li>B0015 transformation in NM522.</li>
+
                        </ul>
-
</ul>
+
-
</description>
+
                         <titre>Kill</titre>
                         <titre>Kill</titre>
-
<description>
+
                        <ul>
-
<ul>
+
                            <li>The transformation results of the 3A ligation ([disp+RBS/GFP+pSB1T3]) was unsuccessful, so it was repeated, this time with both a positive control (strain 39) and a negative one with NM522 culture ;</li>
-
      <li>The transformation of the 3A ligation ([disp+RBS/GFP+pSB1T3]) was successful, so 6 clones were tested on  a plate containing BL media supplemented with Tetracyclin;</li>
+
                            <li>Addition of RNase to the miniprep from pUC57-lysostaphin clones. Gel electrophoresis: there is still a layered cut. However, the bands are as expected.</li>
-
      <li>The fluorescence test of the transformed bacteria containing [disp+RBS/GFP+pSB1T3]  confirm that the promotor is functional</li>
+
                        </ul>
-
      <li>Ligation of the promoter in a Cm resistant iGEM plasmid was made in order to send it to the registry.</li>
+
                        </description>
-
</ul>
+
                        </jour>
-
</description>
+
-
</jour>
+
-
<jour>
+
                        <jour nb="19">
-
<date> Friday, July 20th 2012</date>
+
                        <date> Thursday, July 19th 2012</date>
                         <titre>For all purposes</titre>
                         <titre>For all purposes</titre>
-
<description>
+
                        <description>
-
<ul>
+
                        <ul>
-
    <li>Transformation results : all TSS work (except maybe 1 and 2 with a smaller yield) and prom+pSB1C3 OK → 6 clones are isolated on a GL+Cm plate.</li>
+
                            <li>TSS tests are also made to be sure that all TSS solutions that we have are ok because some transformations did not work;</li>
-
    <li>Quantification and gel electrophoresis of B.subtilis’ genomic DNA.</li>
+
                            <li>A 50ug/mL erythromycin solution is made in order to test the strains’ resistance;</li>
-
    <li>Antibiotic testing of <i>B. thuringensis</i> 407 gfp strain and other strains in BL+Ery growth medium.</li>
+
                            <li>Transformation of yfp, gfp et cfp (from iGEM plates) in NM522;</li>
-
    <li>Failure of transforming pBK5 in <i>B. subtilis</i> 168 with the same protocol as previously. New task: find a new protocol.</li>
+
                            <li>B0015 transformation in NM522.</li>
-
</ul>
+
                        </ul>
-
</description>
+
                         <titre>Kill</titre>
                         <titre>Kill</titre>
-
<description>
+
                        <ul>
-
<ul>
+
                            <li>The transformation of the 3A ligation ([disp+RBS/GFP+pSB1T3]) was successful, so 6 clones were tested on  a plate containing BL media supplemented with Tetracyclin;</li>
-
      <li>Transformation of NM522 strain with the part BBa_K606030 (pBK6) and promoter+dispersin;</li>
+
                            <li>The fluorescence test of the transformed bacteria containing [disp+RBS/GFP+pSB1T3]  confirm that the promotor is functional</li>
-
      <li>Ligation Prom+Dsp in P23 and transformation;</li>
+
                            <li>Ligation of the promoter in a Cm resistant iGEM plasmid was made in order to send it to the registry.</li>
-
      <li>Ligation Lysostaphin in pSB1C3 and transformation;</li>
+
                        </ul>
-
      <li>Isolation of 6 clones of the Term transformation;</li>
+
                        </description>
-
      <li>Transformation results of fluorescent genes: ok, except yfp </li>
+
                        </jour>
-
      <li>NM522 strain containing pUC57-lysostaphin is put in storage under the name of BK12.</li>
+
-
</ul>
+
-
</description>
+
-
</jour>
+
-
<jour>
+
                        <jour nb="20">
-
<date> Monday, July 23rd 2012</date>
+
                        <date> Friday, July 20th 2012</date>
                         <titre>For all purposes</titre>
                         <titre>For all purposes</titre>
-
<description>
+
                        <description>
-
<ul>
+
                        <ul>
-
    <li>Selected clones (NM522+pBK6) are red, meaning that pVeg promoter and RBS from subtilis are recognized by <i>E. coli</i>’s ribosome. 4 clones are streaked in LB+Cm.</li>
+
                            <li>Transformation results : all TSS work (except maybe 1 and 2 with a smaller yield) and prom+pSB1C3 OK → 6 clones are isolated on a GL+Cm plate.</li>
-
    <li>GL+Ery and TSB+Tet Petri plates are made.</li>
+
                            <li>Quantification and gel electrophoresis of B.subtilis’ genomic DNA.</li>
-
    <li>YFP transformation was successful.</li>
+
                            <li>Antibiotic testing of <i>B. thuringensis</i> 407 gfp strain and other strains in BL+Ery growth medium.</li>
-
    <li>GFP and CFP plasmids’ extraction showed a failure in ligation.</li>
+
                            <li>Failure of transforming pBK5 in <i>B. subtilis</i> 168 with the same protocol as previously. New task: find a new protocol.</li>
-
    <li><i>B. subtilis</i> 168 is put in storage (BK14) in TSB medium.</li>
+
                        </ul>
-
    <li>Extraction of B0015 terminator. Gel electrophoresis showed 4 good clones.</li>
+
-
</ul>
+
-
</description>
+
                         <titre>Kill</titre>
                         <titre>Kill</titre>
-
<description>
+
                        <ul>
-
<ul>
+
                            <li>Transformation of NM522 strain with the part BBa_K606030 (pBK6) and promoter+dispersin;</li>
-
      <li>Transformation results</li>
+
                            <li>Ligation Prom+Dsp in P23 and transformation;</li>
-
      <ul>
+
                            <li>Ligation Lysostaphin in pSB1C3 and transformation;</li>
-
              <li>Prom+Dsp in p23 : nothing on the plate;</li>
+
                            <li>Isolation of 6 clones of the Term transformation;</li>
-
              <li>Lysostaphin, negative witness contains bacteria so the plate is put in junk.</li>
+
                            <li>Transformation results of fluorescent genes: ok, except yfp </li>
-
      </ul>
+
                            <li>NM522 strain containing pUC57-lysostaphin is put in storage under the name of BK12.</li>
-
      <li>New digestions, ligations,transformations:</li>
+
                        </ul>
-
      <ul>
+
                        </description>
-
              <li>Lyso+Dsp in pUc57;</li>
+
                        </jour>
-
              <li>Dsp in PSB1C3;</li>
+
-
              <li>Lyso in PSB1C3;</li>
+
-
              <li>Prom+Dsp in p23.</li>
+
-
      </ul>
+
-
      <li>streaking of 4 clones of the transformed strain NM522/pBK6 on a Cm + LB plate. All of them formed red colonies which shows that the constitutive promotor and the RBS specific to the Bacillus subtilis strain are recognized by the RNA polymerase of <i>E coli</i>.</li>
+
-
</ul>
+
-
</description>
+
-
                      <titre>Stick</titre>
+
-
<description>
+
-
PCR of XylR. Gel electrophoresis: the PCR didn’t work.
+
-
</description>
+
                        <jour nb="23">
-
</jour>
+
                        <date> Monday, July 23rd 2012</date>
-
 
