Team:UB Indonesia

From 2014.igem.org

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Indonesia as one of the currently high development countries in science is allowing for synthetic biology to grow rapidly. Prospects for the synthetic biology's development in Indonesia, among others, is the independence of technology in the health sector include the development of a specific diagnosis, the provision of pharmaceutical raw materials, and technology screening for Indonesia natural resources which have potency to treat various types of diseases.<br><br>
Indonesia as one of the currently high development countries in science is allowing for synthetic biology to grow rapidly. Prospects for the synthetic biology's development in Indonesia, among others, is the independence of technology in the health sector include the development of a specific diagnosis, the provision of pharmaceutical raw materials, and technology screening for Indonesia natural resources which have potency to treat various types of diseases.<br><br>
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Brawijaya University iGEM team will develop synthetic biology in order to solve health sector problems, focus in Cervical Cancer. We have three sub-projects, they are: plant engineering for cervical cancer prevention, developing Cervical Cancer Care Program application for smartphone as helpdesk, and scanning technology for natural materials treatment (SCT Kit).</p>
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Brawijaya University iGEM team will develop synthetic biology in order to solve health sector problems, focus in Cervical Cancer. We have three sub-projects, they are: plant engineering for cervical cancer prevention, developing Cervical Cancer Care Program application for smartphone as helpdesk, and scanning technology for natural materials treatment (CHS Kit).</p>
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We try to make an idea to build a new prototype for early detection to cervical cancer, especially caused by HPV 18 and HPV 16. We construct a new specific TALEs that can bind to our target sequences and we called it TALE 1 and TALE 2. In order to make sure the presence of DNA  from HPV 16 and 18, we need reporter which connect to detector.  Fluorescent protein usually used as reporter gene to study about gene expression. It will be connected to detector using linker. When the HPV DNA is bind to detector, blue colour will appear in the second strip. The Intensity of colour will be detected in our software and we can determined the risk level of cervical cancer disease. Dark blue colour show that the amount of  DNA  from HPV 16 and 18 is high and indicate the patient get severe cervical cancer.<br><br>
We try to make an idea to build a new prototype for early detection to cervical cancer, especially caused by HPV 18 and HPV 16. We construct a new specific TALEs that can bind to our target sequences and we called it TALE 1 and TALE 2. In order to make sure the presence of DNA  from HPV 16 and 18, we need reporter which connect to detector.  Fluorescent protein usually used as reporter gene to study about gene expression. It will be connected to detector using linker. When the HPV DNA is bind to detector, blue colour will appear in the second strip. The Intensity of colour will be detected in our software and we can determined the risk level of cervical cancer disease. Dark blue colour show that the amount of  DNA  from HPV 16 and 18 is high and indicate the patient get severe cervical cancer.<br><br>
Beside that, we try to take the advantage of tea plant. Tea plant (Camelia sinensis) has catechin compounds that contains antioxidants.  Catechin family that most effective used as antioxidant is Epigallocathecin gallate (EGCG).  Based on research in vitro or in silico, EGCG is able to inhibit the proliferation of cancer cells because stop over-expression between L1 HPV 16- EGFR (Epithel Growth Factor Receptor) bond but there are few of EGCG content in tea plant. Based on these problems, we would to over- expression EGCG by knockdown non-compound EGCG gene, so hopefully the content of EGCG on tea are more prominent.<br><br>
Beside that, we try to take the advantage of tea plant. Tea plant (Camelia sinensis) has catechin compounds that contains antioxidants.  Catechin family that most effective used as antioxidant is Epigallocathecin gallate (EGCG).  Based on research in vitro or in silico, EGCG is able to inhibit the proliferation of cancer cells because stop over-expression between L1 HPV 16- EGFR (Epithel Growth Factor Receptor) bond but there are few of EGCG content in tea plant. Based on these problems, we would to over- expression EGCG by knockdown non-compound EGCG gene, so hopefully the content of EGCG on tea are more prominent.<br><br>
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CHS (Cancer Herbal Screening) is a kit which contains of hela cells as cervical cancer cells and it was designed to screening the plants that have compund potentially for cervical cancer therapy. Herbs that potentially as a therapy of cervical cancer in the kit are marked by the absence of green or red colors, while the negative results are marked by the emergence of green or red in the kit. The kit is expected to provide convenience to the researchers in the field of cervical cancer and cervical cancer effects can be mitigated with natural compound that not a lot of side effects. <br><br>
