Difference between revisions of "Team:HebrewU/Open Source"

 
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             <li><a href="https://2018.igem.org/Team:HebrewU/Description">Description</a></li>
 
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             <li><a href="https://2018.igem.org/Team:HebrewU/Results">Results</a></li>
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+
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  <div class="w3-center">
 
  <div class="w3-center">
             <img src="https://static.igem.org/mediawiki/2018/2/25/T--hebrewu--Open_Source_HL.png" width="20%">
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             <img src="https://static.igem.org/mediawiki/2018/2/25/T--hebrewu--Open_Source_HL.png" width="30%">
 
           <br /> <br /> <br />
 
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<p style="padding-left:215px;padding-right:230px;text-align:justify;line-height:1.5">
 +
We created an open source platform aimed at helping researchers and organizations worldwide tackle their dioxin pollution. In our open source page, we present the basic foundations necessary to create a viable transgenic plant based on our research and experiments.
 +
<br /><br />
 +
Our open source page features two main programs: our synthetic enzymatic pathway (i.e. optimized gene sequences for each plant, including descriptions), and our proposed plants that are optimal for our pathway.
 +
We chose the plants based on 4 categories: Transformation, dioxin uptake efficiency, sterilization methods, and plant durability. We did our best to gather the necessary information to support it using both academic research and verified gardening sites.<br /><br />
 +
 
 +
Transformation - How many methods are known for the transformation of this plant? How easy and effective are they?<br />
 +
Dioxin uptake efficiency - How well does the plant absorb dioxin from the ground, compared to other plants?<br />
 +
Sterilization methods - With these types of solutions, it is important to be ecologically responsible; releasing genetically engineered plants into the environment is no trivial matter. The ability to sterilize the plants, along with short life expectancies in general, is key for the safe release of transformed plants.<br />
 +
Plant durability - Under what conditions do the plants grow? Where do they grow? Do they grow in regions that are in dire need of solutions to dioxin contaminations?<br />
 +
 
 +
</p>     
 
            
 
            
  
<a href="#cucurbita_main_toggle"><button class="w3-button w3-padding-large w3-large w3-margin-top" style="background-color:#D1F2EB;border-radius: 12px;width:230px;">Cucurbita pepo L. <br/ > <b> Pumpkin & Zucchini </b></button> </a> &nbsp; &nbsp;
+
<a href="#cucurbita_main_toggle"><button class="w3-button w3-padding-large w3-large w3-margin-top" style="color:#616161;background-color:#F0B27A;border-radius: 12px;width:230px;">Cucurbita pepo L. <br/ > <b> Pumpkin & Zucchini </b></button> </a> &nbsp; &nbsp;
<a href="#Brassica_main_toggle"><button class="w3-button w3-padding-large w3-large w3-margin-top" style="background-color:#D1F2EB;border-radius: 12px;width:230px;">Brassica campestris <br/ > <b> Chinese Cabbage </b></button> </a> &nbsp; &nbsp;
+
<a href="#Brassica_main_toggle"><button class="w3-button w3-padding-large w3-large w3-margin-top" style="color:#616161;background-color:#ABEBC6;border-radius: 12px;width:230px;">Brassica rapa <br/ > <b> Chinese Cabbage </b></button> </a> &nbsp; &nbsp;
<a href="#Lycopersicon_main_toggle"><button class="w3-button w3-padding-large w3-large w3-margin-top" style="background-color:#D1F2EB;border-radius: 12px;width:230px;">Lycopersicon esculintum <br/ > <b> Tomato </b></button> </a> &nbsp; &nbsp;
+
<a href="#Lycopersicon_main_toggle"><button class="w3-button w3-padding-large w3-large w3-margin-top" style="color:#616161;background-color:#F1948A;border-radius: 12px;width:230px;">Solanum lycopersicum <br/ > <b> Tomato </b></button> </a> &nbsp; &nbsp;
  
  
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<div class="w3-light-grey">
 
<div class="w3-light-grey">
 
   <div class="w3-container" style="width:80%;background-color:#2196f3a3"> <span class="w3-badge w3-white">1</span>
 
   <div class="w3-container" style="width:80%;background-color:#2196f3a3"> <span class="w3-badge w3-white">1</span>
  &nbsp; Dioxin Uptake</div>
+
  &nbsp; Uptake Rate</div>
 
</div>
 
</div>
  
 
<ul>
 
<ul>
 
     <li>
 
     <li>
         Zucchini`s Roots grow mainly down while pumpkin`s grow mainly to the sides.
+
         Deep root systems.
 
     </li>
 
     </li>
 
     <li>
 
     <li>
         High uptake values of nutrition from soil.
+
         Zucchini roots grow mainly downward, while pumpkin`s grow mainly outward.
 
     </li>
 
     </li>
 
     <li>
 
     <li>
        Able to absorb dioxins in roots and deliver them thought the plant (potential for high speed degradation in whole plant).
+
        High uptake values of nutrition from soil.
 +
    </li>
 +
    <li>
 +
        Able to absorb dioxins through roots and deliver them throughout the plant (potential for high-speed degradation in the plant).
 
     </li>
 
     </li>
 
</ul><br />
 
</ul><br />
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<div class="w3-light-grey">
 
<div class="w3-light-grey">
   <div class="w3-container w3-green" style="width:50%"><span class="w3-badge w3-white">2</span>&nbsp; Ease of growth</div>
+
   <div class="w3-container w3-green" style="width:50%"><span class="w3-badge w3-white">2</span>&nbsp; Growth Conditions</div>
 
</div>
 
</div>
  
 
<ul>
 
<ul>
 
<li>
 
<li>
Short seasoned plants, can be grown only in hot seasons.
+
Short-season plants, grown in hot seasons.
 
</li>
 
</li>
 
<li>
 
<li>
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<div class="w3-light-grey">
 
<div class="w3-light-grey">
   <div class="w3-container w3-red" style="width:40%"><span class="w3-badge w3-white">3</span> &nbsp; Ease of transformation</div>
+
   <div class="w3-container w3-red" style="width:40%"><span class="w3-badge w3-white">3</span> &nbsp; Transformation</div>
 
</div>
 
</div>
  
 
<ul>
 
<ul>
 
     <li>
 
     <li>
         Existing transformation methods using agrobacterium.   
+
         Existing transformation methods use agrobacterium.   
 
     </li>
 
     </li>
 
     <li>
 
     <li>
         Whole genome sequence doesn`t exist yet.
+
         Whole-genome sequence doesn`t exist yet.
 
     </li>
 
     </li>
 
</ul><br />
 
</ul><br />
 
 
  
  
 
<div class="w3-light-grey">
 
<div class="w3-light-grey">
   <div class="w3-container w3-yellow" style="width:30%"><span class="w3-badge w3-white">4</span> &nbsp; Ease of sterilization</div>
+
   <div class="w3-container w3-yellow" style="width:30%"><span class="w3-badge w3-white">4</span> &nbsp; Sterilization</div>
 
</div>
 
</div>
  
 
<ul>
 
<ul>
     <li> none
+
     <li> No specific method was found.
 
     </li>
 
     </li>
 
</ul><br />
 
</ul><br />
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<br /> <br />
 
<br /> <br />
<h2 class="w3-center w3-panel" style="width:100%;background-color:#2196f3a3"> <span class="w3-badge w3-white">1</span> &nbsp; Dioxin Uptake</h2>
+
<h2 class="w3-center w3-panel" style="width:100%;background-color:#2196f3a3"> <span class="w3-badge w3-white">1</span> &nbsp; Uptake Rate</h2>
 
  <p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">  
 
  <p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">  
 
<br /> <br />
 
<br /> <br />
Zucchini plants have been shown to have the most successful uptake mechanisms for PCDD/PCDF's of all plants tested. This includes mechanisms that can translocate dioxins from their roots to their shoot system (including flowers and fruits), as opposed to many other plants that can only absorb dioxins into their roots.
+
As shown in the figure below, zucchini has shown an impressive absorbance ability of dioxins from contaminated soil1<sup>1</sup>. The main advantage zucchini and pumpkin plants have over other plants (that have been studied) are their ability to transfer the dioxins to their shoots, flowers, and fruits, while others cannot<sup>2</sup>, so theoretically we have more dioxin to mass ratio, letting them absorb more dioxins. As such, zucchini and pumpkin are our main candidates for dioxin phytoremediation in case of a suitable climate.
 
