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| <div class="row"> | | <div class="row"> |
| <div class="twelve columns page-content"> | | <div class="twelve columns page-content"> |
− | <h1 class="page-title">Description about Esophageal Cancer</h1> | + | <h1 class="page-title">Description & Design</h1> |
| + | <div class="spacespace twelve columns page-content"></div> |
| + | <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 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> | | <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> |
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| <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> | | <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-title">miRNA as Potential Biomarkers</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 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> | | <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> |
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| <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> | | <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-title">What is Toehold Switch</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 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> |
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| <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> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
− | <img src="https://static.igem.org/mediawiki/2015/8/80/TsinghuaA_Project_1.png" width=40%> | + | <img src="https://static.igem.org/mediawiki/2015/8/80/TsinghuaA_Project_1.png" width="40%"> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
− | <h1 class="page-title">Our Circuit to Detect miRNA-144</h1> | + | <h1 class="page-subtitle2"><span>Our Circuit to Detect miRNA-144</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">There are 3 parts in our circuit in total.</p> | | <p class="page-main" style="text-indent:1em">There are 3 parts in our circuit in total.</p> |
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| <p class="page-main" style="text-indent:1em">We use the experimental data from Salivary MicroRNAs as Promising Biomarkers for Detection of Esophageal Cancer, Zijun Xie et. al. Altogether, there are 58 samples, 46 of which are patients and the rest of which are healthy control.</p> | | <p class="page-main" style="text-indent:1em">We use the experimental data from Salivary MicroRNAs as Promising Biomarkers for Detection of Esophageal Cancer, Zijun Xie et. al. Altogether, there are 58 samples, 46 of which are patients and the rest of which are healthy control.</p> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
− | <h2 class="page-subtitle2">Plotting the ROC curve</h2> | + | <h2 class="page-subtitle2" style="font-size:28px" >Plotting the ROC curve</h2> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
| <p class="page-main" style="text-indent:1em">The ROC curve can be used to test whether a single feature (in our case, the concentration of a particular kind of miRNA in a person’s saliva) is linearly separable. The bigger the area under the ROC curve, the higher the possibility of the single feature being linearly separable is.</p> | | <p class="page-main" style="text-indent:1em">The ROC curve can be used to test whether a single feature (in our case, the concentration of a particular kind of miRNA in a person’s saliva) is linearly separable. The bigger the area under the ROC curve, the higher the possibility of the single feature being linearly separable is.</p> |
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| <p class="page-main" style="text-indent:1em">For the above 3 figures, the first 3 subfigures are the results of 3 kinds of miRNA in the sample’s whole saliva, and the last 4 subfigures are the results of 4 kinds of miRNA in the sample’s saliva supernatant. The results are not satisfying. We assume that it is because the dataset collected is not large enough.</p> | | <p class="page-main" style="text-indent:1em">For the above 3 figures, the first 3 subfigures are the results of 3 kinds of miRNA in the sample’s whole saliva, and the last 4 subfigures are the results of 4 kinds of miRNA in the sample’s saliva supernatant. The results are not satisfying. We assume that it is because the dataset collected is not large enough.</p> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
− | <h2 class="page-subtitle2"> Application of different kinds of classifiers</h2> | + | <h2 class="page-subtitle2" style="font-size:28px"> Application of different kinds of classifiers</h2> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
| <p class="page-main"><span>Fisher Linear Discriminant:</span></p> | | <p class="page-main"><span>Fisher Linear Discriminant:</span></p> |
