Difference between revisions of "Team:USMA-West Point/Notebook"

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{{USMA-West_Point}}
 
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Notebook - iGem 01</title>
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<h1>Notebook</h1>
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<p> Document the dates you worked on your project. This should be a detailed account of the work done each day for your project.</p>
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<li>Chronological notes of what your team is doing.</li>
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<h5>Inspiration</h5>
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<li><a href="https://2014.igem.org/Team:ATOMS-Turkiye/Notebook">2014 ATOMS-Turkiye</a></li>
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<li><a href="https://2014.igem.org/Team:Tec-Monterrey/ITESM14_project.html#tab_notebook">2014 Tec Monterrey</a></li>
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<li><a href="https://2014.igem.org/Team:Kyoto/Notebook/Magnetosome_Formation#title">2014 Kyoto</a></li>
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<a href="#Neurons">Neurons</a> <br>
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<a href="#Perfusion System with Bioreactor Design">Perfusion System with Bioreactor Design</a> <br>
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<a name="Neurons"></a> <br>
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<h3>Neurons</h3>
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9 Jun 2017 <br> WO RG AM KP MM
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<li>Received HT-22 Immortalized Mouse Hippocampal Cell Line and related materials from West Point
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13 Jun 2017 <br> WO RG AM KP MM PB
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15 Jun 2017 <br> WO RG AM KP MM PB
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17 Jun 2017 <br> JG
 
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19 Jun 2017 <br> WO RG MM PB
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21 Jun 2017 <br> WO RG MM PB
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27 Jun 2017 <br> WO RG
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<li>Made and changed media
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30 Jun 2017 <br> WO RG
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<ul>  
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<li>Thawed and plated cells - Passage 2
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5 Jul 2017 <br> WO RG
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<li>Split cells - Passage 3
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7 Jul 2017 <br> WO RG
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<ol><li class="font_7" style="text-align: justify;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">OR vectors were purchased from OriGene and transfected into XL-10 Gold Ultracompetent cells by heat shocking at 42 degrees Celsius</span></span></span><br></li><li class="font_7" style="text-align: justify;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Cells were cultured in LB broth to amplify vectors</span></span></span><br></li><li class="font_7" style="text-align: justify;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">DNA gels were run with specific restriction enzymes to determine multiple cloning sites</span></span></span><br></li><li class="font_7" style="text-align: justify;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Participants</span></span></span><ol><li class="font_7" style="text-align: justify;"><a data-cke-saved-href="https://www.mcdb.ucla.edu/Research/Banerjee/protocols/maxiprep--Qiagen.pdf" href="https://www.mcdb.ucla.edu/Research/Banerjee/protocols/maxiprep--Qiagen.pdf"></a><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Dr. Alexander Mitropoulos, Dr. Ken Wickiser, Dr. Kamil Woronowicz, 2LT Dillon Macky, 2LT Ishmael Raheem, CDT Jason Hug, CDT Elizabeth Huuki, CDT Channah Mills, CDT Matthew McDonough, Isaac Dabkowski</span></span></span><br></li></ol></li></ol>
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10 Jul 2017 <br> WO RG
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<li>Split cells - Passage 4  
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<div id="no-image-holder"  class="preview-image-holder inner-pic-holder" data-menu-name="PREVIEW_INLINE_IMAGE_HOLDER">
  
−
13 Jul 2017 <br> WO RG
+
<div  id="no-image" class="inner-pic preview-element  magic-circle-holder  load-high-res " data-menu-name="PREVIEW_INLINE_IMAGE" style=""  data-orig-width="" data-orig-height="" >
−
<ul>
+
<!-- VIDEO TEMPLATE -->
−
<li>Changed media</li>
+
−
</ul>
+
  
−
17 Jul 2017 <br> JG
+
<div class="element-placeholder" data-elementtype='VIDEO' style="display:none;"></div>
−
<ul>
+
−
<li>Cells were killed</li>
+
−
</ul>
+
  
−
<a name="Perfusion System with Bioreactor Design"></a> <br>
 
−
<h3>Perfusion System with Bioreactor Design</h3>
 
  
−
23 May 2017
+
<!-- MAP TEMPLATE -->
−
<br> WO
+
−
<ul>
+
<div class="element-placeholder" data-elementtype='MAP' style="display:none;"></div>
−
<li>Began bioreactor design based on former models to be used in a perfusion system
+
−
</ul>
+
  
−
25 May 2017
+
<!-- RAW TEMPLATE -->
−
<br>WO
+
−
<ul>
+
<div class="element-placeholder" data-elementtype='RAW' style="display:none;"></div>
−
<li>Used AutoDesk Inventor to design a general bioreactor
+
−
<li>Incorporated shape and general items such as holes for screws and cavity for neuronal culturing
+
−
<li>Determined location of a multielectrode array (MEA) in bioreactor design, where the neurons would be transfected and tested
+
−
</ul>
+
  
