Difference between revisions of "Team:Baltimore Bio-Crew/Contribution"

 
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<h1>Contribution</h1>
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<h3>Bronze Medal Criterion #4</h3>
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<p><b>Standard Tracks:</b> Participate in the Interlab Measurement Study (to be documented on your InterLab page) and/or improve the characterization of an existing BioBrick Part or Device and enter this information on that part's Main Page in the Registry. The part that you are characterizing must NOT be from a 2017 part number range. Teams who are working on improving the characterization of an existing part should document their experimental design here, along with an explanation for why they chose that part to improve. Data can also be shown here, but it MUST also be documented on the part's Main Page in the Registry.
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<b>Special Tracks:</b> Document at least one new substantial contribution to the iGEM community that showcases a project related to BioBricks. This contribution should be central to your project and equivalent in difficulty to making and submitting a BioBrick part.
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          <h1>BALTIMORE BIO-CREW</h1>
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          <h4>Bio-Engineering E.Coli To Degrade Plastic and Save The Baltimore Inner Harbor</h4>
 
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                        <h3> Contributions </h3>
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As our contribution, the Baltimore Biocrew performed an allergenicity screening for some of the most common biobricks. These biobricks have been implemented in countless projects, and therefore have a higher chance of humans interacting with them.  The purpose of the screening is to ensure the safety of using such biobricks. As the topic of safety is of the utmost importance to labs, the possibility of one of the biobricks potentially causing an allergic reaction is cause for concern with all labs using the sequences.
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The Baltimore Biocrew 2017 team discovered that proteins generated through biobrick parts can be evaluated for allergenicity. This information is important to the people using these parts in the lab, as well as when considering using the protein for mass production, or using in the environment. The allergenicity test permits a comparison between the sequences of the biobrick parts and the identified allergen proteins enlisted in a data base.The higher the similarity between the biobricks and the proteins, the more likely the biobrick is allergenic cross-reactive. In the full-length alignments by FASTA, 30% or more amount of similarity signifies that the biobrick has a Precaution Status meaning there is a potential risk with using the part. A 50% or more amount of identity signifies that the biobrick has a Possible Allergen Status. In the sliding window of 80 amino acid segments, greater than 35% signifies similarity to allergens. The percentage of similarity implies the potential of harm biobricks’ potential negative impact to exposed populations. For more information on how to assess your own biobrick part please see the “Allergenicity Testing Protocol” on the following page: <a href="https://2017.igem.org/Team:Baltimore_Bio-Crew/Experiments"> <u>Experiment</u>.</a>
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We evaluated the top 10 coding regions in both the "Frequently used parts" and in the "Well-characterized parts" to characterize them for potential allergen status. Out of these biobrick parts, we discovered 2 potential biobrick coding parts are potential allergens.
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For the biobrick Part:<a href="http://parts.igem.org/Part:BBa_K1172201"><u>BBa_K1172201</u></a> -80 amino acid alignments by FASTA window, there was one match found that is greater than 35% for this biobrick. This means that this part has a Potential Allergen status. Matched to Group V allergen Phl from Phleum pratense at 36.29% <a href=" https://www.ncbi.nlm.nih.gov/protein/3309039"> <u>Identity</u>.</a>
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For the biobrick part, <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_C0079"><u>BBa_C0079</u></a>, there was a 60.0% of identity match and 80% of similarity match to minor allergen Cla 7  <a href="  https://www.ncbi.nlm.nih.gov/protein/467629"> <u> [Davidiella tassiana]</u>.</a>  This means that the biobrick part HAS Potential Allergen Status.
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We would recommend anyone interested in using these parts consider the potential risk in using them to cause an allergic reaction. This is especially important for people using these parts in lab, when using the proteins in production, ​​or working with these parts in the enviroment. ​
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</article>
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The following biobrick parts were also evaluated but were found to have no potential allergen status:
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<ul>
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  <li>BBa_K863005</li>
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  <li>BBa_K863021</li>
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  <li>BBa_E0030</li>
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  <li>B​​Ba_​​K863000</li>
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  <li>BBa_K525515</li>
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  <li>BBa_E0020</li>
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  <li>BBa_K863006</li>
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  <li>BBa_K863001</li>
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  <li>BBa_K1172501</li>
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  <li>BBa_K525710</li>
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  <li>BBa_K863001</li>
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  <li>BBa_​​C0061</li>
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  <li>BBa_C0012</li>
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  <li>BBa_E1010</li>
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  <li>BBa_C0040</li>
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  <li>BBa_E0040</li>
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  <li>BBa_K863022</li>
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  <li>BBa_C0062</li>
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</ul>
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</article>
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</section>
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<section id="Footer" class="footerSection">
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<h2>
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Sponsors
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</h2>
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<h4>
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The Baltimore Bio-Crew thanks our sponsors for their generous support of our team that made our project and travel to the Jamboree possible. Thank you!
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</h4>
  
