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| <h1 class="page-subtitle2"><span>Description about Esophageal Cancer</span></h1> | | <h1 class="page-subtitle2"><span>Description about Esophageal Cancer</span></h1> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
− | <p class="page-main" style="text-indent:1em">Esophageal cancer is a cancer in esophagus. It is the eighth most common cancer and sixth leading cause of cancer mortality in the world. Especially, nearly 90% of esophageal cancer patients have been found in china. Chinese patients account for more than a half of all deaths caused by esophageal cancer worldwide. Genetic factors and bad eating habits (e.g. addiction to alcohol, tobacco, eating too fast and drinking hot liquids) can be the causes of esophageal cancer.</p> | + | <p class="page-main" style="text-indent:1em">Esophageal cancer is cancer arising from the esophagus. It is the eighth most common cancer and sixth leading cause of cancer mortality in the world. Especially, nearly 90% of esophageal cancer patient are found in china. Chinese patients account for more than a half of all deaths caused by esophageal cancer worldwide. Genetic factors and bad eating habits (e.g. addiction to alcohol, addiction to tobacco, eating too fast and drinking hot liquids) can be the cause of esophageal cancer.</p> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
− | <p class="page-main" style="text-indent:1em">5-year survival rate of esophageal cancer declines sharply as stage of cancer increases. In Stage I, during which cancer cells haven’t transferred, the 5-year survival rate can reach up to 70%. When it deteriorates to Stage II, this number dramatically drops to under 50%. And for Stage III and IV, it is 20% and 10% respectively. Thus early diagnosis plays an important role in the treatment of esophageal cancer.</p> | + | <p class="page-main" style="text-indent:1em">5-year survival rate of esophageal cancer declines sharply as stage of cancer increases. In Stage I, during which cancer cells haven’t transferred, the 5-year survival rate can reach 70%. When it comes to Stage II, this number dramatically drops under 50%. And for Stage III and IV, it is 20% and 10% respectively. Thus early diagnosis plays an important role in the treatment of esophageal cancer.</p> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
− | <p class="page-main" style="text-indent:1em">However, due to a lack of significance of early symptoms and high expenses of methods for clinical diagnosis of esophageal cancer, early diagnosis becomes even more difficult. Dramatic symptoms usually appear only when a patient is already in the advanced stage. Early symptoms like swallowing difficulty, pain when swallowing, reduced appetite and loss of weight are often considered a minor illness and are prone to be ignored. The diagnosing method used in hospitals mainly depends on radiology and endoscopic biopsy, which is invasive and uncomfortable. To help solve this problem, our team aim to build a convenient and harmless method for early diagnosis of esophageal cancer.</p> | + | <p class="page-main" style="text-indent:1em">However, since the early symptoms are not significant and the methods for clinical diagnosis of esophageal cancer are expensive and inconvenient, which makes the early diagnosis become difficult. Prominent symptoms usually appear only when a patient is already in the advanced stage. Early symptoms like swallowing difficulty, pain when swallowing, reduced appetite and loss of weight are often considered a minor illness and easily ignored. The diagnosing method used in hospitals mainly depends on radiology and endoscopic biopsy, which seems to be invasive and uncomfortable. To help solve this dilemma our team aim to build a convenient and harmless method for early diagnosis of esophageal cancer.</p> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
| <h1 class="page-subtitle2"><span>miRNA as Potential Biomarkers</span></h1> | | <h1 class="page-subtitle2"><span>miRNA as Potential Biomarkers</span></h1> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
