From 8c24f6c162e3dded8add227b3db884206891d3a0 Mon Sep 17 00:00:00 2001
From: Kong Yangyang <kimmy.kong@cataverse.cn>
Date: Fri, 26 Aug 2022 07:53:03 +0000
Subject: [PATCH] Update wiki/pages/contribution.html

---
 wiki/pages/contribution.html | 201 +++++++++++++++++++++++++++++++++--
 1 file changed, 190 insertions(+), 11 deletions(-)

diff --git a/wiki/pages/contribution.html b/wiki/pages/contribution.html
index d5b10dc..9647270 100644
--- a/wiki/pages/contribution.html
+++ b/wiki/pages/contribution.html
@@ -1,20 +1,199 @@
 {% extends "layout.html" %}
-  
+
 {% block title %}Contribution{% endblock %}
-{% block lead %}Make a useful contribution for future iGEM teams. Use this page to document that contribution.{% endblock %}
 
-{% block page_content %}
+{% block header_content %}
+<img class="sub-header-logo" src="https://static.igem.wiki/teams/4515/wiki/banner.jpg" />
+{% endblock %}
 
-<div class="row mt-4">
-  <div class="col">
-    <div class="bd-callout bd-callout-info">
-      <h4>Bronze Medal Criterion #4</h4>
-      <p>Make a useful contribution for future iGEM teams. Use this page to document that contribution.<p>
-      <p>If you are making a contribution by adding information to an existing Part or creating a new Part, you must document your contribution on the Part's Main Page on the <a href="http://parts.igem.org/Main_Page">Registry</a> for your team to be eligible for this criteria. You can use this page to link to that part and include additional information about your contribution.</p>
-      <hr>
-      <p>Please see the <a href="https://competition.igem.org/judging/medals">2022 Medals Page</a> for more information.</p>
+{% block page_content %}
+<div class="sub-page-bg">
+  <div class="sub-page-content">
+    <div class="content-title">Contribution</div>
+    <div class="title blue-title">Overview</div>
+    <div class="article-content ">
+      Our composite part BBa_K4515012 is the N-butanol pathway we used in Streptococcus Brevis ATCC367. It is improved
+      based on the existing part BBa_K1462040, this is a biological part submitted by iGEM14_SCUT in 2014, with only DNA
+      sequence information and simple text description information. Because the tolerance of Clostridium bacteria to
+      N-butanol is not good enough for large-scale production. Based on this problem, we chose Streptococcus Brevis
+      ATCC367, a lactobacillus with better N-butanol tolerance that has been isolated by researchers, as our host strain
+      in this project. Our team carried out a comprehensive characterization of this part in the laboratory, adding data
+      from fermentation testing to dedicate its function of producing N-butanol. This information can be a good
+      reference for future iGEM teams working on improving the yield of N-butanol.<br />
+      In addition, through literature research, we developed an N-butanol biosynthesis pathway,
+      Pcrt-crt-ter-hbd-Pthl-thl-opt and constructed these genes in the plasmid. What's more, we transferred the
+      recombinant plasmid into Streptococcus Brevis ATCC367 to establish an N-butanol-producing platform and measured
+      the yield of N-butanol. Then, by detecting the growth curve of Streptococcus Brevis ATCC367 transformants, it was
+      further confirmed that Streptococcus Brevis ATCC367 has better tolerance for N-butanol and could be used to
+      produce N-butanol in factories in the future. We upload the DNA sequence information and basic introduction
+      information in the registry of standard biological parts to provide more choices of N-butanol-producing for future
+      iGEM teams.
+    </div>
+    <div class="title blue-title">Add new experimental data to an existing Part BBa_K1462040, crt</div>
+    <div class="article-content ">Gene crt encodes 3-Hydroxybutyryl-CoA dehydratase, which converts 3-Hydroxybutyryl-CoA
+      to Crotonyl-CoA, the third step of the N-butanol pathway. </div>
+    <div class="sub-title">a) Construction of N-butanol biosynthesis pathway with gene crt</div>
+    <div class="article-content ">Gene ctr was promoted by the Pcrt promoter and other related genes, thlA, hbd, and
+      ter, were all amplified from the Lactobacillus Brevis ATCC824 genomic DNA through PCR. The DNA sequences of the
+      Pcrt-crt-ter-hbd-Pthl-thl-opt was inserted into the ApaI and BglII sites of the pIB184 vector, respectively. The
+      certificate of recombinant plasmid sequencing results is as Figure 1.</div>
+    <div class="img-wrap no-margin">
+      <img class="w-80" src="https://static.igem.wiki/teams/4515/wiki/t-east-china-contribution01.jpg" />
+      <span>Figure 1. The results of the sequencing data mapped to the plasmids</span>
+    </div>
+    <div class="sub-title">b) Functional Test</div>
+    <div class="article-content">
+      To confirm if the Pcrt-crt-ter-hbd-Pthl-thl-opt system worked well in the host strain Streptococcus Brevis
+      ATCC367, we also measured the yield of N-butanol through gas chromatography. As shown in Figure 2, the yield of
+      N-butanol is increasing with an increased time of fermenting.