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<footer>
  
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<a href="http://www.bd.com/en-us">
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  <img src="https://upload.wikimedia.org/wikipedia/en/f/f8/Update_Color_BD_PNG_Logo.png" alt="BD Medical Technology, Advancing the World of Health - BD" style="width:100px; height:100px;">
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</a>
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<a href="http://familyleague.org/">
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  <img src="http://baltimoreattendance.org/wp-content/uploads/2015/08/flbcinc-360x230.png" alt="Family League of Baltimore" style="width:100px; height:100px;">
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</a>
  
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                                      <a>
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  <img src="https://static.igem.org/mediawiki/2017/6/6c/T--Baltimore_Bio-Crew--fabian_kolker_small_icon.png" alt="Fabian Kolker Foundation" style="width:100px; height:100px;">
 +
</a>
  
 +
<a href="http://vwrfoundation.org/">
 +
  <img src="https://static.igem.org/mediawiki/2016/1/1a/T--Baltimore_Biocrew--VWR_Foundation_LOGO.jpeg" alt="VWR Charitable Foundation" style="width:100px; height:100px;">
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</a>
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<a href="http://www.marylandrecyclingnetwork.org/">
 +
  <img src="https://media.licdn.com/mpr/mpr/shrink_200_200/AAEAAQAAAAAAAAI8AAAAJDY0ZDg0ZjlkLWVlMTItNGI1Mi1iNWEwLWYzMDVlYWMwMTZhZg.png" alt="Maryland Recycling Network" style="width:100px; height:100px;">
 +
</a>
  
 +
<a href="https://www.rwdfoundation.org/">
 +
  <img src="https://static.igem.org/mediawiki/2016/6/65/T--Baltimore_BioCrew--DeutschFoundation.png" alt="The Robert W. Deutsch Foundation" style="width:100px; height:100px;">
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</a>
  
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Latest revision as of 19:50, 19 November 2017


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Home Team Project Results Design Notebook Composite Part Safety HP Silver Experiment Attribution Collaborations Interlab Contributions


BALTIMORE BIO-CREW

Bio-Engineering E.Coli To Degrade Plastic and Save The Baltimore Inner Harbor

Contributions

As our contribution, the Baltimore Biocrew performed an allergenicity screening for some of the most common biobricks. These biobricks have been implemented in countless projects, and therefore have a higher chance of humans interacting with them. The purpose of the screening is to ensure the safety of using such biobricks. As the topic of safety is of the utmost importance to labs, the possibility of one of the biobricks potentially causing an allergic reaction is cause for concern with all labs using the sequences.
The Baltimore Biocrew 2017 team discovered that proteins generated through biobrick parts can be evaluated for allergenicity. This information is important to the people using these parts in the lab, as well as when considering using the protein for mass production, or using in the environment. The allergenicity test permits a comparison between the sequences of the biobrick parts and the identified allergen proteins enlisted in a data base.The higher the similarity between the biobricks and the proteins, the more likely the biobrick is allergenic cross-reactive. In the full-length alignments by FASTA, 30% or more amount of similarity signifies that the biobrick has a Precaution Status meaning there is a potential risk with using the part. A 50% or more amount of identity signifies that the biobrick has a Possible Allergen Status. In the sliding window of 80 amino acid segments, greater than 35% signifies similarity to allergens. The percentage of similarity implies the potential of harm biobricks’ potential negative impact to exposed populations. For more information on how to assess your own biobrick part please see the “Allergenicity Testing Protocol” on the following page: Experiment.
We evaluated the top 10 coding regions in both the "Frequently used parts" and in the "Well-characterized parts" to characterize them for potential allergen status. Out of these biobrick parts, we discovered 2 potential biobrick coding parts are potential allergens.
For the biobrick Part:BBa_K1172201 -80 amino acid alignments by FASTA window, there was one match found that is greater than 35% for this biobrick. This means that this part has a Potential Allergen status. Matched to Group V allergen Phl from Phleum pratense at 36.29% Identity.
For the biobrick part, BBa_C0079, there was a 60.0% of identity match and 80% of similarity match to minor allergen Cla 7 [Davidiella tassiana]. This means that the biobrick part HAS Potential Allergen Status.
We would recommend anyone interested in using these parts consider the potential risk in using them to cause an allergic reaction. This is especially important for people using these parts in lab, when using the proteins in production, ​​or working with these parts in the enviroment. ​
The following biobrick parts were also evaluated but were found to have no potential allergen status:
  • BBa_K863005
  • BBa_K863021
  • BBa_E0030
  • B​​Ba_​​K863000
  • BBa_K525515
  • BBa_E0020
  • BBa_K863006
  • BBa_K863001
  • BBa_K1172501
  • BBa_K525710
  • BBa_K863001
  • BBa_​​C0061
  • BBa_C0012
  • BBa_E1010
  • BBa_C0040
  • BBa_E0040
  • BBa_K863022
  • BBa_C0062