Difference between revisions of "Team:Thrace/Project Design"

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<img src="https://static.igem.org/mediawiki/2021/2/26/T--Thrace--design.png" style="width: 100%">
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<div style="padding: 10% 10% 5%; border-top: 5px dashed #F3BBAE; border-bottom: 5px dashed #F3BBAE;">
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    <p style+="color: #26456C;
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    font-size: 35px;
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    line-height: 45px;
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    text-align: left;">References
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    </p>
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    <ol style="color: #26456C;
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        text-align: left;">
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            Wu, J., Li, Q., & Fu, X. (2019). Fusobacterium nucleatum Contributes to the Carcinogenesis of Colorectal
 +
            Cancer by Inducing Inflammation and Suppressing Host Immunity. Translational Oncology, 12(6), 846-851.
 +
            <a href="https://doi.org/10.1016/j.tranon.2019.03.003">
 +
                https://doi.org/10.1016/j.tranon.2019.03.003</a>
 +
        </li>
 +
        <li style="color: #47525E;
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        font-size: 26px;
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        line-height: 33px;
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        width: 1168px;
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        text-align: left;">
 +
            Mima, K., Nishihara, R., Qian, Z., Cao, Y., Sukawa, Y., & Nowak, J. et al. (2021). Fusobacterium nucleatum
 +
            in colorectal carcinoma tissue and patient prognosis.
 +
 +
        </li>
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        <li style="color: #47525E;
 +
        font-size: 26px;
 +
        line-height: 33px;
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        width: 1168px;
 +
        text-align: left;">
 +
            Komiya, Y., Shimomura, Y., Higurashi, T., Sugi, Y., Arimoto, J., & Umezawa, S. et al. (2018). Patients with
 +
            colorectal cancer have identical strains of Fusobacterium nucleatum in their colorectal cancer and oral
 +
            cavity. Gut, 68(7), 1335-1337.
 +
            <a href="https://doi.org/10.1136/gutjnl-2018-316661">
 +
                https://doi.org/10.1136/gutjnl-2018-316661</a>
 +
        </li>
 +
        <li style="color: #47525E;
 +
        font-size: 26px;
 +
        line-height: 33px;
 +
        width: 1168px;
 +
        text-align: left;">
 +
            Guven, D., Dizdar, O., Alp, A., Akdoğan Kittana, F., Karakoc, D., & Hamaloglu, E. et al. (2019). Analysis of
 +
            Fusobacterium nucleatum and Streptococcus gallolyticus in saliva of colorectal cancer patients. Biomarkers
 +
            In Medicine, 13(9), 725-735.
 +
            <a href="https://doi.org/10.2217/bmm-2019-0020">
 +
                https://doi.org/10.2217/bmm-2019-0020</a>
 +
        </li>
 +
        <li style="color: #47525E;
 +
        font-size: 26px;
 +
        line-height: 33px;
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        width: 1168px;
 +
        text-align: left;">
 +
            Castellarin, M., Warren, R., Freeman, J., Dreolini, L., Krzywinski, M., & Strauss, J. et al. (2011).
 +
            Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Research, 22(2),
 +
            299-306.
 +
            <a href="https://doi.org/10.1101/gr.126516.111">
 +
                https://doi.org/10.1101/gr.126516.111</a>
 +
        </li>
 +
        <li style="color: #47525E;
 +
        font-size: 26px;