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CHS (Cancer Herbal Screening) is a kit which contains of hela cells as cervical cancer cells and it was designed to screening the plants that have compund potentially for cervical cancer therapy. Herbs that potentially as a therapy of cervical cancer in the kit are marked by the absence of green color, while the negative results are marked by the emergence of green in the kit. The kit is expected to provide convenience to the researchers in the field of cervical cancer and cervical cancer effects can be mitigated with natural compound that not a lot of side effects. <br><br>
From all of above, we bring C3P (Cervical Cancer Program) for iGEM 2014. We named our each project with preventing, screening and therapy. beside, we also do social action in other to socialize our project and be closer to society to inform them how to avoid cervical cancer. <br><br>
From all of above, we bring C3P (Cervical Cancer Program) for iGEM 2014. We named our each project with preventing, screening and therapy. beside, we also do social action in other to socialize our project and be closer to society to inform them how to avoid cervical cancer. <br><br>
The responsible of the scientist is not only the result in the lab, but also share “the right thing” for society. So, thanks to iGEM that gives us an opportunity for doing both, research and social action. <br><br>
The responsible of the scientist is not only the result in the lab, but also share “the right thing” for society. So, thanks to iGEM that gives us an opportunity for doing both, research and social action. <br><br>
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<h2 class="font-thin"><font color="#fff">Overview</font></h2>
<h2 class="font-thin"><font color="#fff">Overview</font></h2>
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<td rowspan="5"><center><img src="https://static.igem.org/mediawiki/2013/7/78/PB_bronzeMedal.gif" width="150" height="200"><br>BRONZE MEDAL</center></td>
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<td>Register for iGEM and attend the Giant Jamboree</td><td><img src="https://static.igem.org/mediawiki/2014/9/9a/UB-Check.PNG" width="" height=""></td>
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<td>Create team wiki</td><td><img src="https://static.igem.org/mediawiki/2014/9/9a/UB-Check.PNG" width="" height=""></td>
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<td>Present a poster and talk at the Giant Jamboree</td><td><img src="https://static.igem.org/mediawiki/2014/6/66/UB-Progress.PNG" width="52" height="43"></td>
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<td>Art and design for synthetic biology</td><td><img src="https://static.igem.org/mediawiki/2014/9/9a/UB-Check.PNG" width="" height=""></td>
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<td>Demonstrate the active engagement of Engineers, Scientists, member of the public and other stakeholder (sponsor)</td><td><img src="https://static.igem.org/mediawiki/2014/9/9a/UB-Check.PNG" width="" height=""></td>
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<td rowspan="5"><center><img src="https://static.igem.org/mediawiki/2013/f/f0/PB_silverMedal.gif" width="150" height="200"><br>SILVER MEDAL</center></td>
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<td>Bronze requirement</td><td><img src="https://static.igem.org/mediawiki/2014/9/9a/UB-Check.PNG" width="" height=""></td>
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<td>Create a short film about or as part at the project and video must be sent to the comitte and iGEM Headquarter</td><td><img src="https://static.igem.org/mediawiki/2014/9/9a/UB-Check.PNG" width="" height=""></td>
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<td>Design and execute a workshop or event for a group of people outside the team</td><td><img src="https://static.igem.org/mediawiki/2014/9/9a/UB-Check.PNG" width="" height=""></td>
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<td>Produce an installation or experiment (contact art design @igem.org to arrange space for presently your project before October 1st</td><td><img src="https://static.igem.org/mediawiki/2014/f/f3/UB-Silang.PNG" width="52" height="43"></td>
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<td rowspan="5"><center><img src="https://static.igem.org/mediawiki/2013/b/b0/PB_goldMedal.gif" width="150" height="200"><br>GOLD MEDAL</center></td>
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<td>Bronze and silver requirement</td><td><img src="https://static.igem.org/mediawiki/2014/6/66/UB-Progress.PNG" width="52" height="43"></td>
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<td>Provoke people to think about synthetic biology & its implication in a new & novel way</td><td><img src="https://static.igem.org/mediawiki/2014/6/66/UB-Progress.PNG" width="52" height="43"></td>
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<td>Collaborate directly with an iGEM team in another track</td><td><img src="https://static.igem.org/mediawiki/2014/9/9a/UB-Check.PNG" width="52" height="43"></td>
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<td>Design new part for iGEM biobrick</td><td><img src="https://static.igem.org/mediawiki/2014/9/9a/UB-Check.PNG" width="52" height="43"></td>
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<td>Human practice about the project</td><td><img src="https://static.igem.org/mediawiki/2014/9/9a/UB-Check.PNG" width="52" height="43"></td>
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</center><br><br>