 +
</div>
 +
 +
</div>
 +
  
−
30 May 2017 <br> WO
+
</div>
−
<ul>
+
</div>
−
<li>Adjusted design of bioreactor design
+
<div class="text-side shrinker-parent">
−
<li>Began a custom design for a MEA
+
<div class="vertical-aligner">
−
</ul>
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<h2 id="vbid-bb2e3d32-e7fsajn5" class="preview-element preview-title magic-circle-holder inner-page text-element quick-text-style-menu  allow-mobile-hide" data-menu-name="PREVIEW_TITLE" >February 2017<br></h2>
 +
 +
</div>
 +
<br class="lower-line-break" />
  
−
31 May 2017 <br> WO RG AM KP
+
−
<ul>
+
−
<li>Continued MEA designing: location of electrodes, leads, contact pad spacing, materials
+
−
</ul>
+
 +
 +
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<br class="upper-line-break" />
 +
<div class="preview-subtitle-holder removable-parent order-handle">
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<h3 id="vbid-bb2e3d32-wtn44f6j" class="preview-element preview-subtitle magic-circle-holder text-element quick-text-style-menu  allow-mobile-hide" data-menu-name="PREVIEW_SUBTITLE">Western Blotting</h3>
  
−
1 Jun 2017 <br> WO RM AM KP
+
</div>
−
<ul>
+
<br class="lower-line-break" />
−
<li>MEA
+
−
<ul>
+
−
<li>Altered the electrode arrangement and size for a single well of a 96 well plate</li>
+
−
<li>Predetermined specifications: Gold or TiN wires, embedded in glass </li>
+
−
</ul>
+
−
</li>
+
−
</ul>
+
  
−
2 Jun 2017<br>
+
−
WO RG AM KP MM
+
−
<ul>
+
−
<li>Determined custom MEA design specs, particularly spacing
+
−
</ul>
+
 +
 +
<br class="upper-line-break" />
 +
<div class="preview-body-holder removable-parent order-handle">
 +
 +
<div id="vbid-bb2e3d32-dpy97wsn" class="preview-element preview-body magic-circle-holder text-element quick-text-style-menu  allow-mobile-hide" data-menu-name="PREVIEW_BODY">
 +
<ol><li style="line-height: 1.8em;"><p class="font_8" style="line-height: 1.8em; font-size: 15px; text-align: left;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">HT-22 cells were lysed in RIPA buffer with phosphate and protease inhibitors</span></span></span><br></p></li><li style="line-height: 1.8em;"><p class="font_8" style="line-height: 1.8em; font-size: 15px; text-align: left;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Protein concentration was measured for each OR</span></span></span><br></p></li><li style="line-height: 1.8em;"><p class="font_8" style="line-height: 1.8em; font-size: 15px; text-align: left;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Proteins were prepared with Laemmle sample buffer before loading into 4% Bis-Tris gels to measure protein purity and size</span></span></span><br></p></li><li class="font_7" style="text-align: justify;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Participants</span></span></span><ol><li class="font_7" style="text-align: justify;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Dr. Alexander Mitropoulos, Dr. Ken Wickiser, Dr. Kamil Woronowicz, 2LT Dillon Macky, 2LT Ishmael Raheem, CDT Jason Hug, CDT Elizabeth Huuki, CDT Channah Mills, CDT Matthew McDonough, Isaac Dabkowski</span></span></span><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">​</span></span></span><br></li></ol></li></ol>
 +
</div>
 +
 +
</div>
 +
<br class="lower-line-break" />
  
−
5 Jun 2017<br>
+
−
WO RG AM KP MM
+
−
<ul>
+
−
<li>Revised MEA spacing
+
−
</ul>
+
</div>
 +
</div>
 +
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 +
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 +
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 +
<div id="element-a27df69d08403e5-holder"  class="preview-image-holder inner-pic-holder" data-menu-name="PREVIEW_INLINE_IMAGE_HOLDER">
  
−
6 Jun 2017 <br>
+
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−
WO RG AM KP MM
+
<!-- VIDEO TEMPLATE -->
−
<ul>
+
−
<li>Discussed the location of holes for media flow and a bubble trap
+
−
</ul>
+
  
−
7 Jun 2017 <br>
+
<div class="element-placeholder" data-elementtype='VIDEO' style="display:none;"></div>
−
WO RG AM KP MM
+
−
<ul>
+
−
<li>Fleshed out design for bubble trap
+
−
<li>Began design for clamp to keep pins on the multielectrode array (extension of bioreactor) - KP
+
−
</ul>
+
  
−
8 Jun 2017 <br> WO RG AM KP MM
 
−
<ul>
 
−
<li>Began discussion on removal of olfactant contaminated media while maintaining a perfusion system via syringes
 
−
<li>Continued clamp design-KP
 
−
<li>Requested a quote for custom MEA
 
−
</ul>
 
  
−
9 Jun 2017 <br> WO RG AM KP MM
+
<!-- MAP TEMPLATE -->
−
<ul>
+
−
<li>Confirmed the use of a peristaltic pump for media flow
+
<div class="element-placeholder" data-elementtype='MAP' style="display:none;"></div>
−
<li>Finalized MEA design
+
−
</ul>
+
  