 +
        line-height: 33px;
 +
        width: 1168px;
 +
        text-align: left;">
 +
            Rapado-González, Majem, Álvarez-Castro, Díaz-Peña, Abalo, & Suárez-Cabrera et al. (2019). A Novel
 +
            Saliva-Based miRNA Signature for Colorectal Cancer Diagnosis. Journal Of Clinical Medicine, 8(12), 2029.
 +
            <a href="https://doi.org/10.3390/jcm8122029">
 +
                https://doi.org/10.3390/jcm8122029</a>
 +
        </li>
 +
        <li style="color: #47525E;
 +
        font-size: 26px;
 +
        line-height: 33px;
 +
        width: 1168px;
 +
        text-align: left;">
 +
            Sazanov, A., Kiselyova, E., Zakharenko, A., Romanov, M., & Zaraysky, M. (2016). Plasma and saliva miR-21
 +
            expression in colorectal cancer patients. Journal Of Applied Genetics, 58(2), 231-237.
 +
            <a href="https://doi.org/10.1007/s13353-016-0379-9">
 +
                https://doi.org/10.1007/s13353-016-0379-9</a>
 +
        </li>
 +
        <li style="color: #47525E;
 +
        font-size: 26px;
 +
        line-height: 33px;
 +
        width: 1168px;
 +
        text-align: left;">
 +
            Kellner, M., Koob, J., Gootenberg, J., Abudayyeh, O., & Zhang, F. (2019). SHERLOCK: nucleic acid detection
 +
            with CRISPR nucleases. Nature Protocols, 14(10), 2986-3012.
 +
            <a href="https://doi.org/10.1038/s41596-019-0210-2">
 +
                https://doi.org/10.1038/s41596-019-0210-2</a>
 +
        </li>
 +
        <li style="color: #47525E;
 +
        font-size: 26px;
 +
        line-height: 33px;
 +
        width: 1168px;
 +
        text-align: left;">
 +
            Lobato, I., & O'Sullivan, C. (2018). Recombinase polymerase amplification: Basics, applications and recent
 +
            advances. Trac Trends In Analytical Chemistry, 98, 19-35.
 +
            <a href="https://doi.org/10.1016/j.trac.2017.10.015">
 +
                https://doi.org/10.1016/j.trac.2017.10.015</a>
 +
        </li>
 +
        <li style="color: #47525E;
 +
        font-size: 26px;
 +
        line-height: 33px;
 +
        width: 1168px;
 +
        text-align: left;">
 +
            Abd El Wahed, A., El-Deeb, A., El-Tholoth, M., Abd El Kader, H., Ahmed, A., & Hassan, S. et al. (2013). A
 +
            Portable Reverse Transcription Recombinase Polymerase Amplification Assay for Rapid Detection of
 +
            Foot-and-Mouth Disease Virus. Plos ONE, 8(8), e71642.
 +
            <a href="https://doi.org/10.1371/journal.pone.0071642">
 +
                https://doi.org/10.1371/journal.pone.0071642</a>
 +
        </li>
 +
        <li style="color: #47525E;
 +
        font-size: 26px;
 +
        line-height: 33px;
 +
        width: 1168px;
 +
        text-align: left;">
 +
            Daher, R., Stewart, G., Boissinot, M., & Bergeron, M. (2016). Recombinase Polymerase Amplification for
 +
            Diagnostic Applications. Clinical Chemistry, 62(7), 947-958.
 +
            <a href="https://doi.org/10.1373/clinchem.2015.24582">
 +
                https://doi.org/10.1373/clinchem.2015.24582</a>
 +
        </li>
 +
        <li style="color: #47525E;
 +
        font-size: 26px;
 +
        line-height: 33px;
 +
        width: 1168px;
 +
        text-align: left;">
 +
            Huang, S., Yang, Z., Zou, D., Dong, D., Liu, A., Liu, W., & Huang, L. (2016). Rapid detection of nusG and
 +
            fadA in Fusobacterium nucleatum by loop-mediated isothermal amplification. Journal Of Medical Microbiology,
 +
            65(8), 760-769.
 +
            <a href="https://doi.org/10.1099/jmm.0.000300">
 +
                https://doi.org/10.1099/jmm.0.000300</a>
 +
        </li>
 +
        <li style="color: #47525E;
 +
        font-size: 26px;
 +
        line-height: 33px;
 +
        width: 1168px;
 +
        text-align: left;">
 +