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<div class="w3-panel w3-blue-gray">
 
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   <p class="w3-large w3-serif">
 
   <i class="fa fa-quote-right w3-xxlarge w3-margin-right"></i>
 
   <i class="fa fa-quote-right w3-xxlarge w3-margin-right"></i>
"Plants have been frequently shown to remove POPs from soils (Zhao et al. 2006; Susarla et al. 2002; Macek et al. 2000). The high propensity of selected Cucurbitaceae to extract PCDDs/PCDFs from soil was first reported by Hülster et al. (1994), who found that C. pepo L. fruits contained double the PCDD/PCDF concentrations of other examined plants. " </p>
+
"Plants have been frequently shown to remove POPs from soils (Zhao et al. 2006; Susarla et al. 2002; Macek et al. 2000). The high propensity of selected Cucurbitaceae to extract PCDDs/PCDFs from soil was first reported by Hülster et al. (1994), who found that C. pepo L. fruits contained double the PCDD/PCDF concentrations of other examined plants."<sup>1</sup> </p>
 
</div> <br /> <br />
 
</div> <br /> <br />
  
<p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">
 
Current results demonstrated that cultivation of C. pepo L. cv. ‘Atena Polka’ reduced total PCDD/PCDF content by a mean value of 37 % in soil amended with sewage sludge and 32 % in soil treated with urban sediment (Fig. 1A1, B1; Table 2S). Mean reduction in TEQ concentrations were 68 and 52 % in soil amended with sewage sludge and sediment, respectively; values almost twice those of PCDD/PCDF content (Fig. 1A2, B2; Table 2S). Wilcoxon matched pair test revealed significant differences in total and TEQ values before and after C. pepo L. cv. ‘Atena Polka’ cultivation at p = 0.067. The greatest decline of total PCDD/PCDF content was observed for control samples (66 % for soil with sewage sludge and 81 % for soil with sediment), while the greatest reduction of TEQ values was detected in samples fertilized with 9 and 18 t/ha of sewage sludge (72 and 73 %, respectively) (Fig. 1; Table 2S). In soil amended with 3 t/ha of sludge, ‘Atena Polka’ cultivation led to a 63 % reduction of TEQ. Other large decreases were also noted for soil amended with 9 and 18 t/ha of urban sediments (59 and 70 %, respectively), while a much smaller reduction (21 %) was noted for a dose of 3 t/ha (Fig. 1; Table 2S). The above declines in soil total and TEQ PCDD/PCDF concentrations are, from one site, a result of ‘Atena Polka’ cultivation, however, the bioremediation activity of soil microorganisms seems to also be an important factor responsible for the obtained reductions (Urbaniak 2013; Field and Sierra-Alvarez 2008).
 
</p>
 
  
 
   <img src="https://static.igem.org/mediawiki/2018/d/d5/T--Hebrewu--Zuccini_info_1_0.jpeg" style="width:60%">
 
   <img src="https://static.igem.org/mediawiki/2018/d/d5/T--Hebrewu--Zuccini_info_1_0.jpeg" style="width:60%">
 
<p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5"> <br />  
 
<p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5"> <br />  
 
Fig. 1:  
 
Fig. 1:  
Mean decreases in total and TEQ PCDD/PCDF concentrations in soil amended with different doses of sewage sludge (A1, A2) and urban sediments (B1–B2) before and after Cucurbita pepo L. cv ‘Atena Polka’ cultivation"
+
"Mean decreases in total and TEQ PCDD/PCDF concentrations in soil amended with different doses of sewage sludge (A1, A2) and urban sediments (B1–B2) before and after Cucurbita pepo L. cv ‘Atena Polka’ cultivation".<sup>3</sup>
 
</p>
 
</p>
  
 
  <br /> <br />
 
  <br /> <br />
  <h2 class="w3-center w3-panel w3-green"><span class="w3-badge w3-white">2</span> &nbsp; Plant Growth</h2>
+
  <h2 class="w3-center w3-panel w3-green"><span class="w3-badge w3-white">2</span> &nbsp; Growth Conditions</h2>
 
  <p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">
 
  <p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">
Zucchini and pumpkin are very sensitive to cold weather, requires warm temperatures of above 16 degrees Celsius to grow, but to warm of a climate (above 38 degrees) will harm the plant. zucchini takes 60 days to mature, by than it produces fruit as long as someone pick them before they rot. Pumpkin requires between 90 to 160 days to mature. They both have a fast growth and as such, high root uptake of nutrition from the ground. both need a lot of water to grow, which oppose some problem if you try to grow it in dry areas. Zucchini don’t spread much and it`s root go mainly deeper in a taproot formation, while pumpkin spread vertically and most of its nutrients are absorbed from the upper half a meter of the soil.
+
Zucchini and pumpkin are very sensitive to cold weather, requires warm temperatures of above 16 degrees Celsius to grow, but to warm of a climate (above 38 degrees) will harm the plant. Zucchini takes about 60 days to mature. By then it produces fruit as long as someone picks them before they rot. Pumpkin requires between 90 to 160 days to mature. They both grow relatively quickly and, as such, have high root-uptake of nutrition from the ground. Both require moderate quantities of water to grow, which may make it more difficult to grow in drier climates; however, pumpkins have been successfully grown in Iraq, for example. Zucchini roots generally extend deeply downward in a taproot formation, while pumpkin roots tend to spread horizontally as well as vertically - most of its nutrients are absorbed from the upper 1/2 meter of the soil. <sup>3,4,5</sup>
 +
 
 +
 
 
  </p>
 
  </p>
 
   
 
   
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  <h2 class="w3-center w3-panel w3-red"> <span class="w3-badge w3-white">3</span> &nbsp; Plant Transformation:</h2>
 
  <h2 class="w3-center w3-panel w3-red"> <span class="w3-badge w3-white">3</span> &nbsp; Plant Transformation:</h2>
 
  <p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">
 
  <p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">
Two-week-old in vitro grown Cucurbita pepo L. intact plants and cotyledons (detached and undetached from the mother-plant) were transformed by Agrobacterium rhizogenes strain NCPPB 1855, grown for 48 h at 25 °C on YMB medium. All infected material formed vigorous hairy roots in about seven days. The transformed roots were successfully grown in liquid MS medium without plant growth regulators for an indefinite number of transfers
+
We know of a few agrobacterium strains able to transform pumpkin plants and zucchini<sup>6,7</sup>. Agrobacterium is one of the most popular methods of plants transformation, widely studied in plant research
 +
 
 
  </p>
 
  </p>
 
<br /> <br />
 
<br /> <br />
 
<h2 class="w3-center w3-panel w3-yellow"><span class="w3-badge w3-white">4</span> &nbsp; Plant Sterility </h2>
 
<h2 class="w3-center w3-panel w3-yellow"><span class="w3-badge w3-white">4</span> &nbsp; Plant Sterility </h2>
 
  <p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">
 
  <p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">
Triploid plants have larger organs, greater biomass, and strong stress resistance by preserving relatively larger amounts of photosynthetic energy. The undesirable spread of non-native invasive crop and horticultural plants into natural areas can also be reduced or eliminated by the use of triploids, because they tend to be sterile and seedless. <br /> <br />
+
Triploid plants<sup>*</sup> have larger organs, greater biomass, and strong stress resistance by preserving relatively larger amounts of photosynthetic energy<sup>8</sup>. The undesirable spread of non-native invasive crop and horticultural plants into natural areas can also be reduced or eliminated by the use of triploids because they tend to be sterile and seedless
 +
 
 
   
 
   
 
  There are few different ways to create triploid plants:
 
  There are few different ways to create triploid plants:
 
     <ul style="text-align:left;padding-left:150px;">
 
     <ul style="text-align:left;padding-left:150px;">
         <li> Natural selection - triploid plants occur in nature, meaning it is possible to look for the desired plant in nature.
+
         <li> - Natural selection - triploid plants occur in nature, meaning it is possible to look for the desired plant in nature.
 