−
12 Jun 2017<br>
+
<!-- RAW TEMPLATE -->
−
WO RG AM KP MM PB
+
−
<ul>
+
<div class="element-placeholder" data-elementtype='RAW' style="display:none;"></div>
−
<li>Contacted other MEA fabrication companies for quotes
+
−
</ul>
+
  
−
13 Jun 2017<br>
+
</div>
−
WO RG AM KP MM PB
+
−
<ul>
+
</div>
−
<li>Continued search of MEA vendors
+
−
<li>Worked on specifics regarding flow into and out of the bioreactor/media reservoirs - decided to use luer locks
+
−
</ul>
+
  
−
14 Jun 2017<br>
+
</div>
−
WO RG AM KP MM PB
+
</div>
−
<ul>
+
<div class="text-side shrinker-parent">
−
<li>Continued contacting MEA vendors
+
<div class="vertical-aligner">
−
</ul>
+
<div class="item-details preview-content-wrapper  multi" style="position:relative;">
 +
<div class="draggable-div-holder"></div>
 +
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<!--  BY SPECIFIC ORDER -->
 +
 +
 +
 +
 +
<br class="upper-line-break" />
 +
<div class="preview-title-holder removable-parent order-handle">
 +
 +
<h2 id="vbid-c9477c3f-y1ukkv8r" class="preview-element preview-title magic-circle-holder inner-page text-element quick-text-style-menu  allow-mobile-hide" data-menu-name="PREVIEW_TITLE" >March 2017<br></h2>
 +
 +
</div>
 +
<br class="lower-line-break" />
  
−
15 Jun 2017<br>
+
−
WO RG AM KP MM PB
+
−
<ul>
+
−
<li>Determined best luer lock connectors for tubing
+
−
<li>Finished printing of clamp design
+
−
<li>Explored photomasking vendors
+
−
</ul>
+
<br class="upper-line-break" />
 +
<div class="preview-subtitle-holder removable-parent order-handle">
 +
 +
<h3 id="vbid-c9477c3f-o0cafyw3" class="preview-element preview-subtitle magic-circle-holder text-element quick-text-style-menu  allow-mobile-hide" data-menu-name="PREVIEW_SUBTITLE">Confocal Microscopy</h3>
  
−
16 Jun 2017<br>
+
</div>
−
WO RG AM KP MM PB
+
<br class="lower-line-break" />
−
<ul>
+
−
<li>Determined design of media reservoirs to be conical flasks 
+
−
<li>Explored pre-made MEA vendors
+
−
</ul>
+
  
−
16 Jun 2017<br>
+
−
WO RG MM PB
+
−
<ul>
+
−
<li>Determined design of media reservoirs to be conical flasks 
+
−
<li>Explored pre-made MEA vendors
+
−
</ul>
+
 +
<br class="upper-line-break" />
 +
<div class="preview-body-holder removable-parent order-handle">
 +
 +
<div id="vbid-c9477c3f-rhbmmfpx" class="preview-element preview-body magic-circle-holder text-element quick-text-style-menu  allow-mobile-hide" data-menu-name="PREVIEW_BODY">
 +
<ol><li style="line-height: 1.8em;"><p class="font_8" style="line-height: 1.8em; font-size: 15px; text-align: left;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">HT-22 cells were fixed with 4% paraformaldehyde and immunohistochemistry with antibodies responsible for individual OR binding followed by secondary antibodies for visualization</span></span></span><br></p></li><li class="font_7" style="text-align: justify;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Participants</span></span></span><ol><li class="font_7" style="text-align: justify;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Dr. Alexander Mitropoulos, Dr. Ken Wickiser, Dr. Kamil Woronowicz, 2LT Dillon Macky, 2LT Ishmael Raheem, CDT Jason Hug, CDT Elizabeth Huuki, CDT Channah Mills, CDT Matthew McDonough, Isaac Dabkowski</span></span></span><br></li></ol></li></ol>
 +
</div>
 +
 +
</div>
 +
<br class="lower-line-break" />
  
−
19 Jun 2017<br>
+
−
WO RG MM PB
+
−
<ul>
+
−
<li>Ordered MEAs from Multichannel Systems
+
−
<li>Researched on systems to control the peristaltic pump from the computer
+
−
</ul>
+
 +
 +
 +
</div>
 +
</div>
 +
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 +
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 +
<div id="no-image" class="background-image-div preview-element image-source magic-circle-holder unfold-left load-high-res" data-menu-name="BACKGROUND_IMAGE" style="">
 +
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<div class="helper-div middle-center" >
 +
<!-- <div class="benet" style="min-height:inherit;"></div> -->
 +
<div class="pic-side">
 +
<div class="vertical-aligner">
 +
<div id="no-image-holder"  class="preview-image-holder inner-pic-holder" data-menu-name="PREVIEW_INLINE_IMAGE_HOLDER">
  
