Team:AUC TURKEY/Human Practices/Future Plan

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<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
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justify;line-height:normal'><span lang=EN-US style='font-size:26.0pt;
 
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color:black'></span></p>
 
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<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
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justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt'>&nbsp;</span></p>
 
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<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
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justify;line-height:normal'><img width=258 height=194
 
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src="https://static.igem.org/mediawiki/2014hs/e/e4/Image0001.jpg" align=left hspace=12><u><span
 
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lang=EN-US style='font-size:16.0pt;color:black'>1) Reporter Systems Overview</span></u><u><span
 
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lang=EN-US style='font-size:11.5pt;color:black'>:</span></u></p>
 
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<p class=MsoNormal style='margin-top:6.0pt;margin-right:0cm;margin-bottom:6.0pt;
 
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margin-left:0cm;text-align:justify;line-height:normal'><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  '>a)  Fluorescent Proteins:
 
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&nbsp;The green fluorescent protein (GFP) is a </span><a
 
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href="http://en.wikipedia.org/wiki/Protein"><span lang=EN-US style='font-size:
 
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11.5pt;color:black;  ;text-decoration:none'>protein</span></a><span
 
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lang=EN-US style='font-size:11.5pt;color:black;  '> &nbsp;that
 
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exhibits bright green </span><a href="http://en.wikipedia.org/wiki/Fluorescence"><span
 
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lang=EN-US style='font-size:11.5pt;color:black;  ;text-decoration:
 
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none'>fluorescence</span></a><span lang=EN-US style='font-size:11.5pt;
 
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color:black;  '> when exposed to light in the blue to </span><a
 
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href="http://en.wikipedia.org/wiki/Ultraviolet"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>ultraviolet</span></a><span
 
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lang=EN-US style='font-size:11.5pt;color:black;  '> range.
 
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&nbsp;Although many other marine organisms have similar green fluorescent proteins,
 
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GFP traditionally refers to the protein first isolated from the </span><a
 
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href="http://en.wikipedia.org/wiki/Jellyfish"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>jellyfish</span></a><span
 
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lang=EN-US style='font-size:11.5pt;color:black;  '> </span><a
 
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href="http://en.wikipedia.org/wiki/Aequorea_victoria"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>Aequorea
 
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victoria</span></a><span lang=EN-US style='font-size:11.5pt;color:black;
 
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  '>. The GFP from A. victoria has a major </span><a
 
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href="http://en.wikipedia.org/wiki/Fluorescence_spectroscopy"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>excitation
 
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peak</span></a><span lang=EN-US style='font-size:11.5pt;color:black;  '> at a </span><a href="http://en.wikipedia.org/wiki/Wavelength"><span
 
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lang=EN-US style='font-size:11.5pt;color:black;  ;text-decoration:
 
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none'>wavelength</span></a><span lang=EN-US style='font-size:11.5pt;color:black;
 
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  '> of 395 nm and a minor one at 475 nm. Its emission peak is at
 
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509 nm, which is in the lower green portion of the </span><a
 
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href="http://en.wikipedia.org/wiki/Visible_spectrum"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>visible
 
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spectrum</span></a><span lang=EN-US style='font-size:11.5pt;color:black;
 
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  '>. The fluorescence </span><a
 
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href="http://en.wikipedia.org/wiki/Quantum_yield"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>quantum
 
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yield</span></a><span lang=EN-US style='font-size:11.5pt;color:black;
 
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  '> (QY) of GFP is 0.79. The GFP from </span><img width=143
 
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height=143 src="https://static.igem.org/mediawiki/2014hs/3/3b/Image0002.jpg" align=right hspace=12><span
 
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lang=EN-US style='font-size:11.5pt;color:black;  '>the </span><a
 
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href="http://en.wikipedia.org/wiki/Sea_pansy"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>sea
 
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pansy</span></a><span lang=EN-US style='font-size:11.5pt;color:black;
 
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  '> (</span><span lang=EN-US style='font-size:12.0pt'><a
 
-
href="http://en.wikipedia.org/wiki/Renilla_reniformis"><span style='font-size:
 
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11.5pt;color:black;  ;text-decoration:none'>Renilla reniformis</span></a></span><span
 
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lang=EN-US style='font-size:11.5pt;color:black;  '>) has a single
 
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major excitation peak at 498 nm. </span></p>
 
-
 
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<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
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justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
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color:black;  '>In </span><a
 
-
href="http://en.wikipedia.org/wiki/Cell_biology"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>cell</span></a><span
 
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lang=EN-US style='font-size:11.5pt;color:black;  '> and </span><a
 
-
href="http://en.wikipedia.org/wiki/Molecular_biology"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>molecular
 
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biology</span></a><span lang=EN-US style='font-size:11.5pt;color:black;
 
