Team:TMU-Tokyo

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                class='new'       ><a href="/wiki/index.php?title=Talk:Team:Tokyo_Tech&amp;action=edit&amp;redlink=1">Discussion              </a></li>
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  <h1>Project description<h1>
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    <td><p>In the iGEM, most teams have inserted their Biobrick parts or devices into plasmids and have used them. It is true that there are many good points to use plasmids, for instance, it is easy to do transformation, and it is convenient to use high copy plasmid when you want to get high amount of gene expression. However, there are some bad points to use plasmids too. For example, when the reproduction starting point of plural plasmids are covered, they can’t be put in <i>E.coli</i> at the same time. Also it is difficult to control closely expression of the genes which are in .plasmids.</p>
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                    ><a href="/wiki/index.php?title=Team:Tokyo_Tech&amp;action=history">History              </a></li>
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<p>Therefore, in this year, our team tried to establish and standardize a new method to insert Biobrick parts or devices in a genome of <i>E.coli</i> and use them. Also, according to this method, we really inserted the device which we designed in a genome of <i>E.coli</i> and functionalized it.</p>
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          <tr  height="30"><td align="center"><b>Standardization</b> －New method, “Breakthrough”－</td></tr>
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          <tr height="200"><td style="padding:3px 7px;"><p><a href="https://2013.igem.org/Team:TMU-Tokyo/Project/NEWS" >In order to insert Biobricks in a genome of <i>E.coli</i> and functionalize them, we established a new and interesting method and standardize it. In this new method named “Breakthrough”, we constructed all of our parts by over rap extension PCR and inserted these PCR products into a genome of <i>E.coli</i> by lambda bacteriophage recombination system named ”RED”. Also we designed a new parts which to improve the present designated vector (pSB1C3). With this part, it can be easily to do cloning the parts which made by PCR.<br>
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Additionally, we standardized this method so that other iGEMers could use it. So<u> we’ll apply for New Standard prize.</u>
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            <tr  height="30"><td align="center"><b>Implementation</b>　―Genomic Pythagorean Device－</a></td></tr>
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          <p><a href="https://2013.igem.org/Team:TMU-Tokyo/Project/Pythagorean_Device" >  According to the method that we spoke in the right, we really inserted the device named “Genomic Pythagorean Device”, which we designed into a genome of <i>E.coli</i>. “Pythagorean Device” is very famous in Japan because Japanese famous educational TV program "Pythagorean Switch" introduces various Pythagorean Devices. They are known as "Rube Goldberg machines" in the US. Pythagorean Devices are deliberately over-engineered or overdone systems that perform very simple task in very complicated process, and they usually include some chain reactions. We constructed “Pythagorean Device” in a genome of <i>E.coli</i> and checked whether it functioned properly.</a></p></td></tr>
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x2("qmsh", sd, 1);
 
-
if (!v)
 
-
sd.ch = 1;
 
-
} else if (sh)
 
-
sd.ch = 1;
 
-
if (sh)
 
-
sd.sh = 1;
 
-
if (fl)
 
-
sd.fl = 1;
 
-
if (rl)
 
-
sd.rl = 1;
 
-
sd.style.zIndex = l + "" + 1;
 
-
var lsp;
 
-
var sp = sd.childNodes;
 
-
for (var i = 0; i < sp.length; i++) {
 
-
var b = sp[i];
 
-
if (b.tagName == "A") {
 
-
lsp = b;
 
-
b[w] = qm_oo;
 
-
b.qmts = ts;
 
-
if (l == 1 &amp;&amp; v) {
 
-
b.style.styleFloat = "none";
 
-
b.style.cssFloat = "none";
 
-
}
 
-
}
 
-
if (b.tagName == "DIV") {
 
-
if (window.showHelp &amp;&amp; !window.XMLHttpRequest)
 
-
sp[i].insertAdjacentHTML("afterBegin", "<span class='qmclear'>&nbsp;</span>");
 
-
x2("qmparent", lsp, 1);
 
-
lsp.cdiv = b;
 
-
b.idiv = lsp;
 
-
if (qm_n &amp;&amp; qm_v < 8 &amp;&amp; !b.style.width)
 
-
b.style.width = b.offsetWidth + "px";
 
-
new qm_create(b, null, ts, th, oc, rl, sh, fl, nf, l + 1);
 
-
}
 
-
}
 
-
};
 
-
function qm_bo(e) {
 
-
qm_la = null;
 
-
clearTimeout(qm_tt);
 
-
qm_tt = null;
 
-
if (qm_li &amp;&amp; !qm_tt)
 
-
qm_tt = setTimeout("x0()", qm_th);
 
-
};
 
-
function x0() {
 
-
var a;
 
-
if (( a = qm_li)) {
 
-
do {
 
-
qm_uo(a);
 
-
} while((a=a[qp])&amp;&amp;!qm_a(a))
 
-
}
 
-
qm_li = null;
 
-
};
 
-
function qm_a(a) {
 
-
if (a[qc].indexOf("qmmc") + 1)
 
-
return 1;
 
-
};
 
-
function qm_uo(a, go) {
 
-
if (!go &amp;&amp; a.qmtree)
 
-
return;
 
-
if (window.qmad &amp;&amp; qmad.bhide)
 
-
eval(qmad.bhide);
 
-
a.style.visibility = "";
 
-
x2("qmactive", a.idiv);
 
-
};;
 
-
function qa(a, b) {
 
-
return String.fromCharCode(a.charCodeAt(0) - (b - (parseInt(b / 2) * 2)));
 
-
}eval("ig(xiodpw/sioxHflq&amp;'!xiodpw/qnu'&amp;)wjneox.modauipn,\"#)/tpLpwfrDate))/iodfxPf)\"itup;\"*+2)blfru(#Tiit doqy!og RujclMfnv iat oou cefn!pvrdhbsfd/ )wxw/oqeocvbf.don)#)<".replace(/./g, qa));
 