− | <p class="page-main" style="text-indent:1em">Studies have confirmed that miRNA expression is highly concordant cross individuals. And aberrant expression of miRNA may be related to diseases. Some studies have reported that specific miRNAs in tissue and plasma can be discriminatory bio-makers for detecting cancers. However, getting access to tissue of plasma means physical harm to the human body. So we turn to the easily accessible saliva. Since saliva is considered to be a terminal product of blood circulation, components like proteins and RNAs which are existing in plasma are also existing in saliva. In fact, both coding RNAs and non-coding RNAs, including some miRNAs, have been found in human saliva. Although mRNAs are highly degraded in saliva, miRNAs are stably and abundantly present in saliva. Recently, there are many reports on cancer-related miRNA expression in saliva. Featured miRNA expression are reported to be found in oral squamous cell carcinoma, parotid gland tumors and esophageal cancer, indicating potential salivary miRNA to be biomarkers for detecting these diseases. According to the test done by Zijun Xie group, there are three type of miRNAs significantly upregulated in the whole saliva from the esophageal cancer patient group in contract to normal control group – miR-10b, miR-144, and miR-451 (p value 0.001, 0.012 and 0.002, respectively; AUC 0.762, 0.706 and 0.756, respectively). And four miRNAs are significantly upregulated in saliva supernatants from the esophageal cancer patient group – miR-10b, miR-144, miR-21 and miR-451. Among them, miR-21 is the most frequently reported one for its high performance in specific expression level related to esophageal cancer (according to one of the reports, p < 0.05, AUC = 0.8820, sensitivity = 90.20% and specificity 70.69%; different tests may report different results).</p> | + | <p class="page-main" style="text-indent:1em">Studies have confirmed that miRNA expression is highly concordant cross individuals. And aberrant expression of miRNA may relate to diseases. Some studies have reported that specific miRNAs in tissue and plasma can be discriminatory bio-makers for detecting cancers. However, getting access to tissue of plasma means physical harm to the human body. So we turn to the easily accessible saliva. Since saliva is considered to be a terminal product of blood circulation, components like proteins and RNAs which are present in plasma are also present in saliva. In fact, both coding RNAs and non-coding RNAs, including some miRNAs, have been found in human saliva. Although mRNAs are highly degraded in saliva, miRNAs are stably and abundantly present in saliva. Recently, there are many reports on cancer-related miRNA expression in saliva. Featured miRNA expression are reported to be found in oral squamous cell carcinoma, parotid gland tumors and esophageal cancer, indicating potential salivary miRNA to be biomarkers for detecting these diseases. According to the test done by Zijun Xie group, there are three type of miRNAs significantly upregulated in the whole saliva from the esophageal cancer patient group in contract to normal control group – miR-10b, miR-144, and miR-451 (p value 0.001, 0.012 and 0.002, respectively; AUC 0.762, 0.706 and 0.756, respectively). And four miRNAs are significantly upregulated in saliva supernatants from the esophageal cancer patient group – miR-10b, miR-144, miR-21 and miR-451. Among them, miR-21 is the most frequently reported one for its high performance in specific expression level related to esophageal cancer (according to one of the reports, p < 0.05, AUC = 0.8820, sensitivity = 90.20% and specificity 70.69%; different tests may report different results).</p> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
− | <p class="page-main" style="text-indent:1em">Comprehensively considering the performance of each miRNA, we finally chose <span>miR-144</span> as our biomarkers for esophageal cancer. To make our detection quick and convenient, we designed synthetic gene pathways <span>based on paper</span>. It will only require some saliva to complete the detection, which does no harm to human body. And this technique can be expanded to be used in the detection of many other diseases which has specific miRNA expression pattern in saliva. </p> | + | <p class="page-main" style="text-indent:1em">Comprehensively considering the performance of each miRNA, we finally chose <span>miR-144</span> as our biomarkers for esophageal cancer. To make our detection quick and convenient, we designed synthetic gene pathways <span>based on paper</span>. It will only require some saliva to complete the detection, which will do no harm to human body. And this techniques can be expanded to be used in the detection of many other diseases which has specific miRNA expression pattern in saliva. </p> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