−
20 Jun 2017<br>
+
<div  id="no-image" class="inner-pic preview-element  magic-circle-holder  load-high-res " data-menu-name="PREVIEW_INLINE_IMAGE" style=""  data-orig-width="" data-orig-height="" >
−
WO RG MM PB
+
<!-- VIDEO TEMPLATE -->
−
<ul>
+
−
<li>Find tubing for bioreactor and pump
+
−
</ul>
+
  
−
21 Jun 2017<br>
+
<div class="element-placeholder" data-elementtype='VIDEO' style="display:none;"></div>
−
WO RG MM PB
+
−
<ul>
+
−
<li>Designed media reservoirs in Inventor, obtaining a cubic appearance, as opposed to the original conical tube appearance
+
−
</ul>
+
  
−
22 Jun 2017<br>
 
−
WO RG MM PB
 
−
<ul>
 
−
<li>Ordered tubing
 
−
</ul>
 
  
−
26 Jun 2017<br>
+
<!-- MAP TEMPLATE -->
−
WO RG MM PB
+
−
<ul>
+
<div class="element-placeholder" data-elementtype='MAP' style="display:none;"></div>
−
<li>Redesigned clamp system for pins using a platform and screws system
+
−
<li>Revised bioreactor design to have internal channels in one side of the bioreactor
+
−
</ul>
+
  
−
27 Jun 2017<br>
+
<!-- RAW TEMPLATE -->
−
WO RG MM PB
+
−
<ul>
+
<div class="element-placeholder" data-elementtype='RAW' style="display:none;"></div>
−
<li>Inserted a conical steeple for the bubble trap
+
−
<li>Made minor modifications to bioreactor design
+
−
</ul>
+
  
−
30 Jun 2017<br>
+
</div>
−
WO RG
+
−
<ul>
+
</div>
−
<li>Inserted threading into media reservoirs
+
−
<li>Made measurements of ordered o-rings to be fitted
+
−
</ul>
+
  
−
3 Jul 2017<br>
+
</div>
−
WO RG
+
</div>
−
<ul>
+
<div class="text-side shrinker-parent">
−
<li>Printed out models to help test fittings for the O-ring
+
<div class="vertical-aligner">
−
</ul>
+
<div class="item-details preview-content-wrapper  multi" style="position:relative;">
 +
<div class="draggable-div-holder"></div>
 +
<div class="preview-content-holder shrinker-content">
 +
 +
<!--  BY SPECIFIC ORDER -->
 +
 +
 +
 +
 +
<br class="upper-line-break" />
 +
<div class="preview-title-holder removable-parent order-handle">
 +
 +
<h2 id="vbid-df58bf33-y1ukkv8r" class="preview-element preview-title magic-circle-holder inner-page text-element quick-text-style-menu  allow-mobile-hide" data-menu-name="PREVIEW_TITLE" >April 2017<br></h2>
 +
 +
</div>
 +
<br class="lower-line-break" />
  
−
5 Jul 2017<br>
+
−
WO RG
+
−
<ul>
+
−
<li>Printed array to narrow down sizing for O-Ring
+
−
<li>Modified media reservoir due to space constraints
+
−
<li>Printed model MEAs to test pin setup and general fittings
+
−
</ul>
+
<br class="upper-line-break" />
 +
<div class="preview-subtitle-holder removable-parent order-handle">
 +
 +
<h3 id="vbid-df58bf33-o0cafyw3" class="preview-element preview-subtitle magic-circle-holder text-element quick-text-style-menu  allow-mobile-hide" data-menu-name="PREVIEW_SUBTITLE">Action Potential Measurements</h3>
  
−
7 Jul 2017<br>
+
</div>
−
WO RG
+
<br class="lower-line-break" />
−
<ul>
+
−
<li>Modified media reservoir for better fluid flow
+
−
</ul>
+
  
−
10 Jul 2017<br>
+
−
WO RG
+
−
<ul>
+
−
<li>Printed first part of bioreactor
+
−
</ul>
+
 +
 +
<br class="upper-line-break" />
 +
<div class="preview-body-holder removable-parent order-handle">
 +
 +
<div id="vbid-df58bf33-rhbmmfpx" class="preview-element preview-body magic-circle-holder text-element quick-text-style-menu  allow-mobile-hide" data-menu-name="PREVIEW_BODY">
 +
<ol><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;"></span></span></span><li style="line-height: 1.8em;"><p class="font_8" style="line-height: 1.8em; font-size: 15px; text-align: left;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Nucleofected HT-22 cells were stimulated with individual odorants</span></span></span><br></p></li><li style="line-height: 1.8em;"><p class="font_8" style="line-height: 1.8em; font-size: 15px; text-align: left;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">The neurons generated action potentials that were measured via a microelectrode array</span></span></span><br></p></li><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;"></span></span></span><li class="font_7" style="text-align: justify;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Participants</span></span></span><ol><li class="font_7" style="text-align: justify;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Dr. Alexander Mitropoulos, Dr. Ken Wickiser, Dr. Kamil Woronowicz, 2LT Dillon Macky, 2LT Ishmael Raheem, CDT Jason Hug, CDT Elizabeth Huuki, CDT Channah Mills, CDT Matthew McDonough, Isaac Dabkowski</span></span></span><br></li></ol></li></ol>
 +
</div>
 +
 +
</div>
 +
<br class="lower-line-break" />
  