-
  '>, the GFP </span><a href="http://en.wikipedia.org/wiki/Gene"><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  ;text-decoration:
 
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none'>gene</span></a><span lang=EN-US style='font-size:11.5pt;color:black;
 
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  '> is frequently used as a </span><a
 
-
href="http://en.wikipedia.org/wiki/Reporter_gene"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>reporter
 
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of expression</span></a><span lang=EN-US style='font-size:11.5pt;color:black;
 
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  '>. In modified forms it has been used to make </span><a
 
-
href="http://en.wikipedia.org/wiki/Biosensor"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>biosensors</span></a><span
 
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lang=EN-US style='font-size:11.5pt;color:black;  '>, and many
 
-
animals have been created that express GFP as a proof-of-concept that a gene
 
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can be expressed throughout a given organism. The GFP gene can be introduced
 
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into organisms and maintained in their genome through breeding, injection with
 
-
a </span><a href="http://en.wikipedia.org/wiki/Viral_vector"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>viral
 
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vector</span></a><span lang=EN-US style='font-size:11.5pt;color:black;
 
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  '>, or cell transformation. To date, the GFP gene has been
 
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introduced and expressed in many </span><a
 
-
href="http://en.wikipedia.org/wiki/Bacteria"><span lang=EN-US style='font-size:
 
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11.5pt;color:black;  ;text-decoration:none'>Bacteria</span></a><span
 
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lang=EN-US style='font-size:11.5pt;color:black;  '>, </span><a
 
-
href="http://en.wikipedia.org/wiki/Yeast"><span lang=EN-US style='font-size:
 
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11.5pt;color:black;  ;text-decoration:none'>Yeast</span></a><span
 
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lang=EN-US style='font-size:11.5pt;color:black;  '> and other </span><a
 
-
href="http://en.wikipedia.org/wiki/Fungi"><span lang=EN-US style='font-size:
 
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11.5pt;color:black;  ;text-decoration:none'>Fungi</span></a><span
 
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lang=EN-US style='font-size:11.5pt;color:black;  '>, fish (such
 
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as </span><a href="http://en.wikipedia.org/wiki/Zebrafish"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>zebrafish</span></a><span
 
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lang=EN-US style='font-size:11.5pt;color:black;  '>), plant, fly,
 
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and mammalian cells, including human. </span><a
 
-
href="http://en.wikipedia.org/wiki/Martin_Chalfie"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>Martin
 
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Chalfie</span></a><span lang=EN-US style='font-size:11.5pt;color:black;
 
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  '>, </span><a
 
-
href="http://en.wikipedia.org/wiki/Osamu_Shimomura"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>Osamu
 
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Shimomura</span></a><span lang=EN-US style='font-size:11.5pt;color:black;
 
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  '>, and </span><a
 
-
href="http://en.wikipedia.org/wiki/Roger_Y._Tsien"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>Roger
 
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Y. Tsien</span></a><span lang=EN-US style='font-size:11.5pt;color:black;
 
-
  '> were awarded the 2008 </span><a
 
-
href="http://en.wikipedia.org/wiki/Nobel_Prize_in_Chemistry"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>Nobel
 
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Prize in Chemistry</span></a><span lang=EN-US style='font-size:11.5pt;
 
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color:black;  '> on 10 October 2008 for their discovery and
 
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development of the green fluorescent protein. </span></p>
 
-
 
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<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
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justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
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color:black'>&nbsp;</span></p>
 
-
 
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<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
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justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
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color:black'>&nbsp;</span></p>
 
-
 
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<p class=MsoListParagraph style='margin-bottom:0cm;margin-bottom:.0001pt;
 
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text-align:justify;text-indent:-18.0pt;line-height:normal'><span lang=EN-US
 
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style='font-size:11.5pt;color:black'>a)<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
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</span></span><span lang=EN-US style='font-size:11.5pt;color:black'> Luciferin:<span
 
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style='  '> Luciferin (from the Latin </span>lucifer,
 
-
&quot;light-bringer&quot;) is a generic term for the light-emitting </span><a
 
-
href="http://en.wikipedia.org/wiki/Chemical_compound"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>compound</span></a><span
 
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lang=EN-US style='font-size:11.5pt;color:black;  '> found in
 
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organisms that generate </span><a
 
-
href="http://en.wikipedia.org/wiki/Bioluminescence"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>bioluminescence</span></a><span
 
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lang=EN-US style='font-size:11.5pt;color:black;  '>. Luciferins
 
-
typically undergo an </span><img width=329 height=219
 
-
src="https://static.igem.org/mediawiki/2014hs/1/1e/Image0003.jpg" align=right hspace=12><a
 
-
href="http://en.wikipedia.org/wiki/Enzyme"><span lang=EN-US style='font-size:
 