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<b>Note:</b><br>
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<tr><td><img src="https://static.igem.org/mediawiki/2014/9/9a/UB-Check.PNG" width="52" height="43"></td><td>=</td><td>Done</td></tr>
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<tr><td><img src="https://static.igem.org/mediawiki/2014/6/66/UB-Progress.PNG" width="52" height="43"></td><td>=</td><td>In Progress</td></tr>
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<tr><td><img src="https://static.igem.org/mediawiki/2014/f/f3/UB-Silang.PNG" width="52" height="43"></td><td>=</td><td>Not yet</td></tr>
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                                        </div>
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                                        <h2 class="font-thin"><font color="#fff">Achievement</font></h2>
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                                         <a href="#preventing" class="fancybox"><p><i class="icon icon-shield"></i></p></a>
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<p align="justify">Indonesia is an agricultural country that most of their society works as farmer. Malang is resite at 440-667 (mdpl) altitude, one of the tourist destinations in East Java because of the potential of natural and climatic owned. Malang climate conditions during 2008 temperatures recorded ranging from 22.7 ° C to 25.1 ° C. While the maximum temperature reached 32.7 ° C and minimum temperature of 18.4 ° C. The average air humidity range 79% - 86%. With a maximum moisture content of 99% and a minimum at 40%. These conditions favor the development of the tea plant (Camellia sinensis).</p> <br>
<p align="justify">Indonesia is an agricultural country that most of their society works as farmer. Malang is resite at 440-667 (mdpl) altitude, one of the tourist destinations in East Java because of the potential of natural and climatic owned. Malang climate conditions during 2008 temperatures recorded ranging from 22.7 ° C to 25.1 ° C. While the maximum temperature reached 32.7 ° C and minimum temperature of 18.4 ° C. The average air humidity range 79% - 86%. With a maximum moisture content of 99% and a minimum at 40%. These conditions favor the development of the tea plant (Camellia sinensis).</p> <br>
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<center><img src="https://static.igem.org/mediawiki/2014/e/ed/UB-Tea.PNG" width="" height=""><br>
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<center><img src="https://static.igem.org/mediawiki/2014/f/f8/UB-G1.jpg" height="300"><br>
Figure 1. Tea Plantation in Lawang, Malang City (Department of Electrical Engineering Brawijaya University, 2014)</center><br>
Figure 1. Tea Plantation in Lawang, Malang City (Department of Electrical Engineering Brawijaya University, 2014)</center><br>
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<td><img src="" width="" height=""><br>Figure 2. EGCG structure 2D (National Center for Biotechnology Information, 2005)</td>
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<td><center><img src="https://static.igem.org/mediawiki/2014/3/36/UB-EGCG_structure_2D.png" width="300" height="300"><br>Figure 2. EGCG structure 2D (National Center for Biotechnology Information, 2005)</center></td>
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<td><img src="" width="" height=""><br>Figure 3. EGCG structure 3D (National Center for Biotechnology Information, 2005)</td>
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<td><center><img src="https://static.igem.org/mediawiki/2014/e/e5/EGCG_structure_3D.png" width="300" height="300"><br>Figure 3. EGCG structure 3D (National Center for Biotechnology Information, 2005)</center></td>
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Plasmid A:
Plasmid A:
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<center><img src="https://static.igem.org/mediawiki/2014/f/fc/UB-Plasmid_A.PNG" width="700px" height="300"><br>
Figure 4 Construct design siRNA LAR BBa_K1367004 inserted in pSB1C3<br><br>
Figure 4 Construct design siRNA LAR BBa_K1367004 inserted in pSB1C3<br><br>
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Plasmid A:
Plasmid A:
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<center><img src="https://static.igem.org/mediawiki/2014/6/67/UB-Plasmid_B.PNG" width="700px" height="300"><br>
Figure 5. Construct design siRNA GFP  BBa_K1367005 inserted in pSB1C3<br><br>
Figure 5. Construct design siRNA GFP  BBa_K1367005 inserted in pSB1C3<br><br>
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<h2 class="font-thin"><font color="#fff">Screening</font></h2>
<h2 class="font-thin"><font color="#fff">Screening</font></h2>
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<p align="justify">
<b>Overview Therapy</b><br>
<b>Overview Therapy</b><br>
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CHS (Cancer Herbal Screening) part is design plasmid which contain  promoter P97 (HPV 16) or P105 (HPV 18). This part has ability in screening chemical compounds of plant for cervical cancer therapy. The herbs have to inhibit transcription factor of P97 and P10. Promoter was combained with fluorescence reporter GFP obtained from biobrick Bba_E0240 (Plate 4, well 11N) to detect the successfull of the herbal compounds.  P97 (HPV 16) and P105(HPV 18) were digested with EcoR1-Xbal, GFP digested with Xbal-Spel, and plasmid backbone PSB1C3 digested with EcoR1-Spel. Then, the HPV promoter and GFP was ligated into palsmid backbone PSB1C3. Plasmid design was transfected into HeLa cells containing some transcripton factor to induced promoter. This part was purposed to help researcher work easier to explore herbal plants for cervical cancer therapy.<br>
