Difference between revisions of "Team:Georgia State/sandbox"

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<h1 style="color:#1F618D; text-align: center; font-size: 36px; line-height: 40px;">Background</h1>
 
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<h1 style="color:#ffffff; background-color:#1F618D;; -moz-border-radius: 15px; -webkit-border-radius: 15px; padding:15px; text-align: center; font-family: Trebuchet MS">What is Lipopolysaccharide?</h1>  <br>
 
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Endotoxin is a Lipopolysaccharide (LPS) it consists of a core oligosaccharide, O-antigen a glycan polymer and the lipid A. The lipid A is a phosphorylated glucosamine disaccharide with multiple fatty acids and is the cause for endotoxin toxicity.  LPS are bacterial poisons and can impact numerous biological activities. When gram-negative bacteria enter the body a complement immune response is initiated. Once the cell wall and/or bacteria are destroyed a significant of endotoxins are released which can lead to endotoxemia the symptoms of which are vomiting, nausea, diarrhea, fever, disseminated intravascular coagulation, vascular collapse, organ failure and possibly death. Antibiotics will not inactivate the endotoxins, therefore detection of the endotoxin before they enter the body is prudent.<br>
 
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<h1 style="color:#ffffff; background-color:#1F618D;; -moz-border-radius: 15px; -webkit-border-radius: 15px; padding:15px; text-align: center; font-family: Trebuchet MS">What do horseshoe crabs have to do with endotoxin?</h1>  <br>
 
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<img src="https://static.igem.org/mediawiki/2017/c/cf/T--Georgia_State--horseshoebranfromaquarium.jpg"  alt="Horseshoe Crab in Aquarium" width="250" height="250" style="float:right;">
 
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<b> Limulus polyphemus (Atlantic horseshoe crab)</b> is protected against infection by their immune system and blood coagulation system. They use hemocyanin to carry oxygen instead of hemoglobin. The blue color of their blood is due to the presence of copper in hemocyanin. The amebocytes (blood cells) are similar to white blood cells. Inside the amebocytes are proteins that are released in response to unwanted organisms like gram-negative bacteria. These proteins bind to and inactivate endotoxin. Assistance in wound control is moderated by components of their blood which prevent bleeding and form a physical barrier against additional infection. <br>
 
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In the presence of endotoxin, a clotting cascade is invoked to activate the proclotting enzyme which is used to transform coagulogen into coagulin. The zymogen Factor C is a glycoprotein that is 123kD, and the only enzyme that is endotoxin sensitive. It consists of an H chain (80kD) and L chain (43kD). Factor C activates in the presence of LPS and undergoes autocatalysis, the phenylalanine- isoleucine bond on the L chain is cleaved resulting in a B chain (34kD) and an A chain (8.5 kD). Factor C then activates Factor B which activates the proclotting enzyme. An activated proclotting enzyme is called the clotting enzyme which converts coagulogen into coagulin. <br>
 
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<img src="https://static.igem.org/mediawiki/2017/9/9a/T--Georgia_State--FactorCcascade.jpg"  alt="Cotting Cascade" width="300" height="300" style="left;">
 
  
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<img src="https://static.igem.org/mediawiki/2017/1/1d/T--Georgia_State--factorcdiagram.jpg" alt="Factor C diagram" width="250" height="250" style="float:right;">
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<h1>Parts</h1>
  
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<p>Each team will make new parts during iGEM and will submit them to the Registry of Standard Biological Parts. The iGEM software provides an easy way to present the parts your team has created. The <code>&lt;groupparts&gt;</code> tag (see below) will generate a table with all of the parts that your team adds to your team sandbox.</p>
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<p>Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without needing to refer to the primary literature. Registry users in future years should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.</p>
  
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<h1 style="color:#ffffff; background-color:#1F618D;; -moz-border-radius: 15px; -webkit-border-radius: 15px; padding:15px; text-align: center; font-family: Trebuchet MS"> What is LAL assay? </h1> 
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<img src= "https://static.igem.org/mediawiki/2017/2/24/T--Georgia_State--LALcascadeandBLUEblood.jpg" alt="Clotting Cascade" width="300" height="300" style="float:right;">
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Limulus Amebocyte Lysate test is an extract of the Limulus polyphemus (Atlantic horseshoe crab) blood cells (amoebocytes) it detects small concentrations of endotoxin.  Horseshoe crabs are bleed through the pericardium. A third of their blood is taken and they are released back into the water. Through centrifugation, their blood cells are separated from the serum. In order to release the chemicals from inside the blood cells, they are placed in distilled water where they burst and form the lysate. Once the lysate is made the test becomes simple. A sample is mixed with lysate and water. If endotoxin is present if coagulation transpires.
 