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11.5pt;color:black;  ;text-decoration:none'>enzyme</span></a><span
 
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lang=EN-US style='font-size:11.5pt;color:black;  '>-catalysed </span><a
 
-
href="http://en.wikipedia.org/wiki/Oxidation"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>oxidation</span></a><span
 
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lang=EN-US style='font-size:11.5pt;color:black;  '> and the
 
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resulting</span><a href="http://en.wikipedia.org/wiki/Excited_state"><span
 
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lang=EN-US style='font-size:11.5pt;color:black;  ;text-decoration:
 
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none'>excited state</span></a><span lang=EN-US style='font-size:11.5pt;
 
-
color:black;  '> intermediate emits light upon decaying to its </span><a
 
-
href="http://en.wikipedia.org/wiki/Ground_state"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>ground
 
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state</span></a><span lang=EN-US style='font-size:11.5pt;color:black;
 
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  '>. This may refer to molecules that are substrates for both </span><a
 
-
href="http://en.wikipedia.org/wiki/Luciferase"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>luciferases</span></a><span
 
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lang=EN-US style='font-size:11.5pt;color:black;  '> and </span><a
 
-
href="http://en.wikipedia.org/wiki/Photoprotein"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>photoproteins</span></a><span
 
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lang=EN-US style='font-size:11.5pt;color:black;  '>. Luciferins
 
-
are a class of small-molecule </span><a
 
-
href="http://en.wikipedia.org/wiki/Substrate_(biochemistry)"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>substrates</span></a><span
 
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lang=EN-US style='font-size:11.5pt;color:black;  '> that are </span><a
 
-
href="http://en.wikipedia.org/wiki/Redox"><span lang=EN-US style='font-size:
 
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11.5pt;color:black;  ;text-decoration:none'>oxidized</span></a><span
 
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lang=EN-US style='font-size:11.5pt;color:black;  '> in the
 
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presence of the enzyme </span><a href="http://en.wikipedia.org/wiki/Luciferase"><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  ;text-decoration:
 
-
none'>luciferase</span></a><span lang=EN-US style='font-size:11.5pt;color:black;
 
-
  '> to produce oxyluciferin and </span><a
 
-
href="http://en.wikipedia.org/wiki/Energy"><span lang=EN-US style='font-size:
 
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11.5pt;color:black;  ;text-decoration:none'>energy</span></a><span
 
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lang=EN-US style='font-size:11.5pt;color:black;  '> in the form
 
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of </span><a href="http://en.wikipedia.org/wiki/Light"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>light</span></a><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '>. It is not
 
-
known just how many types of luciferins there are, but some of the
 
-
better-studied compounds are listed below. There are many types of luciferins,
 
-
yet all share the use of </span><a
 
-
href="http://en.wikipedia.org/wiki/Reactive_oxygen_species"><span lang=EN-US
 
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style='font-size:11.5pt;color:black;  ;text-decoration:none'>reactive
 
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oxygen species</span></a><span lang=EN-US style='font-size:11.5pt;color:black;
 
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  '> to emit light. </span></p>
 
-
 
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<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
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justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
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color:black'>&nbsp;</span></p>
 
-
 
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<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
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justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
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color:black'>b) &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Xgal Reporter System:<span
 
-
style='  '> X-gal </span>is an </span><a
 
-
href="http://en.wikipedia.org/wiki/Organic_compound"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>organic
 
-
compound</span></a><span lang=EN-US style='font-size:11.5pt;color:black;
 
-
  '> consisting of</span><a
 
-
href="http://en.wikipedia.org/wiki/Galactose"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>galactose</span></a><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '> linked to a
 
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substituted </span><a href="http://en.wikipedia.org/wiki/Indole"><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  ;text-decoration:
 
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none'>indole</span></a><span lang=EN-US style='font-size:11.5pt;color:black;
 
-
  '>. The compound was synthesized by </span><a
 
-
href="http://en.wikipedia.org/wiki/Jerome_Horwitz"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>Jerome
 
-
Horwitz</span></a><span lang=EN-US style='font-size:11.5pt;color:black;
 
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  '> and collaborators in Detroit, MI, in 1964. The formal
 
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chemical name is often shortened to less accurate but also less cumbersome
 
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phrases such as bromochloroindoxyl galactoside. The X from </span><a
 
-
href="http://en.wikipedia.org/wiki/Indoxyl"><span lang=EN-US style='font-size:
 
-
11.5pt;color:black;  ;text-decoration:none'>indoxyl</span></a><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '> may well be
 
-
the source of the X in the X-gal contraction. X-gal is much used in </span><a
 
-
href="http://en.wikipedia.org/wiki/Molecular_biology"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>molecular
 
-
biology</span></a><span lang=EN-US style='font-size:11.5pt;color:black;
 