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Cervical cancer is the one of most killing cause of woman. Approximately, 300.000 people deaths by cervical cancer in every year (Frazer, Cox et al., 2006; Lowy and Schiller, 2006).Cervical cancer caused by Human papillomaviruses (HPV) (Martinez et al., 2008).More than 100 types of HPVs have been identified to date (Dell et al., 2001), but the two most common types in cervical cancer are HPV 16 and 18. HPV type 16 and 18 are high risk type that causecervical cancer (Das, 2003). Both of those type responsible for approximately 70 % of all cases (Smith et al., 2007).<br><br>
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<center><img src="https://static.igem.org/mediawiki/2014/5/52/UB-construct-hps.PNG" width="500" height="300"></center>   
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HPV are small double-stranded DNA viruses that contain of two oncogenes E6 and E7 that are involved in cellular transformation. Two viral genes, E6 and E7 are commonly found expressed in these cancer cells (Song, 2000). Transcription of the human papillomavirus type 16 (HPV-16) genome is controlled by several promoters and the P97 promoter is considered to be the main one (Braunstein et al., 1999). P97 is the HPV-16 early promoter involved in the transcription of E6, E7 and other viral genes (Dell and Gaston, 2011; Flores and Lambert, 1997; Hebner and Laimins, 2006. Based on Laura et al (2005), P105 is located to the next E6 start codon and is the main early promoter of HPV-18. AP-1, Sp-1, NF-1, Oct-1, TEF-1, YY-1, KRF-1, Skn-1a, and TFIID known as transcription factors that could stimulate P105 promoter activity. HPV-18 P105 promoter and HPV-16 P97 promoter has equivalent function. E2 repression of P105 promoter activity has been demonstrated in HeLa cells (Thierry and Yaniv, 1987) and in primary human keratinocytes (Bernard et al., 1989). Romanczuk et al(1990), suggested that P97 and P105 promoters both could be regulated by similar mechanisms. A comparison of the sequences upstream of the HPV-16 P97 promoter and the HPV-18 P105 promoter revealed a similar spatial arrangement of the four E2-binding sites, the TATAAAA boxes, and the start sites for transcription in the respective viral LCRs. (Romanczuk et al, 1990).  Based on Chong et al(1991), trancript factor such as NF1, AP-1, and oct-1 were present in higher concentration in HeLa cells. Therefor, HeLa cells can be used as transfection for promoter P97 and promoter P105 so it could be activated.<br><br>
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Indonesia has many potential herb that potentially used as medicine for cervical cancer.  The major goal ofthis research is to create a kit that can screen herb potentially used as medicine for cervical cancer. It can give early information for researcher, doctor and other practical that can be used as reference to continue the research as well as to give scientific. CHS (Cancer Herbal Screening) part is design plasmid which contain  promoter P97 (HPV 16) or P105 (HPV 18). This part has ability in screening chemical compounds of plant for cervical cancer therapy. The herbs have to inhibit transcription factor of P97 and P10. <br><br>
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Promoter was combained with fluorescence reporter GFP obtained from biobrick Bba_E0240 (Plate 4, well 11N) to detect the successfull of the herbal compounds.  P97 (HPV 16) and P105 (HPV 18) were digested with EcoR1-Xbal, GFP digested with Xbal-Pstl, and plasmid backbone pSB1C3 digested with EcoR1-Pstl. Then, the HPV promoter and GFP was ligated into palsmid backbone pSB1C3. Plasmid design was transfected into HeLa cells containing some transcripton factor to induced promoter. Based on Chong et al (1991), trancript factor such as NF1, AP-1, and oct-1 were present in higher concentration in HeLa cells. Therefor, HeLa cells can be used as transfection for promoter P97 and promoter P105 so it could be activated. This part was purposed to help researcher work easier to explore herbal plants for cervical cancer therapy.</p> <br><br>
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<center><img src="https://static.igem.org/mediawiki/2014/e/ef/UB-overview_therapy.PNG" width="500" height="300"><br>
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Figure 1. Construction of CHS (Cancer Herbal Screening) in pSB1C3
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<b>References :</b><br>
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<ul>
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<li>Bernard, B. A., C. Bailly, M.-C. Lenoir, M. Darmon, F. Thierry, and M. Yaniv. 1989. The human papillomavirus type 18 (HPV18) E2 gene product is a repressor of the HPV18 regulatory region in human keratinocytes. J. Virol  63:4317-4324.</li>
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<li>Braunstein TH, BS Madsen, B Gavnholt, MW Rosenstierne, C Koefoed Johnsen and B norrild. 1999. Identification of a new promoter in the early region of the  human papillomaviruses type 16 genome. Journal of General Virology 80: 3241-3250</li>