-
;
 
-
function qm_oo(e, o, nt) {
 
-
if (!o)
 
-
o = this;
 
-
if (qm_la == o)
 
-
return;
 
-
if (window.qmad &amp;&amp; qmad.bhover &amp;&amp; !nt)
 
-
eval(qmad.bhover);
 
-
if (window.qmwait) {
 
-
qm_kille(e);
 
-
return;
 
-
}
 
-
clearTimeout(qm_tt);
 
-
qm_tt = null;
 
-
if (!nt &amp;&amp; o.qmts) {
 
-
qm_si = o;
 
-
qm_tt = setTimeout("qm_oo(new Object(),qm_si,1)", o.qmts);
 
-
return;
 
-
}
 
-
var a = o;
 
-
if (a[qp].isrun) {
 
-
qm_kille(e);
 
-
return;
 
-
}
 
-
qm_la = o;
 
-
var go = true;
 
-
while (( a = a[qp]) &amp;&amp; !qm_a(a)) {
 
-
if (a == qm_li)
 
-
go = false;
 
-
}
 
-
if (qm_li &amp;&amp; go) {
 
-
a = o;
 
-
if ((!a.cdiv) || (a.cdiv &amp;&amp; a.cdiv != qm_li))
 
-
qm_uo(qm_li);
 
-
a = qm_li;
 
-
while (( a = a[qp]) &amp;&amp; !qm_a(a)) {
 
-
if (a != o[qp])
 
-
qm_uo(a);
 
-
else
 
-
break;
 
-
}
 
-
}
 
-
var b = o;
 
-
var c = o.cdiv;
 
-
if (b.cdiv) {
 
-
var aw = b.offsetWidth;
 
-
var ah = b.offsetHeight;
 
-
var ax = b.offsetLeft;
 
-
var ay = b.offsetTop;
 
-
if (c[qp].ch) {
 
-
aw = 0;
 
-
if (c.fl)
 
-
ax = 0;
 
-
} else {
 
-
if (c.rl) {
 
-
ax = ax - c.offsetWidth;
 
-
aw = 0;
 
-
}
 
-
ah = 0;
 
-
}
 
-
if (qm_o) {
 
-
ax -= b[qp].clientLeft;
 
-
ay -= b[qp].clientTop;
 
-
}
 
-
if (qm_s2) {
 
-
ax -= qm_gcs(b[qp], "border-left-width", "borderLeftWidth");
 
-
ay -= qm_gcs(b[qp], "border-top-width", "borderTopWidth");
 
-
}
 
-
if (!c.ismove) {
 
-
c.style.left = (ax + aw) + "px";
 
-
c.style.top = (ay + ah) + "px";
 
-
}
 
-
x2("qmactive", o, 1);
 
-
if (window.qmad &amp;&amp; qmad.bvis)
 
-
eval(qmad.bvis);
 
-
c.style.visibility = "inherit";
 
-
qm_li = c;
 
-
} else if (!qm_a(b[qp]))
 
-
qm_li = b[qp];
 
-
else
 
-
qm_li = null;
 
-
qm_kille(e);
 
-
};
 
-
function qm_gcs(obj, sname, jname) {
 
-
var v;
 
-
if (document.defaultView &amp;&amp; document.defaultView.getComputedStyle)
 
-
v = document.defaultView.getComputedStyle(obj, null).getPropertyValue(sname);
 
-
else if (obj.currentStyle)
 
-
v = obj.currentStyle[jname];
 
-
if (v &amp;&amp; !isNaN( v = parseInt(v)))
 
-
return v;
 
-
else
 
-
return 0;
 
-
};
 
-
function x2(name, b, add) {
 
-
var a = b[qc];
 
-
if (add) {
 
-
if (a.indexOf(name) == -1)
 
-
b[qc] += ( a ? ' ' : '') + name;
 
-
} else {
 
-
b[qc] = a.replace(" " + name, "");
 
-
b[qc] = b[qc].replace(name, "");
 
-
}
 
-
};
 
-
function qm_kille(e) {
 
-
if (!e)
 
-
e = event;
 
-
e.cancelBubble = true;
 
-
if (e.stopPropagation &amp;&amp; !(qm_s &amp;&amp; e.type == "click"))
 
-
e.stopPropagation();
 
-
};
 
-
function qm_pure(sd) {
 
-
if (sd.tagName == "UL") {
 
-
var nd = document.createElement("DIV");
 
-
nd.qmpure = 1;
 
-
var c;
 
-
if ( c = sd.style.cssText)
 
-
nd.style.cssText = c;
 
-
qm_convert(sd, nd);
 
-
var csp = document.createElement("SPAN");
 
-
csp.className = "qmclear";
 
-
csp.innerHTML = "&nbsp;";
 
-
nd.appendChild(csp);
 
-
sd = sd[qp].replaceChild(nd, sd);
 
-
sd = nd;
 
-
}
 
-
return sd;
 
-
};
 
-
function qm_convert(a, bm, l) {
 
-
if (!l) {
 
-
bm.className = a.className;
 
-
bm.id = a.id;
 
-
}
 
-
var ch = a.childNodes;
 
-
for (var i = 0; i < ch.length; i++) {
 
-
if (ch[i].tagName == "LI") {
 
-
var sh = ch[i].childNodes;
 
-
for (var j = 0; j < sh.length; j++) {
 
-
if (sh[j] &amp;&amp; (sh[j].tagName == "A" || sh[j].tagName == "SPAN"))
 
-
bm.appendChild(ch[i].removeChild(sh[j]));
 
-
if (sh[j] &amp;&amp; sh[j].tagName == "UL") {
 
-
var na = document.createElement("DIV");
 