-
  '> to test for the presence of an enzyme, </span><a
 
-
href="http://en.wikipedia.org/wiki/Beta-galactosidase"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>&#946;-galactosidase</span></a><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '>. It is also
 
-
used to detect activity of this enzyme in </span><a
 
-
href="http://en.wikipedia.org/wiki/Histochemistry"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>histochemistry</span></a><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '> and </span><a
 
-
href="http://en.wikipedia.org/wiki/Bacteriology"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>bacteriology</span></a><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '>. X-gal is one
 
-
of many indoxyl glycosides and esters that yield insoluble blue compounds
 
-
similar to </span><a href="http://en.wikipedia.org/wiki/Indigo"><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  ;text-decoration:
 
-
none'>indigo</span></a><span lang=EN-US style='font-size:11.5pt;color:black;
 
-
  '> as a result of enzyme-catalyzed hydrolysis.</span><a
 
-
href="http://en.wikipedia.org/wiki/X-gal#cite_note-2"><sup><span lang=EN-US
 
-
style='font-size:7.0pt;color:black;  ;text-decoration:none'>[2]</span></sup></a><sup><span
 
-
lang=EN-US style='font-size:7.0pt;color:black;  '> </span></sup><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '>X-gal is an </span><a
 
-
href="http://en.wikipedia.org/wiki/Structural_analog"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>analog</span></a><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '> of </span><a
 
-
href="http://en.wikipedia.org/wiki/Lactose"><span lang=EN-US style='font-size:
 
-
11.5pt;color:black;  ;text-decoration:none'>lactose</span></a><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '>, and
 
-
therefore may be hydrolyzed by the </span><a
 
-
href="http://en.wikipedia.org/wiki/Beta-galactosidase"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>&#946;-</span></a><img
 
-
width=218 height=182 src="https://static.igem.org/mediawiki/2014hs/e/e8/Image0004.jpg" align=left
 
-
hspace=12><a href="http://en.wikipedia.org/wiki/Beta-galactosidase"><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  ;text-decoration:
 
-
none'>galactosidase</span></a><span lang=EN-US style='font-size:11.5pt;
 
-
color:black;  '> enzyme which cleaves the &#946;-</span><span
 
-
lang=EN-US style='font-size:12.0pt'><a
 
-
href="http://en.wikipedia.org/wiki/Glycosidic_bond"><span style='font-size:
 
-
11.5pt;color:black;  ;text-decoration:none'>glycosidic bond</span></a></span><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '> in D-lactose.
 
-
X-gal, when cleaved by &#946;-galactosidase, yields galactose and
 
-
5-bromo-4-chloro-3-hydroxyindole. The latter then spontaneously dimerizes and
 
-
is oxidized into 5,5'-dibromo-4,4'-dichloro-indigo, an intensely blue product
 
-
which is insoluble. X-gal itself is colorless, the presence of blue-colored
 
-
product therefore may be used as a test for the presence of an active
 
-
&#946;-galactosidase. This easy identification of an active enzyme allows the
 
-
gene for &#946;-galactosidase (the </span><span lang=EN-US style='font-size:
 
-
11.5pt;color:black'>lacZ gene) to be used as a </span><a
 
-
href="http://en.wikipedia.org/wiki/Reporter_gene"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>reporter
 
-
gene</span></a><span lang=EN-US style='font-size:11.5pt;color:black;  '> in various applications. </span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>c) &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GUS Reporter System: <span
 
-
style='  '>The </span>GUS reporter system (GUS: </span><a
 
-
href="http://en.wikipedia.org/wiki/%CE%92-glucuronidase"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>&#946;-glucuronidase</span></a><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '>) is a </span><a
 
-
href="http://en.wikipedia.org/wiki/Reporter_gene"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>reporter
 
-
gene</span></a><span lang=EN-US style='font-size:11.5pt;color:black;  '> system, particularly useful in plant </span><img width=167 height=249
 
-
src="https://static.igem.org/mediawiki/2014hs/5/51/Image0005.jpg" align=right hspace=12><a
 
-
href="http://en.wikipedia.org/wiki/Molecular_biology"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>molecular
 
-
biology</span></a><span lang=EN-US style='font-size:11.5pt;color:black;
 
-
  '> and microbiology. Several kinds of GUS </span><a
 
-
href="http://en.wikipedia.org/wiki/Reporter_gene_assay"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>reporter
 
-
gene assay</span></a><span lang=EN-US style='font-size:11.5pt;color:black;
 
-
  '> are available, depending on the substrate used. The term </span><span
 
-
lang=EN-US style='font-size:11.5pt;color:black'>GUS staining refers to the most
 
-
common of these, a histochemical technique. The purpose of this technique is to
 
-
analyze the activity of a </span><a
 
-
href="http://en.wikipedia.org/wiki/Promoter_(biology)"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>promoter</span></a><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '> (in terms of </span><a
 