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An injectable healthcare product like a vaccine and any other healthcare product like implantables that come in contact with a patients blood or cerebrospinal fluid must be sterile. However, the process to kill bacteria results in the release of endotoxin into the product because the cell wall can withstand steam sterilization. The products must be tested for endotoxin before use.
 
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<iframe width="450" height="230" align= "float" src="https://www.youtube.com/embed/VgEbcQxFUu8" frameborder="0" allowfullscreen> </iframe>
 
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<img src= "https://static.igem.org/mediawiki/2017/5/52/T--Georgia_State--horseshoecrabbleeding.jpg" alt="horseshoe crab bleeding" width="350" height="450" style="float:right;">
 
  
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<h5>Note</h5>
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<p>Note that parts must be documented on the <a href="http://parts.igem.org/Main_Page"> Registry</a>. This page serves to <i>showcase</i> the parts you have made. Future teams and other users and are much more likely to find parts by looking in the Registry than by looking at your team wiki.</p>
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<h1 style="color:#ffffff; background-color:#1F618D;; -moz-border-radius: 15px; -webkit-border-radius: 15px; padding:15px; text-align: center; font-family: Trebuchet MS">So where does GSU come in to play? </h1> 
 
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Using horseshoe crab blood is an unsustainable practice due to the impact on the crabs and the expense of the LAL assay. A third of the blood is taken from the horseshoe crab before they are realsed back into the water. The theory is that the crabs eventually heal however up to 30% of bled crabs die. The total population is decreasing rapidly while producers are forced to increase harvests to keep up with global demand. The LAL test is expensive to make; a quart of blood is sold for $15,000. Part of affordable healthcare means that the production of the products used also need to be affordable. <br>
 
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Creating an alternative form of testing is unavoidable. Instead of creating a recombinant version of the entire clotting cascade it is more efficient to create a recombinant version of factor c and include a detection mechanism to detect the autocatalysis in the presence of LPS.  Human chorionic gonadotropin (hCG) beta subunit is detected through a human pregnancy test. Using the subunit in tandem with the pregnancy test allows for an efficient and inexpensive autocatalysis detection method. The goal of our project is to create a fusion protein of Factor c with hCG and immobilize it in a solution. When the LPS is exposed to the factor c it will undergo autocatalysis and release hCG into the solution where it is then detected by the pregnancy test. <br>
 
  
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<img src= "https://static.igem.org/mediawiki/2017/4/4b/T--Georgia_State--factorcdiagrampart1.jpg" alt="factorc1" width="350" height="450" style="float:left;">
 
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<img src= "https://static.igem.org/mediawiki/2017/a/a3/T--Georgia_State--factorc2.jpg" alt="factorc1" width="350" height="450" style="float:right;">
 
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<br><br><br> <br> <br> <br>
 
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<a href="https://2017.igem.org/Team:Georgia_State/Parts"><h1 style="color:#ffffff; background-color:#7FB3D5;; -moz-border-radius: 15px; -webkit-border-radius: 15px; padding:15px; text-align: center; font-family: Trebuchet MS">Next: Part Design</h1> </a>
 
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<a href="https://2017.igem.org/Team:Georgia_State"><h1 style="color:#ffffff; background-color:#A9CCE3;; -moz-border-radius: 15px; -webkit-border-radius: 15px; padding:15px; text-align: center; font-family: Trebuchet MS">Back to Home</h1> </a>
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<h5>Adding parts to the registry</h5>
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<b>References</b><br>
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<p>You can add parts to the Registry at our <a href="http://parts.igem.org/Add_a_Part_to_the_Registry">Add a Part to the Registry</a> link.</p>
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- - -B. Akbar John, K.C.A. Jalal, Y.B. Kamaruzzaman and K. Zaleha, 2010.<i>Mechanism in the Clot Formation of Horseshoe Crab Blood during Bacterial Endotoxin Invasion (July 10, 2010). Journal of Applied Sciences, 10: 1930-1936. Retrieved June 11, 2017, from</i><a http://scialert.net/fulltext/?doi=jas.2010.1930.1936">http://scialert.net/fulltext/?doi=jas.2010.1930.1936</a> <br>
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<p>We encourage teams to start completing documentation for their parts on the Registry as soon as you have it available. The sooner you put up your parts, the better you will remember all the details about your parts. Remember, you don't need to send us the DNA sample before you create an entry for a part on the Registry. (However, you <b>do</b> need to send us the DNA sample before the Jamboree. If you don't send us a DNA sample of a part, that part will not be eligible for awards and medal criteria.)</p>
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- - - <i>Elizabeth Cox. (2017,September, 21). Why do we harvest horseshoe crab blood?  [Video file]. </i> <a href="https://www.youtube.com/watch?v=VgEbcQxFUu8/"> https://www.youtube.com/watch?v=VgEbcQxFUu8/</a> <br>
 