         </li>
 
         </li>
         <li> Artificial hybridization - by sexual hybridization of different ploidy, one can create a triploid offspring.
+
         <li> - Artificial hybridization - by sexual hybridization of different ploidy, one can create a triploid offspring.
 
         </li>
 
         </li>
           <li> Endosperm culture in vitro - endosperm is a triploid tissue. Successful regeneration of a plant from an endosperm tissue would result in triploid plant.
+
           <li> - Endosperm culture in vitro - endosperm is a triploid tissue. Successful regeneration of a plant from an endosperm tissue would result in a triploid plant.
 
         </li>
 
         </li>
 
     </ul>
 
     </ul>
 
  </p>
 
  </p>
 +
<p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">
 +
• Triploid plants contain 3 sets of chromosomes, meaning they have 3n chromosomes. Triploid organisms, in general, tend to be sterile, as in most plants.
 +
</p>
 +
 +
  <h2 align="center" style="color:#F0B27A">Optimized genes for Cucurbita pepo: </h2>
 +
<p style="text-align:center;padding-left:60px;color:#F0B27A"> <a onClick="openTab(this)" name="https://static.igem.org/mediawiki/2018/3/33/T--hebrewu--cucurbita_seq.txt"><button class="w3-button w3-padding-large w3-large w3-margin-top" style="color:#616161;background-color:#F0B27A;border-radius: 12px;width:230px;">View sequences</button></a><br /><br />
 +
* In order to optimize the genes, we used our <a onClick="openTab(this)" name="https://2018.igem.org/Team:HebrewU/Software">MOOLTi codon optimizer</a>. We originally designed <a onClick="openTab(this)" name="https://2018.igem.org/Team:HebrewU/Software">MOOLTi </a>to perform optimizations for multiple organisms simultaneously, but it is also capable of optimizing for a single organism with ease.
 +
 +
 +
</p>
 +
 
   
 
   
 
  <h2 align="left"> References: </h2>
 
  <h2 align="left"> References: </h2>
 
  <p style="text-align:left">
 
  <p style="text-align:left">
1. <a href="https://link.springer.com/article/10.1023/A:1005955012372">Cucurbita pepo L. can be transformed by Agrobacterium rhizogenes By Luigi Sanità di Toppi, Nicola Pecchioni, Mauro Durante - Nov 1997 </a> <br />
+
1. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978765/">"Potential for Phytoremediation of PCDD/PCDF-Contaminated Sludge and Sediments Using Cucurbitaceae Plants: A Pilot Study" Magdalena Urbaniak et al. (2016).<br />
2. <a href="https://www.agriculturejournals.cz/publicFiles/186537.pdf">Breeding Triploid Plants: A Review
+
2. <a href="https://www.sciencedirect.com/science/article/pii/S0045653509006730?via%3Dihub#tbl2">"Uptake by roots and translocation to shoots of polychlorinated dibenzo-p-dioxins and dibenzofurans in typical crop plants" Haijun Zhang et al. (2009). </a><br />
By Xiling WANG, Zong-Ming (Max) CHENG, Shuang ZHI and Fengxiang XU - 2016. </a><br />
+
3. <a href="https://www.almanac.com/plant/pumpkins">"Planting, growing, and harvesting pumpking" The Old Farmer'S Almanac website (2010). </a><br />
3. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978765/">Potential for Phytoremediation of PCDD/PCDF-Contaminated Sludge and Sediments Using Cucurbitaceae Plants: A Pilot Study By Magdalena Urbaniak, Anna Wyrwicka, Marek Zieliński, Joanna Mankiewicz-Boczek. - Jun 2016
+
4. <a href="http://www.spadespatula.com/2012/09/14/how-to-grow-zucchini-a-squash-vocabulary-lesson/">"How to Grow Zucchini: A Squash Vocabulary Lesson"
 +
Charity Shumway (2012).</a><br />
 +
5. <a href="https://homeguides.sfgate.com/life-expectancy-zucchini-plants-58679.html">"What Is the Life Expectancy of Zucchini Plants?" Karen Carter. </a><br />
 +
6. <a href="https://link.springer.com/article/10.1023/A:1005955012372">"Cucurbita pepo L. can be transformed by Agrobacterium rhizogenes" Luigi Sanità di Toppi et al. (1997). </a> <br />
 +
7. <a href="https://www.sciencedirect.com/science/article/pii/S0045653509006730?via%3Dihub#tbl2">"A simple method for transient transformation of pumpkin (Cucurbita maxima) seedlings" Francisco Arturo Ramírez-Ortega et al. (2015).</a><br />
 +
8. <a href="https://www.agriculturejournals.cz/publicFiles/186537.pdf">"Breeding Triploid Plants: A Review"
 +
Xiling Wang et al. (2016). </a><br />
 
</a><br />
 
</a><br />
4. <a href="https://www.sciencedirect.com/science/article/pii/S0045653509006730?via%3Dihub#tbl2">A simple method for transient transformation of pumpkin (Cucurbita maxima) seedlings By Francisco Arturo Ramírez-Ortega, Beatriz Xoconostle-Cázares, Roberto Toscano-Morales, Roberto Ruiz-Medrano - 2015.</a><br />
+
 
5. <a href="https://www.sciencedirect.com/science/article/pii/S0045653509006730?via%3Dihub#tbl2">Uptake by roots and translocation to shoots of polychlorinated dibenzo-p-dioxins and dibenzofurans in typical crop plants By Haijun Zhang, Jiping Chen, Yuwen Ni, Qing Zhang, Liang Zhao - Aug 2009. </a><br />
+
 
6. <a href="https://www.almanac.com/plant/pumpkins">PLANTING, GROWING, AND HARVESTING PUMPKINS
+
Oct 2010. </a><br />
+
7. <a href="http://www.spadespatula.com/2012/09/14/how-to-grow-zucchini-a-squash-vocabulary-lesson/">How to Grow Zucchini: A Squash Vocabulary Lesson
+
By Charity Shumway | September 14th, 2012.</a><br />
+
8. <a href="https://homeguides.sfgate.com/life-expectancy-zucchini-plants-58679.html">What Is the Life Expectancy of Zucchini Plants?
+
By Karen Carter. </a><br />
+
 
  </p>  
 
  </p>  
 
  <br /> <br />
 
  <br /> <br />
Line 419: Line 493:
  
 
   
 
   
</div>
 
 
</div>
 
</div>
 
</div>
 
</div>
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   <div class="w3-content">
 
   <div class="w3-content">
 
     <div class="w3-third w3-center">
 
     <div class="w3-third w3-center">
<img src="https://static.igem.org/mediawiki/2018/0/04/T--Hebrewu--lettuce.png" width="100%" style="padding-top:80px;">
+
<img src="https://static.igem.org/mediawiki/2018/d/da/T--hebrewu--cabbage.png" width="100%" style="padding-top:80px;">
 
     </div>
 
     </div>
  
 
     <div class="w3-twothird">
 
     <div class="w3-twothird">
       <h1>Brassica campestris (Chinese Cabbage) </h1>
+
       <h1>Brassica rapa (Chinese cabbage) </h1>
 
     <br /><br />
 
     <br /><br />
  
 
<div class="w3-light-grey">
 
<div class="w3-light-grey">
 
   <div class="w3-container" style="width:60%;background-color:#2196f3a3"> <span class="w3-badge w3-white">1</span>
 
   <div class="w3-container" style="width:60%;background-color:#2196f3a3"> <span class="w3-badge w3-white">1</span>
  &nbsp; Dioxin Uptake</div>
+
  &nbsp; Uptake Rate</div>
 
</div>
 
</div>
  
 
<ul>
 
<ul>
 
     <li>
 
     <li>
         Roots does not go deep or wide relatively to other plants checked.
+
         Roots do not extend deeply or widely relative to other plants.
 