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<li>Chong, T., D. Apt, B. Gloss, M. Isa, and H. U. Bernard. 1991. The enhancer of human papillomavirus type 16: binding sites for the ubiquitous transcription factors Oct-1, NFA, TEF-2, NF1, and AP1 participate in epithelial cell-specific transcription. J. Virol. 65:5933–5943. </li>
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<li>Das, B.C. 2003. Cellular control of human papillomavirus gene activity in cervical cancer. Proc.Indian natn Sci Acan. B69 No.1 pp23-24. </li>
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<li>Dell, G., and K. Gaston. 2001. Contributions in the domain of cancer research:review of human papillomaviruses and their role in cervical cancer.Cell. Mol. Life Sci.58:1923–1942. </li>
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<li>Flores, E. R., and P. F. Lambert. 1997. Evidence for a switch in the mode of human papillomavirus type 16 DNA replication during the viral life cycle. J. Virol. 71:7167–7179. </li>
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<li>Frazer, I. H., J. T. Cox, et al. 2006. Advances in prevention of cervical cancer and other human papillomavirus-related diseases.Pediatr Infect Dis J 25(2 Suppl): S65-81, quiz S82. </li>
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<li>Hebner, C. M., and L. A. Laimins. 2006. Human papillomaviruses: basic mechanisms of pathogenesis and oncogenicity. Rev. Med. Virol16:83–97. </li>
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<li>Laura Sichero, Eduardo Luis Franco, and Luisa Lina Villa. 2005. Different P105 Promoter Activities among Natural Variants of Human Papillomavirus Type 18. The Journal of Infectious Diseases191:739–42. </li>
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<li>Lowy, D. R. and J. T. Schiller. 2006. Prophylactic human papillomavirus vaccines. J Clin Invest 116(5): 1167-73. </li>
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<li>Martinez., AS Gardiner, KF Board, FA Monzon, RP Edwards and SA Khan. 2008. Human papillomavirus type 16 reduces the expression of microRNA-218 in cervical carcinoma cells. Oncogene 27:2575-2582</li>
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<li>Romanczuk H., F Thierry and P M Howley. 1990.Mutational analysis of cis elements involved in E2 modulation of human papillomavirus type 16 P97 and type 18 P105 promoters. J. Virol64(6):2849. </li>
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<li>Smith JS, Lindsay L, Hoots B, Keys J, Franceschi S, Winer R, et al. 2007. Human papillomavirus type distribution in invasive cervical cancer and high-grade cervical lesions: a meta-analysis update. International journal of cancer121:621-32. </li>
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<li>Song, Shiyu., Amy Liem, James A., Miller and Paul F Lambert. 2000. Human Papillomavirus Types 16 E6 and E7 Contribute Differently to Carcinogenesis. Virology 267:141-150. </li>
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<li>Thierry, F., and M. Yaniv. 1987. The BPV1-E2 trans-acting protein can be either an activator or a repressor of the HPV 18 regulatory region. EMBO J6:3391-3397. </li>
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<li>Thierry, F., J. M. Heard, K. Dartmann, and M. Yaniv. 1987. Characterization of a transcriptional promoter of human papillomavirus 18 and modulation of its expression by simian virus 40 and adenovirus early antigens. J. Virol61:134-142. </li>
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</ul>
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<h2 class="font-thin"><font color="#fff">Therapy</font></h2>
<h2 class="font-thin"><font color="#fff">Therapy</font></h2>
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<ul>
<ul>
<li>Week 1</li>
<li>Week 1</li>
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Splitting HeLa cells. The confluence HeLa cells (80 – 90%) splitting into another flask then incubate in 37ᵒC.
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Splitting HeLa cells. The confluence HeLa cells (80 – 90%) splitting into another flask then incubate in 37ᵒC.<br>
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<center>https://static.igem.org/mediawiki/2014/0/0f/UB-HELA.jpg</center>
<li>Week 2</li>
<li>Week 2</li>
Cell observation. The splitting HeLa cells observed to control the growth.
Cell observation. The splitting HeLa cells observed to control the growth.
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Figure 4. There are two TALES we tried to synthesize, TALE 1 and TALE 2. Every TALE has triplo but only T1-2, T2-1, and T2-2 succesfully assembled.</center><br>
Figure 4. There are two TALES we tried to synthesize, TALE 1 and TALE 2. Every TALE has triplo but only T1-2, T2-1, and T2-2 succesfully assembled.</center><br>
<p align="justify">
<p align="justify">
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We collected as many as possible references for the application content. Our application is android mobile based and we started to encode it. The application consist of preventing and therapy suggestion also screening method information. Special feature from our application is snap tool that can detect the kit result.
+
We collected as many as possible references for the application content. Our application is android mobile based and we started to encode it. The application consist of preventing and therapy suggestion also screening method information. Special feature from our application is snap tool that can detect the kit result.<br><br>
 +
 