-
href="http://en.wikipedia.org/wiki/Gene_expression"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>expression</span></a><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '> of a gene
 
-
under that promoter) either in a quantitative way or through visualization of
 
-
its activity in different </span><a
 
-
href="http://en.wikipedia.org/wiki/Biological_tissue"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>tissues</span></a><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '>. The
 
-
technique is based on </span><a
 
-
href="http://en.wikipedia.org/wiki/%CE%92-glucuronidase"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>&#946;-glucuronidase</span></a><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '>, an enzyme
 
-
from the bacterium </span><a
 
-
href="http://en.wikipedia.org/wiki/Escherichia_coli"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>Escherichia
 
-
coli</span></a><span lang=EN-US style='font-size:11.5pt;color:black;  '>; this enzyme, when incubated with some specific colorless or non-fluorescent
 
-
</span><a href="http://en.wikipedia.org/wiki/Substrate_(biology)"><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  ;text-decoration:
 
-
none'>substrates</span></a><span lang=EN-US style='font-size:11.5pt;color:black;
 
-
  '>, can transform them into </span><a
 
-
href="http://en.wikipedia.org/wiki/Color"><span lang=EN-US style='font-size:
 
-
11.5pt;color:black;  ;text-decoration:none'>coloured</span></a><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '> or </span><a
 
-
href="http://en.wikipedia.org/wiki/Fluorescence"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>fluorescent</span></a><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '> products. </span></p>
 
-
 
-
<p class=MsoNormal style='margin-top:6.0pt;margin-right:0cm;margin-bottom:6.0pt;
 
-
margin-left:0cm;text-align:justify;line-height:normal'><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  '>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-top:6.0pt;margin-right:0cm;margin-bottom:6.0pt;
 
-
margin-left:0cm;text-align:justify;line-height:normal'><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  '>d) Chloramphenicol
 
-
acetyltransferase (CAT) System: Chloramphenicol acetyltransferase (or CAT) is a
 
-
</span><a href="http://en.wikipedia.org/wiki/Bacteria"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>bacterial</span></a><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '> </span><a
 
-
href="http://en.wikipedia.org/wiki/Enzyme"><span lang=EN-US style='font-size:
 
-
11.5pt;color:black;  ;text-decoration:none'>enzyme</span></a><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '> (</span><a
 
-
href="http://en.wikipedia.org/wiki/Enzyme_Commission_number"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>EC</span></a><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '> </span><a
 
-
href="http://enzyme.expasy.org/EC/2.3.1.28"><span lang=EN-US style='font-size:
 
-
11.5pt;color:black;  ;text-decoration:none'>2.3.1.28</span></a><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '>) that
 
-
detoxifies the </span><a href="http://en.wikipedia.org/wiki/Antibiotic"><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  ;text-decoration:
 
-
none'>antibiotic</span></a><a
 
-
href="http://en.wikipedia.org/wiki/Chloramphenicol"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>chloramphenicol</span></a><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '> and is
 
-
responsible for chloramphenicol resistance in bacteria. This enzyme covalently
 
-
attaches an</span><a href="http://en.wikipedia.org/wiki/Acetyl"><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  ;text-decoration:
 
-
none'>acetyl</span></a><span lang=EN-US style='font-size:11.5pt;color:black;
 
-
  '> group from </span><a
 
-
href="http://en.wikipedia.org/wiki/Acetyl-CoA"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>acetyl-CoA</span></a><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '> to
 
-
chloramphenicol, which prevents chloramphenicol from binding to </span><a
 
-
href="http://en.wikipedia.org/wiki/Ribosome"><span lang=EN-US style='font-size:
 
-
11.5pt;color:black;  ;text-decoration:none'>ribosomes</span></a><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '>. A histidine
 
-
residue, located in the C-terminal section of the enzyme, plays a central role
 
-
in its catalytic mechanism.</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black;  '>The crystal structure of the type III enzyme from
 
-
</span><a href="http://en.wikipedia.org/wiki/Escherichia_coli"><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  ;text-decoration:
 
-
none'>Escherichia coli</span></a><span lang=EN-US style='font-size:11.5pt;
 
-
color:black;  '> with chloramphenicol bound has been determined.
 