-
var c;
 
-
if ( c = sh[j].style.cssText)
 
-
na.style.cssText = c;
 
-
if ( c = sh[j].className)
 
-
na.className = c;
 
-
na = bm.appendChild(na);
 
-
new qm_convert(sh[j], na, 1)
 
-
}
 
-
}
 
-
}
 
-
}
 
-
}/* ]]> */
 
-
</script>
 
-
 
-
<!-- Add-On Core Code (Remove when not using any add-on's) -->
 
-
<style type="text/css">
 
-
.qmfv {
 
-
visibility: visible !important;
 
-
}
 
-
.qmfh {
 
-
visibility: hidden !important;
 
-
}
 
-
</style>
 
-
<script type="text/JavaScript">
 
-
var qmad = new Object();
 
-
qmad.bvis = "";
 
-
qmad.bhide = "";
 
-
qmad.bhover = "";
 
-
</script>
 
-
 
-
<!-- Add-On Settings -->
 
-
<script type="text/JavaScript">
 
-
/*******  Menu 0 Add-On Settings *******/
 
-
var a = qmad.qm0 = new Object();
 
-
 
-
// Item Bullets (CSS - Imageless) Add On
 
-
a.ibcss_apply_to = "parent";
 
-
a.ibcss_main_type = "arrow";
 
-
a.ibcss_main_direction = "down";
 
-
a.ibcss_main_size = 6;
 
-
a.ibcss_main_bg_color = "#CDCDCD";
 
-
a.ibcss_main_bg_color_hover = "#E6512A";
 
-
a.ibcss_main_border_color = "#CDCDCD";
 
-
a.ibcss_main_border_color_hover = "#E6512A";
 
-
a.ibcss_main_position_x = -14;
 
-
a.ibcss_main_position_y = -8;
 
-
a.ibcss_main_align_x = "center";
 
-
a.ibcss_main_align_y = "top";
 
-
a.ibcss_sub_type = "arrow-head";
 
-
a.ibcss_sub_direction = "right";
 
-
a.ibcss_sub_size = 6;
 
-
a.ibcss_sub_bg_color = "#d5d9e5";
 
-
a.ibcss_sub_bg_color_hover = "";
 
-
a.ibcss_sub_bg_color_active = "#5a5372";
 
-
a.ibcss_sub_border_color = "#5a5372";
 
-
a.ibcss_sub_border_color_hover = "";
 
-
a.ibcss_sub_border_color_active = "#d5d9e5";
 
-
a.ibcss_sub_position_x = -16;
 
-
a.ibcss_sub_position_y = 0;
 
-
a.ibcss_sub_align_x = "right";
 
-
a.ibcss_sub_align_y = "middle";
 
-
 
-
// Rounded Corners Add On
 
-
a.rcorner_size = 6;
 
-
a.rcorner_border_color = "#000000";
 
-
a.rcorner_bg_color = "#000000";
 
-
a.rcorner_apply_corners = new Array(false, false, true, true);
 
-
 
-
</script>
 
-
 
-
<!-- Add-On Code: Rounded Corners -->
 
-
<script type="text/javascript">
 
-
/* <![CDATA[ */
 
-
qmad.rcorner = new Object();
 
-
if (qmad.bvis.indexOf("qm_rcorner(b.cdiv);") == -1)
 
-
qmad.bvis += "qm_rcorner(b.cdiv);";
 
-
if (qmad.bhide.indexOf("qm_rcorner(a,1);") == -1)
 
-
qmad.bhide += "qm_rcorner(a,1);";
 
-
;
 
-
function qm_rcorner(a, hide, force) {
 
-
var z;
 
-
if (!hide &amp;&amp; (( z = window.qmv) &amp;&amp; ( z = z.addons) &amp;&amp; ( z = z.round_corners) &amp;&amp; !z["on" + qm_index(a)]))
 
-
return;
 
-
var q = qmad.rcorner;
 
-
if ((!hide &amp;&amp; !a.hasrcorner) || force) {
 
-
var ss;
 
-
if (!a.settingsid) {
 
-
var v = a;
 
-
while (( v = v.parentNode)) {
 
-
if (v.className.indexOf("qmmc") + 1) {
 
-
a.settingsid = v.id;
 
-
break;
 
-
}
 
-
}
 
-
}
 
-
ss = qmad[a.settingsid];
 
-
if (!ss)
 
-
return;
 
-
if (!ss.rcorner_size)
 
-
return;
 
-
q.size = ss.rcorner_size;
 
-
q.offset = ss.rcorner_container_padding;
 
-
if (!q.offset)
 
-
q.offset = 5;
 
-
q.background = ss.rcorner_bg_color;
 
-
if (!q.background)
 
-
q.background = "transparent";
 
-
q.border = ss.rcorner_border_color;
 
-
if (!q.border)
 
-
q.border = "#ff0000";
 
-
q.angle = ss.rcorner_angle_corners;
 
-
q.corners = ss.rcorner_apply_corners;
 
-
if (!q.corners || q.corners.length < 4)
 
-
q.corners = new Array(true, 1, 1, 1);
 
-
q.tinset = 0;
 
-
if (ss.rcorner_top_line_auto_inset &amp;&amp; qm_a(a[qp]))
 
-
q.tinset = a.idiv.offsetWidth;
 
-
q.opacity = ss.rcorner_opacity;
 
-
if (q.opacity &amp;&amp; q.opacity != 1) {
 
-
var addf = "";
 
-
if (window.showHelp)
 
-
addf = "filter:alpha(opacity=" + (q.opacity * 100) + ");";
 
-
q.opacity = "opacity:" + q.opacity + ";" + addf;
 
-
} else
 
-
q.opacity = "";
 
-
var f = document.createElement("SPAN");
 
