Difference between revisions of "Team:UChicago/Description"

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{{UChicago/Header}}
 
{{UChicago/Header}}
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<h3>Background</h3>
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Circadian rhythms are found in a diverse range of species, using a series of oscillatory proteins to govern everything from sleep in humans to cell cycle progression in fungi. The well characterized Kai ABC circadian oscillator in cyanobacteria has been demonstrated to regulate photosynthesis, cell division, nitrogen fixation, and a host of other essential cell processes. Because of this wide range of down stream functionality, the ability to reconstitute this robust oscillator would allow us to control the production of a target molecule on a 24 hour time scale, such as caffeine or melatonin.
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The Kai ABC system is composed of three proteins, Kai A, Kai B, and Kai C. Kai A acts to autophosphorylate Kai C at one of 2 sites, either T431 (T) or S432 (S). Kai B then acts to auto-dephosphorylate Kai C. Previous research (cite that one paper)has shown that Kai B and Kai C are present in equal stoichiometries, and that the oscillatory character of the system is due to a change in Kai A concentration.  
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The 2015 iGem team has 3 main goals: The first is to reconstitute the Kai ABC oscillator in E. Coli. The oscillator is native to cyanobacteria, and reconstituting it in the most widely used model organism in biomedical research serves as a proof of concept for further applications of the oscillatory system.  
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The second goal is to develop a readout system to allow us to assay the downstream effect of the system at various time points during its oscillation by investigating the proteins RpaA, SasA, and CikA. RpaA, SasA, and CikA are components of an expression system directly downstream of KaiABC. RpaA is a master transcription factor that connects the circadian pattern occurring on the protein-protein level in KaiABC to gene expression. SasA and CikA act in similar manner to KaiA and KaiB, phoshporylating and dephosphorylating their substrate RpaA respectively. SasA and CikA directly bind and interact with the KaiABC proteins as well as act on RpaA. While previous studies of transplanting the KaiABC system have demonstrated the ability of SasA and KaiC-P interaction to drive expression, we hope to show oscillations of the RpaA master regulator itself. With the inclusion of the negative regulator CikA, we hope to generate oscillations of RpaA and a downstream kaibc promoter which were not reported in previous studies.  
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The third goal is to link the oscillation to the expression and secretion of AANAT
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−
</html>
+
<body lang=EN-US style='tab-interval:.5in'>
−
[[File:UChicagoOscillatorDiagram.png]]
+
−
<html>
+
  
−
<h2> Project Description </h2>
+
<div class=WordSection1>
  
−
<p>Tell us about your project, describe what moves you and why this is something important for your team.</p>
+
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
−
<br />
+
normal'><b style='mso-bidi-font-weight:normal'><span style='font-size:16.0pt;
 +
font-family:"Georgia",serif;mso-fareast-font-family:"Times New Roman";
 +
mso-bidi-font-family:Arial;color:black;background:white'>Yay, we can’t believe
 +
you fell for the clickbait. Here’s a picture of a cute cat for no reason:<o:p></o:p></span></b></p>
  
−
<h5>What should this page contain?</h5>
+
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
−
<ul>
+
normal'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype id="_x0000_t75"
−
   <li> A clear and concise description of your project.</li>
+
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−
   <li>A detailed explanation of why your team chose to work on this particular project.</li>
+
filled="f" stroked="f">
−
   <li>References and sources to document your research.</li>
+
<v:stroke joinstyle="miter"/>
−
   <li>Use illustrations and other visual resources to explain your project.</li>
+
<v:formulas>
−
</ul>
+
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 +
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 +
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 +
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 +
src="../File:UChicago002.jpg"
 +
alt="../File:UChicago002.jpg"
 +
v:shapes="Picture_x0020_1"><![endif]></span><b style='mso-bidi-font-weight:
 +
normal'><span style='font-size:16.0pt;font-family:"Georgia",serif;mso-fareast-font-family:
 +
"Times New Roman";mso-bidi-font-family:Arial;color:black;background:white'>Anyways,
 +
onto our project:<o:p></o:p></span></b></p>
  
 +
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
 +
normal'><b style='mso-bidi-font-weight:normal'><span style='font-size:16.0pt;
 +
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 +
mso-bidi-font-family:Arial;color:black;background:white'><o:p>&nbsp;</o:p></span></b></p>
  
−
<br />
+
<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
−
<h4>Advice on writing your Project Description</h4>
+
id="Picture_x0020_2" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:468.75pt;
 +
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−
<p>
+
<p class=MsoNormal><o:p>&nbsp;</o:p></p>
−
We encourage you to put up a lot of information and content on your wiki, but we also encourage you to include summaries as much as possible. If you think of the sections in your project description as the sections in a publication, you should try to be consist, accurate and unambiguous in your achievements.
+
−
</p>
+
  