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| <h2 class="page-subtitle2"><span>Diagnosis and Treatment</span></h2> | | <h2 class="page-subtitle2"><span>Diagnosis and Treatment</span></h2> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
| + | <img src="https://static.igem.org/mediawiki/2015/2/20/TsinghuaA_HP_pic4.jpeg"> |
| <h2 class="page-subtitle2"><span>Preventive Tips</span></h2> | | <h2 class="page-subtitle2"><span>Preventive Tips</span></h2> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
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| <p class="page-main" style="text-indent:1em"> It’s a really interesting one. Your test paper can work as a preliminary screening of esophageal cancer high risk people, because it’s convenient and noninvasive. To do this, you need to ensure the sensitivity, not specificity, of the test paper. Though at present you may not be able to work out a test paper that can be used in clinically, it’s a very good idea, or concept. </p> | | <p class="page-main" style="text-indent:1em"> It’s a really interesting one. Your test paper can work as a preliminary screening of esophageal cancer high risk people, because it’s convenient and noninvasive. To do this, you need to ensure the sensitivity, not specificity, of the test paper. Though at present you may not be able to work out a test paper that can be used in clinically, it’s a very good idea, or concept. </p> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
− | <img src="https://static.igem.org/mediawiki/2015/c/c9/TsinghuaA_HP_CL1.jpg"> | + | <img src="https://static.igem.org/mediawiki/2015/c/c9/TsinghuaA_HP_CL1.jpg" width="80%"> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
− | <img src="https://static.igem.org/mediawiki/2015/9/93/TsinghuaA_HP_CL2.jpg"> | + | <img src="https://static.igem.org/mediawiki/2015/9/93/TsinghuaA_HP_CL2.jpg" width="80%"> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
| </div> | | </div> |
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| <div class="twelve columns page-content"> | | <div class="twelve columns page-content"> |
| <h1 class="page-title">The Result of Our Questionnaire</h1> | | <h1 class="page-title">The Result of Our Questionnaire</h1> |
| + | <div class="spacespace twelve columns page-content"></div> |
| + | <p class="page-main" style="text-indent:1em"><span>Q1: Our country(China) is one of the areas of high incidence of esophageal cancer in the world, there are more than ten million people died of esophageal cancer each year. Do you know the causes of esophageal cancer? (Nitrosamines and other chemical carcinogens, fungi, micronutrient deficiencies, poor diet, genetic factors, etc.)</span></p> |
| + | <div class="spacespace twelve columns page-content"></div> |
| + | <img src="https://static.igem.org/mediawiki/2015/5/52/TsinghuaA_HP_a.jpeg"> |
| + | <div class="spacespace twelve columns page-content"></div> |
| + | <p class="page-main" style="text-indent:1em"><span>Q2: Have you ever heard which poor eating habits are related to esophageal cancer? (Tobacco and alcohol addiction, swallowing hot or irritating esophagus excellent food, etc.)</span></p> |
| + | <div class="spacespace twelve columns page-content"></div> |
| + | <img src="https://static.igem.org/mediawiki/2015/e/e5/TsinghuaA_HP_b.jpeg"> |
| + | <div class="spacespace twelve columns page-content"></div> |
| + | <p class="page-main" style="text-indent:1em"><span>Q3: Do you know how the hospital diagnose esophageal cancer? (Ultrasound, barium meal, endoscopy, etc.)</span></p> |
| + | <div class="spacespace twelve columns page-content"></div> |
| + | <img src="https://static.igem.org/mediawiki/2015/e/ec/TsinghuaA_HP_c.jpeg"> |
| + | <div class="spacespace twelve columns page-content"></div> |
| + | <p class="page-main" style="text-indent:1em"><span>Q4: Do you know the symptoms of esophageal cancer? (Weight plummeted, vomiting, difficulty swallowing, indigestion, etc.)</span></p> |
| + | <div class="spacespace twelve columns page-content"></div> |
| + | <img src="https://static.igem.org/mediawiki/2015/9/9c/TsinghuaA_HP_d.jpeg"> |
| + | <div class="spacespace twelve columns page-content"></div> |
| + | <p class="page-main" style="text-indent:1em"><span>Q5: If there is a strange feeling esophagus (such as dysphagia, pain, etc.), will you immediately go to the hospital to check it?</span></p> |
| + | <div class="spacespace twelve columns page-content"></div> |
| + | <img src="https://static.igem.org/mediawiki/2015/7/79/TsinghuaA_HP_e.jpeg"> |
| + | <div class="spacespace twelve columns page-content"></div> |
| + | <p class="page-main" style="text-indent:1em"><span>Q6: Which of the following is the main reason that you do not choose to go to the hospital to check?</span></p> |