+    </div>
+    <div class="img-wrap no-margin">
+      <img class="w-80" src="https://static.igem.wiki/teams/4515/wiki/t-east-china-contribution02.jpg" />
+      <span>Figure 2. After pLY15-opt was transformed into Streptococcus Brevis, N-butanol production of ply15-opt
+        strain was measured at different times (48h, 69h, 95h, and 159h)</span>
+    </div>
+    <div class="title blue-title">Add new information to the Part BBa_K4515012, BBa_K4515010, and BBa_K4515014</div>
+    <div class="sub-title">a) BBa_K4515012, Pcrt-crt-ter-hbd-Pthl-thl-opt:</div>
+    <div class="article-content">
+      Genes thlA, crt, hbd, and ter, play important roles in the N-butanol biosynthesis pathway. Those genes were
+      codon-optimized. Gene thlA is coding for acetyl-CoA acetyltransferase and converts Acetyl-CoA into Acetoacetyl-CoA
+      in the N-butanol biosynthesis pathway. Gene hbd, encodes β-Hydroxybutyryl-CoA dehydrogenase and converts
+      Acetoacetyl-CoA into 3-Hydroxybutyryl-CoA. Gene crt encodes 3-Hydroxybutyryl-CoA dehydratase, which converts
+      3-Hydroxybutyryl-CoA to Crotonyl-CoA, the third step of the N-butanol pathway. In this part, genes crt, ter and
+      hbd were promoted by Pcrt promoter, gene thl was promoted by Pthl promoter, and these DNA fragments were ligated
+      in order into pIB184 vector.
+    </div>
+    <div class="sub-title">b) BBa_K4515010, pIB184-vector</div>
+    <div class="article-content">pIB184-vector is an E. coli - Streptococci shuttle plasmid for gene expression in
+      streptococci with P23 promoter. This plasmid is a low-copy plasmid and Erythromycin resistance can be used to
+      screen the correct colony in bacteria. This vector contains MCS-A. The backbone of this vector is based on pOri23.
+    </div>
+    <div class="sub-title">c) BBa_K4515014, pLY15-opt</div>
+    <div class="article-content">
+      This composite part is the recombinant plasmid constructed by Pcrt-crt-ter-hbd-Pthl-thl-opt fusion DNA fragment
+      (BBa_K4515012) and pIB184-vector (BBa_K4515010). This plasmid could be transferred into Streptococcus Brevis
+      ATCC367 to produce N-butanol.<br />
+      Above all, we look forward to the future iGEM team making new additions, explorations, and explanations to our
+      biological components.
+    </div>
+    <div class="title blue-title">Reference</div>
+    <div class="article-content">
+      1. 张云贤, 张华西, 余维新, 李杰灵, & 谭平华. (2015). 正丁醇的合成进展简述. 2015 中国化工学会学术年会. <br />
+      2. Li, J., Zhao, J. B., Zhao, M., Yang, Y. L., Jiang, W. H., & Yang, S. (2010). Screening and characterization of
+      butanol-tolerant micro-organisms. Letters in applied microbiology, 50(4), 373–379.
+      https://doi.org/10.1111/j.1472-765X.2010.02808.x <br />
+      3. Berezina, O. V., Zakharova, N. V., Brandt, A., Yarotsky, S. V., Schwarz, W. H., & Zverlov, V. V. (2010).
+      Reconstructing the clostridial n-butanol metabolic pathway in Lactobacillus brevis. Applied microbiology and
+      biotechnology, 87(2), 635–646. https://doi.org/10.1007/s00253-010-2480-z <br />
+      4. Inui M, Suda M, Kimura S, Yasuda K, Suzuki H, Toda H, Yamamoto S, Okino S, Suzuki N, Yukawa H (2008) Expression
+      of Clostridium acetobutylicum butanol synthetic genes in Escherichia coli. Appl Microbiol Biot 77:1305–1316.