−
12 Jul 2017<br>
+
−
WO RG
+
−
<ul>
+
−
<li>Adjusted dimensions and reprinted first part of bioreactor
+
−
</ul>
+
</div>
 +
</div>
 +
</div>
 +
</div>
 +
</div>
 +
</div>
 +
</div>
 +
</div>
 +
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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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 +
<!-- ARRANGER SETTINGS -->
 +
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 +
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 +
data-ARRANGER_COLS="0"
 +
data-ARRANGER_ITEM_MAX_WIDTH="400"
 +
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 +
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 +
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 +
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 +
 +
<div class="page-wrapper item-wrapper ">
 +
 +
<div class="item-content leaf multi_layout page content -container" data-self="vbid-3d4ff3cd-o0ba9iw8" data-preview-style="style-3d4ff3cd-2p5gmo8r" data-style="style-4e411-yq39oaomol" data-orig-thumb-height="2592" data-orig-thumb-width="3872" data-vbid="vbid-3d4ff3cd-o0ba9iw8" data-bgimg="https://lh3.googleusercontent.com/nQjKEktNrFksk3oBSUBL3If8TXXgu24pvw-GIvFjuubu69TyFY8NZ70THN-wjFOgWzmB74i6JQav4HMj">
 +
<div  class="multi-container preview image-cover" >
 +
<div class="Picture item-preview">
 +
<div class="preview-image-holder">
 +
<div id="no-image" class="background-image-div preview-element image-source magic-circle-holder unfold-left load-high-res" data-menu-name="BACKGROUND_IMAGE" style="">
 +
</div>
 +
<div class="helper-div middle-left" >
 +
<!-- <div class="benet" style="min-height:inherit;"></div> -->
 +
<div class="pic-side">
 +
<div class="vertical-aligner">
 +
<div id="element-cdcf73d3fbcac92-holder"  class="preview-image-holder inner-pic-holder" data-menu-name="PREVIEW_INLINE_IMAGE_HOLDER">
  
−
13 Jul 2017<br> WO RG
+
<div  id="element-cdcf73d3fbcac92" class="inner-pic preview-element  magic-circle-holder  load-high-res " data-menu-name="PREVIEW_INLINE_IMAGE" style="background-image:url(https://lh3.googleusercontent.com/nQjKEktNrFksk3oBSUBL3If8TXXgu24pvw-GIvFjuubu69TyFY8NZ70THN-wjFOgWzmB74i6JQav4HMj=s300);"  data-orig-width="3872" data-orig-height="2592" >
−
<ul>
+
<!-- VIDEO TEMPLATE -->
−
<li>Adjusted dimensions and printed a third version of the first part of bioreactor</li>
+
−
</ul>
+
  
−
14 Jul 2017<br> WO RG
+
<div class="element-placeholder" data-elementtype='VIDEO' style="display:none;"></div>
−
<ul>
+
−
<li>Printed array to determine necessary dimensions to fit luer locks </li>
+
−
</ul>
+
  
−
17 Jul 2017<br> WO RG
 
−
<ul>
 
−
<li>Applied dimension changes to bioreactor design and reprinted the first part of bioreactor</li>
 
−
</ul>
 
  
−
18 Jul 2017<br> WO RG
+
<!-- MAP TEMPLATE -->
−
<ul>
+
−
<li>Determined screw size and lengths needed to apply appropriate pressure on pins</li>
+
<div class="element-placeholder" data-elementtype='MAP' style="display:none;"></div>
−
</ul>
+
  
−
19 Jul 2017<br> WO RG
+
<!-- RAW TEMPLATE -->
−
<ul>
+
−
<li>Printed out top and bottom of bioreactor and clamp</li>
+
<div class="element-placeholder" data-elementtype='RAW' style="display:none;"></div>
−
<li>Perforated MEA Bioreactor modified</li>
+
−
<li>Verified operation of the pump</li>
+
−
<li>Tested calibration of pump</li>
+
−
</ul>
+
−
<a name="Programming and Electronics"></a> <br>
+
−
<h3>Programming and Electronics (Bioreactor focus)</h3>
+
  
−
23 May 2017 <br>
+
</div>
−
WO
+
−
<ul>
+
</div>
−
<li>Introduced to labview - use to take voltage readings from electrodes
+
−
<li>Determined to set peak threshold to +/- 2 SD of base activity
+
−
</ul>
+
  
−
25 May 2017 <br>
+
</div>
−
WO
+
</div>
−
<ul>
+
<div class="text-side shrinker-parent">
−
<li>Built time-averaging method to determine frequency and amplitude of peaks
+
<div class="vertical-aligner">
−
<li>Generated preliminary statistics for data
+
<div class="item-details preview-content-wrapper  multi" style="position:relative;">
−
<li>Built code to write to a file
+
<div class="draggable-div-holder"></div>
−
</ul>
+
<div class="preview-content-holder shrinker-content">
 +
 +
<!--  BY SPECIFIC ORDER -->
 +
 +
 +
 +
 +
<br class="upper-line-break" />
 +
<div class="preview-title-holder removable-parent order-handle">
 +
 +
<h2 id="vbid-3d4ff3cd-kekeilno" class="preview-element preview-title magic-circle-holder inner-page text-element quick-text-style-menu  allow-mobile-hide" data-menu-name="PREVIEW_TITLE" >May 2017<br></h2>
 +
 +
</div>
 +
<br class="lower-line-break" />
  