| + | <div class="spacespace twelve columns page-content"></div> |
| + | <img src="https://static.igem.org/mediawiki/2015/b/b4/TsinghuaA_HP_f.jpeg"> |
| + | <div class="spacespace twelve columns page-content"></div> |
| + | <p class="page-main" style="text-indent:1em"><span>Q7: How much would you like to pay for the test paper if it’s result is trustful?</span></p> |
| + | <div class="spacespace twelve columns page-content"></div> |
| + | <img src="https://static.igem.org/mediawiki/2015/9/92/TsinghuaA_HP_g.jpeg"> |
| + | <div class="spacespace twelve columns page-content"></div> |
| + | <p class="page-main" style="text-indent:1em"><span>Q8: Which of the following choice is the most acceptable one for you to diagnose cancer?</span></p> |
| + | <div class="spacespace twelve columns page-content"></div> |
| + | <img src="https://static.igem.org/mediawiki/2015/f/ff/TsinghuaA_HP_h.jpeg"> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
| </div> | | </div> |
| + | |
| | | |
| <div class="twelve columns page-content"> | | <div class="twelve columns page-content"> |
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| <h1 class="page-title">Communication & Collabroation</h1> | | <h1 class="page-title">Communication & Collabroation</h1> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
− | <h2 class="page-subtitle2"><span>Help Tianjin-China with the Modeling</span></h2> | + | <h2 class="page-subtitle2"><span>Help Tianjin with the Modeling</span></h2> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
− | <p class="page-main" style="text-indent:1em">From July 24 to 26, team member from the Tianjin-China visited us in Beijing. During the three-day stay here, we discussed about our ideas, our projects and team and team management.</p> | + | <p class="page-main" style="text-indent:1em">From July 24 to 26, team member from the Tianjin visited us in Beijing. During the three-day stay here, we discussed about our ideas, our projects and team and team management.</p> |
| <p class="page-main" style="text-indent:1em">Then we helped Tianjin-IGEM in their programming. In their modelling, they want to make the model visible by stimulating their processes using Matlab. So we help them abstract calculation process from real reactions.</p> | | <p class="page-main" style="text-indent:1em">Then we helped Tianjin-IGEM in their programming. In their modelling, they want to make the model visible by stimulating their processes using Matlab. So we help them abstract calculation process from real reactions.</p> |
| <p class="page-main" style="text-indent:1em">The basic method is Monte Carlo.</p> | | <p class="page-main" style="text-indent:1em">The basic method is Monte Carlo.</p> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
− | <img src="https://static.igem.org/mediawiki/2015/d/d5/TsinghuaA_HP_TJ1.jpg"> | + | <img src="https://static.igem.org/mediawiki/2015/d/d5/TsinghuaA_HP_TJ1.jpg" width="80%"> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
− | <img src="https://static.igem.org/mediawiki/2015/4/49/TsinghuaA_HP_TJ2.jpg"> | + | <img src="https://static.igem.org/mediawiki/2015/4/49/TsinghuaA_HP_TJ2.jpg" width="80%"> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
| <h2 class="page-subtitle2"><span>Participate in CCIC</span></h2> | | <h2 class="page-subtitle2"><span>Participate in CCIC</span></h2> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
| <p class="page-main" style="text-indent:1em">During Aug 14th-15th, our team participated in CCIC(Conference of China iGEMer Committee) in PKU. We gave ‘peer’ review to other iGEM team and gained feedback from others. We enjoyed the process reaching out to other teams, asking for advice and talking about ideas. In the CCIC, the young, ambitious and creative synthetic biologist got together and had fun with each other.</p> | | <p class="page-main" style="text-indent:1em">During Aug 14th-15th, our team participated in CCIC(Conference of China iGEMer Committee) in PKU. We gave ‘peer’ review to other iGEM team and gained feedback from others. We enjoyed the process reaching out to other teams, asking for advice and talking about ideas. In the CCIC, the young, ambitious and creative synthetic biologist got together and had fun with each other.</p> |
− | <img src="https://static.igem.org/mediawiki/2015/7/73/NYU_Shanghai_Day_47.jpg"> | + | <div class="spacespace twelve columns page-content"></div> |
| + | <img src="https://static.igem.org/mediawiki/2015/7/73/NYU_Shanghai_Day_47.jpg" width="80%"> |
| <div class="spacespace twelve columns page-content"></div> | | <div class="spacespace twelve columns page-content"></div> |
| </div> | | </div> |