 +
<b>July Week 1– August</b><br>
 +
<table width="100%">
 +
<tr><td>Discussion about the material and tool which complete the task of the devices. We  looked for some well known, user friendly, easy handle, effective, and efficient. We also get some material recommendation and suggestion for our device. Then, by some review and consideration, we decided to use a test pack for the tool (hardware) and colour intensity as the diagnostic result.</td>
 +
<td><img src="https://static.igem.org/mediawiki/2014/4/49/Ub-Test_pack_1.jpg" width="400" height="200"></td></tr>
 +
 
 +
</table><br>
 +
 
 +
<b>August 4th – August 8th (Week 2)</b><br>
 +
<table width="100%">
 +
<tr><td><img src="https://static.igem.org/mediawiki/2014/5/56/UB-Test_pack_2.jpg" width="400" height="150"></td>
 +
<td>Chose and bought some test pack to be learned. Here, we got some model of test pack to study and determine the model from one of common trademark as the basic model of ours.</td></tr>
 +
</table><br>
 +
 
 +
<b>September 8th – September 12th  (Week 2)</b><br>
 +
We try to put the enzyme into model and observed the result. We performed some test in different variable to determine its reliability.<br>
 +
<table width="100%">
 +
<tr><td align="right"><img src="https://static.igem.org/mediawiki/2014/d/db/UB-TP_1.jpg" width="300" height="100"></td>
 +
<td><img src="https://static.igem.org/mediawiki/2014/8/8c/UB-TP_2.jpg" width="300" height="100"></td></tr>
 +
<tr><td align="right"><img src="https://static.igem.org/mediawiki/2014/0/02/UB-TP_3.jpg" width="300" height="100"></td>
 +
<td><img src="https://static.igem.org/mediawiki/2014/7/77/UB-TP_4.jpg" width="300" height="100"></td></tr>
 +
</table><br>
 +
 
 +
<b>September 15th – September 19th (Week 3)</b><br>
 +
Still continue to test the device and get more result.<br><br>
 +
 
 +
<b>September 22nd – September 26th (Week 4)</b><br>
 +
Get some suggestion and more explanation from our lecturer in Biology about the result <br><br>
 +
 
 +
<b>September 29th – October 3rd </b><br>
 +
Performed stability test to know more about the device. We even did it with a little various differentiation.<br><br>
 +
 
 +
<b>October 2th – October 5th  (Week 1)</b><br>
 +
We designed the software content and review it from some journals and articles.<br>
 +
<center>
 +
<img src="https://static.igem.org/mediawiki/2014/c/cf/Ub-software1.jpg" width="300" height="500"><br><br>
 +
<img src="https://static.igem.org/mediawiki/2014/1/1e/Ub-software2.jpg" width="300" height="500"><br><br>
 +
<img src="https://static.igem.org/mediawiki/2014/d/da/Ub-software3.jpg" width="300" height="500"><br><br>
 +
<img src="https://static.igem.org/mediawiki/2014/4/41/Ub-software4.jpg" width="300" height="500"><br><br>
 +
<img src="https://static.igem.org/mediawiki/2014/c/c9/Ub-software5.jpg" width="300" height="500"><br><br>
 +
</center>
 +
 
 +
<b>October 6th – October 10th  (Week 2)</b><br>
 +
Collected the results and put it into results table to be presented.<br>
 +
We try to develop the software with ECLIPSE program .<br><br>
</p>
</p>
</ul>
</ul>
Line 453: Line 598:
<li>Mix well and spin down.</li>
<li>Mix well and spin down.</li>
<li>Incubate the restriction digest at 37˚C for 30minutes, and then 80˚C for 20minutes.</li>
<li>Incubate the restriction digest at 37˚C for 30minutes, and then 80˚C for 20minutes.</li>
-
<li>Arranges sequence of P97 and P105 then combined with restriction enzyme sequence (EcoRI and Xbal). Order the synthetic sequence into IDT (Integrated DNA Technology). </li>
 
-
<li>Getting P97 and P105 synthetic sequence from IDT. </li>
 
-
<li>Ligase the P97 and P105 synthetic sequence into PJET plasmid vector. Each plasmid vector ligase with P97 sequence or P105 sequence. Cloned. </li>
 