+      https://doi.org/10.1007/s00253-007-1257-5 <br />
+      5. Mitchell WJ (1998) Physiology of carbohydrate to solvent conversion by Clostridia. In: Poole RK (ed) Advances
+      in Microbial Physiology, vol 39. pp 31–130 <br />
+      6. Bowles LK, Ellefson WL (1985) Effects of butanol on Clostridium-acetobutylicum. Appl Environ Microb
+      50:1165–1170<br />
+      7. Biswas I, Jha JK, Fromm N. (2008) Shuttle expression plasmids for genetic studies in Streptococcus mutans.
+      Microbiology (Reading). Aug;154(Pt 8):2275-2282. doi: 10.1099/mic.0.2008/019265-0.
     </div>
   </div>
 </div>
+{% endblock %}{% extends "layout.html" %}
+
+{% block title %}Contribution{% endblock %}
 
+{% block header_content %}
+<img class="sub-header-logo" src="https://static.igem.wiki/teams/4515/wiki/banner.jpg" />
+{% endblock %}
+
+{% block page_content %}
+<div class="sub-page-bg">
+  <div class="sub-page-content">
+    <div class="content-title">Contribution</div>
+    <div class="title blue-title">Overview</div>
+    <div class="article-content ">
+      Our composite part BBa_K4515012 is the N-butanol pathway we used in Streptococcus Brevis ATCC367. It is improved
+      based on the existing part BBa_K1462040, this is a biological part submitted by iGEM14_SCUT in 2014, with only DNA
+      sequence information and simple text description information. Because the tolerance of Clostridium bacteria to
+      N-butanol is not good enough for large-scale production. Based on this problem, we chose Streptococcus Brevis
+      ATCC367, a lactobacillus with better N-butanol tolerance that has been isolated by researchers, as our host strain
+      in this project. Our team carried out a comprehensive characterization of this part in the laboratory, adding data
+      from fermentation testing to dedicate its function of producing N-butanol. This information can be a good
+      reference for future iGEM teams working on improving the yield of N-butanol.<br />
+      In addition, through literature research, we developed an N-butanol biosynthesis pathway,
+      Pcrt-crt-ter-hbd-Pthl-thl-opt and constructed these genes in the plasmid. What's more, we transferred the
+      recombinant plasmid into Streptococcus Brevis ATCC367 to establish an N-butanol-producing platform and measured
+      the yield of N-butanol. Then, by detecting the growth curve of Streptococcus Brevis ATCC367 transformants, it was
+      further confirmed that Streptococcus Brevis ATCC367 has better tolerance for N-butanol and could be used to
+      produce N-butanol in factories in the future. We upload the DNA sequence information and basic introduction
+      information in the registry of standard biological parts to provide more choices of N-butanol-producing for future
+      iGEM teams.
+    </div>
+    <div class="title blue-title">Add new experimental data to an existing Part BBa_K1462040, crt</div>
+    <div class="article-content ">Gene crt encodes 3-Hydroxybutyryl-CoA dehydratase, which converts 3-Hydroxybutyryl-CoA
+      to Crotonyl-CoA, the third step of the N-butanol pathway. </div>
+    <div class="sub-title">a) Construction of N-butanol biosynthesis pathway with gene crt</div>
+    <div class="article-content ">Gene ctr was promoted by the Pcrt promoter and other related genes, thlA, hbd, and
+      ter, were all amplified from the Lactobacillus Brevis ATCC824 genomic DNA through PCR. The DNA sequences of the
+      Pcrt-crt-ter-hbd-Pthl-thl-opt was inserted into the ApaI and BglII sites of the pIB184 vector, respectively. The
+      certificate of recombinant plasmid sequencing results is as Figure 1.</div>
+    <div class="img-wrap no-margin">
+      <img class="w-80" src="https://static.igem.wiki/teams/4515/wiki/t-east-china-contribution01.jpg" />
+      <span>Figure 1. The results of the sequencing data mapped to the plasmids</span>
+    </div>
+    <div class="sub-title">b) Functional Test</div>
+    <div class="article-content">
+      To confirm if the Pcrt-crt-ter-hbd-Pthl-thl-opt system worked well in the host strain Streptococcus Brevis
+      ATCC367, we also measured the yield of N-butanol through gas chromatography. As shown in Figure 2, the yield of
+      N-butanol is increasing with an increased time of fermenting.
