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

Line 93: Line 93:
 
<!-- Menu End -->
 
<!-- Menu End -->
 
                        
 
                        
            <div class="container">
+
        {{Georgia_State_sand}}
                <div class="featured-heading">
+
<html>
                    <h1><i><font style="text-transform: none;">"There are two possible outcomes: if the result confirms the hypothesis, then you've made a measurement. If the result is contrary to the hypothesis, then you've made a discovery."</font></i></h2>
+
<br>
                    <h2>Enrico Fermi</h4>
+
<h1 style="color:#1F618D; text-align: center; font-size: 36px; line-height: 40px;">Background</h1>
                                    </div>
+
<br>
            </div>
+
<h1 style="color:#ffffff; background-color:#1A5276;; -moz-border-radius: 15px; -webkit-border-radius: 15px; padding:15px; text-align: center; font-family: Trebuchet MS">What is Lipopolysaccharide?</h1> <br><br>
 +
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>
 +
<br>
  
<div class="container" >
+
<h1 style="color:#ffffff; background-color:#1A5276;; -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>
 +
<img src= "https://2017.igem.org/File:T--Georgia_State--horseshoebranfromaquarium.jpg" alt = 'Horseshoe Crab' style="float:left;"  margin: "5px 5px 5px 5px";>
 +
<br><br>
  
<p>Here you can describe the results of your project and your future plans. </p>
+
<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>
 +
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><br>  
  
<h5>What should this page contain?</h5>
 
<ul>
 
<li> Clearly and objectively describe the results of your work.</li>
 
<li> Future plans for the project. </li>
 
<li> Considerations for replicating the experiments. </li>
 
</ul>
 
  
<h5>You should also describe what your results mean: </h5>
+
<br><br><br>
 +
<h1 style="color:#ffffff; background-color:#1A5276;; -moz-border-radius: 15px; -webkit-border-radius: 15px; padding:15px; text-align: center; font-family: Trebuchet MS"> What is LAL assay? </h1>
  
<ul>
+
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.
<li> Interpretation of the results obtained during your project. Don't just show a plot/figure/graph/other, tell us what you think the data means. This is an important part of your project that the judges will look for. </li>
+
<br>
<li> Show data, but remember all measurement and characterization data must be on part pages in the Registry. </li>
+
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.
<li> Consider including an analysis summary section to discuss what your results mean. Judges like to read what you think your data means, beyond all the data you have acquired during your project. </li>
+
<br><br>
</ul>
+
  
</div>
 
  
<div class="clear"></div>
 
  
<div class="container" >
+
<h1 style="color:#ffffff; background-color:#1A5276;; -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> 
 +
<br>
 +
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>
  
 +
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 its autocatalysis in the presence of LPS.
  
<h5> Project Achievements </h5>
+
<br><br>
  
<p>You can also include a list of bullet points (and links) of the successes and failures you have had over your summer. It is a quick reference page for the judges to see what you achieved during your summer.</p>
+
<a href="https://2016.igem.org/Team:MIT/Experiments"><h1 style="color:#ffffff; background-color:#1A5276;; -moz-border-radius: 15px; -webkit-border-radius: 15px; padding:15px; text-align: center; font-family: Trebuchet MS">Next: Experimental Design</h1> </a>
 
+
<ul class="img-home">
<ul>
+
<li>
<li>A list of linked bullet points of the successful results during your project</li>
+
    <a href="https://2016.igem.org/Team:MIT/Experiments/Promoters">
<li>A list of linked bullet points of the unsuccessful results during your project. This is about being scientifically honest. If you worked on an area for a long time with no success, tell us so we know where you put your effort.</li>
+
      <img src="https://static.igem.org/mediawiki/2016/1/16/T--MIT--synpromobutton.svg" alt="Promoters" >
 +
      <span class="text-content"><span><br><br><br><br><br><br><br>We created new, synthetic promoters to respond to this disease marker<br><br></span></span>
 +
    </a>
 +
</li>
 +
<li> 
 +
    <a href="https://2016.igem.org/Team:MIT/Experiments/miRNA">
 +
      <img src="https://static.igem.org/mediawiki/2016/8/89/T--MIT--miRNAsensorsbutton.svg" alt="miRNA" >
 +
      <span class="text-content"><span><br><br><br><br><br><br><br>We characterized microRNA profiles in model cells under varying conditions<br><br></span></span>
 +
    </a>
 +
  </li>
 +
<li>
 +
    <a href="https://2016.igem.org/Team:MIT/Experiments/Recombinases">
 +
      <img src="https://static.igem.org/mediawiki/2016/e/e2/T--MIT--recombinasesbutton.svg" alt="Recombinases" >
 +
      <span class="text-content"><span><br><br><br><br><br><br>We characterized a serine integrase, TP901, that could give a genetic circuit memory across a cycle<br><br></span></span>
 +
    </a>
 +
  </li>
 