+
-
<jour>
+
-
<date> Tuesday, July 24th 2012</date>
+
                         <titre>For all purposes</titre>
                         <titre>For all purposes</titre>
-
<description>
+
                        <description>
-
<ul>
+
                        <ul>
-
    <li>Plasmid extraction from Bacillus strain (BT407 GFP). We tested 2 methods in parallel. However, only the one using the extraction kit seems to work.</li>
+
                            <li>Selected clones (NM522+pBK6) are red, meaning that pVeg promoter and RBS from subtilis are recognized by <i>E. coli</i>’s ribosome. 4 clones are streaked in LB+Cm.</li>
-
    <li>Extraction of gfp, cfp, yfp ;  test => OK : put in storage.</li>
+
                            <li>GL+Ery and TSB+Tet Petri plates are made.</li>
-
    <li>YFP transformation was successful.</li>
+
                            <li>YFP transformation was successful.</li>
-
    <li>Extraction of the pHT 315 GFP plasmid of <i>B. thuringiensis</i> 407 GFP to build a shuttle vector <i>B. subtilis</i> ⇔ <i>E. coli</i>. Transformation in NM522 strain and selection on Ampicillin media : ok.</li>
+
                            <li>GFP and CFP plasmids’ extraction showed a failure in ligation.</li>
-
    <li><i>B. subtilis</i> 168 is put in storage (BK14) in TSB medium.</li>
+
                            <li><i>B. subtilis</i> 168 is put in storage (BK14) in TSB medium.</li>
-
    <li><i>S. epidermidis</i> is put in storage in TSB media under the reference BK15.</li>
+
                            <li>Extraction of B0015 terminator. Gel electrophoresis showed 4 good clones.</li>
-
</ul>
+
                        </ul>
-
</description>
+
                         <titre>Kill</titre>
                         <titre>Kill</titre>
-
<description>
+
                        <ul>
-
<ul>
+
                            <li>Transformation results</li>
-
      <li>Transformation results:
+
                            <ul>
-
      <ul>
+
                                <li>Prom+Dsp in p23 : nothing on the plate;</li>
-
              <li>Lyso+Dsp in pUc57 : the plate is covered of clones;</li>
+
                                <li>Lysostaphin, negative witness contains bacteria so the plate is put in junk.</li>
-
              <li>Promoter+Dsp : nothing on the plate;</li>
+
                            </ul>
-
              <li>Dsp in PSB1C3 : a lot of clones;</li>
+
                            <li>New digestions, ligations,transformations:</li>
-
              <li>Lyso in PSB1C3 : a lot of clones.</li>
+
                            <ul>
-
      </ul>
+
                                <li>Lyso+Dsp in pUc57;</li>
-
      Selection of 4 clones of each lyso+igem plasmid and dsp+igem plasmid on Cm plate and in a liquid culture. Isolation of lyso+dsp (because there are too many clones!)</li>
+
                                <li>Dsp in PSB1C3;</li>
 +
                                <li>Lyso in PSB1C3;</li>
 +
                                <li>Prom+Dsp in p23.</li>
 +
                            </ul>
 +
                            <li>streaking of 4 clones of the transformed strain NM522/pBK6 on a Cm + LB plate. All of them formed red colonies which shows that the constitutive promotor and the RBS specific to the Bacillus subtilis strain are recognized by the RNA polymerase of <i>E coli</i>.</li>
 +
                        </ul>
 +
                        <titre>Stick</titre>
 +
                        PCR of XylR. Gel electrophoresis: the PCR didn’t work.
-
      <li>Extraction of the plasmidic DNA [Promoter in PSB1C3].</li>
+
                        </description>
-
      <li>Extraction of pBK6 from the transformed strain.</li>
+
                        </jour>
-