−
<p>
+
<p class=MsoNormal><i style='mso-bidi-font-style:normal'><span
−
Judges like to read your wiki and know exactly what you have achieved. This is how you should think about these sections; from the point of view of the judge evaluating you at the end of the year.
+
style='font-family:"Arial",sans-serif'>Figure 2: Schematic of how <span
−
</p>
+
class=SpellE>KaiB</span> and <span class=SpellE>KaiA</span> stimulate different
 +
phosphorylation states of <span class=SpellE>KaiC</span> in a circadian rhythm.
 +
CATS.</span></i><span style='font-family:"Arial",sans-serif'><o:p></o:p></span></p>
  
 +
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
 +
normal'><b style='mso-bidi-font-weight:normal'><span style='font-size:16.0pt;
 +
font-family:"Georgia",serif;mso-fareast-font-family:"Times New Roman";
 +
mso-bidi-font-family:Arial;color:black;background:white'><o:p>&nbsp;</o:p></span></b></p>
  
−
<br />
+
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
−
<h4>References</h4>
+
normal'><span style='font-size:10.0pt;font-family:"Georgia",serif;mso-fareast-font-family:
−
<p>iGEM teams are encouraged to record references you use during the course of your research. They should be posted somewhere on your wiki so that judges and other visitors can see how you though about your project and what works inspired you.</p>
+
"Times New Roman";mso-bidi-font-family:Arial;color:black;background:white'><o:p>&nbsp;</o:p></span></p>
  
 +
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
 +
normal'><span style='font-size:15.0pt;font-family:"Garamond",serif;mso-fareast-font-family:
 +
"Times New Roman";mso-bidi-font-family:Arial;color:black;background:white'>Circadian
 +
rhythms are found in a diverse range of species, using a series of oscillatory
 +
proteins to govern everything from sleep in humans to cell cycle progression in
 +
fungi. The well characterized Kai ABC circadian oscillator in cyanobacteria has
 +
been demonstrated to regulate photosynthesis, cell division, nitrogen fixation,
 +
and a host of other essential cell processes. Because of this wide range of
 +
downstream functionality, the ability to reconstitute this robust oscillator
 +
would allow us to control the production of a target molecule on a 24 hour time
 +
scale, such as caffeine or melatonin.</span><span style='font-size:15.0pt;
 +
font-family:"Garamond",serif;mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
  
 +
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
 +
normal'><span style='font-size:15.0pt;font-family:"Garamond",serif;mso-fareast-font-family:
 +
"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
  
−
<h4>Inspiration</h4>
+
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
−
<p>See how other teams have described and presented their projects: </p>
+
normal'><span style='font-size:15.0pt;font-family:"Garamond",serif;mso-fareast-font-family:
 +
"Times New Roman";mso-bidi-font-family:Arial;color:black;background:white'>The
 +
Kai ABC system is composed of three proteins, Kai A, Kai B, and Kai C. Kai A
 +
acts to <span class=SpellE>autophosphorylate</span> Kai C at one of 2 sites,
 +
either T431 (T) or S432 (S). Kai B then acts to auto-dephosphorylate Kai C.
 +
Previous research (cite that one paper)has shown that Kai B and Kai C are
 +
present in equal <span class=SpellE>stoichiometries</span>, and that the
 +
oscillatory character of the system is due to a change in Kai A concentration. </span><span
 +
style='font-size:15.0pt;font-family:"Garamond",serif;mso-fareast-font-family:
 +
"Times New Roman"'><o:p></o:p></span></p>
  
−
<ul>
+
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
−
  <li><a href="https://2014.igem.org/Team:Imperial/Project"> Imperial</a></li>
+
normal'><span style='font-size:15.0pt;font-family:"Garamond",serif;mso-fareast-font-family:
−
  <li><a href="https://2014.igem.org/Team:UC_Davis/Project_Overview"> UC Davis</a></li>
+
"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
−
  <li><a href="https://2014.igem.org/Team:SYSU-Software/Overview">SYSU Software</a></li>
+
 
−
</ul>
+
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
 +
normal'><span style='font-size:15.0pt;font-family:"Garamond",serif;mso-fareast-font-family:
 +
"Times New Roman";mso-bidi-font-family:Arial;color:black;background:white'>The
 +
2015 <span class=SpellE>iGem</span> team has <b style='mso-bidi-font-weight:
 +
normal'>3 main goals</b>:<o:p></o:p></span></p>
 +
 