     </li>
 
     </li>
 
     <li>
 
     <li>
        High uptake of dioxins in roots.
+
        High uptake of dioxins in roots.
 
     </li>
 
     </li>
 
     <li>
 
     <li>
Line 455: Line 528:
  
 
<div class="w3-light-grey">
 
<div class="w3-light-grey">
   <div class="w3-container w3-green" style="width:85%"><span class="w3-badge w3-white">2</span>&nbsp; Ease of growth</div>
+
   <div class="w3-container w3-green" style="width:85%"><span class="w3-badge w3-white">2</span>&nbsp; Growth Conditions</div>
 
</div>
 
</div>
  
 
<ul>
 
<ul>
 
<li>
 
<li>
Grow in most parts of the world, mostly in somewhat cold areas
+
Grows in most parts of the world, mostly in temperate-cold areas.
 
</li>
 
</li>
 
<li>
 
<li>
Line 468: Line 541:
  
 
<div class="w3-light-grey">
 
<div class="w3-light-grey">
   <div class="w3-container w3-red" style="width:90%"><span class="w3-badge w3-white">3</span> &nbsp; Ease of transformation</div>
+
   <div class="w3-container w3-red" style="width:90%"><span class="w3-badge w3-white">3</span> &nbsp; Transformation</div>
 
</div>
 
</div>
  
 
<ul>
 
<ul>
 
     <li>
 
     <li>
         Abundance of agrobacterium strains known to be effective.  
+
         An abundance of agrobacterium strains known to be effective.  
 
     </li>
 
     </li>
 
     <li>
 
     <li>
         Whole genome sequenced.
+
         Whole genome sequenced<sup>1</sup>.
 
     </li>
 
     </li>
 
         <li>
 
         <li>
         Susceptible for hybridization.
+
         Susceptible to hybridization.
 
     </li>
 
     </li>
 
</ul><br />
 
</ul><br />
Line 487: Line 560:
  
 
<div class="w3-light-grey">
 
<div class="w3-light-grey">
   <div class="w3-container w3-yellow" style="width:90%"><span class="w3-badge w3-white">4</span> &nbsp; Ease of sterilization</div>
+
   <div class="w3-container w3-yellow" style="width:90%"><span class="w3-badge w3-white">4</span> &nbsp; Sterilization</div>
 
</div>
 
</div>
  
Line 500: Line 573:
  
 
</div>   
 
</div>   
</div>
 
 
</div>
 
</div>
  
Line 507: Line 579:
 
<br /> <br />
 
<br /> <br />
  
<h2 class="w3-center w3-panel" style="width:100%;background-color:#2196f3a3"> <span class="w3-badge w3-white">1</span> &nbsp; Dioxin Uptake</h2>
+
<h2 class="w3-center w3-panel" style="width:100%;background-color:#2196f3a3"> <span class="w3-badge w3-white">1</span> &nbsp; Uptake Rate</h2>
 
  <p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">  
 
  <p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">  
 
<br /> <br />
 
<br /> <br />
Although zucchini and pumpkin have showed the best overall uptake of dioxins, primarily showing an extraordinary shoot uptake of dioxins, Chinese cabbage have showed a specially high uptake of dioxins in root only according to table 2. as our proposed method takes effect in roots as well as the shoots, a high root uptake would work perfectly.
+
Although zucchini and pumpkin have shown the best overall uptake of dioxins, primarily showing an extraordinary shoot uptake of dioxins, Chinese cabbage has shown an especially high uptake of dioxins in their roots only according to Table 2<sup>2</sup>. Since our proposed method takes effect in roots as well as the shoots, a high enough root uptake should suffice.
 
  </p>   
 
  </p>   
  
Line 519: Line 591:
  
  
  <h2 class="w3-center w3-panel w3-green"><span class="w3-badge w3-white">2</span> &nbsp; Plant Growth</h2>
+
  <h2 class="w3-center w3-panel w3-green"><span class="w3-badge w3-white">2</span> &nbsp; Growth Conditions</h2>
 
  <p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">
 
  <p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">
Chinese cabbage requires cool temperatures between 7-17 degrees Celsius to grow and takes between 50-85 days to mature. It`s roots grow in taproot formation, spreading about 30 cm foot radius and go 75 cm deep, where the deeper the roots are, the less branched they are. The plant doesn`t require a large amount of water and able to keep growing without much (although that would make the roots go deeper and spread less).
+
Chinese cabbage requires cool temperatures, between 7-17 degrees Celsius, to grow and it takes between 50-85 days to mature. It`s roots grow in taproot formation, spreading into about 30 cm radius and 75 cm deep. The deeper the roots are, the less branched they are. This plant doesn`t require a large amount of water and is able to keep growing without too much intervention.<sup>3</sup>
 
  </p>
 
  </p>
 
   
 
   
Line 528: Line 600:
 
  <h2 class="w3-center w3-panel w3-red"> <span class="w3-badge w3-white">3</span> &nbsp; Plant Transformation:</h2>
 
  <h2 class="w3-center w3-panel w3-red"> <span class="w3-badge w3-white">3</span> &nbsp; Plant Transformation:</h2>
 
  <p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">
 
  <p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">
An abundance of papers exists describing the transformation of Chinese cabbage using different agrobacterium strains, presenting 1-3% transformations rates.  
+
An abundance of research exists that describes the transformation of Chinese cabbage using different agrobacterium strains, presenting 1-3% transformation rates. <sup>4,5,6</sup>
 
  </p>
 
  </p>
 
<br /> <br />
 
<br /> <br />
 
<h2 class="w3-center w3-panel w3-yellow"><span class="w3-badge w3-white">4</span> &nbsp; Plant Sterility </h2>
 
<h2 class="w3-center w3-panel w3-yellow"><span class="w3-badge w3-white">4</span> &nbsp; Plant Sterility </h2>
 
   <p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">  
 
   <p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">  
<br /> <br />
+
Both female and male sterile strains exist for the Chinese cabbage<sup>7,8,9</sup>. The protocols for molecular techniques and the creation of hybrid strains are available for this plant.
Both female and male sterile strains exist for the Chinese cabbage. Both molecular biology techniques or creation of hybrid strains protocols are available for recreation of sterile plants.
+
 
</p>   
 
</p>   
 
   
 
   
 
  <p class="w3-large w3-serif">
 
  <p class="w3-large w3-serif">
 
   <i class="fa fa-quote-right w3-xxlarge w3-margin-right"></i>
 
   <i class="fa fa-quote-right w3-xxlarge w3-margin-right"></i>
"compared to the wild-type line ‘FT,’ the fsm plants exhibited pistil abortion. Whether the fsm mutant was self-pollinated or used as the female parent to accept foreign pollen (wild-type line ‘FT’), the seed setting rates of fsm were both zero. The results showed that the female sterility of fsm was stable." </p>
+
"..…compared to the wild-type line ‘FT,’ the fsm plants exhibited pistil abortion. Whether the fsm mutant was self-pollinated or used as the female parent to accept foreign pollen (wild-type line ‘FT’), the seed setting rates of fsm were both zero. The results showed that the female sterility of fsm was stable."
  