      <li>Extraction of the [Promoter+RBS+GFP] in pBK 23 (Tet R) by miniprep and check by electrophoresis after digesting by EcoRI and PstI : gel ok. Congrats (pBK12) -> 122,6 ng/µL.</li>
+
-
      <li>Extraction of the pBK6 plasmid (PVeg+RBS+RFP in psB1C3). The electrophoresis confirms the plasmid’s structure.</li>
+
-
      <li>- Liquid culture of Bs168 pWG100 overnight in order to do the first lysostaphin tests on plates.</li>
+
-
</ul>
+
-
</description>
+
-
                      <titre>Stick</titre>
+
-
<description>
+
-
New PCR of XylR with some modifications in the protocol : the PCR didn’t work.
+
-
</description>
+
                        </month>
-
</jour>
+
                        </project>
 +
                        </xml>
 +
                    </div>
-
<jour>
+
                    <div id="contentPage">
-
<date> Wednesday, July 25th 2012</date>
+
                        <br>
-
                         <titre>For all purposes</titre>
+
                         <h1>The Notebooks</h1>
-
<description>
+
                        <br>
-
<ul>
+
                         <div id="monthSelection">
-
    <li>Strains are put in storage :</li>
+
                            <div class="month">July</div>
-
    <ul>
+
                            <div class="month">August</div>
-
            <li><i>S. epidermidis</i> on TSB+Tet (BK17);</li>
+
                            <div class="month">September</div>
-
            <li><i>B. thuringensis</i> 407 GFP on GL+Ery (BK16).</li>
+
                            <div class="month">October</div>
-
    </ul>
+
                        </div>
-
    <li>Minipreps to extract the plasmidic DNA of the clones NM522 + pHT 315 GFP and check by electrophoresis : plasmid ok (digested by E, X, S, P and no digested).</li>
+
                        <br>
-
    <li>Transformation attempt of Bs 168 by pBK5 with a new procedure : Failure ⇒ the fault of the plasmid which seems not to be the plasmid waited...Try again with the shuttle vector pHT 315 (GFP or not).</li>
+
-
    <li>The plasmid extraction protocol from <i>B. subtilis</i> was tested once again, with a few modifications. The results were unsatisfying. After electrophoresis, only genomic DNA was observed.</li>
+
-
</ul>
+
-
</description>
+
-
                         <titre>Kill</titre>
+
-
<description>
+
-
<ul>
+
-
      <li>Check of the plasmidic DNA extracted of the clones transformed by [Promoter in pSB1C3] : none of the 4 clones is ok.</li>
+
-
      <li>Selection of 4 clones transformed by [lyso+dsp] on LB+Amp plates and on liquid cultures.</li>
+
-
      <li>Miniprep to extract [Lyso+Cm] and [Disp+Cm] → Digestion.</li>
+
-
      <li>3A ligation between : lysostaphin in puc57 + Terminator in pSB1K3 + pSB1C3. Check by electrophoresis : Lysostaphin, terminator and vector are ok but not the ligation (no DNA).</li>
+
-
      <li>Lysostaphin tests (Bs 168 pWG100 supernatant) on antibiograms (diameter : 6mm) applied on GL+Tet plates having a biofilm already etablished and in development of <i>S. epidermidis.</i></li>
+
-
</ul>
+
-
</description>
+
-
                      <titre>Stick</titre>
+
-
<description>
+
-
PCR on the <i>B. subtilis</i> 168 genome using universal primers of Phil Oger, and positive control with <i>Bulkhoderia cepacia</i> genome provided by Phil Oger. Goal : determine if the PCR problems come from the primers or the low concentration of genomic DNA of <i>B. subtilis</i> 168.
+
-
</description>
+
-
</jour>
+
-
<jour>
+
                        <!-- MODIF LUCAS -->
-
<date> Thursday, July 26th 2012</date>
+
                         <div id="monthDays">
-
                         <titre>For all purposes</titre>
+
                            <ul>
-
<description>
+
                                   