 +
<p class=MsoListParagraphCxSpFirst style='margin-bottom:0in;margin-bottom:.0001pt;
 +
mso-add-space:auto;text-indent:-.25in;line-height:normal;mso-list:l0 level1 lfo1'><![if !supportLists]><span
 +
style='font-size:10.0pt;mso-bidi-font-size:15.0pt;font-family:"Garamond",serif;
 +
mso-fareast-font-family:Garamond;mso-bidi-font-family:Garamond;color:black'><span
 +
style='mso-list:Ignore'>1)<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 +
</span></span></span><![endif]><span style='font-size:15.0pt;font-family:"Garamond",serif;
 +
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Arial;
 +
color:black;background:white'><span style='mso-spacerun:yes'> </span>The first
 +
is to reconstitute the Kai ABC oscillator in E. <span class=GramE>Coli</span>.
 +
The oscillator is native to cyanobacteria, and reconstituting it in the most
 +
widely used model organism in biomedical research serves as a proof of concept
 +
for further applications of the oscillatory system. </span><span
 +
style='font-size:15.0pt;font-family:"Garamond",serif;mso-fareast-font-family:
 +
"Times New Roman"'><o:p></o:p></span></p>
 +
 
 +
<p class=MsoListParagraphCxSpLast style='margin-bottom:0in;margin-bottom:.0001pt;
 +
mso-add-space:auto;text-indent:-.25in;line-height:normal;mso-list:l0 level1 lfo1'><![if !supportLists]><span
 +
style='font-size:10.0pt;mso-bidi-font-size:15.0pt;font-family:"Garamond",serif;
 +
mso-fareast-font-family:Garamond;mso-bidi-font-family:Garamond;color:black'><span
 +
style='mso-list:Ignore'>2)<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 +
</span></span></span><![endif]><span style='font-size:15.0pt;font-family:"Garamond",serif;
 +
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Arial;
 +
color:black;background:white'>3) The second goal is to develop a readout system
 +
to allow us to assay the downstream effect of the system at various time points
 +
during its oscillation by investigating the proteins <span class=SpellE>RpaA</span>,
 +
<span class=SpellE>SasA</span>, and <span class=SpellE>CikA</span>. <span
 +
class=SpellE>RpaA</span>, <span class=SpellE>SasA</span>, and <span
 +
class=SpellE>CikA</span> are components of an expression system directly
 +
downstream of <span class=SpellE>KaiABC</span>. <span class=SpellE>RpaA</span>
 +
is a master transcription factor that connects the circadian pattern occurring
 +
on the protein-protein level in <span class=SpellE>KaiABC</span> to gene
 +
expression. <span class=SpellE>SasA</span> and <span class=SpellE>CikA</span>
 +
act in similar manner to <span class=SpellE>KaiA</span> and <span class=SpellE>KaiB</span>,
 +
<span class=SpellE>phoshporylating</span> and dephosphorylating their substrate
 +
<span class=SpellE>RpaA</span> respectively. <span class=SpellE>SasA</span> and
 +
<span class=SpellE>CikA</span> directly bind and interact with the <span
 +
class=SpellE>KaiABC</span> proteins as well as act on <span class=SpellE>RpaA</span>.
 +
While previous studies of transplanting the <span class=SpellE>KaiABC</span>
 +
system have demonstrated the ability of <span class=SpellE>SasA</span> and <span
 +
class=SpellE>KaiC</span>-P interaction to drive expression, we hope to show
 +
oscillations of the <span class=SpellE>RpaA</span> master regulator itself.
 +
With the inclusion of the negative regulator <span class=SpellE>CikA</span>, we
 +
hope to generate oscillations of <span class=SpellE>RpaA</span> and a
 +
downstream <span class=SpellE>kaibc</span> promoter which were not reported in
 +
previous studies. </span><span style='font-size:15.0pt;font-family:"Garamond",serif;
 +
mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
 +
 
 +
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
 +
normal'><span style='font-size:15.0pt;font-family:"Garamond",serif;mso-fareast-font-family:
 +
"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
 +
normal'><span style='font-size:15.0pt;font-family:"Garamond",serif;mso-fareast-font-family:
 +
"Times New Roman";mso-bidi-font-family:Arial;color:black;background:white'>The
 +
third goal is to link the oscillation to the expression and secretion of AANAT <a
 +
style='mso-comment-reference:KY_1;mso-comment-date:20150917T0012'><b
 +
style='mso-bidi-font-weight:normal'>(and if ben could explain more here that
 +
would also be great, cause I really have no idea what’s happening with this </b></a><span
 +
class=GramE><span style='mso-comment-continuation:1'><b style='mso-bidi-font-weight:
 +
normal'>part )</b></span></span></span><span class=MsoCommentReference><span
 +
style='font-size:8.0pt'><![if !supportAnnotations]><a class=msocomanchor
 +
id="_anchor_1" onmouseover="msoCommentShow('_anchor_1','_com_1')"
 +
onmouseout="msoCommentHide('_com_1')" href="#_msocom_1" language=JavaScript
 +
name="_msoanchor_1">[KY1]</a><![endif]><span style='mso-special-character:comment'>&nbsp;</span></span></span><span
 +
style='font-size:15.0pt;font-family:"Garamond",serif;mso-fareast-font-family:
 +
"Times New Roman"'><o:p></o:p></span></p>
 +
 
