Guide selection using a CRISPRa system to activate parkin gene related to parkinson's disease
Parkinson's Disease (PD) is a neurodegenerative disorder that causes a loss in motor capabilities, tremors, bradykinesia, cognitive capacity, and sometimes dementia. The Parkin gene is an essential gene that has a fundamental role in the ubiquitination of proteins and the maintenance of mitocho...
- Autores:
-
Sotelo Montero, Sebastián
- Tipo de recurso:
- Trabajo de grado de pregrado
- Fecha de publicación:
- 2023
- Institución:
- Universidad de los Andes
- Repositorio:
- Séneca: repositorio Uniandes
- Idioma:
- eng
- OAI Identifier:
- oai:repositorio.uniandes.edu.co:1992/64471
- Acceso en línea:
- http://hdl.handle.net/1992/64471
- Palabra clave:
- CRISPRa
DH10B
E. coli
Parkinson's disease
DH5 alpha
Microbiología
- Rights
- openAccess
- License
- Attribution-NonCommercial-NoDerivatives 4.0 Internacional
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Guide selection using a CRISPRa system to activate parkin gene related to parkinson's disease |
| title |
Guide selection using a CRISPRa system to activate parkin gene related to parkinson's disease |
| spellingShingle |
Guide selection using a CRISPRa system to activate parkin gene related to parkinson's disease CRISPRa DH10B E. coli Parkinson's disease DH5 alpha Microbiología |
| title_short |
Guide selection using a CRISPRa system to activate parkin gene related to parkinson's disease |
| title_full |
Guide selection using a CRISPRa system to activate parkin gene related to parkinson's disease |
| title_fullStr |
Guide selection using a CRISPRa system to activate parkin gene related to parkinson's disease |
| title_full_unstemmed |
Guide selection using a CRISPRa system to activate parkin gene related to parkinson's disease |
| title_sort |
Guide selection using a CRISPRa system to activate parkin gene related to parkinson's disease |
| dc.creator.fl_str_mv |
Sotelo Montero, Sebastián |
| dc.contributor.advisor.none.fl_str_mv |
Bloch Morel, Natasha Ivonne Bernal Giraldo, Adriana Jimena |
| dc.contributor.author.none.fl_str_mv |
Sotelo Montero, Sebastián |
| dc.contributor.other.none.fl_str_mv |
Esmeral Lascano, Natalia Paola |
| dc.contributor.researchgroup.es_CO.fl_str_mv |
Neurogenética y Comportamiento |
| dc.subject.keyword.none.fl_str_mv |
CRISPRa DH10B E. coli Parkinson's disease DH5 alpha |
| topic |
CRISPRa DH10B E. coli Parkinson's disease DH5 alpha Microbiología |
| dc.subject.themes.es_CO.fl_str_mv |
Microbiología |
| description |
Parkinson's Disease (PD) is a neurodegenerative disorder that causes a loss in motor capabilities, tremors, bradykinesia, cognitive capacity, and sometimes dementia. The Parkin gene is an essential gene that has a fundamental role in the ubiquitination of proteins and the maintenance of mitochondria. Mutations in the Parkin gene are related to PD. In this study, we got the required DNA to activate the Parkin gene through a CRISPR activation system as a therapeutical objective. We show that using the DH5 alpha strain of E. coli is not the best option to transform and clone the plasmids that have the genetic information. The DH10B strain is a better option for obtaining linearized DNA. It strains requires fewer steps to achieve colonies with the plasmid, and the amount of DNA recovered is notably more significant than with the DH5 alpha. |
| publishDate |
2023 |
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2023-02-01T15:30:54Z |
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2023-02-01T15:30:54Z |
| dc.date.issued.none.fl_str_mv |
2023-01-31 |
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Trabajo de grado - Pregrado |
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info:eu-repo/semantics/bachelorThesis |