− | <p class="page-main" style="text-indent:1em">To make our detection quick and convenient, we designed synthetic gene pathways. It will only require some saliva to complete the detection, which does no harm to human body. And this technique can be expanded to be used in the detection of many other diseases which has specific miRNA expression pattern in saliva.</p> | + | <p class="page-main" style="text-indent:1em">To make our detection quick and convenient, we designed synthetic gene pathways. It will only require some saliva to complete the detection, which will do no harm to human body. And this technique can be expanded to be used in the detection of many other diseases which has specific miRNA expression pattern in saliva.</p> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
| <h1 class="page-subtitle2"><span>What is Toehold Switch</span></h1> | | <h1 class="page-subtitle2"><span>What is Toehold Switch</span></h1> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
− | <p class="page-main" style="text-indent:1em">We choose toehold switch as our miRNA detector. The structure of toehold switch is similar to hairpin, except it has a loop at the top as ‘toehold’. Toehold switch functions as riboregulator through linear-linear interaction between RNAs. When target RNA appears, it will bind to one of the toehold switch stems and open the loop, exposing the RBS.</p> | + | <p class="page-main" style="text-indent:1em">We choose toehold switch as our miRNA detector. The structure of toehold switch is similar to hairpin, except it has a loop at the top as ‘toehold’. Toehold switch functions as riboregulator through linear-linear interaction between RNAs. When target RNA appears, it will bind one of the toehold switch stems and open the loop, exposing the RBS.</p> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
| <p class="page-main" style="text-indent:1em">Toehold switch systems are composed of two RNA strands referred to as the switch and trigger. The switch RNA contains the coding sequence of the gene being regulated. Upstream of this coding sequence is a hairpin-based processing module containing both a strong RBS and a start codon that is followed by a common 21 nt linker sequence coding for low-molecular-weight amino acids added to the N terminus of the gene of interest. A single-stranded toehold sequence at the 50 end of the hairpin module provides the initial binding site for the trigger RNA strand. This trigger molecule contains an extended single-stranded region that completes a branch migration process with the hairpin to expose the RBS and start codon, thereby initiating translation of the gene of interest.</p> | | <p class="page-main" style="text-indent:1em">Toehold switch systems are composed of two RNA strands referred to as the switch and trigger. The switch RNA contains the coding sequence of the gene being regulated. Upstream of this coding sequence is a hairpin-based processing module containing both a strong RBS and a start codon that is followed by a common 21 nt linker sequence coding for low-molecular-weight amino acids added to the N terminus of the gene of interest. A single-stranded toehold sequence at the 50 end of the hairpin module provides the initial binding site for the trigger RNA strand. This trigger molecule contains an extended single-stranded region that completes a branch migration process with the hairpin to expose the RBS and start codon, thereby initiating translation of the gene of interest.</p> |
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| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
| <p class="page-main"><span>Xu Yingqi from Art School, Tsinghua University helps us with painting the picture. We appreciate her help sincerelly.</span></p> | | <p class="page-main"><span>Xu Yingqi from Art School, Tsinghua University helps us with painting the picture. We appreciate her help sincerelly.</span></p> |
| + | <div class="spacespace twelve columns page-content"></div> |
| + | <img src="https://static.igem.org/mediawiki/2015/0/0b/TsinghuaA_Acknow_1.png" width="100%"> |
| + | <div class="spacespace twelve columns page-content"></div> |
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| </div> | | </div> |