-
<ul>
+
                            </ul>
-
    <li>Transformation of NM522 strain with pHT304 and pHT315 (2 shuttle vectors for <i>B. subtilis</i> and <i>E. coli</i>).</li>
+
                        </div>
-
    <li>gDNA extraction with 2 differents protocols : the first for <i>Bacillus subtilis</i> 168 and the second for Gram- bacteria with some modifications. The first protocol gives a better yield.</li>
+
                        <!-- //MODIF LUCAS -->
-
    <li>PCR of ARNr 16s on B.s. 168 to test if PCR works in the bacteria without being lysed : it works.</li>
+
                     
-
    <li>NM522 + gfp, cfp and yfp in storage.</li>
+
                         <div id="descJour">
-
    <li>pHT 315 GFP put in storage under the reference pBK 18.</li>
+
                            <div id="jourPrecedent"><img src="./igem_files/Precedent.gif" width="30px" height="30px"><br>Previous day</div>
-
    <li>NM522 + pHT 315 GFP strain put in storage under the reference BK 21.</li>
+
-
</ul>
+
-
</description>
+
-
                         <titre>Kill</titre>
+
-
<description>
+
-
<ul>
+
-
      <li>Other clones transformed with the Constitutive Promoter in pSB1C3 are selected in order to do other check by extracting their plasmidic DNA. ( bur they are not good again).</li>
+
-
      <li>Extraction of the plasmidic DNA of the clones transformed with Lyso+Disp in pBK2 and check by electrophoresis gel. The clones are not right.</li>
+
-
</ul>
+
-
</description>
+
-
                      <titre>Surfactant</titre>
+
-
<description>
+
-
3A assembly rbs-gfp (pbk7-pbk14) in psb1K3 = L1. Transformation of L1 in NM522.
+
-
</description>
+
-
</jour>
+
-
<jour>
+
                            <div id="noteBookTextContent">
-
<date> Friday, July 27th 2012</date>
+
                                <div class="scrollbar disable" style="height: 300px; "><div class="track" style="height: 300px; "><div class="thumb" style="height: 300px; "><div class="end"></div></div></div></div>
-
                        <titre>For all purposes</titre>
+
                                <div class="viewport">  
-
<description>
+
                                    <div class="overview textContent" style="top: 0px; ">                    
-
Extraction of transformed clones (NM522/pHT304 et NM522/pHT315). The electrophoresis showed that the plasmids had approximately 7kb  and the restriction sites XbaI, EcorI and PstI as expected. However, there is a SpeI site which was not mapped.
+
                                    </div>
-
</description>
+
                                </div>
-
                        <titre>Kill</titre>
+
                            </div>
-
<description>
+
-
<ul>
+
-
      <li>Extraction of plasmidic DNA : clones Lysostaphin in PSB1C3, Promoter in pSB1C3.</li>
+
-
      <li>Plasmidic DNA check by digestion and electrophoresis : Clones Lysostaphin okay and Promoter clones are not okay.</li>
+
-
      <li>New 3A ligation with Lyso/Terminator/pSB1C3 and transformation in NM522 strain.</li>
+
-
      <li>Results of the lysostaphin tests on plates : no effect (regular biofilms)</li>
+
-
</ul>
+
-
</description>
+
-
                      <titre>Surfactant</titre>
+
-
<description>
+
-
<ul>
+
-
      <li>sfp (surfactin part 1) and abrB put in storage : pBK16 et pBK17.</li>
+
-
      <li>Failure of transformation of L1 in NM522.</li>
+
-
      <li>3A assembly of RBS-CFP (pBK7-pBK13) in pSB1C3 = L2. (!! the part2 construction already has a terminator)</li>
+
-
      <li>3A assembly of sfp-part2(lacI)-term (pBK4-pBK10) in pSB1C3 = IV.</li>
+
-
</ul>
+
-
</description>
+
-
                      <titre>Stick</titre>
+
-
<description>
+
-
<ul>
+
-
      <li>PCR of xylR from gDNA extracted yesterday. Test on gel : PCR successful !!</li>
+
-
      <li>3A ligation of RBS (pBK7) and XylR (produced by PCR) in pSB1C3 ( ! the vector plamid has the same resistance as the plasmid containing the RBS...).</li>
+
-
</ul>
+
-
</description>
+
-
</jour>
+
-
<jour>
 