            Li, H., Xing, S., Xu, J., He, Y., Lai, Y., & Wang, Y. et al. (2021). Aptamer-based CRISPR/Cas12a assay for
 +
            the ultrasensitive detection of extracellular vesicle proteins. Talanta, 221, 121670.
 +
            <a href="https://doi.org/10.1016/j.talanta.2020.121670">
 +
                https://doi.org/10.1016/j.talanta.2020.121670</a>
 +
        </li>
 +
        <li style="color: #47525E;
 +
        font-size: 26px;
 +
        line-height: 33px;
 +
        width: 1168px;
 +
        text-align: left;">
 +
            Dai, Y., Somoza, R., Wang, L., Welter, J., Li, Y., Caplan, A., & Liu, C. (2019). Exploring the
 +
            Trans‐Cleavage Activity of CRISPR‐Cas12a (cpf1) for the Development of a Universal Electrochemical
 +
            Biosensor. Angewandte Chemie, 131(48), 17560-17566.
 +
            <a href="https://doi.org/10.1002/ange.201910772">
 +
                https://doi.org/10.1002/ange.201910772</a>
 +
        </li>
 +
        <li style="color: #47525E;
 +
        font-size: 26px;
 +
        line-height: 33px;
 +
        width: 1168px;
 +
        text-align: left;">
 +
            Concordet, J., & Haeussler, M. (2018). CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing
 +
            experiments and screens. Nucleic Acids Research, 46(W1), W242-W245.
 +
            <a href="https://doi.org/10.1093/nar/gky354">
 +
                https://doi.org/10.1093/nar/gky354</a>
 +
        </li>
 +
        <li style="color: #47525E;
 +
        font-size: 26px;
 +
        line-height: 33px;
 +
        width: 1168px;
 +
        text-align: left;">
 +
            De Puig, H., Lee, R., Najjar, D., Tan, X., Soenksen, L., & Angenent-Mari, N. et al. (2021). Minimally
 +
            instrumented SHERLOCK (miSHERLOCK) for CRISPR-based point-of-care diagnosis of SARS-CoV-2 and emerging
 +
            variants. Science Advances, 7(32).
 +
            <a href="https://doi.org/10.1126/sciadv.abh2944">
 +
                https://doi.org/10.1126/sciadv.abh2944</a>
 +
        </li>
 +
        <li style="color: #47525E;
 +
        font-size: 26px;
 +
        line-height: 33px;
 +
        width: 1168px;
 +
        text-align: left;">
 +
            Kramer, M. (2011). Stem‐Loop RT‐qPCR for miRNAs. Current Protocols In Molecular Biology, 95(1).
 +
            <a href="https://doi.org/10.1002/0471142727.mb1510s95">
 +
                https://doi.org/10.1093/nar/gni178</a>
 +
        </li>
 +
        <li style="color: #47525E;
 +
        font-size: 26px;
 +
        line-height: 33px;
 +
        width: 1168px;
 +
        text-align: left;">
 +
            Chen, C. (2005). Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Research, 33(20),
 +
            e179-e179.
 +
            <a href="https://doi.org/10.1093/nar/gni178">
 +
                https://doi.org/10.1093/nar/gni178</a>
 +
        </li>
 +
    </ol>
 +
    <p style="color: #47525E;
 +
    font-size: 26px;
 +
    line-height: 33px;
 +
    width: 1168px;
 +
    text-align: left;">Figure 1: RPA mechanism
 +
        Bhat A.I., Rao G.P. (2020) Recombinase Polymerase Amplification. In: Characterization of Plant Viruses. Springer
 +
        Protocols Handbooks. Humana, New York, NY.
 +
        <a href="https://doi.org/10.1007/978-1-0716-0334-5_40">
 +
            https://doi.org/10.1007/978-1-0716-0334-5_40</a>
 +
    </p>
 +
    <p style="color: #47525E;
 +
    font-size: 26px;
 +
    line-height: 33px;
 +
    width: 1168px;
 +
    text-align: left;">Figure 2: SHERLOCK mechanism
 +
        Mustafa, M., & Makhawi, A. (2021). SHERLOCK and DETECTR: CRISPR-Cas Systems as Potential Rapid Diagnostic Tools
 +
        for Emerging Infectious Diseases. Journal Of Clinical Microbiology, 59(3).
 +
        <a href="https://doi.org/10.1128/jcm.00745-20">
 +
            https://doi.org/10.1128/jcm.00745-20 </a>
 +
    </p>
 +
</div>
  