<div style="text-align:center">
+
  <h2 align="center" style="color:#ABEBC6">Optimized genes for Brassica rapa: </h2>
<br /> <img src="https://static.igem.org/mediawiki/2018/3/32/T--hebrewu--Open_Source_Table1.jpg" style="width:80%"> <br />
+
<p style="text-align:center;padding-left:60px;color:#ABEBC6"> <a onClick="openTab(this)" name="https://static.igem.org/mediawiki/2018/b/b5/T--hebrewu--brassica_seq.txt"><button class="w3-button w3-padding-large w3-large w3-margin-top" style="color:#616161;background-color:#ABEBC6;border-radius: 12px;width:230px;">View sequences</button></a><br /><br />
</div>
+
* In order to optimize the genes, we used our <a onClick="openTab(this)" name="https://2018.igem.org/Team:HebrewU/Software">MOOLTi codon optimizer</a>. We originally designed <a onClick="openTab(this)" name="https://2018.igem.org/Team:HebrewU/Software">MOOLTi </a>to perform optimizations for multiple organisms simultaneously, but it is also capable of optimizing for a single organism with ease.
  
<p style="padding-left:10%;padding-right:90px;text-align:justify;line-height:1.5">
 
** CMS - Cytoplasmic Male Sterility.
 
</p>
 
 
 
   
 
   
 +
</p>
 +
 +
 
  <h2 align="left"> References: </h2>
 
  <h2 align="left"> References: </h2>
 
  <p style="text-align:left">
 
  <p style="text-align:left">
1. <a href="https://www.sciencedirect.com/science/article/pii/S0045653509006730?via%3Dihub#tbl2">"Uptake by roots and translocation to shoots of polychlorinated dibenzo-p-dioxins and dibenzofurans in typical crop plants" by Haijun Zhang and Liang Zhao (2009).
+
 +
1. <a href="https://www.ncbi.nlm.nih.gov/pubmed?Db=pubmed&Cmd=ShowDetailView&TermToSearch=21873998">"The genome of the mesopolyploid crop species Brassica rapa" Wang X and Zhang Z (Brassica rapa Genome Sequencing Project Consortium, 2011). </a><br />
 +
 +
2. <a href="https://www.sciencedirect.com/science/article/pii/S0045653509006730?via%3Dihub#tbl2">"Uptake by roots and translocation to shoots of polychlorinated dibenzo-p-dioxins and dibenzofurans in typical crop plants" Haijun Zhang et al. (2009).
 
  </a> <br />
 
  </a> <br />
2. <a href="https://link.springer.com/article/10.1007/s10681-015-1595-9">"Interspecific hybridisation of cytoplasmic male-sterile rapeseed with Oguracytoplasm and Brassica rapa var. pekinensis as a method to obtain male-sterile Chinese cabbage inbred lines" by Piotr Kamiński and Elżbieta Starzycka-Korbas (2016).
+
 +
3. <a href="https://harvesttotable.com/how_to_grow_chinese_cabbage/">"HOW TO GROW CHINESE CABBAGE" Steve Albert (2018). </a><br />
 +
 
 +
4. <a href="https://link.springer.com/article/10.1007/s002990050775">"Agrobacterium-mediated transformation of cotyledonary explants of Chinese cabbage (Brassica campestris L. ssp. pekinensis)" F.-L, Zhang and M. Watanabe (2000).
 
  </a><br />
 
  </a><br />
3. <a href="https://www.frontiersin.org/articles/10.3389/fpls.2017.00546/full">"Transcriptome Analysis of a Female-sterile Mutant (fsm) in Chinese Cabbage (Brassica campestris ssp. pekinensis)" by Shengnan Huang and Hui Feng (2017).
+
 +
5. <a href="https://www.ncbi.nlm.nih.gov/pubmed/17021847">"Successful genetic transformation of Chinese cabbage using phosphomannose isomerase as a selection marker" Min BW and Harn CH (2007).</a><br />
 +
 
 +
6. <a href="https://www.ncbi.nlm.nih.gov/pubmed/24194308">"Agrobacterium-mediated transformation and regeneration of fertile transgenic plants of chinese cabbage (brassica campestris ssp. pekinensis cv. 'spring flavor')" Jun S 2nd and Paek KH(1995). </a><br />
 +
 
 +
7. <a href="https://link.springer.com/article/10.1007/s10681-015-1595-9">"Interspecific hybridisation of cytoplasmic male-sterile rapeseed with Oguracytoplasm and Brassica rapa var. pekinensis as a method to obtain male-sterile Chinese cabbage inbred lines" Piotr Kamiński et al. (2016).
 +
</a><br />
 +
 +
8. <a href="https://www.frontiersin.org/articles/10.3389/fpls.2017.00546/full">"Transcriptome Analysis of a Female-sterile Mutant (fsm) in Chinese Cabbage (Brassica campestris ssp. pekinensis)" Shengnan Huang et al. (2017).
  
 
</a><br />
 
</a><br />
4. <a href="https://www.ncbi.nlm.nih.gov/pubmed/19436990">"SSR and SCAR mapping of a multiple-allele male-sterile gene in Chinese cabbage (Brassica rapa L.)" by Feng and Lim YP (2009).
+
9. <a href="https://www.ncbi.nlm.nih.gov/pubmed/19436990">"SSR and SCAR mapping of a multiple-allele male-sterile gene in Chinese cabbage (Brassica rapa L.)" Feng and Lim YP (2009).
 
</a><br />
 
</a><br />
5. <a href="https://www.ncbi.nlm.nih.gov/pubmed?Db=pubmed&Cmd=ShowDetailView&TermToSearch=21873998">"The genome of the mesopolyploid crop species Brassica rapa" by Wang X and Zhang Z (Brassica rapa Genome Sequencing Project Consortium, 2011). </a><br />
 
  
6. <a href="https://www.ncbi.nlm.nih.gov/pubmed/24194308">"Agrobacterium-mediated transformation and regeneration of fertile transgenic plants of chinese cabbage (brassica campestris ssp. pekinensis cv. 'spring flavor')" by Jun S 2nd and Paek KH(1995). </a><br />
 
  
7. <a href="https://www.ncbi.nlm.nih.gov/pubmed/17021847">"Successful genetic transformation of Chinese cabbage using phosphomannose isomerase as a selection marker" By Min BW and Harn CH (2007).</a><br />
 
  
9. <a href="https://link.springer.com/article/10.1007/s002990050775">"Agrobacterium-mediated transformation of cotyledonary explants of Chinese cabbage (Brassica campestris L. ssp. pekinensis)" by F.-L, Zhang and M. Watanabe (2000).
 
</a><br />
 
9. <a href="https://harvesttotable.com/how_to_grow_chinese_cabbage/">"HOW TO GROW CHINESE CABBAGE" by Steve Albert (2018). </a><br />
 
  
10. <a href="https://homeguides.sfgate.com/deep-lettuce-roots-grow-101837.html">"How Deep Do Lettuce Roots Grow?" by Teo Spengler.
+
 
</a><br />
+
 
 +
 
 
  </p>  
 
  </p>  
 
  <br /> <br />
 
  <br /> <br />
Line 578: Line 657:
  
 
   
 
   
</div>
 
 
</div>
 
</div>
 
</div>
 
</div>
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   <div class="w3-content">
 
   <div class="w3-content">
 
     <div class="w3-twothird">
 
     <div class="w3-twothird">
       <h1> Lycopersicon esculentum (Tomato) </h1>
+
       <h1> Solanum lycopersicum (Tomato) </h1>
 
       <br /><br />
 
       <br /><br />
  
Line 600: Line 678:
 
<div class="w3-light-grey">
 
<div class="w3-light-grey">
 
  <div class="w3-container" style="width:30%;background-color:#2196f3a3"> <span class="w3-badge w3-white">1</span>
 
  <div class="w3-container" style="width:30%;background-color:#2196f3a3"> <span class="w3-badge w3-white">1</span>
  &nbsp; Dioxin Uptake</div>
+
  &nbsp;Uptake Rate</div>
 
</div>
 
</div>
  
 
<ul>
 
<ul>
 
     <li>
 
     <li>
         Roots go deep and wide.
+
         Roots grow deep and wide.
 