-
CAT is a trimer of identical subunits (monomer Mr 25,000) and the trimeric
 
-
structure is stabilised by a number of hydrogen bonds, some of which result in
 
-
the extension of a beta-sheet across the subunit interface. Chloramphenicol
 
-
binds in a deep pocket located at the boundary between adjacent subunits of the
 
-
trimer, such that the majority of residues forming the binding pocket belong to
 
-
one subunit while the catalytically essential histidine belongs to the adjacent
 
-
subunit. His195 is appropriately positioned to act as a general base catalyst
 
-
in the reaction, and the required tautomeric stabilisation is provided by an
 
-
unusual interaction with a main-chain carbonyl oxygen. CAT is used as a
 
-
reporter system to measure the level of a promoter or its tissue-specific
 
-
expression. The CAT assay involves monitoring acetylation of radioactively
 
-
labeled chloramphenicol on a </span><a
 
-
href="http://en.wikipedia.org/wiki/Thin_layer_chromatography"><span lang=EN-US
 
-
style='font-size:11.5pt;color:black;  ;text-decoration:none'>TLC</span></a><span
 
-
lang=EN-US style='font-size:11.5pt;color:black;  '> plate; CAT
 
-
activity is determined by looking for the acetylated forms of chloramphenicol,
 
-
which have a significantly increased migration rate as compared to the
 
-
unacetylated form.</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>d) &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Other Response Systems:
 
-
Some fast response systems were for constructed based on traditional response
 
-
systems like GFP or luciferin reporter system through protein engineering.
 
-
Although these response systems give fast response, they have high costs and/or
 
-
difficulty in implementation. The systems are devised by major genetics
 
-
companies that synthesize these systems using high cost equipment thus
 
-
reflecting the costs to the buyers resulting in very expensive prices making it
 
-
almost impossible for most of the iGEM teams to obtain them.</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><u><span lang=EN-US style='font-size:16.0pt;
 
-
color:black'>2) Advantages of DegradEColor: </span></u></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>a) <i>Our system aims to operate faster because it focuses on the
 
-
prencipal which is making the produced enzyme effect more substrata in which
 
-
are dyes instead of continuously producing new proteins. </i></span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><i><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>Our system works in a way that is suitable for different dyes and
 
-
peroxidase enzymes of the project it is going to be applied. </span></i></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>c)  <i>Also our system ables scientists to; develop dyes suitable
 
-
for their works, and chose the suitable enzyme for their subject living
 
-
material </i></span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><u><span lang=EN-US style='font-size:16.0pt;
 
-
color:black'>3) Disadvantages of DegradEColor: </span></u></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>a) </span><span style='color:black'>Our protein is produced by
 
-
HRP-C enzyme which is taken by horseradish plant, and the other one LiP-1 is
 
-
taken by white rot fungus. Since our enzymes are taken from living material in
 
-
nature it might make things harder for people who wishes to use them on
 
-
different livings.</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>b) </span><span style='color:black'>The dyes we use alongside of
 
-
our enzymes origins are used in histologic and genetic studies in order to
 
-
colour DNA, RNA and other parts of cell, this situation is the reason why
 
-
&nbsp;our dyes does not to include the molecules we need which will increase
 
-
the efficiency of our project.</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:16.0pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p style='margin:0cm;margin-bottom:.0001pt;text-align:justify'><u><span
 
-
lang=EN-US style='font-size:16.0pt;font-family:"Calibri","sans-serif";
 
-
color:black'>4) Planned Improvements of DegradEColor:</span></u></p>
 
-
 
-
<p style='margin:0cm;margin-bottom:.0001pt;text-align:justify'><span
 
-
lang=EN-US style='font-size:16.0pt;font-family:"Calibri","sans-serif";
 
-
color:black'> </span><span lang=EN-US style='font-family:"Calibri","sans-serif";
 
-
color:black'>The dyes and enzymes we used should be engineered to be suitable
 
-
for our project if it is going to be used as a reliable reporter system which
 
-
will be used in synthetic biology and genetics in future. </span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><u><span lang=EN-US style='font-size:16.0pt;
 
-
color:black'>a) Dye Improvements:</span></u></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:200%'><span lang=EN-US style='font-size:11.5pt;line-height:
 
-
200%;color:black'>One of the actions that we conducted to further develop our
 
-
future plans was to meet up with organic chemistry experts specialized in the
 
-
field of dye synthesis. As a result of the meetings, we learned that it would
 
-
be possible to further develop the structure of our selected dyes in respect to
 
-
the speed of degradation thus reducing the total time of the process. </span><span
 
-
lang=EN-US style='font-size:12.0pt;line-height:200%;color:black'>. Our stops
 
-
were Prof. Dr. Cihangir Tanyeli from METU, and Doc. Dr. Zeynel Seferoğlu from
 
-
Gazi University. We took their thoughts about the possibility and any point
 
-
that can be advanced of our project. With this way, our project has been
 
-
approved and developed by experts.</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><u><span lang=EN-US style='font-size:16.0pt;
 
-
color:black'>Prof. Dr. Cihangir Tanyeli</span></u></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><u><span lang=EN-US style='font-size:16.0pt;
 
-
color:black'>METU Faculty of Organic Chemistry</span></u></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><img width=389 height=292
 