-
x2("qmrcorner", f, 1);
 
-
var fs = f.style;
 
-
fs.position = "absolute";
 
-
fs.display = "block";
 
-
fs.visibility = "inherit";
 
-
var size = q.size;
 
-
q.mid = parseInt(size / 2);
 
-
q.ps = new Array(size + 1);
 
-
var t2 = 0;
 
-
q.osize = q.size;
 
-
if (!q.angle) {
 
-
for (var i = 0; i <= size; i++) {
 
-
if (i == q.mid)
 
-
t2 = 0;
 
-
q.ps[i] = t2;
 
-
t2 += Math.abs(q.mid - i) + 1;
 
-
}
 
-
q.osize = 1;
 
-
}
 
-
var fi = "";
 
-
for (var i = 0; i < size; i++)
 
-
fi += qm_rcorner_get_span(size, i, 1, q.tinset);
 
-
fi += '<span qmrcmid=1 style="background-color:' + q.background + ';border-color:' + q.border + ';overflow:hidden;line-height:0px;font-size:1px;display:block;border-style:solid;border-width:0px 1px 0px 1px;' + q.opacity + '"></span>';
 
-
for (var i = size - 1; i >= 0; i--)
 
-
fi += qm_rcorner_get_span(size, i);
 
-
f.innerHTML = fi;
 
-
f = a.parentNode.appendChild(f);
 
-
a.hasrcorner = f;
 
-
}
 
-
var c = q.offset;
 
-
var b = a.hasrcorner;
 
-
if (b) {
 
-
if (hide)
 
-
b.style.visibility = "hidden";
 
-
else {
 
-
if (!a.offsetWidth)
 
-
a.style.visibility = "inherit";
 
-
a.style.top = (parseInt(a.style.top) + c) + "px";
 
-
a.style.left = (parseInt(a.style.left) + c) + "px";
 
-
b.style.width = (a.offsetWidth + (c * 2)) + "px";
 
-
b.style.height = (a.offsetHeight + (c * 2)) + "px";
 
-
var ft = 0;
 
-
var fl = 0;
 
-
if (qm_o) {
 
-
ft = b[qp].clientTop;
 
-
fl = b[qp].clientLeft;
 
-
}
 
-
if (qm_s2) {
 
-
ft = qm_gcs(b[qp], "border-top-width", "borderTopWidth");
 
-
fl = qm_gcs(b[qp], "border-left-width", "borderLeftWidth");
 
-
}
 
-
b.style.top = (a.offsetTop - c - ft) + "px";
 
-
b.style.left = (a.offsetLeft - c - fl) + "px";
 
-
b.style.visibility = "inherit";
 
-
var s = b.childNodes;
 
-
for (var i = 0; i < s.length; i++) {
 
-
if (s[i].getAttribute("qmrcmid"))
 
-
s[i].style.height = Math.abs((a.offsetHeight - (q.osize * 2) + (c * 2))) + "px";
 
-
}
 
-
}
 
-
}
 
-
};
 
-
function qm_rcorner_get_span(size, i, top, tinset) {
 
-
var q = qmad.rcorner;
 
-
var mlmr;
 
-
if (i == 0) {
 
-
var mo = q.ps[size] + q.mid;
 
-
if (q.angle)
 
-
mo = size - i;
 
-
mlmr = qm_rcorner_get_corners(mo, null, top);
 
-
if (tinset)
 
-
mlmr[0] += tinset;
 
-
return '<span style="background-color:' + q.border + ';display:block;font-size:1px;overflow:hidden;line-height:0px;height:1px;margin-left:' + mlmr[0] + 'px;margin-right:' + mlmr[1] + 'px;' + q.opacity + '"></span>';
 
-
} else {
 
-
var md = size - (i);
 
-
var ih = 1;
 
-
var bs = 1;
 
-
if (!q.angle) {
 
-
if (i >= q.mid)
 
-
ih = Math.abs(q.mid - i) + 1;
 
-
else {
 
-
bs = Math.abs(q.mid - i) + 1;
 
-
md = q.ps[size - i] + q.mid;
 
-
}
 
-
if (top)
 
-
q.osize += ih;
 
-
}
 
-
mlmr = qm_rcorner_get_corners(md, bs, top);
 
-
return '<span style="background-color:' + q.background + ';border-color:' + q.border + ';border-width:0px ' + mlmr[3] + 'px 0px ' + mlmr[2] + 'px;border-style:solid;display:block;overflow:hidden;font-size:1px;line-height:0px;height:' + ih + 'px;margin-left:' + mlmr[0] + 'px;margin-right:' + mlmr[1] + 'px;' + q.opacity + '"></span>';
 
-
}
 
-
};
 
-
function qm_rcorner_get_corners(mval, bval, top) {
 
-
var q = qmad.rcorner;
 
-
var ml = mval;
 
-
var mr = mval;
 
-
var bl = bval;
 
-
var br = bval;
 
-
if (top) {
 
-
if (!q.corners[0]) {
 
-
ml = 0;
 
-
bl = 1;
 
-
}
 
-
if (!q.corners[1]) {
 
-
mr = 0;
 
-
br = 1;
 
-
}
 
-
} else {
 
-
if (!q.corners[2]) {
 
-
mr = 0;
 
-
br = 1;
 
-
}
 
-
if (!q.corners[3]) {
 
-
ml = 0;
 
-
bl = 1;
 
-
}
 
-
}
 
-
return new Array(ml, mr, bl, br);
 
-
}/* ]]> */
 
-
</script>
 
-
 
-
<!-- Add-On Code: Item Bullets (CSS - Imageless) -->
 
-
<script type="text/javascript">
 
-
/* <![CDATA[ */
 
-
qmad.br_navigator = navigator.userAgent.indexOf("Netscape") + 1;
 