     </li>
 
     </li>
 
     <li>
 
     <li>
Line 614: Line 692:
  
 
<div class="w3-light-grey">
 
<div class="w3-light-grey">
   <div class="w3-container w3-green" style="width:75%"><span class="w3-badge w3-white">2</span>&nbsp; Ease of growth</div>
+
   <div class="w3-container w3-green" style="width:75%"><span class="w3-badge w3-white">2</span>&nbsp; Growth Conditions</div>
 
</div>
 
</div>
  
 
<ul>
 
<ul>
 
     <li>
 
     <li>
         Grow in most parts of the world, require direct sunlight.
+
         Grows in most parts of the world, requires direct sunlight.
 
     </li>
 
     </li>
 
     <li>
 
     <li>
Line 630: Line 708:
  
 
<div class="w3-light-grey">
 
<div class="w3-light-grey">
   <div class="w3-container w3-red" style="width:96%"><span class="w3-badge w3-white">3</span> &nbsp; Ease of transformation</div>
+
   <div class="w3-container w3-red" style="width:96%"><span class="w3-badge w3-white">3</span> &nbsp; Transformation</div>
 
</div>
 
</div>
  
Line 638: Line 716:
 
     </li>
 
     </li>
 
     <li>
 
     <li>
         Whole genome sequenced.
+
         Whole genome sequenced.<sup>1</sup>
 
     </li>
 
     </li>
 
</ul><br />
 
</ul><br />
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<div class="w3-light-grey">
 
<div class="w3-light-grey">
   <div class="w3-container w3-yellow" style="width:96%"><span class="w3-badge w3-white">4</span> &nbsp; Ease of sterilization</div>
+
   <div class="w3-container w3-yellow" style="width:96%"><span class="w3-badge w3-white">4</span> &nbsp; Sterilization</div>
 
</div>
 
</div>
  
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     <li> Known male and female sterile mutants.
 
     <li> Known male and female sterile mutants.
 
     </li>
 
     </li>
         <li> Known CRISPER methods for seedless fruits.
+
         <li> Known CRISPR methods for seedless fruits.
 
     </li>
 
     </li>
         <li> Reproduce easily vegetativaly.
+
         <li> Problem of vegetative growths regarding the spread of transgenic plants.
 
     </li>
 
     </li>
 
</ul><br />
 
</ul><br />
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     </div>
 
     </div>
 
   </div>
 
   </div>
</div>
 
</div>
 
 
<div id="tomato_full" class="collapse">
 
<div id="tomato_full" class="collapse">
<div class="w3-dark-grey w3-center" style="padding-left:10%;padding-right:10%">
+
  <div class="w3-dark-grey w3-center" style="padding-left:10%;padding-right:10%">
 
<br /> <br />
 
<br /> <br />
  
<h2 class="w3-center w3-panel" style="width:100%;background-color:#2196f3a3"> <span class="w3-badge w3-white">1</span> &nbsp; Dioxin Uptake</h2>
+
<h2 class="w3-center w3-panel" style="width:100%;background-color:#2196f3a3"> <span class="w3-badge w3-white">1</span> &nbsp; Uptake Rate</h2>
 
  <p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">  
 
  <p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">  
 
<br /> <br />
 
<br /> <br />
Much like the Chinese cabbage, tomato plants have high dioxin uptake in their roots but very poor transfer to shoots through the xylem. Main difference between the two is higher root uptake in Chinese cabbage, against easier transformation and longer life expectancy of tomatoes.
+
Much like the Chinese cabbage, tomato plants have high dioxin uptake in their roots but very poor transfer to shoots through the xylem<sup>2</sup>. The main difference between the two [plants] is higher root uptake in Chinese cabbage, while tomatoes have an easier transformation and longer life expectancy.
 +
 
 
  </p>   
 
  </p>   
  
Line 683: Line 760:
  
  
  <h2 class="w3-center w3-panel w3-green"><span class="w3-badge w3-white">2</span> &nbsp; Plant Growth</h2>
+
  <h2 class="w3-center w3-panel w3-green"><span class="w3-badge w3-white">2</span> &nbsp; Growth Conditions</h2>
 
  <p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">
 
  <p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">
 
Tomato plants come in different sizes and varieties. Tomato plants are perennials, mostly requiring direct sunlight to grow and love warm temperatures, able to grow in most areas of the world. It`s roots form a taproot formation, reaching half a meter to a meter and a half deep and 1 meter in diameter.  
 
Tomato plants come in different sizes and varieties. Tomato plants are perennials, mostly requiring direct sunlight to grow and love warm temperatures, able to grow in most areas of the world. It`s roots form a taproot formation, reaching half a meter to a meter and a half deep and 1 meter in diameter.  
</p>
+
</p>
 
   
 
   
 
   
 
   
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  <h2 class="w3-center w3-panel w3-red"> <span class="w3-badge w3-white">3</span> &nbsp; Plant Transformation:</h2>
 
  <h2 class="w3-center w3-panel w3-red"> <span class="w3-badge w3-white">3</span> &nbsp; Plant Transformation:</h2>
 
  <p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">
 
  <p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">
Plant transformation using agrobacterium is considered robust, with transformation frequencies of 40%+. On top of that a whole genome sequence, being continuously studied for several decades now give us superb knowledge of tomato transformation possibilities.
+
Plant transformation using agrobacterium is considered robust, with transformation frequencies of 40%+<sup>3</sup>. On top of that, a whole genome sequence, being continuously studied for several decades now, gives us superb knowledge of tomato transformation possibilities.
 
  </p>
 
  </p>
 
<br /> <br />
 
<br /> <br />
 
<h2 class="w3-center w3-panel w3-yellow"><span class="w3-badge w3-white">4</span> &nbsp; Plant Sterility </h2>
 
<h2 class="w3-center w3-panel w3-yellow"><span class="w3-badge w3-white">4</span> &nbsp; Plant Sterility </h2>
 
   <p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">  
 
   <p style="padding-left:90px;padding-right:90px;text-align:justify;line-height:1.5">  
<br /> <br />
+
A technique for promoting fruit formation without seed creation using CRISPR/Cas9 exists<sup>4</sup> as well as known male and female sterile strains<sup>5</sup>.
A technique for promoting fruit formation without seed creation using CRISPER/Cas9 exist on top of known male and female sterile strains.
+
On the downside, the plant is known for its ability to form roots everywhere on its stem, meaning it can easily spread by vegetative means.<sup>6</sup>
On the down side, the plant is known for its ability to form roots everywhere on its stem, meaning it can easily spread by vegetative means.
+
</p>  <br /><br />
</p>   
+
 
   
 
   
 +
  <h2 align="center" style="color:#F1948A">Optimized genes for Solanum lycopersicum: </h2>
 +
<p style="text-align:center;padding-left:60px;color:#F1948A"> <a onClick="openTab(this)" name="https://static.igem.org/mediawiki/2018/7/75/T--Hebrewu--tomato_seq.txt"><button class="w3-button w3-padding-large w3-large w3-margin-top" style="color:#616161;background-color:#F1948A;border-radius: 12px;width:230px;">View sequences</button></a><br /><br />
 +
* In order to optimize the genes, we used our <a onClick="openTab(this)" name="https://2018.igem.org/Team:HebrewU/Software">MOOLTi codon optimizer</a>. We originally designed <a onClick="openTab(this)" name="https://2018.igem.org/Team:HebrewU/Software">MOOLTi </a>to perform optimizations for multiple organisms simultaneously, but it is also capable of optimizing for a single organism with ease.
 +
 
   
 
   
 +
</p>
 +
 
  <h2 align="left"> References: </h2>
 
  <h2 align="left"> References: </h2>
 
  <p style="text-align:left">
 
  <p style="text-align:left">
1. <a href="https://www.sgn.cornell.edu">"Tomato gene sequence".
+
1. <a href="https://www.sgn.cornell.edu">"Tomato gene sequence" Fernandez-Pozo et al (2014).
 