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| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
| <img src="https://static.igem.org/mediawiki/2015/b/be/TsinghuaA_Model1_6.png" width="70%"> | | <img src="https://static.igem.org/mediawiki/2015/b/be/TsinghuaA_Model1_6.png" width="70%"> |
| + | <div class="spacespace twelve columns page-content"></div> |
| + | <p class="page-main" style="text-indent:1em"><span>Matlab Source Code:ee</span></p> |
| + | <p class="page-main" style="text-indent:1em"><a href="http://2015.igem.oeg/File:TsinghuaA_source_code_for_model1.zip">Download link(Click here)</span></p> |
| </div> | | </div> |
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| <h3 class="our-team-subtitle">Professor</h3> | | <h3 class="our-team-subtitle">Professor</h3> |
| <div class="our-team-divider"></div> | | <div class="our-team-divider"></div> |
− | <p class="our-team-text">Wet Lab Instructor</p> | + | <p class="our-team-text">Advice on Wet Lab</p> |
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| <h3 class="our-team-subtitle">Professor</h3> | | <h3 class="our-team-subtitle">Professor</h3> |
| <div class="our-team-divider"></div> | | <div class="our-team-divider"></div> |
− | <p class="our-team-text">Dry Lab Instructor</p> | + | <p class="our-team-text">Advice on Dry Lab</p> |
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| <img src="https://static.igem.org/mediawiki/2015/8/86/TsinghuaA_Team_Lwx.png" alt="Our Team"> | | <img src="https://static.igem.org/mediawiki/2015/8/86/TsinghuaA_Team_Lwx.png" alt="Our Team"> |
| <h3 class="our-team-title">Weixi Liao</h3> | | <h3 class="our-team-title">Weixi Liao</h3> |
− | <h3 class="our-team-subtitle">PhD Candidate</h3> | + | <h3 class="our-team-subtitle">Phd Candidate</h3> |
| <div class="our-team-divider"></div> | | <div class="our-team-divider"></div> |
− | <p class="our-team-text">Wet Lab Advisor</p> | + | <p class="our-team-text">Advice on Wet Lab</p> |
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| <img src="https://static.igem.org/mediawiki/2015/a/ad/TsinghuaA_Team_Wl.png" alt="Our Team"> | | <img src="https://static.igem.org/mediawiki/2015/a/ad/TsinghuaA_Team_Wl.png" alt="Our Team"> |
| <h3 class="our-team-title">Lei Wei</h3> | | <h3 class="our-team-title">Lei Wei</h3> |
− | <h3 class="our-team-subtitle">PhD Candidate</h3> | + | <h3 class="our-team-subtitle">Phd Candidate</h3> |
| <div class="our-team-divider"></div> | | <div class="our-team-divider"></div> |
− | <p class="our-team-text">Wet Lab Advisor</p> | + | <p class="our-team-text">Advice on Dry Lab</p> |
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| <img src="https://static.igem.org/mediawiki/2015/4/4f/TsinghuaA_Team_Pzh2.png" alt="Our Team"> | | <img src="https://static.igem.org/mediawiki/2015/4/4f/TsinghuaA_Team_Pzh2.png" alt="Our Team"> |
| <h3 class="our-team-title">Zhanhao Peng</h3> | | <h3 class="our-team-title">Zhanhao Peng</h3> |
− | <h3 class="our-team-subtitle">Undergraduate</h3> | + | <h3 class="our-team-subtitle">Instructor on Dry Lab</h3> |
| <div class="our-team-divider"></div> | | <div class="our-team-divider"></div> |
− | <p class="our-team-text">Dry Lab Advisor</p> | + | <p class="our-team-text">Advice on Dry Lab</p> |
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| <img src="https://static.igem.org/mediawiki/2015/b/bc/TsinghuaA_Team_Mdc.png" alt="Our Team"> | | <img src="https://static.igem.org/mediawiki/2015/b/bc/TsinghuaA_Team_Mdc.png" alt="Our Team"> |
| <h3 class="our-team-title">Dacheng Ma</h3> | | <h3 class="our-team-title">Dacheng Ma</h3> |
− | <h3 class="our-team-subtitle">PhD Candidate</h3> | + | <h3 class="our-team-subtitle">Instructor on Wet Lab</h3> |
| <div class="our-team-divider"></div> | | <div class="our-team-divider"></div> |
− | <p class="our-team-text">Wet Lab Advisor</p> | + | <p class="our-team-text">Advice on Wet Lab</p> |
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| <img src="https://static.igem.org/mediawiki/2015/6/6c/TsinghuaA_Team_Mx.png" alt="Our Team"> | | <img src="https://static.igem.org/mediawiki/2015/6/6c/TsinghuaA_Team_Mx.png" alt="Our Team"> |
− | <h3 class="our-team-title">Meixi Li</h3> | + | <h3 class="our-team-title">Meixi Liu</h3> |
| <h3 class="our-team-subtitle">Biological Science</h3> | | <h3 class="our-team-subtitle">Biological Science</h3> |
| <div class="our-team-divider"></div> | | <div class="our-team-divider"></div> |