-
<li>Digest the plasmid vector that contain of P97 and P105 synthetic sequence with restriction enzyme EcoRI and Xbal. Then, digest the PSB1C3 plasmid backbone with same restriction enzyme. </li>
 
-
<li>Confirm the digested P97 and P105 synthetic sequence and PSB1C3 plasmid backbone using electrophoresis. </li>
 
-
<li>The electrophoresis gel which contain of digested P97 and P105 synthetic sequence and PSB1C3 plasmid backbone, extraction using DNA extraction gel kit. </li>
 
-
<li>Ligase the P97 and P105 synthetic sequence with PSB1C3 plasmid backbone become reccombination plasmid. </li>
 
-
<li>Comfirm the reccombination plasmid using electrophoresis and cloned.</li>
 
-
 
</ul><br>
</ul><br>
<b>SiRNADigestion</b><br>
<b>SiRNADigestion</b><br>
Line 752: Line 888:
<p align="justify">UB iGEM Team had collaboration with UI iGEM Team and ITB iGEM team in holding Synthetic Biology for Indonesia Community. The aim of this community is to form a synthetic biology  association in Indonesia.Programs that have been done previously is an online course in facebook group named “Synthetic Biology for Indonesia” and already got approximately 121 members from all over Indonesia.<br><br>
<p align="justify">UB iGEM Team had collaboration with UI iGEM Team and ITB iGEM team in holding Synthetic Biology for Indonesia Community. The aim of this community is to form a synthetic biology  association in Indonesia.Programs that have been done previously is an online course in facebook group named “Synthetic Biology for Indonesia” and already got approximately 121 members from all over Indonesia.<br><br>
For developing this community, we conducted a forum for us to meet up with others synbio community all over Indonesia. This forum (meet up) was initiated by UB iGEM Team, ITB iGEM Team and UI iGEM Team. For this year, 2014, the meeting was held in Brawijaya University, Malang, East Java, Indonesia on September, 27th 2014. The event combined with seminar and workshop in synthetic biology. We also invited synthetic biology community of Gadjah Mada University, synthetic biology community of Sumbawa Technology University, Biology department of Airlangga University and Biology department of State of Malang University.<br><br>
For developing this community, we conducted a forum for us to meet up with others synbio community all over Indonesia. This forum (meet up) was initiated by UB iGEM Team, ITB iGEM Team and UI iGEM Team. For this year, 2014, the meeting was held in Brawijaya University, Malang, East Java, Indonesia on September, 27th 2014. The event combined with seminar and workshop in synthetic biology. We also invited synthetic biology community of Gadjah Mada University, synthetic biology community of Sumbawa Technology University, Biology department of Airlangga University and Biology department of State of Malang University.<br><br>
-
We tend to do annual meet up for discussing anything about synthetic biology, start from research until social action. In the other hand, each of the university member will link together to be strengthen community and cooperate with government, practitioners and scientist in Indonesia.</p>
+
We tend to do annual meet up for discussing anything about synthetic biology, start from research until social action. In the other hand, each of the university member will link together to be strengthen community and cooperate with government, practitioners and scientist in Indonesia.</p><br><br>
 +
<b>Collaboration part with ITB teams are some cloned parts :</b><br>
 +
<ul>
 +
<li> Syntethic sequence (P97 and P105) inserted into plasmid pJET.</li>
 +
<li> GFP reporter in plate 4 well 11N inserted into plasmid PSB1A3 with Ampicillin resistance.</li>
 +
<li> Promoter CMV in plate 1 well 21P inserted into PSB1C3 with chloramphenicol resistance.</li>
 +
</ul>
 +
"We acknowledge to all members of IGEM ITB team for helping us doing of parts project."<br><br>
 +
 
 +
For developing TALE 1 and TALE 2, we've got the material- GATE Assembly Kit, pTALEN and pTAL-TF -from BIOSS at University of Freiburg by Nicole Gensch. <br>
 +
<img src="https://static.igem.org/mediawiki/2014/d/dd/UB-Bioss.jpg" height="200" width="400">
 +
 