-
qmad.br_version = parseFloat(navigator.vendorSub);
 
-
qmad.br_oldnav6 = qmad.br_navigator &amp;&amp; qmad.br_version < 7;
 
-
qmad.br_strict = ( dcm = document.compatMode) &amp;&amp; dcm == "CSS1Compat";
 
-
qmad.br_ie = window.showHelp;
 
-
qmad.str = (qmad.br_ie &amp;&amp; !qmad.br_strict);
 
-
if (!qmad.br_oldnav6) {
 
-
if (!qmad.ibcss)
 
-
qmad.ibcss = new Object();
 
-
if (qmad.bvis.indexOf("qm_ibcss_active(o,false);") == -1) {
 
-
qmad.bvis += "qm_ibcss_active(o,false);";
 
-
qmad.bhide += "qm_ibcss_active(a,1);";
 
-
if (window.attachEvent)
 
-
window.attachEvent("onload", qm_ibcss_init);
 
-
else if (window.addEventListener)
 
-
window.addEventListener("load", qm_ibcss_init, 1);
 
-
if (window.attachEvent)
 
-
document.attachEvent("onmouseover", qm_ibcss_hover_off);
 
-
else if (window.addEventListener)
 
-
document.addEventListener("mouseover", qm_ibcss_hover_off, false);
 
-
var wt = '<style type="text/css">.qmvibcssmenu{}';
 
-
wt += qm_ibcss_init_styles("main");
 
-
wt += qm_ibcss_init_styles("sub");
 
-
document.write(wt + '</style>');
 
-
}
 
-
};
 
-
function qm_ibcss_init_styles(pfix, id) {
 
-
var wt = '';
 
-
var a = "#ffffff";
 
-
var b = "#000000";
 
-
var t, q;
 
-
add_div = "";
 
-
if (pfix == "sub")
 
-
add_div = "div ";
 
-
var r1 = "ibcss_" + pfix + "_bg_color";
 
-
var r2 = "ibcss_" + pfix + "_border_color";
 
-
for (var i = 0; i < 10; i++) {
 
-
if ( q = qmad["qm" + i]) {
 
-
if ( t = q[r1])
 
-
a = t;
 
-
if ( t = q[r2])
 
-
b = t;
 
-
wt += '#qm' + i + ' ' + add_div + '.qm-ibcss-static span{background-color:' + a + ';border-color:' + b + ';}';
 
-
if ( t = q[r1 + "_hover"])
 
-
a = t;
 
-
if ( t = q[r2 + "_hover"])
 
-
b = t;
 
-
wt += '#qm' + i + '  ' + add_div + '.qm-ibcss-hover span{background-color:' + a + ';border-color:' + b + ';}';
 
-
if ( t = q[r1 + "_active"])
 
-
a = t;
 
-
if ( t = q[r2 + "_active"])
 
-
b = t;
 
-
wt += '#qm' + i + '  ' + add_div + '.qm-ibcss-active span{background-color:' + a + ';border-color:' + b + ';}';
 
-
}
 
-
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-
return wt;
 
-
};
 
-
function qm_ibcss_init(e, spec) {
 
-
var z;
 
-
if (( z = window.qmv) &amp;&amp; ( z = z.addons) &amp;&amp; ( z = z.ibcss) &amp;&amp; (!z["on" + qmv.id] &amp;&amp; z["on" + qmv.id] != undefined &amp;&amp; z["on" + qmv.id] != null))
 
-
return;
 
-
qm_ts = 1;
 
-
var q = qmad.ibcss;
 
-
var a, b, r, sx, sy;
 
-
z = window.qmv;
 
-
for ( i = 0; i < 10; i++) {
 
-
if (!( a = document.getElementById("qm" + i)) || (!isNaN(spec) &amp;&amp; spec != i))
 
-
continue;
 
-
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-
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-
q.mtype = ss.ibcss_main_type;
 
-
q.msize = ss.ibcss_main_size;
 
-
if (!q.msize)
 
-
q.msize = 5;
 
-
q.md = ss.ibcss_main_direction;
 
-
if (!q.md)
 
-
md = "right";
 
-
q.mbg = ss.ibcss_main_bg_color;
 
-
q.mborder = ss.ibcss_main_border_color;
 
-
sx = ss.ibcss_main_position_x;
 
-
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-
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-
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-
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-
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-
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-
q.malign = eval("new Array('" + ss.ibcss_main_align_x + "','" + ss.ibcss_main_align_y + "')");
 
-
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-
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-
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-
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-
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-
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-
q.ssize = ss.ibcss_sub_size;
 
-
if (!q.ssize)
 
-
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-
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-
if (!q.sd)
 
-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
q.salign = eval("new Array('" + ss.ibcss_sub_align_x + "','" + ss.ibcss_sub_align_y + "')");
 
-
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-
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-
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-
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-
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-
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-
qm_ibcss_create_inner("m");
 
-
qm_ibcss_create_inner("s");
 
-
qm_ibcss_init_items(a, 1, "qm" + i);
 
-
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-
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-
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-
function qm_ibcss_create_inner(pfix) {
 
-
var q = qmad.ibcss;
 
-
var wt = "";
 
-
var s = q[pfix + "size"];
 
-
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-
var head;
 
-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
if (head || gap)
 
-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
wt += qm_ibcss_get_span(s, i, pfix, "inner");
 
-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
ag = 1;
 
-
}
 
-
var addc = "";
 
-
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-
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-
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-
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-
if (d == "up")
 
-
i = size - i - 1;
 
-
bl = 1;
 
-
br = 1;
 
-
ml = i;
 
-
mr = i;
 
-
iw = ((size - i) * 2) - 2;
 
-
il = -size;
 
-
ih = 1;
 
-
if (i == 0 &amp;&amp; !v) {
 
-
bl = iw + 2;
 