-
<date> Monday, July 30th 2012</date>
 
-
                        <titre>For all purposes</titre>
 
-
<description>
 
-
<ul>
 
-
      <li>Meeting at 9 o’clock.</li>
 
-
      <li><i>It was also a fire day : a man’s hair and a lab bench on fire !!!! As the saying goes, ”everything comes in threes, if it's happened twice, it'll happen a third time ” (we’re still waiting for the third fire...).</i></li>
 
-
</ul>
 
-
</description>
 
-
                        <titre>Kill</titre>
 
-
<description>
 
-
<ul>
 
-
      <li>Digestion test and gel of pBK2 (prom + lyso) by EcoRI and SpeI, pBK3 (disp + term) by XbaI and PstI and pSB1C3 by EcoRI and Pst1.</li>
 
-
      <li>We got 3 clones for the transformation of NM522 bacteria with the ligation’s product Lyso+Terminater-pSB1C3 : the plasmidic DNA of these 3 clones is extracted and tested by electrophoresis gel ⇒ the 3 clones aren’t right.</li>
 
-
      <li>Lysostaphin test on plate : this time, by trying with biofilm in formation less dense (OD = 0,5, dilution the culture x100, 1000 and 10 000).</li>
 
-
</ul>
 
-
</description>
 
-
                      <titre>Surfactant</titre>
 
-
<description>
 
-
<ul>
 
-
      <li>Transformation of L1, L2 et IV in NM522.</li>
 
-
      <li>Transformation of sfp and abrB in NM522.</li>
 
-
</ul>
 
-
</description>
 
-
                      <titre>Stick</titre>
 
-
<description>
 
-
Purification of XylR, produced by PCR.
 