</ul>
 
</ul>
 +
<br><br>
 +
<a href="https://2016.igem.org/Team:MIT"><h1 style="color:#ffffff; background-color:#F20253;; -moz-border-radius: 15px; -webkit-border-radius: 15px; padding:15px; text-align: center; font-family: Trebuchet MS">Back to Home</h1> </a>
  
</div>
+
<ol style="font-size: 8pt;">
 +
<b>References</b><br>
 +
- - - C. Nezhat et al 2012. <i>Endometriosis: Ancient disease, ancient treatments.</i><a href="http://www.nezhat.org/file/Endometriosis-Article.pdf">http://www.nezhat.org/file/Endometriosis-Article.pdf</a> <br>
  
 +
- - - <i>Do you have Endo? </i>Endometriosis Research Center. <a href="https://www.endocenter.org/do-you-have-endo/">https://www.endocenter.org/do-you-have-endo/</a> <br>
  
<div class="container" >
+
- - - <i>FAQ.</i> MIT Center for Gynepathology Research. <a href="http://web.mit.edu/cgr/faq---links.html">http://web.mit.edu/cgr/faq---links.html</a><br>
 +
 
 +
- - - <i>Altered expression of microRNA-451 in eutopic endometrium of baboons (Papio anubis) with endometriosis.</i> Joshi NR <i>et al.</i> 2015.<br> NCBI <a href="https://www.ncbi.nlm.nih.gov/pubmed/26370665">https://www.ncbi.nlm.nih.gov/pubmed/26370665</a><br>
 +
 
 +
- - - <i>Gene Expression Analysis of Endometrium Reveals Progesterone Resistance and Candidate Susceptibility Genes in Women<br> with Endometriosis</i> R. O. Burney <i> et all</i> 2009. Endocrinology <a href="http://press.endocrine.org/doi/full/10.1210/en.2006-1692">http://press.endocrine.org/doi/full/10.1210/en.2006-1692</a><br>
 +
 
 +
- - - <i> What is Endometriosis?. </i>Endometriosis Foundation of America. <a href="http://www.endofound.org/endometriosis">http://www.endofound.org/endometriosis</a><br>
 +
 
 +
 
 +
</ol>
  
<h5>Inspiration</h5>
 
<p>See how other teams presented their results.</p>
 
<ul>
 
<li><a href="https://2014.igem.org/Team:TU_Darmstadt/Results/Pathway">2014 TU Darmstadt </a></li>
 
<li><a href="https://2014.igem.org/Team:Imperial/Results">2014 Imperial </a></li>
 
<li><a href="https://2014.igem.org/Team:Paris_Bettencourt/Results">2014 Paris Bettencourt </a></li>
 
</ul>
 
  
</div>
 
  
  
  
 
</html>
 
</html>

Revision as of 16:55, 31 October 2017

{{Georgia_State_sand}}

Background


What is Lipopolysaccharide?



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.

What do Horseshoe crabs have to do with endotoxin?


Horseshoe Crab

Limulus polyphemus (Atlantic horseshoe crab) 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.
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.




What is LAL assay?

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.
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.

So where does GSU come in to play?


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.
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 its autocatalysis in the presence of LPS.

Next: Experimental Design



Back to Home

    References
    - - - C. Nezhat et al 2012. Endometriosis: Ancient disease, ancient treatments.http://www.nezhat.org/file/Endometriosis-Article.pdf
    - - - Do you have Endo? Endometriosis Research Center. https://www.endocenter.org/do-you-have-endo/
    - - - FAQ. MIT Center for Gynepathology Research. http://web.mit.edu/cgr/faq---links.html
    - - - Altered expression of microRNA-451 in eutopic endometrium of baboons (Papio anubis) with endometriosis. Joshi NR et al. 2015.
    NCBI https://www.ncbi.nlm.nih.gov/pubmed/26370665
    - - - Gene Expression Analysis of Endometrium Reveals Progesterone Resistance and Candidate Susceptibility Genes in Women
    with Endometriosis
    R. O. Burney et all 2009. Endocrinology http://press.endocrine.org/doi/full/10.1210/en.2006-1692
    - - - What is Endometriosis?. Endometriosis Foundation of America. http://www.endofound.org/endometriosis