-
src="https://static.igem.org/mediawiki/2014hs/9/98/Image0006.jpg" align=left hspace=12><span
 
-
lang=EN-US style='font-size:12.0pt;color:black'>One of the first questions we
 
-
asked to Mr Tanyeli was: What different technique or techniques can we increase
 
-
the effectiveness of Horse radish peroxidase and lignin peroxidase or how can
 
-
we make our dyes more sensitive and suitable through our enzymes and be able to
 
-
improve the usage field of our project?</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt;
 
-
color:black'>He focused on re-designing the dyes to make them suitable for
 
-
enzymes which was his main field of study and he offered us 2 different
 
-
methods.</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt;
 
-
color:black'>1st Method: We can develop the dye matter by using 4-amino-TEMPO.
 
-
This is a good redox system. By this way that we won’t need hydrogen peroxidase
 
-
for Oxidation</span><sub><span lang=EN-US style='font-size:7.5pt;color:black'> </span></sub><span
 
-
lang=EN-US style='font-size:12.0pt;color:black'>system. A polymer can be taken
 
-
as a Matrix. 4-amino-TEMPO can be immobilized to biodegradable polymer. With
 
-
the way that, sodium hypochlorite (NaClO) can be used as an alternative to
 
-
hydrogen peroxide. Since this is a macro molecular system, it can be
 
-
precipitated to water and regained this will provide us an ease of researching.
 
-
When used in a bulk system in the nature, most usable metalloporphirins have
 
-
silica like systems that has Si main structure, are more solid and hard to
 
-
degrade, but still, if the biodegradable systems are used catalytic activity
 
-
can be decreased and be a system that can fit to nature instead of being waste.</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt;
 
-
color:black'>In order to block the degrading ability of the 4-amino-TEMPO
 
-
system, antioxidants like ascorbic acid can be used this happens by radical
 
-
group gets silenced by ascorbic acid which goes into a reaction with Bleach. He
 
-
also stated that we can use other antioxidants that alternatives of ascorbic
 
-
acid. In the other hand,. NaClO(Bleach instrument) is could be harmful for the
 
-
environment. 4 amino tempo system we suggested has an incredible balance with
 
-
bleach insturemuer so we for the nature we can chose the most envorment insrtie
 
-
, destroying its harms for environment because bleach + tempo system &nbsp;In
 
-
this method we focus on 4 amino tempos.. The reason we use amino instead of
 
-
hydroxide, we want our TEMPO molecule (oxidation instruments) can easily
 
-
interact with some organic molecules that can be produce by organisms with
 
-
amino group..</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt;
 
-
color:black'>2</span><sup><span lang=EN-US style='font-size:7.5pt;color:black'>nd</span></sup><span
 
-
lang=EN-US style='font-size:12.0pt;color:black'> method: Some functional groups
 
-
can be placed on Carbon Nanotubes. Carboxylic acid can be placed on Carbon
 
-
Nanotubes with desiccation. Also 4-amino-TEMPO added on Carboxylic acid
 
-
functional group with direct covalent immobilization approach. If the 4-amino-TEMPO
 
-
stated gets inserted on and bleach instruments like NaClO added the environment
 
-
dye degradation will be happen. Big advantages of Carbon nanotubes that can be
 
-
regained with filtration and precipitation and this make this system more efficient
 
-
and economic and using over and over.</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt;
 
-
color:black'>Both of this methods are using with switch systems that working
 
-
with pH or temperature control by an enzymes, or a bacteria or a bio systems.</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt;
 
-
color:black'>We stated that time used by the systems used currently used around
 
-
the world takes 16 hours is decreased to a few hours by our system while we
 
-
were talking to our precious scholar. He gave us valuable information. We thank
 
-
to him for giving us time.</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:13.0pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><u><span lang=EN-US style='font-size:16.0pt;
 
-
color:black'>Doc. Dr. Zeynel SEFEROĞLU</span></u></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><u><span lang=EN-US style='font-size:16.0pt;
 
-
color:black'>Gazi University Faculty of Organic Chemistry</span></u></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><img width=319 height=240
 
-
src="https://static.igem.org/mediawiki/2014hs/5/5c/Image0007.jpg" align=left hspace=12><span
 
-
lang=EN-US style='font-size:12.0pt;color:black'>We started our conservation
 
-
with our scholar how we can make our dyes more suitable for our dyes and make
 
-
it fit right in to our project. He suggested us to make a research on quantum
 
-
efficient dyes and increase our knowledge on functional fluorescence dyes. When
 
-
we first mentioned our project he liked it and stated that this could be used
 
-
easily and efficiently in genetic and synthetic biology world. He gave us some
 
-
articles that might help. He also stated that it is important to introduce to
 
-
science to the world since iGEM is already doing that we made someone else like
 