 
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Latest revision as of 03:32, 22 October 2021

References

  1. Wu, J., Li, Q., & Fu, X. (2019). Fusobacterium nucleatum Contributes to the Carcinogenesis of Colorectal Cancer by Inducing Inflammation and Suppressing Host Immunity. Translational Oncology, 12(6), 846-851. https://doi.org/10.1016/j.tranon.2019.03.003
  2. Mima, K., Nishihara, R., Qian, Z., Cao, Y., Sukawa, Y., & Nowak, J. et al. (2021). Fusobacterium nucleatum in colorectal carcinoma tissue and patient prognosis.
  3. Komiya, Y., Shimomura, Y., Higurashi, T., Sugi, Y., Arimoto, J., & Umezawa, S. et al. (2018). Patients with colorectal cancer have identical strains of Fusobacterium nucleatum in their colorectal cancer and oral cavity. Gut, 68(7), 1335-1337. https://doi.org/10.1136/gutjnl-2018-316661
  4. Guven, D., Dizdar, O., Alp, A., Akdoğan Kittana, F., Karakoc, D., & Hamaloglu, E. et al. (2019). Analysis of Fusobacterium nucleatum and Streptococcus gallolyticus in saliva of colorectal cancer patients. Biomarkers In Medicine, 13(9), 725-735. https://doi.org/10.2217/bmm-2019-0020
  5. Castellarin, M., Warren, R., Freeman, J., Dreolini, L., Krzywinski, M., & Strauss, J. et al. (2011). Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Research, 22(2), 299-306. https://doi.org/10.1101/gr.126516.111
  6. Rapado-González, Majem, Álvarez-Castro, Díaz-Peña, Abalo, & Suárez-Cabrera et al. (2019). A Novel Saliva-Based miRNA Signature for Colorectal Cancer Diagnosis. Journal Of Clinical Medicine, 8(12), 2029. https://doi.org/10.3390/jcm8122029
  7. Sazanov, A., Kiselyova, E., Zakharenko, A., Romanov, M., & Zaraysky, M. (2016). Plasma and saliva miR-21 expression in colorectal cancer patients. Journal Of Applied Genetics, 58(2), 231-237. https://doi.org/10.1007/s13353-016-0379-9
  8. Kellner, M., Koob, J., Gootenberg, J., Abudayyeh, O., & Zhang, F. (2019). SHERLOCK: nucleic acid detection with CRISPR nucleases. Nature Protocols, 14(10), 2986-3012. https://doi.org/10.1038/s41596-019-0210-2
  9. Lobato, I., & O'Sullivan, C. (2018). Recombinase polymerase amplification: Basics, applications and recent advances. Trac Trends In Analytical Chemistry, 98, 19-35. https://doi.org/10.1016/j.trac.2017.10.015
  10. Abd El Wahed, A., El-Deeb, A., El-Tholoth, M., Abd El Kader, H., Ahmed, A., & Hassan, S. et al. (2013). A Portable Reverse Transcription Recombinase Polymerase Amplification Assay for Rapid Detection of Foot-and-Mouth Disease Virus. Plos ONE, 8(8), e71642. https://doi.org/10.1371/journal.pone.0071642
  11. Daher, R., Stewart, G., Boissinot, M., & Bergeron, M. (2016). Recombinase Polymerase Amplification for Diagnostic Applications. Clinical Chemistry, 62(7), 947-958. https://doi.org/10.1373/clinchem.2015.24582
  12. Huang, S., Yang, Z., Zou, D., Dong, D., Liu, A., Liu, W., & Huang, L. (2016). Rapid detection of nusG and fadA in Fusobacterium nucleatum by loop-mediated isothermal amplification. Journal Of Medical Microbiology, 65(8), 760-769. https://doi.org/10.1099/jmm.0.000300
  13. Li, H., Xing, S., Xu, J., He, Y., Lai, Y., & Wang, Y. et al. (2021). Aptamer-based CRISPR/Cas12a assay for the ultrasensitive detection of extracellular vesicle proteins. Talanta, 221, 121670. https://doi.org/10.1016/j.talanta.2020.121670
  14. Dai, Y., Somoza, R., Wang, L., Welter, J., Li, Y., Caplan, A., & Liu, C. (2019). Exploring the Trans‐Cleavage Activity of CRISPR‐Cas12a (cpf1) for the Development of a Universal Electrochemical Biosensor. Angewandte Chemie, 131(48), 17560-17566. https://doi.org/10.1002/ange.201910772
  15. Concordet, J., & Haeussler, M. (2018). CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens. Nucleic Acids Research, 46(W1), W242-W245. https://doi.org/10.1093/nar/gky354
  16. De Puig, H., Lee, R., Najjar, D., Tan, X., Soenksen, L., & Angenent-Mari, N. et al. (2021). Minimally instrumented SHERLOCK (miSHERLOCK) for CRISPR-based point-of-care diagnosis of SARS-CoV-2 and emerging variants. Science Advances, 7(32). https://doi.org/10.1126/sciadv.abh2944
  17. Kramer, M. (2011). Stem‐Loop RT‐qPCR for miRNAs. Current Protocols In Molecular Biology, 95(1). https://doi.org/10.1093/nar/gni178
  18. Chen, C. (2005). Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Research, 33(20), e179-e179. https://doi.org/10.1093/nar/gni178

Figure 1: RPA mechanism Bhat A.I., Rao G.P. (2020) Recombinase Polymerase Amplification. In: Characterization of Plant Viruses. Springer Protocols Handbooks. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0334-5_40

Figure 2: SHERLOCK mechanism Mustafa, M., & Makhawi, A. (2021). SHERLOCK and DETECTR: CRISPR-Cas Systems as Potential Rapid Diagnostic Tools for Emerging Infectious Diseases. Journal Of Clinical Microbiology, 59(3). https://doi.org/10.1128/jcm.00745-20

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