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info:eu-repo/semantics/acceptedVersion |
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http://hdl.handle.net/1992/64471 |
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eng |
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| dc.relation.references.es_CO.fl_str_mv |
Bittar, A. F., Bloch, N. I., Reyes, L. H., & Bernal, A. J. (2020.). Diseño y construcción de sistemas CRISPRa y CRISPRi para el desarrollo de una terapia génica para el Parkinson. TESIS DE GRADO PARA OPTAR EL TÍTULO DE: Microbiólogo. Universidad de los Andes. Dawson, T. M., & Dawson, V. L. (2010). The role of parkin in familial and sporadic Parkinson's disease. Movement Disorders, 25(SUPPL. 1). https://doi.org/10.1002/mds.22798 Durfee, T., Nelson, R., Baldwin, S., Plunkett, G., Burland, V., Mau, B., Petrosino, J. F., Qin, X., Muzny, D. M., Ayele, M., Gibbs, R. A., Csörgo, B., Pósfai, G., Weinstock, G. M., & Blattner, F. R. (2008). The complete genome sequence of Escherichia coli DH10B: Insights into the biology of a laboratory workhorse. Journal of Bacteriology, 190(7), 2597-2606. https://doi.org/10.1128/JB.01695-07 Dy, Lady, Chalasani, S., & Essani, K. (1993). Isolation of Escherichia coli mutants lacking methylcytosine-dependent restriction systems for cloning extensively methylated frog virus 3 DNA. Gene, 131(1), 87-91. https://doi.org/https://doi.org/10.1016/0378-1119(93)90673-Q Fields, C. R., Bengoa-Vergniory, N., & Wade-Martins, R. (2019). Targeting Alpha-Synuclein as a Therapy for Parkinson's Disease. In Frontiers in Molecular Neuroscience (Vol. 12). Frontiers Media S.A. https://doi.org/10.3389/fnmol.2019.00299 Freundt, E. C., Maynard, N., Clancy, E. K., Roy, S., Bousset, L., Sourigues, Y., Covert, M., Melki, R., Kirkegaard, K., & Brahic, M. (2012). Neuron-to-neuron transmission of alpha-synuclein fibrils through axonal transport. Annals of Neurology, 72(4), 517-524. https://doi.org/10.1002/ana.23747 Hidalgo-Cantabrana, C., Goh, Y. J., Pan, M., Sanozky-Dawes, R., & Barrangou, R. (2019). Genome editing using the endogenous type I CRISPR-Cas system in Lactobacillus crispatus. Proceedings of the National Academy of Sciences of the United States of America, 116(32), 15774-15783. https://doi.org/10.1073/pnas.1905421116 Kanafi, M. M., & Tavallaei, M. (2022). Overview of advances in CRISPR/deadCas9 technology and its applications in human diseases. Gene, 830, 146518. https://doi.org/https://doi.org/10.1016/j.gene.2022.146518 Kamienieva, I., Duszynski, J., & Szczepanowska, J. (2021). Multitasking guardian of mitochondrial quality: Parkin function and Parkinson's disease. In Translational Neurodegeneration (Vol. 10, Issue 1). BioMed Central Ltd. https://doi.org/10.1186/s40035-020-00229-8 Klein, C., & Westenberger, A. (2012). Genetics of Parkinson's disease. Cold Spring Harbor Perspectives in Medicine, 2(1). https://doi.org/10.1101/cshperspect.a008888 Konermann, S., Brigham, M. D., Trevino, A. E., Joung, J., Abudayyeh, O. O., Barcena, C., Hsu, P. D., Habib, N., Gootenberg, J. S., Nishimasu, H., Nureki, O., & Zhang, F. (2015). Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature, 517(7536), 583-588. https://doi.org/10.1038/nature14136 Korczyn, A. D. (2022). Drug treatment of Parkinson's disease. In Dialogues in Clinical Neuroscience (Vol. 6, Issue 3, pp. 315-322). https://doi.org/10.31887/dcns.2004.6.3/akorczyn Kostylev, M., Otwell, A. E., Richardson, R. E., & Suzuki, Y. (2015). Cloning should be simple: Escherichia coli DH5á-mediated assembly of multiple DNA fragments with short end homologies. PLoS ONE, 10(9). https://doi.org/10.1371/journal.pone.0137466 Liu, W., Zhu, X., Lei, M., Xia, Q., Botella, J. R., Zhu, J. K., & Mao, Y. (2015). A detailed procedure for CRISPR/Cas9-mediated gene editing in Arabidopsis thaliana. Science Bulletin, 60(15), 