  </a> <br />
 
  </a> <br />
2. <a href="https://www.ncbi.nlm.nih.gov/pubmed/19805904">"A simple and efficient Agrobacterium-mediated procedure for transformation of tomato" by Sharma MK and Sharma AK (2009).
+
 +
2. <a href="https://www.sciencedirect.com/science/article/pii/S0045653509006730?via%3Dihub#tbl2">"Uptake by roots and translocation to shoots of polychlorinated dibenzo-p-dioxins and dibenzofurans in typical crop plants" Haijun Zhang et al. Chemosphere; Volume 76, Issue 6, Pages 740-746 (2009).
 
  </a><br />
 
  </a><br />
3. <a href="https://homeguides.sfgate.com/deep-wide-fullgrown-tomato-plant-grow-59872.html">"How Deep & Wide Does a Full-Grown Tomato Plant Grow?
 
" by Julie Christensen (2018).
 
  
</a><br />
+
3. <a href="https://www.ncbi.nlm.nih.gov/pubmed/19805904">"A simple and efficient Agrobacterium-mediated procedure for transformation of tomato" Sharma MK and Sharma AK (2009).
4. <a href="https://www.almanac.com/plant/tomatoes">"PLANTING, GROWING, AND HARVESTING TOMATOES" by "The Old Farmer's Almanac" (2018).
+
</a><br />
 +
 +
4. <a href="https://www.sciencedirect.com/science/article/pii/S0045653509006730?via%3Dihub#tbl2">"Rapid breeding of parthenocarpic tomato plants using CRISPR/Cas9" Risa Ueta et al. Scientific Reports; volume 7, Article number: 507 (2017).
 +
</a><br />
 +
 +
5. <a href="https://www.sciencedirect.com/science/article/pii/S0045653509006730?via%3Dihub#tbl2">" SEXUAL STERILITY is Essential for Both Male and Female Gametogenesis in Tomato." Hao S et al. Plant Cell Physiol 58(1):22–34 (2017).
 +
</a><br />
 +
 +
</a>
 +
6. <a href="https://www.almanac.com/plant/tomatoes">"Planting, growing, and harvesting tomatoes" The Old Farmer's Almanac website (2018).
 
</a><br />
 
</a><br />
 
  </p>  
 
  </p>  
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Latest revision as of 17:34, 12 December 2018

HebrewU HujiGEM 2018






We created an open source platform aimed at helping researchers and organizations worldwide tackle their dioxin pollution. In our open source page, we present the basic foundations necessary to create a viable transgenic plant based on our research and experiments.

Our open source page features two main programs: our synthetic enzymatic pathway (i.e. optimized gene sequences for each plant, including descriptions), and our proposed plants that are optimal for our pathway. We chose the plants based on 4 categories: Transformation, dioxin uptake efficiency, sterilization methods, and plant durability. We did our best to gather the necessary information to support it using both academic research and verified gardening sites.

Transformation - How many methods are known for the transformation of this plant? How easy and effective are they?
Dioxin uptake efficiency - How well does the plant absorb dioxin from the ground, compared to other plants?
Sterilization methods - With these types of solutions, it is important to be ecologically responsible; releasing genetically engineered plants into the environment is no trivial matter. The ability to sterilize the plants, along with short life expectancies in general, is key for the safe release of transformed plants.
Plant durability - Under what conditions do the plants grow? Where do they grow? Do they grow in regions that are in dire need of solutions to dioxin contaminations?

           

Cucurbita pepo L. (Pumpkin & Zucchini)



1   Uptake Rate
  • Deep root systems.
  • Zucchini roots grow mainly downward, while pumpkin`s grow mainly outward.
  • High uptake values of nutrition from soil.
  • Able to absorb dioxins through roots and deliver them throughout the plant (potential for high-speed degradation in the plant).

2  Growth Conditions
  • Short-season plants, grown in hot seasons.
  • Easily grown in most areas of the world.

3   Transformation
  • Existing transformation methods use agrobacterium.
  • Whole-genome sequence doesn`t exist yet.

4   Sterilization
  • No specific method was found.








1   Uptake Rate



As shown in the figure below, zucchini has shown an impressive absorbance ability of dioxins from contaminated soil11. The main advantage zucchini and pumpkin plants have over other plants (that have been studied) are their ability to transfer the dioxins to their shoots, flowers, and fruits, while others cannot2, so theoretically we have more dioxin to mass ratio, letting them absorb more dioxins. As such, zucchini and pumpkin are our main candidates for dioxin phytoremediation in case of a suitable climate.

"Plants have been frequently shown to remove POPs from soils (Zhao et al. 2006; Susarla et al. 2002; Macek et al. 2000). The high propensity of selected Cucurbitaceae to extract PCDDs/PCDFs from soil was first reported by Hülster et al. (1994), who found that C. pepo L. fruits contained double the PCDD/PCDF concentrations of other examined plants."1




Fig. 1: "Mean decreases in total and TEQ PCDD/PCDF concentrations in soil amended with different doses of sewage sludge (A1, A2) and urban sediments (B1–B2) before and after Cucurbita pepo L. cv ‘Atena Polka’ cultivation".3



2   Growth Conditions

Zucchini and pumpkin are very sensitive to cold weather, requires warm temperatures of above 16 degrees Celsius to grow, but to warm of a climate (above 38 degrees) will harm the plant. Zucchini takes about 60 days to mature. By then it produces fruit as long as someone picks them before they rot. Pumpkin requires between 90 to 160 days to mature. They both grow relatively quickly and, as such, have high root-uptake of nutrition from the ground. Both require moderate quantities of water to grow, which may make it more difficult to grow in drier climates; however, pumpkins have been successfully grown in Iraq, for example. Zucchini roots generally extend deeply downward in a taproot formation, while pumpkin roots tend to spread horizontally as well as vertically - most of its nutrients are absorbed from the upper 1/2 meter of the soil. 3,4,5



3   Plant Transformation:

We know of a few agrobacterium strains able to transform pumpkin plants and zucchini6,7. Agrobacterium is one of the most popular methods of plants transformation, widely studied in plant research. 



4   Plant Sterility

Triploid plants* have larger organs, greater biomass, and strong stress resistance by preserving relatively larger amounts of photosynthetic energy8. The undesirable spread of non-native invasive crop and horticultural plants into natural areas can also be reduced or eliminated by the use of triploids because they tend to be sterile and seedless There are few different ways to create triploid plants:

  • - Natural selection - triploid plants occur in nature, meaning it is possible to look for the desired plant in nature.
  • - Artificial hybridization - by sexual hybridization of different ploidy, one can create a triploid offspring.
  • - Endosperm culture in vitro - endosperm is a triploid tissue. Successful regeneration of a plant from an endosperm tissue would result in a triploid plant.

• Triploid plants contain 3 sets of chromosomes, meaning they have 3n chromosomes. Triploid organisms, in general, tend to be sterile, as in most plants.