 +
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;line-height:
 +
normal'><span style='font-size:15.0pt;font-family:"Garamond",serif;mso-fareast-font-family:
 +
"Times New Roman"'>Next, want to ****** the ***** of your ****? Click here!<o:p></o:p></span></p>
 +
 
 +
</div>
 +
 
 +
<div style='mso-element:comment-list'><![if !supportAnnotations]>
 +
 
 +
<hr class=msocomoff align=left size=1 width="33%">
 +
 
 +
<![endif]>
 +
 
 +
<div style='mso-element:comment'><![if !supportAnnotations]>
 +
 
 +
<div id="_com_1" class=msocomtxt language=JavaScript
 +
onmouseover="msoCommentShow('_anchor_1','_com_1')"
 +
onmouseout="msoCommentHide('_com_1')"><![endif]><span style='mso-comment-author:
 +
"Kevin Yang";mso-comment-providerid:"Windows Live";mso-comment-userid:dd5da70c2fbc3965'><![if !supportAnnotations]><a
 +
name="_msocom_1"></a><![endif]></span>
 +
 
 +
<p class=MsoCommentText><span class=MsoCommentReference><span style='font-size:
 +
8.0pt'><span style='mso-special-character:comment'>&nbsp;<![if !supportAnnotations]><a
 +
href="#_msoanchor_1" class=msocomoff>[KY1]</a><![endif]></span></span></span>This
 +
would be not good to include in the final wiki lol</p>
 +
 
 +
<![if !supportAnnotations]></div>
 +
 
 +
<![endif]></div>
 +
 
 +
</div>
 +
 
 +
</body>
  
 
</html>
 
</html>
 +
  
 
{{UChicago/Footer}}
 
{{UChicago/Footer}}

Revision as of 07:18, 17 September 2015

Team UChicago banner.jpg

Yay, we can’t believe you fell for the clickbait. Here’s a picture of a cute cat for no reason:

../File:UChicago002.jpgAnyways, onto our project:

 

 

Figure 2: Schematic of how KaiB and KaiA stimulate different phosphorylation states of KaiC in a circadian rhythm. CATS.

 

 

Circadian rhythms are found in a diverse range of species, using a series of oscillatory proteins to govern everything from sleep in humans to cell cycle progression in fungi. The well characterized Kai ABC circadian oscillator in cyanobacteria has been demonstrated to regulate photosynthesis, cell division, nitrogen fixation, and a host of other essential cell processes. Because of this wide range of downstream functionality, the ability to reconstitute this robust oscillator would allow us to control the production of a target molecule on a 24 hour time scale, such as caffeine or melatonin.

 

The Kai ABC system is composed of three proteins, Kai A, Kai B, and Kai C. Kai A acts to autophosphorylate Kai C at one of 2 sites, either T431 (T) or S432 (S). Kai B then acts to auto-dephosphorylate Kai C. Previous research (cite that one paper)has shown that Kai B and Kai C are present in equal stoichiometries, and that the oscillatory character of the system is due to a change in Kai A concentration.

 

The 2015 iGem team has 3 main goals:

1)        The first is to reconstitute the Kai ABC oscillator in E. Coli. The oscillator is native to cyanobacteria, and reconstituting it in the most widely used model organism in biomedical research serves as a proof of concept for further applications of the oscillatory system.

2)       3) The second goal is to develop a readout system to allow us to assay the downstream effect of the system at various time points during its oscillation by investigating the proteins RpaA, SasA, and CikA. RpaA, SasA, and CikA are components of an expression system directly downstream of KaiABC. RpaA is a master transcription factor that connects the circadian pattern occurring on the protein-protein level in KaiABC to gene expression. SasA and CikA act in similar manner to KaiA and KaiB, phoshporylating and dephosphorylating their substrate RpaA respectively. SasA and CikA directly bind and interact with the KaiABC proteins as well as act on RpaA. While previous studies of transplanting the KaiABC system have demonstrated the ability of SasA and KaiC-P interaction to drive expression, we hope to show oscillations of the RpaA master regulator itself. With the inclusion of the negative regulator CikA, we hope to generate oscillations of RpaA and a downstream kaibc promoter which were not reported in previous studies.

 

The third goal is to link the oscillation to the expression and secretion of AANAT (and if ben could explain more here that would also be great, cause I really have no idea what’s happening with this part )[KY1] 

Next, want to ****** the ***** of your ****? Click here!

 [KY1]This would be not good to include in the final wiki lol


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