1332-1347. https://doi.org/10.1007/s11434-015-0848-2 Lowder, L. G., Zhou, J., Zhang, Y., Malzahn, A., Zhong, Z., Hsieh, T. F., Voytas, D. F., Zhang, Y., & Qi, Y. (2018). Robust Transcriptional Activation in Plants Using Multiplexed CRISPR-Act2.0 and mTALE-Act Systems. Molecular Plant, 11(2), 245-256. https://doi.org/10.1016/j.molp.2017.11.010 Oertel, W., & Schulz, J. B. (2016). Current and experimental treatments of Parkinson's disease: A guide for neuroscientists. In Journal of Neurochemistry (pp. 325-337). Blackwell Publishing Ltd. https://doi.org/10.1111/jnc.13750 Orozco, J. L., Valderrama-Chaparro, J. A., Pinilla-Monsalve, G. D., Molina-Echeverry, M. I., Castaño, A. M. P., Ariza-Araújo, Y., Prada, S. I., & Takeuchi, Y. (2020). Parkinson's disease prevalence, colombiaage distribution, and staging in. Neurology International, 12(1), 9-14. https://doi.org/10.4081/ni.2020.8401 Ou, Z., Pan, J., Tang, S., Duan, D., Yu, D., Nong, H., & Wang, Z. (2021). Global Trends in the Incidence, Prevalence, and Years Lived With Disability of Parkinson's Disease in 204 Countries/Territories From 1990 to 2019. Frontiers in Public Health, 9. https://doi.org/10.3389/fpubh.2021.776847 Poewe, W., Seppi, K., Tanner, C. M., Halliday, G. M., Brundin, P., Volkmann, J., Schrag, A. E., & Lang, A. E. (2017). Parkinson disease. Nature Reviews Disease Primers, 3, 1-21. https://doi.org/10.1038/nrdp.2017.13 Schapira, A. H. V. (2005). Present and future drug treatment for Parkinson's disease. In Journal of Neurology, Neurosurgery, and Psychiatry (Vol. 76, Issue 11, pp. 1472-1478). BMJ Publishing Group. https://doi.org/10.1136/jnnp.2004.035980 Schapira, A. H. V. (2009). Neurobiology and treatment of Parkinson's disease. In Trends in Pharmacological Sciences (Vol. 30, Issue 1, pp. 41-47). https://doi.org/10.1016/j.tips.2008.10.005 Simon, D. K., Tanner, C. M. & Brundin. (2020). P. Parkinson's Disease Epidemiology, Pathology, Genetics, and Pathophysiology. Clin Geriatr Med 36, 1-12. https://doi.org/10.1016/j.cger.2019.08.002 Wani, M. A., & Ganaie, A. A. (2019). Generation of CRISPR-cas9 construct for knockout of genes encoding chromatin-associated proteins. Bulletin of the National Research Centre, 43(1). https://doi.org/10.1186/s42269-019-0141-7 Wirdefeldt, K., Adami, H. O., Cole, P., Trichopoulos, D., & Mandel, J. (2011). Epidemiology and etiology of Parkinson's disease: A review of the evidence. In European Journal of Epidemiology (Vol. 26, Issue SUPPL. 1). https://doi.org/10.1007/s10654-011-9581-6 Wooley, R. E., Gibbs, P. S., Dickerson, H. W., Brown, J., & Nolan, L. K. (1996). Analysis of plasmids cloned from a virulent avian Escherichia coli and transformed into Escherichia coli DH5 alpha. Avian diseases, 40(3), 533-539. Wu, Z., Chen, Z., Gao, X., Li, J., & Shang, G. (2019). Combination of ssDNA recombineering and CRISPR-Cas9 for Pseudomonas putida KT2440 genome editing. Applied Microbiology and Biotechnology, 103(6), 2783-2795. https://doi.org/10.1007/s00253-019-09654-w |
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Attribution-NonCommercial-NoDerivatives 4.0 Internacionalhttps://repositorio.uniandes.edu.co/static/pdf/aceptacion_uso_es.pdfinfo:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Bloch Morel, Natasha Ivonneb751f88a-6344-4f6c-b4c3-f4f1041d3a6e600Bernal Giraldo, Adriana Jimenavirtual::5011-1Sotelo Montero, Sebastián68ad3cbf-2ec5-4491-978c-e4be9aff478b600Esmeral Lascano, Natalia PaolaNeurogenética y Comportamiento2023-02-01T15:30:54Z2023-02-01T15:30:54Z2023-01-31http://hdl.handle.net/1992/64471instname:Universidad de los Andesreponame:Repositorio Institucional Sénecarepourl:https://repositorio.uniandes.edu.co/Parkinson's Disease (PD) is a neurodegenerative disorder that causes a loss in motor capabilities, tremors, bradykinesia, cognitive capacity, and sometimes