-
</description>
 
-
</jour>
 
-
<jour>
+
                            <div id="jourSuivant"><img style="float:right;" src="./igem_files/Suivant.gif" width="30px" height="30px"><br>Next day</div>
-
<date> Tuesday, July 31st 2012</date>
+
                            <div id="leDiapo">
-
                        <titre>Kill</titre>
+
                                <div id="titreDiapo">Watch us in action !</div>
-
<description>
+
                                <div class="diapoContent" style="width:320px;height:240px;padding:14px"><object width="320" height="240"><param name="movie" value="http://pf.kizoa.com/sflite.swf?did=3106662&amp;k=3963711"><param name="wmode" value="transparent"><param name="allowFullScreen" value="true"><embed src="http://pf.kizoa.com/sflite.swf?did=3106662&amp;k=3963711" type="application/x-shockwave-flash" wmode="transparent" width="320" height="240" allowfullscreen="true"></object><br></div>
-
Results of the lysostaphin tests on plates : negative. There is no biofilm : too diluated but even though, the colonies do not seem to be affected by the presence of Bs 168 pWG100 supernatant ⇒ the Bs 168 pWG100 have lost their plasmide ? (are cultivated without selection pressure, that is whitout erythromycin).
+
                            </div>
-
</description>
+
                        </div>
-
                      <titre>Surfactant</titre>
+
                    </div>
-
<description>
+
-
<ul>
+
-
      <li>Given the fact that the previous transformation didn’t work, we made an other transformation of NM522 strain with the abrB and sfp parts.</li>
+
-
      <li>Results of the transformations of L1, L2 and IV : ok. Selection of some clones in order to do minipreps.</li>
+
-
</ul>
+
-
</description>
+
-
                      <titre>Stick</titre>
+
-
<description>
+
-
Ligation of RBS and XylR and transformation in NM522 strain.
+
-
</description>
+
-
</jour>
+
-
</month>
+
-
<month name="August">
 
-
<jour>
 
-
<titre>For all purposes</titre>
 
-
<date> Wednesday, August 1st 2012</date>
 
-
<description>
 
-
 
-
<p>The transformation protocol for Bacillus was tested using the pHT315 GFP plasmid extracted from the <i>B. thuringiensis</i> BT407GFP strain.</p>
 
-
 
-
</description>
 
-
                        <titre>Kill</titre>
 
-
<description>
 
-
<ul>
 
-
      <li>Transformation results :
 
-
      <ul>
 
-
              <li>Lysostaphin+terminator : nothing;</li>
 
-
              <li>Lysostaphin+dispersin : a lot of clones.</li>
 
-
      </ul>
 
-
      Cultures in liquid LB of Lyso+Dsp are launched.</li>
 
-
      <li>Digestion of Promoter clones and lysostaphin clones followed by an electophoresis : lysostaphin clones are okay, promoter clones are not okay.</li>
 
-
      <li>pUC57 with Dsp put in storage : pBK3.</li>
 
-
      <li>Lysostaphin test : the come back ! This time, we used more <i>S. epidermidis</i> (DO= 0.75 diluted 1000 times) and  a control for the stability of the pWG100 plasmid (spreading of 200 µL on GL + Ery plates), after the liquid culture without selective pressure. Spreading on LB plates without Tetracycline (but addition of Tetracycline into the Bs 168 pWG100 supernatant).</li>
 
-
</ul>
 
-
</description>
 
-
                      <titre>Surfactant</titre>
 
-
<description>
 
-
<ul>
 
-
      <li>The strain NM522/pBK6 was put in storage under the reference BK22.</li>
 
-
      <li>Transformations of the NM522 strain with the ordered constructions (sfp and abrB in pUC57 AmpR). The transformation was unsuccessful, so we did it again.</li>
 
-
      <li>Quantification of Sfp and abrB constructions provided by Genecust using the Nanodrop.</li>
 
-
      <li>Miniprep of the L1, L2 and IV ligations : it didn’t work.</li>
 
-
</ul>
 
-
</description>
 
-
</jour>
 
-
 
-
                <jour>
 
-
<titre>For all purposes</titre>
 
-
<date> Thursday, August 2nd 2012</date>
 
-
<description>
 
-
<ul>
 
-
      <li>The transformation of the Bacillus strain failed because of contaminated LB media, so a new transformation was attempted.</li>
 
-
      <li>pHT 304 and pHT 315 plasmids supernumerary site SpeI deletion attempt by digestion, filling-in,  ligation and transformation in NM522.</li>
 
-
</ul>
 
-
</description>
 
-
                      <titre>Kill</titre>
 
-
<description>
 
-
<ul>
 
-
      <li>Extraction of plasmidic DNA from the Lysostaphin + Dispersin clones in Cm iGEM plasmid (pSB1C3) and from the BK12 strain clones. Plasmidic DNA is checked by digestions.<br /> Lysostaphin+Dsp clones digestion : clones not okay.</li>
 