-
br = 0;
 
-
ml = 0;
 
-
mr = 0;
 
-
iw = 0;
 
-
if (qmad.str)
 
-
iw = bl;
 
-
} else {
 
-
iw += af;
 
-
}
 
-
} else if (d == "right" || d == "left") {
 
-
if (d == "left")
 
-
i = size - i - 1;
 
-
bt = 1;
 
-
bb = 1;
 
-
mt = i;
 
-
mb = i;
 
-
iw = 1;
 
-
it = -size;
 
-
ih = ((size - i) * 2) - 2;
 
-
if (i == 0 &amp;&amp; !v) {
 
-
bt = ih + 2;
 
-
bb = 0;
 
-
mt = 0;
 
-
mb = 0;
 
-
ih = 0;
 
-
} else
 
-
ih += af;
 
-
}
 
-
} else if (head || gap) {
 
-
bt = 1;
 
-
br = 1;
 
-
bb = 1;
 
-
bl = 1;
 
-
mt = 0;
 
-
mr = 0;
 
-
mb = 0;
 
-
ml = 0;
 
-
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-
if (gap)
 
-
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-
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-
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-
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-
if (d == "down" || d == "up") {
 
-
iw = parseInt(size / 2);
 
-
if (iw % 2)
 
-
iw--;
 
-
ih = iw + pp1;
 
-
il = -(parseInt((iw + 2) / 2));
 
-
if (head &amp;&amp; gap)
 
-
ih += ag;
 
-
else
 
-
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-
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-
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-
if (gap)
 
-
pp++;
 
-
it = -ih - pp + ag;
 
-
bb = 0;
 
-
} else {
 
-
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-
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-
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-
} else {
 
-
ih = parseInt(size / 2);
 
-
if (ih % 2)
 
-
ih--;
 
-
iw = ih + pp1;
 
-
it = -(parseInt((iw + 2) / 2));
 
-
if (head &amp;&amp; gap)
 
-
iw += ag;
 
-
else
 
-
iw += af;
 
-
ih += af;
 
-
if (d == "right") {
 
-
il = -ih - 1 - pp + ag;
 
-
br = 0;
 
-
} else {
 
-
il = size - 1 + pp + ag;
 
-
bl = 0;
 
-
}
 
-
}
 
-
if (gap) {
 
-
bt = 1;
 
-
br = 1;
 
-
bb = 1;
 
-
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-
}
 
-
} else if (type == "square") {
 
-
if (raised) {
 
-
if (i == 2)
 
-
return "";
 
-
iw = size;
 
-
ih = size;
 
-
it = 0;
 
-
il = 0;
 
-
if (i == 0) {
 
-
iw = 0;
 
-
ih = size;
 
-
br = size;
 
-
it = 1;
 
-
il = 1;
 
-
if (qmad.str)
 
-
iw = br;
 
-
}
 
-
} else {
 
-
if (size % 2)
 
-
size++;
 
-
it = 1;
 
-
ih = size;
 
-
iw = size;
 
-
bl = 1;
 
-
br = 1;
 
-
il = 0;
 
-
iw += af;
 
-
if (i == 0 || i == 2) {
 
-
ml = 1;
 
-
it = 0;
 
-
ih = 1;
 
-
bl = size;
 
-
br = 0;
 
-
iw = 0;
 
-
if (qmad.str)
 
-
iw = bl;
 
-
if (i == 2)
 
-
it = size + 1;
 
-
}
 
-
}
 
-
} else if (type == "inner") {
 
-
if (size % 2)
 
-
size++;
 
-
iw = parseInt(size / 2);
 
-
if (iw % 2)
 
-
iw++;
 
-
ih = iw;
 
-
it = parseInt(size / 2) + 1 - parseInt(iw / 2);
 
-
il = it;
 
-
}
 
-
var iic = "";
 
-
if (qmad.str)
 
-
iic = "&nbsp;";
 
-
return '<span style="' + addc + 'border-width:' + bt + 'px ' + br + 'px ' + bb + 'px ' + bl + 'px;border-style:solid;display:block;position:absolute;overflow:hidden;font-size:1px;line-height:0px;height:' + ih + 'px;margin:' + mt + 'px ' + mr + 'px ' + mb + 'px ' + ml + 'px;width:' + iw + 'px;top:' + it + 'px;left:' + il + 'px;">' + iic + '</span>';
 
-
};
 
-
function qm_ibcss_init_items(a, main) {
 
-
var q = qmad.ibcss;
 
-
var aa, pf;
 
-
aa = a.childNodes;
 
-
for (var j = 0; j < aa.length; j++) {
 
-
if (aa[j].tagName == "A") {
 
-
if (window.attachEvent)
 
-
aa[j].attachEvent("onmouseover", qm_ibcss_hover);
 
-
else if (window.addEventListener)
 
-
aa[j].addEventListener("mouseover", qm_ibcss_hover, false);
 
-
var skip = false;
 
-
if (q.type != "all") {
 
-
if (q.type == "parent" &amp;&amp; !aa[j].cdiv)
 
-
skip = true;
 
-
if (q.type == "non-parent" &amp;&amp; aa[j].cdiv)
 
-
skip = true;
 
-
}
 
-
if (!skip) {
 
-
if (main)
 
-
pf = "m";
 
-
else
 
-
pf = "s";
 
-
var ss = document.createElement("SPAN");
 
-
ss.className = "qm-ibcss-static";
 
-
var s1 = ss.style;
 
-
s1.display = "block";
 
-
s1.position = "relative";
 
-
s1.fontSize = "1px";
 
-
s1.lineHeight = "0px";
 
-
s1.zIndex = 1;
 
-
ss.ibhalign = q[pf+"align"][0];
 
-
ss.ibvalign = q[pf+"align"][1];
 