Optimized genes for Cucurbita pepo:



* In order to optimize the genes, we used our MOOLTi codon optimizer. We originally designed MOOLTi to perform optimizations for multiple organisms simultaneously, but it is also capable of optimizing for a single organism with ease.

References:

1. "Potential for Phytoremediation of PCDD/PCDF-Contaminated Sludge and Sediments Using Cucurbitaceae Plants: A Pilot Study" Magdalena Urbaniak et al. (2016).
2.
"Uptake by roots and translocation to shoots of polychlorinated dibenzo-p-dioxins and dibenzofurans in typical crop plants" Haijun Zhang et al. (2009).
3. "Planting, growing, and harvesting pumpking" The Old Farmer'S Almanac website (2010).
4. "How to Grow Zucchini: A Squash Vocabulary Lesson" Charity Shumway (2012).
5. "What Is the Life Expectancy of Zucchini Plants?" Karen Carter.
6. "Cucurbita pepo L. can be transformed by Agrobacterium rhizogenes" Luigi Sanità di Toppi et al. (1997).
7. "A simple method for transient transformation of pumpkin (Cucurbita maxima) seedlings" Francisco Arturo Ramírez-Ortega et al. (2015).
8. "Breeding Triploid Plants: A Review" Xiling Wang et al. (2016).





Brassica rapa (Chinese cabbage)



1   Uptake Rate
  • Roots do not extend deeply or widely relative to other plants.
  • High uptake of dioxins in roots.
  • Very low transfer of dioxins from roots to shoots.

2  Growth Conditions
  • Grows in most parts of the world, mostly in temperate-cold areas.
  • Grown all year round.

3   Transformation
  • An abundance of agrobacterium strains known to be effective.
  • Whole genome sequenced1.
  • Susceptible to hybridization.

4   Sterilization
  • Known male and female sterile mutants.







1   Uptake Rate



Although zucchini and pumpkin have shown the best overall uptake of dioxins, primarily showing an extraordinary shoot uptake of dioxins, Chinese cabbage has shown an especially high uptake of dioxins in their roots only according to Table 22. Since our proposed method takes effect in roots as well as the shoots, a high enough root uptake should suffice.



2   Growth Conditions

Chinese cabbage requires cool temperatures, between 7-17 degrees Celsius, to grow and it takes between 50-85 days to mature. It`s roots grow in taproot formation, spreading into about 30 cm radius and 75 cm deep. The deeper the roots are, the less branched they are. This plant doesn`t require a large amount of water and is able to keep growing without too much intervention.3



3   Plant Transformation:

An abundance of research exists that describes the transformation of Chinese cabbage using different agrobacterium strains, presenting 1-3% transformation rates. 4,5,6



4   Plant Sterility

Both female and male sterile strains exist for the Chinese cabbage7,8,9. The protocols for molecular techniques and the creation of hybrid strains are available for this plant.

"..…compared to the wild-type line ‘FT,’ the fsm plants exhibited pistil abortion. Whether the fsm mutant was self-pollinated or used as the female parent to accept foreign pollen (wild-type line ‘FT’), the seed setting rates of fsm were both zero. The results showed that the female sterility of fsm was stable."

Optimized genes for Brassica rapa:



* In order to optimize the genes, we used our MOOLTi codon optimizer. We originally designed MOOLTi to perform optimizations for multiple organisms simultaneously, but it is also capable of optimizing for a single organism with ease.

References:

1. "The genome of the mesopolyploid crop species Brassica rapa" Wang X and Zhang Z (Brassica rapa Genome Sequencing Project Consortium, 2011).
2. "Uptake by roots and translocation to shoots of polychlorinated dibenzo-p-dioxins and dibenzofurans in typical crop plants" Haijun Zhang et al. (2009).
3. "HOW TO GROW CHINESE CABBAGE" Steve Albert (2018).
4. "Agrobacterium-mediated transformation of cotyledonary explants of Chinese cabbage (Brassica campestris L. ssp. pekinensis)" F.-L, Zhang and M. Watanabe (2000).
5. "Successful genetic transformation of Chinese cabbage using phosphomannose isomerase as a selection marker" Min BW and Harn CH (2007).
6. "Agrobacterium-mediated transformation and regeneration of fertile transgenic plants of chinese cabbage (brassica campestris ssp. pekinensis cv. 'spring flavor')" Jun S 2nd and Paek KH(1995).
7. "Interspecific hybridisation of cytoplasmic male-sterile rapeseed with Oguracytoplasm and Brassica rapa var. pekinensis as a method to obtain male-sterile Chinese cabbage inbred lines" Piotr Kamiński et al. (2016).
8. "Transcriptome Analysis of a Female-sterile Mutant (fsm) in Chinese Cabbage (Brassica campestris ssp. pekinensis)" Shengnan Huang et al. (2017).
9. "SSR and SCAR mapping of a multiple-allele male-sterile gene in Chinese cabbage (Brassica rapa L.)" Feng and Lim YP (2009).





Solanum lycopersicum (Tomato)



1  Uptake Rate
  • Roots grow deep and wide.
  • Very low transfer of dioxins from roots to shoots.

2  Growth Conditions
  • Grows in most parts of the world, requires direct sunlight.
  • Grown all year round.
  • Perennial plant.

3   Transformation
  • Very effective agrobacterium transformation (40%+ transformation frequency).
  • Whole genome sequenced.1

4   Sterilization
  • Known male and female sterile mutants.
  • Known CRISPR methods for seedless fruits.
  • Problem of vegetative growths regarding the spread of transgenic plants.





1   Uptake Rate



Much like the Chinese cabbage, tomato plants have high dioxin uptake in their roots but very poor transfer to shoots through the xylem2. The main difference between the two [plants] is higher root uptake in Chinese cabbage, while tomatoes have an easier transformation and longer life expectancy.



2   Growth Conditions

Tomato plants come in different sizes and varieties. Tomato plants are perennials, mostly requiring direct sunlight to grow and love warm temperatures, able to grow in most areas of the world. It`s roots form a taproot formation, reaching half a meter to a meter and a half deep and 1 meter in diameter.



3   Plant Transformation:

Plant transformation using agrobacterium is considered robust, with transformation frequencies of 40%+3. On top of that, a whole genome sequence, being continuously studied for several decades now, gives us superb knowledge of tomato transformation possibilities.



4   Plant Sterility

A technique for promoting fruit formation without seed creation using CRISPR/Cas9 exists4 as well as known male and female sterile strains5. On the downside, the plant is known for its ability to form roots everywhere on its stem, meaning it can easily spread by vegetative means.6



Optimized genes for Solanum lycopersicum:



* In order to optimize the genes, we used our MOOLTi codon optimizer. We originally designed MOOLTi to perform optimizations for multiple organisms simultaneously, but it is also capable of optimizing for a single organism with ease.

References:

1. "Tomato gene sequence" Fernandez-Pozo et al (2014).
2. "Uptake by roots and translocation to shoots of polychlorinated dibenzo-p-dioxins and dibenzofurans in typical crop plants" Haijun Zhang et al. Chemosphere; Volume 76, Issue 6, Pages 740-746 (2009).
3. "A simple and efficient Agrobacterium-mediated procedure for transformation of tomato" Sharma MK and Sharma AK (2009).
4. "Rapid breeding of parthenocarpic tomato plants using CRISPR/Cas9" Risa Ueta et al. Scientific Reports; volume 7, Article number: 507 (2017).
5. " SEXUAL STERILITY is Essential for Both Male and Female Gametogenesis in Tomato." Hao S et al. Plant Cell Physiol 58(1):22–34 (2017).
6. "Planting, growing, and harvesting tomatoes" The Old Farmer's Almanac website (2018).