  
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- - - <i>Ecological Research & Development Group. (2013). <br> Horseshoe Crabs and Endotoxin Testing . . Retrieved October 31, 2017, from </i> <a href="http://www.horseshoecrab.org/med/sustainable.html"> http://www.horseshoecrab.org/med/sustainable.html</a><br>
 
  
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- - - <i>Ecological Research & Development Group. (2013). [Copper Based "Blue blood" and Cascade of Enzymes and Proteins ]. </i> JRetrieved October 31, 2017, from<br> <a href="http://www.horseshoecrab.org/med/testing.html">http://www.horseshoecrab.org/med/testing.html</a><br>
 
  
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- - - <i>PBS. (2014, February 26). A still for the PBS Nature documentary Crash [Digital image]. Retrieved October 31, 2017, from <br><a href="https://www.theatlantic.com/technology/archive/2014/02/the-blood-harvest/284078/">https://www.theatlantic.com/technology/archive/2014/02/the-blood-harvest/284078/</a><br>
 
  
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<h5>What information do I need to start putting my parts on the Registry?</h5>
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<p>The information needed to initially create a part on the Registry is:</p>
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<li>Part Name</li>
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<li>Part type</li>
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<li>Creator</li>
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<li>Sequence</li>
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<li>Short Description (60 characters on what the DNA does)</li>
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<li>Long Description (Longer description of what the DNA does)</li>
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<li>Design considerations</li>
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<p>
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We encourage you to put up <em>much more</em> information as you gather it over the summer. If you have images, plots, characterization data and other information, please also put it up on the part page. </p>
  
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<h5>Inspiration</h5>
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<p>We have a created  a <a href="http://parts.igem.org/Well_Documented_Parts">collection of well documented parts</a> that can help you get started.</p>
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<p> You can also take a look at how other teams have documented their parts in their wiki:</p>
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<ul>
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<li><a href="https://2014.igem.org/Team:MIT/Parts"> 2014 MIT </a></li>
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<li><a href="https://2014.igem.org/Team:Heidelberg/Parts"> 2014 Heidelberg</a></li>
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<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">2014 Tokyo Tech</a></li>
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</ul>
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<h5>Part Table </h5>
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<p>Please include a table of all the parts your team has made during your project on this page. Remember part characterization and measurement data must go on your team part pages on the Registry. </p>
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<groupparts>iGEM17 Georgia_State</groupparts>
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Revision as of 22:30, 31 October 2017

{{Georgia_State}}

Parts

Each team will make new parts during iGEM and will submit them to the Registry of Standard Biological Parts. The iGEM software provides an easy way to present the parts your team has created. The <groupparts> tag (see below) will generate a table with all of the parts that your team adds to your team sandbox.

Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without needing to refer to the primary literature. Registry users in future years should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.

Note

Note that parts must be documented on the Registry. This page serves to showcase the parts you have made. Future teams and other users and are much more likely to find parts by looking in the Registry than by looking at your team wiki.

Adding parts to the registry

You can add parts to the Registry at our Add a Part to the Registry link.

We encourage teams to start completing documentation for their parts on the Registry as soon as you have it available. The sooner you put up your parts, the better you will remember all the details about your parts. Remember, you don't need to send us the DNA sample before you create an entry for a part on the Registry. (However, you do need to send us the DNA sample before the Jamboree. If you don't send us a DNA sample of a part, that part will not be eligible for awards and medal criteria.)

What information do I need to start putting my parts on the Registry?

The information needed to initially create a part on the Registry is:

  • Part Name
  • Part type
  • Creator
  • Sequence
  • Short Description (60 characters on what the DNA does)
  • Long Description (Longer description of what the DNA does)
  • Design considerations

We encourage you to put up much more information as you gather it over the summer. If you have images, plots, characterization data and other information, please also put it up on the part page.

Inspiration

We have a created a collection of well documented parts that can help you get started.

You can also take a look at how other teams have documented their parts in their wiki:

Part Table

Please include a table of all the parts your team has made during your project on this page. Remember part characterization and measurement data must go on your team part pages on the Registry.

<groupparts>iGEM17 Georgia_State</groupparts>