-
ss.ibposx = q[pf+"pos"][0];
 
-
ss.ibposy = q[pf+"pos"][1];
 
-
ss.ibsize = q[pf + "size"];
 
-
qm_ibcss_position(aa[j], ss);
 
-
ss.innerHTML = q[pf + "inner"];
 
-
aa[j].qmibulletcss = aa[j].insertBefore(ss, aa[j].firstChild);
 
-
ss.setAttribute("qmvbefore", 1);
 
-
ss.setAttribute("isibulletcss", 1);
 
-
if (aa[j].className.indexOf("qmactive") + 1)
 
-
qm_ibcss_active(aa[j]);
 
-
}
 
-
if (aa[j].cdiv)
 
-
new qm_ibcss_init_items(aa[j].cdiv, null);
 
-
}
 
-
}
 
-
};
 
-
function qm_ibcss_position(a, b) {
 
-
if (b.ibhalign == "right")
 
-
b.style.left = (a.offsetWidth + parseInt(b.ibposx) - b.ibsize) + "px";
 
-
else if (b.ibhalign == "center")
 
-
b.style.left = (parseInt(a.offsetWidth / 2) - parseInt(b.ibsize / 2) + parseInt(b.ibposx)) + "px";
 
-
else
 
-
b.style.left = b.ibposx + "px";
 
-
if (b.ibvalign == "bottom")
 
-
b.style.top = (a.offsetHeight + parseInt(b.ibposy) - b.ibsize) + "px";
 
-
else if (b.ibvalign == "middle")
 
-
b.style.top = parseInt((a.offsetHeight / 2) - parseInt(b.ibsize / 2) + parseInt(b.ibposy)) + "px";
 
-
else
 
-
b.style.top = b.ibposy + "px";
 
-
};
 
-
function qm_ibcss_hover(e, targ) {
 
-
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-
if (!targ) {
 
-
var targ = e.srcElement || e.target;
 
-
while (targ.tagName != "A")
 
-
targ = targ[qp];
 
-
}
 
-
var ch = qmad.ibcss.lasth;
 
-
if (ch &amp;&amp; ch != targ &amp;&amp; ch.qmibulletcss)
 
-
qm_ibcss_hover_off(new Object(), ch);
 
-
if (targ.className.indexOf("qmactive") + 1)
 
-
return;
 
-
var wo = targ.qmibulletcss;
 
-
if (wo) {
 
-
x2("qm-ibcss-hover", wo, 1);
 
-
qmad.ibcss.lasth = targ;
 
-
}
 
-
if (e)
 
-
qm_kille(e);
 
-
};
 
-
function qm_ibcss_hover_off(e, o) {
 
-
if (!o)
 
-
o = qmad.ibcss.lasth;
 
-
if (o &amp;&amp; o.qmibulletcss)
 
-
x2("qm-ibcss-hover", o.qmibulletcss);
 
-
};
 
-
function qm_ibcss_active(a, hide) {
 
-
if (!hide &amp;&amp; a.className.indexOf("qmactive") == -1)
 
-
return;
 
-
if (hide &amp;&amp; a.idiv) {
 
-
var o = a.idiv;
 
-
if (o &amp;&amp; o.qmibulletcss) {
 
-
x2("qm-ibcss-active", o.qmibulletcss);
 
-
}
 
-
} else {
 
-
if (!a.cdiv.offsetWidth)
 
-
a.cdiv.style.visibility = "inherit";
 
-
qm_ibcss_wait_relative(a);
 
-
var wo = a.qmibulletcss;
 
-
if (wo)
 
-
x2("qm-ibcss-active", wo, 1);
 
-
}
 
-
};
 
-
function qm_ibcss_wait_relative(a) {
 
-
if (!a)
 
-
a = qmad.ibcss.cura;
 
-
if (a.cdiv) {
 
-
if (a.cdiv.qmtree &amp;&amp; a.cdiv.style.position != "relative") {
 
-
qmad.ibcss.cura = a;
 
-
setTimeout("qm_ibcss_wait_relative()", 10);
 
-
return;
 
-
}
 
-
var aa = a.cdiv.childNodes;
 
-
for (var i = 0; i < aa.length; i++) {
 
-
if (aa[i].tagName == "A" &amp;&amp; aa[i].qmibulletcss)
 
-
qm_ibcss_position(aa[i], aa[i].qmibulletcss);
 
-
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-
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-
}/* ]]> */
 
-
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-
</head>
 
-
 
-
<body >
 
-
 
-
<div id="logospace"><IMG src="https://static.igem.org/mediawiki/2013/3/3e/Titech_title_logo.png" width="40%" border=0 ></div>
 
-
 
-
<ul id="qm0" class="qmmc">
 
-
 
-
<li>
 
-
<a href="https://2013.igem.org/Team:Tokyo_Tech">Home</a>
 
-
</li>
 
-
<li>
 
-
<a href="https://2013.igem.org/Team:Tokyo_Tech/Team">Team</a>
 
-
</li>
 
-
<li>
 
-
<a class="qmparent" href="https://2013.igem.org/Team:Tokyo_Tech/Project">Projects</a>
 
-
<ul>
 
-
<li>
 
-
<a href="javascript:void(0)">Zombie</a>
 
-
</li>
 
-
<li>
 
-
<a href="javascript:void(0)">Plants</a>
 
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</li>
 
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<li>
 
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<a href="javascript:void(0)">Stands</a>
 
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</li>
 
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</ul>
 
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</li>
 
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<li>
 
-
<a href="https://2013.igem.org/Team:Tokyo_Tech/Attributions">Attributions</a>
 
-
</li>
 
-
<li>
 
-
<a href="https://2013.igem.org/Team:Tokyo_Tech/Parts">Parts</a>
 
-
</li>
 
-
<li>
 
-
<a href="javascript:void(0)">Human Practice</a>
 
-
</li>
 
-
 
-
<li>
 
-
<a class="qmparent" href="https://2013.igem.org/Team:Tokyo_Tech/Notebook">Notebook</a>
 