−
30 May 2017 <br>
+
−
WO
+
−
<ul>
+
−
<li>Inserted method to adjust thresholds before data collection
+
−
</ul>
+
 +
 +
<br class="upper-line-break" />
 +
<div class="preview-subtitle-holder removable-parent order-handle">
 +
 +
<h3 id="vbid-3d4ff3cd-bb0e8gwp" class="preview-element preview-subtitle magic-circle-holder text-element quick-text-style-menu  allow-mobile-hide" data-menu-name="PREVIEW_SUBTITLE">USMA Projects Day</h3>
  
−
29 Jun 2017 <br>
+
</div>
−
WO
+
<br class="lower-line-break" />
−
<ul>
+
−
<li>Adjusted labview program to read in data from electrodes using Intan codes (as opposed to theoretical inputs)
+
−
<li>Finished labview program - can select filename/type
+
−
</ul>
+
  
−
12 Jun 2017 <br>
+
−
WO
+
−
<ul>
+
−
<li>Implemented impedance program from Intan to determine the presence of cells on electrodes
+
−
</ul>
+
 +
 +
<br class="upper-line-break" />
 +
<div class="preview-body-holder removable-parent order-handle">
 +
 +
<div id="vbid-3d4ff3cd-4adbl1bh" class="preview-element preview-body magic-circle-holder text-element quick-text-style-menu  allow-mobile-hide" data-menu-name="PREVIEW_BODY">
 +
<ol><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;"></span></span></span><li style="line-height: 1.8em;"><p class="font_8" style="line-height: 1.8em; font-size: 15px; text-align: left;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Presented research at United States Military Academy Projects Day, a day where students present projects concerning research in various fields</span></span></span><br></p></li><li style="line-height: 1.8em;"><p class="font_8" style="line-height: 1.8em; font-size: 15px; text-align: left;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Reports put together for eNOSE</span></span></span><br></p></li><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;"></span></span></span><li class="font_7" style="text-align: justify;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Participants</span></span></span><ol><li class="font_7" style="text-align: justify;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Dr. Alexander Mitropoulos, Dr. Ken Wickiser, Dr. Kamil Woronowicz, 2LT Dillon Macky, 2LT Ishmael Raheem, CDT Jason Hug, CDT Elizabeth Huuki, CDT Channah Mills, CDT Matthew McDonough, Isaac Dabkowski</span></span></span><br></li></ol></li></ol>
 +
</div>
 +
 +
</div>
 +
<br class="lower-line-break" />
 +
 
 +
 +
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 +
 +
 +
 +
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 +
</div>
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</div>
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</div>
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 +
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 +
</div>
 +
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 +
<!-- LAYOUT SETTINGS -->
 +
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 +
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 +
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 +
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 +
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 +
 