dementia. The Parkin gene is an essential gene that has a fundamental role in the ubiquitination of proteins and the maintenance of mitochondria. Mutations in the Parkin gene are related to PD. In this study, we got the required DNA to activate the Parkin gene through a CRISPR activation system as a therapeutical objective. We show that using the DH5 alpha strain of E. coli is not the best option to transform and clone the plasmids that have the genetic information. The DH10B strain is a better option for obtaining linearized DNA. It strains requires fewer steps to achieve colonies with the plasmid, and the amount of DNA recovered is notably more significant than with the DH5 alpha.MincienciasMicrobiólogoPregradoIngeniería genética14 páginasapplication/pdfengUniversidad de los AndesMicrobiologíaFacultad de CienciasDepartamento de Ciencias BiológicasGuide selection using a CRISPRa system to activate parkin gene related to parkinson's diseaseTrabajo de grado - Pregradoinfo:eu-repo/semantics/bachelorThesisinfo:eu-repo/semantics/acceptedVersionhttp://purl.org/coar/resource_type/c_7a1fTexthttp://purl.org/redcol/resource_type/TPCRISPRaDH10BE. coliParkinson's diseaseDH5 alphaMicrobiologíaBittar, A. F., Bloch, N. I., Reyes, L. H., & Bernal, A. J. (2020.). Diseño y construcción de sistemas CRISPRa y CRISPRi para el desarrollo de una terapia génica para el Parkinson. TESIS DE GRADO PARA OPTAR EL TÍTULO DE: Microbiólogo. Universidad de los Andes.Dawson, T. M., & Dawson, V. L. (2010). The role of parkin in familial and sporadic Parkinson's disease. Movement Disorders, 25(SUPPL. 1). https://doi.org/10.1002/mds.22798Durfee, T., Nelson, R., Baldwin, S., Plunkett, G., Burland, V., Mau, B., Petrosino, J. F., Qin, X., Muzny, D. M., Ayele, M., Gibbs, R. A., Csörgo, B., Pósfai, G., Weinstock, G. M., & Blattner, F. R. (2008). The complete genome sequence of Escherichia coli DH10B: Insights into the biology of a laboratory workhorse. Journal of Bacteriology, 190(7), 2597-2606. https://doi.org/10.1128/JB.01695-07Dy, Lady, Chalasani, S., & Essani, K. (1993). Isolation of Escherichia coli mutants lacking methylcytosine-dependent restriction systems for cloning extensively methylated frog virus 3 DNA. Gene, 131(1), 87-91. https://doi.org/https://doi.org/10.1016/0378-1119(93)90673-QFields, C. R., Bengoa-Vergniory, N., & Wade-Martins, R. (2019). Targeting Alpha-Synuclein as a Therapy for Parkinson's Disease. In Frontiers in Molecular Neuroscience (Vol. 12). Frontiers Media S.A. https://doi.org/10.3389/fnmol.2019.00299Freundt, E. C., Maynard, N., Clancy, E. K., Roy, S., Bousset, L., Sourigues, Y., Covert, M., Melki, R., Kirkegaard, K., & Brahic, M. (2012). Neuron-to-neuron transmission of alpha-synuclein fibrils through axonal transport. Annals of Neurology, 72(4), 517-524. https://doi.org/10.1002/ana.23747Hidalgo-Cantabrana, C., Goh, Y. J., Pan, M., Sanozky-Dawes, R., & Barrangou, R. (2019). Genome editing using the endogenous type I CRISPR-Cas system in Lactobacillus crispatus. Proceedings of the National Academy of Sciences of the United States of America, 116(32), 15774-15783. https://doi.org/10.1073/pnas.1905421116Kanafi, M. M., & Tavallaei, M. (2022). Overview of advances in CRISPR/deadCas9 technology and its applications in human diseases. Gene, 830, 146518. https://doi.org/https://doi.org/10.1016/j.gene.2022.146518Kamienieva, I., Duszynski, J., & Szczepanowska, J. (2021). Multitasking guardian of mitochondrial quality: Parkin function and Parkinson's disease. In Translational Neurodegeneration (Vol. 10, Issue 1). BioMed Central Ltd. https://doi.org/10.1186/s40035-020-00229-8Klein, C., & Westenberger, A. (2012). Genetics of Parkinson's disease. Cold Spring Harbor Perspectives in Medicine, 2(1). https://doi.org/10.1101/cshperspect.a008888Konermann, S., Brigham, M. D., Trevino, A. E., Joung, J., Abudayyeh, O. O., Barcena, C., Hsu, P. D., Habib, N., Gootenberg, J. S., Nishimasu, H., Nureki, O., & Zhang, F. (2015). Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature, 517(7536), 583-588. https://doi.org/10.1038/nature14136Korczyn, A. D. (2022). Drug treatment of Parkinson's disease. In Dialogues in Clinical Neuroscience (Vol. 6, Issue 3, pp. 315-322). https://doi.org/10.31887/dcns.2004.6.3/akorczynKostylev, M., Otwell, A. E., Richardson, R. E., & Suzuki, Y. (2015). Cloning should be simple: Escherichia coli DH5á-mediated assembly of multiple DNA fragments with short end homologies. PLoS ONE, 10(9). https://doi.org/10.1371/journal.pone.0137466Liu, W., Zhu, X., Lei, M., Xia, Q., Botella, J. R., Zhu, J. K., & Mao, Y. (2015). A detailed procedure for CRISPR/Cas9-mediated gene editing in Arabidopsis thaliana. Science Bulletin, 60(15), 1332-1347. https://doi.org/10.1007/s11434-015-0848-2Lowder, L. G., Zhou, J., Zhang, Y., Malzahn, A., Zhong, Z., Hsieh, T. F., Voytas, D. F., Zhang, Y., & Qi, Y. (2018). Robust Transcriptional Activation in Plants Using Multiplexed CRISPR-Act2.0 and mTALE-Act Systems. Molecular Plant, 11(2), 245-256. https://doi.org/10.1016/j.molp.2017.11.010Oertel, W., & Schulz, J. B. (2016). Current and experimental treatments of Parkinson's disease: A guide for neuroscientists. In Journal of Neurochemistry (pp. 325-337). Blackwell Publishing Ltd. https://doi.org/10.1111/jnc.13750Orozco, J. L., Valderrama-Chaparro, J. A., Pinilla-Monsalve, G. D., Molina-Echeverry, M. I., Castaño, A. M. P., Ariza-Araújo, Y., Prada, S. I., & Takeuchi, Y. (2020). Parkinson's disease prevalence, colombiaage distribution, and staging in. Neurology International, 12(1), 9-14. https://doi.org/10.4081/ni.2020.8401Ou, Z., Pan, J., Tang, S., Duan, D., Yu, D., Nong, H., & Wang, Z. (2021). Global Trends in the Incidence, Prevalence, and Years Lived With Disability of Parkinson's Disease in 204 Countries/Territories From 1990 to 2019. Frontiers in Public Health, 9. https://doi.org/10.3389/fpubh.2021.776847Poewe, W., Seppi, K., Tanner, C. M., Halliday, G. M., Brundin, P., Volkmann, J., Schrag, A. E., & Lang, A. E. (2017). Parkinson disease. Nature Reviews Disease Primers, 3, 1-21. https://doi.org/10.1038/nrdp.2017.13Schapira, A. H. V. (2005). Present and future drug treatment for Parkinson's disease. In Journal of Neurology, Neurosurgery, and Psychiatry (Vol. 76, Issue 11, pp. 1472-1478). BMJ Publishing Group. https://doi.org/10.1136/jnnp.2004.035980Schapira, A. H. V. (2009). Neurobiology and treatment of Parkinson's disease. In Trends in Pharmacological Sciences (Vol. 30, Issue 1, pp. 41-47). https://doi.org/10.1016/j.tips.2008.10.005Simon, D. K., Tanner, C. M. & Brundin. (2020). P. Parkinson's Disease Epidemiology, Pathology, Genetics, and Pathophysiology. Clin Geriatr Med 36, 1-12. https://doi.org/10.1016/j.cger.2019.08.002Wani, M. A., & Ganaie, A. A. (2019). Generation of CRISPR-cas9 construct for knockout of genes encoding chromatin-associated proteins. Bulletin of the National Research Centre, 43(1). https://doi.org/10.1186/s42269-019-0141-7Wirdefeldt, K., Adami, H. O., Cole, P., Trichopoulos, D., & Mandel, J. (2011). Epidemiology and etiology of Parkinson's disease: A review of the evidence. In European Journal of Epidemiology (Vol. 26, Issue SUPPL. 1). https://doi.org/10.1007/s10654-011-9581-6Wooley, R. E., Gibbs, P. S., Dickerson, H. W., Brown, J., & Nolan, L. K. (1996). Analysis of plasmids cloned from a virulent avian Escherichia coli and transformed into Escherichia coli DH5 alpha. Avian diseases, 40(3), 533-539.Wu, Z., Chen, Z., Gao, X., Li, J., & Shang, G. (2019). Combination of ssDNA recombineering and CRISPR-Cas9 for Pseudomonas putida KT2440 genome editing. 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