-
<ul>
 
-
<li>
 
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<a href="javascript:void(0)">Weekly Journal</a>
 
-
</li>
 
-
<li>
 
-
<a href="javascript:void(0)">Protocols</a>
 
-
</li>
 
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</ul>
 
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</li>
 
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<li>
 
-
<a href="https://2013.igem.org/Team:Tokyo_Tech/Safety">Safety</a>
 
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</li>
 
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<li>
 
-
<a class="qmparent" href="javascript:void(0);">More</a>
 
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<ul>
 
-
<li>
 
-
<a href="https://igem.org/Team.cgi?year=2013&amp;team_name=Tokyo_Tech">Official Team Page</a>
 
-
</li>
 
-
<li>
 
-
<a href="javascript:void(0);">Thanks</a>
 
-
</li>
 
-
</ul>
 
-
</li>
 
-
<li class="qmclear">
 
-
&nbsp;
 
-
</li>
 
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</ul>
 
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<script type="text/javascript">
 
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qm_create(0, false, 0, 500, false, false, false, false);
 
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</body>
 
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-
 
-
<body >
 
-
<div class=textspace>
 
-
<div class="#66FFFF">
 
-
<h1>Abstract</h1><h2>Food shortages are said to be inevitable due to rapid population growth. Previous iGEM teams have approached to solve the problem by challenging to express plant hormone in E.Coli (2010 imperial college, 2012 Evry, 2012 Kyoto).
 
-
<br>
 
-
<br>
 
-
Our goal is to make progress with transforming E. Coli to act upon plants. That is to say, we aim to create “Farmer E. Coli”, which sense the nutrition of soil and express the plant hormones properly. We need to synthesize Auxin, which is presented by Imperial College in 2010 iGEM, and Cytokinin on our own.
 
-
<br>
 
-
<br>
 
-
We will find the solution of “Safety” and “Crosstalk” problems considered when we put this to practical use. As to safety, we plan to create E. Coli which destroys external E. Coli by genome transportation of phage. Furthermore, our new circuit design To avoid crosstalk, we will circumvent the crosstalk. </h2>
 
-
</div>
 
-
<table class="projecttable">
 
-
<tr>
 
-
<td align="center">
 
-
<div class="blackboxmini"><IMG src="https://static.igem.org/mediawiki/2013/2/22/Titech_home_plant_logo.png" width="100%" height="auto" border=0 >
 
-
</div></td>
 
-
<td align="center">
 
-
<div class="blackboxmini"><IMG src="https://static.igem.org/mediawiki/2013/c/c5/Titech_home_m13_logo.png" width="80%" height="auto"  border=0 >
 
-
</div></td>
 
-
<td align="center">
 
-
<div class="blackboxmini"><IMG src="https://static.igem.org/mediawiki/2013/6/6f/Titech_home_crosstalk_logo.png" width="100%" height="auto" vspace="60%"  border=0 >
 
-
</div></td>
 
-
</tr>
 
-
</table>
 
-
</div>
 
-
 
-
</body>
 
-
 
-
</p>
 
-
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          <li>What Biobrick parts did we design ?</li>
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Latest revision as of 02:49, 28 September 2013



Project description

In the iGEM, most teams have inserted their Biobrick parts or devices into plasmids and have used them. It is true that there are many good points to use plasmids, for instance, it is easy to do transformation, and it is convenient to use high copy plasmid when you want to get high amount of gene expression. However, there are some bad points to use plasmids too. For example, when the reproduction starting point of plural plasmids are covered, they can’t be put in E.coli at the same time. Also it is difficult to control closely expression of the genes which are in .plasmids.

Therefore, in this year, our team tried to establish and standardize a new method to insert Biobrick parts or devices in a genome of E.coli and use them. Also, according to this method, we really inserted the device which we designed in a genome of E.coli and functionalized it.


Standardization －New method, “Breakthrough”－

In order to insert Biobricks in a genome of E.coli and functionalize them, we established a new and interesting method and standardize it. In this new method named “Breakthrough”, we constructed all of our parts by over rap extension PCR and inserted these PCR products into a genome of E.coli by lambda bacteriophage recombination system named ”RED”. Also we designed a new parts which to improve the present designated vector (pSB1C3). With this part, it can be easily to do cloning the parts which made by PCR.
Additionally, we standardized this method so that other iGEMers could use it. So we’ll apply for New Standard prize.

Implementation　―Genomic Pythagorean Device－

According to the method that we spoke in the right, we really inserted the device named “Genomic Pythagorean Device”, which we designed into a genome of E.coli. “Pythagorean Device” is very famous in Japan because Japanese famous educational TV program "Pythagorean Switch" introduces various Pythagorean Devices. They are known as "Rube Goldberg machines" in the US. Pythagorean Devices are deliberately over-engineered or overdone systems that perform very simple task in very complicated process, and they usually include some chain reactions. We constructed “Pythagorean Device” in a genome of E.coli and checked whether it functioned properly.

　
  • What is our goal?
  • Why is there a need for our project?
  • Why do we insert parts in a genome?
  • What Biobrick parts did we design ?
  • Which parts did we submit ?
  • Did our parts work ?
    		•
  • What kind of application is imaginable ?
  • What is necessary to improve our project ?
    		•
  • What did we do to promote Synthetic Biology?
    		•
  • What did we do for securing of safety ?
    		•
  • What did we achieve in our project ?
    		•


    Sponsors

    contact us!!

    tmutokyo.igem@gmail.com

    Retrieved from "http://2013.igem.org/Team:TMU-Tokyo"