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<h2 id="vbid-252908aa-x6d0iiuy" class="preview-element preview-title magic-circle-holder inner-page text-element quick-text-style-menu  allow-mobile-hide" data-menu-name="PREVIEW_TITLE" >June 2017<br></h2>
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<h3 id="vbid-252908aa-ywwepk8k" class="preview-element preview-subtitle magic-circle-holder text-element quick-text-style-menu  allow-mobile-hide" data-menu-name="PREVIEW_SUBTITLE">Further Trials and Biosensor Design</h3>
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<ol><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;"></span></span></span><li style="line-height: 1.8em;"><p class="font_8" style="line-height: 1.8em; font-size: 15px; text-align: left;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Cells amplified</span></span></span><br></p></li><li style="line-height: 1.8em;"><p class="font_8" style="line-height: 1.8em; font-size: 15px; text-align: left;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Focused on designing a biosensor</span></span></span></p><ul><li style="line-height: 1.8em; text-align: left;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Bioreactor</span></span></span></li><li style="line-height: 1.8em; text-align: left;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Microelectrode array (MEA)</span></span></span></li><li style="line-height: 1.8em; text-align: left;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Perfusion system</span></span></span></li><li style="line-height: 1.8em; text-align: left;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Signal Processor</span></span></span><br></li></ul></li><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;"></span></span></span><li class="font_7" style="text-align: justify;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Participants</span></span></span><ol><li class="font_7" style="text-align: justify;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Dr. Kirk Pirlo, Dr. Joel Gaston, Winston Ou, Rayonna Gordon, CDT Angela Marsh, CDT Kanak Pal, CDT Payton Boylston, CDT Matthew McDonough</span></span></span><br></li></ol></li></ol>
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<ol><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;"></span></span></span><li style="line-height: 1.8em;"><p class="font_8" style="line-height: 1.8em; font-size: 15px; text-align: left;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Finalized biosensor design as necessary parts were delivered</span></span></span><br></p></li><li style="line-height: 1.8em; text-align: left;">Prepared for trials with updated biosensor</li><li style="line-height: 1.8em; text-align: left;">Additional transformations<span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;"></span></span></span><br></li><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;"></span></span></span><li class="font_7" style="text-align: justify;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Participants</span></span></span><ol><li class="font_7" style="text-align: justify;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Dr. Kirk Pirlo, Dr. Joel Gaston, Winston Ou, Rayonna Gordon, Dr. Alex Mitropoulos</span></span></span><br></li></ol></li></ol>
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<ol><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;"></span></span></span><li style="line-height: 1.8em;"><p class="font_8" style="line-height: 1.8em; font-size: 15px; text-align: left;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Ran successful trials with updated biosensor</span></span></span><br></p></li><li style="line-height: 1.8em;"><p class="font_8" style="line-height: 1.8em; font-size: 15px; text-align: left;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Collected more data for device</span></span></span><br></p></li><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;"></span></span></span><li class="font_7" style="text-align: justify;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Participants</span></span></span><ol><li class="font_7" style="text-align: justify;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Dr. Kirk Pirlo, Dr. Joel Gaston, Winston Ou, Rayonna Gordon, Dr. Alex Mitropoulos</span></span></span><br></li></ol></li></ol>
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<h3 id="vbid-b49c473a-bd4ey2ss" class="preview-element preview-subtitle magic-circle-holder text-element quick-text-style-menu  allow-mobile-hide" data-menu-name="PREVIEW_SUBTITLE">Interlab Protocol and iGEM Plasmid</h3>
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<ol><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;"></span></span></span><li style="line-height: 1.8em;"><p class="font_8" style="line-height: 1.8em; font-size: 15px; text-align: left;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Completed Interlab protocol and collected data</span></span></span><br></p></li><li style="line-height: 1.8em;"><p class="font_8" style="line-height: 1.8em; font-size: 15px; text-align: left;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Developed iGEM plasmid by transfection and amplification</span></span></span></p></li><li style="line-height: 1.8em;"><p class="font_8" style="line-height: 1.8em; font-size: 15px; text-align: left;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Ran gel of plasmids to evaluate</span></span></span><br></p></li><li class="font_7" style="text-align: justify;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Participants</span></span></span><ol><li class="font_7" style="text-align: justify;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Dr. Alexander Mitropoulos, Dr. Ken Wickiser, Dr. Kamil Woronowicz, Dr. John Cave, CDT Jason Hug, CDT Zachary Andersen, CDT Kylor Keisewetter, CDT Alana Appel, CDT Elizabeth Huuki​, CDT Channah Mills, CDT Matthew McDonough, CDT James Pruneski</span></span></span><br></li></ol></li></ol>
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<h2 id="vbid-1be02fa7-mbbndz1n" class="preview-element preview-title magic-circle-holder inner-page text-element quick-text-style-menu  allow-mobile-hide" data-menu-name="PREVIEW_TITLE" >October 2017<br></h2>
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<h3 id="vbid-1be02fa7-oiwczuaa" class="preview-element preview-subtitle magic-circle-holder text-element quick-text-style-menu  allow-mobile-hide" data-menu-name="PREVIEW_SUBTITLE">Preparation for iGEM</h3>
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<ol><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;"></span></span></span><li style="line-height: 1.8em;"><p class="font_8" style="line-height: 1.8em; font-size: 15px; text-align: left;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Finalized results</span></span></span><br></p></li><li style="line-height: 1.8em;"><p class="font_8" style="line-height: 1.8em; font-size: 15px; text-align: left;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Design and develop parts</span></span></span><br></p></li><li style="line-height: 1.8em;"><p class="font_8" style="line-height: 1.8em; font-size: 15px; text-align: left;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Prepared iGEM wiki and presentation</span></span></span><br></p></li><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;"></span></span></span><li class="font_7" style="text-align: justify;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Participants</span></span></span><ol><li class="font_7" style="text-align: justify;"><span style="color: rgb(0, 0, 0);"><span style="font-size: 15px;"><span style="font-family: helvetica-w01-light,helvetica-w02-light,sans-serif;">Dr. Alexander Mitropoulos, Dr. Ken Wickiser, Dr. Kamil Woronowicz, Dr. John Cave, CDT Jason Hug, CDT Zachary Andersen, CDT Kylor Keisewetter, CDT Alana Appel, CDT Elizabeth Huuki​, CDT Channah Mills, CDT Matthew McDonough, CDT James Pruneski</span></span></span><br></li></ol></li></ol>
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Latest revision as of 23:16, 1 November 2017