-
      <li>Ligations of :
 
-
      <ul>
 
-
              <li>Constitutive promoter in Cm iGEM plasmid;</li>
 
-
              <li>Dispersin in Cm iGEM plasmid.</li>
 
-
      </ul>
 
-
      Ligation were verified by electrophoresis.</li>
 
-
      <li>Results of the Lysostaphin tests : some Bs 168 pWG100 contaminated the plate. However, we noticed a halo of 2-3 mm around the Bacillus colonies  where the <i>S. epidermidis</i> didn’t grow due to lysostaphin activity.</li>
 
-
      <li>New Lysostaphin test on LB+Tet plate with a negative control (10 µL of Ampicillin).</li>
 
-
</ul>
 
-
</description>
 
-
                      <titre>Stick</titre>
 
-
<description>
 
-
<ul>
 
-
      <li>Miniprep of 5 clones of the transformed NM522 strain with RBS-xylR and 2 clones of the NM522 transformed with the abrB construction. Given the fact that the NM522 strain used for the transformations was contaminated, the electrophoresis showed unexpected results.</li>
 
-
      <li>New ligation of RBS and XylR in pSB1A3 and transformation in NM522 strain.</li>
 
-
</ul>
 
-
</description>
 
-
                      <titre>Surfactant</titre>
 
-
<description>
 
-
The transformation of Sfp and abrB in NM522 strain didn’t work.
 
-
</description>
 
-
</jour>
 
-
 
-
<jour>
 
-
<date> Friday, August 3rd 2012</date>
 
-
                        <titre>For all purposes</titre>
 
-
<description>
 
-
<ul>
 
-
      <li>Meeting at 9 o’clock.</li>
 
-
      <li>Purification of the NM 522 strain (because of the problems on the negativ control during the transformation) and resistance tests on the purified clones.</li>
 
-
      <li>The results of Bacillus transformation are inconclusive : there are only a few clones on the plate. However, the negative control has a few colonies too. Despite this result, we decided to verify six clones and extract their DNA.</li>
 
-
      <li>A lot of clones for the transformation of the pHT 304 and pHT 315 plasmids (without SpeI site) on LB+Amp plates ⇒ Purification of 12 clones of each.</li>
 
-
</ul>
 
-
</description>
 
-
                      <titre>Kill</titre>
 
-
<description>
 
-
<ul>
 
-
      <li>Replication with velvet of the Lysostaphin+Dispersin in pSB1C3 transformation plate on LB + Amp.</li>
 
-
      <li>Antibiotic resistance checked for 5 clones Lysostaphin+Dispersin in iGEM plasmid (clones 1 to 5).</li>
 
-
      <li>BK12 strain check : spread on LB ampicillin.</li>
 
-
      <li>Ligation Promoter+Dispersin in Cm iGEM plasmid followed by transformation of the 3 ligations.</li>
 
-
      Ligation were verified by electrophoresis.</li>
 
-
      <li>Transformation of Promoter+Dispersin ligation.</li>
 
-
      <li>PCR to check the presence of the promoter in the clones Promoter in Cm iGEM plasmid.</li>
 
-
      <li>Preliminary test of the liquid lysostaphin (10 µL of tetracycline to kill <i>Bacillus</i>, 500 µL of BS 168 pWG100 supernatant, 500 µL of <i>S. epidermidis</i> with OD=1,2 (the strains are cultivated overnight at 30°C). This test shows a possible effect of lysostaphin (decrease of the OD with the time, during 3h30). To be repeated with a negative control without Bs 168 pWG100.</li>
 
-
</ul>
 
-
</description>
 
-
                      <titre>Surfactant</titre>
 
-
<description>
 
-
<ul>
 
-
      <li>Ligation (3A protocol) of pBK7, pBK13 and iGEM backbone pSB1K3 (=RBS+CFP+pSB1K3).</li>
 
-
      <li>Ligation (3A protocol) of pBK7, pBK14 and iGEM backbone pSB1K3 (=RBS+GFP+pSB1K3).</li>
 
-
      <li>Because of the difficulties to transform the bacteria with the plasmids containing Sfp and abrB, we decided to do an electrophoresis directly on the constructions sent by Genecust. Result : the genes were not inserted in a pUC57 plasmid.</li>
 
-
      <li>Ligation of abrB and sfp in pSB1K3 and transformation in NM522.</li>
 
-
</ul>
 
-
</description>
 
-
                      <titre>Stick</titre>
 
-
<description>
 
-
New ligation between RBS and XylR in pSB1A3 and transformation in NM522 strain.
 