+    </div>
+    <div class="img-wrap no-margin">
+      <img class="w-80" src="https://static.igem.wiki/teams/4515/wiki/t-east-china-contribution02.jpg" />
+      <span>Figure 2. After pLY15-opt was transformed into Streptococcus Brevis, N-butanol production of ply15-opt
+        strain was measured at different times (48h, 69h, 95h, and 159h)</span>
+    </div>
+    <div class="title blue-title">Add new information to the Part BBa_K4515012, BBa_K4515010, and BBa_K4515014</div>
+    <div class="sub-title">a) BBa_K4515012, Pcrt-crt-ter-hbd-Pthl-thl-opt:</div>
+    <div class="article-content">
+      Genes thlA, crt, hbd, and ter, play important roles in the N-butanol biosynthesis pathway. Those genes were
+      codon-optimized. Gene thlA is coding for acetyl-CoA acetyltransferase and converts Acetyl-CoA into Acetoacetyl-CoA
+      in the N-butanol biosynthesis pathway. Gene hbd, encodes β-Hydroxybutyryl-CoA dehydrogenase and converts
+      Acetoacetyl-CoA into 3-Hydroxybutyryl-CoA. Gene crt encodes 3-Hydroxybutyryl-CoA dehydratase, which converts
+      3-Hydroxybutyryl-CoA to Crotonyl-CoA, the third step of the N-butanol pathway. In this part, genes crt, ter and
+      hbd were promoted by Pcrt promoter, gene thl was promoted by Pthl promoter, and these DNA fragments were ligated
+      in order into pIB184 vector.
+    </div>
+    <div class="sub-title">b) BBa_K4515010, pIB184-vector</div>
+    <div class="article-content">pIB184-vector is an E. coli - Streptococci shuttle plasmid for gene expression in
+      streptococci with P23 promoter. This plasmid is a low-copy plasmid and Erythromycin resistance can be used to
+      screen the correct colony in bacteria. This vector contains MCS-A. The backbone of this vector is based on pOri23.
+    </div>
+    <div class="sub-title">c) BBa_K4515014, pLY15-opt</div>
+    <div class="article-content">
+      This composite part is the recombinant plasmid constructed by Pcrt-crt-ter-hbd-Pthl-thl-opt fusion DNA fragment
+      (BBa_K4515012) and pIB184-vector (BBa_K4515010). This plasmid could be transferred into Streptococcus Brevis
+      ATCC367 to produce N-butanol.<br />
+      Above all, we look forward to the future iGEM team making new additions, explorations, and explanations to our
+      biological components.
+    </div>
+    <div class="title blue-title">Reference</div>
+    <div class="article-content">
+      1. 张云贤, 张华西, 余维新, 李杰灵, & 谭平华. (2015). 正丁醇的合成进展简述. 2015 中国化工学会学术年会. <br />
+      2. Li, J., Zhao, J. B., Zhao, M., Yang, Y. L., Jiang, W. H., & Yang, S. (2010). Screening and characterization of
+      butanol-tolerant micro-organisms. Letters in applied microbiology, 50(4), 373–379.
+      https://doi.org/10.1111/j.1472-765X.2010.02808.x <br />
+      3. Berezina, O. V., Zakharova, N. V., Brandt, A., Yarotsky, S. V., Schwarz, W. H., & Zverlov, V. V. (2010).
+      Reconstructing the clostridial n-butanol metabolic pathway in Lactobacillus brevis. Applied microbiology and
+      biotechnology, 87(2), 635–646. https://doi.org/10.1007/s00253-010-2480-z <br />
+      4. Inui M, Suda M, Kimura S, Yasuda K, Suzuki H, Toda H, Yamamoto S, Okino S, Suzuki N, Yukawa H (2008) Expression
+      of Clostridium acetobutylicum butanol synthetic genes in Escherichia coli. Appl Microbiol Biot 77:1305–1316.
+      https://doi.org/10.1007/s00253-007-1257-5 <br />
+      5. Mitchell WJ (1998) Physiology of carbohydrate to solvent conversion by Clostridia. In: Poole RK (ed) Advances
+      in Microbial Physiology, vol 39. pp 31–130 <br />
+      6. Bowles LK, Ellefson WL (1985) Effects of butanol on Clostridium-acetobutylicum. Appl Environ Microb
+      50:1165–1170<br />
+      7. Biswas I, Jha JK, Fromm N. (2008) Shuttle expression plasmids for genetic studies in Streptococcus mutans.
+      Microbiology (Reading). Aug;154(Pt 8):2275-2282. doi: 10.1099/mic.0.2008/019265-0.
+    </div>
+  </div>
+</div>
 {% endblock %}
-- 
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