                                         </div>
                                         </div>
<h2 class="font-thin"><font color="#fff">SYNBIO FOR INDONESIA</font></h2>
<h2 class="font-thin"><font color="#fff">SYNBIO FOR INDONESIA</font></h2>
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<a href="#fav-parts" class="fancybox"><p><i class="icon icon-group"></i></p></a>
<a href="#fav-parts" class="fancybox"><p><i class="icon icon-group"></i></p></a>
                                         <div id="fav-parts" style="display:none;width:700px;">
                                         <div id="fav-parts" style="display:none;width:700px;">
-
<h2><center>“”</center></h2>
+
<h2><center>Favorite Parts</center></h2><br>
-
<p align="justify"></p>
+
<a href="http://parts.igem.org/Part:BBa_E0240:Design"><b>Bba_E0240 GFP_Generator </b></a><br><br>
 +
<center>
 +
<img src="https://static.igem.org/mediawiki/2014/0/0b/UB-GFP_1.PNG" width="200" height="100"><br>
 +
<img src="https://static.igem.org/mediawiki/2014/d/d9/UB-GFP-PLASMID_2.PNG" width="500" height="500"></center><br><br>
 +
 
 +
<a href="http://parts.igem.org/Part:BBa_K747012"><b>Bba_K747012 TALE_Protein_TA1_Direpeat </b></a><br><br>
 +
<center><img src="https://static.igem.org/mediawiki/2014/9/9b/UB-TALE-PLASMID_2.PNG" width="500" height="500"></center>
                                         </div>
                                         </div>
<h2 class="font-thin"><font color="#fff">Favorite Parts</font></h2>
<h2 class="font-thin"><font color="#fff">Favorite Parts</font></h2>
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<a href="#testimoni" class="fancybox"><p><i class="icon icon-comment"></i></p></a>
<a href="#testimoni" class="fancybox"><p><i class="icon icon-comment"></i></p></a>
                                         <div id="testimoni" style="display:none;width:700px;">
                                         <div id="testimoni" style="display:none;width:700px;">
 +
<h2>What People Says About iGEM UB ?</h2><br>
 +
<ul>
 +
<li><b>GAMANANTA Support UB iGEM Team 2014</b></li><br>
 +
<center><img src="https://static.igem.org/mediawiki/2014/0/0f/UB-GAMANANTA.jpg" width="500" height="200"></center><br>
 +
<p align="justify">
 +
When i was a child, i’m educated by my parents about the importance of healthiness. Because we believe that healthiness is expensive. Therefore, eventhough we can not avoid sickness, prevention action is better than curing. Especially disease that spread by HPV virus on cervical cancer which generally attacks women. Men can also suffered from this disease.<br><br>
 +
Seeing the description of the outline of project brought by the IGEM team Biology FMIPA at UB, I become understand how important their steps. The program brings the C3P (Cervical Cancer Care - Preventing, Screening, Treatment) that are currently in progress of development, IGEM team Biology FMIPA offers a real solution on prevention of cervical cancer at early stages. A solution with a very good prospect. Shows the path of the light that prevention is indeed better.<br><br>
 +
For me personally, with GAMANANTA friends as travelling community that loves to have a trip, fully support that program. I openly invite friends to not underestimate cervical cancer because its deadly impact. We often underestimate influenza that can disturb our trip. It will not very sad if our dream travel to various quarters of destination both domestic and foreign disturbed by the presence of a virus diseases might threaten at any time.<br><br>
 +
I hope, among IGEM team Biology FMIPA UB and their program objectives could have a positive relation. Thus, it feel easier if both components work together. Awareness program objectives are not easily changed, but does not mean impossible. And C3P development program is one solutive step to increase awareness of program objectives . Time to beat the "drums of war" against cervical cancer and together achieve a better future.<br><br></p>
 +
<p align="left">Warm regards,<br>
 +
<b>Rifqy Faiza Rahman<br>
 +
Founder & Commissioner of GAMANANTA</b></p><br><br>
 +
<li><b>YPKAI Support UB iGEM Team 2014</b></li><br>
 +
<center><img src="https://static.igem.org/mediawiki/2014/e/e3/UB-YPKAI.jpg" width="500" height="200"></center><br>
 +
<p align="justify">"Salute to UB team for the attention and care in cervical cancer, especially this cancer increasingly higher numbers of sufferers. Hopefully the research can have a positive effect in reducing the risk and treatment of cancer, as well as support the careness of cancer risk which threaten anyone from amongst any and all ages. Hopefully the results of this work can also inspire young people of Indonesia to continue to work for the nation and each other."</p><br><br>
 +
<p align="left">Warm regards,<br>
 +
<b>Indonesia Child Cancer Care (YPKAI)<br>
 +
Together reaching hope for kid with cancer</b></p>
 +
</ul>
                                         </div>
                                         </div>
<h2 class="font-thin"><font color="#fff">People Says</font></h2>
<h2 class="font-thin"><font color="#fff">People Says</font></h2>

Latest revision as of 01:15, 18 October 2014

iGEM2014 | UB INDONESIA

BRAWIJAYA UNIVERSITY , INDONESIA

This is team wiki to share our iGEM experience



iGEM UB
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iGEM2014
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