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USMA-West_Point


Notebook - iGem 01

usMA-WEST POINT


NOTEBOOK



Day to Day activity inside the lab



January 2017



Transformation of Bacteria Cells



  1. OR vectors were purchased from OriGene and transfected into XL-10 Gold Ultracompetent cells by heat shocking at 42 degrees Celsius
  2. Cells were cultured in LB broth to amplify vectors
  3. DNA gels were run with specific restriction enzymes to determine multiple cloning sites
  4. Participants
    1. Dr. Alexander Mitropoulos, Dr. Ken Wickiser, Dr. Kamil Woronowicz, 2LT Dillon Macky, 2LT Ishmael Raheem, CDT Jason Hug, CDT Elizabeth Huuki, CDT Channah Mills, CDT Matthew McDonough, Isaac Dabkowski


February 2017



Western Blotting



  1. HT-22 cells were lysed in RIPA buffer with phosphate and protease inhibitors

  2. Protein concentration was measured for each OR

  3. Proteins were prepared with Laemmle sample buffer before loading into 4% Bis-Tris gels to measure protein purity and size

  4. Participants
    1. Dr. Alexander Mitropoulos, Dr. Ken Wickiser, Dr. Kamil Woronowicz, 2LT Dillon Macky, 2LT Ishmael Raheem, CDT Jason Hug, CDT Elizabeth Huuki, CDT Channah Mills, CDT Matthew McDonough, Isaac Dabkowski​


March 2017



Confocal Microscopy



  1. HT-22 cells were fixed with 4% paraformaldehyde and immunohistochemistry with antibodies responsible for individual OR binding followed by secondary antibodies for visualization

  2. Participants
    1. Dr. Alexander Mitropoulos, Dr. Ken Wickiser, Dr. Kamil Woronowicz, 2LT Dillon Macky, 2LT Ishmael Raheem, CDT Jason Hug, CDT Elizabeth Huuki, CDT Channah Mills, CDT Matthew McDonough, Isaac Dabkowski


April 2017



Action Potential Measurements



  1. Nucleofected HT-22 cells were stimulated with individual odorants

  2. The neurons generated action potentials that were measured via a microelectrode array

  3. Participants
    1. Dr. Alexander Mitropoulos, Dr. Ken Wickiser, Dr. Kamil Woronowicz, 2LT Dillon Macky, 2LT Ishmael Raheem, CDT Jason Hug, CDT Elizabeth Huuki, CDT Channah Mills, CDT Matthew McDonough, Isaac Dabkowski


May 2017



USMA Projects Day



  1. Presented research at United States Military Academy Projects Day, a day where students present projects concerning research in various fields

  2. Reports put together for eNOSE

  3. Participants
    1. Dr. Alexander Mitropoulos, Dr. Ken Wickiser, Dr. Kamil Woronowicz, 2LT Dillon Macky, 2LT Ishmael Raheem, CDT Jason Hug, CDT Elizabeth Huuki, CDT Channah Mills, CDT Matthew McDonough, Isaac Dabkowski


June 2017



Further Trials and Biosensor Design



  1. Cells amplified

  2. Focused on designing a biosensor

    • Bioreactor
    • Microelectrode array (MEA)
    • Perfusion system
    • Signal Processor
  3. Participants
    1. Dr. Kirk Pirlo, Dr. Joel Gaston, Winston Ou, Rayonna Gordon, CDT Angela Marsh, CDT Kanak Pal, CDT Payton Boylston, CDT Matthew McDonough


July 2017



Finalizing Design



  1. Finalized biosensor design as necessary parts were delivered

  2. Prepared for trials with updated biosensor
  3. Additional transformations
  4. Participants
    1. Dr. Kirk Pirlo, Dr. Joel Gaston, Winston Ou, Rayonna Gordon, Dr. Alex Mitropoulos


August 2017



Trials with Updated Device



  1. Ran successful trials with updated biosensor

  2. Collected more data for device

  3. Participants
    1. Dr. Kirk Pirlo, Dr. Joel Gaston, Winston Ou, Rayonna Gordon, Dr. Alex Mitropoulos


September 2017



Interlab Protocol and iGEM Plasmid



  1. Completed Interlab protocol and collected data

  2. Developed iGEM plasmid by transfection and amplification

  3. Ran gel of plasmids to evaluate

  4. Participants
    1. Dr. Alexander Mitropoulos, Dr. Ken Wickiser, Dr. Kamil Woronowicz, Dr. John Cave, CDT Jason Hug, CDT Zachary Andersen, CDT Kylor Keisewetter, CDT Alana Appel, CDT Elizabeth Huuki​, CDT Channah Mills, CDT Matthew McDonough, CDT James Pruneski


October 2017



Preparation for iGEM



  1. Finalized results

  2. Design and develop parts

  3. Prepared iGEM wiki and presentation

  4. Participants
    1. Dr. Alexander Mitropoulos, Dr. Ken Wickiser, Dr. Kamil Woronowicz, Dr. John Cave, CDT Jason Hug, CDT Zachary Andersen, CDT Kylor Keisewetter, CDT Alana Appel, CDT Elizabeth Huuki​, CDT Channah Mills, CDT Matthew McDonough, CDT James Pruneski


DEPARTMENT OF CHEMISTRY AND LIFE SCIENCE



BARTLETT HALL, ROOM 400, WEST POINT, NY 10996, USA


TEL: 845.938.3915