-
</description>
 
-
</jour>
 
-
 
-
<jour>
 
-
<date> Saturday, August 4th 2012</date>
 
-
                        <titre>Kill</titre>
 
-
<description>
 
-
<ul>
 
-
      <li>Transformation results :
 
-
      <ul>
 
-
              <li>The negative control is ok;</li>
 
-
              <li>There are clones on every transformation plates (Promoter in pSB1C3, Dispersin in pSB1C3, Promoter+Dispersin in pSB1C3).</li>
 
-
      </ul>
 
-
      8 clones per type of transformation are chosen and spread on LB+Cm and LB+Amp plates.</li>
 
-
</ul>
 
-
</description>
 
-
                      <titre>Surfactant</titre>
 
-
<description>
 
-
<ul>
 
-
      <li>Transormations of abrB and sfp are a success !! :D</li>
 
-
      <li>Liquid cultures of abrB and sfp clones are launched to do plasmid extractions.</li>
 
-
</ul>
 
-
</description>
 
-
                      <titre>Stick</titre>
 
-
<description>
 
-
Sorting of the RBS + xylR clones to eliminate the clones having two plasmids religated.
 
-
</description>
 
-
</jour>
 
-
 
-
<jour>
 
-
<date> Sunday, August 5th 2012</date>
 
-
                        <titre>For all purposes</titre>
 
-
<description>
 
-
Liquid culture of 6 NM522 clones with pHT 304 S and 6 clones pHT 315 S.
 
-
</description>
 
-
                      <titre>Surfactant</titre>
 
-
<description>
 
-
Plasmid extractions from 3 clones NM522/abrB and 5 clones NM522/sfp. The electrophoresis of the digested plasmids with EcoRI and PstI confirmed the presence of sfp construction (at 800 bp) and abrB construction  (at 500 bp).
 
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</description>
 
-
                      <titre>Stick</titre>
 
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<description>
 
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Liquid cultures of RBS+XylR clones are launched to do plasmid extractions.
 
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</description>
 
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</jour>
 
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</month>
 
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</project>
 
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  </xml>
 
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</div>
 
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<div id="contentPage">
 
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<br/>
 
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<h1>The Notebook</h1>
 
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<br/>
 
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<div  id="monthSelection">
 
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<div class="month">July</div>
 
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        <div class="month">August</div>
 
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                        <div class="month">September</div>
 
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                        <div class="month">October</div>
 
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</div>
 
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<br/>
 
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                <div id="descJour">
 
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  <div id="jourPrecedent"><img src="https://static.igem.org/mediawiki/igem.org/8/8c/Precedent.gif" width="30px" height="30px"/><br/>Previous day</div>
 
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<div id="noteBookTextContent">
 
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<div class="scrollbar"><div class="track"><div class="thumb"><div class="end"></div></div></div></div>
 
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    <div class="viewport">  
 
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<div class="overview textContent">                   
 
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</div>
 
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</div>
 
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</div>
 
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                  <div id="jourSuivant"><img style="float:right;" src="https://static.igem.org/mediawiki/igem.org/0/08/Suivant.gif" width="30px" height="30px"/><br/>Next day</div>
 
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                  <div id="leDiapo">
 
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                  <div id="titreDiapo">Watch us in action !</div>
 
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                  <div class="diapoContent" style="width:320px;height:240px;padding:14px"><object width="320" height="240"><param name="movie" value="http://pf.kizoa.com/sflite.swf?did=3106662&k=3963711"></param><param name="wmode" value="transparent"></param><param name="allowFullScreen" value="true"></param><embed src="http://pf.kizoa.com/sflite.swf?did=3106662&k=3963711" type="application/x-shockwave-flash" wmode="transparent" width="320" height="240" allowFullScreen="true"></embed></object><br /></div>
 
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</div>
 
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                </div>
 
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</div>
 
</body>
</body>

Revision as of 09:46, 6 September 2012


The Notebooks


July
August
September
October


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Next day
Watch us in action !

Retrieved from "http://2012.igem.org/Team:Lyon-INSA/notebook"