-
iGEM. We thank our scholar for giving us opportunity to have this conservation.</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><u><span lang=EN-US style='font-size:16.0pt;
 
-
color:black;  '>ALFA Dye</span></u><u><span lang=EN-US
 
-
style='font-size:16.0pt;color:black;  '> and &nbsp;Chemistry</span></u></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><img width=238 height=394
 
-
src="https://static.igem.org/mediawiki/2014hs/f/f6/Image0008.jpg" align=left hspace=12><span
 
-
lang=EN-US style='font-size:12.0pt;color:black;  '>We wanted to
 
-
inform the local companies about iGEM and our project. Our first target was a
 
-
professional corporation Alfa Dye. Here we talked about the possibility and
 
-
usage in daily life and received some information on industrial dyes. We
 
-
learned the dyes used in histologic dying are an addition to pigments as
 
-
connecting molecules. So if we want to add other activities other than
 
-
bioremediation of dye wastes we should add some small systems which will cleave
 
-
such connections. With this visit we had new a perspective through the future.
 
-
The company got happy for us to be in such competition. They sacrificed their
 
-
time in order to give us directions we thank them for that.</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><u><span lang=EN-US style='font-size:16.0pt;
 
-
color:black'>b) Enzyme and Genetic Dyes Improvements:</span></u></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:11.5pt;
 
-
color:black'>Another activity to further develop our future plans was to
 
-
consult genetic, biology and biochemistry experts and genetics companies to
 
-
assist in the development of the theory of our project. The feedback that we
 
-
received was indicating that through the development of the binding sites of
 
-
the enzymes with protein engineering the project could be improved and that the
 
-
project beared great potential for the improvision of synthetic biology.</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:12.0pt;text-align:justify;line-height:
 
-
normal'><span lang=EN-US style='font-size:12.0pt'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><u><span lang=EN-US style='font-size:16.0pt;
 
-
color:black'>Prof. Dr. Sadık Çiğdem</span></u></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><u><span lang=EN-US style='font-size:16.0pt;
 
-
color:black'>Tsukuba University Genetic Faculty Japan</span></u></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><img width=343 height=258
 
-
src="https://static.igem.org/mediawiki/2014hs/4/4e/Image0009.jpg" align=left hspace=12><span
 
-
lang=EN-US style='font-size:12.0pt;color:black'>He is one of the guest
 
-
scientist of Turgut Ozal University Genetic Department. When we mentioned him
 
-
about our project DegradEColor he is really impressed about the idea behind our
 
-
project and also he gave us some advice and information about our HRP enzyme.
 
-
He informed us that one of our enzyme HRP is used by ELISA and Western-Blot
 
-
experiments. HRP is added on antibodies in Western Blot and also ELISA and
 
-
cause the substrate ECL give response. We thanked to him for this opportunity. </span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><u><span lang=EN-US style='font-size:16.0pt;
 
-
color:black'>Prof. Dr. Esra Gündüz</span></u></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><u><span lang=EN-US style='font-size:16.0pt;
 
-
color:black'>Turgut Özal University Faculty of Medicine</span></u></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt;
 
-
color:black'>&nbsp;</span></p>
 
-
 
-
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
-
justify;line-height:normal'><img width=387 height=290
 
-
src="https://static.igem.org/mediawiki/2014hs/5/5d/Image0010.jpg" align=left hspace=12><span
 
-
lang=EN-US style='font-size:12.0pt;color:black'>We informed her about our iGEM
 
-
HS Project DegradEColor, she really interested on our project. She was very
 
-
pleased when she saw us, doing such work at this young age. She stated that she
 
-
will provide any support she can. &nbsp;&nbsp;</span></p>
 
-
 
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<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
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<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
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color:black'>&nbsp;</span></p>
 
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<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
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justify;line-height:normal'><span lang=EN-US style='font-size:12.0pt;
 
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color:black'>&nbsp;</span></p>
 
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<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align:
 
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justify;line-height:normal'><u><span lang=EN-US style='font-size:16.0pt;
 
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color:black'>Burak Yılmaz</span></u></p>
 
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justify;line-height:normal'><u><span lang=EN-US style='font-size:16.0pt;
 
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color:black'>The founder of SENTEGEN and its CEO</span></u></p>
 
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src="https://static.igem.org/mediawiki/2014hs/a/a7/Image0011.jpg" align=left hspace=12><span
 
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lang=EN-US style='font-size:12.0pt;color:black'>We impressed Mr. Yılmaz with
 
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our project and aim to reduce the time of response systems. He stated managing
 
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time is a very big problem for companies. The company which will use our system
 
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will manage their time 14~15 times more efficient. He said “This advantage can’t
 
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be ignored”. He congratulated us for coming up with such a wonderful idea we
 
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thank him for this.</span></p>
 
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Revision as of 21:44, 18 February 2015